1

2

BIO 300BIO 300BIOLOGICAL TECHNIQUES AND SKILLSBIOLOGICAL TECHNIQUES AND SKILLS

SARINI BINTI AHMAD WAKIDSARINI BINTI AHMAD WAKIDFACULTY OF APPLIED SCIENCEFACULTY OF APPLIED SCIENCE

BIO 300BIO 300BIOLOGICAL TECHNIQUES AND SKILLSBIOLOGICAL TECHNIQUES AND SKILLS

SARINI BINTI AHMAD WAKIDSARINI BINTI AHMAD WAKIDFACULTY OF APPLIED SCIENCEFACULTY OF APPLIED SCIENCE

3

Techniques in field Techniques in field investigationinvestigation

4

Population EcologyPopulation Ecology

Populationmdash A group of individuals of the same

species living in a particular geographic area

Population Ecologymdash Concentrates mainly on the factors

that affect how many individuals of a particular species live in an area

5

What is a sample

ldquoA portion piece or segment that is representative of a wholerdquo

6

Why do we sample

Because it is usually impossible tocount all the plants or animals presentin a given areandash eg dragonfly larvae in a pondndash eg plant cover on a river terracendash eg species of plants in the estate

7

NON-INVASIVE SAMPLING

Avoid any degradation of the habitat when

sampling1048698 Removal of whole or parts of organismsshould be limited to species that can

quickly recover

8

REPRESENTATIVE SAMPLINGTake a number of samples from around the

sampling site so as to be reasonably sure that the samples represent the site in general

Necessitieshellip1048698 the samples represent the wholendash It is necessary to take enough samples so

that an accurate representation is obtainedndash It is necessary to avoid bias when sampling

9

SAMPLING UNITS

Type determined by the organisms and the physical nature of the habitat being sampled

ndash Area of ground surfacendash Volume of air water or soil1048698 Standard units enable comparison of

results

10

QUADRATS

A standard area sampling unit consisting of a square frame1048698 Consistent size and shape is essential for comparing

samples from different places andor timesQuadrat sizeChosen to suit sampling goals1048698 A balance between what is best and what is practical is

always necessary1048698 Should suitndash practical constraintsndash habitatndash organism

11

Quadrat Method A Quadrat is a sampling area of any

shape randomly deployed Each individual within the quadrat is counted and those numbers are used to extrapolate population size Example a 100 square centimeter metal

rectangle is randomly thrown four times and all of the beetles of a particular species within the square are counted each time 19 21 17 and 19 This translates to 19 beetles per 100 cm2 or 1900 per m2

12

QUADRAT amp TRANSECT ACTIVITIESHow Where amp Why Scientists Do SamplingScientists often collect data ldquoin the fieldrdquo which couldmean underwater in a forest in a cave on a reef oreven the moon Two essential methods to gatherecological information in a standardized way areTransect Sampling (using a single line) and

QuadratSampling (counted within a grid) These samplingmethods provide more accurate data than randomsampling or simply guessing but they take less timethan counting every specimen in a certain area

13

Quadrats- a sturdily built

wooden frame

can be folded for easy transport and storage

14

Quadrats

- When placed on the ground the species present within the frame are identified and their abundance recorded

- Sampling could be random or systematic

Using a quadrat along a belt transect

15

Practical Constraints

Small quadrats are quicker to survey but yield a smaller individual sample of habitat

ndash Often require a larger of samples to represent the habitat

1048698 Large quadrats require more time and effort to survey but provide a larger individual sample of habitat

ndash Often require a smaller of samples to represent the habitat

16

Habitat sizeAppropriate sample unit size depends on size scale

of the habitatndash Small scale habitats require smaller sized samples1048698 Ex Bouldersndash Large scale habitats require larger sized samples1048698 Ex Forests

17

Organism size and density

Depends on size and density of organisms

ndash Small dense organisms require smaller samples

1048698 Ex grassndash Large scattered organisms require

larger samples1048698 Ex Trees

18

TYPES OF SAMPLING

1048698 Systematic 1048698 Stratified 1048698 Random

19

SYSTEMATIC SAMPLING

1048698 Often used when the area being studied is varied not very large or

when time is available 1048698 Samples are taken at fixed intervals

20

How to sample systematicallySystematic samples are usually taken along a transect line marked by a tape measure

1048698 Transect- a line laid across an area

21

Sampling along gradients

Transects are setup along aenvironmentalgradientsndash down a hillsidendash across a streambedndash out from a source ofpollution

22

Types of transect sampling 1048698 Line transect 1048698 Belt transect

23

Line transect methodA measured line is laidacross the area in thedirection of theenvironmental gradientndash The species touching theline can be recordedalong the whole length ofthe line (continuoussampling) or at specificpoints along the line(systematic sampling)

24

Line Transect- useful where a transition of flora andor fauna

occurs- a string or tape is stretched out along the

ground in a straight line record the organisms touching or covering

the line all along its length or at regular intervals

- Profile transect when there is appreciable height change along the transect and thus affecting the distribution of its species

25

Belt transect method

Similar to line transect butwidens the sampling areandash Transect line is laid outndash Samples are taken bydetermining abundance or cover in an area that is adefined distance from the linendash Samples can be taken all

theway along the line at specificintervals or even randomly

26

Belt TransectIt is a strip usually a metre wide marked by putting a

second line parallel to the other The species between the lines are carefully recorded working a metre at a time

Alternatively a frame quadrat in conjunction with a single line transect could be used

Using a quadrat along a belt transect eg ladder transect (every 5m)

27

Point Frames- for grassland field study of dense vegetation

28

STRATIFIED SAMPLING1048698 Often used whenthere are smallareas within alarger habitat thatare clearly different1048698 Strata- majordifferences withincommunitiesrecognized beforesampling begins

29

RANDOM SAMPLING

1048698 Often used when the area being studied isfairly uniform very large or when there is alimited amount of time available1048698 Random = chosen by chance rather thanaccording to a plan all outcomes are

equallylikely1048698 Samples are taken from different positionswithin a habitat and those positions arechosen randomly

30

How to sample randomly

Choose individuals or Placeldquosampling unitsrdquo

haphazardlyndash This is rarely completely

random1048698 ORhellip1048698 Assign numbers to the

areasor individuals to be sampledndash Use a random number

table toselect which areas or

individualswill be sample

31

Population Attributes Density ndash size of a population in relation to a definite

unit of space Affected by

Natality ndash the reproductive output (birth rate) of a population

Mortality ndash the death rate of organisms in a population

Immigration ndash number of organisms moving into the area occupied by the population

Emigration ndash number of organisms moving out of the area occupied by the population

32

Population Density

Four primary population parameters

33

Two Types of Density Estimates

bull Absolute Density ndash a known density such as m2

bull Relative Density ndash we know when one area has more individuals than another

34

Measuring Absolute Density

Total Count ndash count the number of organisms living in an area Human census number of oak trees in a

wooded lot number of singing birds in an area

Total counts generally are not used very often

Sampling Methods ndash use a sample to estimate population size Either use the quadrat or capture-

recapture method

35

Measurement of Environmental ParametersAbiotic factors are important in determining

both the distribution of the organisms and their physical and physiological adaptations

Temperature- diurnal and seasonal temperature variations

are significant in affecting different species of plants and animals

- equipment mercury thermometer maximum-minimum thermometer

miniaturized thermistor

36

pH

-measure pH of a solution by universal indicator pH paper pH meter etc

Light

-measure its duration and intensity duration by predication from Royal Observatory intensity by photographic light meter

pH meter in use

37

Humidity

Relative humidity the water content of a given volume of air relative to the same volume of fully saturated air

- equipment whirling hygrometer

38

Wind and Water Speed- wind speed- anemometer or wind

gauges- water speed - time the movement of a

floating object over a measured distance

39

Salinity

- using a conductivity meter greater salinity has greater conductivity

Oxygen Level

- using an oxygen meter or chemical method (Winkler method)

40

Collecting MethodsCollecting all organisms within a habitat is normally

impractical and therefore small areas are selected Remember to return all material to its original position

after searching amp collecting sufficient specimens Some collecting apparatus for general use are listed

below

41

1 specimen tube

2 screwed-topped jars

3 polythene bags

4 forceps

5 paint brush

6 bulb pipette

7 pooter

42

8 widger 9 sieve 10 hand lens

11 enamel dish 12 beating tray 13 light traps

14 Tullgren funnel 15 Baermann funnel 16 mammal traps

17 pitfall traps 18 netting

43

Estimating Population Size

The exact methods used for estimation depend not only the nature of the habitat but also on the organisms involved

eg animals - population

plants - percentage cover

44

Using Quadrats

- By sampling an area using quadrats and counting the number of individuals within each quadrat it is possible to estimate the total number of individuals within the area

- confined to plants and sessile or very slow-moving animals

- fast-moving animals are disturbed and run away

45

Capture-recapture Techniques- useful for mobile animals which can be marked

- capture marked released randomly recaptured

and marked individuals recorded

no of marked individuals recaptured total no of individuals in 1st sample

-------------------------------------------- = ------------------------------------------

total no of individuals in 2nd sample estimated size of population

(the Lincoln Index)

46

Capture-recapture Techniques Factors affecting the accuracy of the estimation

deaths migration individuals become more liable to predation etc

Examples

- arthropods marked on their backs with non-toxic paint

- fish have tags attached to opercula - mammals have tags clipped to their ears

birds have their legs ringed

47

Capture-recapture Method Important tool for estimating density birth

rate and death rate for mobile animals Method

Collect a sample of individuals mark them and then release them

After a period collect more individuals from the wild and count the number that have marks

We assume that a sample if random will contain the same proportion of marked individuals as the population does

Estimate population density

48

Assumptions For All Capture-Recapture Studies Marking technique does not increase

mortality of marked animals Marked individuals are allowed to mix

with population Marking technique does not affect catch

probability Marks are not lost or overlooked No significant immigration or emigration No significant mortality or natality

49

Marked animals in second sample

Total caught in second sample

Marked animals in first sample

Total population size

=

520 N

16=

Peterson Method or Lincoln Index

N = 64N = (20)(16)5

50

Some Indices Used

Traps Number of Fecal

Pellets Vocalization

Frequency Pelt Records Catch per Unit

Fishing Effort

Number of Artifacts Questionnaires Cover Feeding Capacity Roadside Counts

51

Abundance Scales

The population size may be fairly accurately determined by making some form of frequency assessment

These are subjective and involve an experimenter making some estimate of the number of individuals in a given area or the cover of a particular species

This is especially useful where individuals are very numerous eg barnacles on a rocky shore or where it is difficult to distinguish individuals eg grass plants in a meadow

52

The assessments are usually made on an abundance scale of 5 categories

Abundance Common Frequent Occasional Rare

Barnacles exposed at low water

53

Environmental resistance are the factors which limit the growth of a particular population

eg predation disease availability of light food water oxygen and shelter the accumulation of toxic wastes and even the size of the population itself

54

Density-dependent Growth A population is a density-dependent when its size

(or density) affects its growth rate because of density-dependent factors such as food availability and toxic waste accumulation

Density-independent Growth In this type of growth a population increases until

some factor causes a sudden reduction in its size Its effect is the same regardless of the size of the

population eg temperature fires floods storms etc

55

Regulation of Population Size Fecundity is the reproductive capacity of individual

females of a species Birth rate or natality is used to measure fecundity Death rate or mortality is the number of individuals

of a species which die per unit time Immigration occurs when individuals join a

population from neighbouring ones Emigration occurs when individuals depart from a

population A cycle occurs when the size of a population

fluctuates on a regular basis

56

Ecological Sampling

57

Why Do We Sample Determine presence andor

abundance

Monitor population fluctuations

Assess lsquoecological damagersquo

Assess quality of habitat

Assess population responses

58

What Do We Sample

Physical Environment Temperature DO pH salinity clarity

flow sediment

Biotic Environment All living things

59

Physical Habitat Temperature

Mercury thermometer Electronic thermometer Long-term thermometers

Dissolved Oxygen Winkler method (titration) DO meter (electrode)

pH Litmus paper pH meter (electrode)

Salinity Salinity Meter YSI 550A DO Meter w12 cable

60

Water Clarity Secchi Disk

Disk is attached to a calibrated rope The disk is lowered into the water until the white parts can no longer be seen Secchi disk depth is then recorded and serves as the waters transparency index The clearer the water the greater the secchi disk depth

Secchi Disk

61

Current Velocity (flow) Floating-orange method

Put an orange (or something else that floats just below the water surface) and measure the time it takes it to float across a known distance

Odometer-type flow meter Number of revolutions the propeller

makes for a given time is calibrated to flow velocity

62

Sediment Sediment size is important to many

aquatic organisms Sieversquos are used to separate and

grade sediment samples Percent of each size grade can be

determined

63

Water Sample

Water and plankton from various depths can be collected

A trigger mechanism is used to close the sampler Sample is then brought back to the

surface

64

Small Mammals

Mouserat Traps Fatal

Pit Falls Bucket is placed in the ground Sometimes have lsquoleadsrsquo to the buckets

Live traps Havahart Sherman

Spot-light

Sherman trapHavahart trap

65

Birds Stick-under-the-box method Bird-trap

Works like a minnow trap Mist net

Captures birds in flight Rocket net

Uses a propellant to throw a net over birds

66

Terrestrial Insects

Sticky paper flies

Baited Traps Fire ants

Nets butterflies

Foggers Collect insects from tree canopies

67

Aquatic Insects Drift Net

Place net in flowing water Kick Net

lsquoKickrsquo sediment upstream from block net and the flow will wash them into the net

Wash bucket Serber or Hess Sampler

Stir up known area of sediment

Animals are collected by a catch net

Multi-plate Sampler Become colonized

68

Crawfish and Crab Traps

69

Fish Larvae Light Traps

Larvae are attracted to the light Ichthyoplankton nets

Can be towed at various depths Fish collect at the lsquocodrsquoend

70

Fish Lift net

Net is placed down and after a set amount of time it is quickly lifted

Pop-net Similar to a lift net but

floats are attached to a framed net

Operated by a trigger mechanism

Throw net A net attached to a heavy

frame is thrown and every thing inside is netted out Throw net

Pop-net

Lift net

71

Minnow trap

Usually use bait to attract small fish Light is used sometimes as an attractant

72

Fish Electrofishing

Electricity is put into the water Fish are temporarily stunned and usually

swim towards the electricity source Usually non-fatal but may cause some

damage

73

Fish Gill Net

Gill nets resemble tennis nets Fish can not swim completely through the

net and get caught Gill nets are size selective (based on mesh

size) Square Mesh

Bar mesh

Stretch mesh

74

Fish Trammel Net

Three panels two large mesh on the outside and a small mesh on the inside

Fish swim through the outer mesh pushes the small mesh through the other side and becomes entangled

75

Hoop nets (and other similar nets) can have bait or not

Fyke nets have leads to help guide fish to the net

76

Seine Seines are nets that are pulled

through shallow water to catch fish

77

Purse Seine Used to encircle entire schools of fish

Usually involves a spotter plane and a second boat

78

Trotline (longline) A series of baited drop lines

connected to a main line

Can be deployed by tying one end to the bank and tying the other end with a heavy weight

79

Shrimp (or fish) Trawl Net pulled behind

a boat along the bottom Either a beam or

otter boards keep the net open

80

Tagging Individuals Coded Wire Tags

Microwire that has a unique label

Magnetic wand detects the tag

Tag retention should be determined

T-Bar tags Can be individually

numbered External tag

PIT tags (Passive Integrated Transponders) Wand induces the tag to

transmit individual number is displayed

81

Other Tagging Methods

Toe clip Amphibian and reptile Clip of one or more toes

to identify individuals

Bird Band Place a metal band on a

bird leg Generally has

identification information

82

Preserving plant specimens Pressing and drying Long-term

preservation and storage

Alternative drying techniques

Special preservation and processing techniques

Mounting

83

Pressing and drying Techniques for pressing and drying specimens have been

established for many years There are minor variations in recommended methods but they are essentially the same worldwide

The best specimens are plants that are pressed as soon as possible after collection before wilting and shrivelling Most plants may be kept in sealed containers such as plastic bags for up to a day if it is inconvenient to press immediately However some plants show such rapid wilting particularly of the flowers that such delays are best avoided Flowers with a lot of nectar may go mouldy very quickly if excess nectar is not shaken off before pressing

Specimens are pressed flat and dried between sheets of absorbent blotters or semi-absorbent paper such as newspaper Papers with a glossy surface should be avoided because they are not absorbent enough to aid drying The plant should be carefully laid out between the drying sheets as their form at this stage largely determines their ultimate appearance The flowers should be spread out with the petals carefully arranged wilted leaves should be straightened and unnecessary shoots of excessively twiggy shrubs may be cut away

84

Microwave ovens Small numbers of specimens can be dried using a microwave

oven The technique recommended in the literature is to place the specimens between unprinted absorbent paper for example butchers paper not newspaper which is unsuitable because the chemicals present in the ink may cause a fire The specimens should be put in a special press which should be of a microwave-safe material (wood acrylic or polycarbonate sheeting eg plexiglass or perspex NO metal components) If such a press is not available sheets of cardboard can be placed above and below the specimens and then weighted down

Drying time depends on the power of your oven In most cases drying is accomplished by irradiating at maximum power for 1-2 minutes per specimen although it is often a case of trial and error It is best to process no more than 10-12 specimens of average thickness per batch Specimens are usually dried after the moisture that characteristically appears on the glass door has disappeared If the specimen is damp when taken out of the oven allow it to stand before re-radiating as moisture continues to evaporate from the specimen for some time Care must be taken not to irradiate the specimens for too long

It should be noted that microwave treatment damages seeds and the cellular structure of the plants which may reduce the long-term value of the specimens

85

Alternative drying techniquesSilica gelother desiccants amp freeze drying Alternative methods of drying plant specimens have been

used for some time but are mostly restricted to special purpose collections The main alternatives are freeze-drying and drying in a desiccant powder such as desiccant silica gel In general these techniques are used where it is essential to preserve the shape of a delicate plant of organ of the plant such as the flower Freeze-drying has also been used to preserve the chemical composition of a plant as accurately as possible for later study

Disadvantages and special conservation problems of specimens dried in these manners are that they are particularly susceptible to damage The dried parts are fragile lack support and often catch on packing materials They must therefore be packed especially carefully and stored in small boxes or tubes with some appropriate packing material that does not snag and break small projections Acid-free tissue paper is often used Drying in desiccant silica gel crystals or powder can also have the disadvantage that it is difficult to remove all traces of the silica gel after drying

86

Special preservation and processing techniquesWet or spirit collections

Very fleshy or delicate structures including small algae and orchid flowers are best preserved in an air-tight glass or plastic jar with a liquid preservative rather than by drying The type of preservative used should be clearly labelled in the jar Such material is often referred to as a spirit collection or wet collection

Most material can be satisfactorily preserved in 70 ethyl alcohol (or 70 methylated spirit or denatured alcohol) with 30 water Colours will fade quickly in spirit however so it is a good idea to keep comprehensive notes and photographs

87

Small algae Microscopic algae are often collected in a jar and in the

water in which they were found If the algae are to be stored for more than 2-3 days a preservative needs to be used Traditionally this has been the extremely toxic formalin - a small amount can be added to the water to make a 5 final solution and the container labelled This must not be sent through the post or by courier

There are some other equally toxic options for example propylene phenoxytol but none should be sent through the post A safer option is to add sufficient concentrated alcohol or methylated spirits to the water containing the algae to make a final solution of 70 alcohol This treatment dilutes the algae making them difficult to find so if they can be concentrated somehow first (eg by filtering) they can be stored in much less liquid Another option is to fix the algae in formalin (or something similar) first and then prepare a microscope glass slide with a permanent water-soluble mounting medium

88

Mounting Mounting specimens prevents most fragile material from

fragmenting and prevents specimens becoming separated from their labels If the plant collection is a long-term project specimens should be mounted on sheets of archival (permanent) cardboard or paper with archival-quality fixing media These include stitching with cotton thread dental floss nickel-plated copper wire (for heavier specimens) narrow strips of archival paper linen tape or by using an archival adhesive such as methyl cellulose adhesive

One disadvantage of mounting specimens is that it can make parts of the specimen inaccessible for examination so it is essential that this be borne in mind during specimen arrangement and mounting For example easily reversible mounting media should be used specimens should be strapped to the sheet rather than glued all over and the specimen should be carefully arranged before it is attached so that it shows all features

89

Full-size herbarium mounting sheets are usually about 43 cm long x 28 cm wide The plant name and accompanying field notes should be transcribed on a permanent label stuck to one corner of the herbarium sheet (the bottom right-hand corner being the most common) or sometimes annotations may be written directly on the sheet or card

Small pieces of material which may have become separated from the specimen (eg seeds) can be placed in small plastic bags and pinned to the sheet

90

Long-term preservation and storage The long-term preservation of dry plant

specimens is largely dependent on protection from insect attack Specimens collected by Linnaeus in the eighteenth century and by Banks and Solander on the Endeavour voyage in 1788 are still excellently preserved

91

Pests and their control A range of pests attack dried plant material The

most common pests are insects and fungi though rodents and other large animals can cause damage in poor storage conditions Insects eat the material the paper surrounding the material and the adhesives and mounting media

Such insect pests range from psocids (book lice) which attack mainly the softer parts such as flowers and soft fruits to tobacco beetles and carpet beetles which can bore holes through the toughest of specimens Many insects are particularly sensitive to relative humidity levels and do not thrive at levels below 50

92

The most common and acceptable specimen treatments for insect control are Freezing Microwave Poisoning Insect deterrents Fungal pests

93

Storage

Dried and pressed plant specimens can be stored in cardboard or plastic boxes or tied in bundles in light-weight cardboard folders placed in pigeon holes

Alternatively they can be placed in protective plastic jackets and displayed in ring folders which is recommended if they are to be frequently handled such as for a reference collection

94

Filing

Specimens should be filed in a systematic order if a relatively permanent collection is being made The major groups ie ferns and fern allies cycads conifers dicotyledons and monocotyledons are best kept separately or according to some classification scheme such as that given in a flora or handbook

Similarly the genera within each family and the species within each genus may be filed alphabetically or following some such classification

95

Preservation of entire animals

Types of collection specimens of an entire animal For reference collections mammals can be prepared as a variety of specimens The condition of the specimen may determine possible ways to preserve it if for instance decomposition of the skin has loosened the hair of a carcass so much that it can easily be pulled out or removed by rubbing (ldquoslippingrdquo fur) it will be very difficult or impossible to produce a study skin or mounted specimen The most usual types of specimens (based on Nagorsen and Peterson 1980) are 1) entire fluid-preserved animals (for studying anatomy and histology fluid preservation may change the fur colour) 2) study skins with accompanying skulls partial skeletons (some bones remain in the skin) for studying pelage colour hair quality and moulting patterns 3) mounted skins with accompanying partial or entire skeleton (some bones may remain in the skin dependant on the method of preservation) or freeze-dried specimens 4) entire skeletons for instance for studying anatomy geographic variation or for age determination (entire skeletons are poorly represented in collections so Nagorsen and Peterson (1980) recommend preparation of at least one male and one female skeleton per species

96

Preservation of specimens in the field Formalin preservation Preservation in alcohol Preservation by cooling or freezing

97

Formalin preservation After weighing and measuring the animal and attaching an

adequate label very small specimens (up to 100 g) can be fixed whole by submerging them in 10 buffered formalin (tissue - formalin solution ratio of at least 1 12) the body cavity can be filled with formalin solution by injection until it is turgid and firm some formalin may also be injected under the skin into the body cavity larger muscles and organs If hypodermic needles are not available the body cavity can be opened ventrally by making a slit instead allowing the formalin to enter

Keeping the mouth open with a piece of wood or cotton may later allow examination of teeth Then the whole body can be immersed in formalin in the posture in which it is supposed to stay permanently because it will harden The ratio of formalin to carcass must be at least 12 to 1 to assure a good fixation Tissues can be left in buffered neutralized formalin for several months but formalin hardens specimens therefore after fixation longterm storage in alcohol may be better After preservation the carcass should therefore be washed in water and transferred into ethanol for permanent storage

Disadvantages for instance it discolours the fur after a longish immersion softens the bones and prevents further examination for microbiology

98

Preservation in alcohol

After weighing a whole animal can be preserved in a container of alcohol (70-90) Removal of the intestine prior to storage of the animal in alcohol is recommended

99

Preservation by cooling or freezing Removal of the skin with insulating fur

before cooling or freezing may help to cool the carcass down more quickly

Freezing is not recommended if histological examination is planned

100

THANK YOU

2

BIO 300BIO 300BIOLOGICAL TECHNIQUES AND SKILLSBIOLOGICAL TECHNIQUES AND SKILLS

SARINI BINTI AHMAD WAKIDSARINI BINTI AHMAD WAKIDFACULTY OF APPLIED SCIENCEFACULTY OF APPLIED SCIENCE

BIO 300BIO 300BIOLOGICAL TECHNIQUES AND SKILLSBIOLOGICAL TECHNIQUES AND SKILLS

SARINI BINTI AHMAD WAKIDSARINI BINTI AHMAD WAKIDFACULTY OF APPLIED SCIENCEFACULTY OF APPLIED SCIENCE

3

Techniques in field Techniques in field investigationinvestigation

4

Population EcologyPopulation Ecology

Populationmdash A group of individuals of the same

species living in a particular geographic area

Population Ecologymdash Concentrates mainly on the factors

that affect how many individuals of a particular species live in an area

5

What is a sample

ldquoA portion piece or segment that is representative of a wholerdquo

6

Why do we sample

Because it is usually impossible tocount all the plants or animals presentin a given areandash eg dragonfly larvae in a pondndash eg plant cover on a river terracendash eg species of plants in the estate

7

NON-INVASIVE SAMPLING

Avoid any degradation of the habitat when

sampling1048698 Removal of whole or parts of organismsshould be limited to species that can

quickly recover

8

REPRESENTATIVE SAMPLINGTake a number of samples from around the

sampling site so as to be reasonably sure that the samples represent the site in general

Necessitieshellip1048698 the samples represent the wholendash It is necessary to take enough samples so

that an accurate representation is obtainedndash It is necessary to avoid bias when sampling

9

SAMPLING UNITS

Type determined by the organisms and the physical nature of the habitat being sampled

ndash Area of ground surfacendash Volume of air water or soil1048698 Standard units enable comparison of

results

10

QUADRATS

A standard area sampling unit consisting of a square frame1048698 Consistent size and shape is essential for comparing

samples from different places andor timesQuadrat sizeChosen to suit sampling goals1048698 A balance between what is best and what is practical is

always necessary1048698 Should suitndash practical constraintsndash habitatndash organism

11

Quadrat Method A Quadrat is a sampling area of any

shape randomly deployed Each individual within the quadrat is counted and those numbers are used to extrapolate population size Example a 100 square centimeter metal

rectangle is randomly thrown four times and all of the beetles of a particular species within the square are counted each time 19 21 17 and 19 This translates to 19 beetles per 100 cm2 or 1900 per m2

12

QUADRAT amp TRANSECT ACTIVITIESHow Where amp Why Scientists Do SamplingScientists often collect data ldquoin the fieldrdquo which couldmean underwater in a forest in a cave on a reef oreven the moon Two essential methods to gatherecological information in a standardized way areTransect Sampling (using a single line) and

QuadratSampling (counted within a grid) These samplingmethods provide more accurate data than randomsampling or simply guessing but they take less timethan counting every specimen in a certain area

13

Quadrats- a sturdily built

wooden frame

can be folded for easy transport and storage

14

Quadrats

- When placed on the ground the species present within the frame are identified and their abundance recorded

- Sampling could be random or systematic

Using a quadrat along a belt transect

15

Practical Constraints

Small quadrats are quicker to survey but yield a smaller individual sample of habitat

ndash Often require a larger of samples to represent the habitat

1048698 Large quadrats require more time and effort to survey but provide a larger individual sample of habitat

ndash Often require a smaller of samples to represent the habitat

16

Habitat sizeAppropriate sample unit size depends on size scale

of the habitatndash Small scale habitats require smaller sized samples1048698 Ex Bouldersndash Large scale habitats require larger sized samples1048698 Ex Forests

17

Organism size and density

Depends on size and density of organisms

ndash Small dense organisms require smaller samples

1048698 Ex grassndash Large scattered organisms require

larger samples1048698 Ex Trees

18

TYPES OF SAMPLING

1048698 Systematic 1048698 Stratified 1048698 Random

19

SYSTEMATIC SAMPLING

1048698 Often used when the area being studied is varied not very large or

when time is available 1048698 Samples are taken at fixed intervals

20

How to sample systematicallySystematic samples are usually taken along a transect line marked by a tape measure

1048698 Transect- a line laid across an area

21

Sampling along gradients

Transects are setup along aenvironmentalgradientsndash down a hillsidendash across a streambedndash out from a source ofpollution

22

Types of transect sampling 1048698 Line transect 1048698 Belt transect

23

Line transect methodA measured line is laidacross the area in thedirection of theenvironmental gradientndash The species touching theline can be recordedalong the whole length ofthe line (continuoussampling) or at specificpoints along the line(systematic sampling)

24

Line Transect- useful where a transition of flora andor fauna

occurs- a string or tape is stretched out along the

ground in a straight line record the organisms touching or covering

the line all along its length or at regular intervals

- Profile transect when there is appreciable height change along the transect and thus affecting the distribution of its species

25

Belt transect method

Similar to line transect butwidens the sampling areandash Transect line is laid outndash Samples are taken bydetermining abundance or cover in an area that is adefined distance from the linendash Samples can be taken all

theway along the line at specificintervals or even randomly

26

Belt TransectIt is a strip usually a metre wide marked by putting a

second line parallel to the other The species between the lines are carefully recorded working a metre at a time

Alternatively a frame quadrat in conjunction with a single line transect could be used

Using a quadrat along a belt transect eg ladder transect (every 5m)

27

Point Frames- for grassland field study of dense vegetation

28

STRATIFIED SAMPLING1048698 Often used whenthere are smallareas within alarger habitat thatare clearly different1048698 Strata- majordifferences withincommunitiesrecognized beforesampling begins

29

RANDOM SAMPLING

1048698 Often used when the area being studied isfairly uniform very large or when there is alimited amount of time available1048698 Random = chosen by chance rather thanaccording to a plan all outcomes are

equallylikely1048698 Samples are taken from different positionswithin a habitat and those positions arechosen randomly

30

How to sample randomly

Choose individuals or Placeldquosampling unitsrdquo

haphazardlyndash This is rarely completely

random1048698 ORhellip1048698 Assign numbers to the

areasor individuals to be sampledndash Use a random number

table toselect which areas or

individualswill be sample

31

Population Attributes Density ndash size of a population in relation to a definite

unit of space Affected by

Natality ndash the reproductive output (birth rate) of a population

Mortality ndash the death rate of organisms in a population

Immigration ndash number of organisms moving into the area occupied by the population

Emigration ndash number of organisms moving out of the area occupied by the population

32

Population Density

Four primary population parameters

33

Two Types of Density Estimates

bull Absolute Density ndash a known density such as m2

bull Relative Density ndash we know when one area has more individuals than another

34

Measuring Absolute Density

Total Count ndash count the number of organisms living in an area Human census number of oak trees in a

wooded lot number of singing birds in an area

Total counts generally are not used very often

Sampling Methods ndash use a sample to estimate population size Either use the quadrat or capture-

recapture method

35

Measurement of Environmental ParametersAbiotic factors are important in determining

both the distribution of the organisms and their physical and physiological adaptations

Temperature- diurnal and seasonal temperature variations

are significant in affecting different species of plants and animals

- equipment mercury thermometer maximum-minimum thermometer

miniaturized thermistor

36

pH

-measure pH of a solution by universal indicator pH paper pH meter etc

Light

-measure its duration and intensity duration by predication from Royal Observatory intensity by photographic light meter

pH meter in use

37

Humidity

Relative humidity the water content of a given volume of air relative to the same volume of fully saturated air

- equipment whirling hygrometer

38

Wind and Water Speed- wind speed- anemometer or wind

gauges- water speed - time the movement of a

floating object over a measured distance

39

Salinity

- using a conductivity meter greater salinity has greater conductivity

Oxygen Level

- using an oxygen meter or chemical method (Winkler method)

40

Collecting MethodsCollecting all organisms within a habitat is normally

impractical and therefore small areas are selected Remember to return all material to its original position

after searching amp collecting sufficient specimens Some collecting apparatus for general use are listed

below

41

1 specimen tube

2 screwed-topped jars

3 polythene bags

4 forceps

5 paint brush

6 bulb pipette

7 pooter

42

8 widger 9 sieve 10 hand lens

11 enamel dish 12 beating tray 13 light traps

14 Tullgren funnel 15 Baermann funnel 16 mammal traps

17 pitfall traps 18 netting

43

Estimating Population Size

The exact methods used for estimation depend not only the nature of the habitat but also on the organisms involved

eg animals - population

plants - percentage cover

44

Using Quadrats

- By sampling an area using quadrats and counting the number of individuals within each quadrat it is possible to estimate the total number of individuals within the area

- confined to plants and sessile or very slow-moving animals

- fast-moving animals are disturbed and run away

45

Capture-recapture Techniques- useful for mobile animals which can be marked

- capture marked released randomly recaptured

and marked individuals recorded

no of marked individuals recaptured total no of individuals in 1st sample

-------------------------------------------- = ------------------------------------------

total no of individuals in 2nd sample estimated size of population

(the Lincoln Index)

46

Capture-recapture Techniques Factors affecting the accuracy of the estimation

deaths migration individuals become more liable to predation etc

Examples

- arthropods marked on their backs with non-toxic paint

- fish have tags attached to opercula - mammals have tags clipped to their ears

birds have their legs ringed

47

Capture-recapture Method Important tool for estimating density birth

rate and death rate for mobile animals Method

Collect a sample of individuals mark them and then release them

After a period collect more individuals from the wild and count the number that have marks

We assume that a sample if random will contain the same proportion of marked individuals as the population does

Estimate population density

48

Assumptions For All Capture-Recapture Studies Marking technique does not increase

mortality of marked animals Marked individuals are allowed to mix

with population Marking technique does not affect catch

probability Marks are not lost or overlooked No significant immigration or emigration No significant mortality or natality

49

Marked animals in second sample

Total caught in second sample

Marked animals in first sample

Total population size

=

520 N

16=

Peterson Method or Lincoln Index

N = 64N = (20)(16)5

50

Some Indices Used

Traps Number of Fecal

Pellets Vocalization

Frequency Pelt Records Catch per Unit

Fishing Effort

Number of Artifacts Questionnaires Cover Feeding Capacity Roadside Counts

51

Abundance Scales

The population size may be fairly accurately determined by making some form of frequency assessment

These are subjective and involve an experimenter making some estimate of the number of individuals in a given area or the cover of a particular species

This is especially useful where individuals are very numerous eg barnacles on a rocky shore or where it is difficult to distinguish individuals eg grass plants in a meadow

52

The assessments are usually made on an abundance scale of 5 categories

Abundance Common Frequent Occasional Rare

Barnacles exposed at low water

53

Environmental resistance are the factors which limit the growth of a particular population

eg predation disease availability of light food water oxygen and shelter the accumulation of toxic wastes and even the size of the population itself

54

Density-dependent Growth A population is a density-dependent when its size

(or density) affects its growth rate because of density-dependent factors such as food availability and toxic waste accumulation

Density-independent Growth In this type of growth a population increases until

some factor causes a sudden reduction in its size Its effect is the same regardless of the size of the

population eg temperature fires floods storms etc

55

Regulation of Population Size Fecundity is the reproductive capacity of individual

females of a species Birth rate or natality is used to measure fecundity Death rate or mortality is the number of individuals

of a species which die per unit time Immigration occurs when individuals join a

population from neighbouring ones Emigration occurs when individuals depart from a

population A cycle occurs when the size of a population

fluctuates on a regular basis

56

Ecological Sampling

57

Why Do We Sample Determine presence andor

abundance

Monitor population fluctuations

Assess lsquoecological damagersquo

Assess quality of habitat

Assess population responses

58

What Do We Sample

Physical Environment Temperature DO pH salinity clarity

flow sediment

Biotic Environment All living things

59

Physical Habitat Temperature

Mercury thermometer Electronic thermometer Long-term thermometers

Dissolved Oxygen Winkler method (titration) DO meter (electrode)

pH Litmus paper pH meter (electrode)

Salinity Salinity Meter YSI 550A DO Meter w12 cable

60

Water Clarity Secchi Disk

Disk is attached to a calibrated rope The disk is lowered into the water until the white parts can no longer be seen Secchi disk depth is then recorded and serves as the waters transparency index The clearer the water the greater the secchi disk depth

Secchi Disk

61

Current Velocity (flow) Floating-orange method

Put an orange (or something else that floats just below the water surface) and measure the time it takes it to float across a known distance

Odometer-type flow meter Number of revolutions the propeller

makes for a given time is calibrated to flow velocity

62

Sediment Sediment size is important to many

aquatic organisms Sieversquos are used to separate and

grade sediment samples Percent of each size grade can be

determined

63

Water Sample

Water and plankton from various depths can be collected

A trigger mechanism is used to close the sampler Sample is then brought back to the

surface

64

Small Mammals

Mouserat Traps Fatal

Pit Falls Bucket is placed in the ground Sometimes have lsquoleadsrsquo to the buckets

Live traps Havahart Sherman

Spot-light

Sherman trapHavahart trap

65

Birds Stick-under-the-box method Bird-trap

Works like a minnow trap Mist net

Captures birds in flight Rocket net

Uses a propellant to throw a net over birds

66

Terrestrial Insects

Sticky paper flies

Baited Traps Fire ants

Nets butterflies

Foggers Collect insects from tree canopies

67

Aquatic Insects Drift Net

Place net in flowing water Kick Net

lsquoKickrsquo sediment upstream from block net and the flow will wash them into the net

Wash bucket Serber or Hess Sampler

Stir up known area of sediment

Animals are collected by a catch net

Multi-plate Sampler Become colonized

68

Crawfish and Crab Traps

69

Fish Larvae Light Traps

Larvae are attracted to the light Ichthyoplankton nets

Can be towed at various depths Fish collect at the lsquocodrsquoend

70

Fish Lift net

Net is placed down and after a set amount of time it is quickly lifted

Pop-net Similar to a lift net but

floats are attached to a framed net

Operated by a trigger mechanism

Throw net A net attached to a heavy

frame is thrown and every thing inside is netted out Throw net

Pop-net

Lift net

71

Minnow trap

Usually use bait to attract small fish Light is used sometimes as an attractant

72

Fish Electrofishing

Electricity is put into the water Fish are temporarily stunned and usually

swim towards the electricity source Usually non-fatal but may cause some

damage

73

Fish Gill Net

Gill nets resemble tennis nets Fish can not swim completely through the

net and get caught Gill nets are size selective (based on mesh

size) Square Mesh

Bar mesh

Stretch mesh

74

Fish Trammel Net

Three panels two large mesh on the outside and a small mesh on the inside

Fish swim through the outer mesh pushes the small mesh through the other side and becomes entangled

75

Hoop nets (and other similar nets) can have bait or not

Fyke nets have leads to help guide fish to the net

76

Seine Seines are nets that are pulled

through shallow water to catch fish

77

Purse Seine Used to encircle entire schools of fish

Usually involves a spotter plane and a second boat

78

Trotline (longline) A series of baited drop lines

connected to a main line

Can be deployed by tying one end to the bank and tying the other end with a heavy weight

79

Shrimp (or fish) Trawl Net pulled behind

a boat along the bottom Either a beam or

otter boards keep the net open

80

Tagging Individuals Coded Wire Tags

Microwire that has a unique label

Magnetic wand detects the tag

Tag retention should be determined

T-Bar tags Can be individually

numbered External tag

PIT tags (Passive Integrated Transponders) Wand induces the tag to

transmit individual number is displayed

81

Other Tagging Methods

Toe clip Amphibian and reptile Clip of one or more toes

to identify individuals

Bird Band Place a metal band on a

bird leg Generally has

identification information

82

Preserving plant specimens Pressing and drying Long-term

preservation and storage

Alternative drying techniques

Special preservation and processing techniques

Mounting

83

Pressing and drying Techniques for pressing and drying specimens have been

established for many years There are minor variations in recommended methods but they are essentially the same worldwide

The best specimens are plants that are pressed as soon as possible after collection before wilting and shrivelling Most plants may be kept in sealed containers such as plastic bags for up to a day if it is inconvenient to press immediately However some plants show such rapid wilting particularly of the flowers that such delays are best avoided Flowers with a lot of nectar may go mouldy very quickly if excess nectar is not shaken off before pressing

Specimens are pressed flat and dried between sheets of absorbent blotters or semi-absorbent paper such as newspaper Papers with a glossy surface should be avoided because they are not absorbent enough to aid drying The plant should be carefully laid out between the drying sheets as their form at this stage largely determines their ultimate appearance The flowers should be spread out with the petals carefully arranged wilted leaves should be straightened and unnecessary shoots of excessively twiggy shrubs may be cut away

84

Microwave ovens Small numbers of specimens can be dried using a microwave

oven The technique recommended in the literature is to place the specimens between unprinted absorbent paper for example butchers paper not newspaper which is unsuitable because the chemicals present in the ink may cause a fire The specimens should be put in a special press which should be of a microwave-safe material (wood acrylic or polycarbonate sheeting eg plexiglass or perspex NO metal components) If such a press is not available sheets of cardboard can be placed above and below the specimens and then weighted down

Drying time depends on the power of your oven In most cases drying is accomplished by irradiating at maximum power for 1-2 minutes per specimen although it is often a case of trial and error It is best to process no more than 10-12 specimens of average thickness per batch Specimens are usually dried after the moisture that characteristically appears on the glass door has disappeared If the specimen is damp when taken out of the oven allow it to stand before re-radiating as moisture continues to evaporate from the specimen for some time Care must be taken not to irradiate the specimens for too long

It should be noted that microwave treatment damages seeds and the cellular structure of the plants which may reduce the long-term value of the specimens

85

Alternative drying techniquesSilica gelother desiccants amp freeze drying Alternative methods of drying plant specimens have been

used for some time but are mostly restricted to special purpose collections The main alternatives are freeze-drying and drying in a desiccant powder such as desiccant silica gel In general these techniques are used where it is essential to preserve the shape of a delicate plant of organ of the plant such as the flower Freeze-drying has also been used to preserve the chemical composition of a plant as accurately as possible for later study

Disadvantages and special conservation problems of specimens dried in these manners are that they are particularly susceptible to damage The dried parts are fragile lack support and often catch on packing materials They must therefore be packed especially carefully and stored in small boxes or tubes with some appropriate packing material that does not snag and break small projections Acid-free tissue paper is often used Drying in desiccant silica gel crystals or powder can also have the disadvantage that it is difficult to remove all traces of the silica gel after drying

86

Special preservation and processing techniquesWet or spirit collections

Very fleshy or delicate structures including small algae and orchid flowers are best preserved in an air-tight glass or plastic jar with a liquid preservative rather than by drying The type of preservative used should be clearly labelled in the jar Such material is often referred to as a spirit collection or wet collection

Most material can be satisfactorily preserved in 70 ethyl alcohol (or 70 methylated spirit or denatured alcohol) with 30 water Colours will fade quickly in spirit however so it is a good idea to keep comprehensive notes and photographs

87

Small algae Microscopic algae are often collected in a jar and in the

water in which they were found If the algae are to be stored for more than 2-3 days a preservative needs to be used Traditionally this has been the extremely toxic formalin - a small amount can be added to the water to make a 5 final solution and the container labelled This must not be sent through the post or by courier

There are some other equally toxic options for example propylene phenoxytol but none should be sent through the post A safer option is to add sufficient concentrated alcohol or methylated spirits to the water containing the algae to make a final solution of 70 alcohol This treatment dilutes the algae making them difficult to find so if they can be concentrated somehow first (eg by filtering) they can be stored in much less liquid Another option is to fix the algae in formalin (or something similar) first and then prepare a microscope glass slide with a permanent water-soluble mounting medium

88

Mounting Mounting specimens prevents most fragile material from

fragmenting and prevents specimens becoming separated from their labels If the plant collection is a long-term project specimens should be mounted on sheets of archival (permanent) cardboard or paper with archival-quality fixing media These include stitching with cotton thread dental floss nickel-plated copper wire (for heavier specimens) narrow strips of archival paper linen tape or by using an archival adhesive such as methyl cellulose adhesive

One disadvantage of mounting specimens is that it can make parts of the specimen inaccessible for examination so it is essential that this be borne in mind during specimen arrangement and mounting For example easily reversible mounting media should be used specimens should be strapped to the sheet rather than glued all over and the specimen should be carefully arranged before it is attached so that it shows all features

89

Full-size herbarium mounting sheets are usually about 43 cm long x 28 cm wide The plant name and accompanying field notes should be transcribed on a permanent label stuck to one corner of the herbarium sheet (the bottom right-hand corner being the most common) or sometimes annotations may be written directly on the sheet or card

Small pieces of material which may have become separated from the specimen (eg seeds) can be placed in small plastic bags and pinned to the sheet

90

Long-term preservation and storage The long-term preservation of dry plant

specimens is largely dependent on protection from insect attack Specimens collected by Linnaeus in the eighteenth century and by Banks and Solander on the Endeavour voyage in 1788 are still excellently preserved

91

Pests and their control A range of pests attack dried plant material The

most common pests are insects and fungi though rodents and other large animals can cause damage in poor storage conditions Insects eat the material the paper surrounding the material and the adhesives and mounting media

Such insect pests range from psocids (book lice) which attack mainly the softer parts such as flowers and soft fruits to tobacco beetles and carpet beetles which can bore holes through the toughest of specimens Many insects are particularly sensitive to relative humidity levels and do not thrive at levels below 50

92

The most common and acceptable specimen treatments for insect control are Freezing Microwave Poisoning Insect deterrents Fungal pests

93

Storage

Dried and pressed plant specimens can be stored in cardboard or plastic boxes or tied in bundles in light-weight cardboard folders placed in pigeon holes

Alternatively they can be placed in protective plastic jackets and displayed in ring folders which is recommended if they are to be frequently handled such as for a reference collection

94

Filing

Specimens should be filed in a systematic order if a relatively permanent collection is being made The major groups ie ferns and fern allies cycads conifers dicotyledons and monocotyledons are best kept separately or according to some classification scheme such as that given in a flora or handbook

Similarly the genera within each family and the species within each genus may be filed alphabetically or following some such classification

95

Preservation of entire animals

Types of collection specimens of an entire animal For reference collections mammals can be prepared as a variety of specimens The condition of the specimen may determine possible ways to preserve it if for instance decomposition of the skin has loosened the hair of a carcass so much that it can easily be pulled out or removed by rubbing (ldquoslippingrdquo fur) it will be very difficult or impossible to produce a study skin or mounted specimen The most usual types of specimens (based on Nagorsen and Peterson 1980) are 1) entire fluid-preserved animals (for studying anatomy and histology fluid preservation may change the fur colour) 2) study skins with accompanying skulls partial skeletons (some bones remain in the skin) for studying pelage colour hair quality and moulting patterns 3) mounted skins with accompanying partial or entire skeleton (some bones may remain in the skin dependant on the method of preservation) or freeze-dried specimens 4) entire skeletons for instance for studying anatomy geographic variation or for age determination (entire skeletons are poorly represented in collections so Nagorsen and Peterson (1980) recommend preparation of at least one male and one female skeleton per species

96

Preservation of specimens in the field Formalin preservation Preservation in alcohol Preservation by cooling or freezing

97

Formalin preservation After weighing and measuring the animal and attaching an

adequate label very small specimens (up to 100 g) can be fixed whole by submerging them in 10 buffered formalin (tissue - formalin solution ratio of at least 1 12) the body cavity can be filled with formalin solution by injection until it is turgid and firm some formalin may also be injected under the skin into the body cavity larger muscles and organs If hypodermic needles are not available the body cavity can be opened ventrally by making a slit instead allowing the formalin to enter

Keeping the mouth open with a piece of wood or cotton may later allow examination of teeth Then the whole body can be immersed in formalin in the posture in which it is supposed to stay permanently because it will harden The ratio of formalin to carcass must be at least 12 to 1 to assure a good fixation Tissues can be left in buffered neutralized formalin for several months but formalin hardens specimens therefore after fixation longterm storage in alcohol may be better After preservation the carcass should therefore be washed in water and transferred into ethanol for permanent storage

Disadvantages for instance it discolours the fur after a longish immersion softens the bones and prevents further examination for microbiology

98

Preservation in alcohol

After weighing a whole animal can be preserved in a container of alcohol (70-90) Removal of the intestine prior to storage of the animal in alcohol is recommended

99

Preservation by cooling or freezing Removal of the skin with insulating fur

before cooling or freezing may help to cool the carcass down more quickly

Freezing is not recommended if histological examination is planned

100

THANK YOU

3

Techniques in field Techniques in field investigationinvestigation

4

Population EcologyPopulation Ecology

Populationmdash A group of individuals of the same

species living in a particular geographic area

Population Ecologymdash Concentrates mainly on the factors

that affect how many individuals of a particular species live in an area

5

What is a sample

ldquoA portion piece or segment that is representative of a wholerdquo

6

Why do we sample

Because it is usually impossible tocount all the plants or animals presentin a given areandash eg dragonfly larvae in a pondndash eg plant cover on a river terracendash eg species of plants in the estate

7

NON-INVASIVE SAMPLING

Avoid any degradation of the habitat when

sampling1048698 Removal of whole or parts of organismsshould be limited to species that can

quickly recover

8

REPRESENTATIVE SAMPLINGTake a number of samples from around the

sampling site so as to be reasonably sure that the samples represent the site in general

Necessitieshellip1048698 the samples represent the wholendash It is necessary to take enough samples so

that an accurate representation is obtainedndash It is necessary to avoid bias when sampling

9

SAMPLING UNITS

Type determined by the organisms and the physical nature of the habitat being sampled

ndash Area of ground surfacendash Volume of air water or soil1048698 Standard units enable comparison of

results

10

QUADRATS

A standard area sampling unit consisting of a square frame1048698 Consistent size and shape is essential for comparing

samples from different places andor timesQuadrat sizeChosen to suit sampling goals1048698 A balance between what is best and what is practical is

always necessary1048698 Should suitndash practical constraintsndash habitatndash organism

11

Quadrat Method A Quadrat is a sampling area of any

shape randomly deployed Each individual within the quadrat is counted and those numbers are used to extrapolate population size Example a 100 square centimeter metal

rectangle is randomly thrown four times and all of the beetles of a particular species within the square are counted each time 19 21 17 and 19 This translates to 19 beetles per 100 cm2 or 1900 per m2

12

QUADRAT amp TRANSECT ACTIVITIESHow Where amp Why Scientists Do SamplingScientists often collect data ldquoin the fieldrdquo which couldmean underwater in a forest in a cave on a reef oreven the moon Two essential methods to gatherecological information in a standardized way areTransect Sampling (using a single line) and

QuadratSampling (counted within a grid) These samplingmethods provide more accurate data than randomsampling or simply guessing but they take less timethan counting every specimen in a certain area

13

Quadrats- a sturdily built

wooden frame

can be folded for easy transport and storage

14

Quadrats

- When placed on the ground the species present within the frame are identified and their abundance recorded

- Sampling could be random or systematic

Using a quadrat along a belt transect

15

Practical Constraints

Small quadrats are quicker to survey but yield a smaller individual sample of habitat

ndash Often require a larger of samples to represent the habitat

1048698 Large quadrats require more time and effort to survey but provide a larger individual sample of habitat

ndash Often require a smaller of samples to represent the habitat

16

Habitat sizeAppropriate sample unit size depends on size scale

of the habitatndash Small scale habitats require smaller sized samples1048698 Ex Bouldersndash Large scale habitats require larger sized samples1048698 Ex Forests

17

Organism size and density

Depends on size and density of organisms

ndash Small dense organisms require smaller samples

1048698 Ex grassndash Large scattered organisms require

larger samples1048698 Ex Trees

18

TYPES OF SAMPLING

1048698 Systematic 1048698 Stratified 1048698 Random

19

SYSTEMATIC SAMPLING

1048698 Often used when the area being studied is varied not very large or

when time is available 1048698 Samples are taken at fixed intervals

20

How to sample systematicallySystematic samples are usually taken along a transect line marked by a tape measure

1048698 Transect- a line laid across an area

21

Sampling along gradients

Transects are setup along aenvironmentalgradientsndash down a hillsidendash across a streambedndash out from a source ofpollution

22

Types of transect sampling 1048698 Line transect 1048698 Belt transect

23

Line transect methodA measured line is laidacross the area in thedirection of theenvironmental gradientndash The species touching theline can be recordedalong the whole length ofthe line (continuoussampling) or at specificpoints along the line(systematic sampling)

24

Line Transect- useful where a transition of flora andor fauna

occurs- a string or tape is stretched out along the

ground in a straight line record the organisms touching or covering

the line all along its length or at regular intervals

- Profile transect when there is appreciable height change along the transect and thus affecting the distribution of its species

25

Belt transect method

Similar to line transect butwidens the sampling areandash Transect line is laid outndash Samples are taken bydetermining abundance or cover in an area that is adefined distance from the linendash Samples can be taken all

theway along the line at specificintervals or even randomly

26

Belt TransectIt is a strip usually a metre wide marked by putting a

second line parallel to the other The species between the lines are carefully recorded working a metre at a time

Alternatively a frame quadrat in conjunction with a single line transect could be used

Using a quadrat along a belt transect eg ladder transect (every 5m)

27

Point Frames- for grassland field study of dense vegetation

28

STRATIFIED SAMPLING1048698 Often used whenthere are smallareas within alarger habitat thatare clearly different1048698 Strata- majordifferences withincommunitiesrecognized beforesampling begins

29

RANDOM SAMPLING

1048698 Often used when the area being studied isfairly uniform very large or when there is alimited amount of time available1048698 Random = chosen by chance rather thanaccording to a plan all outcomes are

equallylikely1048698 Samples are taken from different positionswithin a habitat and those positions arechosen randomly

30

How to sample randomly

Choose individuals or Placeldquosampling unitsrdquo

haphazardlyndash This is rarely completely

random1048698 ORhellip1048698 Assign numbers to the

areasor individuals to be sampledndash Use a random number

table toselect which areas or

individualswill be sample

31

Population Attributes Density ndash size of a population in relation to a definite

unit of space Affected by

Natality ndash the reproductive output (birth rate) of a population

Mortality ndash the death rate of organisms in a population

Immigration ndash number of organisms moving into the area occupied by the population

Emigration ndash number of organisms moving out of the area occupied by the population

32

Population Density

Four primary population parameters

33

Two Types of Density Estimates

bull Absolute Density ndash a known density such as m2

bull Relative Density ndash we know when one area has more individuals than another

34

Measuring Absolute Density

Total Count ndash count the number of organisms living in an area Human census number of oak trees in a

wooded lot number of singing birds in an area

Total counts generally are not used very often

Sampling Methods ndash use a sample to estimate population size Either use the quadrat or capture-

recapture method

35

Measurement of Environmental ParametersAbiotic factors are important in determining

both the distribution of the organisms and their physical and physiological adaptations

Temperature- diurnal and seasonal temperature variations

are significant in affecting different species of plants and animals

- equipment mercury thermometer maximum-minimum thermometer

miniaturized thermistor

36

pH

-measure pH of a solution by universal indicator pH paper pH meter etc

Light

-measure its duration and intensity duration by predication from Royal Observatory intensity by photographic light meter

pH meter in use

37

Humidity

Relative humidity the water content of a given volume of air relative to the same volume of fully saturated air

- equipment whirling hygrometer

38

Wind and Water Speed- wind speed- anemometer or wind

gauges- water speed - time the movement of a

floating object over a measured distance

39

Salinity

- using a conductivity meter greater salinity has greater conductivity

Oxygen Level

- using an oxygen meter or chemical method (Winkler method)

40

Collecting MethodsCollecting all organisms within a habitat is normally

impractical and therefore small areas are selected Remember to return all material to its original position

after searching amp collecting sufficient specimens Some collecting apparatus for general use are listed

below

41

1 specimen tube

2 screwed-topped jars

3 polythene bags

4 forceps

5 paint brush

6 bulb pipette

7 pooter

42

8 widger 9 sieve 10 hand lens

11 enamel dish 12 beating tray 13 light traps

14 Tullgren funnel 15 Baermann funnel 16 mammal traps

17 pitfall traps 18 netting

43

Estimating Population Size

The exact methods used for estimation depend not only the nature of the habitat but also on the organisms involved

eg animals - population

plants - percentage cover

44

Using Quadrats

- By sampling an area using quadrats and counting the number of individuals within each quadrat it is possible to estimate the total number of individuals within the area

- confined to plants and sessile or very slow-moving animals

- fast-moving animals are disturbed and run away

45

Capture-recapture Techniques- useful for mobile animals which can be marked

- capture marked released randomly recaptured

and marked individuals recorded

no of marked individuals recaptured total no of individuals in 1st sample

-------------------------------------------- = ------------------------------------------

total no of individuals in 2nd sample estimated size of population

(the Lincoln Index)

46

Capture-recapture Techniques Factors affecting the accuracy of the estimation

deaths migration individuals become more liable to predation etc

Examples

- arthropods marked on their backs with non-toxic paint

- fish have tags attached to opercula - mammals have tags clipped to their ears

birds have their legs ringed

47

Capture-recapture Method Important tool for estimating density birth

rate and death rate for mobile animals Method

Collect a sample of individuals mark them and then release them

After a period collect more individuals from the wild and count the number that have marks

We assume that a sample if random will contain the same proportion of marked individuals as the population does

Estimate population density

48

Assumptions For All Capture-Recapture Studies Marking technique does not increase

mortality of marked animals Marked individuals are allowed to mix

with population Marking technique does not affect catch

probability Marks are not lost or overlooked No significant immigration or emigration No significant mortality or natality

49

Marked animals in second sample

Total caught in second sample

Marked animals in first sample

Total population size

=

520 N

16=

Peterson Method or Lincoln Index

N = 64N = (20)(16)5

50

Some Indices Used

Traps Number of Fecal

Pellets Vocalization

Frequency Pelt Records Catch per Unit

Fishing Effort

Number of Artifacts Questionnaires Cover Feeding Capacity Roadside Counts

51

Abundance Scales

The population size may be fairly accurately determined by making some form of frequency assessment

These are subjective and involve an experimenter making some estimate of the number of individuals in a given area or the cover of a particular species

This is especially useful where individuals are very numerous eg barnacles on a rocky shore or where it is difficult to distinguish individuals eg grass plants in a meadow

52

The assessments are usually made on an abundance scale of 5 categories

Abundance Common Frequent Occasional Rare

Barnacles exposed at low water

53

Environmental resistance are the factors which limit the growth of a particular population

eg predation disease availability of light food water oxygen and shelter the accumulation of toxic wastes and even the size of the population itself

54

Density-dependent Growth A population is a density-dependent when its size

(or density) affects its growth rate because of density-dependent factors such as food availability and toxic waste accumulation

Density-independent Growth In this type of growth a population increases until

some factor causes a sudden reduction in its size Its effect is the same regardless of the size of the

population eg temperature fires floods storms etc

55

Regulation of Population Size Fecundity is the reproductive capacity of individual

females of a species Birth rate or natality is used to measure fecundity Death rate or mortality is the number of individuals

of a species which die per unit time Immigration occurs when individuals join a

population from neighbouring ones Emigration occurs when individuals depart from a

population A cycle occurs when the size of a population

fluctuates on a regular basis

56

Ecological Sampling

57

Why Do We Sample Determine presence andor

abundance

Monitor population fluctuations

Assess lsquoecological damagersquo

Assess quality of habitat

Assess population responses

58

What Do We Sample

Physical Environment Temperature DO pH salinity clarity

flow sediment

Biotic Environment All living things

59

Physical Habitat Temperature

Mercury thermometer Electronic thermometer Long-term thermometers

Dissolved Oxygen Winkler method (titration) DO meter (electrode)

pH Litmus paper pH meter (electrode)

Salinity Salinity Meter YSI 550A DO Meter w12 cable

60

Water Clarity Secchi Disk

Disk is attached to a calibrated rope The disk is lowered into the water until the white parts can no longer be seen Secchi disk depth is then recorded and serves as the waters transparency index The clearer the water the greater the secchi disk depth

Secchi Disk

61

Current Velocity (flow) Floating-orange method

Put an orange (or something else that floats just below the water surface) and measure the time it takes it to float across a known distance

Odometer-type flow meter Number of revolutions the propeller

makes for a given time is calibrated to flow velocity

62

Sediment Sediment size is important to many

aquatic organisms Sieversquos are used to separate and

grade sediment samples Percent of each size grade can be

determined

63

Water Sample

Water and plankton from various depths can be collected

A trigger mechanism is used to close the sampler Sample is then brought back to the

surface

64

Small Mammals

Mouserat Traps Fatal

Pit Falls Bucket is placed in the ground Sometimes have lsquoleadsrsquo to the buckets

Live traps Havahart Sherman

Spot-light

Sherman trapHavahart trap

65

Birds Stick-under-the-box method Bird-trap

Works like a minnow trap Mist net

Captures birds in flight Rocket net

Uses a propellant to throw a net over birds

66

Terrestrial Insects

Sticky paper flies

Baited Traps Fire ants

Nets butterflies

Foggers Collect insects from tree canopies

67

Aquatic Insects Drift Net

Place net in flowing water Kick Net

lsquoKickrsquo sediment upstream from block net and the flow will wash them into the net

Wash bucket Serber or Hess Sampler

Stir up known area of sediment

Animals are collected by a catch net

Multi-plate Sampler Become colonized

68

Crawfish and Crab Traps

69

Fish Larvae Light Traps

Larvae are attracted to the light Ichthyoplankton nets

Can be towed at various depths Fish collect at the lsquocodrsquoend

70

Fish Lift net

Net is placed down and after a set amount of time it is quickly lifted

Pop-net Similar to a lift net but

floats are attached to a framed net

Operated by a trigger mechanism

Throw net A net attached to a heavy

frame is thrown and every thing inside is netted out Throw net

Pop-net

Lift net

71

Minnow trap

Usually use bait to attract small fish Light is used sometimes as an attractant

72

Fish Electrofishing

Electricity is put into the water Fish are temporarily stunned and usually

swim towards the electricity source Usually non-fatal but may cause some

damage

73

Fish Gill Net

Gill nets resemble tennis nets Fish can not swim completely through the

net and get caught Gill nets are size selective (based on mesh

size) Square Mesh

Bar mesh

Stretch mesh

74

Fish Trammel Net

Three panels two large mesh on the outside and a small mesh on the inside

Fish swim through the outer mesh pushes the small mesh through the other side and becomes entangled

75

Hoop nets (and other similar nets) can have bait or not

Fyke nets have leads to help guide fish to the net

76

Seine Seines are nets that are pulled

through shallow water to catch fish

77

Purse Seine Used to encircle entire schools of fish

Usually involves a spotter plane and a second boat

78

Trotline (longline) A series of baited drop lines

connected to a main line

Can be deployed by tying one end to the bank and tying the other end with a heavy weight

79

Shrimp (or fish) Trawl Net pulled behind

a boat along the bottom Either a beam or

otter boards keep the net open

80

Tagging Individuals Coded Wire Tags

Microwire that has a unique label

Magnetic wand detects the tag

Tag retention should be determined

T-Bar tags Can be individually

numbered External tag

PIT tags (Passive Integrated Transponders) Wand induces the tag to

transmit individual number is displayed

81

Other Tagging Methods

Toe clip Amphibian and reptile Clip of one or more toes

to identify individuals

Bird Band Place a metal band on a

bird leg Generally has

identification information

82

Preserving plant specimens Pressing and drying Long-term

preservation and storage

Alternative drying techniques

Special preservation and processing techniques

Mounting

83

Pressing and drying Techniques for pressing and drying specimens have been

established for many years There are minor variations in recommended methods but they are essentially the same worldwide

The best specimens are plants that are pressed as soon as possible after collection before wilting and shrivelling Most plants may be kept in sealed containers such as plastic bags for up to a day if it is inconvenient to press immediately However some plants show such rapid wilting particularly of the flowers that such delays are best avoided Flowers with a lot of nectar may go mouldy very quickly if excess nectar is not shaken off before pressing

Specimens are pressed flat and dried between sheets of absorbent blotters or semi-absorbent paper such as newspaper Papers with a glossy surface should be avoided because they are not absorbent enough to aid drying The plant should be carefully laid out between the drying sheets as their form at this stage largely determines their ultimate appearance The flowers should be spread out with the petals carefully arranged wilted leaves should be straightened and unnecessary shoots of excessively twiggy shrubs may be cut away

84

Microwave ovens Small numbers of specimens can be dried using a microwave

oven The technique recommended in the literature is to place the specimens between unprinted absorbent paper for example butchers paper not newspaper which is unsuitable because the chemicals present in the ink may cause a fire The specimens should be put in a special press which should be of a microwave-safe material (wood acrylic or polycarbonate sheeting eg plexiglass or perspex NO metal components) If such a press is not available sheets of cardboard can be placed above and below the specimens and then weighted down

Drying time depends on the power of your oven In most cases drying is accomplished by irradiating at maximum power for 1-2 minutes per specimen although it is often a case of trial and error It is best to process no more than 10-12 specimens of average thickness per batch Specimens are usually dried after the moisture that characteristically appears on the glass door has disappeared If the specimen is damp when taken out of the oven allow it to stand before re-radiating as moisture continues to evaporate from the specimen for some time Care must be taken not to irradiate the specimens for too long

It should be noted that microwave treatment damages seeds and the cellular structure of the plants which may reduce the long-term value of the specimens

85

Alternative drying techniquesSilica gelother desiccants amp freeze drying Alternative methods of drying plant specimens have been

used for some time but are mostly restricted to special purpose collections The main alternatives are freeze-drying and drying in a desiccant powder such as desiccant silica gel In general these techniques are used where it is essential to preserve the shape of a delicate plant of organ of the plant such as the flower Freeze-drying has also been used to preserve the chemical composition of a plant as accurately as possible for later study

Disadvantages and special conservation problems of specimens dried in these manners are that they are particularly susceptible to damage The dried parts are fragile lack support and often catch on packing materials They must therefore be packed especially carefully and stored in small boxes or tubes with some appropriate packing material that does not snag and break small projections Acid-free tissue paper is often used Drying in desiccant silica gel crystals or powder can also have the disadvantage that it is difficult to remove all traces of the silica gel after drying

86

Special preservation and processing techniquesWet or spirit collections

Very fleshy or delicate structures including small algae and orchid flowers are best preserved in an air-tight glass or plastic jar with a liquid preservative rather than by drying The type of preservative used should be clearly labelled in the jar Such material is often referred to as a spirit collection or wet collection

Most material can be satisfactorily preserved in 70 ethyl alcohol (or 70 methylated spirit or denatured alcohol) with 30 water Colours will fade quickly in spirit however so it is a good idea to keep comprehensive notes and photographs

87

Small algae Microscopic algae are often collected in a jar and in the

water in which they were found If the algae are to be stored for more than 2-3 days a preservative needs to be used Traditionally this has been the extremely toxic formalin - a small amount can be added to the water to make a 5 final solution and the container labelled This must not be sent through the post or by courier

There are some other equally toxic options for example propylene phenoxytol but none should be sent through the post A safer option is to add sufficient concentrated alcohol or methylated spirits to the water containing the algae to make a final solution of 70 alcohol This treatment dilutes the algae making them difficult to find so if they can be concentrated somehow first (eg by filtering) they can be stored in much less liquid Another option is to fix the algae in formalin (or something similar) first and then prepare a microscope glass slide with a permanent water-soluble mounting medium

88

Mounting Mounting specimens prevents most fragile material from

fragmenting and prevents specimens becoming separated from their labels If the plant collection is a long-term project specimens should be mounted on sheets of archival (permanent) cardboard or paper with archival-quality fixing media These include stitching with cotton thread dental floss nickel-plated copper wire (for heavier specimens) narrow strips of archival paper linen tape or by using an archival adhesive such as methyl cellulose adhesive

One disadvantage of mounting specimens is that it can make parts of the specimen inaccessible for examination so it is essential that this be borne in mind during specimen arrangement and mounting For example easily reversible mounting media should be used specimens should be strapped to the sheet rather than glued all over and the specimen should be carefully arranged before it is attached so that it shows all features

89

Full-size herbarium mounting sheets are usually about 43 cm long x 28 cm wide The plant name and accompanying field notes should be transcribed on a permanent label stuck to one corner of the herbarium sheet (the bottom right-hand corner being the most common) or sometimes annotations may be written directly on the sheet or card

Small pieces of material which may have become separated from the specimen (eg seeds) can be placed in small plastic bags and pinned to the sheet

90

Long-term preservation and storage The long-term preservation of dry plant

specimens is largely dependent on protection from insect attack Specimens collected by Linnaeus in the eighteenth century and by Banks and Solander on the Endeavour voyage in 1788 are still excellently preserved

91

Pests and their control A range of pests attack dried plant material The

most common pests are insects and fungi though rodents and other large animals can cause damage in poor storage conditions Insects eat the material the paper surrounding the material and the adhesives and mounting media

Such insect pests range from psocids (book lice) which attack mainly the softer parts such as flowers and soft fruits to tobacco beetles and carpet beetles which can bore holes through the toughest of specimens Many insects are particularly sensitive to relative humidity levels and do not thrive at levels below 50

92

The most common and acceptable specimen treatments for insect control are Freezing Microwave Poisoning Insect deterrents Fungal pests

93

Storage

Dried and pressed plant specimens can be stored in cardboard or plastic boxes or tied in bundles in light-weight cardboard folders placed in pigeon holes

Alternatively they can be placed in protective plastic jackets and displayed in ring folders which is recommended if they are to be frequently handled such as for a reference collection

94

Filing

Specimens should be filed in a systematic order if a relatively permanent collection is being made The major groups ie ferns and fern allies cycads conifers dicotyledons and monocotyledons are best kept separately or according to some classification scheme such as that given in a flora or handbook

Similarly the genera within each family and the species within each genus may be filed alphabetically or following some such classification

95

Preservation of entire animals

Types of collection specimens of an entire animal For reference collections mammals can be prepared as a variety of specimens The condition of the specimen may determine possible ways to preserve it if for instance decomposition of the skin has loosened the hair of a carcass so much that it can easily be pulled out or removed by rubbing (ldquoslippingrdquo fur) it will be very difficult or impossible to produce a study skin or mounted specimen The most usual types of specimens (based on Nagorsen and Peterson 1980) are 1) entire fluid-preserved animals (for studying anatomy and histology fluid preservation may change the fur colour) 2) study skins with accompanying skulls partial skeletons (some bones remain in the skin) for studying pelage colour hair quality and moulting patterns 3) mounted skins with accompanying partial or entire skeleton (some bones may remain in the skin dependant on the method of preservation) or freeze-dried specimens 4) entire skeletons for instance for studying anatomy geographic variation or for age determination (entire skeletons are poorly represented in collections so Nagorsen and Peterson (1980) recommend preparation of at least one male and one female skeleton per species

96

Preservation of specimens in the field Formalin preservation Preservation in alcohol Preservation by cooling or freezing

97

Formalin preservation After weighing and measuring the animal and attaching an

adequate label very small specimens (up to 100 g) can be fixed whole by submerging them in 10 buffered formalin (tissue - formalin solution ratio of at least 1 12) the body cavity can be filled with formalin solution by injection until it is turgid and firm some formalin may also be injected under the skin into the body cavity larger muscles and organs If hypodermic needles are not available the body cavity can be opened ventrally by making a slit instead allowing the formalin to enter

Keeping the mouth open with a piece of wood or cotton may later allow examination of teeth Then the whole body can be immersed in formalin in the posture in which it is supposed to stay permanently because it will harden The ratio of formalin to carcass must be at least 12 to 1 to assure a good fixation Tissues can be left in buffered neutralized formalin for several months but formalin hardens specimens therefore after fixation longterm storage in alcohol may be better After preservation the carcass should therefore be washed in water and transferred into ethanol for permanent storage

Disadvantages for instance it discolours the fur after a longish immersion softens the bones and prevents further examination for microbiology

98

Preservation in alcohol

After weighing a whole animal can be preserved in a container of alcohol (70-90) Removal of the intestine prior to storage of the animal in alcohol is recommended

99

Preservation by cooling or freezing Removal of the skin with insulating fur

before cooling or freezing may help to cool the carcass down more quickly

Freezing is not recommended if histological examination is planned

100

THANK YOU

4

Population EcologyPopulation Ecology

Populationmdash A group of individuals of the same

species living in a particular geographic area

Population Ecologymdash Concentrates mainly on the factors

that affect how many individuals of a particular species live in an area

5

What is a sample

ldquoA portion piece or segment that is representative of a wholerdquo

6

Why do we sample

Because it is usually impossible tocount all the plants or animals presentin a given areandash eg dragonfly larvae in a pondndash eg plant cover on a river terracendash eg species of plants in the estate

7

NON-INVASIVE SAMPLING

Avoid any degradation of the habitat when

sampling1048698 Removal of whole or parts of organismsshould be limited to species that can

quickly recover

8

REPRESENTATIVE SAMPLINGTake a number of samples from around the

sampling site so as to be reasonably sure that the samples represent the site in general

Necessitieshellip1048698 the samples represent the wholendash It is necessary to take enough samples so

that an accurate representation is obtainedndash It is necessary to avoid bias when sampling

9

SAMPLING UNITS

Type determined by the organisms and the physical nature of the habitat being sampled

ndash Area of ground surfacendash Volume of air water or soil1048698 Standard units enable comparison of

results

10

QUADRATS

A standard area sampling unit consisting of a square frame1048698 Consistent size and shape is essential for comparing

samples from different places andor timesQuadrat sizeChosen to suit sampling goals1048698 A balance between what is best and what is practical is

always necessary1048698 Should suitndash practical constraintsndash habitatndash organism

11

Quadrat Method A Quadrat is a sampling area of any

shape randomly deployed Each individual within the quadrat is counted and those numbers are used to extrapolate population size Example a 100 square centimeter metal

rectangle is randomly thrown four times and all of the beetles of a particular species within the square are counted each time 19 21 17 and 19 This translates to 19 beetles per 100 cm2 or 1900 per m2

12

QUADRAT amp TRANSECT ACTIVITIESHow Where amp Why Scientists Do SamplingScientists often collect data ldquoin the fieldrdquo which couldmean underwater in a forest in a cave on a reef oreven the moon Two essential methods to gatherecological information in a standardized way areTransect Sampling (using a single line) and

QuadratSampling (counted within a grid) These samplingmethods provide more accurate data than randomsampling or simply guessing but they take less timethan counting every specimen in a certain area

13

Quadrats- a sturdily built

wooden frame

can be folded for easy transport and storage

14

Quadrats

- When placed on the ground the species present within the frame are identified and their abundance recorded

- Sampling could be random or systematic

Using a quadrat along a belt transect

15

Practical Constraints

Small quadrats are quicker to survey but yield a smaller individual sample of habitat

ndash Often require a larger of samples to represent the habitat

1048698 Large quadrats require more time and effort to survey but provide a larger individual sample of habitat

ndash Often require a smaller of samples to represent the habitat

16

Habitat sizeAppropriate sample unit size depends on size scale

of the habitatndash Small scale habitats require smaller sized samples1048698 Ex Bouldersndash Large scale habitats require larger sized samples1048698 Ex Forests

17

Organism size and density

Depends on size and density of organisms

ndash Small dense organisms require smaller samples

1048698 Ex grassndash Large scattered organisms require

larger samples1048698 Ex Trees

18

TYPES OF SAMPLING

1048698 Systematic 1048698 Stratified 1048698 Random

19

SYSTEMATIC SAMPLING

1048698 Often used when the area being studied is varied not very large or

when time is available 1048698 Samples are taken at fixed intervals

20

How to sample systematicallySystematic samples are usually taken along a transect line marked by a tape measure

1048698 Transect- a line laid across an area

21

Sampling along gradients

Transects are setup along aenvironmentalgradientsndash down a hillsidendash across a streambedndash out from a source ofpollution

22

Types of transect sampling 1048698 Line transect 1048698 Belt transect

23

Line transect methodA measured line is laidacross the area in thedirection of theenvironmental gradientndash The species touching theline can be recordedalong the whole length ofthe line (continuoussampling) or at specificpoints along the line(systematic sampling)

24

Line Transect- useful where a transition of flora andor fauna

occurs- a string or tape is stretched out along the

ground in a straight line record the organisms touching or covering

the line all along its length or at regular intervals

- Profile transect when there is appreciable height change along the transect and thus affecting the distribution of its species

25

Belt transect method

Similar to line transect butwidens the sampling areandash Transect line is laid outndash Samples are taken bydetermining abundance or cover in an area that is adefined distance from the linendash Samples can be taken all

theway along the line at specificintervals or even randomly

26

Belt TransectIt is a strip usually a metre wide marked by putting a

second line parallel to the other The species between the lines are carefully recorded working a metre at a time

Alternatively a frame quadrat in conjunction with a single line transect could be used

Using a quadrat along a belt transect eg ladder transect (every 5m)

27

Point Frames- for grassland field study of dense vegetation

28

STRATIFIED SAMPLING1048698 Often used whenthere are smallareas within alarger habitat thatare clearly different1048698 Strata- majordifferences withincommunitiesrecognized beforesampling begins

29

RANDOM SAMPLING

1048698 Often used when the area being studied isfairly uniform very large or when there is alimited amount of time available1048698 Random = chosen by chance rather thanaccording to a plan all outcomes are

equallylikely1048698 Samples are taken from different positionswithin a habitat and those positions arechosen randomly

30

How to sample randomly

Choose individuals or Placeldquosampling unitsrdquo

haphazardlyndash This is rarely completely

random1048698 ORhellip1048698 Assign numbers to the

areasor individuals to be sampledndash Use a random number

table toselect which areas or

individualswill be sample

31

Population Attributes Density ndash size of a population in relation to a definite

unit of space Affected by

Natality ndash the reproductive output (birth rate) of a population

Mortality ndash the death rate of organisms in a population

Immigration ndash number of organisms moving into the area occupied by the population

Emigration ndash number of organisms moving out of the area occupied by the population

32

Population Density

Four primary population parameters

33

Two Types of Density Estimates

bull Absolute Density ndash a known density such as m2

bull Relative Density ndash we know when one area has more individuals than another

34

Measuring Absolute Density

Total Count ndash count the number of organisms living in an area Human census number of oak trees in a

wooded lot number of singing birds in an area

Total counts generally are not used very often

Sampling Methods ndash use a sample to estimate population size Either use the quadrat or capture-

recapture method

35

Measurement of Environmental ParametersAbiotic factors are important in determining

both the distribution of the organisms and their physical and physiological adaptations

Temperature- diurnal and seasonal temperature variations

are significant in affecting different species of plants and animals

- equipment mercury thermometer maximum-minimum thermometer

miniaturized thermistor

36

pH

-measure pH of a solution by universal indicator pH paper pH meter etc

Light

-measure its duration and intensity duration by predication from Royal Observatory intensity by photographic light meter

pH meter in use

37

Humidity

Relative humidity the water content of a given volume of air relative to the same volume of fully saturated air

- equipment whirling hygrometer

38

Wind and Water Speed- wind speed- anemometer or wind

gauges- water speed - time the movement of a

floating object over a measured distance

39

Salinity

- using a conductivity meter greater salinity has greater conductivity

Oxygen Level

- using an oxygen meter or chemical method (Winkler method)

40

Collecting MethodsCollecting all organisms within a habitat is normally

impractical and therefore small areas are selected Remember to return all material to its original position

after searching amp collecting sufficient specimens Some collecting apparatus for general use are listed

below

41

1 specimen tube

2 screwed-topped jars

3 polythene bags

4 forceps

5 paint brush

6 bulb pipette

7 pooter

42

8 widger 9 sieve 10 hand lens

11 enamel dish 12 beating tray 13 light traps

14 Tullgren funnel 15 Baermann funnel 16 mammal traps

17 pitfall traps 18 netting

43

Estimating Population Size

The exact methods used for estimation depend not only the nature of the habitat but also on the organisms involved

eg animals - population

plants - percentage cover

44

Using Quadrats

- By sampling an area using quadrats and counting the number of individuals within each quadrat it is possible to estimate the total number of individuals within the area

- confined to plants and sessile or very slow-moving animals

- fast-moving animals are disturbed and run away

45

Capture-recapture Techniques- useful for mobile animals which can be marked

- capture marked released randomly recaptured

and marked individuals recorded

no of marked individuals recaptured total no of individuals in 1st sample

-------------------------------------------- = ------------------------------------------

total no of individuals in 2nd sample estimated size of population

(the Lincoln Index)

46

Capture-recapture Techniques Factors affecting the accuracy of the estimation

deaths migration individuals become more liable to predation etc

Examples

- arthropods marked on their backs with non-toxic paint

- fish have tags attached to opercula - mammals have tags clipped to their ears

birds have their legs ringed

47

Capture-recapture Method Important tool for estimating density birth

rate and death rate for mobile animals Method

Collect a sample of individuals mark them and then release them

After a period collect more individuals from the wild and count the number that have marks

We assume that a sample if random will contain the same proportion of marked individuals as the population does

Estimate population density

48

Assumptions For All Capture-Recapture Studies Marking technique does not increase

mortality of marked animals Marked individuals are allowed to mix

with population Marking technique does not affect catch

probability Marks are not lost or overlooked No significant immigration or emigration No significant mortality or natality

49

Marked animals in second sample

Total caught in second sample

Marked animals in first sample

Total population size

=

520 N

16=

Peterson Method or Lincoln Index

N = 64N = (20)(16)5

50

Some Indices Used

Traps Number of Fecal

Pellets Vocalization

Frequency Pelt Records Catch per Unit

Fishing Effort

Number of Artifacts Questionnaires Cover Feeding Capacity Roadside Counts

51

Abundance Scales

The population size may be fairly accurately determined by making some form of frequency assessment

These are subjective and involve an experimenter making some estimate of the number of individuals in a given area or the cover of a particular species

This is especially useful where individuals are very numerous eg barnacles on a rocky shore or where it is difficult to distinguish individuals eg grass plants in a meadow

52

The assessments are usually made on an abundance scale of 5 categories

Abundance Common Frequent Occasional Rare

Barnacles exposed at low water

53

Environmental resistance are the factors which limit the growth of a particular population

eg predation disease availability of light food water oxygen and shelter the accumulation of toxic wastes and even the size of the population itself

54

Density-dependent Growth A population is a density-dependent when its size

(or density) affects its growth rate because of density-dependent factors such as food availability and toxic waste accumulation

Density-independent Growth In this type of growth a population increases until

some factor causes a sudden reduction in its size Its effect is the same regardless of the size of the

population eg temperature fires floods storms etc

55

Regulation of Population Size Fecundity is the reproductive capacity of individual

females of a species Birth rate or natality is used to measure fecundity Death rate or mortality is the number of individuals

of a species which die per unit time Immigration occurs when individuals join a

population from neighbouring ones Emigration occurs when individuals depart from a

population A cycle occurs when the size of a population

fluctuates on a regular basis

56

Ecological Sampling

57

Why Do We Sample Determine presence andor

abundance

Monitor population fluctuations

Assess lsquoecological damagersquo

Assess quality of habitat

Assess population responses

58

What Do We Sample

Physical Environment Temperature DO pH salinity clarity

flow sediment

Biotic Environment All living things

59

Physical Habitat Temperature

Mercury thermometer Electronic thermometer Long-term thermometers

Dissolved Oxygen Winkler method (titration) DO meter (electrode)

pH Litmus paper pH meter (electrode)

Salinity Salinity Meter YSI 550A DO Meter w12 cable

60

Water Clarity Secchi Disk

Disk is attached to a calibrated rope The disk is lowered into the water until the white parts can no longer be seen Secchi disk depth is then recorded and serves as the waters transparency index The clearer the water the greater the secchi disk depth

Secchi Disk

61

Current Velocity (flow) Floating-orange method

Put an orange (or something else that floats just below the water surface) and measure the time it takes it to float across a known distance

Odometer-type flow meter Number of revolutions the propeller

makes for a given time is calibrated to flow velocity

62

Sediment Sediment size is important to many

aquatic organisms Sieversquos are used to separate and

grade sediment samples Percent of each size grade can be

determined

63

Water Sample

Water and plankton from various depths can be collected

A trigger mechanism is used to close the sampler Sample is then brought back to the

surface

64

Small Mammals

Mouserat Traps Fatal

Pit Falls Bucket is placed in the ground Sometimes have lsquoleadsrsquo to the buckets

Live traps Havahart Sherman

Spot-light

Sherman trapHavahart trap

65

Birds Stick-under-the-box method Bird-trap

Works like a minnow trap Mist net

Captures birds in flight Rocket net

Uses a propellant to throw a net over birds

66

Terrestrial Insects

Sticky paper flies

Baited Traps Fire ants

Nets butterflies

Foggers Collect insects from tree canopies

67

Aquatic Insects Drift Net

Place net in flowing water Kick Net

lsquoKickrsquo sediment upstream from block net and the flow will wash them into the net

Wash bucket Serber or Hess Sampler

Stir up known area of sediment

Animals are collected by a catch net

Multi-plate Sampler Become colonized

68

Crawfish and Crab Traps

69

Fish Larvae Light Traps

Larvae are attracted to the light Ichthyoplankton nets

Can be towed at various depths Fish collect at the lsquocodrsquoend

70

Fish Lift net

Net is placed down and after a set amount of time it is quickly lifted

Pop-net Similar to a lift net but

floats are attached to a framed net

Operated by a trigger mechanism

Throw net A net attached to a heavy

frame is thrown and every thing inside is netted out Throw net

Pop-net

Lift net

71

Minnow trap

Usually use bait to attract small fish Light is used sometimes as an attractant

72

Fish Electrofishing

Electricity is put into the water Fish are temporarily stunned and usually

swim towards the electricity source Usually non-fatal but may cause some

damage

73

Fish Gill Net

Gill nets resemble tennis nets Fish can not swim completely through the

net and get caught Gill nets are size selective (based on mesh

size) Square Mesh

Bar mesh

Stretch mesh

74

Fish Trammel Net

Three panels two large mesh on the outside and a small mesh on the inside

Fish swim through the outer mesh pushes the small mesh through the other side and becomes entangled

75

Hoop nets (and other similar nets) can have bait or not

Fyke nets have leads to help guide fish to the net

76

Seine Seines are nets that are pulled

through shallow water to catch fish

77

Purse Seine Used to encircle entire schools of fish

Usually involves a spotter plane and a second boat

78

Trotline (longline) A series of baited drop lines

connected to a main line

Can be deployed by tying one end to the bank and tying the other end with a heavy weight

79

Shrimp (or fish) Trawl Net pulled behind

a boat along the bottom Either a beam or

otter boards keep the net open

80

Tagging Individuals Coded Wire Tags

Microwire that has a unique label

Magnetic wand detects the tag

Tag retention should be determined

T-Bar tags Can be individually

numbered External tag

PIT tags (Passive Integrated Transponders) Wand induces the tag to

transmit individual number is displayed

81

Other Tagging Methods

Toe clip Amphibian and reptile Clip of one or more toes

to identify individuals

Bird Band Place a metal band on a

bird leg Generally has

identification information

82

Preserving plant specimens Pressing and drying Long-term

preservation and storage

Alternative drying techniques

Special preservation and processing techniques

Mounting

83

Pressing and drying Techniques for pressing and drying specimens have been

established for many years There are minor variations in recommended methods but they are essentially the same worldwide

The best specimens are plants that are pressed as soon as possible after collection before wilting and shrivelling Most plants may be kept in sealed containers such as plastic bags for up to a day if it is inconvenient to press immediately However some plants show such rapid wilting particularly of the flowers that such delays are best avoided Flowers with a lot of nectar may go mouldy very quickly if excess nectar is not shaken off before pressing

Specimens are pressed flat and dried between sheets of absorbent blotters or semi-absorbent paper such as newspaper Papers with a glossy surface should be avoided because they are not absorbent enough to aid drying The plant should be carefully laid out between the drying sheets as their form at this stage largely determines their ultimate appearance The flowers should be spread out with the petals carefully arranged wilted leaves should be straightened and unnecessary shoots of excessively twiggy shrubs may be cut away

84

Microwave ovens Small numbers of specimens can be dried using a microwave

oven The technique recommended in the literature is to place the specimens between unprinted absorbent paper for example butchers paper not newspaper which is unsuitable because the chemicals present in the ink may cause a fire The specimens should be put in a special press which should be of a microwave-safe material (wood acrylic or polycarbonate sheeting eg plexiglass or perspex NO metal components) If such a press is not available sheets of cardboard can be placed above and below the specimens and then weighted down

Drying time depends on the power of your oven In most cases drying is accomplished by irradiating at maximum power for 1-2 minutes per specimen although it is often a case of trial and error It is best to process no more than 10-12 specimens of average thickness per batch Specimens are usually dried after the moisture that characteristically appears on the glass door has disappeared If the specimen is damp when taken out of the oven allow it to stand before re-radiating as moisture continues to evaporate from the specimen for some time Care must be taken not to irradiate the specimens for too long

It should be noted that microwave treatment damages seeds and the cellular structure of the plants which may reduce the long-term value of the specimens

85

Alternative drying techniquesSilica gelother desiccants amp freeze drying Alternative methods of drying plant specimens have been

used for some time but are mostly restricted to special purpose collections The main alternatives are freeze-drying and drying in a desiccant powder such as desiccant silica gel In general these techniques are used where it is essential to preserve the shape of a delicate plant of organ of the plant such as the flower Freeze-drying has also been used to preserve the chemical composition of a plant as accurately as possible for later study

Disadvantages and special conservation problems of specimens dried in these manners are that they are particularly susceptible to damage The dried parts are fragile lack support and often catch on packing materials They must therefore be packed especially carefully and stored in small boxes or tubes with some appropriate packing material that does not snag and break small projections Acid-free tissue paper is often used Drying in desiccant silica gel crystals or powder can also have the disadvantage that it is difficult to remove all traces of the silica gel after drying

86

Special preservation and processing techniquesWet or spirit collections

Very fleshy or delicate structures including small algae and orchid flowers are best preserved in an air-tight glass or plastic jar with a liquid preservative rather than by drying The type of preservative used should be clearly labelled in the jar Such material is often referred to as a spirit collection or wet collection

Most material can be satisfactorily preserved in 70 ethyl alcohol (or 70 methylated spirit or denatured alcohol) with 30 water Colours will fade quickly in spirit however so it is a good idea to keep comprehensive notes and photographs

87

Small algae Microscopic algae are often collected in a jar and in the

water in which they were found If the algae are to be stored for more than 2-3 days a preservative needs to be used Traditionally this has been the extremely toxic formalin - a small amount can be added to the water to make a 5 final solution and the container labelled This must not be sent through the post or by courier

There are some other equally toxic options for example propylene phenoxytol but none should be sent through the post A safer option is to add sufficient concentrated alcohol or methylated spirits to the water containing the algae to make a final solution of 70 alcohol This treatment dilutes the algae making them difficult to find so if they can be concentrated somehow first (eg by filtering) they can be stored in much less liquid Another option is to fix the algae in formalin (or something similar) first and then prepare a microscope glass slide with a permanent water-soluble mounting medium

88

Mounting Mounting specimens prevents most fragile material from

fragmenting and prevents specimens becoming separated from their labels If the plant collection is a long-term project specimens should be mounted on sheets of archival (permanent) cardboard or paper with archival-quality fixing media These include stitching with cotton thread dental floss nickel-plated copper wire (for heavier specimens) narrow strips of archival paper linen tape or by using an archival adhesive such as methyl cellulose adhesive

One disadvantage of mounting specimens is that it can make parts of the specimen inaccessible for examination so it is essential that this be borne in mind during specimen arrangement and mounting For example easily reversible mounting media should be used specimens should be strapped to the sheet rather than glued all over and the specimen should be carefully arranged before it is attached so that it shows all features

89

Full-size herbarium mounting sheets are usually about 43 cm long x 28 cm wide The plant name and accompanying field notes should be transcribed on a permanent label stuck to one corner of the herbarium sheet (the bottom right-hand corner being the most common) or sometimes annotations may be written directly on the sheet or card

Small pieces of material which may have become separated from the specimen (eg seeds) can be placed in small plastic bags and pinned to the sheet

90

Long-term preservation and storage The long-term preservation of dry plant

specimens is largely dependent on protection from insect attack Specimens collected by Linnaeus in the eighteenth century and by Banks and Solander on the Endeavour voyage in 1788 are still excellently preserved

91

Pests and their control A range of pests attack dried plant material The

most common pests are insects and fungi though rodents and other large animals can cause damage in poor storage conditions Insects eat the material the paper surrounding the material and the adhesives and mounting media

Such insect pests range from psocids (book lice) which attack mainly the softer parts such as flowers and soft fruits to tobacco beetles and carpet beetles which can bore holes through the toughest of specimens Many insects are particularly sensitive to relative humidity levels and do not thrive at levels below 50

92

The most common and acceptable specimen treatments for insect control are Freezing Microwave Poisoning Insect deterrents Fungal pests

93

Storage

Dried and pressed plant specimens can be stored in cardboard or plastic boxes or tied in bundles in light-weight cardboard folders placed in pigeon holes

Alternatively they can be placed in protective plastic jackets and displayed in ring folders which is recommended if they are to be frequently handled such as for a reference collection

94

Filing

Specimens should be filed in a systematic order if a relatively permanent collection is being made The major groups ie ferns and fern allies cycads conifers dicotyledons and monocotyledons are best kept separately or according to some classification scheme such as that given in a flora or handbook

Similarly the genera within each family and the species within each genus may be filed alphabetically or following some such classification

95

Preservation of entire animals

Types of collection specimens of an entire animal For reference collections mammals can be prepared as a variety of specimens The condition of the specimen may determine possible ways to preserve it if for instance decomposition of the skin has loosened the hair of a carcass so much that it can easily be pulled out or removed by rubbing (ldquoslippingrdquo fur) it will be very difficult or impossible to produce a study skin or mounted specimen The most usual types of specimens (based on Nagorsen and Peterson 1980) are 1) entire fluid-preserved animals (for studying anatomy and histology fluid preservation may change the fur colour) 2) study skins with accompanying skulls partial skeletons (some bones remain in the skin) for studying pelage colour hair quality and moulting patterns 3) mounted skins with accompanying partial or entire skeleton (some bones may remain in the skin dependant on the method of preservation) or freeze-dried specimens 4) entire skeletons for instance for studying anatomy geographic variation or for age determination (entire skeletons are poorly represented in collections so Nagorsen and Peterson (1980) recommend preparation of at least one male and one female skeleton per species

96

Preservation of specimens in the field Formalin preservation Preservation in alcohol Preservation by cooling or freezing

97

Formalin preservation After weighing and measuring the animal and attaching an

adequate label very small specimens (up to 100 g) can be fixed whole by submerging them in 10 buffered formalin (tissue - formalin solution ratio of at least 1 12) the body cavity can be filled with formalin solution by injection until it is turgid and firm some formalin may also be injected under the skin into the body cavity larger muscles and organs If hypodermic needles are not available the body cavity can be opened ventrally by making a slit instead allowing the formalin to enter

Keeping the mouth open with a piece of wood or cotton may later allow examination of teeth Then the whole body can be immersed in formalin in the posture in which it is supposed to stay permanently because it will harden The ratio of formalin to carcass must be at least 12 to 1 to assure a good fixation Tissues can be left in buffered neutralized formalin for several months but formalin hardens specimens therefore after fixation longterm storage in alcohol may be better After preservation the carcass should therefore be washed in water and transferred into ethanol for permanent storage

Disadvantages for instance it discolours the fur after a longish immersion softens the bones and prevents further examination for microbiology

98

Preservation in alcohol

After weighing a whole animal can be preserved in a container of alcohol (70-90) Removal of the intestine prior to storage of the animal in alcohol is recommended

99

Preservation by cooling or freezing Removal of the skin with insulating fur

before cooling or freezing may help to cool the carcass down more quickly

Freezing is not recommended if histological examination is planned

100

THANK YOU

5

What is a sample

ldquoA portion piece or segment that is representative of a wholerdquo

6

Why do we sample

Because it is usually impossible tocount all the plants or animals presentin a given areandash eg dragonfly larvae in a pondndash eg plant cover on a river terracendash eg species of plants in the estate

7

NON-INVASIVE SAMPLING

Avoid any degradation of the habitat when

sampling1048698 Removal of whole or parts of organismsshould be limited to species that can

quickly recover

8

REPRESENTATIVE SAMPLINGTake a number of samples from around the

sampling site so as to be reasonably sure that the samples represent the site in general

Necessitieshellip1048698 the samples represent the wholendash It is necessary to take enough samples so

that an accurate representation is obtainedndash It is necessary to avoid bias when sampling

9

SAMPLING UNITS

Type determined by the organisms and the physical nature of the habitat being sampled

ndash Area of ground surfacendash Volume of air water or soil1048698 Standard units enable comparison of

results

10

QUADRATS

A standard area sampling unit consisting of a square frame1048698 Consistent size and shape is essential for comparing

samples from different places andor timesQuadrat sizeChosen to suit sampling goals1048698 A balance between what is best and what is practical is

always necessary1048698 Should suitndash practical constraintsndash habitatndash organism

11

Quadrat Method A Quadrat is a sampling area of any

shape randomly deployed Each individual within the quadrat is counted and those numbers are used to extrapolate population size Example a 100 square centimeter metal

rectangle is randomly thrown four times and all of the beetles of a particular species within the square are counted each time 19 21 17 and 19 This translates to 19 beetles per 100 cm2 or 1900 per m2

12

QUADRAT amp TRANSECT ACTIVITIESHow Where amp Why Scientists Do SamplingScientists often collect data ldquoin the fieldrdquo which couldmean underwater in a forest in a cave on a reef oreven the moon Two essential methods to gatherecological information in a standardized way areTransect Sampling (using a single line) and

QuadratSampling (counted within a grid) These samplingmethods provide more accurate data than randomsampling or simply guessing but they take less timethan counting every specimen in a certain area

13

Quadrats- a sturdily built

wooden frame

can be folded for easy transport and storage

14

Quadrats

- When placed on the ground the species present within the frame are identified and their abundance recorded

- Sampling could be random or systematic

Using a quadrat along a belt transect

15

Practical Constraints

Small quadrats are quicker to survey but yield a smaller individual sample of habitat

ndash Often require a larger of samples to represent the habitat

1048698 Large quadrats require more time and effort to survey but provide a larger individual sample of habitat

ndash Often require a smaller of samples to represent the habitat

16

Habitat sizeAppropriate sample unit size depends on size scale

of the habitatndash Small scale habitats require smaller sized samples1048698 Ex Bouldersndash Large scale habitats require larger sized samples1048698 Ex Forests

17

Organism size and density

Depends on size and density of organisms

ndash Small dense organisms require smaller samples

1048698 Ex grassndash Large scattered organisms require

larger samples1048698 Ex Trees

18

TYPES OF SAMPLING

1048698 Systematic 1048698 Stratified 1048698 Random

19

SYSTEMATIC SAMPLING

1048698 Often used when the area being studied is varied not very large or

when time is available 1048698 Samples are taken at fixed intervals

20

How to sample systematicallySystematic samples are usually taken along a transect line marked by a tape measure

1048698 Transect- a line laid across an area

21

Sampling along gradients

Transects are setup along aenvironmentalgradientsndash down a hillsidendash across a streambedndash out from a source ofpollution

22

Types of transect sampling 1048698 Line transect 1048698 Belt transect

23

Line transect methodA measured line is laidacross the area in thedirection of theenvironmental gradientndash The species touching theline can be recordedalong the whole length ofthe line (continuoussampling) or at specificpoints along the line(systematic sampling)

24

Line Transect- useful where a transition of flora andor fauna

occurs- a string or tape is stretched out along the

ground in a straight line record the organisms touching or covering

the line all along its length or at regular intervals

- Profile transect when there is appreciable height change along the transect and thus affecting the distribution of its species

25

Belt transect method

Similar to line transect butwidens the sampling areandash Transect line is laid outndash Samples are taken bydetermining abundance or cover in an area that is adefined distance from the linendash Samples can be taken all

theway along the line at specificintervals or even randomly

26

Belt TransectIt is a strip usually a metre wide marked by putting a

second line parallel to the other The species between the lines are carefully recorded working a metre at a time

Alternatively a frame quadrat in conjunction with a single line transect could be used

Using a quadrat along a belt transect eg ladder transect (every 5m)

27

Point Frames- for grassland field study of dense vegetation

28

STRATIFIED SAMPLING1048698 Often used whenthere are smallareas within alarger habitat thatare clearly different1048698 Strata- majordifferences withincommunitiesrecognized beforesampling begins

29

RANDOM SAMPLING

1048698 Often used when the area being studied isfairly uniform very large or when there is alimited amount of time available1048698 Random = chosen by chance rather thanaccording to a plan all outcomes are

equallylikely1048698 Samples are taken from different positionswithin a habitat and those positions arechosen randomly

30

How to sample randomly

Choose individuals or Placeldquosampling unitsrdquo

haphazardlyndash This is rarely completely

random1048698 ORhellip1048698 Assign numbers to the

areasor individuals to be sampledndash Use a random number

table toselect which areas or

individualswill be sample

31

Population Attributes Density ndash size of a population in relation to a definite

unit of space Affected by

Natality ndash the reproductive output (birth rate) of a population

Mortality ndash the death rate of organisms in a population

Immigration ndash number of organisms moving into the area occupied by the population

Emigration ndash number of organisms moving out of the area occupied by the population

32

Population Density

Four primary population parameters

33

Two Types of Density Estimates

bull Absolute Density ndash a known density such as m2

bull Relative Density ndash we know when one area has more individuals than another

34

Measuring Absolute Density

Total Count ndash count the number of organisms living in an area Human census number of oak trees in a

wooded lot number of singing birds in an area

Total counts generally are not used very often

Sampling Methods ndash use a sample to estimate population size Either use the quadrat or capture-

recapture method

35

Measurement of Environmental ParametersAbiotic factors are important in determining

both the distribution of the organisms and their physical and physiological adaptations

Temperature- diurnal and seasonal temperature variations

are significant in affecting different species of plants and animals

- equipment mercury thermometer maximum-minimum thermometer

miniaturized thermistor

36

pH

-measure pH of a solution by universal indicator pH paper pH meter etc

Light

-measure its duration and intensity duration by predication from Royal Observatory intensity by photographic light meter

pH meter in use

37

Humidity

Relative humidity the water content of a given volume of air relative to the same volume of fully saturated air

- equipment whirling hygrometer

38

Wind and Water Speed- wind speed- anemometer or wind

gauges- water speed - time the movement of a

floating object over a measured distance

39

Salinity

- using a conductivity meter greater salinity has greater conductivity

Oxygen Level

- using an oxygen meter or chemical method (Winkler method)

40

Collecting MethodsCollecting all organisms within a habitat is normally

impractical and therefore small areas are selected Remember to return all material to its original position

after searching amp collecting sufficient specimens Some collecting apparatus for general use are listed

below

41

1 specimen tube

2 screwed-topped jars

3 polythene bags

4 forceps

5 paint brush

6 bulb pipette

7 pooter

42

8 widger 9 sieve 10 hand lens

11 enamel dish 12 beating tray 13 light traps

14 Tullgren funnel 15 Baermann funnel 16 mammal traps

17 pitfall traps 18 netting

43

Estimating Population Size

The exact methods used for estimation depend not only the nature of the habitat but also on the organisms involved

eg animals - population

plants - percentage cover

44

Using Quadrats

- By sampling an area using quadrats and counting the number of individuals within each quadrat it is possible to estimate the total number of individuals within the area

- confined to plants and sessile or very slow-moving animals

- fast-moving animals are disturbed and run away

45

Capture-recapture Techniques- useful for mobile animals which can be marked

- capture marked released randomly recaptured

and marked individuals recorded

no of marked individuals recaptured total no of individuals in 1st sample

-------------------------------------------- = ------------------------------------------

total no of individuals in 2nd sample estimated size of population

(the Lincoln Index)

46

Capture-recapture Techniques Factors affecting the accuracy of the estimation

deaths migration individuals become more liable to predation etc

Examples

- arthropods marked on their backs with non-toxic paint

- fish have tags attached to opercula - mammals have tags clipped to their ears

birds have their legs ringed

47

Capture-recapture Method Important tool for estimating density birth

rate and death rate for mobile animals Method

Collect a sample of individuals mark them and then release them

After a period collect more individuals from the wild and count the number that have marks

We assume that a sample if random will contain the same proportion of marked individuals as the population does

Estimate population density

48

Assumptions For All Capture-Recapture Studies Marking technique does not increase

mortality of marked animals Marked individuals are allowed to mix

with population Marking technique does not affect catch

probability Marks are not lost or overlooked No significant immigration or emigration No significant mortality or natality

49

Marked animals in second sample

Total caught in second sample

Marked animals in first sample

Total population size

=

520 N

16=

Peterson Method or Lincoln Index

N = 64N = (20)(16)5

50

Some Indices Used

Traps Number of Fecal

Pellets Vocalization

Frequency Pelt Records Catch per Unit

Fishing Effort

Number of Artifacts Questionnaires Cover Feeding Capacity Roadside Counts

51

Abundance Scales

The population size may be fairly accurately determined by making some form of frequency assessment

These are subjective and involve an experimenter making some estimate of the number of individuals in a given area or the cover of a particular species

This is especially useful where individuals are very numerous eg barnacles on a rocky shore or where it is difficult to distinguish individuals eg grass plants in a meadow

52

The assessments are usually made on an abundance scale of 5 categories

Abundance Common Frequent Occasional Rare

Barnacles exposed at low water

53

Environmental resistance are the factors which limit the growth of a particular population

eg predation disease availability of light food water oxygen and shelter the accumulation of toxic wastes and even the size of the population itself

54

Density-dependent Growth A population is a density-dependent when its size

(or density) affects its growth rate because of density-dependent factors such as food availability and toxic waste accumulation

Density-independent Growth In this type of growth a population increases until

some factor causes a sudden reduction in its size Its effect is the same regardless of the size of the

population eg temperature fires floods storms etc

55

Regulation of Population Size Fecundity is the reproductive capacity of individual

females of a species Birth rate or natality is used to measure fecundity Death rate or mortality is the number of individuals

of a species which die per unit time Immigration occurs when individuals join a

population from neighbouring ones Emigration occurs when individuals depart from a

population A cycle occurs when the size of a population

fluctuates on a regular basis

56

Ecological Sampling

57

Why Do We Sample Determine presence andor

abundance

Monitor population fluctuations

Assess lsquoecological damagersquo

Assess quality of habitat

Assess population responses

58

What Do We Sample

Physical Environment Temperature DO pH salinity clarity

flow sediment

Biotic Environment All living things

59

Physical Habitat Temperature

Mercury thermometer Electronic thermometer Long-term thermometers

Dissolved Oxygen Winkler method (titration) DO meter (electrode)

pH Litmus paper pH meter (electrode)

Salinity Salinity Meter YSI 550A DO Meter w12 cable

60

Water Clarity Secchi Disk

Disk is attached to a calibrated rope The disk is lowered into the water until the white parts can no longer be seen Secchi disk depth is then recorded and serves as the waters transparency index The clearer the water the greater the secchi disk depth

Secchi Disk

61

Current Velocity (flow) Floating-orange method

Put an orange (or something else that floats just below the water surface) and measure the time it takes it to float across a known distance

Odometer-type flow meter Number of revolutions the propeller

makes for a given time is calibrated to flow velocity

62

Sediment Sediment size is important to many

aquatic organisms Sieversquos are used to separate and

grade sediment samples Percent of each size grade can be

determined

63

Water Sample

Water and plankton from various depths can be collected

A trigger mechanism is used to close the sampler Sample is then brought back to the

surface

64

Small Mammals

Mouserat Traps Fatal

Pit Falls Bucket is placed in the ground Sometimes have lsquoleadsrsquo to the buckets

Live traps Havahart Sherman

Spot-light

Sherman trapHavahart trap

65

Birds Stick-under-the-box method Bird-trap

Works like a minnow trap Mist net

Captures birds in flight Rocket net

Uses a propellant to throw a net over birds

66

Terrestrial Insects

Sticky paper flies

Baited Traps Fire ants

Nets butterflies

Foggers Collect insects from tree canopies

67

Aquatic Insects Drift Net

Place net in flowing water Kick Net

lsquoKickrsquo sediment upstream from block net and the flow will wash them into the net

Wash bucket Serber or Hess Sampler

Stir up known area of sediment

Animals are collected by a catch net

Multi-plate Sampler Become colonized

68

Crawfish and Crab Traps

69

Fish Larvae Light Traps

Larvae are attracted to the light Ichthyoplankton nets

Can be towed at various depths Fish collect at the lsquocodrsquoend

70

Fish Lift net

Net is placed down and after a set amount of time it is quickly lifted

Pop-net Similar to a lift net but

floats are attached to a framed net

Operated by a trigger mechanism

Throw net A net attached to a heavy

frame is thrown and every thing inside is netted out Throw net

Pop-net

Lift net

71

Minnow trap

Usually use bait to attract small fish Light is used sometimes as an attractant

72

Fish Electrofishing

Electricity is put into the water Fish are temporarily stunned and usually

swim towards the electricity source Usually non-fatal but may cause some

damage

73

Fish Gill Net

Gill nets resemble tennis nets Fish can not swim completely through the

net and get caught Gill nets are size selective (based on mesh

size) Square Mesh

Bar mesh

Stretch mesh

74

Fish Trammel Net

Three panels two large mesh on the outside and a small mesh on the inside

Fish swim through the outer mesh pushes the small mesh through the other side and becomes entangled

75

Hoop nets (and other similar nets) can have bait or not

Fyke nets have leads to help guide fish to the net

76

Seine Seines are nets that are pulled

through shallow water to catch fish

77

Purse Seine Used to encircle entire schools of fish

Usually involves a spotter plane and a second boat

78

Trotline (longline) A series of baited drop lines

connected to a main line

Can be deployed by tying one end to the bank and tying the other end with a heavy weight

79

Shrimp (or fish) Trawl Net pulled behind

a boat along the bottom Either a beam or

otter boards keep the net open

80

Tagging Individuals Coded Wire Tags

Microwire that has a unique label

Magnetic wand detects the tag

Tag retention should be determined

T-Bar tags Can be individually

numbered External tag

PIT tags (Passive Integrated Transponders) Wand induces the tag to

transmit individual number is displayed

81

Other Tagging Methods

Toe clip Amphibian and reptile Clip of one or more toes

to identify individuals

Bird Band Place a metal band on a

bird leg Generally has

identification information

82

Preserving plant specimens Pressing and drying Long-term

preservation and storage

Alternative drying techniques

Special preservation and processing techniques

Mounting

83

Pressing and drying Techniques for pressing and drying specimens have been

established for many years There are minor variations in recommended methods but they are essentially the same worldwide

The best specimens are plants that are pressed as soon as possible after collection before wilting and shrivelling Most plants may be kept in sealed containers such as plastic bags for up to a day if it is inconvenient to press immediately However some plants show such rapid wilting particularly of the flowers that such delays are best avoided Flowers with a lot of nectar may go mouldy very quickly if excess nectar is not shaken off before pressing

Specimens are pressed flat and dried between sheets of absorbent blotters or semi-absorbent paper such as newspaper Papers with a glossy surface should be avoided because they are not absorbent enough to aid drying The plant should be carefully laid out between the drying sheets as their form at this stage largely determines their ultimate appearance The flowers should be spread out with the petals carefully arranged wilted leaves should be straightened and unnecessary shoots of excessively twiggy shrubs may be cut away

84

Microwave ovens Small numbers of specimens can be dried using a microwave

oven The technique recommended in the literature is to place the specimens between unprinted absorbent paper for example butchers paper not newspaper which is unsuitable because the chemicals present in the ink may cause a fire The specimens should be put in a special press which should be of a microwave-safe material (wood acrylic or polycarbonate sheeting eg plexiglass or perspex NO metal components) If such a press is not available sheets of cardboard can be placed above and below the specimens and then weighted down

Drying time depends on the power of your oven In most cases drying is accomplished by irradiating at maximum power for 1-2 minutes per specimen although it is often a case of trial and error It is best to process no more than 10-12 specimens of average thickness per batch Specimens are usually dried after the moisture that characteristically appears on the glass door has disappeared If the specimen is damp when taken out of the oven allow it to stand before re-radiating as moisture continues to evaporate from the specimen for some time Care must be taken not to irradiate the specimens for too long

It should be noted that microwave treatment damages seeds and the cellular structure of the plants which may reduce the long-term value of the specimens

85

Alternative drying techniquesSilica gelother desiccants amp freeze drying Alternative methods of drying plant specimens have been

used for some time but are mostly restricted to special purpose collections The main alternatives are freeze-drying and drying in a desiccant powder such as desiccant silica gel In general these techniques are used where it is essential to preserve the shape of a delicate plant of organ of the plant such as the flower Freeze-drying has also been used to preserve the chemical composition of a plant as accurately as possible for later study

Disadvantages and special conservation problems of specimens dried in these manners are that they are particularly susceptible to damage The dried parts are fragile lack support and often catch on packing materials They must therefore be packed especially carefully and stored in small boxes or tubes with some appropriate packing material that does not snag and break small projections Acid-free tissue paper is often used Drying in desiccant silica gel crystals or powder can also have the disadvantage that it is difficult to remove all traces of the silica gel after drying

86

Special preservation and processing techniquesWet or spirit collections

Very fleshy or delicate structures including small algae and orchid flowers are best preserved in an air-tight glass or plastic jar with a liquid preservative rather than by drying The type of preservative used should be clearly labelled in the jar Such material is often referred to as a spirit collection or wet collection

Most material can be satisfactorily preserved in 70 ethyl alcohol (or 70 methylated spirit or denatured alcohol) with 30 water Colours will fade quickly in spirit however so it is a good idea to keep comprehensive notes and photographs

87

Small algae Microscopic algae are often collected in a jar and in the

water in which they were found If the algae are to be stored for more than 2-3 days a preservative needs to be used Traditionally this has been the extremely toxic formalin - a small amount can be added to the water to make a 5 final solution and the container labelled This must not be sent through the post or by courier

There are some other equally toxic options for example propylene phenoxytol but none should be sent through the post A safer option is to add sufficient concentrated alcohol or methylated spirits to the water containing the algae to make a final solution of 70 alcohol This treatment dilutes the algae making them difficult to find so if they can be concentrated somehow first (eg by filtering) they can be stored in much less liquid Another option is to fix the algae in formalin (or something similar) first and then prepare a microscope glass slide with a permanent water-soluble mounting medium

88

Mounting Mounting specimens prevents most fragile material from

fragmenting and prevents specimens becoming separated from their labels If the plant collection is a long-term project specimens should be mounted on sheets of archival (permanent) cardboard or paper with archival-quality fixing media These include stitching with cotton thread dental floss nickel-plated copper wire (for heavier specimens) narrow strips of archival paper linen tape or by using an archival adhesive such as methyl cellulose adhesive

One disadvantage of mounting specimens is that it can make parts of the specimen inaccessible for examination so it is essential that this be borne in mind during specimen arrangement and mounting For example easily reversible mounting media should be used specimens should be strapped to the sheet rather than glued all over and the specimen should be carefully arranged before it is attached so that it shows all features

89

Full-size herbarium mounting sheets are usually about 43 cm long x 28 cm wide The plant name and accompanying field notes should be transcribed on a permanent label stuck to one corner of the herbarium sheet (the bottom right-hand corner being the most common) or sometimes annotations may be written directly on the sheet or card

Small pieces of material which may have become separated from the specimen (eg seeds) can be placed in small plastic bags and pinned to the sheet

90

Long-term preservation and storage The long-term preservation of dry plant

specimens is largely dependent on protection from insect attack Specimens collected by Linnaeus in the eighteenth century and by Banks and Solander on the Endeavour voyage in 1788 are still excellently preserved

91

Pests and their control A range of pests attack dried plant material The

most common pests are insects and fungi though rodents and other large animals can cause damage in poor storage conditions Insects eat the material the paper surrounding the material and the adhesives and mounting media

Such insect pests range from psocids (book lice) which attack mainly the softer parts such as flowers and soft fruits to tobacco beetles and carpet beetles which can bore holes through the toughest of specimens Many insects are particularly sensitive to relative humidity levels and do not thrive at levels below 50

92

The most common and acceptable specimen treatments for insect control are Freezing Microwave Poisoning Insect deterrents Fungal pests

93

Storage

Dried and pressed plant specimens can be stored in cardboard or plastic boxes or tied in bundles in light-weight cardboard folders placed in pigeon holes

Alternatively they can be placed in protective plastic jackets and displayed in ring folders which is recommended if they are to be frequently handled such as for a reference collection

94

Filing

Specimens should be filed in a systematic order if a relatively permanent collection is being made The major groups ie ferns and fern allies cycads conifers dicotyledons and monocotyledons are best kept separately or according to some classification scheme such as that given in a flora or handbook

Similarly the genera within each family and the species within each genus may be filed alphabetically or following some such classification

95

Preservation of entire animals

Types of collection specimens of an entire animal For reference collections mammals can be prepared as a variety of specimens The condition of the specimen may determine possible ways to preserve it if for instance decomposition of the skin has loosened the hair of a carcass so much that it can easily be pulled out or removed by rubbing (ldquoslippingrdquo fur) it will be very difficult or impossible to produce a study skin or mounted specimen The most usual types of specimens (based on Nagorsen and Peterson 1980) are 1) entire fluid-preserved animals (for studying anatomy and histology fluid preservation may change the fur colour) 2) study skins with accompanying skulls partial skeletons (some bones remain in the skin) for studying pelage colour hair quality and moulting patterns 3) mounted skins with accompanying partial or entire skeleton (some bones may remain in the skin dependant on the method of preservation) or freeze-dried specimens 4) entire skeletons for instance for studying anatomy geographic variation or for age determination (entire skeletons are poorly represented in collections so Nagorsen and Peterson (1980) recommend preparation of at least one male and one female skeleton per species

96

Preservation of specimens in the field Formalin preservation Preservation in alcohol Preservation by cooling or freezing

97

Formalin preservation After weighing and measuring the animal and attaching an

adequate label very small specimens (up to 100 g) can be fixed whole by submerging them in 10 buffered formalin (tissue - formalin solution ratio of at least 1 12) the body cavity can be filled with formalin solution by injection until it is turgid and firm some formalin may also be injected under the skin into the body cavity larger muscles and organs If hypodermic needles are not available the body cavity can be opened ventrally by making a slit instead allowing the formalin to enter

Keeping the mouth open with a piece of wood or cotton may later allow examination of teeth Then the whole body can be immersed in formalin in the posture in which it is supposed to stay permanently because it will harden The ratio of formalin to carcass must be at least 12 to 1 to assure a good fixation Tissues can be left in buffered neutralized formalin for several months but formalin hardens specimens therefore after fixation longterm storage in alcohol may be better After preservation the carcass should therefore be washed in water and transferred into ethanol for permanent storage

Disadvantages for instance it discolours the fur after a longish immersion softens the bones and prevents further examination for microbiology

98

Preservation in alcohol

After weighing a whole animal can be preserved in a container of alcohol (70-90) Removal of the intestine prior to storage of the animal in alcohol is recommended

99

Preservation by cooling or freezing Removal of the skin with insulating fur

before cooling or freezing may help to cool the carcass down more quickly

Freezing is not recommended if histological examination is planned

100

THANK YOU

6

Why do we sample

Because it is usually impossible tocount all the plants or animals presentin a given areandash eg dragonfly larvae in a pondndash eg plant cover on a river terracendash eg species of plants in the estate

7

NON-INVASIVE SAMPLING

Avoid any degradation of the habitat when

sampling1048698 Removal of whole or parts of organismsshould be limited to species that can

quickly recover

8

REPRESENTATIVE SAMPLINGTake a number of samples from around the

sampling site so as to be reasonably sure that the samples represent the site in general

Necessitieshellip1048698 the samples represent the wholendash It is necessary to take enough samples so

that an accurate representation is obtainedndash It is necessary to avoid bias when sampling

9

SAMPLING UNITS

Type determined by the organisms and the physical nature of the habitat being sampled

ndash Area of ground surfacendash Volume of air water or soil1048698 Standard units enable comparison of

results

10

QUADRATS

A standard area sampling unit consisting of a square frame1048698 Consistent size and shape is essential for comparing

samples from different places andor timesQuadrat sizeChosen to suit sampling goals1048698 A balance between what is best and what is practical is

always necessary1048698 Should suitndash practical constraintsndash habitatndash organism

11

Quadrat Method A Quadrat is a sampling area of any

shape randomly deployed Each individual within the quadrat is counted and those numbers are used to extrapolate population size Example a 100 square centimeter metal

rectangle is randomly thrown four times and all of the beetles of a particular species within the square are counted each time 19 21 17 and 19 This translates to 19 beetles per 100 cm2 or 1900 per m2

12

QUADRAT amp TRANSECT ACTIVITIESHow Where amp Why Scientists Do SamplingScientists often collect data ldquoin the fieldrdquo which couldmean underwater in a forest in a cave on a reef oreven the moon Two essential methods to gatherecological information in a standardized way areTransect Sampling (using a single line) and

QuadratSampling (counted within a grid) These samplingmethods provide more accurate data than randomsampling or simply guessing but they take less timethan counting every specimen in a certain area

13

Quadrats- a sturdily built

wooden frame

can be folded for easy transport and storage

14

Quadrats

- When placed on the ground the species present within the frame are identified and their abundance recorded

- Sampling could be random or systematic

Using a quadrat along a belt transect

15

Practical Constraints

Small quadrats are quicker to survey but yield a smaller individual sample of habitat

ndash Often require a larger of samples to represent the habitat

1048698 Large quadrats require more time and effort to survey but provide a larger individual sample of habitat

ndash Often require a smaller of samples to represent the habitat

16

Habitat sizeAppropriate sample unit size depends on size scale

of the habitatndash Small scale habitats require smaller sized samples1048698 Ex Bouldersndash Large scale habitats require larger sized samples1048698 Ex Forests

17

Organism size and density

Depends on size and density of organisms

ndash Small dense organisms require smaller samples

1048698 Ex grassndash Large scattered organisms require

larger samples1048698 Ex Trees

18

TYPES OF SAMPLING

1048698 Systematic 1048698 Stratified 1048698 Random

19

SYSTEMATIC SAMPLING

1048698 Often used when the area being studied is varied not very large or

when time is available 1048698 Samples are taken at fixed intervals

20

How to sample systematicallySystematic samples are usually taken along a transect line marked by a tape measure

1048698 Transect- a line laid across an area

21

Sampling along gradients

Transects are setup along aenvironmentalgradientsndash down a hillsidendash across a streambedndash out from a source ofpollution

22

Types of transect sampling 1048698 Line transect 1048698 Belt transect

23

Line transect methodA measured line is laidacross the area in thedirection of theenvironmental gradientndash The species touching theline can be recordedalong the whole length ofthe line (continuoussampling) or at specificpoints along the line(systematic sampling)

24

Line Transect- useful where a transition of flora andor fauna

occurs- a string or tape is stretched out along the

ground in a straight line record the organisms touching or covering

the line all along its length or at regular intervals

- Profile transect when there is appreciable height change along the transect and thus affecting the distribution of its species

25

Belt transect method

Similar to line transect butwidens the sampling areandash Transect line is laid outndash Samples are taken bydetermining abundance or cover in an area that is adefined distance from the linendash Samples can be taken all

theway along the line at specificintervals or even randomly

26

Belt TransectIt is a strip usually a metre wide marked by putting a

second line parallel to the other The species between the lines are carefully recorded working a metre at a time

Alternatively a frame quadrat in conjunction with a single line transect could be used

Using a quadrat along a belt transect eg ladder transect (every 5m)

27

Point Frames- for grassland field study of dense vegetation

28

STRATIFIED SAMPLING1048698 Often used whenthere are smallareas within alarger habitat thatare clearly different1048698 Strata- majordifferences withincommunitiesrecognized beforesampling begins

29

RANDOM SAMPLING

1048698 Often used when the area being studied isfairly uniform very large or when there is alimited amount of time available1048698 Random = chosen by chance rather thanaccording to a plan all outcomes are

equallylikely1048698 Samples are taken from different positionswithin a habitat and those positions arechosen randomly

30

How to sample randomly

Choose individuals or Placeldquosampling unitsrdquo

haphazardlyndash This is rarely completely

random1048698 ORhellip1048698 Assign numbers to the

areasor individuals to be sampledndash Use a random number

table toselect which areas or

individualswill be sample

31

Population Attributes Density ndash size of a population in relation to a definite

unit of space Affected by

Natality ndash the reproductive output (birth rate) of a population

Mortality ndash the death rate of organisms in a population

Immigration ndash number of organisms moving into the area occupied by the population

Emigration ndash number of organisms moving out of the area occupied by the population

32

Population Density

Four primary population parameters

33

Two Types of Density Estimates

bull Absolute Density ndash a known density such as m2

bull Relative Density ndash we know when one area has more individuals than another

34

Measuring Absolute Density

Total Count ndash count the number of organisms living in an area Human census number of oak trees in a

wooded lot number of singing birds in an area

Total counts generally are not used very often

Sampling Methods ndash use a sample to estimate population size Either use the quadrat or capture-

recapture method

35

Measurement of Environmental ParametersAbiotic factors are important in determining

both the distribution of the organisms and their physical and physiological adaptations

Temperature- diurnal and seasonal temperature variations

are significant in affecting different species of plants and animals

- equipment mercury thermometer maximum-minimum thermometer

miniaturized thermistor

36

pH

-measure pH of a solution by universal indicator pH paper pH meter etc

Light

-measure its duration and intensity duration by predication from Royal Observatory intensity by photographic light meter

pH meter in use

37

Humidity

Relative humidity the water content of a given volume of air relative to the same volume of fully saturated air

- equipment whirling hygrometer

38

Wind and Water Speed- wind speed- anemometer or wind

gauges- water speed - time the movement of a

floating object over a measured distance

39

Salinity

- using a conductivity meter greater salinity has greater conductivity

Oxygen Level

- using an oxygen meter or chemical method (Winkler method)

40

Collecting MethodsCollecting all organisms within a habitat is normally

impractical and therefore small areas are selected Remember to return all material to its original position

after searching amp collecting sufficient specimens Some collecting apparatus for general use are listed

below

41

1 specimen tube

2 screwed-topped jars

3 polythene bags

4 forceps

5 paint brush

6 bulb pipette

7 pooter

42

8 widger 9 sieve 10 hand lens

11 enamel dish 12 beating tray 13 light traps

14 Tullgren funnel 15 Baermann funnel 16 mammal traps

17 pitfall traps 18 netting

43

Estimating Population Size

The exact methods used for estimation depend not only the nature of the habitat but also on the organisms involved

eg animals - population

plants - percentage cover

44

Using Quadrats

- By sampling an area using quadrats and counting the number of individuals within each quadrat it is possible to estimate the total number of individuals within the area

- confined to plants and sessile or very slow-moving animals

- fast-moving animals are disturbed and run away

45

Capture-recapture Techniques- useful for mobile animals which can be marked

- capture marked released randomly recaptured

and marked individuals recorded

no of marked individuals recaptured total no of individuals in 1st sample

-------------------------------------------- = ------------------------------------------

total no of individuals in 2nd sample estimated size of population

(the Lincoln Index)

46

Capture-recapture Techniques Factors affecting the accuracy of the estimation

deaths migration individuals become more liable to predation etc

Examples

- arthropods marked on their backs with non-toxic paint

- fish have tags attached to opercula - mammals have tags clipped to their ears

birds have their legs ringed

47

Capture-recapture Method Important tool for estimating density birth

rate and death rate for mobile animals Method

Collect a sample of individuals mark them and then release them

After a period collect more individuals from the wild and count the number that have marks

We assume that a sample if random will contain the same proportion of marked individuals as the population does

Estimate population density

48

Assumptions For All Capture-Recapture Studies Marking technique does not increase

mortality of marked animals Marked individuals are allowed to mix

with population Marking technique does not affect catch

probability Marks are not lost or overlooked No significant immigration or emigration No significant mortality or natality

49

Marked animals in second sample

Total caught in second sample

Marked animals in first sample

Total population size

=

520 N

16=

Peterson Method or Lincoln Index

N = 64N = (20)(16)5

50

Some Indices Used

Traps Number of Fecal

Pellets Vocalization

Frequency Pelt Records Catch per Unit

Fishing Effort

Number of Artifacts Questionnaires Cover Feeding Capacity Roadside Counts

51

Abundance Scales

The population size may be fairly accurately determined by making some form of frequency assessment

These are subjective and involve an experimenter making some estimate of the number of individuals in a given area or the cover of a particular species

This is especially useful where individuals are very numerous eg barnacles on a rocky shore or where it is difficult to distinguish individuals eg grass plants in a meadow

52

The assessments are usually made on an abundance scale of 5 categories

Abundance Common Frequent Occasional Rare

Barnacles exposed at low water

53

Environmental resistance are the factors which limit the growth of a particular population

eg predation disease availability of light food water oxygen and shelter the accumulation of toxic wastes and even the size of the population itself

54

Density-dependent Growth A population is a density-dependent when its size

(or density) affects its growth rate because of density-dependent factors such as food availability and toxic waste accumulation

Density-independent Growth In this type of growth a population increases until

some factor causes a sudden reduction in its size Its effect is the same regardless of the size of the

population eg temperature fires floods storms etc

55

Regulation of Population Size Fecundity is the reproductive capacity of individual

females of a species Birth rate or natality is used to measure fecundity Death rate or mortality is the number of individuals

of a species which die per unit time Immigration occurs when individuals join a

population from neighbouring ones Emigration occurs when individuals depart from a

population A cycle occurs when the size of a population

fluctuates on a regular basis

56

Ecological Sampling

57

Why Do We Sample Determine presence andor

abundance

Monitor population fluctuations

Assess lsquoecological damagersquo

Assess quality of habitat

Assess population responses

58

What Do We Sample

Physical Environment Temperature DO pH salinity clarity

flow sediment

Biotic Environment All living things

59

Physical Habitat Temperature

Mercury thermometer Electronic thermometer Long-term thermometers

Dissolved Oxygen Winkler method (titration) DO meter (electrode)

pH Litmus paper pH meter (electrode)

Salinity Salinity Meter YSI 550A DO Meter w12 cable

60

Water Clarity Secchi Disk

Disk is attached to a calibrated rope The disk is lowered into the water until the white parts can no longer be seen Secchi disk depth is then recorded and serves as the waters transparency index The clearer the water the greater the secchi disk depth

Secchi Disk

61

Current Velocity (flow) Floating-orange method

Put an orange (or something else that floats just below the water surface) and measure the time it takes it to float across a known distance

Odometer-type flow meter Number of revolutions the propeller

makes for a given time is calibrated to flow velocity

62

Sediment Sediment size is important to many

aquatic organisms Sieversquos are used to separate and

grade sediment samples Percent of each size grade can be

determined

63

Water Sample

Water and plankton from various depths can be collected

A trigger mechanism is used to close the sampler Sample is then brought back to the

surface

64

Small Mammals

Mouserat Traps Fatal

Pit Falls Bucket is placed in the ground Sometimes have lsquoleadsrsquo to the buckets

Live traps Havahart Sherman

Spot-light

Sherman trapHavahart trap

65

Birds Stick-under-the-box method Bird-trap

Works like a minnow trap Mist net

Captures birds in flight Rocket net

Uses a propellant to throw a net over birds

66

Terrestrial Insects

Sticky paper flies

Baited Traps Fire ants

Nets butterflies

Foggers Collect insects from tree canopies

67

Aquatic Insects Drift Net

Place net in flowing water Kick Net

lsquoKickrsquo sediment upstream from block net and the flow will wash them into the net

Wash bucket Serber or Hess Sampler

Stir up known area of sediment

Animals are collected by a catch net

Multi-plate Sampler Become colonized

68

Crawfish and Crab Traps

69

Fish Larvae Light Traps

Larvae are attracted to the light Ichthyoplankton nets

Can be towed at various depths Fish collect at the lsquocodrsquoend

70

Fish Lift net

Net is placed down and after a set amount of time it is quickly lifted

Pop-net Similar to a lift net but

floats are attached to a framed net

Operated by a trigger mechanism

Throw net A net attached to a heavy

frame is thrown and every thing inside is netted out Throw net

Pop-net

Lift net

71

Minnow trap

Usually use bait to attract small fish Light is used sometimes as an attractant

72

Fish Electrofishing

Electricity is put into the water Fish are temporarily stunned and usually

swim towards the electricity source Usually non-fatal but may cause some

damage

73

Fish Gill Net

Gill nets resemble tennis nets Fish can not swim completely through the

net and get caught Gill nets are size selective (based on mesh

size) Square Mesh

Bar mesh

Stretch mesh

74

Fish Trammel Net

Three panels two large mesh on the outside and a small mesh on the inside

Fish swim through the outer mesh pushes the small mesh through the other side and becomes entangled

75

Hoop nets (and other similar nets) can have bait or not

Fyke nets have leads to help guide fish to the net

76

Seine Seines are nets that are pulled

through shallow water to catch fish

77

Purse Seine Used to encircle entire schools of fish

Usually involves a spotter plane and a second boat

78

Trotline (longline) A series of baited drop lines

connected to a main line

Can be deployed by tying one end to the bank and tying the other end with a heavy weight

79

Shrimp (or fish) Trawl Net pulled behind

a boat along the bottom Either a beam or

otter boards keep the net open

80

Tagging Individuals Coded Wire Tags

Microwire that has a unique label

Magnetic wand detects the tag

Tag retention should be determined

T-Bar tags Can be individually

numbered External tag

PIT tags (Passive Integrated Transponders) Wand induces the tag to

transmit individual number is displayed

81

Other Tagging Methods

Toe clip Amphibian and reptile Clip of one or more toes

to identify individuals

Bird Band Place a metal band on a

bird leg Generally has

identification information

82

Preserving plant specimens Pressing and drying Long-term

preservation and storage

Alternative drying techniques

Special preservation and processing techniques

Mounting

83

Pressing and drying Techniques for pressing and drying specimens have been

established for many years There are minor variations in recommended methods but they are essentially the same worldwide

The best specimens are plants that are pressed as soon as possible after collection before wilting and shrivelling Most plants may be kept in sealed containers such as plastic bags for up to a day if it is inconvenient to press immediately However some plants show such rapid wilting particularly of the flowers that such delays are best avoided Flowers with a lot of nectar may go mouldy very quickly if excess nectar is not shaken off before pressing

Specimens are pressed flat and dried between sheets of absorbent blotters or semi-absorbent paper such as newspaper Papers with a glossy surface should be avoided because they are not absorbent enough to aid drying The plant should be carefully laid out between the drying sheets as their form at this stage largely determines their ultimate appearance The flowers should be spread out with the petals carefully arranged wilted leaves should be straightened and unnecessary shoots of excessively twiggy shrubs may be cut away

84

Microwave ovens Small numbers of specimens can be dried using a microwave

oven The technique recommended in the literature is to place the specimens between unprinted absorbent paper for example butchers paper not newspaper which is unsuitable because the chemicals present in the ink may cause a fire The specimens should be put in a special press which should be of a microwave-safe material (wood acrylic or polycarbonate sheeting eg plexiglass or perspex NO metal components) If such a press is not available sheets of cardboard can be placed above and below the specimens and then weighted down

Drying time depends on the power of your oven In most cases drying is accomplished by irradiating at maximum power for 1-2 minutes per specimen although it is often a case of trial and error It is best to process no more than 10-12 specimens of average thickness per batch Specimens are usually dried after the moisture that characteristically appears on the glass door has disappeared If the specimen is damp when taken out of the oven allow it to stand before re-radiating as moisture continues to evaporate from the specimen for some time Care must be taken not to irradiate the specimens for too long

It should be noted that microwave treatment damages seeds and the cellular structure of the plants which may reduce the long-term value of the specimens

85

Alternative drying techniquesSilica gelother desiccants amp freeze drying Alternative methods of drying plant specimens have been

used for some time but are mostly restricted to special purpose collections The main alternatives are freeze-drying and drying in a desiccant powder such as desiccant silica gel In general these techniques are used where it is essential to preserve the shape of a delicate plant of organ of the plant such as the flower Freeze-drying has also been used to preserve the chemical composition of a plant as accurately as possible for later study

Disadvantages and special conservation problems of specimens dried in these manners are that they are particularly susceptible to damage The dried parts are fragile lack support and often catch on packing materials They must therefore be packed especially carefully and stored in small boxes or tubes with some appropriate packing material that does not snag and break small projections Acid-free tissue paper is often used Drying in desiccant silica gel crystals or powder can also have the disadvantage that it is difficult to remove all traces of the silica gel after drying

86

Special preservation and processing techniquesWet or spirit collections

Very fleshy or delicate structures including small algae and orchid flowers are best preserved in an air-tight glass or plastic jar with a liquid preservative rather than by drying The type of preservative used should be clearly labelled in the jar Such material is often referred to as a spirit collection or wet collection

Most material can be satisfactorily preserved in 70 ethyl alcohol (or 70 methylated spirit or denatured alcohol) with 30 water Colours will fade quickly in spirit however so it is a good idea to keep comprehensive notes and photographs

87

Small algae Microscopic algae are often collected in a jar and in the

water in which they were found If the algae are to be stored for more than 2-3 days a preservative needs to be used Traditionally this has been the extremely toxic formalin - a small amount can be added to the water to make a 5 final solution and the container labelled This must not be sent through the post or by courier

There are some other equally toxic options for example propylene phenoxytol but none should be sent through the post A safer option is to add sufficient concentrated alcohol or methylated spirits to the water containing the algae to make a final solution of 70 alcohol This treatment dilutes the algae making them difficult to find so if they can be concentrated somehow first (eg by filtering) they can be stored in much less liquid Another option is to fix the algae in formalin (or something similar) first and then prepare a microscope glass slide with a permanent water-soluble mounting medium

88

Mounting Mounting specimens prevents most fragile material from

fragmenting and prevents specimens becoming separated from their labels If the plant collection is a long-term project specimens should be mounted on sheets of archival (permanent) cardboard or paper with archival-quality fixing media These include stitching with cotton thread dental floss nickel-plated copper wire (for heavier specimens) narrow strips of archival paper linen tape or by using an archival adhesive such as methyl cellulose adhesive

One disadvantage of mounting specimens is that it can make parts of the specimen inaccessible for examination so it is essential that this be borne in mind during specimen arrangement and mounting For example easily reversible mounting media should be used specimens should be strapped to the sheet rather than glued all over and the specimen should be carefully arranged before it is attached so that it shows all features

89

Full-size herbarium mounting sheets are usually about 43 cm long x 28 cm wide The plant name and accompanying field notes should be transcribed on a permanent label stuck to one corner of the herbarium sheet (the bottom right-hand corner being the most common) or sometimes annotations may be written directly on the sheet or card

Small pieces of material which may have become separated from the specimen (eg seeds) can be placed in small plastic bags and pinned to the sheet

90

Long-term preservation and storage The long-term preservation of dry plant

specimens is largely dependent on protection from insect attack Specimens collected by Linnaeus in the eighteenth century and by Banks and Solander on the Endeavour voyage in 1788 are still excellently preserved

91

Pests and their control A range of pests attack dried plant material The

most common pests are insects and fungi though rodents and other large animals can cause damage in poor storage conditions Insects eat the material the paper surrounding the material and the adhesives and mounting media

Such insect pests range from psocids (book lice) which attack mainly the softer parts such as flowers and soft fruits to tobacco beetles and carpet beetles which can bore holes through the toughest of specimens Many insects are particularly sensitive to relative humidity levels and do not thrive at levels below 50

92

The most common and acceptable specimen treatments for insect control are Freezing Microwave Poisoning Insect deterrents Fungal pests

93

Storage

Dried and pressed plant specimens can be stored in cardboard or plastic boxes or tied in bundles in light-weight cardboard folders placed in pigeon holes

Alternatively they can be placed in protective plastic jackets and displayed in ring folders which is recommended if they are to be frequently handled such as for a reference collection

94

Filing

Specimens should be filed in a systematic order if a relatively permanent collection is being made The major groups ie ferns and fern allies cycads conifers dicotyledons and monocotyledons are best kept separately or according to some classification scheme such as that given in a flora or handbook

Similarly the genera within each family and the species within each genus may be filed alphabetically or following some such classification

95

Preservation of entire animals

Types of collection specimens of an entire animal For reference collections mammals can be prepared as a variety of specimens The condition of the specimen may determine possible ways to preserve it if for instance decomposition of the skin has loosened the hair of a carcass so much that it can easily be pulled out or removed by rubbing (ldquoslippingrdquo fur) it will be very difficult or impossible to produce a study skin or mounted specimen The most usual types of specimens (based on Nagorsen and Peterson 1980) are 1) entire fluid-preserved animals (for studying anatomy and histology fluid preservation may change the fur colour) 2) study skins with accompanying skulls partial skeletons (some bones remain in the skin) for studying pelage colour hair quality and moulting patterns 3) mounted skins with accompanying partial or entire skeleton (some bones may remain in the skin dependant on the method of preservation) or freeze-dried specimens 4) entire skeletons for instance for studying anatomy geographic variation or for age determination (entire skeletons are poorly represented in collections so Nagorsen and Peterson (1980) recommend preparation of at least one male and one female skeleton per species

96

Preservation of specimens in the field Formalin preservation Preservation in alcohol Preservation by cooling or freezing

97

Formalin preservation After weighing and measuring the animal and attaching an

adequate label very small specimens (up to 100 g) can be fixed whole by submerging them in 10 buffered formalin (tissue - formalin solution ratio of at least 1 12) the body cavity can be filled with formalin solution by injection until it is turgid and firm some formalin may also be injected under the skin into the body cavity larger muscles and organs If hypodermic needles are not available the body cavity can be opened ventrally by making a slit instead allowing the formalin to enter

Keeping the mouth open with a piece of wood or cotton may later allow examination of teeth Then the whole body can be immersed in formalin in the posture in which it is supposed to stay permanently because it will harden The ratio of formalin to carcass must be at least 12 to 1 to assure a good fixation Tissues can be left in buffered neutralized formalin for several months but formalin hardens specimens therefore after fixation longterm storage in alcohol may be better After preservation the carcass should therefore be washed in water and transferred into ethanol for permanent storage

Disadvantages for instance it discolours the fur after a longish immersion softens the bones and prevents further examination for microbiology

98

Preservation in alcohol

After weighing a whole animal can be preserved in a container of alcohol (70-90) Removal of the intestine prior to storage of the animal in alcohol is recommended

99

Preservation by cooling or freezing Removal of the skin with insulating fur

before cooling or freezing may help to cool the carcass down more quickly

Freezing is not recommended if histological examination is planned

100

THANK YOU

7

NON-INVASIVE SAMPLING

Avoid any degradation of the habitat when

sampling1048698 Removal of whole or parts of organismsshould be limited to species that can

quickly recover

8

REPRESENTATIVE SAMPLINGTake a number of samples from around the

sampling site so as to be reasonably sure that the samples represent the site in general

Necessitieshellip1048698 the samples represent the wholendash It is necessary to take enough samples so

that an accurate representation is obtainedndash It is necessary to avoid bias when sampling

9

SAMPLING UNITS

Type determined by the organisms and the physical nature of the habitat being sampled

ndash Area of ground surfacendash Volume of air water or soil1048698 Standard units enable comparison of

results

10

QUADRATS

A standard area sampling unit consisting of a square frame1048698 Consistent size and shape is essential for comparing

samples from different places andor timesQuadrat sizeChosen to suit sampling goals1048698 A balance between what is best and what is practical is

always necessary1048698 Should suitndash practical constraintsndash habitatndash organism

11

Quadrat Method A Quadrat is a sampling area of any

shape randomly deployed Each individual within the quadrat is counted and those numbers are used to extrapolate population size Example a 100 square centimeter metal

rectangle is randomly thrown four times and all of the beetles of a particular species within the square are counted each time 19 21 17 and 19 This translates to 19 beetles per 100 cm2 or 1900 per m2

12

QUADRAT amp TRANSECT ACTIVITIESHow Where amp Why Scientists Do SamplingScientists often collect data ldquoin the fieldrdquo which couldmean underwater in a forest in a cave on a reef oreven the moon Two essential methods to gatherecological information in a standardized way areTransect Sampling (using a single line) and

QuadratSampling (counted within a grid) These samplingmethods provide more accurate data than randomsampling or simply guessing but they take less timethan counting every specimen in a certain area

13

Quadrats- a sturdily built

wooden frame

can be folded for easy transport and storage

14

Quadrats

- When placed on the ground the species present within the frame are identified and their abundance recorded

- Sampling could be random or systematic

Using a quadrat along a belt transect

15

Practical Constraints

Small quadrats are quicker to survey but yield a smaller individual sample of habitat

ndash Often require a larger of samples to represent the habitat

1048698 Large quadrats require more time and effort to survey but provide a larger individual sample of habitat

ndash Often require a smaller of samples to represent the habitat

16

Habitat sizeAppropriate sample unit size depends on size scale

of the habitatndash Small scale habitats require smaller sized samples1048698 Ex Bouldersndash Large scale habitats require larger sized samples1048698 Ex Forests

17

Organism size and density

Depends on size and density of organisms

ndash Small dense organisms require smaller samples

1048698 Ex grassndash Large scattered organisms require

larger samples1048698 Ex Trees

18

TYPES OF SAMPLING

1048698 Systematic 1048698 Stratified 1048698 Random

19

SYSTEMATIC SAMPLING

1048698 Often used when the area being studied is varied not very large or

when time is available 1048698 Samples are taken at fixed intervals

20

How to sample systematicallySystematic samples are usually taken along a transect line marked by a tape measure

1048698 Transect- a line laid across an area

21

Sampling along gradients

Transects are setup along aenvironmentalgradientsndash down a hillsidendash across a streambedndash out from a source ofpollution

22

Types of transect sampling 1048698 Line transect 1048698 Belt transect

23

Line transect methodA measured line is laidacross the area in thedirection of theenvironmental gradientndash The species touching theline can be recordedalong the whole length ofthe line (continuoussampling) or at specificpoints along the line(systematic sampling)

24

Line Transect- useful where a transition of flora andor fauna

occurs- a string or tape is stretched out along the

ground in a straight line record the organisms touching or covering

the line all along its length or at regular intervals

- Profile transect when there is appreciable height change along the transect and thus affecting the distribution of its species

25

Belt transect method

Similar to line transect butwidens the sampling areandash Transect line is laid outndash Samples are taken bydetermining abundance or cover in an area that is adefined distance from the linendash Samples can be taken all

theway along the line at specificintervals or even randomly

26

Belt TransectIt is a strip usually a metre wide marked by putting a

second line parallel to the other The species between the lines are carefully recorded working a metre at a time

Alternatively a frame quadrat in conjunction with a single line transect could be used

Using a quadrat along a belt transect eg ladder transect (every 5m)

27

Point Frames- for grassland field study of dense vegetation

28

STRATIFIED SAMPLING1048698 Often used whenthere are smallareas within alarger habitat thatare clearly different1048698 Strata- majordifferences withincommunitiesrecognized beforesampling begins

29

RANDOM SAMPLING

1048698 Often used when the area being studied isfairly uniform very large or when there is alimited amount of time available1048698 Random = chosen by chance rather thanaccording to a plan all outcomes are

equallylikely1048698 Samples are taken from different positionswithin a habitat and those positions arechosen randomly

30

How to sample randomly

Choose individuals or Placeldquosampling unitsrdquo

haphazardlyndash This is rarely completely

random1048698 ORhellip1048698 Assign numbers to the

areasor individuals to be sampledndash Use a random number

table toselect which areas or

individualswill be sample

31

Population Attributes Density ndash size of a population in relation to a definite

unit of space Affected by

Natality ndash the reproductive output (birth rate) of a population

Mortality ndash the death rate of organisms in a population

Immigration ndash number of organisms moving into the area occupied by the population

Emigration ndash number of organisms moving out of the area occupied by the population

32

Population Density

Four primary population parameters

33

Two Types of Density Estimates

bull Absolute Density ndash a known density such as m2

bull Relative Density ndash we know when one area has more individuals than another

34

Measuring Absolute Density

Total Count ndash count the number of organisms living in an area Human census number of oak trees in a

wooded lot number of singing birds in an area

Total counts generally are not used very often

Sampling Methods ndash use a sample to estimate population size Either use the quadrat or capture-

recapture method

35

Measurement of Environmental ParametersAbiotic factors are important in determining

both the distribution of the organisms and their physical and physiological adaptations

Temperature- diurnal and seasonal temperature variations

are significant in affecting different species of plants and animals

- equipment mercury thermometer maximum-minimum thermometer

miniaturized thermistor

36

pH

-measure pH of a solution by universal indicator pH paper pH meter etc

Light

-measure its duration and intensity duration by predication from Royal Observatory intensity by photographic light meter

pH meter in use

37

Humidity

Relative humidity the water content of a given volume of air relative to the same volume of fully saturated air

- equipment whirling hygrometer

38

Wind and Water Speed- wind speed- anemometer or wind

gauges- water speed - time the movement of a

floating object over a measured distance

39

Salinity

- using a conductivity meter greater salinity has greater conductivity

Oxygen Level

- using an oxygen meter or chemical method (Winkler method)

40

Collecting MethodsCollecting all organisms within a habitat is normally

impractical and therefore small areas are selected Remember to return all material to its original position

after searching amp collecting sufficient specimens Some collecting apparatus for general use are listed

below

41

1 specimen tube

2 screwed-topped jars

3 polythene bags

4 forceps

5 paint brush

6 bulb pipette

7 pooter

42

8 widger 9 sieve 10 hand lens

11 enamel dish 12 beating tray 13 light traps

14 Tullgren funnel 15 Baermann funnel 16 mammal traps

17 pitfall traps 18 netting

43

Estimating Population Size

The exact methods used for estimation depend not only the nature of the habitat but also on the organisms involved

eg animals - population

plants - percentage cover

44

Using Quadrats

- By sampling an area using quadrats and counting the number of individuals within each quadrat it is possible to estimate the total number of individuals within the area

- confined to plants and sessile or very slow-moving animals

- fast-moving animals are disturbed and run away

45

Capture-recapture Techniques- useful for mobile animals which can be marked

- capture marked released randomly recaptured

and marked individuals recorded

no of marked individuals recaptured total no of individuals in 1st sample

-------------------------------------------- = ------------------------------------------

total no of individuals in 2nd sample estimated size of population

(the Lincoln Index)

46

Capture-recapture Techniques Factors affecting the accuracy of the estimation

deaths migration individuals become more liable to predation etc

Examples

- arthropods marked on their backs with non-toxic paint

- fish have tags attached to opercula - mammals have tags clipped to their ears

birds have their legs ringed

47

Capture-recapture Method Important tool for estimating density birth

rate and death rate for mobile animals Method

Collect a sample of individuals mark them and then release them

After a period collect more individuals from the wild and count the number that have marks

We assume that a sample if random will contain the same proportion of marked individuals as the population does

Estimate population density

48

Assumptions For All Capture-Recapture Studies Marking technique does not increase

mortality of marked animals Marked individuals are allowed to mix

with population Marking technique does not affect catch

probability Marks are not lost or overlooked No significant immigration or emigration No significant mortality or natality

49

Marked animals in second sample

Total caught in second sample

Marked animals in first sample

Total population size

=

520 N

16=

Peterson Method or Lincoln Index

N = 64N = (20)(16)5

50

Some Indices Used

Traps Number of Fecal

Pellets Vocalization

Frequency Pelt Records Catch per Unit

Fishing Effort

Number of Artifacts Questionnaires Cover Feeding Capacity Roadside Counts

51

Abundance Scales

The population size may be fairly accurately determined by making some form of frequency assessment

These are subjective and involve an experimenter making some estimate of the number of individuals in a given area or the cover of a particular species

This is especially useful where individuals are very numerous eg barnacles on a rocky shore or where it is difficult to distinguish individuals eg grass plants in a meadow

52

The assessments are usually made on an abundance scale of 5 categories

Abundance Common Frequent Occasional Rare

Barnacles exposed at low water

53

Environmental resistance are the factors which limit the growth of a particular population

eg predation disease availability of light food water oxygen and shelter the accumulation of toxic wastes and even the size of the population itself

54

Density-dependent Growth A population is a density-dependent when its size

(or density) affects its growth rate because of density-dependent factors such as food availability and toxic waste accumulation

Density-independent Growth In this type of growth a population increases until

some factor causes a sudden reduction in its size Its effect is the same regardless of the size of the

population eg temperature fires floods storms etc

55

Regulation of Population Size Fecundity is the reproductive capacity of individual

females of a species Birth rate or natality is used to measure fecundity Death rate or mortality is the number of individuals

of a species which die per unit time Immigration occurs when individuals join a

population from neighbouring ones Emigration occurs when individuals depart from a

population A cycle occurs when the size of a population

fluctuates on a regular basis

56

Ecological Sampling

57

Why Do We Sample Determine presence andor

abundance

Monitor population fluctuations

Assess lsquoecological damagersquo

Assess quality of habitat

Assess population responses

58

What Do We Sample

Physical Environment Temperature DO pH salinity clarity

flow sediment

Biotic Environment All living things

59

Physical Habitat Temperature

Mercury thermometer Electronic thermometer Long-term thermometers

Dissolved Oxygen Winkler method (titration) DO meter (electrode)

pH Litmus paper pH meter (electrode)

Salinity Salinity Meter YSI 550A DO Meter w12 cable

60

Water Clarity Secchi Disk

Disk is attached to a calibrated rope The disk is lowered into the water until the white parts can no longer be seen Secchi disk depth is then recorded and serves as the waters transparency index The clearer the water the greater the secchi disk depth

Secchi Disk

61

Current Velocity (flow) Floating-orange method

Put an orange (or something else that floats just below the water surface) and measure the time it takes it to float across a known distance

Odometer-type flow meter Number of revolutions the propeller

makes for a given time is calibrated to flow velocity

62

Sediment Sediment size is important to many

aquatic organisms Sieversquos are used to separate and

grade sediment samples Percent of each size grade can be

determined

63

Water Sample

Water and plankton from various depths can be collected

A trigger mechanism is used to close the sampler Sample is then brought back to the

surface

64

Small Mammals

Mouserat Traps Fatal

Pit Falls Bucket is placed in the ground Sometimes have lsquoleadsrsquo to the buckets

Live traps Havahart Sherman

Spot-light

Sherman trapHavahart trap

65

Birds Stick-under-the-box method Bird-trap

Works like a minnow trap Mist net

Captures birds in flight Rocket net

Uses a propellant to throw a net over birds

66

Terrestrial Insects

Sticky paper flies

Baited Traps Fire ants

Nets butterflies

Foggers Collect insects from tree canopies

67

Aquatic Insects Drift Net

Place net in flowing water Kick Net

lsquoKickrsquo sediment upstream from block net and the flow will wash them into the net

Wash bucket Serber or Hess Sampler

Stir up known area of sediment

Animals are collected by a catch net

Multi-plate Sampler Become colonized

68

Crawfish and Crab Traps

69

Fish Larvae Light Traps

Larvae are attracted to the light Ichthyoplankton nets

Can be towed at various depths Fish collect at the lsquocodrsquoend

70

Fish Lift net

Net is placed down and after a set amount of time it is quickly lifted

Pop-net Similar to a lift net but

floats are attached to a framed net

Operated by a trigger mechanism

Throw net A net attached to a heavy

frame is thrown and every thing inside is netted out Throw net

Pop-net

Lift net

71

Minnow trap

Usually use bait to attract small fish Light is used sometimes as an attractant

72

Fish Electrofishing

Electricity is put into the water Fish are temporarily stunned and usually

swim towards the electricity source Usually non-fatal but may cause some

damage

73

Fish Gill Net

Gill nets resemble tennis nets Fish can not swim completely through the

net and get caught Gill nets are size selective (based on mesh

size) Square Mesh

Bar mesh

Stretch mesh

74

Fish Trammel Net

Three panels two large mesh on the outside and a small mesh on the inside

Fish swim through the outer mesh pushes the small mesh through the other side and becomes entangled

75

Hoop nets (and other similar nets) can have bait or not

Fyke nets have leads to help guide fish to the net

76

Seine Seines are nets that are pulled

through shallow water to catch fish

77

Purse Seine Used to encircle entire schools of fish

Usually involves a spotter plane and a second boat

78

Trotline (longline) A series of baited drop lines

connected to a main line

Can be deployed by tying one end to the bank and tying the other end with a heavy weight

79

Shrimp (or fish) Trawl Net pulled behind

a boat along the bottom Either a beam or

otter boards keep the net open

80

Tagging Individuals Coded Wire Tags

Microwire that has a unique label

Magnetic wand detects the tag

Tag retention should be determined

T-Bar tags Can be individually

numbered External tag

PIT tags (Passive Integrated Transponders) Wand induces the tag to

transmit individual number is displayed

81

Other Tagging Methods

Toe clip Amphibian and reptile Clip of one or more toes

to identify individuals

Bird Band Place a metal band on a

bird leg Generally has

identification information

82

Preserving plant specimens Pressing and drying Long-term

preservation and storage

Alternative drying techniques

Special preservation and processing techniques

Mounting

83

Pressing and drying Techniques for pressing and drying specimens have been

established for many years There are minor variations in recommended methods but they are essentially the same worldwide

The best specimens are plants that are pressed as soon as possible after collection before wilting and shrivelling Most plants may be kept in sealed containers such as plastic bags for up to a day if it is inconvenient to press immediately However some plants show such rapid wilting particularly of the flowers that such delays are best avoided Flowers with a lot of nectar may go mouldy very quickly if excess nectar is not shaken off before pressing

Specimens are pressed flat and dried between sheets of absorbent blotters or semi-absorbent paper such as newspaper Papers with a glossy surface should be avoided because they are not absorbent enough to aid drying The plant should be carefully laid out between the drying sheets as their form at this stage largely determines their ultimate appearance The flowers should be spread out with the petals carefully arranged wilted leaves should be straightened and unnecessary shoots of excessively twiggy shrubs may be cut away

84

Microwave ovens Small numbers of specimens can be dried using a microwave

oven The technique recommended in the literature is to place the specimens between unprinted absorbent paper for example butchers paper not newspaper which is unsuitable because the chemicals present in the ink may cause a fire The specimens should be put in a special press which should be of a microwave-safe material (wood acrylic or polycarbonate sheeting eg plexiglass or perspex NO metal components) If such a press is not available sheets of cardboard can be placed above and below the specimens and then weighted down

Drying time depends on the power of your oven In most cases drying is accomplished by irradiating at maximum power for 1-2 minutes per specimen although it is often a case of trial and error It is best to process no more than 10-12 specimens of average thickness per batch Specimens are usually dried after the moisture that characteristically appears on the glass door has disappeared If the specimen is damp when taken out of the oven allow it to stand before re-radiating as moisture continues to evaporate from the specimen for some time Care must be taken not to irradiate the specimens for too long

It should be noted that microwave treatment damages seeds and the cellular structure of the plants which may reduce the long-term value of the specimens

85

Alternative drying techniquesSilica gelother desiccants amp freeze drying Alternative methods of drying plant specimens have been

used for some time but are mostly restricted to special purpose collections The main alternatives are freeze-drying and drying in a desiccant powder such as desiccant silica gel In general these techniques are used where it is essential to preserve the shape of a delicate plant of organ of the plant such as the flower Freeze-drying has also been used to preserve the chemical composition of a plant as accurately as possible for later study

Disadvantages and special conservation problems of specimens dried in these manners are that they are particularly susceptible to damage The dried parts are fragile lack support and often catch on packing materials They must therefore be packed especially carefully and stored in small boxes or tubes with some appropriate packing material that does not snag and break small projections Acid-free tissue paper is often used Drying in desiccant silica gel crystals or powder can also have the disadvantage that it is difficult to remove all traces of the silica gel after drying

86

Special preservation and processing techniquesWet or spirit collections

Very fleshy or delicate structures including small algae and orchid flowers are best preserved in an air-tight glass or plastic jar with a liquid preservative rather than by drying The type of preservative used should be clearly labelled in the jar Such material is often referred to as a spirit collection or wet collection

Most material can be satisfactorily preserved in 70 ethyl alcohol (or 70 methylated spirit or denatured alcohol) with 30 water Colours will fade quickly in spirit however so it is a good idea to keep comprehensive notes and photographs

87

Small algae Microscopic algae are often collected in a jar and in the

water in which they were found If the algae are to be stored for more than 2-3 days a preservative needs to be used Traditionally this has been the extremely toxic formalin - a small amount can be added to the water to make a 5 final solution and the container labelled This must not be sent through the post or by courier

There are some other equally toxic options for example propylene phenoxytol but none should be sent through the post A safer option is to add sufficient concentrated alcohol or methylated spirits to the water containing the algae to make a final solution of 70 alcohol This treatment dilutes the algae making them difficult to find so if they can be concentrated somehow first (eg by filtering) they can be stored in much less liquid Another option is to fix the algae in formalin (or something similar) first and then prepare a microscope glass slide with a permanent water-soluble mounting medium

88

Mounting Mounting specimens prevents most fragile material from

fragmenting and prevents specimens becoming separated from their labels If the plant collection is a long-term project specimens should be mounted on sheets of archival (permanent) cardboard or paper with archival-quality fixing media These include stitching with cotton thread dental floss nickel-plated copper wire (for heavier specimens) narrow strips of archival paper linen tape or by using an archival adhesive such as methyl cellulose adhesive

One disadvantage of mounting specimens is that it can make parts of the specimen inaccessible for examination so it is essential that this be borne in mind during specimen arrangement and mounting For example easily reversible mounting media should be used specimens should be strapped to the sheet rather than glued all over and the specimen should be carefully arranged before it is attached so that it shows all features

89

Full-size herbarium mounting sheets are usually about 43 cm long x 28 cm wide The plant name and accompanying field notes should be transcribed on a permanent label stuck to one corner of the herbarium sheet (the bottom right-hand corner being the most common) or sometimes annotations may be written directly on the sheet or card

Small pieces of material which may have become separated from the specimen (eg seeds) can be placed in small plastic bags and pinned to the sheet

90

Long-term preservation and storage The long-term preservation of dry plant

specimens is largely dependent on protection from insect attack Specimens collected by Linnaeus in the eighteenth century and by Banks and Solander on the Endeavour voyage in 1788 are still excellently preserved

91

Pests and their control A range of pests attack dried plant material The

most common pests are insects and fungi though rodents and other large animals can cause damage in poor storage conditions Insects eat the material the paper surrounding the material and the adhesives and mounting media

Such insect pests range from psocids (book lice) which attack mainly the softer parts such as flowers and soft fruits to tobacco beetles and carpet beetles which can bore holes through the toughest of specimens Many insects are particularly sensitive to relative humidity levels and do not thrive at levels below 50

92

The most common and acceptable specimen treatments for insect control are Freezing Microwave Poisoning Insect deterrents Fungal pests

93

Storage

Dried and pressed plant specimens can be stored in cardboard or plastic boxes or tied in bundles in light-weight cardboard folders placed in pigeon holes

Alternatively they can be placed in protective plastic jackets and displayed in ring folders which is recommended if they are to be frequently handled such as for a reference collection

94

Filing

Specimens should be filed in a systematic order if a relatively permanent collection is being made The major groups ie ferns and fern allies cycads conifers dicotyledons and monocotyledons are best kept separately or according to some classification scheme such as that given in a flora or handbook

Similarly the genera within each family and the species within each genus may be filed alphabetically or following some such classification

95

Preservation of entire animals

Types of collection specimens of an entire animal For reference collections mammals can be prepared as a variety of specimens The condition of the specimen may determine possible ways to preserve it if for instance decomposition of the skin has loosened the hair of a carcass so much that it can easily be pulled out or removed by rubbing (ldquoslippingrdquo fur) it will be very difficult or impossible to produce a study skin or mounted specimen The most usual types of specimens (based on Nagorsen and Peterson 1980) are 1) entire fluid-preserved animals (for studying anatomy and histology fluid preservation may change the fur colour) 2) study skins with accompanying skulls partial skeletons (some bones remain in the skin) for studying pelage colour hair quality and moulting patterns 3) mounted skins with accompanying partial or entire skeleton (some bones may remain in the skin dependant on the method of preservation) or freeze-dried specimens 4) entire skeletons for instance for studying anatomy geographic variation or for age determination (entire skeletons are poorly represented in collections so Nagorsen and Peterson (1980) recommend preparation of at least one male and one female skeleton per species

96

Preservation of specimens in the field Formalin preservation Preservation in alcohol Preservation by cooling or freezing

97

Formalin preservation After weighing and measuring the animal and attaching an

adequate label very small specimens (up to 100 g) can be fixed whole by submerging them in 10 buffered formalin (tissue - formalin solution ratio of at least 1 12) the body cavity can be filled with formalin solution by injection until it is turgid and firm some formalin may also be injected under the skin into the body cavity larger muscles and organs If hypodermic needles are not available the body cavity can be opened ventrally by making a slit instead allowing the formalin to enter

Keeping the mouth open with a piece of wood or cotton may later allow examination of teeth Then the whole body can be immersed in formalin in the posture in which it is supposed to stay permanently because it will harden The ratio of formalin to carcass must be at least 12 to 1 to assure a good fixation Tissues can be left in buffered neutralized formalin for several months but formalin hardens specimens therefore after fixation longterm storage in alcohol may be better After preservation the carcass should therefore be washed in water and transferred into ethanol for permanent storage

Disadvantages for instance it discolours the fur after a longish immersion softens the bones and prevents further examination for microbiology

98

Preservation in alcohol

After weighing a whole animal can be preserved in a container of alcohol (70-90) Removal of the intestine prior to storage of the animal in alcohol is recommended

99

Preservation by cooling or freezing Removal of the skin with insulating fur

before cooling or freezing may help to cool the carcass down more quickly

Freezing is not recommended if histological examination is planned

100

THANK YOU

8

REPRESENTATIVE SAMPLINGTake a number of samples from around the

sampling site so as to be reasonably sure that the samples represent the site in general

Necessitieshellip1048698 the samples represent the wholendash It is necessary to take enough samples so

that an accurate representation is obtainedndash It is necessary to avoid bias when sampling

9

SAMPLING UNITS

Type determined by the organisms and the physical nature of the habitat being sampled

ndash Area of ground surfacendash Volume of air water or soil1048698 Standard units enable comparison of

results

10

QUADRATS

A standard area sampling unit consisting of a square frame1048698 Consistent size and shape is essential for comparing

samples from different places andor timesQuadrat sizeChosen to suit sampling goals1048698 A balance between what is best and what is practical is

always necessary1048698 Should suitndash practical constraintsndash habitatndash organism

11

Quadrat Method A Quadrat is a sampling area of any

shape randomly deployed Each individual within the quadrat is counted and those numbers are used to extrapolate population size Example a 100 square centimeter metal

rectangle is randomly thrown four times and all of the beetles of a particular species within the square are counted each time 19 21 17 and 19 This translates to 19 beetles per 100 cm2 or 1900 per m2

12

QUADRAT amp TRANSECT ACTIVITIESHow Where amp Why Scientists Do SamplingScientists often collect data ldquoin the fieldrdquo which couldmean underwater in a forest in a cave on a reef oreven the moon Two essential methods to gatherecological information in a standardized way areTransect Sampling (using a single line) and

QuadratSampling (counted within a grid) These samplingmethods provide more accurate data than randomsampling or simply guessing but they take less timethan counting every specimen in a certain area

13

Quadrats- a sturdily built

wooden frame

can be folded for easy transport and storage

14

Quadrats

- When placed on the ground the species present within the frame are identified and their abundance recorded

- Sampling could be random or systematic

Using a quadrat along a belt transect

15

Practical Constraints

Small quadrats are quicker to survey but yield a smaller individual sample of habitat

ndash Often require a larger of samples to represent the habitat

1048698 Large quadrats require more time and effort to survey but provide a larger individual sample of habitat

ndash Often require a smaller of samples to represent the habitat

16

Habitat sizeAppropriate sample unit size depends on size scale

of the habitatndash Small scale habitats require smaller sized samples1048698 Ex Bouldersndash Large scale habitats require larger sized samples1048698 Ex Forests

17

Organism size and density

Depends on size and density of organisms

ndash Small dense organisms require smaller samples

1048698 Ex grassndash Large scattered organisms require

larger samples1048698 Ex Trees

18

TYPES OF SAMPLING

1048698 Systematic 1048698 Stratified 1048698 Random

19

SYSTEMATIC SAMPLING

1048698 Often used when the area being studied is varied not very large or

when time is available 1048698 Samples are taken at fixed intervals

20

How to sample systematicallySystematic samples are usually taken along a transect line marked by a tape measure

1048698 Transect- a line laid across an area

21

Sampling along gradients

Transects are setup along aenvironmentalgradientsndash down a hillsidendash across a streambedndash out from a source ofpollution

22

Types of transect sampling 1048698 Line transect 1048698 Belt transect

23

Line transect methodA measured line is laidacross the area in thedirection of theenvironmental gradientndash The species touching theline can be recordedalong the whole length ofthe line (continuoussampling) or at specificpoints along the line(systematic sampling)

24

Line Transect- useful where a transition of flora andor fauna

occurs- a string or tape is stretched out along the

ground in a straight line record the organisms touching or covering

the line all along its length or at regular intervals

- Profile transect when there is appreciable height change along the transect and thus affecting the distribution of its species

25

Belt transect method

Similar to line transect butwidens the sampling areandash Transect line is laid outndash Samples are taken bydetermining abundance or cover in an area that is adefined distance from the linendash Samples can be taken all

theway along the line at specificintervals or even randomly

26

Belt TransectIt is a strip usually a metre wide marked by putting a

second line parallel to the other The species between the lines are carefully recorded working a metre at a time

Alternatively a frame quadrat in conjunction with a single line transect could be used

Using a quadrat along a belt transect eg ladder transect (every 5m)

27

Point Frames- for grassland field study of dense vegetation

28

STRATIFIED SAMPLING1048698 Often used whenthere are smallareas within alarger habitat thatare clearly different1048698 Strata- majordifferences withincommunitiesrecognized beforesampling begins

29

RANDOM SAMPLING

1048698 Often used when the area being studied isfairly uniform very large or when there is alimited amount of time available1048698 Random = chosen by chance rather thanaccording to a plan all outcomes are

equallylikely1048698 Samples are taken from different positionswithin a habitat and those positions arechosen randomly

30

How to sample randomly

Choose individuals or Placeldquosampling unitsrdquo

haphazardlyndash This is rarely completely

random1048698 ORhellip1048698 Assign numbers to the

areasor individuals to be sampledndash Use a random number

table toselect which areas or

individualswill be sample

31

Population Attributes Density ndash size of a population in relation to a definite

unit of space Affected by

Natality ndash the reproductive output (birth rate) of a population

Mortality ndash the death rate of organisms in a population

Immigration ndash number of organisms moving into the area occupied by the population

Emigration ndash number of organisms moving out of the area occupied by the population

32

Population Density

Four primary population parameters

33

Two Types of Density Estimates

bull Absolute Density ndash a known density such as m2

bull Relative Density ndash we know when one area has more individuals than another

34

Measuring Absolute Density

Total Count ndash count the number of organisms living in an area Human census number of oak trees in a

wooded lot number of singing birds in an area

Total counts generally are not used very often

Sampling Methods ndash use a sample to estimate population size Either use the quadrat or capture-

recapture method

35

Measurement of Environmental ParametersAbiotic factors are important in determining

both the distribution of the organisms and their physical and physiological adaptations

Temperature- diurnal and seasonal temperature variations

are significant in affecting different species of plants and animals

- equipment mercury thermometer maximum-minimum thermometer

miniaturized thermistor

36

pH

-measure pH of a solution by universal indicator pH paper pH meter etc

Light

-measure its duration and intensity duration by predication from Royal Observatory intensity by photographic light meter

pH meter in use

37

Humidity

Relative humidity the water content of a given volume of air relative to the same volume of fully saturated air

- equipment whirling hygrometer

38

Wind and Water Speed- wind speed- anemometer or wind

gauges- water speed - time the movement of a

floating object over a measured distance

39

Salinity

- using a conductivity meter greater salinity has greater conductivity

Oxygen Level

- using an oxygen meter or chemical method (Winkler method)

40

Collecting MethodsCollecting all organisms within a habitat is normally

impractical and therefore small areas are selected Remember to return all material to its original position

after searching amp collecting sufficient specimens Some collecting apparatus for general use are listed

below

41

1 specimen tube

2 screwed-topped jars

3 polythene bags

4 forceps

5 paint brush

6 bulb pipette

7 pooter

42

8 widger 9 sieve 10 hand lens

11 enamel dish 12 beating tray 13 light traps

14 Tullgren funnel 15 Baermann funnel 16 mammal traps

17 pitfall traps 18 netting

43

Estimating Population Size

The exact methods used for estimation depend not only the nature of the habitat but also on the organisms involved

eg animals - population

plants - percentage cover

44

Using Quadrats

- By sampling an area using quadrats and counting the number of individuals within each quadrat it is possible to estimate the total number of individuals within the area

- confined to plants and sessile or very slow-moving animals

- fast-moving animals are disturbed and run away

45

Capture-recapture Techniques- useful for mobile animals which can be marked

- capture marked released randomly recaptured

and marked individuals recorded

no of marked individuals recaptured total no of individuals in 1st sample

-------------------------------------------- = ------------------------------------------

total no of individuals in 2nd sample estimated size of population

(the Lincoln Index)

46

Capture-recapture Techniques Factors affecting the accuracy of the estimation

deaths migration individuals become more liable to predation etc

Examples

- arthropods marked on their backs with non-toxic paint

- fish have tags attached to opercula - mammals have tags clipped to their ears

birds have their legs ringed

47

Capture-recapture Method Important tool for estimating density birth

rate and death rate for mobile animals Method

Collect a sample of individuals mark them and then release them

After a period collect more individuals from the wild and count the number that have marks

We assume that a sample if random will contain the same proportion of marked individuals as the population does

Estimate population density

48

Assumptions For All Capture-Recapture Studies Marking technique does not increase

mortality of marked animals Marked individuals are allowed to mix

with population Marking technique does not affect catch

probability Marks are not lost or overlooked No significant immigration or emigration No significant mortality or natality

49

Marked animals in second sample

Total caught in second sample

Marked animals in first sample

Total population size

=

520 N

16=

Peterson Method or Lincoln Index

N = 64N = (20)(16)5

50

Some Indices Used

Traps Number of Fecal

Pellets Vocalization

Frequency Pelt Records Catch per Unit

Fishing Effort

Number of Artifacts Questionnaires Cover Feeding Capacity Roadside Counts

51

Abundance Scales

The population size may be fairly accurately determined by making some form of frequency assessment

These are subjective and involve an experimenter making some estimate of the number of individuals in a given area or the cover of a particular species

This is especially useful where individuals are very numerous eg barnacles on a rocky shore or where it is difficult to distinguish individuals eg grass plants in a meadow

52

The assessments are usually made on an abundance scale of 5 categories

Abundance Common Frequent Occasional Rare

Barnacles exposed at low water

53

Environmental resistance are the factors which limit the growth of a particular population

eg predation disease availability of light food water oxygen and shelter the accumulation of toxic wastes and even the size of the population itself

54

Density-dependent Growth A population is a density-dependent when its size

(or density) affects its growth rate because of density-dependent factors such as food availability and toxic waste accumulation

Density-independent Growth In this type of growth a population increases until

some factor causes a sudden reduction in its size Its effect is the same regardless of the size of the

population eg temperature fires floods storms etc

55

Regulation of Population Size Fecundity is the reproductive capacity of individual

females of a species Birth rate or natality is used to measure fecundity Death rate or mortality is the number of individuals

of a species which die per unit time Immigration occurs when individuals join a

population from neighbouring ones Emigration occurs when individuals depart from a

population A cycle occurs when the size of a population

fluctuates on a regular basis

56

Ecological Sampling

57

Why Do We Sample Determine presence andor

abundance

Monitor population fluctuations

Assess lsquoecological damagersquo

Assess quality of habitat

Assess population responses

58

What Do We Sample

Physical Environment Temperature DO pH salinity clarity

flow sediment

Biotic Environment All living things

59

Physical Habitat Temperature

Mercury thermometer Electronic thermometer Long-term thermometers

Dissolved Oxygen Winkler method (titration) DO meter (electrode)

pH Litmus paper pH meter (electrode)

Salinity Salinity Meter YSI 550A DO Meter w12 cable

60

Water Clarity Secchi Disk

Disk is attached to a calibrated rope The disk is lowered into the water until the white parts can no longer be seen Secchi disk depth is then recorded and serves as the waters transparency index The clearer the water the greater the secchi disk depth

Secchi Disk

61

Current Velocity (flow) Floating-orange method

Put an orange (or something else that floats just below the water surface) and measure the time it takes it to float across a known distance

Odometer-type flow meter Number of revolutions the propeller

makes for a given time is calibrated to flow velocity

62

Sediment Sediment size is important to many

aquatic organisms Sieversquos are used to separate and

grade sediment samples Percent of each size grade can be

determined

63

Water Sample

Water and plankton from various depths can be collected

A trigger mechanism is used to close the sampler Sample is then brought back to the

surface

64

Small Mammals

Mouserat Traps Fatal

Pit Falls Bucket is placed in the ground Sometimes have lsquoleadsrsquo to the buckets

Live traps Havahart Sherman

Spot-light

Sherman trapHavahart trap

65

Birds Stick-under-the-box method Bird-trap

Works like a minnow trap Mist net

Captures birds in flight Rocket net

Uses a propellant to throw a net over birds

66

Terrestrial Insects

Sticky paper flies

Baited Traps Fire ants

Nets butterflies

Foggers Collect insects from tree canopies

67

Aquatic Insects Drift Net

Place net in flowing water Kick Net

lsquoKickrsquo sediment upstream from block net and the flow will wash them into the net

Wash bucket Serber or Hess Sampler

Stir up known area of sediment

Animals are collected by a catch net

Multi-plate Sampler Become colonized

68

Crawfish and Crab Traps

69

Fish Larvae Light Traps

Larvae are attracted to the light Ichthyoplankton nets

Can be towed at various depths Fish collect at the lsquocodrsquoend

70

Fish Lift net

Net is placed down and after a set amount of time it is quickly lifted

Pop-net Similar to a lift net but

floats are attached to a framed net

Operated by a trigger mechanism

Throw net A net attached to a heavy

frame is thrown and every thing inside is netted out Throw net

Pop-net

Lift net

71

Minnow trap

Usually use bait to attract small fish Light is used sometimes as an attractant

72

Fish Electrofishing

Electricity is put into the water Fish are temporarily stunned and usually

swim towards the electricity source Usually non-fatal but may cause some

damage

73

Fish Gill Net

Gill nets resemble tennis nets Fish can not swim completely through the

net and get caught Gill nets are size selective (based on mesh

size) Square Mesh

Bar mesh

Stretch mesh

74

Fish Trammel Net

Three panels two large mesh on the outside and a small mesh on the inside

Fish swim through the outer mesh pushes the small mesh through the other side and becomes entangled

75

Hoop nets (and other similar nets) can have bait or not

Fyke nets have leads to help guide fish to the net

76

Seine Seines are nets that are pulled

through shallow water to catch fish

77

Purse Seine Used to encircle entire schools of fish

Usually involves a spotter plane and a second boat

78

Trotline (longline) A series of baited drop lines

connected to a main line

Can be deployed by tying one end to the bank and tying the other end with a heavy weight

79

Shrimp (or fish) Trawl Net pulled behind

a boat along the bottom Either a beam or

otter boards keep the net open

80

Tagging Individuals Coded Wire Tags

Microwire that has a unique label

Magnetic wand detects the tag

Tag retention should be determined

T-Bar tags Can be individually

numbered External tag

PIT tags (Passive Integrated Transponders) Wand induces the tag to

transmit individual number is displayed

81

Other Tagging Methods

Toe clip Amphibian and reptile Clip of one or more toes

to identify individuals

Bird Band Place a metal band on a

bird leg Generally has

identification information

82

Preserving plant specimens Pressing and drying Long-term

preservation and storage

Alternative drying techniques

Special preservation and processing techniques

Mounting

83

Pressing and drying Techniques for pressing and drying specimens have been

established for many years There are minor variations in recommended methods but they are essentially the same worldwide

The best specimens are plants that are pressed as soon as possible after collection before wilting and shrivelling Most plants may be kept in sealed containers such as plastic bags for up to a day if it is inconvenient to press immediately However some plants show such rapid wilting particularly of the flowers that such delays are best avoided Flowers with a lot of nectar may go mouldy very quickly if excess nectar is not shaken off before pressing

Specimens are pressed flat and dried between sheets of absorbent blotters or semi-absorbent paper such as newspaper Papers with a glossy surface should be avoided because they are not absorbent enough to aid drying The plant should be carefully laid out between the drying sheets as their form at this stage largely determines their ultimate appearance The flowers should be spread out with the petals carefully arranged wilted leaves should be straightened and unnecessary shoots of excessively twiggy shrubs may be cut away

84

Microwave ovens Small numbers of specimens can be dried using a microwave

oven The technique recommended in the literature is to place the specimens between unprinted absorbent paper for example butchers paper not newspaper which is unsuitable because the chemicals present in the ink may cause a fire The specimens should be put in a special press which should be of a microwave-safe material (wood acrylic or polycarbonate sheeting eg plexiglass or perspex NO metal components) If such a press is not available sheets of cardboard can be placed above and below the specimens and then weighted down

Drying time depends on the power of your oven In most cases drying is accomplished by irradiating at maximum power for 1-2 minutes per specimen although it is often a case of trial and error It is best to process no more than 10-12 specimens of average thickness per batch Specimens are usually dried after the moisture that characteristically appears on the glass door has disappeared If the specimen is damp when taken out of the oven allow it to stand before re-radiating as moisture continues to evaporate from the specimen for some time Care must be taken not to irradiate the specimens for too long

It should be noted that microwave treatment damages seeds and the cellular structure of the plants which may reduce the long-term value of the specimens

85

Alternative drying techniquesSilica gelother desiccants amp freeze drying Alternative methods of drying plant specimens have been

used for some time but are mostly restricted to special purpose collections The main alternatives are freeze-drying and drying in a desiccant powder such as desiccant silica gel In general these techniques are used where it is essential to preserve the shape of a delicate plant of organ of the plant such as the flower Freeze-drying has also been used to preserve the chemical composition of a plant as accurately as possible for later study

Disadvantages and special conservation problems of specimens dried in these manners are that they are particularly susceptible to damage The dried parts are fragile lack support and often catch on packing materials They must therefore be packed especially carefully and stored in small boxes or tubes with some appropriate packing material that does not snag and break small projections Acid-free tissue paper is often used Drying in desiccant silica gel crystals or powder can also have the disadvantage that it is difficult to remove all traces of the silica gel after drying

86

Special preservation and processing techniquesWet or spirit collections

Very fleshy or delicate structures including small algae and orchid flowers are best preserved in an air-tight glass or plastic jar with a liquid preservative rather than by drying The type of preservative used should be clearly labelled in the jar Such material is often referred to as a spirit collection or wet collection

Most material can be satisfactorily preserved in 70 ethyl alcohol (or 70 methylated spirit or denatured alcohol) with 30 water Colours will fade quickly in spirit however so it is a good idea to keep comprehensive notes and photographs

87

Small algae Microscopic algae are often collected in a jar and in the

water in which they were found If the algae are to be stored for more than 2-3 days a preservative needs to be used Traditionally this has been the extremely toxic formalin - a small amount can be added to the water to make a 5 final solution and the container labelled This must not be sent through the post or by courier

There are some other equally toxic options for example propylene phenoxytol but none should be sent through the post A safer option is to add sufficient concentrated alcohol or methylated spirits to the water containing the algae to make a final solution of 70 alcohol This treatment dilutes the algae making them difficult to find so if they can be concentrated somehow first (eg by filtering) they can be stored in much less liquid Another option is to fix the algae in formalin (or something similar) first and then prepare a microscope glass slide with a permanent water-soluble mounting medium

88

Mounting Mounting specimens prevents most fragile material from

fragmenting and prevents specimens becoming separated from their labels If the plant collection is a long-term project specimens should be mounted on sheets of archival (permanent) cardboard or paper with archival-quality fixing media These include stitching with cotton thread dental floss nickel-plated copper wire (for heavier specimens) narrow strips of archival paper linen tape or by using an archival adhesive such as methyl cellulose adhesive

One disadvantage of mounting specimens is that it can make parts of the specimen inaccessible for examination so it is essential that this be borne in mind during specimen arrangement and mounting For example easily reversible mounting media should be used specimens should be strapped to the sheet rather than glued all over and the specimen should be carefully arranged before it is attached so that it shows all features

89

Full-size herbarium mounting sheets are usually about 43 cm long x 28 cm wide The plant name and accompanying field notes should be transcribed on a permanent label stuck to one corner of the herbarium sheet (the bottom right-hand corner being the most common) or sometimes annotations may be written directly on the sheet or card

Small pieces of material which may have become separated from the specimen (eg seeds) can be placed in small plastic bags and pinned to the sheet

90

Long-term preservation and storage The long-term preservation of dry plant

specimens is largely dependent on protection from insect attack Specimens collected by Linnaeus in the eighteenth century and by Banks and Solander on the Endeavour voyage in 1788 are still excellently preserved

91

Pests and their control A range of pests attack dried plant material The

most common pests are insects and fungi though rodents and other large animals can cause damage in poor storage conditions Insects eat the material the paper surrounding the material and the adhesives and mounting media

Such insect pests range from psocids (book lice) which attack mainly the softer parts such as flowers and soft fruits to tobacco beetles and carpet beetles which can bore holes through the toughest of specimens Many insects are particularly sensitive to relative humidity levels and do not thrive at levels below 50

92

The most common and acceptable specimen treatments for insect control are Freezing Microwave Poisoning Insect deterrents Fungal pests

93

Storage

Dried and pressed plant specimens can be stored in cardboard or plastic boxes or tied in bundles in light-weight cardboard folders placed in pigeon holes

Alternatively they can be placed in protective plastic jackets and displayed in ring folders which is recommended if they are to be frequently handled such as for a reference collection

94

Filing

Specimens should be filed in a systematic order if a relatively permanent collection is being made The major groups ie ferns and fern allies cycads conifers dicotyledons and monocotyledons are best kept separately or according to some classification scheme such as that given in a flora or handbook

Similarly the genera within each family and the species within each genus may be filed alphabetically or following some such classification

95

Preservation of entire animals

Types of collection specimens of an entire animal For reference collections mammals can be prepared as a variety of specimens The condition of the specimen may determine possible ways to preserve it if for instance decomposition of the skin has loosened the hair of a carcass so much that it can easily be pulled out or removed by rubbing (ldquoslippingrdquo fur) it will be very difficult or impossible to produce a study skin or mounted specimen The most usual types of specimens (based on Nagorsen and Peterson 1980) are 1) entire fluid-preserved animals (for studying anatomy and histology fluid preservation may change the fur colour) 2) study skins with accompanying skulls partial skeletons (some bones remain in the skin) for studying pelage colour hair quality and moulting patterns 3) mounted skins with accompanying partial or entire skeleton (some bones may remain in the skin dependant on the method of preservation) or freeze-dried specimens 4) entire skeletons for instance for studying anatomy geographic variation or for age determination (entire skeletons are poorly represented in collections so Nagorsen and Peterson (1980) recommend preparation of at least one male and one female skeleton per species

96

Preservation of specimens in the field Formalin preservation Preservation in alcohol Preservation by cooling or freezing

97

Formalin preservation After weighing and measuring the animal and attaching an

adequate label very small specimens (up to 100 g) can be fixed whole by submerging them in 10 buffered formalin (tissue - formalin solution ratio of at least 1 12) the body cavity can be filled with formalin solution by injection until it is turgid and firm some formalin may also be injected under the skin into the body cavity larger muscles and organs If hypodermic needles are not available the body cavity can be opened ventrally by making a slit instead allowing the formalin to enter

Keeping the mouth open with a piece of wood or cotton may later allow examination of teeth Then the whole body can be immersed in formalin in the posture in which it is supposed to stay permanently because it will harden The ratio of formalin to carcass must be at least 12 to 1 to assure a good fixation Tissues can be left in buffered neutralized formalin for several months but formalin hardens specimens therefore after fixation longterm storage in alcohol may be better After preservation the carcass should therefore be washed in water and transferred into ethanol for permanent storage

Disadvantages for instance it discolours the fur after a longish immersion softens the bones and prevents further examination for microbiology

98

Preservation in alcohol

After weighing a whole animal can be preserved in a container of alcohol (70-90) Removal of the intestine prior to storage of the animal in alcohol is recommended

99

Preservation by cooling or freezing Removal of the skin with insulating fur

before cooling or freezing may help to cool the carcass down more quickly

Freezing is not recommended if histological examination is planned

100

THANK YOU

9

SAMPLING UNITS

Type determined by the organisms and the physical nature of the habitat being sampled

ndash Area of ground surfacendash Volume of air water or soil1048698 Standard units enable comparison of

results

10

QUADRATS

A standard area sampling unit consisting of a square frame1048698 Consistent size and shape is essential for comparing

samples from different places andor timesQuadrat sizeChosen to suit sampling goals1048698 A balance between what is best and what is practical is

always necessary1048698 Should suitndash practical constraintsndash habitatndash organism

11

Quadrat Method A Quadrat is a sampling area of any

shape randomly deployed Each individual within the quadrat is counted and those numbers are used to extrapolate population size Example a 100 square centimeter metal

rectangle is randomly thrown four times and all of the beetles of a particular species within the square are counted each time 19 21 17 and 19 This translates to 19 beetles per 100 cm2 or 1900 per m2

12

QUADRAT amp TRANSECT ACTIVITIESHow Where amp Why Scientists Do SamplingScientists often collect data ldquoin the fieldrdquo which couldmean underwater in a forest in a cave on a reef oreven the moon Two essential methods to gatherecological information in a standardized way areTransect Sampling (using a single line) and

QuadratSampling (counted within a grid) These samplingmethods provide more accurate data than randomsampling or simply guessing but they take less timethan counting every specimen in a certain area

13

Quadrats- a sturdily built

wooden frame

can be folded for easy transport and storage

14

Quadrats

- When placed on the ground the species present within the frame are identified and their abundance recorded

- Sampling could be random or systematic

Using a quadrat along a belt transect

15

Practical Constraints

Small quadrats are quicker to survey but yield a smaller individual sample of habitat

ndash Often require a larger of samples to represent the habitat

1048698 Large quadrats require more time and effort to survey but provide a larger individual sample of habitat

ndash Often require a smaller of samples to represent the habitat

16

Habitat sizeAppropriate sample unit size depends on size scale

of the habitatndash Small scale habitats require smaller sized samples1048698 Ex Bouldersndash Large scale habitats require larger sized samples1048698 Ex Forests

17

Organism size and density

Depends on size and density of organisms

ndash Small dense organisms require smaller samples

1048698 Ex grassndash Large scattered organisms require

larger samples1048698 Ex Trees

18

TYPES OF SAMPLING

1048698 Systematic 1048698 Stratified 1048698 Random

19

SYSTEMATIC SAMPLING

1048698 Often used when the area being studied is varied not very large or

when time is available 1048698 Samples are taken at fixed intervals

20

How to sample systematicallySystematic samples are usually taken along a transect line marked by a tape measure

1048698 Transect- a line laid across an area

21

Sampling along gradients

Transects are setup along aenvironmentalgradientsndash down a hillsidendash across a streambedndash out from a source ofpollution

22

Types of transect sampling 1048698 Line transect 1048698 Belt transect

23

Line transect methodA measured line is laidacross the area in thedirection of theenvironmental gradientndash The species touching theline can be recordedalong the whole length ofthe line (continuoussampling) or at specificpoints along the line(systematic sampling)

24

Line Transect- useful where a transition of flora andor fauna

occurs- a string or tape is stretched out along the

ground in a straight line record the organisms touching or covering

the line all along its length or at regular intervals

- Profile transect when there is appreciable height change along the transect and thus affecting the distribution of its species

25

Belt transect method

Similar to line transect butwidens the sampling areandash Transect line is laid outndash Samples are taken bydetermining abundance or cover in an area that is adefined distance from the linendash Samples can be taken all

theway along the line at specificintervals or even randomly

26

Belt TransectIt is a strip usually a metre wide marked by putting a

second line parallel to the other The species between the lines are carefully recorded working a metre at a time

Alternatively a frame quadrat in conjunction with a single line transect could be used

Using a quadrat along a belt transect eg ladder transect (every 5m)

27

Point Frames- for grassland field study of dense vegetation

28

STRATIFIED SAMPLING1048698 Often used whenthere are smallareas within alarger habitat thatare clearly different1048698 Strata- majordifferences withincommunitiesrecognized beforesampling begins

29

RANDOM SAMPLING

1048698 Often used when the area being studied isfairly uniform very large or when there is alimited amount of time available1048698 Random = chosen by chance rather thanaccording to a plan all outcomes are

equallylikely1048698 Samples are taken from different positionswithin a habitat and those positions arechosen randomly

30

How to sample randomly

Choose individuals or Placeldquosampling unitsrdquo

haphazardlyndash This is rarely completely

random1048698 ORhellip1048698 Assign numbers to the

areasor individuals to be sampledndash Use a random number

table toselect which areas or

individualswill be sample

31

Population Attributes Density ndash size of a population in relation to a definite

unit of space Affected by

Natality ndash the reproductive output (birth rate) of a population

Mortality ndash the death rate of organisms in a population

Immigration ndash number of organisms moving into the area occupied by the population

Emigration ndash number of organisms moving out of the area occupied by the population

32

Population Density

Four primary population parameters

33

Two Types of Density Estimates

bull Absolute Density ndash a known density such as m2

bull Relative Density ndash we know when one area has more individuals than another

34

Measuring Absolute Density

Total Count ndash count the number of organisms living in an area Human census number of oak trees in a

wooded lot number of singing birds in an area

Total counts generally are not used very often

Sampling Methods ndash use a sample to estimate population size Either use the quadrat or capture-

recapture method

35

Measurement of Environmental ParametersAbiotic factors are important in determining

both the distribution of the organisms and their physical and physiological adaptations

Temperature- diurnal and seasonal temperature variations

are significant in affecting different species of plants and animals

- equipment mercury thermometer maximum-minimum thermometer

miniaturized thermistor

36

pH

-measure pH of a solution by universal indicator pH paper pH meter etc

Light

-measure its duration and intensity duration by predication from Royal Observatory intensity by photographic light meter

pH meter in use

37

Humidity

Relative humidity the water content of a given volume of air relative to the same volume of fully saturated air

- equipment whirling hygrometer

38

Wind and Water Speed- wind speed- anemometer or wind

gauges- water speed - time the movement of a

floating object over a measured distance

39

Salinity

- using a conductivity meter greater salinity has greater conductivity

Oxygen Level

- using an oxygen meter or chemical method (Winkler method)

40

Collecting MethodsCollecting all organisms within a habitat is normally

impractical and therefore small areas are selected Remember to return all material to its original position

after searching amp collecting sufficient specimens Some collecting apparatus for general use are listed

below

41

1 specimen tube

2 screwed-topped jars

3 polythene bags

4 forceps

5 paint brush

6 bulb pipette

7 pooter

42

8 widger 9 sieve 10 hand lens

11 enamel dish 12 beating tray 13 light traps

14 Tullgren funnel 15 Baermann funnel 16 mammal traps

17 pitfall traps 18 netting

43

Estimating Population Size

The exact methods used for estimation depend not only the nature of the habitat but also on the organisms involved

eg animals - population

plants - percentage cover

44

Using Quadrats

- By sampling an area using quadrats and counting the number of individuals within each quadrat it is possible to estimate the total number of individuals within the area

- confined to plants and sessile or very slow-moving animals

- fast-moving animals are disturbed and run away

45

Capture-recapture Techniques- useful for mobile animals which can be marked

- capture marked released randomly recaptured

and marked individuals recorded

no of marked individuals recaptured total no of individuals in 1st sample

-------------------------------------------- = ------------------------------------------

total no of individuals in 2nd sample estimated size of population

(the Lincoln Index)

46

Capture-recapture Techniques Factors affecting the accuracy of the estimation

deaths migration individuals become more liable to predation etc

Examples

- arthropods marked on their backs with non-toxic paint

- fish have tags attached to opercula - mammals have tags clipped to their ears

birds have their legs ringed

47

Capture-recapture Method Important tool for estimating density birth

rate and death rate for mobile animals Method

Collect a sample of individuals mark them and then release them

After a period collect more individuals from the wild and count the number that have marks

We assume that a sample if random will contain the same proportion of marked individuals as the population does

Estimate population density

48

Assumptions For All Capture-Recapture Studies Marking technique does not increase

mortality of marked animals Marked individuals are allowed to mix

with population Marking technique does not affect catch

probability Marks are not lost or overlooked No significant immigration or emigration No significant mortality or natality

49

Marked animals in second sample

Total caught in second sample

Marked animals in first sample

Total population size

=

520 N

16=

Peterson Method or Lincoln Index

N = 64N = (20)(16)5

50

Some Indices Used

Traps Number of Fecal

Pellets Vocalization

Frequency Pelt Records Catch per Unit

Fishing Effort

Number of Artifacts Questionnaires Cover Feeding Capacity Roadside Counts

51

Abundance Scales

The population size may be fairly accurately determined by making some form of frequency assessment

These are subjective and involve an experimenter making some estimate of the number of individuals in a given area or the cover of a particular species

This is especially useful where individuals are very numerous eg barnacles on a rocky shore or where it is difficult to distinguish individuals eg grass plants in a meadow

52

The assessments are usually made on an abundance scale of 5 categories

Abundance Common Frequent Occasional Rare

Barnacles exposed at low water

53

Environmental resistance are the factors which limit the growth of a particular population

eg predation disease availability of light food water oxygen and shelter the accumulation of toxic wastes and even the size of the population itself

54

Density-dependent Growth A population is a density-dependent when its size

(or density) affects its growth rate because of density-dependent factors such as food availability and toxic waste accumulation

Density-independent Growth In this type of growth a population increases until

some factor causes a sudden reduction in its size Its effect is the same regardless of the size of the

population eg temperature fires floods storms etc

55

Regulation of Population Size Fecundity is the reproductive capacity of individual

females of a species Birth rate or natality is used to measure fecundity Death rate or mortality is the number of individuals

of a species which die per unit time Immigration occurs when individuals join a

population from neighbouring ones Emigration occurs when individuals depart from a

population A cycle occurs when the size of a population

fluctuates on a regular basis

56

Ecological Sampling

57

Why Do We Sample Determine presence andor

abundance

Monitor population fluctuations

Assess lsquoecological damagersquo

Assess quality of habitat

Assess population responses

58

What Do We Sample

Physical Environment Temperature DO pH salinity clarity

flow sediment

Biotic Environment All living things

59

Physical Habitat Temperature

Mercury thermometer Electronic thermometer Long-term thermometers

Dissolved Oxygen Winkler method (titration) DO meter (electrode)

pH Litmus paper pH meter (electrode)

Salinity Salinity Meter YSI 550A DO Meter w12 cable

60

Water Clarity Secchi Disk

Disk is attached to a calibrated rope The disk is lowered into the water until the white parts can no longer be seen Secchi disk depth is then recorded and serves as the waters transparency index The clearer the water the greater the secchi disk depth

Secchi Disk

61

Current Velocity (flow) Floating-orange method

Put an orange (or something else that floats just below the water surface) and measure the time it takes it to float across a known distance

Odometer-type flow meter Number of revolutions the propeller

makes for a given time is calibrated to flow velocity

62

Sediment Sediment size is important to many

aquatic organisms Sieversquos are used to separate and

grade sediment samples Percent of each size grade can be

determined

63

Water Sample

Water and plankton from various depths can be collected

A trigger mechanism is used to close the sampler Sample is then brought back to the

surface

64

Small Mammals

Mouserat Traps Fatal

Pit Falls Bucket is placed in the ground Sometimes have lsquoleadsrsquo to the buckets

Live traps Havahart Sherman

Spot-light

Sherman trapHavahart trap

65

Birds Stick-under-the-box method Bird-trap

Works like a minnow trap Mist net

Captures birds in flight Rocket net

Uses a propellant to throw a net over birds

66

Terrestrial Insects

Sticky paper flies

Baited Traps Fire ants

Nets butterflies

Foggers Collect insects from tree canopies

67

Aquatic Insects Drift Net

Place net in flowing water Kick Net

lsquoKickrsquo sediment upstream from block net and the flow will wash them into the net

Wash bucket Serber or Hess Sampler

Stir up known area of sediment

Animals are collected by a catch net

Multi-plate Sampler Become colonized

68

Crawfish and Crab Traps

69

Fish Larvae Light Traps

Larvae are attracted to the light Ichthyoplankton nets

Can be towed at various depths Fish collect at the lsquocodrsquoend

70

Fish Lift net

Net is placed down and after a set amount of time it is quickly lifted

Pop-net Similar to a lift net but

floats are attached to a framed net

Operated by a trigger mechanism

Throw net A net attached to a heavy

frame is thrown and every thing inside is netted out Throw net

Pop-net

Lift net

71

Minnow trap

Usually use bait to attract small fish Light is used sometimes as an attractant

72

Fish Electrofishing

Electricity is put into the water Fish are temporarily stunned and usually

swim towards the electricity source Usually non-fatal but may cause some

damage

73

Fish Gill Net

Gill nets resemble tennis nets Fish can not swim completely through the

net and get caught Gill nets are size selective (based on mesh

size) Square Mesh

Bar mesh

Stretch mesh

74

Fish Trammel Net

Three panels two large mesh on the outside and a small mesh on the inside

Fish swim through the outer mesh pushes the small mesh through the other side and becomes entangled

75

Hoop nets (and other similar nets) can have bait or not

Fyke nets have leads to help guide fish to the net

76

Seine Seines are nets that are pulled

through shallow water to catch fish

77

Purse Seine Used to encircle entire schools of fish

Usually involves a spotter plane and a second boat

78

Trotline (longline) A series of baited drop lines

connected to a main line

Can be deployed by tying one end to the bank and tying the other end with a heavy weight

79

Shrimp (or fish) Trawl Net pulled behind

a boat along the bottom Either a beam or

otter boards keep the net open

80

Tagging Individuals Coded Wire Tags

Microwire that has a unique label

Magnetic wand detects the tag

Tag retention should be determined

T-Bar tags Can be individually

numbered External tag

PIT tags (Passive Integrated Transponders) Wand induces the tag to

transmit individual number is displayed

81

Other Tagging Methods

Toe clip Amphibian and reptile Clip of one or more toes

to identify individuals

Bird Band Place a metal band on a

bird leg Generally has

identification information

82

Preserving plant specimens Pressing and drying Long-term

preservation and storage

Alternative drying techniques

Special preservation and processing techniques

Mounting

83

Pressing and drying Techniques for pressing and drying specimens have been

established for many years There are minor variations in recommended methods but they are essentially the same worldwide

The best specimens are plants that are pressed as soon as possible after collection before wilting and shrivelling Most plants may be kept in sealed containers such as plastic bags for up to a day if it is inconvenient to press immediately However some plants show such rapid wilting particularly of the flowers that such delays are best avoided Flowers with a lot of nectar may go mouldy very quickly if excess nectar is not shaken off before pressing

Specimens are pressed flat and dried between sheets of absorbent blotters or semi-absorbent paper such as newspaper Papers with a glossy surface should be avoided because they are not absorbent enough to aid drying The plant should be carefully laid out between the drying sheets as their form at this stage largely determines their ultimate appearance The flowers should be spread out with the petals carefully arranged wilted leaves should be straightened and unnecessary shoots of excessively twiggy shrubs may be cut away

84

Microwave ovens Small numbers of specimens can be dried using a microwave

oven The technique recommended in the literature is to place the specimens between unprinted absorbent paper for example butchers paper not newspaper which is unsuitable because the chemicals present in the ink may cause a fire The specimens should be put in a special press which should be of a microwave-safe material (wood acrylic or polycarbonate sheeting eg plexiglass or perspex NO metal components) If such a press is not available sheets of cardboard can be placed above and below the specimens and then weighted down

Drying time depends on the power of your oven In most cases drying is accomplished by irradiating at maximum power for 1-2 minutes per specimen although it is often a case of trial and error It is best to process no more than 10-12 specimens of average thickness per batch Specimens are usually dried after the moisture that characteristically appears on the glass door has disappeared If the specimen is damp when taken out of the oven allow it to stand before re-radiating as moisture continues to evaporate from the specimen for some time Care must be taken not to irradiate the specimens for too long

It should be noted that microwave treatment damages seeds and the cellular structure of the plants which may reduce the long-term value of the specimens

85

Alternative drying techniquesSilica gelother desiccants amp freeze drying Alternative methods of drying plant specimens have been

used for some time but are mostly restricted to special purpose collections The main alternatives are freeze-drying and drying in a desiccant powder such as desiccant silica gel In general these techniques are used where it is essential to preserve the shape of a delicate plant of organ of the plant such as the flower Freeze-drying has also been used to preserve the chemical composition of a plant as accurately as possible for later study

Disadvantages and special conservation problems of specimens dried in these manners are that they are particularly susceptible to damage The dried parts are fragile lack support and often catch on packing materials They must therefore be packed especially carefully and stored in small boxes or tubes with some appropriate packing material that does not snag and break small projections Acid-free tissue paper is often used Drying in desiccant silica gel crystals or powder can also have the disadvantage that it is difficult to remove all traces of the silica gel after drying

86

Special preservation and processing techniquesWet or spirit collections

Very fleshy or delicate structures including small algae and orchid flowers are best preserved in an air-tight glass or plastic jar with a liquid preservative rather than by drying The type of preservative used should be clearly labelled in the jar Such material is often referred to as a spirit collection or wet collection

Most material can be satisfactorily preserved in 70 ethyl alcohol (or 70 methylated spirit or denatured alcohol) with 30 water Colours will fade quickly in spirit however so it is a good idea to keep comprehensive notes and photographs

87

Small algae Microscopic algae are often collected in a jar and in the

water in which they were found If the algae are to be stored for more than 2-3 days a preservative needs to be used Traditionally this has been the extremely toxic formalin - a small amount can be added to the water to make a 5 final solution and the container labelled This must not be sent through the post or by courier

There are some other equally toxic options for example propylene phenoxytol but none should be sent through the post A safer option is to add sufficient concentrated alcohol or methylated spirits to the water containing the algae to make a final solution of 70 alcohol This treatment dilutes the algae making them difficult to find so if they can be concentrated somehow first (eg by filtering) they can be stored in much less liquid Another option is to fix the algae in formalin (or something similar) first and then prepare a microscope glass slide with a permanent water-soluble mounting medium

88

Mounting Mounting specimens prevents most fragile material from

fragmenting and prevents specimens becoming separated from their labels If the plant collection is a long-term project specimens should be mounted on sheets of archival (permanent) cardboard or paper with archival-quality fixing media These include stitching with cotton thread dental floss nickel-plated copper wire (for heavier specimens) narrow strips of archival paper linen tape or by using an archival adhesive such as methyl cellulose adhesive

One disadvantage of mounting specimens is that it can make parts of the specimen inaccessible for examination so it is essential that this be borne in mind during specimen arrangement and mounting For example easily reversible mounting media should be used specimens should be strapped to the sheet rather than glued all over and the specimen should be carefully arranged before it is attached so that it shows all features

89

Full-size herbarium mounting sheets are usually about 43 cm long x 28 cm wide The plant name and accompanying field notes should be transcribed on a permanent label stuck to one corner of the herbarium sheet (the bottom right-hand corner being the most common) or sometimes annotations may be written directly on the sheet or card

Small pieces of material which may have become separated from the specimen (eg seeds) can be placed in small plastic bags and pinned to the sheet

90

Long-term preservation and storage The long-term preservation of dry plant

specimens is largely dependent on protection from insect attack Specimens collected by Linnaeus in the eighteenth century and by Banks and Solander on the Endeavour voyage in 1788 are still excellently preserved

91

Pests and their control A range of pests attack dried plant material The

most common pests are insects and fungi though rodents and other large animals can cause damage in poor storage conditions Insects eat the material the paper surrounding the material and the adhesives and mounting media

Such insect pests range from psocids (book lice) which attack mainly the softer parts such as flowers and soft fruits to tobacco beetles and carpet beetles which can bore holes through the toughest of specimens Many insects are particularly sensitive to relative humidity levels and do not thrive at levels below 50

92

The most common and acceptable specimen treatments for insect control are Freezing Microwave Poisoning Insect deterrents Fungal pests

93

Storage

Dried and pressed plant specimens can be stored in cardboard or plastic boxes or tied in bundles in light-weight cardboard folders placed in pigeon holes

Alternatively they can be placed in protective plastic jackets and displayed in ring folders which is recommended if they are to be frequently handled such as for a reference collection

94

Filing

Specimens should be filed in a systematic order if a relatively permanent collection is being made The major groups ie ferns and fern allies cycads conifers dicotyledons and monocotyledons are best kept separately or according to some classification scheme such as that given in a flora or handbook

Similarly the genera within each family and the species within each genus may be filed alphabetically or following some such classification

95

Preservation of entire animals

Types of collection specimens of an entire animal For reference collections mammals can be prepared as a variety of specimens The condition of the specimen may determine possible ways to preserve it if for instance decomposition of the skin has loosened the hair of a carcass so much that it can easily be pulled out or removed by rubbing (ldquoslippingrdquo fur) it will be very difficult or impossible to produce a study skin or mounted specimen The most usual types of specimens (based on Nagorsen and Peterson 1980) are 1) entire fluid-preserved animals (for studying anatomy and histology fluid preservation may change the fur colour) 2) study skins with accompanying skulls partial skeletons (some bones remain in the skin) for studying pelage colour hair quality and moulting patterns 3) mounted skins with accompanying partial or entire skeleton (some bones may remain in the skin dependant on the method of preservation) or freeze-dried specimens 4) entire skeletons for instance for studying anatomy geographic variation or for age determination (entire skeletons are poorly represented in collections so Nagorsen and Peterson (1980) recommend preparation of at least one male and one female skeleton per species

96

Preservation of specimens in the field Formalin preservation Preservation in alcohol Preservation by cooling or freezing

97

Formalin preservation After weighing and measuring the animal and attaching an

adequate label very small specimens (up to 100 g) can be fixed whole by submerging them in 10 buffered formalin (tissue - formalin solution ratio of at least 1 12) the body cavity can be filled with formalin solution by injection until it is turgid and firm some formalin may also be injected under the skin into the body cavity larger muscles and organs If hypodermic needles are not available the body cavity can be opened ventrally by making a slit instead allowing the formalin to enter

Keeping the mouth open with a piece of wood or cotton may later allow examination of teeth Then the whole body can be immersed in formalin in the posture in which it is supposed to stay permanently because it will harden The ratio of formalin to carcass must be at least 12 to 1 to assure a good fixation Tissues can be left in buffered neutralized formalin for several months but formalin hardens specimens therefore after fixation longterm storage in alcohol may be better After preservation the carcass should therefore be washed in water and transferred into ethanol for permanent storage

Disadvantages for instance it discolours the fur after a longish immersion softens the bones and prevents further examination for microbiology

98

Preservation in alcohol

After weighing a whole animal can be preserved in a container of alcohol (70-90) Removal of the intestine prior to storage of the animal in alcohol is recommended

99

Preservation by cooling or freezing Removal of the skin with insulating fur

before cooling or freezing may help to cool the carcass down more quickly

Freezing is not recommended if histological examination is planned

100

THANK YOU

10

QUADRATS

A standard area sampling unit consisting of a square frame1048698 Consistent size and shape is essential for comparing

samples from different places andor timesQuadrat sizeChosen to suit sampling goals1048698 A balance between what is best and what is practical is

always necessary1048698 Should suitndash practical constraintsndash habitatndash organism

11

Quadrat Method A Quadrat is a sampling area of any

shape randomly deployed Each individual within the quadrat is counted and those numbers are used to extrapolate population size Example a 100 square centimeter metal

rectangle is randomly thrown four times and all of the beetles of a particular species within the square are counted each time 19 21 17 and 19 This translates to 19 beetles per 100 cm2 or 1900 per m2

12

QUADRAT amp TRANSECT ACTIVITIESHow Where amp Why Scientists Do SamplingScientists often collect data ldquoin the fieldrdquo which couldmean underwater in a forest in a cave on a reef oreven the moon Two essential methods to gatherecological information in a standardized way areTransect Sampling (using a single line) and

QuadratSampling (counted within a grid) These samplingmethods provide more accurate data than randomsampling or simply guessing but they take less timethan counting every specimen in a certain area

13

Quadrats- a sturdily built

wooden frame

can be folded for easy transport and storage

14

Quadrats

- When placed on the ground the species present within the frame are identified and their abundance recorded

- Sampling could be random or systematic

Using a quadrat along a belt transect

15

Practical Constraints

Small quadrats are quicker to survey but yield a smaller individual sample of habitat

ndash Often require a larger of samples to represent the habitat

1048698 Large quadrats require more time and effort to survey but provide a larger individual sample of habitat

ndash Often require a smaller of samples to represent the habitat

16

Habitat sizeAppropriate sample unit size depends on size scale

of the habitatndash Small scale habitats require smaller sized samples1048698 Ex Bouldersndash Large scale habitats require larger sized samples1048698 Ex Forests

17

Organism size and density

Depends on size and density of organisms

ndash Small dense organisms require smaller samples

1048698 Ex grassndash Large scattered organisms require

larger samples1048698 Ex Trees

18

TYPES OF SAMPLING

1048698 Systematic 1048698 Stratified 1048698 Random

19

SYSTEMATIC SAMPLING

1048698 Often used when the area being studied is varied not very large or

when time is available 1048698 Samples are taken at fixed intervals

20

How to sample systematicallySystematic samples are usually taken along a transect line marked by a tape measure

1048698 Transect- a line laid across an area

21

Sampling along gradients

Transects are setup along aenvironmentalgradientsndash down a hillsidendash across a streambedndash out from a source ofpollution

22

Types of transect sampling 1048698 Line transect 1048698 Belt transect

23

Line transect methodA measured line is laidacross the area in thedirection of theenvironmental gradientndash The species touching theline can be recordedalong the whole length ofthe line (continuoussampling) or at specificpoints along the line(systematic sampling)

24

Line Transect- useful where a transition of flora andor fauna

occurs- a string or tape is stretched out along the

ground in a straight line record the organisms touching or covering

the line all along its length or at regular intervals

- Profile transect when there is appreciable height change along the transect and thus affecting the distribution of its species

25

Belt transect method

Similar to line transect butwidens the sampling areandash Transect line is laid outndash Samples are taken bydetermining abundance or cover in an area that is adefined distance from the linendash Samples can be taken all

theway along the line at specificintervals or even randomly

26

Belt TransectIt is a strip usually a metre wide marked by putting a

second line parallel to the other The species between the lines are carefully recorded working a metre at a time

Alternatively a frame quadrat in conjunction with a single line transect could be used

Using a quadrat along a belt transect eg ladder transect (every 5m)

27

Point Frames- for grassland field study of dense vegetation

28

STRATIFIED SAMPLING1048698 Often used whenthere are smallareas within alarger habitat thatare clearly different1048698 Strata- majordifferences withincommunitiesrecognized beforesampling begins

29

RANDOM SAMPLING

1048698 Often used when the area being studied isfairly uniform very large or when there is alimited amount of time available1048698 Random = chosen by chance rather thanaccording to a plan all outcomes are

equallylikely1048698 Samples are taken from different positionswithin a habitat and those positions arechosen randomly

30

How to sample randomly

Choose individuals or Placeldquosampling unitsrdquo

haphazardlyndash This is rarely completely

random1048698 ORhellip1048698 Assign numbers to the

areasor individuals to be sampledndash Use a random number

table toselect which areas or

individualswill be sample

31

Population Attributes Density ndash size of a population in relation to a definite

unit of space Affected by

Natality ndash the reproductive output (birth rate) of a population

Mortality ndash the death rate of organisms in a population

Immigration ndash number of organisms moving into the area occupied by the population

Emigration ndash number of organisms moving out of the area occupied by the population

32

Population Density

Four primary population parameters

33

Two Types of Density Estimates

bull Absolute Density ndash a known density such as m2

bull Relative Density ndash we know when one area has more individuals than another

34

Measuring Absolute Density

Total Count ndash count the number of organisms living in an area Human census number of oak trees in a

wooded lot number of singing birds in an area

Total counts generally are not used very often

Sampling Methods ndash use a sample to estimate population size Either use the quadrat or capture-

recapture method

35

Measurement of Environmental ParametersAbiotic factors are important in determining

both the distribution of the organisms and their physical and physiological adaptations

Temperature- diurnal and seasonal temperature variations

are significant in affecting different species of plants and animals

- equipment mercury thermometer maximum-minimum thermometer

miniaturized thermistor

36

pH

-measure pH of a solution by universal indicator pH paper pH meter etc

Light

-measure its duration and intensity duration by predication from Royal Observatory intensity by photographic light meter

pH meter in use

37

Humidity

Relative humidity the water content of a given volume of air relative to the same volume of fully saturated air

- equipment whirling hygrometer

38

Wind and Water Speed- wind speed- anemometer or wind

gauges- water speed - time the movement of a

floating object over a measured distance

39

Salinity

- using a conductivity meter greater salinity has greater conductivity

Oxygen Level

- using an oxygen meter or chemical method (Winkler method)

40

Collecting MethodsCollecting all organisms within a habitat is normally

impractical and therefore small areas are selected Remember to return all material to its original position

after searching amp collecting sufficient specimens Some collecting apparatus for general use are listed

below

41

1 specimen tube

2 screwed-topped jars

3 polythene bags

4 forceps

5 paint brush

6 bulb pipette

7 pooter

42

8 widger 9 sieve 10 hand lens

11 enamel dish 12 beating tray 13 light traps

14 Tullgren funnel 15 Baermann funnel 16 mammal traps

17 pitfall traps 18 netting

43

Estimating Population Size

The exact methods used for estimation depend not only the nature of the habitat but also on the organisms involved

eg animals - population

plants - percentage cover

44

Using Quadrats

- By sampling an area using quadrats and counting the number of individuals within each quadrat it is possible to estimate the total number of individuals within the area

- confined to plants and sessile or very slow-moving animals

- fast-moving animals are disturbed and run away

45

Capture-recapture Techniques- useful for mobile animals which can be marked

- capture marked released randomly recaptured

and marked individuals recorded

no of marked individuals recaptured total no of individuals in 1st sample

-------------------------------------------- = ------------------------------------------

total no of individuals in 2nd sample estimated size of population

(the Lincoln Index)

46

Capture-recapture Techniques Factors affecting the accuracy of the estimation

deaths migration individuals become more liable to predation etc

Examples

- arthropods marked on their backs with non-toxic paint

- fish have tags attached to opercula - mammals have tags clipped to their ears

birds have their legs ringed

47

Capture-recapture Method Important tool for estimating density birth

rate and death rate for mobile animals Method

Collect a sample of individuals mark them and then release them

After a period collect more individuals from the wild and count the number that have marks

We assume that a sample if random will contain the same proportion of marked individuals as the population does

Estimate population density

48

Assumptions For All Capture-Recapture Studies Marking technique does not increase

mortality of marked animals Marked individuals are allowed to mix

with population Marking technique does not affect catch

probability Marks are not lost or overlooked No significant immigration or emigration No significant mortality or natality

49

Marked animals in second sample

Total caught in second sample

Marked animals in first sample

Total population size

=

520 N

16=

Peterson Method or Lincoln Index

N = 64N = (20)(16)5

50

Some Indices Used

Traps Number of Fecal

Pellets Vocalization

Frequency Pelt Records Catch per Unit

Fishing Effort

Number of Artifacts Questionnaires Cover Feeding Capacity Roadside Counts

51

Abundance Scales

The population size may be fairly accurately determined by making some form of frequency assessment

These are subjective and involve an experimenter making some estimate of the number of individuals in a given area or the cover of a particular species

This is especially useful where individuals are very numerous eg barnacles on a rocky shore or where it is difficult to distinguish individuals eg grass plants in a meadow

52

The assessments are usually made on an abundance scale of 5 categories

Abundance Common Frequent Occasional Rare

Barnacles exposed at low water

53

Environmental resistance are the factors which limit the growth of a particular population

eg predation disease availability of light food water oxygen and shelter the accumulation of toxic wastes and even the size of the population itself

54

Density-dependent Growth A population is a density-dependent when its size

(or density) affects its growth rate because of density-dependent factors such as food availability and toxic waste accumulation

Density-independent Growth In this type of growth a population increases until

some factor causes a sudden reduction in its size Its effect is the same regardless of the size of the

population eg temperature fires floods storms etc

55

Regulation of Population Size Fecundity is the reproductive capacity of individual

females of a species Birth rate or natality is used to measure fecundity Death rate or mortality is the number of individuals

of a species which die per unit time Immigration occurs when individuals join a

population from neighbouring ones Emigration occurs when individuals depart from a

population A cycle occurs when the size of a population

fluctuates on a regular basis

56

Ecological Sampling

57

Why Do We Sample Determine presence andor

abundance

Monitor population fluctuations

Assess lsquoecological damagersquo

Assess quality of habitat

Assess population responses

58

What Do We Sample

Physical Environment Temperature DO pH salinity clarity

flow sediment

Biotic Environment All living things

59

Physical Habitat Temperature

Mercury thermometer Electronic thermometer Long-term thermometers

Dissolved Oxygen Winkler method (titration) DO meter (electrode)

pH Litmus paper pH meter (electrode)

Salinity Salinity Meter YSI 550A DO Meter w12 cable

60

Water Clarity Secchi Disk

Disk is attached to a calibrated rope The disk is lowered into the water until the white parts can no longer be seen Secchi disk depth is then recorded and serves as the waters transparency index The clearer the water the greater the secchi disk depth

Secchi Disk

61

Current Velocity (flow) Floating-orange method

Put an orange (or something else that floats just below the water surface) and measure the time it takes it to float across a known distance

Odometer-type flow meter Number of revolutions the propeller

makes for a given time is calibrated to flow velocity

62

Sediment Sediment size is important to many

aquatic organisms Sieversquos are used to separate and

grade sediment samples Percent of each size grade can be

determined

63

Water Sample

Water and plankton from various depths can be collected

A trigger mechanism is used to close the sampler Sample is then brought back to the

surface

64

Small Mammals

Mouserat Traps Fatal

Pit Falls Bucket is placed in the ground Sometimes have lsquoleadsrsquo to the buckets

Live traps Havahart Sherman

Spot-light

Sherman trapHavahart trap

65

Birds Stick-under-the-box method Bird-trap

Works like a minnow trap Mist net

Captures birds in flight Rocket net

Uses a propellant to throw a net over birds

66

Terrestrial Insects

Sticky paper flies

Baited Traps Fire ants

Nets butterflies

Foggers Collect insects from tree canopies

67

Aquatic Insects Drift Net

Place net in flowing water Kick Net

lsquoKickrsquo sediment upstream from block net and the flow will wash them into the net

Wash bucket Serber or Hess Sampler

Stir up known area of sediment

Animals are collected by a catch net

Multi-plate Sampler Become colonized

68

Crawfish and Crab Traps

69

Fish Larvae Light Traps

Larvae are attracted to the light Ichthyoplankton nets

Can be towed at various depths Fish collect at the lsquocodrsquoend

70

Fish Lift net

Net is placed down and after a set amount of time it is quickly lifted

Pop-net Similar to a lift net but

floats are attached to a framed net

Operated by a trigger mechanism

Throw net A net attached to a heavy

frame is thrown and every thing inside is netted out Throw net

Pop-net

Lift net

71

Minnow trap

Usually use bait to attract small fish Light is used sometimes as an attractant

72

Fish Electrofishing

Electricity is put into the water Fish are temporarily stunned and usually

swim towards the electricity source Usually non-fatal but may cause some

damage

73

Fish Gill Net

Gill nets resemble tennis nets Fish can not swim completely through the

net and get caught Gill nets are size selective (based on mesh

size) Square Mesh

Bar mesh

Stretch mesh

74

Fish Trammel Net

Three panels two large mesh on the outside and a small mesh on the inside

Fish swim through the outer mesh pushes the small mesh through the other side and becomes entangled

75

Hoop nets (and other similar nets) can have bait or not

Fyke nets have leads to help guide fish to the net

76

Seine Seines are nets that are pulled

through shallow water to catch fish

77

Purse Seine Used to encircle entire schools of fish

Usually involves a spotter plane and a second boat

78

Trotline (longline) A series of baited drop lines

connected to a main line

Can be deployed by tying one end to the bank and tying the other end with a heavy weight

79

Shrimp (or fish) Trawl Net pulled behind

a boat along the bottom Either a beam or

otter boards keep the net open

80

Tagging Individuals Coded Wire Tags

Microwire that has a unique label

Magnetic wand detects the tag

Tag retention should be determined

T-Bar tags Can be individually

numbered External tag

PIT tags (Passive Integrated Transponders) Wand induces the tag to

transmit individual number is displayed

81

Other Tagging Methods

Toe clip Amphibian and reptile Clip of one or more toes

to identify individuals

Bird Band Place a metal band on a

bird leg Generally has

identification information

82

Preserving plant specimens Pressing and drying Long-term

preservation and storage

Alternative drying techniques

Special preservation and processing techniques

Mounting

83

Pressing and drying Techniques for pressing and drying specimens have been

established for many years There are minor variations in recommended methods but they are essentially the same worldwide

The best specimens are plants that are pressed as soon as possible after collection before wilting and shrivelling Most plants may be kept in sealed containers such as plastic bags for up to a day if it is inconvenient to press immediately However some plants show such rapid wilting particularly of the flowers that such delays are best avoided Flowers with a lot of nectar may go mouldy very quickly if excess nectar is not shaken off before pressing

Specimens are pressed flat and dried between sheets of absorbent blotters or semi-absorbent paper such as newspaper Papers with a glossy surface should be avoided because they are not absorbent enough to aid drying The plant should be carefully laid out between the drying sheets as their form at this stage largely determines their ultimate appearance The flowers should be spread out with the petals carefully arranged wilted leaves should be straightened and unnecessary shoots of excessively twiggy shrubs may be cut away

84

Microwave ovens Small numbers of specimens can be dried using a microwave

oven The technique recommended in the literature is to place the specimens between unprinted absorbent paper for example butchers paper not newspaper which is unsuitable because the chemicals present in the ink may cause a fire The specimens should be put in a special press which should be of a microwave-safe material (wood acrylic or polycarbonate sheeting eg plexiglass or perspex NO metal components) If such a press is not available sheets of cardboard can be placed above and below the specimens and then weighted down

Drying time depends on the power of your oven In most cases drying is accomplished by irradiating at maximum power for 1-2 minutes per specimen although it is often a case of trial and error It is best to process no more than 10-12 specimens of average thickness per batch Specimens are usually dried after the moisture that characteristically appears on the glass door has disappeared If the specimen is damp when taken out of the oven allow it to stand before re-radiating as moisture continues to evaporate from the specimen for some time Care must be taken not to irradiate the specimens for too long

It should be noted that microwave treatment damages seeds and the cellular structure of the plants which may reduce the long-term value of the specimens

85

Alternative drying techniquesSilica gelother desiccants amp freeze drying Alternative methods of drying plant specimens have been

used for some time but are mostly restricted to special purpose collections The main alternatives are freeze-drying and drying in a desiccant powder such as desiccant silica gel In general these techniques are used where it is essential to preserve the shape of a delicate plant of organ of the plant such as the flower Freeze-drying has also been used to preserve the chemical composition of a plant as accurately as possible for later study

Disadvantages and special conservation problems of specimens dried in these manners are that they are particularly susceptible to damage The dried parts are fragile lack support and often catch on packing materials They must therefore be packed especially carefully and stored in small boxes or tubes with some appropriate packing material that does not snag and break small projections Acid-free tissue paper is often used Drying in desiccant silica gel crystals or powder can also have the disadvantage that it is difficult to remove all traces of the silica gel after drying

86

Special preservation and processing techniquesWet or spirit collections

Very fleshy or delicate structures including small algae and orchid flowers are best preserved in an air-tight glass or plastic jar with a liquid preservative rather than by drying The type of preservative used should be clearly labelled in the jar Such material is often referred to as a spirit collection or wet collection

Most material can be satisfactorily preserved in 70 ethyl alcohol (or 70 methylated spirit or denatured alcohol) with 30 water Colours will fade quickly in spirit however so it is a good idea to keep comprehensive notes and photographs

87

Small algae Microscopic algae are often collected in a jar and in the

water in which they were found If the algae are to be stored for more than 2-3 days a preservative needs to be used Traditionally this has been the extremely toxic formalin - a small amount can be added to the water to make a 5 final solution and the container labelled This must not be sent through the post or by courier

There are some other equally toxic options for example propylene phenoxytol but none should be sent through the post A safer option is to add sufficient concentrated alcohol or methylated spirits to the water containing the algae to make a final solution of 70 alcohol This treatment dilutes the algae making them difficult to find so if they can be concentrated somehow first (eg by filtering) they can be stored in much less liquid Another option is to fix the algae in formalin (or something similar) first and then prepare a microscope glass slide with a permanent water-soluble mounting medium

88

Mounting Mounting specimens prevents most fragile material from

fragmenting and prevents specimens becoming separated from their labels If the plant collection is a long-term project specimens should be mounted on sheets of archival (permanent) cardboard or paper with archival-quality fixing media These include stitching with cotton thread dental floss nickel-plated copper wire (for heavier specimens) narrow strips of archival paper linen tape or by using an archival adhesive such as methyl cellulose adhesive

One disadvantage of mounting specimens is that it can make parts of the specimen inaccessible for examination so it is essential that this be borne in mind during specimen arrangement and mounting For example easily reversible mounting media should be used specimens should be strapped to the sheet rather than glued all over and the specimen should be carefully arranged before it is attached so that it shows all features

89

Full-size herbarium mounting sheets are usually about 43 cm long x 28 cm wide The plant name and accompanying field notes should be transcribed on a permanent label stuck to one corner of the herbarium sheet (the bottom right-hand corner being the most common) or sometimes annotations may be written directly on the sheet or card

Small pieces of material which may have become separated from the specimen (eg seeds) can be placed in small plastic bags and pinned to the sheet

90

Long-term preservation and storage The long-term preservation of dry plant

specimens is largely dependent on protection from insect attack Specimens collected by Linnaeus in the eighteenth century and by Banks and Solander on the Endeavour voyage in 1788 are still excellently preserved

91

Pests and their control A range of pests attack dried plant material The

most common pests are insects and fungi though rodents and other large animals can cause damage in poor storage conditions Insects eat the material the paper surrounding the material and the adhesives and mounting media

Such insect pests range from psocids (book lice) which attack mainly the softer parts such as flowers and soft fruits to tobacco beetles and carpet beetles which can bore holes through the toughest of specimens Many insects are particularly sensitive to relative humidity levels and do not thrive at levels below 50

92

The most common and acceptable specimen treatments for insect control are Freezing Microwave Poisoning Insect deterrents Fungal pests

93

Storage

Dried and pressed plant specimens can be stored in cardboard or plastic boxes or tied in bundles in light-weight cardboard folders placed in pigeon holes

Alternatively they can be placed in protective plastic jackets and displayed in ring folders which is recommended if they are to be frequently handled such as for a reference collection

94

Filing

Specimens should be filed in a systematic order if a relatively permanent collection is being made The major groups ie ferns and fern allies cycads conifers dicotyledons and monocotyledons are best kept separately or according to some classification scheme such as that given in a flora or handbook

Similarly the genera within each family and the species within each genus may be filed alphabetically or following some such classification

95

Preservation of entire animals

Types of collection specimens of an entire animal For reference collections mammals can be prepared as a variety of specimens The condition of the specimen may determine possible ways to preserve it if for instance decomposition of the skin has loosened the hair of a carcass so much that it can easily be pulled out or removed by rubbing (ldquoslippingrdquo fur) it will be very difficult or impossible to produce a study skin or mounted specimen The most usual types of specimens (based on Nagorsen and Peterson 1980) are 1) entire fluid-preserved animals (for studying anatomy and histology fluid preservation may change the fur colour) 2) study skins with accompanying skulls partial skeletons (some bones remain in the skin) for studying pelage colour hair quality and moulting patterns 3) mounted skins with accompanying partial or entire skeleton (some bones may remain in the skin dependant on the method of preservation) or freeze-dried specimens 4) entire skeletons for instance for studying anatomy geographic variation or for age determination (entire skeletons are poorly represented in collections so Nagorsen and Peterson (1980) recommend preparation of at least one male and one female skeleton per species

96

Preservation of specimens in the field Formalin preservation Preservation in alcohol Preservation by cooling or freezing

97

Formalin preservation After weighing and measuring the animal and attaching an

adequate label very small specimens (up to 100 g) can be fixed whole by submerging them in 10 buffered formalin (tissue - formalin solution ratio of at least 1 12) the body cavity can be filled with formalin solution by injection until it is turgid and firm some formalin may also be injected under the skin into the body cavity larger muscles and organs If hypodermic needles are not available the body cavity can be opened ventrally by making a slit instead allowing the formalin to enter

Keeping the mouth open with a piece of wood or cotton may later allow examination of teeth Then the whole body can be immersed in formalin in the posture in which it is supposed to stay permanently because it will harden The ratio of formalin to carcass must be at least 12 to 1 to assure a good fixation Tissues can be left in buffered neutralized formalin for several months but formalin hardens specimens therefore after fixation longterm storage in alcohol may be better After preservation the carcass should therefore be washed in water and transferred into ethanol for permanent storage

Disadvantages for instance it discolours the fur after a longish immersion softens the bones and prevents further examination for microbiology

98

Preservation in alcohol

After weighing a whole animal can be preserved in a container of alcohol (70-90) Removal of the intestine prior to storage of the animal in alcohol is recommended

99

Preservation by cooling or freezing Removal of the skin with insulating fur

before cooling or freezing may help to cool the carcass down more quickly

Freezing is not recommended if histological examination is planned

100

THANK YOU

11

Quadrat Method A Quadrat is a sampling area of any

shape randomly deployed Each individual within the quadrat is counted and those numbers are used to extrapolate population size Example a 100 square centimeter metal

rectangle is randomly thrown four times and all of the beetles of a particular species within the square are counted each time 19 21 17 and 19 This translates to 19 beetles per 100 cm2 or 1900 per m2

12

QUADRAT amp TRANSECT ACTIVITIESHow Where amp Why Scientists Do SamplingScientists often collect data ldquoin the fieldrdquo which couldmean underwater in a forest in a cave on a reef oreven the moon Two essential methods to gatherecological information in a standardized way areTransect Sampling (using a single line) and

QuadratSampling (counted within a grid) These samplingmethods provide more accurate data than randomsampling or simply guessing but they take less timethan counting every specimen in a certain area

13

Quadrats- a sturdily built

wooden frame

can be folded for easy transport and storage

14

Quadrats

- When placed on the ground the species present within the frame are identified and their abundance recorded

- Sampling could be random or systematic

Using a quadrat along a belt transect

15

Practical Constraints

Small quadrats are quicker to survey but yield a smaller individual sample of habitat

ndash Often require a larger of samples to represent the habitat

1048698 Large quadrats require more time and effort to survey but provide a larger individual sample of habitat

ndash Often require a smaller of samples to represent the habitat

16

Habitat sizeAppropriate sample unit size depends on size scale

of the habitatndash Small scale habitats require smaller sized samples1048698 Ex Bouldersndash Large scale habitats require larger sized samples1048698 Ex Forests

17

Organism size and density

Depends on size and density of organisms

ndash Small dense organisms require smaller samples

1048698 Ex grassndash Large scattered organisms require

larger samples1048698 Ex Trees

18

TYPES OF SAMPLING

1048698 Systematic 1048698 Stratified 1048698 Random

19

SYSTEMATIC SAMPLING

1048698 Often used when the area being studied is varied not very large or

when time is available 1048698 Samples are taken at fixed intervals

20

How to sample systematicallySystematic samples are usually taken along a transect line marked by a tape measure

1048698 Transect- a line laid across an area

21

Sampling along gradients

Transects are setup along aenvironmentalgradientsndash down a hillsidendash across a streambedndash out from a source ofpollution

22

Types of transect sampling 1048698 Line transect 1048698 Belt transect

23

Line transect methodA measured line is laidacross the area in thedirection of theenvironmental gradientndash The species touching theline can be recordedalong the whole length ofthe line (continuoussampling) or at specificpoints along the line(systematic sampling)

24

Line Transect- useful where a transition of flora andor fauna

occurs- a string or tape is stretched out along the

ground in a straight line record the organisms touching or covering

the line all along its length or at regular intervals

- Profile transect when there is appreciable height change along the transect and thus affecting the distribution of its species

25

Belt transect method

Similar to line transect butwidens the sampling areandash Transect line is laid outndash Samples are taken bydetermining abundance or cover in an area that is adefined distance from the linendash Samples can be taken all

theway along the line at specificintervals or even randomly

26

Belt TransectIt is a strip usually a metre wide marked by putting a

second line parallel to the other The species between the lines are carefully recorded working a metre at a time

Alternatively a frame quadrat in conjunction with a single line transect could be used

Using a quadrat along a belt transect eg ladder transect (every 5m)

27

Point Frames- for grassland field study of dense vegetation

28

STRATIFIED SAMPLING1048698 Often used whenthere are smallareas within alarger habitat thatare clearly different1048698 Strata- majordifferences withincommunitiesrecognized beforesampling begins

29

RANDOM SAMPLING

1048698 Often used when the area being studied isfairly uniform very large or when there is alimited amount of time available1048698 Random = chosen by chance rather thanaccording to a plan all outcomes are

equallylikely1048698 Samples are taken from different positionswithin a habitat and those positions arechosen randomly

30

How to sample randomly

Choose individuals or Placeldquosampling unitsrdquo

haphazardlyndash This is rarely completely

random1048698 ORhellip1048698 Assign numbers to the

areasor individuals to be sampledndash Use a random number

table toselect which areas or

individualswill be sample

31

Population Attributes Density ndash size of a population in relation to a definite

unit of space Affected by

Natality ndash the reproductive output (birth rate) of a population

Mortality ndash the death rate of organisms in a population

Immigration ndash number of organisms moving into the area occupied by the population

Emigration ndash number of organisms moving out of the area occupied by the population

32

Population Density

Four primary population parameters

33

Two Types of Density Estimates

bull Absolute Density ndash a known density such as m2

bull Relative Density ndash we know when one area has more individuals than another

34

Measuring Absolute Density

Total Count ndash count the number of organisms living in an area Human census number of oak trees in a

wooded lot number of singing birds in an area

Total counts generally are not used very often

Sampling Methods ndash use a sample to estimate population size Either use the quadrat or capture-

recapture method

35

Measurement of Environmental ParametersAbiotic factors are important in determining

both the distribution of the organisms and their physical and physiological adaptations

Temperature- diurnal and seasonal temperature variations

are significant in affecting different species of plants and animals

- equipment mercury thermometer maximum-minimum thermometer

miniaturized thermistor

36

pH

-measure pH of a solution by universal indicator pH paper pH meter etc

Light

-measure its duration and intensity duration by predication from Royal Observatory intensity by photographic light meter

pH meter in use

37

Humidity

Relative humidity the water content of a given volume of air relative to the same volume of fully saturated air

- equipment whirling hygrometer

38

Wind and Water Speed- wind speed- anemometer or wind

gauges- water speed - time the movement of a

floating object over a measured distance

39

Salinity

- using a conductivity meter greater salinity has greater conductivity

Oxygen Level

- using an oxygen meter or chemical method (Winkler method)

40

Collecting MethodsCollecting all organisms within a habitat is normally

impractical and therefore small areas are selected Remember to return all material to its original position

after searching amp collecting sufficient specimens Some collecting apparatus for general use are listed

below

41

1 specimen tube

2 screwed-topped jars

3 polythene bags

4 forceps

5 paint brush

6 bulb pipette

7 pooter

42

8 widger 9 sieve 10 hand lens

11 enamel dish 12 beating tray 13 light traps

14 Tullgren funnel 15 Baermann funnel 16 mammal traps

17 pitfall traps 18 netting

43

Estimating Population Size

The exact methods used for estimation depend not only the nature of the habitat but also on the organisms involved

eg animals - population

plants - percentage cover

44

Using Quadrats

- By sampling an area using quadrats and counting the number of individuals within each quadrat it is possible to estimate the total number of individuals within the area

- confined to plants and sessile or very slow-moving animals

- fast-moving animals are disturbed and run away

45

Capture-recapture Techniques- useful for mobile animals which can be marked

- capture marked released randomly recaptured

and marked individuals recorded

no of marked individuals recaptured total no of individuals in 1st sample

-------------------------------------------- = ------------------------------------------

total no of individuals in 2nd sample estimated size of population

(the Lincoln Index)

46

Capture-recapture Techniques Factors affecting the accuracy of the estimation

deaths migration individuals become more liable to predation etc

Examples

- arthropods marked on their backs with non-toxic paint

- fish have tags attached to opercula - mammals have tags clipped to their ears

birds have their legs ringed

47

Capture-recapture Method Important tool for estimating density birth

rate and death rate for mobile animals Method

Collect a sample of individuals mark them and then release them

After a period collect more individuals from the wild and count the number that have marks

We assume that a sample if random will contain the same proportion of marked individuals as the population does

Estimate population density

48

Assumptions For All Capture-Recapture Studies Marking technique does not increase

mortality of marked animals Marked individuals are allowed to mix

with population Marking technique does not affect catch

probability Marks are not lost or overlooked No significant immigration or emigration No significant mortality or natality

49

Marked animals in second sample

Total caught in second sample

Marked animals in first sample

Total population size

=

520 N

16=

Peterson Method or Lincoln Index

N = 64N = (20)(16)5

50

Some Indices Used

Traps Number of Fecal

Pellets Vocalization

Frequency Pelt Records Catch per Unit

Fishing Effort

Number of Artifacts Questionnaires Cover Feeding Capacity Roadside Counts

51

Abundance Scales

The population size may be fairly accurately determined by making some form of frequency assessment

These are subjective and involve an experimenter making some estimate of the number of individuals in a given area or the cover of a particular species

This is especially useful where individuals are very numerous eg barnacles on a rocky shore or where it is difficult to distinguish individuals eg grass plants in a meadow

52

The assessments are usually made on an abundance scale of 5 categories

Abundance Common Frequent Occasional Rare

Barnacles exposed at low water

53

Environmental resistance are the factors which limit the growth of a particular population

eg predation disease availability of light food water oxygen and shelter the accumulation of toxic wastes and even the size of the population itself

54

Density-dependent Growth A population is a density-dependent when its size

(or density) affects its growth rate because of density-dependent factors such as food availability and toxic waste accumulation

Density-independent Growth In this type of growth a population increases until

some factor causes a sudden reduction in its size Its effect is the same regardless of the size of the

population eg temperature fires floods storms etc

55

Regulation of Population Size Fecundity is the reproductive capacity of individual

females of a species Birth rate or natality is used to measure fecundity Death rate or mortality is the number of individuals

of a species which die per unit time Immigration occurs when individuals join a

population from neighbouring ones Emigration occurs when individuals depart from a

population A cycle occurs when the size of a population

fluctuates on a regular basis

56

Ecological Sampling

57

Why Do We Sample Determine presence andor

abundance

Monitor population fluctuations

Assess lsquoecological damagersquo

Assess quality of habitat

Assess population responses

58

What Do We Sample

Physical Environment Temperature DO pH salinity clarity

flow sediment

Biotic Environment All living things

59

Physical Habitat Temperature

Mercury thermometer Electronic thermometer Long-term thermometers

Dissolved Oxygen Winkler method (titration) DO meter (electrode)

pH Litmus paper pH meter (electrode)

Salinity Salinity Meter YSI 550A DO Meter w12 cable

60

Water Clarity Secchi Disk

Disk is attached to a calibrated rope The disk is lowered into the water until the white parts can no longer be seen Secchi disk depth is then recorded and serves as the waters transparency index The clearer the water the greater the secchi disk depth

Secchi Disk

61

Current Velocity (flow) Floating-orange method

Put an orange (or something else that floats just below the water surface) and measure the time it takes it to float across a known distance

Odometer-type flow meter Number of revolutions the propeller

makes for a given time is calibrated to flow velocity

62

Sediment Sediment size is important to many

aquatic organisms Sieversquos are used to separate and

grade sediment samples Percent of each size grade can be

determined

63

Water Sample

Water and plankton from various depths can be collected

A trigger mechanism is used to close the sampler Sample is then brought back to the

surface

64

Small Mammals

Mouserat Traps Fatal

Pit Falls Bucket is placed in the ground Sometimes have lsquoleadsrsquo to the buckets

Live traps Havahart Sherman

Spot-light

Sherman trapHavahart trap

65

Birds Stick-under-the-box method Bird-trap

Works like a minnow trap Mist net

Captures birds in flight Rocket net

Uses a propellant to throw a net over birds

66

Terrestrial Insects

Sticky paper flies

Baited Traps Fire ants

Nets butterflies

Foggers Collect insects from tree canopies

67

Aquatic Insects Drift Net

Place net in flowing water Kick Net

lsquoKickrsquo sediment upstream from block net and the flow will wash them into the net

Wash bucket Serber or Hess Sampler

Stir up known area of sediment

Animals are collected by a catch net

Multi-plate Sampler Become colonized

68

Crawfish and Crab Traps

69

Fish Larvae Light Traps

Larvae are attracted to the light Ichthyoplankton nets

Can be towed at various depths Fish collect at the lsquocodrsquoend

70

Fish Lift net

Net is placed down and after a set amount of time it is quickly lifted

Pop-net Similar to a lift net but

floats are attached to a framed net

Operated by a trigger mechanism

Throw net A net attached to a heavy

frame is thrown and every thing inside is netted out Throw net

Pop-net

Lift net

71

Minnow trap

Usually use bait to attract small fish Light is used sometimes as an attractant

72

Fish Electrofishing

Electricity is put into the water Fish are temporarily stunned and usually

swim towards the electricity source Usually non-fatal but may cause some

damage

73

Fish Gill Net

Gill nets resemble tennis nets Fish can not swim completely through the

net and get caught Gill nets are size selective (based on mesh

size) Square Mesh

Bar mesh

Stretch mesh

74

Fish Trammel Net

Three panels two large mesh on the outside and a small mesh on the inside

Fish swim through the outer mesh pushes the small mesh through the other side and becomes entangled

75

Hoop nets (and other similar nets) can have bait or not

Fyke nets have leads to help guide fish to the net

76

Seine Seines are nets that are pulled

through shallow water to catch fish

77

Purse Seine Used to encircle entire schools of fish

Usually involves a spotter plane and a second boat

78

Trotline (longline) A series of baited drop lines

connected to a main line

Can be deployed by tying one end to the bank and tying the other end with a heavy weight

79

Shrimp (or fish) Trawl Net pulled behind

a boat along the bottom Either a beam or

otter boards keep the net open

80

Tagging Individuals Coded Wire Tags

Microwire that has a unique label

Magnetic wand detects the tag

Tag retention should be determined

T-Bar tags Can be individually

numbered External tag

PIT tags (Passive Integrated Transponders) Wand induces the tag to

transmit individual number is displayed

81

Other Tagging Methods

Toe clip Amphibian and reptile Clip of one or more toes

to identify individuals

Bird Band Place a metal band on a

bird leg Generally has

identification information

82

Preserving plant specimens Pressing and drying Long-term

preservation and storage

Alternative drying techniques

Special preservation and processing techniques

Mounting

83

Pressing and drying Techniques for pressing and drying specimens have been

established for many years There are minor variations in recommended methods but they are essentially the same worldwide

The best specimens are plants that are pressed as soon as possible after collection before wilting and shrivelling Most plants may be kept in sealed containers such as plastic bags for up to a day if it is inconvenient to press immediately However some plants show such rapid wilting particularly of the flowers that such delays are best avoided Flowers with a lot of nectar may go mouldy very quickly if excess nectar is not shaken off before pressing

Specimens are pressed flat and dried between sheets of absorbent blotters or semi-absorbent paper such as newspaper Papers with a glossy surface should be avoided because they are not absorbent enough to aid drying The plant should be carefully laid out between the drying sheets as their form at this stage largely determines their ultimate appearance The flowers should be spread out with the petals carefully arranged wilted leaves should be straightened and unnecessary shoots of excessively twiggy shrubs may be cut away

84

Microwave ovens Small numbers of specimens can be dried using a microwave

oven The technique recommended in the literature is to place the specimens between unprinted absorbent paper for example butchers paper not newspaper which is unsuitable because the chemicals present in the ink may cause a fire The specimens should be put in a special press which should be of a microwave-safe material (wood acrylic or polycarbonate sheeting eg plexiglass or perspex NO metal components) If such a press is not available sheets of cardboard can be placed above and below the specimens and then weighted down

Drying time depends on the power of your oven In most cases drying is accomplished by irradiating at maximum power for 1-2 minutes per specimen although it is often a case of trial and error It is best to process no more than 10-12 specimens of average thickness per batch Specimens are usually dried after the moisture that characteristically appears on the glass door has disappeared If the specimen is damp when taken out of the oven allow it to stand before re-radiating as moisture continues to evaporate from the specimen for some time Care must be taken not to irradiate the specimens for too long

It should be noted that microwave treatment damages seeds and the cellular structure of the plants which may reduce the long-term value of the specimens

85

Alternative drying techniquesSilica gelother desiccants amp freeze drying Alternative methods of drying plant specimens have been

used for some time but are mostly restricted to special purpose collections The main alternatives are freeze-drying and drying in a desiccant powder such as desiccant silica gel In general these techniques are used where it is essential to preserve the shape of a delicate plant of organ of the plant such as the flower Freeze-drying has also been used to preserve the chemical composition of a plant as accurately as possible for later study

Disadvantages and special conservation problems of specimens dried in these manners are that they are particularly susceptible to damage The dried parts are fragile lack support and often catch on packing materials They must therefore be packed especially carefully and stored in small boxes or tubes with some appropriate packing material that does not snag and break small projections Acid-free tissue paper is often used Drying in desiccant silica gel crystals or powder can also have the disadvantage that it is difficult to remove all traces of the silica gel after drying

86

Special preservation and processing techniquesWet or spirit collections

Very fleshy or delicate structures including small algae and orchid flowers are best preserved in an air-tight glass or plastic jar with a liquid preservative rather than by drying The type of preservative used should be clearly labelled in the jar Such material is often referred to as a spirit collection or wet collection

Most material can be satisfactorily preserved in 70 ethyl alcohol (or 70 methylated spirit or denatured alcohol) with 30 water Colours will fade quickly in spirit however so it is a good idea to keep comprehensive notes and photographs

87

Small algae Microscopic algae are often collected in a jar and in the

water in which they were found If the algae are to be stored for more than 2-3 days a preservative needs to be used Traditionally this has been the extremely toxic formalin - a small amount can be added to the water to make a 5 final solution and the container labelled This must not be sent through the post or by courier

There are some other equally toxic options for example propylene phenoxytol but none should be sent through the post A safer option is to add sufficient concentrated alcohol or methylated spirits to the water containing the algae to make a final solution of 70 alcohol This treatment dilutes the algae making them difficult to find so if they can be concentrated somehow first (eg by filtering) they can be stored in much less liquid Another option is to fix the algae in formalin (or something similar) first and then prepare a microscope glass slide with a permanent water-soluble mounting medium

88

Mounting Mounting specimens prevents most fragile material from

fragmenting and prevents specimens becoming separated from their labels If the plant collection is a long-term project specimens should be mounted on sheets of archival (permanent) cardboard or paper with archival-quality fixing media These include stitching with cotton thread dental floss nickel-plated copper wire (for heavier specimens) narrow strips of archival paper linen tape or by using an archival adhesive such as methyl cellulose adhesive

One disadvantage of mounting specimens is that it can make parts of the specimen inaccessible for examination so it is essential that this be borne in mind during specimen arrangement and mounting For example easily reversible mounting media should be used specimens should be strapped to the sheet rather than glued all over and the specimen should be carefully arranged before it is attached so that it shows all features

89

Full-size herbarium mounting sheets are usually about 43 cm long x 28 cm wide The plant name and accompanying field notes should be transcribed on a permanent label stuck to one corner of the herbarium sheet (the bottom right-hand corner being the most common) or sometimes annotations may be written directly on the sheet or card

Small pieces of material which may have become separated from the specimen (eg seeds) can be placed in small plastic bags and pinned to the sheet

90

Long-term preservation and storage The long-term preservation of dry plant

specimens is largely dependent on protection from insect attack Specimens collected by Linnaeus in the eighteenth century and by Banks and Solander on the Endeavour voyage in 1788 are still excellently preserved

91

Pests and their control A range of pests attack dried plant material The

most common pests are insects and fungi though rodents and other large animals can cause damage in poor storage conditions Insects eat the material the paper surrounding the material and the adhesives and mounting media

Such insect pests range from psocids (book lice) which attack mainly the softer parts such as flowers and soft fruits to tobacco beetles and carpet beetles which can bore holes through the toughest of specimens Many insects are particularly sensitive to relative humidity levels and do not thrive at levels below 50

92

The most common and acceptable specimen treatments for insect control are Freezing Microwave Poisoning Insect deterrents Fungal pests

93

Storage

Dried and pressed plant specimens can be stored in cardboard or plastic boxes or tied in bundles in light-weight cardboard folders placed in pigeon holes

Alternatively they can be placed in protective plastic jackets and displayed in ring folders which is recommended if they are to be frequently handled such as for a reference collection

94

Filing

Specimens should be filed in a systematic order if a relatively permanent collection is being made The major groups ie ferns and fern allies cycads conifers dicotyledons and monocotyledons are best kept separately or according to some classification scheme such as that given in a flora or handbook

Similarly the genera within each family and the species within each genus may be filed alphabetically or following some such classification

95

Preservation of entire animals

Types of collection specimens of an entire animal For reference collections mammals can be prepared as a variety of specimens The condition of the specimen may determine possible ways to preserve it if for instance decomposition of the skin has loosened the hair of a carcass so much that it can easily be pulled out or removed by rubbing (ldquoslippingrdquo fur) it will be very difficult or impossible to produce a study skin or mounted specimen The most usual types of specimens (based on Nagorsen and Peterson 1980) are 1) entire fluid-preserved animals (for studying anatomy and histology fluid preservation may change the fur colour) 2) study skins with accompanying skulls partial skeletons (some bones remain in the skin) for studying pelage colour hair quality and moulting patterns 3) mounted skins with accompanying partial or entire skeleton (some bones may remain in the skin dependant on the method of preservation) or freeze-dried specimens 4) entire skeletons for instance for studying anatomy geographic variation or for age determination (entire skeletons are poorly represented in collections so Nagorsen and Peterson (1980) recommend preparation of at least one male and one female skeleton per species

96

Preservation of specimens in the field Formalin preservation Preservation in alcohol Preservation by cooling or freezing

97

Formalin preservation After weighing and measuring the animal and attaching an

adequate label very small specimens (up to 100 g) can be fixed whole by submerging them in 10 buffered formalin (tissue - formalin solution ratio of at least 1 12) the body cavity can be filled with formalin solution by injection until it is turgid and firm some formalin may also be injected under the skin into the body cavity larger muscles and organs If hypodermic needles are not available the body cavity can be opened ventrally by making a slit instead allowing the formalin to enter

Keeping the mouth open with a piece of wood or cotton may later allow examination of teeth Then the whole body can be immersed in formalin in the posture in which it is supposed to stay permanently because it will harden The ratio of formalin to carcass must be at least 12 to 1 to assure a good fixation Tissues can be left in buffered neutralized formalin for several months but formalin hardens specimens therefore after fixation longterm storage in alcohol may be better After preservation the carcass should therefore be washed in water and transferred into ethanol for permanent storage

Disadvantages for instance it discolours the fur after a longish immersion softens the bones and prevents further examination for microbiology

98

Preservation in alcohol

After weighing a whole animal can be preserved in a container of alcohol (70-90) Removal of the intestine prior to storage of the animal in alcohol is recommended

99

Preservation by cooling or freezing Removal of the skin with insulating fur

before cooling or freezing may help to cool the carcass down more quickly

Freezing is not recommended if histological examination is planned

100

THANK YOU

12

QUADRAT amp TRANSECT ACTIVITIESHow Where amp Why Scientists Do SamplingScientists often collect data ldquoin the fieldrdquo which couldmean underwater in a forest in a cave on a reef oreven the moon Two essential methods to gatherecological information in a standardized way areTransect Sampling (using a single line) and

QuadratSampling (counted within a grid) These samplingmethods provide more accurate data than randomsampling or simply guessing but they take less timethan counting every specimen in a certain area

13

Quadrats- a sturdily built

wooden frame

can be folded for easy transport and storage

14

Quadrats

- When placed on the ground the species present within the frame are identified and their abundance recorded

- Sampling could be random or systematic

Using a quadrat along a belt transect

15

Practical Constraints

Small quadrats are quicker to survey but yield a smaller individual sample of habitat

ndash Often require a larger of samples to represent the habitat

1048698 Large quadrats require more time and effort to survey but provide a larger individual sample of habitat

ndash Often require a smaller of samples to represent the habitat

16

Habitat sizeAppropriate sample unit size depends on size scale

of the habitatndash Small scale habitats require smaller sized samples1048698 Ex Bouldersndash Large scale habitats require larger sized samples1048698 Ex Forests

17

Organism size and density

Depends on size and density of organisms

ndash Small dense organisms require smaller samples

1048698 Ex grassndash Large scattered organisms require

larger samples1048698 Ex Trees

18

TYPES OF SAMPLING

1048698 Systematic 1048698 Stratified 1048698 Random

19

SYSTEMATIC SAMPLING

1048698 Often used when the area being studied is varied not very large or

when time is available 1048698 Samples are taken at fixed intervals

20

How to sample systematicallySystematic samples are usually taken along a transect line marked by a tape measure

1048698 Transect- a line laid across an area

21

Sampling along gradients

Transects are setup along aenvironmentalgradientsndash down a hillsidendash across a streambedndash out from a source ofpollution

22

Types of transect sampling 1048698 Line transect 1048698 Belt transect

23

Line transect methodA measured line is laidacross the area in thedirection of theenvironmental gradientndash The species touching theline can be recordedalong the whole length ofthe line (continuoussampling) or at specificpoints along the line(systematic sampling)

24

Line Transect- useful where a transition of flora andor fauna

occurs- a string or tape is stretched out along the

ground in a straight line record the organisms touching or covering

the line all along its length or at regular intervals

- Profile transect when there is appreciable height change along the transect and thus affecting the distribution of its species

25

Belt transect method

Similar to line transect butwidens the sampling areandash Transect line is laid outndash Samples are taken bydetermining abundance or cover in an area that is adefined distance from the linendash Samples can be taken all

theway along the line at specificintervals or even randomly

26

Belt TransectIt is a strip usually a metre wide marked by putting a

second line parallel to the other The species between the lines are carefully recorded working a metre at a time

Alternatively a frame quadrat in conjunction with a single line transect could be used

Using a quadrat along a belt transect eg ladder transect (every 5m)

27

Point Frames- for grassland field study of dense vegetation

28

STRATIFIED SAMPLING1048698 Often used whenthere are smallareas within alarger habitat thatare clearly different1048698 Strata- majordifferences withincommunitiesrecognized beforesampling begins

29

RANDOM SAMPLING

1048698 Often used when the area being studied isfairly uniform very large or when there is alimited amount of time available1048698 Random = chosen by chance rather thanaccording to a plan all outcomes are

equallylikely1048698 Samples are taken from different positionswithin a habitat and those positions arechosen randomly

30

How to sample randomly

Choose individuals or Placeldquosampling unitsrdquo

haphazardlyndash This is rarely completely

random1048698 ORhellip1048698 Assign numbers to the

areasor individuals to be sampledndash Use a random number

table toselect which areas or

individualswill be sample

31

Population Attributes Density ndash size of a population in relation to a definite

unit of space Affected by

Natality ndash the reproductive output (birth rate) of a population

Mortality ndash the death rate of organisms in a population

Immigration ndash number of organisms moving into the area occupied by the population

Emigration ndash number of organisms moving out of the area occupied by the population

32

Population Density

Four primary population parameters

33

Two Types of Density Estimates

bull Absolute Density ndash a known density such as m2

bull Relative Density ndash we know when one area has more individuals than another

34

Measuring Absolute Density

Total Count ndash count the number of organisms living in an area Human census number of oak trees in a

wooded lot number of singing birds in an area

Total counts generally are not used very often

Sampling Methods ndash use a sample to estimate population size Either use the quadrat or capture-

recapture method

35

Measurement of Environmental ParametersAbiotic factors are important in determining

both the distribution of the organisms and their physical and physiological adaptations

Temperature- diurnal and seasonal temperature variations

are significant in affecting different species of plants and animals

- equipment mercury thermometer maximum-minimum thermometer

miniaturized thermistor

36

pH

-measure pH of a solution by universal indicator pH paper pH meter etc

Light

-measure its duration and intensity duration by predication from Royal Observatory intensity by photographic light meter

pH meter in use

37

Humidity

Relative humidity the water content of a given volume of air relative to the same volume of fully saturated air

- equipment whirling hygrometer

38

Wind and Water Speed- wind speed- anemometer or wind

gauges- water speed - time the movement of a

floating object over a measured distance

39

Salinity

- using a conductivity meter greater salinity has greater conductivity

Oxygen Level

- using an oxygen meter or chemical method (Winkler method)

40

Collecting MethodsCollecting all organisms within a habitat is normally

impractical and therefore small areas are selected Remember to return all material to its original position

after searching amp collecting sufficient specimens Some collecting apparatus for general use are listed

below

41

1 specimen tube

2 screwed-topped jars

3 polythene bags

4 forceps

5 paint brush

6 bulb pipette

7 pooter

42

8 widger 9 sieve 10 hand lens

11 enamel dish 12 beating tray 13 light traps

14 Tullgren funnel 15 Baermann funnel 16 mammal traps

17 pitfall traps 18 netting

43

Estimating Population Size

The exact methods used for estimation depend not only the nature of the habitat but also on the organisms involved

eg animals - population

plants - percentage cover

44

Using Quadrats

- By sampling an area using quadrats and counting the number of individuals within each quadrat it is possible to estimate the total number of individuals within the area

- confined to plants and sessile or very slow-moving animals

- fast-moving animals are disturbed and run away

45

Capture-recapture Techniques- useful for mobile animals which can be marked

- capture marked released randomly recaptured

and marked individuals recorded

no of marked individuals recaptured total no of individuals in 1st sample

-------------------------------------------- = ------------------------------------------

total no of individuals in 2nd sample estimated size of population

(the Lincoln Index)

46

Capture-recapture Techniques Factors affecting the accuracy of the estimation

deaths migration individuals become more liable to predation etc

Examples

- arthropods marked on their backs with non-toxic paint

- fish have tags attached to opercula - mammals have tags clipped to their ears

birds have their legs ringed

47

Capture-recapture Method Important tool for estimating density birth

rate and death rate for mobile animals Method

Collect a sample of individuals mark them and then release them

After a period collect more individuals from the wild and count the number that have marks

We assume that a sample if random will contain the same proportion of marked individuals as the population does

Estimate population density

48

Assumptions For All Capture-Recapture Studies Marking technique does not increase

mortality of marked animals Marked individuals are allowed to mix

with population Marking technique does not affect catch

probability Marks are not lost or overlooked No significant immigration or emigration No significant mortality or natality

49

Marked animals in second sample

Total caught in second sample

Marked animals in first sample

Total population size

=

520 N

16=

Peterson Method or Lincoln Index

N = 64N = (20)(16)5

50

Some Indices Used

Traps Number of Fecal

Pellets Vocalization

Frequency Pelt Records Catch per Unit

Fishing Effort

Number of Artifacts Questionnaires Cover Feeding Capacity Roadside Counts

51

Abundance Scales

The population size may be fairly accurately determined by making some form of frequency assessment

These are subjective and involve an experimenter making some estimate of the number of individuals in a given area or the cover of a particular species

This is especially useful where individuals are very numerous eg barnacles on a rocky shore or where it is difficult to distinguish individuals eg grass plants in a meadow

52

The assessments are usually made on an abundance scale of 5 categories

Abundance Common Frequent Occasional Rare

Barnacles exposed at low water

53

Environmental resistance are the factors which limit the growth of a particular population

eg predation disease availability of light food water oxygen and shelter the accumulation of toxic wastes and even the size of the population itself

54

Density-dependent Growth A population is a density-dependent when its size

(or density) affects its growth rate because of density-dependent factors such as food availability and toxic waste accumulation

Density-independent Growth In this type of growth a population increases until

some factor causes a sudden reduction in its size Its effect is the same regardless of the size of the

population eg temperature fires floods storms etc

55

Regulation of Population Size Fecundity is the reproductive capacity of individual

females of a species Birth rate or natality is used to measure fecundity Death rate or mortality is the number of individuals

of a species which die per unit time Immigration occurs when individuals join a

population from neighbouring ones Emigration occurs when individuals depart from a

population A cycle occurs when the size of a population

fluctuates on a regular basis

56

Ecological Sampling

57

Why Do We Sample Determine presence andor

abundance

Monitor population fluctuations

Assess lsquoecological damagersquo

Assess quality of habitat

Assess population responses

58

What Do We Sample

Physical Environment Temperature DO pH salinity clarity

flow sediment

Biotic Environment All living things

59

Physical Habitat Temperature

Mercury thermometer Electronic thermometer Long-term thermometers

Dissolved Oxygen Winkler method (titration) DO meter (electrode)

pH Litmus paper pH meter (electrode)

Salinity Salinity Meter YSI 550A DO Meter w12 cable

60

Water Clarity Secchi Disk

Disk is attached to a calibrated rope The disk is lowered into the water until the white parts can no longer be seen Secchi disk depth is then recorded and serves as the waters transparency index The clearer the water the greater the secchi disk depth

Secchi Disk

61

Current Velocity (flow) Floating-orange method

Put an orange (or something else that floats just below the water surface) and measure the time it takes it to float across a known distance

Odometer-type flow meter Number of revolutions the propeller

makes for a given time is calibrated to flow velocity

62

Sediment Sediment size is important to many

aquatic organisms Sieversquos are used to separate and

grade sediment samples Percent of each size grade can be

determined

63

Water Sample

Water and plankton from various depths can be collected

A trigger mechanism is used to close the sampler Sample is then brought back to the

surface

64

Small Mammals

Mouserat Traps Fatal

Pit Falls Bucket is placed in the ground Sometimes have lsquoleadsrsquo to the buckets

Live traps Havahart Sherman

Spot-light

Sherman trapHavahart trap

65

Birds Stick-under-the-box method Bird-trap

Works like a minnow trap Mist net

Captures birds in flight Rocket net

Uses a propellant to throw a net over birds

66

Terrestrial Insects

Sticky paper flies

Baited Traps Fire ants

Nets butterflies

Foggers Collect insects from tree canopies

67

Aquatic Insects Drift Net

Place net in flowing water Kick Net

lsquoKickrsquo sediment upstream from block net and the flow will wash them into the net

Wash bucket Serber or Hess Sampler

Stir up known area of sediment

Animals are collected by a catch net

Multi-plate Sampler Become colonized

68

Crawfish and Crab Traps

69

Fish Larvae Light Traps

Larvae are attracted to the light Ichthyoplankton nets

Can be towed at various depths Fish collect at the lsquocodrsquoend

70

Fish Lift net

Net is placed down and after a set amount of time it is quickly lifted

Pop-net Similar to a lift net but

floats are attached to a framed net

Operated by a trigger mechanism

Throw net A net attached to a heavy

frame is thrown and every thing inside is netted out Throw net

Pop-net

Lift net

71

Minnow trap

Usually use bait to attract small fish Light is used sometimes as an attractant

72

Fish Electrofishing

Electricity is put into the water Fish are temporarily stunned and usually

swim towards the electricity source Usually non-fatal but may cause some

damage

73

Fish Gill Net

Gill nets resemble tennis nets Fish can not swim completely through the

net and get caught Gill nets are size selective (based on mesh

size) Square Mesh

Bar mesh

Stretch mesh

74

Fish Trammel Net

Three panels two large mesh on the outside and a small mesh on the inside

Fish swim through the outer mesh pushes the small mesh through the other side and becomes entangled

75

Hoop nets (and other similar nets) can have bait or not

Fyke nets have leads to help guide fish to the net

76

Seine Seines are nets that are pulled

through shallow water to catch fish

77

Purse Seine Used to encircle entire schools of fish

Usually involves a spotter plane and a second boat

78

Trotline (longline) A series of baited drop lines

connected to a main line

Can be deployed by tying one end to the bank and tying the other end with a heavy weight

79

Shrimp (or fish) Trawl Net pulled behind

a boat along the bottom Either a beam or

otter boards keep the net open

80

Tagging Individuals Coded Wire Tags

Microwire that has a unique label

Magnetic wand detects the tag

Tag retention should be determined

T-Bar tags Can be individually

numbered External tag

PIT tags (Passive Integrated Transponders) Wand induces the tag to

transmit individual number is displayed

81

Other Tagging Methods

Toe clip Amphibian and reptile Clip of one or more toes

to identify individuals

Bird Band Place a metal band on a

bird leg Generally has

identification information

82

Preserving plant specimens Pressing and drying Long-term

preservation and storage

Alternative drying techniques

Special preservation and processing techniques

Mounting

83

Pressing and drying Techniques for pressing and drying specimens have been

established for many years There are minor variations in recommended methods but they are essentially the same worldwide

The best specimens are plants that are pressed as soon as possible after collection before wilting and shrivelling Most plants may be kept in sealed containers such as plastic bags for up to a day if it is inconvenient to press immediately However some plants show such rapid wilting particularly of the flowers that such delays are best avoided Flowers with a lot of nectar may go mouldy very quickly if excess nectar is not shaken off before pressing

Specimens are pressed flat and dried between sheets of absorbent blotters or semi-absorbent paper such as newspaper Papers with a glossy surface should be avoided because they are not absorbent enough to aid drying The plant should be carefully laid out between the drying sheets as their form at this stage largely determines their ultimate appearance The flowers should be spread out with the petals carefully arranged wilted leaves should be straightened and unnecessary shoots of excessively twiggy shrubs may be cut away

84

Microwave ovens Small numbers of specimens can be dried using a microwave

oven The technique recommended in the literature is to place the specimens between unprinted absorbent paper for example butchers paper not newspaper which is unsuitable because the chemicals present in the ink may cause a fire The specimens should be put in a special press which should be of a microwave-safe material (wood acrylic or polycarbonate sheeting eg plexiglass or perspex NO metal components) If such a press is not available sheets of cardboard can be placed above and below the specimens and then weighted down

Drying time depends on the power of your oven In most cases drying is accomplished by irradiating at maximum power for 1-2 minutes per specimen although it is often a case of trial and error It is best to process no more than 10-12 specimens of average thickness per batch Specimens are usually dried after the moisture that characteristically appears on the glass door has disappeared If the specimen is damp when taken out of the oven allow it to stand before re-radiating as moisture continues to evaporate from the specimen for some time Care must be taken not to irradiate the specimens for too long

It should be noted that microwave treatment damages seeds and the cellular structure of the plants which may reduce the long-term value of the specimens

85

Alternative drying techniquesSilica gelother desiccants amp freeze drying Alternative methods of drying plant specimens have been

used for some time but are mostly restricted to special purpose collections The main alternatives are freeze-drying and drying in a desiccant powder such as desiccant silica gel In general these techniques are used where it is essential to preserve the shape of a delicate plant of organ of the plant such as the flower Freeze-drying has also been used to preserve the chemical composition of a plant as accurately as possible for later study

Disadvantages and special conservation problems of specimens dried in these manners are that they are particularly susceptible to damage The dried parts are fragile lack support and often catch on packing materials They must therefore be packed especially carefully and stored in small boxes or tubes with some appropriate packing material that does not snag and break small projections Acid-free tissue paper is often used Drying in desiccant silica gel crystals or powder can also have the disadvantage that it is difficult to remove all traces of the silica gel after drying

86

Special preservation and processing techniquesWet or spirit collections

Very fleshy or delicate structures including small algae and orchid flowers are best preserved in an air-tight glass or plastic jar with a liquid preservative rather than by drying The type of preservative used should be clearly labelled in the jar Such material is often referred to as a spirit collection or wet collection

Most material can be satisfactorily preserved in 70 ethyl alcohol (or 70 methylated spirit or denatured alcohol) with 30 water Colours will fade quickly in spirit however so it is a good idea to keep comprehensive notes and photographs

87

Small algae Microscopic algae are often collected in a jar and in the

water in which they were found If the algae are to be stored for more than 2-3 days a preservative needs to be used Traditionally this has been the extremely toxic formalin - a small amount can be added to the water to make a 5 final solution and the container labelled This must not be sent through the post or by courier

There are some other equally toxic options for example propylene phenoxytol but none should be sent through the post A safer option is to add sufficient concentrated alcohol or methylated spirits to the water containing the algae to make a final solution of 70 alcohol This treatment dilutes the algae making them difficult to find so if they can be concentrated somehow first (eg by filtering) they can be stored in much less liquid Another option is to fix the algae in formalin (or something similar) first and then prepare a microscope glass slide with a permanent water-soluble mounting medium

88

Mounting Mounting specimens prevents most fragile material from

fragmenting and prevents specimens becoming separated from their labels If the plant collection is a long-term project specimens should be mounted on sheets of archival (permanent) cardboard or paper with archival-quality fixing media These include stitching with cotton thread dental floss nickel-plated copper wire (for heavier specimens) narrow strips of archival paper linen tape or by using an archival adhesive such as methyl cellulose adhesive

One disadvantage of mounting specimens is that it can make parts of the specimen inaccessible for examination so it is essential that this be borne in mind during specimen arrangement and mounting For example easily reversible mounting media should be used specimens should be strapped to the sheet rather than glued all over and the specimen should be carefully arranged before it is attached so that it shows all features

89

Full-size herbarium mounting sheets are usually about 43 cm long x 28 cm wide The plant name and accompanying field notes should be transcribed on a permanent label stuck to one corner of the herbarium sheet (the bottom right-hand corner being the most common) or sometimes annotations may be written directly on the sheet or card

Small pieces of material which may have become separated from the specimen (eg seeds) can be placed in small plastic bags and pinned to the sheet

90

Long-term preservation and storage The long-term preservation of dry plant

specimens is largely dependent on protection from insect attack Specimens collected by Linnaeus in the eighteenth century and by Banks and Solander on the Endeavour voyage in 1788 are still excellently preserved

91

Pests and their control A range of pests attack dried plant material The

most common pests are insects and fungi though rodents and other large animals can cause damage in poor storage conditions Insects eat the material the paper surrounding the material and the adhesives and mounting media

Such insect pests range from psocids (book lice) which attack mainly the softer parts such as flowers and soft fruits to tobacco beetles and carpet beetles which can bore holes through the toughest of specimens Many insects are particularly sensitive to relative humidity levels and do not thrive at levels below 50

92

The most common and acceptable specimen treatments for insect control are Freezing Microwave Poisoning Insect deterrents Fungal pests

93

Storage

Dried and pressed plant specimens can be stored in cardboard or plastic boxes or tied in bundles in light-weight cardboard folders placed in pigeon holes

Alternatively they can be placed in protective plastic jackets and displayed in ring folders which is recommended if they are to be frequently handled such as for a reference collection

94

Filing

Specimens should be filed in a systematic order if a relatively permanent collection is being made The major groups ie ferns and fern allies cycads conifers dicotyledons and monocotyledons are best kept separately or according to some classification scheme such as that given in a flora or handbook

Similarly the genera within each family and the species within each genus may be filed alphabetically or following some such classification

95

Preservation of entire animals

Types of collection specimens of an entire animal For reference collections mammals can be prepared as a variety of specimens The condition of the specimen may determine possible ways to preserve it if for instance decomposition of the skin has loosened the hair of a carcass so much that it can easily be pulled out or removed by rubbing (ldquoslippingrdquo fur) it will be very difficult or impossible to produce a study skin or mounted specimen The most usual types of specimens (based on Nagorsen and Peterson 1980) are 1) entire fluid-preserved animals (for studying anatomy and histology fluid preservation may change the fur colour) 2) study skins with accompanying skulls partial skeletons (some bones remain in the skin) for studying pelage colour hair quality and moulting patterns 3) mounted skins with accompanying partial or entire skeleton (some bones may remain in the skin dependant on the method of preservation) or freeze-dried specimens 4) entire skeletons for instance for studying anatomy geographic variation or for age determination (entire skeletons are poorly represented in collections so Nagorsen and Peterson (1980) recommend preparation of at least one male and one female skeleton per species

96

Preservation of specimens in the field Formalin preservation Preservation in alcohol Preservation by cooling or freezing

97

Formalin preservation After weighing and measuring the animal and attaching an

adequate label very small specimens (up to 100 g) can be fixed whole by submerging them in 10 buffered formalin (tissue - formalin solution ratio of at least 1 12) the body cavity can be filled with formalin solution by injection until it is turgid and firm some formalin may also be injected under the skin into the body cavity larger muscles and organs If hypodermic needles are not available the body cavity can be opened ventrally by making a slit instead allowing the formalin to enter

Keeping the mouth open with a piece of wood or cotton may later allow examination of teeth Then the whole body can be immersed in formalin in the posture in which it is supposed to stay permanently because it will harden The ratio of formalin to carcass must be at least 12 to 1 to assure a good fixation Tissues can be left in buffered neutralized formalin for several months but formalin hardens specimens therefore after fixation longterm storage in alcohol may be better After preservation the carcass should therefore be washed in water and transferred into ethanol for permanent storage

Disadvantages for instance it discolours the fur after a longish immersion softens the bones and prevents further examination for microbiology

98

Preservation in alcohol

After weighing a whole animal can be preserved in a container of alcohol (70-90) Removal of the intestine prior to storage of the animal in alcohol is recommended

99

Preservation by cooling or freezing Removal of the skin with insulating fur

before cooling or freezing may help to cool the carcass down more quickly

Freezing is not recommended if histological examination is planned

100

THANK YOU

13

Quadrats- a sturdily built

wooden frame

can be folded for easy transport and storage

14

Quadrats

- When placed on the ground the species present within the frame are identified and their abundance recorded

- Sampling could be random or systematic

Using a quadrat along a belt transect

15

Practical Constraints

Small quadrats are quicker to survey but yield a smaller individual sample of habitat

ndash Often require a larger of samples to represent the habitat

1048698 Large quadrats require more time and effort to survey but provide a larger individual sample of habitat

ndash Often require a smaller of samples to represent the habitat

16

Habitat sizeAppropriate sample unit size depends on size scale

of the habitatndash Small scale habitats require smaller sized samples1048698 Ex Bouldersndash Large scale habitats require larger sized samples1048698 Ex Forests

17

Organism size and density

Depends on size and density of organisms

ndash Small dense organisms require smaller samples

1048698 Ex grassndash Large scattered organisms require

larger samples1048698 Ex Trees

18

TYPES OF SAMPLING

1048698 Systematic 1048698 Stratified 1048698 Random

19

SYSTEMATIC SAMPLING

1048698 Often used when the area being studied is varied not very large or

when time is available 1048698 Samples are taken at fixed intervals

20

How to sample systematicallySystematic samples are usually taken along a transect line marked by a tape measure

1048698 Transect- a line laid across an area

21

Sampling along gradients

Transects are setup along aenvironmentalgradientsndash down a hillsidendash across a streambedndash out from a source ofpollution

22

Types of transect sampling 1048698 Line transect 1048698 Belt transect

23

Line transect methodA measured line is laidacross the area in thedirection of theenvironmental gradientndash The species touching theline can be recordedalong the whole length ofthe line (continuoussampling) or at specificpoints along the line(systematic sampling)

24

Line Transect- useful where a transition of flora andor fauna

occurs- a string or tape is stretched out along the

ground in a straight line record the organisms touching or covering

the line all along its length or at regular intervals

- Profile transect when there is appreciable height change along the transect and thus affecting the distribution of its species

25

Belt transect method

Similar to line transect butwidens the sampling areandash Transect line is laid outndash Samples are taken bydetermining abundance or cover in an area that is adefined distance from the linendash Samples can be taken all

theway along the line at specificintervals or even randomly

26

Belt TransectIt is a strip usually a metre wide marked by putting a

second line parallel to the other The species between the lines are carefully recorded working a metre at a time

Alternatively a frame quadrat in conjunction with a single line transect could be used

Using a quadrat along a belt transect eg ladder transect (every 5m)

27

Point Frames- for grassland field study of dense vegetation

28

STRATIFIED SAMPLING1048698 Often used whenthere are smallareas within alarger habitat thatare clearly different1048698 Strata- majordifferences withincommunitiesrecognized beforesampling begins

29

RANDOM SAMPLING

1048698 Often used when the area being studied isfairly uniform very large or when there is alimited amount of time available1048698 Random = chosen by chance rather thanaccording to a plan all outcomes are

equallylikely1048698 Samples are taken from different positionswithin a habitat and those positions arechosen randomly

30

How to sample randomly

Choose individuals or Placeldquosampling unitsrdquo

haphazardlyndash This is rarely completely

random1048698 ORhellip1048698 Assign numbers to the

areasor individuals to be sampledndash Use a random number

table toselect which areas or

individualswill be sample

31

Population Attributes Density ndash size of a population in relation to a definite

unit of space Affected by

Natality ndash the reproductive output (birth rate) of a population

Mortality ndash the death rate of organisms in a population

Immigration ndash number of organisms moving into the area occupied by the population

Emigration ndash number of organisms moving out of the area occupied by the population

32

Population Density

Four primary population parameters

33

Two Types of Density Estimates

bull Absolute Density ndash a known density such as m2

bull Relative Density ndash we know when one area has more individuals than another

34

Measuring Absolute Density

Total Count ndash count the number of organisms living in an area Human census number of oak trees in a

wooded lot number of singing birds in an area

Total counts generally are not used very often

Sampling Methods ndash use a sample to estimate population size Either use the quadrat or capture-

recapture method

35

Measurement of Environmental ParametersAbiotic factors are important in determining

both the distribution of the organisms and their physical and physiological adaptations

Temperature- diurnal and seasonal temperature variations

are significant in affecting different species of plants and animals

- equipment mercury thermometer maximum-minimum thermometer

miniaturized thermistor

36

pH

-measure pH of a solution by universal indicator pH paper pH meter etc

Light

-measure its duration and intensity duration by predication from Royal Observatory intensity by photographic light meter

pH meter in use

37

Humidity

Relative humidity the water content of a given volume of air relative to the same volume of fully saturated air

- equipment whirling hygrometer

38

Wind and Water Speed- wind speed- anemometer or wind

gauges- water speed - time the movement of a

floating object over a measured distance

39

Salinity

- using a conductivity meter greater salinity has greater conductivity

Oxygen Level

- using an oxygen meter or chemical method (Winkler method)

40

Collecting MethodsCollecting all organisms within a habitat is normally

impractical and therefore small areas are selected Remember to return all material to its original position

after searching amp collecting sufficient specimens Some collecting apparatus for general use are listed

below

41

1 specimen tube

2 screwed-topped jars

3 polythene bags

4 forceps

5 paint brush

6 bulb pipette

7 pooter

42

8 widger 9 sieve 10 hand lens

11 enamel dish 12 beating tray 13 light traps

14 Tullgren funnel 15 Baermann funnel 16 mammal traps

17 pitfall traps 18 netting

43

Estimating Population Size

The exact methods used for estimation depend not only the nature of the habitat but also on the organisms involved

eg animals - population

plants - percentage cover

44

Using Quadrats

- By sampling an area using quadrats and counting the number of individuals within each quadrat it is possible to estimate the total number of individuals within the area

- confined to plants and sessile or very slow-moving animals

- fast-moving animals are disturbed and run away

45

Capture-recapture Techniques- useful for mobile animals which can be marked

- capture marked released randomly recaptured

and marked individuals recorded

no of marked individuals recaptured total no of individuals in 1st sample

-------------------------------------------- = ------------------------------------------

total no of individuals in 2nd sample estimated size of population

(the Lincoln Index)

46

Capture-recapture Techniques Factors affecting the accuracy of the estimation

deaths migration individuals become more liable to predation etc

Examples

- arthropods marked on their backs with non-toxic paint

- fish have tags attached to opercula - mammals have tags clipped to their ears

birds have their legs ringed

47

Capture-recapture Method Important tool for estimating density birth

rate and death rate for mobile animals Method

Collect a sample of individuals mark them and then release them

After a period collect more individuals from the wild and count the number that have marks

We assume that a sample if random will contain the same proportion of marked individuals as the population does

Estimate population density

48

Assumptions For All Capture-Recapture Studies Marking technique does not increase

mortality of marked animals Marked individuals are allowed to mix

with population Marking technique does not affect catch

probability Marks are not lost or overlooked No significant immigration or emigration No significant mortality or natality

49

Marked animals in second sample

Total caught in second sample

Marked animals in first sample

Total population size

=

520 N

16=

Peterson Method or Lincoln Index

N = 64N = (20)(16)5

50

Some Indices Used

Traps Number of Fecal

Pellets Vocalization

Frequency Pelt Records Catch per Unit

Fishing Effort

Number of Artifacts Questionnaires Cover Feeding Capacity Roadside Counts

51

Abundance Scales

The population size may be fairly accurately determined by making some form of frequency assessment

These are subjective and involve an experimenter making some estimate of the number of individuals in a given area or the cover of a particular species

This is especially useful where individuals are very numerous eg barnacles on a rocky shore or where it is difficult to distinguish individuals eg grass plants in a meadow

52

The assessments are usually made on an abundance scale of 5 categories

Abundance Common Frequent Occasional Rare

Barnacles exposed at low water

53

Environmental resistance are the factors which limit the growth of a particular population

eg predation disease availability of light food water oxygen and shelter the accumulation of toxic wastes and even the size of the population itself

54

Density-dependent Growth A population is a density-dependent when its size

(or density) affects its growth rate because of density-dependent factors such as food availability and toxic waste accumulation

Density-independent Growth In this type of growth a population increases until

some factor causes a sudden reduction in its size Its effect is the same regardless of the size of the

population eg temperature fires floods storms etc

55

Regulation of Population Size Fecundity is the reproductive capacity of individual

females of a species Birth rate or natality is used to measure fecundity Death rate or mortality is the number of individuals

of a species which die per unit time Immigration occurs when individuals join a

population from neighbouring ones Emigration occurs when individuals depart from a

population A cycle occurs when the size of a population

fluctuates on a regular basis

56

Ecological Sampling

57

Why Do We Sample Determine presence andor

abundance

Monitor population fluctuations

Assess lsquoecological damagersquo

Assess quality of habitat

Assess population responses

58

What Do We Sample

Physical Environment Temperature DO pH salinity clarity

flow sediment

Biotic Environment All living things

59

Physical Habitat Temperature

Mercury thermometer Electronic thermometer Long-term thermometers

Dissolved Oxygen Winkler method (titration) DO meter (electrode)

pH Litmus paper pH meter (electrode)

Salinity Salinity Meter YSI 550A DO Meter w12 cable

60

Water Clarity Secchi Disk

Disk is attached to a calibrated rope The disk is lowered into the water until the white parts can no longer be seen Secchi disk depth is then recorded and serves as the waters transparency index The clearer the water the greater the secchi disk depth

Secchi Disk

61

Current Velocity (flow) Floating-orange method

Put an orange (or something else that floats just below the water surface) and measure the time it takes it to float across a known distance

Odometer-type flow meter Number of revolutions the propeller

makes for a given time is calibrated to flow velocity

62

Sediment Sediment size is important to many

aquatic organisms Sieversquos are used to separate and

grade sediment samples Percent of each size grade can be

determined

63

Water Sample

Water and plankton from various depths can be collected

A trigger mechanism is used to close the sampler Sample is then brought back to the

surface

64

Small Mammals

Mouserat Traps Fatal

Pit Falls Bucket is placed in the ground Sometimes have lsquoleadsrsquo to the buckets

Live traps Havahart Sherman

Spot-light

Sherman trapHavahart trap

65

Birds Stick-under-the-box method Bird-trap

Works like a minnow trap Mist net

Captures birds in flight Rocket net

Uses a propellant to throw a net over birds

66

Terrestrial Insects

Sticky paper flies

Baited Traps Fire ants

Nets butterflies

Foggers Collect insects from tree canopies

67

Aquatic Insects Drift Net

Place net in flowing water Kick Net

lsquoKickrsquo sediment upstream from block net and the flow will wash them into the net

Wash bucket Serber or Hess Sampler

Stir up known area of sediment

Animals are collected by a catch net

Multi-plate Sampler Become colonized

68

Crawfish and Crab Traps

69

Fish Larvae Light Traps

Larvae are attracted to the light Ichthyoplankton nets

Can be towed at various depths Fish collect at the lsquocodrsquoend

70

Fish Lift net

Net is placed down and after a set amount of time it is quickly lifted

Pop-net Similar to a lift net but

floats are attached to a framed net

Operated by a trigger mechanism

Throw net A net attached to a heavy

frame is thrown and every thing inside is netted out Throw net

Pop-net

Lift net

71

Minnow trap

Usually use bait to attract small fish Light is used sometimes as an attractant

72

Fish Electrofishing

Electricity is put into the water Fish are temporarily stunned and usually

swim towards the electricity source Usually non-fatal but may cause some

damage

73

Fish Gill Net

Gill nets resemble tennis nets Fish can not swim completely through the

net and get caught Gill nets are size selective (based on mesh

size) Square Mesh

Bar mesh

Stretch mesh

74

Fish Trammel Net

Three panels two large mesh on the outside and a small mesh on the inside

Fish swim through the outer mesh pushes the small mesh through the other side and becomes entangled

75

Hoop nets (and other similar nets) can have bait or not

Fyke nets have leads to help guide fish to the net

76

Seine Seines are nets that are pulled

through shallow water to catch fish

77

Purse Seine Used to encircle entire schools of fish

Usually involves a spotter plane and a second boat

78

Trotline (longline) A series of baited drop lines

connected to a main line

Can be deployed by tying one end to the bank and tying the other end with a heavy weight

79

Shrimp (or fish) Trawl Net pulled behind

a boat along the bottom Either a beam or

otter boards keep the net open

80

Tagging Individuals Coded Wire Tags

Microwire that has a unique label

Magnetic wand detects the tag

Tag retention should be determined

T-Bar tags Can be individually

numbered External tag

PIT tags (Passive Integrated Transponders) Wand induces the tag to

transmit individual number is displayed

81

Other Tagging Methods

Toe clip Amphibian and reptile Clip of one or more toes

to identify individuals

Bird Band Place a metal band on a

bird leg Generally has

identification information

82

Preserving plant specimens Pressing and drying Long-term

preservation and storage

Alternative drying techniques

Special preservation and processing techniques

Mounting

83

Pressing and drying Techniques for pressing and drying specimens have been

established for many years There are minor variations in recommended methods but they are essentially the same worldwide

The best specimens are plants that are pressed as soon as possible after collection before wilting and shrivelling Most plants may be kept in sealed containers such as plastic bags for up to a day if it is inconvenient to press immediately However some plants show such rapid wilting particularly of the flowers that such delays are best avoided Flowers with a lot of nectar may go mouldy very quickly if excess nectar is not shaken off before pressing

Specimens are pressed flat and dried between sheets of absorbent blotters or semi-absorbent paper such as newspaper Papers with a glossy surface should be avoided because they are not absorbent enough to aid drying The plant should be carefully laid out between the drying sheets as their form at this stage largely determines their ultimate appearance The flowers should be spread out with the petals carefully arranged wilted leaves should be straightened and unnecessary shoots of excessively twiggy shrubs may be cut away

84

Microwave ovens Small numbers of specimens can be dried using a microwave

oven The technique recommended in the literature is to place the specimens between unprinted absorbent paper for example butchers paper not newspaper which is unsuitable because the chemicals present in the ink may cause a fire The specimens should be put in a special press which should be of a microwave-safe material (wood acrylic or polycarbonate sheeting eg plexiglass or perspex NO metal components) If such a press is not available sheets of cardboard can be placed above and below the specimens and then weighted down

Drying time depends on the power of your oven In most cases drying is accomplished by irradiating at maximum power for 1-2 minutes per specimen although it is often a case of trial and error It is best to process no more than 10-12 specimens of average thickness per batch Specimens are usually dried after the moisture that characteristically appears on the glass door has disappeared If the specimen is damp when taken out of the oven allow it to stand before re-radiating as moisture continues to evaporate from the specimen for some time Care must be taken not to irradiate the specimens for too long

It should be noted that microwave treatment damages seeds and the cellular structure of the plants which may reduce the long-term value of the specimens

85

Alternative drying techniquesSilica gelother desiccants amp freeze drying Alternative methods of drying plant specimens have been

used for some time but are mostly restricted to special purpose collections The main alternatives are freeze-drying and drying in a desiccant powder such as desiccant silica gel In general these techniques are used where it is essential to preserve the shape of a delicate plant of organ of the plant such as the flower Freeze-drying has also been used to preserve the chemical composition of a plant as accurately as possible for later study

Disadvantages and special conservation problems of specimens dried in these manners are that they are particularly susceptible to damage The dried parts are fragile lack support and often catch on packing materials They must therefore be packed especially carefully and stored in small boxes or tubes with some appropriate packing material that does not snag and break small projections Acid-free tissue paper is often used Drying in desiccant silica gel crystals or powder can also have the disadvantage that it is difficult to remove all traces of the silica gel after drying

86

Special preservation and processing techniquesWet or spirit collections

Very fleshy or delicate structures including small algae and orchid flowers are best preserved in an air-tight glass or plastic jar with a liquid preservative rather than by drying The type of preservative used should be clearly labelled in the jar Such material is often referred to as a spirit collection or wet collection

Most material can be satisfactorily preserved in 70 ethyl alcohol (or 70 methylated spirit or denatured alcohol) with 30 water Colours will fade quickly in spirit however so it is a good idea to keep comprehensive notes and photographs

87

Small algae Microscopic algae are often collected in a jar and in the

water in which they were found If the algae are to be stored for more than 2-3 days a preservative needs to be used Traditionally this has been the extremely toxic formalin - a small amount can be added to the water to make a 5 final solution and the container labelled This must not be sent through the post or by courier

There are some other equally toxic options for example propylene phenoxytol but none should be sent through the post A safer option is to add sufficient concentrated alcohol or methylated spirits to the water containing the algae to make a final solution of 70 alcohol This treatment dilutes the algae making them difficult to find so if they can be concentrated somehow first (eg by filtering) they can be stored in much less liquid Another option is to fix the algae in formalin (or something similar) first and then prepare a microscope glass slide with a permanent water-soluble mounting medium

88

Mounting Mounting specimens prevents most fragile material from

fragmenting and prevents specimens becoming separated from their labels If the plant collection is a long-term project specimens should be mounted on sheets of archival (permanent) cardboard or paper with archival-quality fixing media These include stitching with cotton thread dental floss nickel-plated copper wire (for heavier specimens) narrow strips of archival paper linen tape or by using an archival adhesive such as methyl cellulose adhesive

One disadvantage of mounting specimens is that it can make parts of the specimen inaccessible for examination so it is essential that this be borne in mind during specimen arrangement and mounting For example easily reversible mounting media should be used specimens should be strapped to the sheet rather than glued all over and the specimen should be carefully arranged before it is attached so that it shows all features

89

Full-size herbarium mounting sheets are usually about 43 cm long x 28 cm wide The plant name and accompanying field notes should be transcribed on a permanent label stuck to one corner of the herbarium sheet (the bottom right-hand corner being the most common) or sometimes annotations may be written directly on the sheet or card

Small pieces of material which may have become separated from the specimen (eg seeds) can be placed in small plastic bags and pinned to the sheet

90

Long-term preservation and storage The long-term preservation of dry plant

specimens is largely dependent on protection from insect attack Specimens collected by Linnaeus in the eighteenth century and by Banks and Solander on the Endeavour voyage in 1788 are still excellently preserved

91

Pests and their control A range of pests attack dried plant material The

most common pests are insects and fungi though rodents and other large animals can cause damage in poor storage conditions Insects eat the material the paper surrounding the material and the adhesives and mounting media

Such insect pests range from psocids (book lice) which attack mainly the softer parts such as flowers and soft fruits to tobacco beetles and carpet beetles which can bore holes through the toughest of specimens Many insects are particularly sensitive to relative humidity levels and do not thrive at levels below 50

92

The most common and acceptable specimen treatments for insect control are Freezing Microwave Poisoning Insect deterrents Fungal pests

93

Storage

Dried and pressed plant specimens can be stored in cardboard or plastic boxes or tied in bundles in light-weight cardboard folders placed in pigeon holes

Alternatively they can be placed in protective plastic jackets and displayed in ring folders which is recommended if they are to be frequently handled such as for a reference collection

94

Filing

Specimens should be filed in a systematic order if a relatively permanent collection is being made The major groups ie ferns and fern allies cycads conifers dicotyledons and monocotyledons are best kept separately or according to some classification scheme such as that given in a flora or handbook

Similarly the genera within each family and the species within each genus may be filed alphabetically or following some such classification

95

Preservation of entire animals

Types of collection specimens of an entire animal For reference collections mammals can be prepared as a variety of specimens The condition of the specimen may determine possible ways to preserve it if for instance decomposition of the skin has loosened the hair of a carcass so much that it can easily be pulled out or removed by rubbing (ldquoslippingrdquo fur) it will be very difficult or impossible to produce a study skin or mounted specimen The most usual types of specimens (based on Nagorsen and Peterson 1980) are 1) entire fluid-preserved animals (for studying anatomy and histology fluid preservation may change the fur colour) 2) study skins with accompanying skulls partial skeletons (some bones remain in the skin) for studying pelage colour hair quality and moulting patterns 3) mounted skins with accompanying partial or entire skeleton (some bones may remain in the skin dependant on the method of preservation) or freeze-dried specimens 4) entire skeletons for instance for studying anatomy geographic variation or for age determination (entire skeletons are poorly represented in collections so Nagorsen and Peterson (1980) recommend preparation of at least one male and one female skeleton per species

96

Preservation of specimens in the field Formalin preservation Preservation in alcohol Preservation by cooling or freezing

97

Formalin preservation After weighing and measuring the animal and attaching an

adequate label very small specimens (up to 100 g) can be fixed whole by submerging them in 10 buffered formalin (tissue - formalin solution ratio of at least 1 12) the body cavity can be filled with formalin solution by injection until it is turgid and firm some formalin may also be injected under the skin into the body cavity larger muscles and organs If hypodermic needles are not available the body cavity can be opened ventrally by making a slit instead allowing the formalin to enter

Keeping the mouth open with a piece of wood or cotton may later allow examination of teeth Then the whole body can be immersed in formalin in the posture in which it is supposed to stay permanently because it will harden The ratio of formalin to carcass must be at least 12 to 1 to assure a good fixation Tissues can be left in buffered neutralized formalin for several months but formalin hardens specimens therefore after fixation longterm storage in alcohol may be better After preservation the carcass should therefore be washed in water and transferred into ethanol for permanent storage

Disadvantages for instance it discolours the fur after a longish immersion softens the bones and prevents further examination for microbiology

98

Preservation in alcohol

After weighing a whole animal can be preserved in a container of alcohol (70-90) Removal of the intestine prior to storage of the animal in alcohol is recommended

99

Preservation by cooling or freezing Removal of the skin with insulating fur

before cooling or freezing may help to cool the carcass down more quickly

Freezing is not recommended if histological examination is planned

100

THANK YOU

14

Quadrats

- When placed on the ground the species present within the frame are identified and their abundance recorded

- Sampling could be random or systematic

Using a quadrat along a belt transect

15

Practical Constraints

Small quadrats are quicker to survey but yield a smaller individual sample of habitat

ndash Often require a larger of samples to represent the habitat

1048698 Large quadrats require more time and effort to survey but provide a larger individual sample of habitat

ndash Often require a smaller of samples to represent the habitat

16

Habitat sizeAppropriate sample unit size depends on size scale

of the habitatndash Small scale habitats require smaller sized samples1048698 Ex Bouldersndash Large scale habitats require larger sized samples1048698 Ex Forests

17

Organism size and density

Depends on size and density of organisms

ndash Small dense organisms require smaller samples

1048698 Ex grassndash Large scattered organisms require

larger samples1048698 Ex Trees

18

TYPES OF SAMPLING

1048698 Systematic 1048698 Stratified 1048698 Random

19

SYSTEMATIC SAMPLING

1048698 Often used when the area being studied is varied not very large or

when time is available 1048698 Samples are taken at fixed intervals

20

How to sample systematicallySystematic samples are usually taken along a transect line marked by a tape measure

1048698 Transect- a line laid across an area

21

Sampling along gradients

Transects are setup along aenvironmentalgradientsndash down a hillsidendash across a streambedndash out from a source ofpollution

22

Types of transect sampling 1048698 Line transect 1048698 Belt transect

23

Line transect methodA measured line is laidacross the area in thedirection of theenvironmental gradientndash The species touching theline can be recordedalong the whole length ofthe line (continuoussampling) or at specificpoints along the line(systematic sampling)

24

Line Transect- useful where a transition of flora andor fauna

occurs- a string or tape is stretched out along the

ground in a straight line record the organisms touching or covering

the line all along its length or at regular intervals

- Profile transect when there is appreciable height change along the transect and thus affecting the distribution of its species

25

Belt transect method

Similar to line transect butwidens the sampling areandash Transect line is laid outndash Samples are taken bydetermining abundance or cover in an area that is adefined distance from the linendash Samples can be taken all

theway along the line at specificintervals or even randomly

26

Belt TransectIt is a strip usually a metre wide marked by putting a

second line parallel to the other The species between the lines are carefully recorded working a metre at a time

Alternatively a frame quadrat in conjunction with a single line transect could be used

Using a quadrat along a belt transect eg ladder transect (every 5m)

27

Point Frames- for grassland field study of dense vegetation

28

STRATIFIED SAMPLING1048698 Often used whenthere are smallareas within alarger habitat thatare clearly different1048698 Strata- majordifferences withincommunitiesrecognized beforesampling begins

29

RANDOM SAMPLING

1048698 Often used when the area being studied isfairly uniform very large or when there is alimited amount of time available1048698 Random = chosen by chance rather thanaccording to a plan all outcomes are

equallylikely1048698 Samples are taken from different positionswithin a habitat and those positions arechosen randomly

30

How to sample randomly

Choose individuals or Placeldquosampling unitsrdquo

haphazardlyndash This is rarely completely

random1048698 ORhellip1048698 Assign numbers to the

areasor individuals to be sampledndash Use a random number

table toselect which areas or

individualswill be sample

31

Population Attributes Density ndash size of a population in relation to a definite

unit of space Affected by

Natality ndash the reproductive output (birth rate) of a population

Mortality ndash the death rate of organisms in a population

Immigration ndash number of organisms moving into the area occupied by the population

Emigration ndash number of organisms moving out of the area occupied by the population

32

Population Density

Four primary population parameters

33

Two Types of Density Estimates

bull Absolute Density ndash a known density such as m2

bull Relative Density ndash we know when one area has more individuals than another

34

Measuring Absolute Density

Total Count ndash count the number of organisms living in an area Human census number of oak trees in a

wooded lot number of singing birds in an area

Total counts generally are not used very often

Sampling Methods ndash use a sample to estimate population size Either use the quadrat or capture-

recapture method

35

Measurement of Environmental ParametersAbiotic factors are important in determining

both the distribution of the organisms and their physical and physiological adaptations

Temperature- diurnal and seasonal temperature variations

are significant in affecting different species of plants and animals

- equipment mercury thermometer maximum-minimum thermometer

miniaturized thermistor

36

pH

-measure pH of a solution by universal indicator pH paper pH meter etc

Light

-measure its duration and intensity duration by predication from Royal Observatory intensity by photographic light meter

pH meter in use

37

Humidity

Relative humidity the water content of a given volume of air relative to the same volume of fully saturated air

- equipment whirling hygrometer

38

Wind and Water Speed- wind speed- anemometer or wind

gauges- water speed - time the movement of a

floating object over a measured distance

39

Salinity

- using a conductivity meter greater salinity has greater conductivity

Oxygen Level

- using an oxygen meter or chemical method (Winkler method)

40

Collecting MethodsCollecting all organisms within a habitat is normally

impractical and therefore small areas are selected Remember to return all material to its original position

after searching amp collecting sufficient specimens Some collecting apparatus for general use are listed

below

41

1 specimen tube

2 screwed-topped jars

3 polythene bags

4 forceps

5 paint brush

6 bulb pipette

7 pooter

42

8 widger 9 sieve 10 hand lens

11 enamel dish 12 beating tray 13 light traps

14 Tullgren funnel 15 Baermann funnel 16 mammal traps

17 pitfall traps 18 netting

43

Estimating Population Size

The exact methods used for estimation depend not only the nature of the habitat but also on the organisms involved

eg animals - population

plants - percentage cover

44

Using Quadrats

- By sampling an area using quadrats and counting the number of individuals within each quadrat it is possible to estimate the total number of individuals within the area

- confined to plants and sessile or very slow-moving animals

- fast-moving animals are disturbed and run away

45

Capture-recapture Techniques- useful for mobile animals which can be marked

- capture marked released randomly recaptured

and marked individuals recorded

no of marked individuals recaptured total no of individuals in 1st sample

-------------------------------------------- = ------------------------------------------

total no of individuals in 2nd sample estimated size of population

(the Lincoln Index)

46

Capture-recapture Techniques Factors affecting the accuracy of the estimation

deaths migration individuals become more liable to predation etc

Examples

- arthropods marked on their backs with non-toxic paint

- fish have tags attached to opercula - mammals have tags clipped to their ears

birds have their legs ringed

47

Capture-recapture Method Important tool for estimating density birth

rate and death rate for mobile animals Method

Collect a sample of individuals mark them and then release them

After a period collect more individuals from the wild and count the number that have marks

We assume that a sample if random will contain the same proportion of marked individuals as the population does

Estimate population density

48

Assumptions For All Capture-Recapture Studies Marking technique does not increase

mortality of marked animals Marked individuals are allowed to mix

with population Marking technique does not affect catch

probability Marks are not lost or overlooked No significant immigration or emigration No significant mortality or natality

49

Marked animals in second sample

Total caught in second sample

Marked animals in first sample

Total population size

=

520 N

16=

Peterson Method or Lincoln Index

N = 64N = (20)(16)5

50

Some Indices Used

Traps Number of Fecal

Pellets Vocalization

Frequency Pelt Records Catch per Unit

Fishing Effort

Number of Artifacts Questionnaires Cover Feeding Capacity Roadside Counts

51

Abundance Scales

The population size may be fairly accurately determined by making some form of frequency assessment

These are subjective and involve an experimenter making some estimate of the number of individuals in a given area or the cover of a particular species

This is especially useful where individuals are very numerous eg barnacles on a rocky shore or where it is difficult to distinguish individuals eg grass plants in a meadow

52

The assessments are usually made on an abundance scale of 5 categories

Abundance Common Frequent Occasional Rare

Barnacles exposed at low water

53

Environmental resistance are the factors which limit the growth of a particular population

eg predation disease availability of light food water oxygen and shelter the accumulation of toxic wastes and even the size of the population itself

54

Density-dependent Growth A population is a density-dependent when its size

(or density) affects its growth rate because of density-dependent factors such as food availability and toxic waste accumulation

Density-independent Growth In this type of growth a population increases until

some factor causes a sudden reduction in its size Its effect is the same regardless of the size of the

population eg temperature fires floods storms etc

55

Regulation of Population Size Fecundity is the reproductive capacity of individual

females of a species Birth rate or natality is used to measure fecundity Death rate or mortality is the number of individuals

of a species which die per unit time Immigration occurs when individuals join a

population from neighbouring ones Emigration occurs when individuals depart from a

population A cycle occurs when the size of a population

fluctuates on a regular basis

56

Ecological Sampling

57

Why Do We Sample Determine presence andor

abundance

Monitor population fluctuations

Assess lsquoecological damagersquo

Assess quality of habitat

Assess population responses

58

What Do We Sample

Physical Environment Temperature DO pH salinity clarity

flow sediment

Biotic Environment All living things

59

Physical Habitat Temperature

Mercury thermometer Electronic thermometer Long-term thermometers

Dissolved Oxygen Winkler method (titration) DO meter (electrode)

pH Litmus paper pH meter (electrode)

Salinity Salinity Meter YSI 550A DO Meter w12 cable

60

Water Clarity Secchi Disk

Disk is attached to a calibrated rope The disk is lowered into the water until the white parts can no longer be seen Secchi disk depth is then recorded and serves as the waters transparency index The clearer the water the greater the secchi disk depth

Secchi Disk

61

Current Velocity (flow) Floating-orange method

Put an orange (or something else that floats just below the water surface) and measure the time it takes it to float across a known distance

Odometer-type flow meter Number of revolutions the propeller

makes for a given time is calibrated to flow velocity

62

Sediment Sediment size is important to many

aquatic organisms Sieversquos are used to separate and

grade sediment samples Percent of each size grade can be

determined

63

Water Sample

Water and plankton from various depths can be collected

A trigger mechanism is used to close the sampler Sample is then brought back to the

surface

64

Small Mammals

Mouserat Traps Fatal

Pit Falls Bucket is placed in the ground Sometimes have lsquoleadsrsquo to the buckets

Live traps Havahart Sherman

Spot-light

Sherman trapHavahart trap

65

Birds Stick-under-the-box method Bird-trap

Works like a minnow trap Mist net

Captures birds in flight Rocket net

Uses a propellant to throw a net over birds

66

Terrestrial Insects

Sticky paper flies

Baited Traps Fire ants

Nets butterflies

Foggers Collect insects from tree canopies

67

Aquatic Insects Drift Net

Place net in flowing water Kick Net

lsquoKickrsquo sediment upstream from block net and the flow will wash them into the net

Wash bucket Serber or Hess Sampler

Stir up known area of sediment

Animals are collected by a catch net

Multi-plate Sampler Become colonized

68

Crawfish and Crab Traps

69

Fish Larvae Light Traps

Larvae are attracted to the light Ichthyoplankton nets

Can be towed at various depths Fish collect at the lsquocodrsquoend

70

Fish Lift net

Net is placed down and after a set amount of time it is quickly lifted

Pop-net Similar to a lift net but

floats are attached to a framed net

Operated by a trigger mechanism

Throw net A net attached to a heavy

frame is thrown and every thing inside is netted out Throw net

Pop-net

Lift net

71

Minnow trap

Usually use bait to attract small fish Light is used sometimes as an attractant

72

Fish Electrofishing

Electricity is put into the water Fish are temporarily stunned and usually

swim towards the electricity source Usually non-fatal but may cause some

damage

73

Fish Gill Net

Gill nets resemble tennis nets Fish can not swim completely through the

net and get caught Gill nets are size selective (based on mesh

size) Square Mesh

Bar mesh

Stretch mesh

74

Fish Trammel Net

Three panels two large mesh on the outside and a small mesh on the inside

Fish swim through the outer mesh pushes the small mesh through the other side and becomes entangled

75

Hoop nets (and other similar nets) can have bait or not

Fyke nets have leads to help guide fish to the net

76

Seine Seines are nets that are pulled

through shallow water to catch fish

77

Purse Seine Used to encircle entire schools of fish

Usually involves a spotter plane and a second boat

78

Trotline (longline) A series of baited drop lines

connected to a main line

Can be deployed by tying one end to the bank and tying the other end with a heavy weight

79

Shrimp (or fish) Trawl Net pulled behind

a boat along the bottom Either a beam or

otter boards keep the net open

80

Tagging Individuals Coded Wire Tags

Microwire that has a unique label

Magnetic wand detects the tag

Tag retention should be determined

T-Bar tags Can be individually

numbered External tag

PIT tags (Passive Integrated Transponders) Wand induces the tag to

transmit individual number is displayed

81

Other Tagging Methods

Toe clip Amphibian and reptile Clip of one or more toes

to identify individuals

Bird Band Place a metal band on a

bird leg Generally has

identification information

82

Preserving plant specimens Pressing and drying Long-term

preservation and storage

Alternative drying techniques

Special preservation and processing techniques

Mounting

83

Pressing and drying Techniques for pressing and drying specimens have been

established for many years There are minor variations in recommended methods but they are essentially the same worldwide

The best specimens are plants that are pressed as soon as possible after collection before wilting and shrivelling Most plants may be kept in sealed containers such as plastic bags for up to a day if it is inconvenient to press immediately However some plants show such rapid wilting particularly of the flowers that such delays are best avoided Flowers with a lot of nectar may go mouldy very quickly if excess nectar is not shaken off before pressing

Specimens are pressed flat and dried between sheets of absorbent blotters or semi-absorbent paper such as newspaper Papers with a glossy surface should be avoided because they are not absorbent enough to aid drying The plant should be carefully laid out between the drying sheets as their form at this stage largely determines their ultimate appearance The flowers should be spread out with the petals carefully arranged wilted leaves should be straightened and unnecessary shoots of excessively twiggy shrubs may be cut away

84

Microwave ovens Small numbers of specimens can be dried using a microwave

oven The technique recommended in the literature is to place the specimens between unprinted absorbent paper for example butchers paper not newspaper which is unsuitable because the chemicals present in the ink may cause a fire The specimens should be put in a special press which should be of a microwave-safe material (wood acrylic or polycarbonate sheeting eg plexiglass or perspex NO metal components) If such a press is not available sheets of cardboard can be placed above and below the specimens and then weighted down

Drying time depends on the power of your oven In most cases drying is accomplished by irradiating at maximum power for 1-2 minutes per specimen although it is often a case of trial and error It is best to process no more than 10-12 specimens of average thickness per batch Specimens are usually dried after the moisture that characteristically appears on the glass door has disappeared If the specimen is damp when taken out of the oven allow it to stand before re-radiating as moisture continues to evaporate from the specimen for some time Care must be taken not to irradiate the specimens for too long

It should be noted that microwave treatment damages seeds and the cellular structure of the plants which may reduce the long-term value of the specimens

85

Alternative drying techniquesSilica gelother desiccants amp freeze drying Alternative methods of drying plant specimens have been

used for some time but are mostly restricted to special purpose collections The main alternatives are freeze-drying and drying in a desiccant powder such as desiccant silica gel In general these techniques are used where it is essential to preserve the shape of a delicate plant of organ of the plant such as the flower Freeze-drying has also been used to preserve the chemical composition of a plant as accurately as possible for later study

Disadvantages and special conservation problems of specimens dried in these manners are that they are particularly susceptible to damage The dried parts are fragile lack support and often catch on packing materials They must therefore be packed especially carefully and stored in small boxes or tubes with some appropriate packing material that does not snag and break small projections Acid-free tissue paper is often used Drying in desiccant silica gel crystals or powder can also have the disadvantage that it is difficult to remove all traces of the silica gel after drying

86

Special preservation and processing techniquesWet or spirit collections

Very fleshy or delicate structures including small algae and orchid flowers are best preserved in an air-tight glass or plastic jar with a liquid preservative rather than by drying The type of preservative used should be clearly labelled in the jar Such material is often referred to as a spirit collection or wet collection

Most material can be satisfactorily preserved in 70 ethyl alcohol (or 70 methylated spirit or denatured alcohol) with 30 water Colours will fade quickly in spirit however so it is a good idea to keep comprehensive notes and photographs

87

Small algae Microscopic algae are often collected in a jar and in the

water in which they were found If the algae are to be stored for more than 2-3 days a preservative needs to be used Traditionally this has been the extremely toxic formalin - a small amount can be added to the water to make a 5 final solution and the container labelled This must not be sent through the post or by courier

There are some other equally toxic options for example propylene phenoxytol but none should be sent through the post A safer option is to add sufficient concentrated alcohol or methylated spirits to the water containing the algae to make a final solution of 70 alcohol This treatment dilutes the algae making them difficult to find so if they can be concentrated somehow first (eg by filtering) they can be stored in much less liquid Another option is to fix the algae in formalin (or something similar) first and then prepare a microscope glass slide with a permanent water-soluble mounting medium

88

Mounting Mounting specimens prevents most fragile material from

fragmenting and prevents specimens becoming separated from their labels If the plant collection is a long-term project specimens should be mounted on sheets of archival (permanent) cardboard or paper with archival-quality fixing media These include stitching with cotton thread dental floss nickel-plated copper wire (for heavier specimens) narrow strips of archival paper linen tape or by using an archival adhesive such as methyl cellulose adhesive

One disadvantage of mounting specimens is that it can make parts of the specimen inaccessible for examination so it is essential that this be borne in mind during specimen arrangement and mounting For example easily reversible mounting media should be used specimens should be strapped to the sheet rather than glued all over and the specimen should be carefully arranged before it is attached so that it shows all features

89

Full-size herbarium mounting sheets are usually about 43 cm long x 28 cm wide The plant name and accompanying field notes should be transcribed on a permanent label stuck to one corner of the herbarium sheet (the bottom right-hand corner being the most common) or sometimes annotations may be written directly on the sheet or card

Small pieces of material which may have become separated from the specimen (eg seeds) can be placed in small plastic bags and pinned to the sheet

90

Long-term preservation and storage The long-term preservation of dry plant

specimens is largely dependent on protection from insect attack Specimens collected by Linnaeus in the eighteenth century and by Banks and Solander on the Endeavour voyage in 1788 are still excellently preserved

91

Pests and their control A range of pests attack dried plant material The

most common pests are insects and fungi though rodents and other large animals can cause damage in poor storage conditions Insects eat the material the paper surrounding the material and the adhesives and mounting media

Such insect pests range from psocids (book lice) which attack mainly the softer parts such as flowers and soft fruits to tobacco beetles and carpet beetles which can bore holes through the toughest of specimens Many insects are particularly sensitive to relative humidity levels and do not thrive at levels below 50

92

The most common and acceptable specimen treatments for insect control are Freezing Microwave Poisoning Insect deterrents Fungal pests

93

Storage

Dried and pressed plant specimens can be stored in cardboard or plastic boxes or tied in bundles in light-weight cardboard folders placed in pigeon holes

Alternatively they can be placed in protective plastic jackets and displayed in ring folders which is recommended if they are to be frequently handled such as for a reference collection

94

Filing

Specimens should be filed in a systematic order if a relatively permanent collection is being made The major groups ie ferns and fern allies cycads conifers dicotyledons and monocotyledons are best kept separately or according to some classification scheme such as that given in a flora or handbook

Similarly the genera within each family and the species within each genus may be filed alphabetically or following some such classification

95

Preservation of entire animals

Types of collection specimens of an entire animal For reference collections mammals can be prepared as a variety of specimens The condition of the specimen may determine possible ways to preserve it if for instance decomposition of the skin has loosened the hair of a carcass so much that it can easily be pulled out or removed by rubbing (ldquoslippingrdquo fur) it will be very difficult or impossible to produce a study skin or mounted specimen The most usual types of specimens (based on Nagorsen and Peterson 1980) are 1) entire fluid-preserved animals (for studying anatomy and histology fluid preservation may change the fur colour) 2) study skins with accompanying skulls partial skeletons (some bones remain in the skin) for studying pelage colour hair quality and moulting patterns 3) mounted skins with accompanying partial or entire skeleton (some bones may remain in the skin dependant on the method of preservation) or freeze-dried specimens 4) entire skeletons for instance for studying anatomy geographic variation or for age determination (entire skeletons are poorly represented in collections so Nagorsen and Peterson (1980) recommend preparation of at least one male and one female skeleton per species

96

Preservation of specimens in the field Formalin preservation Preservation in alcohol Preservation by cooling or freezing

97

Formalin preservation After weighing and measuring the animal and attaching an

adequate label very small specimens (up to 100 g) can be fixed whole by submerging them in 10 buffered formalin (tissue - formalin solution ratio of at least 1 12) the body cavity can be filled with formalin solution by injection until it is turgid and firm some formalin may also be injected under the skin into the body cavity larger muscles and organs If hypodermic needles are not available the body cavity can be opened ventrally by making a slit instead allowing the formalin to enter

Keeping the mouth open with a piece of wood or cotton may later allow examination of teeth Then the whole body can be immersed in formalin in the posture in which it is supposed to stay permanently because it will harden The ratio of formalin to carcass must be at least 12 to 1 to assure a good fixation Tissues can be left in buffered neutralized formalin for several months but formalin hardens specimens therefore after fixation longterm storage in alcohol may be better After preservation the carcass should therefore be washed in water and transferred into ethanol for permanent storage

Disadvantages for instance it discolours the fur after a longish immersion softens the bones and prevents further examination for microbiology

98

Preservation in alcohol

After weighing a whole animal can be preserved in a container of alcohol (70-90) Removal of the intestine prior to storage of the animal in alcohol is recommended

99

Preservation by cooling or freezing Removal of the skin with insulating fur

before cooling or freezing may help to cool the carcass down more quickly

Freezing is not recommended if histological examination is planned

100

THANK YOU

15

Practical Constraints

Small quadrats are quicker to survey but yield a smaller individual sample of habitat

ndash Often require a larger of samples to represent the habitat

1048698 Large quadrats require more time and effort to survey but provide a larger individual sample of habitat

ndash Often require a smaller of samples to represent the habitat

16

Habitat sizeAppropriate sample unit size depends on size scale

of the habitatndash Small scale habitats require smaller sized samples1048698 Ex Bouldersndash Large scale habitats require larger sized samples1048698 Ex Forests

17

Organism size and density

Depends on size and density of organisms

ndash Small dense organisms require smaller samples

1048698 Ex grassndash Large scattered organisms require

larger samples1048698 Ex Trees

18

TYPES OF SAMPLING

1048698 Systematic 1048698 Stratified 1048698 Random

19

SYSTEMATIC SAMPLING

1048698 Often used when the area being studied is varied not very large or

when time is available 1048698 Samples are taken at fixed intervals

20

How to sample systematicallySystematic samples are usually taken along a transect line marked by a tape measure

1048698 Transect- a line laid across an area

21

Sampling along gradients

Transects are setup along aenvironmentalgradientsndash down a hillsidendash across a streambedndash out from a source ofpollution

22

Types of transect sampling 1048698 Line transect 1048698 Belt transect

23

Line transect methodA measured line is laidacross the area in thedirection of theenvironmental gradientndash The species touching theline can be recordedalong the whole length ofthe line (continuoussampling) or at specificpoints along the line(systematic sampling)

24

Line Transect- useful where a transition of flora andor fauna

occurs- a string or tape is stretched out along the

ground in a straight line record the organisms touching or covering

the line all along its length or at regular intervals

- Profile transect when there is appreciable height change along the transect and thus affecting the distribution of its species

25

Belt transect method

Similar to line transect butwidens the sampling areandash Transect line is laid outndash Samples are taken bydetermining abundance or cover in an area that is adefined distance from the linendash Samples can be taken all

theway along the line at specificintervals or even randomly

26

Belt TransectIt is a strip usually a metre wide marked by putting a

second line parallel to the other The species between the lines are carefully recorded working a metre at a time

Alternatively a frame quadrat in conjunction with a single line transect could be used

Using a quadrat along a belt transect eg ladder transect (every 5m)

27

Point Frames- for grassland field study of dense vegetation

28

STRATIFIED SAMPLING1048698 Often used whenthere are smallareas within alarger habitat thatare clearly different1048698 Strata- majordifferences withincommunitiesrecognized beforesampling begins

29

RANDOM SAMPLING

1048698 Often used when the area being studied isfairly uniform very large or when there is alimited amount of time available1048698 Random = chosen by chance rather thanaccording to a plan all outcomes are

equallylikely1048698 Samples are taken from different positionswithin a habitat and those positions arechosen randomly

30

How to sample randomly

Choose individuals or Placeldquosampling unitsrdquo

haphazardlyndash This is rarely completely

random1048698 ORhellip1048698 Assign numbers to the

areasor individuals to be sampledndash Use a random number

table toselect which areas or

individualswill be sample

31

Population Attributes Density ndash size of a population in relation to a definite

unit of space Affected by

Natality ndash the reproductive output (birth rate) of a population

Mortality ndash the death rate of organisms in a population

Immigration ndash number of organisms moving into the area occupied by the population

Emigration ndash number of organisms moving out of the area occupied by the population

32

Population Density

Four primary population parameters

33

Two Types of Density Estimates

bull Absolute Density ndash a known density such as m2

bull Relative Density ndash we know when one area has more individuals than another

34

Measuring Absolute Density

Total Count ndash count the number of organisms living in an area Human census number of oak trees in a

wooded lot number of singing birds in an area

Total counts generally are not used very often

Sampling Methods ndash use a sample to estimate population size Either use the quadrat or capture-

recapture method

35

Measurement of Environmental ParametersAbiotic factors are important in determining

both the distribution of the organisms and their physical and physiological adaptations

Temperature- diurnal and seasonal temperature variations

are significant in affecting different species of plants and animals

- equipment mercury thermometer maximum-minimum thermometer

miniaturized thermistor

36

pH

-measure pH of a solution by universal indicator pH paper pH meter etc

Light

-measure its duration and intensity duration by predication from Royal Observatory intensity by photographic light meter

pH meter in use

37

Humidity

Relative humidity the water content of a given volume of air relative to the same volume of fully saturated air

- equipment whirling hygrometer

38

Wind and Water Speed- wind speed- anemometer or wind

gauges- water speed - time the movement of a

floating object over a measured distance

39

Salinity

- using a conductivity meter greater salinity has greater conductivity

Oxygen Level

- using an oxygen meter or chemical method (Winkler method)

40

Collecting MethodsCollecting all organisms within a habitat is normally

impractical and therefore small areas are selected Remember to return all material to its original position

after searching amp collecting sufficient specimens Some collecting apparatus for general use are listed

below

41

1 specimen tube

2 screwed-topped jars

3 polythene bags

4 forceps

5 paint brush

6 bulb pipette

7 pooter

42

8 widger 9 sieve 10 hand lens

11 enamel dish 12 beating tray 13 light traps

14 Tullgren funnel 15 Baermann funnel 16 mammal traps

17 pitfall traps 18 netting

43

Estimating Population Size

The exact methods used for estimation depend not only the nature of the habitat but also on the organisms involved

eg animals - population

plants - percentage cover

44

Using Quadrats

- By sampling an area using quadrats and counting the number of individuals within each quadrat it is possible to estimate the total number of individuals within the area

- confined to plants and sessile or very slow-moving animals

- fast-moving animals are disturbed and run away

45

Capture-recapture Techniques- useful for mobile animals which can be marked

- capture marked released randomly recaptured

and marked individuals recorded

no of marked individuals recaptured total no of individuals in 1st sample

-------------------------------------------- = ------------------------------------------

total no of individuals in 2nd sample estimated size of population

(the Lincoln Index)

46

Capture-recapture Techniques Factors affecting the accuracy of the estimation

deaths migration individuals become more liable to predation etc

Examples

- arthropods marked on their backs with non-toxic paint

- fish have tags attached to opercula - mammals have tags clipped to their ears

birds have their legs ringed

47

Capture-recapture Method Important tool for estimating density birth

rate and death rate for mobile animals Method

Collect a sample of individuals mark them and then release them

After a period collect more individuals from the wild and count the number that have marks

We assume that a sample if random will contain the same proportion of marked individuals as the population does

Estimate population density

48

Assumptions For All Capture-Recapture Studies Marking technique does not increase

mortality of marked animals Marked individuals are allowed to mix

with population Marking technique does not affect catch

probability Marks are not lost or overlooked No significant immigration or emigration No significant mortality or natality

49

Marked animals in second sample

Total caught in second sample

Marked animals in first sample

Total population size

=

520 N

16=

Peterson Method or Lincoln Index

N = 64N = (20)(16)5

50

Some Indices Used

Traps Number of Fecal

Pellets Vocalization

Frequency Pelt Records Catch per Unit

Fishing Effort

Number of Artifacts Questionnaires Cover Feeding Capacity Roadside Counts

51

Abundance Scales

The population size may be fairly accurately determined by making some form of frequency assessment

These are subjective and involve an experimenter making some estimate of the number of individuals in a given area or the cover of a particular species

This is especially useful where individuals are very numerous eg barnacles on a rocky shore or where it is difficult to distinguish individuals eg grass plants in a meadow

52

The assessments are usually made on an abundance scale of 5 categories

Abundance Common Frequent Occasional Rare

Barnacles exposed at low water

53

Environmental resistance are the factors which limit the growth of a particular population

eg predation disease availability of light food water oxygen and shelter the accumulation of toxic wastes and even the size of the population itself

54

Density-dependent Growth A population is a density-dependent when its size

(or density) affects its growth rate because of density-dependent factors such as food availability and toxic waste accumulation

Density-independent Growth In this type of growth a population increases until

some factor causes a sudden reduction in its size Its effect is the same regardless of the size of the

population eg temperature fires floods storms etc

55

Regulation of Population Size Fecundity is the reproductive capacity of individual

females of a species Birth rate or natality is used to measure fecundity Death rate or mortality is the number of individuals

of a species which die per unit time Immigration occurs when individuals join a

population from neighbouring ones Emigration occurs when individuals depart from a

population A cycle occurs when the size of a population

fluctuates on a regular basis

56

Ecological Sampling

57

Why Do We Sample Determine presence andor

abundance

Monitor population fluctuations

Assess lsquoecological damagersquo

Assess quality of habitat

Assess population responses

58

What Do We Sample

Physical Environment Temperature DO pH salinity clarity

flow sediment

Biotic Environment All living things

59

Physical Habitat Temperature

Mercury thermometer Electronic thermometer Long-term thermometers

Dissolved Oxygen Winkler method (titration) DO meter (electrode)

pH Litmus paper pH meter (electrode)

Salinity Salinity Meter YSI 550A DO Meter w12 cable

60

Water Clarity Secchi Disk

Disk is attached to a calibrated rope The disk is lowered into the water until the white parts can no longer be seen Secchi disk depth is then recorded and serves as the waters transparency index The clearer the water the greater the secchi disk depth

Secchi Disk

61

Current Velocity (flow) Floating-orange method

Put an orange (or something else that floats just below the water surface) and measure the time it takes it to float across a known distance

Odometer-type flow meter Number of revolutions the propeller

makes for a given time is calibrated to flow velocity

62

Sediment Sediment size is important to many

aquatic organisms Sieversquos are used to separate and

grade sediment samples Percent of each size grade can be

determined

63

Water Sample

Water and plankton from various depths can be collected

A trigger mechanism is used to close the sampler Sample is then brought back to the

surface

64

Small Mammals

Mouserat Traps Fatal

Pit Falls Bucket is placed in the ground Sometimes have lsquoleadsrsquo to the buckets

Live traps Havahart Sherman

Spot-light

Sherman trapHavahart trap

65

Birds Stick-under-the-box method Bird-trap

Works like a minnow trap Mist net

Captures birds in flight Rocket net

Uses a propellant to throw a net over birds

66

Terrestrial Insects

Sticky paper flies

Baited Traps Fire ants

Nets butterflies

Foggers Collect insects from tree canopies

67

Aquatic Insects Drift Net

Place net in flowing water Kick Net

lsquoKickrsquo sediment upstream from block net and the flow will wash them into the net

Wash bucket Serber or Hess Sampler

Stir up known area of sediment

Animals are collected by a catch net

Multi-plate Sampler Become colonized

68

Crawfish and Crab Traps

69

Fish Larvae Light Traps

Larvae are attracted to the light Ichthyoplankton nets

Can be towed at various depths Fish collect at the lsquocodrsquoend

70

Fish Lift net

Net is placed down and after a set amount of time it is quickly lifted

Pop-net Similar to a lift net but

floats are attached to a framed net

Operated by a trigger mechanism

Throw net A net attached to a heavy

frame is thrown and every thing inside is netted out Throw net

Pop-net

Lift net

71

Minnow trap

Usually use bait to attract small fish Light is used sometimes as an attractant

72

Fish Electrofishing

Electricity is put into the water Fish are temporarily stunned and usually

swim towards the electricity source Usually non-fatal but may cause some

damage

73

Fish Gill Net

Gill nets resemble tennis nets Fish can not swim completely through the

net and get caught Gill nets are size selective (based on mesh

size) Square Mesh

Bar mesh

Stretch mesh

74

Fish Trammel Net

Three panels two large mesh on the outside and a small mesh on the inside

Fish swim through the outer mesh pushes the small mesh through the other side and becomes entangled

75

Hoop nets (and other similar nets) can have bait or not

Fyke nets have leads to help guide fish to the net

76

Seine Seines are nets that are pulled

through shallow water to catch fish

77

Purse Seine Used to encircle entire schools of fish

Usually involves a spotter plane and a second boat

78

Trotline (longline) A series of baited drop lines

connected to a main line

Can be deployed by tying one end to the bank and tying the other end with a heavy weight

79

Shrimp (or fish) Trawl Net pulled behind

a boat along the bottom Either a beam or

otter boards keep the net open

80

Tagging Individuals Coded Wire Tags

Microwire that has a unique label

Magnetic wand detects the tag

Tag retention should be determined

T-Bar tags Can be individually

numbered External tag

PIT tags (Passive Integrated Transponders) Wand induces the tag to

transmit individual number is displayed

81

Other Tagging Methods

Toe clip Amphibian and reptile Clip of one or more toes

to identify individuals

Bird Band Place a metal band on a

bird leg Generally has

identification information

82

Preserving plant specimens Pressing and drying Long-term

preservation and storage

Alternative drying techniques

Special preservation and processing techniques

Mounting

83

Pressing and drying Techniques for pressing and drying specimens have been

established for many years There are minor variations in recommended methods but they are essentially the same worldwide

The best specimens are plants that are pressed as soon as possible after collection before wilting and shrivelling Most plants may be kept in sealed containers such as plastic bags for up to a day if it is inconvenient to press immediately However some plants show such rapid wilting particularly of the flowers that such delays are best avoided Flowers with a lot of nectar may go mouldy very quickly if excess nectar is not shaken off before pressing

Specimens are pressed flat and dried between sheets of absorbent blotters or semi-absorbent paper such as newspaper Papers with a glossy surface should be avoided because they are not absorbent enough to aid drying The plant should be carefully laid out between the drying sheets as their form at this stage largely determines their ultimate appearance The flowers should be spread out with the petals carefully arranged wilted leaves should be straightened and unnecessary shoots of excessively twiggy shrubs may be cut away

84

Microwave ovens Small numbers of specimens can be dried using a microwave

oven The technique recommended in the literature is to place the specimens between unprinted absorbent paper for example butchers paper not newspaper which is unsuitable because the chemicals present in the ink may cause a fire The specimens should be put in a special press which should be of a microwave-safe material (wood acrylic or polycarbonate sheeting eg plexiglass or perspex NO metal components) If such a press is not available sheets of cardboard can be placed above and below the specimens and then weighted down

Drying time depends on the power of your oven In most cases drying is accomplished by irradiating at maximum power for 1-2 minutes per specimen although it is often a case of trial and error It is best to process no more than 10-12 specimens of average thickness per batch Specimens are usually dried after the moisture that characteristically appears on the glass door has disappeared If the specimen is damp when taken out of the oven allow it to stand before re-radiating as moisture continues to evaporate from the specimen for some time Care must be taken not to irradiate the specimens for too long

It should be noted that microwave treatment damages seeds and the cellular structure of the plants which may reduce the long-term value of the specimens

85

Alternative drying techniquesSilica gelother desiccants amp freeze drying Alternative methods of drying plant specimens have been

used for some time but are mostly restricted to special purpose collections The main alternatives are freeze-drying and drying in a desiccant powder such as desiccant silica gel In general these techniques are used where it is essential to preserve the shape of a delicate plant of organ of the plant such as the flower Freeze-drying has also been used to preserve the chemical composition of a plant as accurately as possible for later study

Disadvantages and special conservation problems of specimens dried in these manners are that they are particularly susceptible to damage The dried parts are fragile lack support and often catch on packing materials They must therefore be packed especially carefully and stored in small boxes or tubes with some appropriate packing material that does not snag and break small projections Acid-free tissue paper is often used Drying in desiccant silica gel crystals or powder can also have the disadvantage that it is difficult to remove all traces of the silica gel after drying

86

Special preservation and processing techniquesWet or spirit collections

Very fleshy or delicate structures including small algae and orchid flowers are best preserved in an air-tight glass or plastic jar with a liquid preservative rather than by drying The type of preservative used should be clearly labelled in the jar Such material is often referred to as a spirit collection or wet collection

Most material can be satisfactorily preserved in 70 ethyl alcohol (or 70 methylated spirit or denatured alcohol) with 30 water Colours will fade quickly in spirit however so it is a good idea to keep comprehensive notes and photographs

87

Small algae Microscopic algae are often collected in a jar and in the

water in which they were found If the algae are to be stored for more than 2-3 days a preservative needs to be used Traditionally this has been the extremely toxic formalin - a small amount can be added to the water to make a 5 final solution and the container labelled This must not be sent through the post or by courier

There are some other equally toxic options for example propylene phenoxytol but none should be sent through the post A safer option is to add sufficient concentrated alcohol or methylated spirits to the water containing the algae to make a final solution of 70 alcohol This treatment dilutes the algae making them difficult to find so if they can be concentrated somehow first (eg by filtering) they can be stored in much less liquid Another option is to fix the algae in formalin (or something similar) first and then prepare a microscope glass slide with a permanent water-soluble mounting medium

88

Mounting Mounting specimens prevents most fragile material from

fragmenting and prevents specimens becoming separated from their labels If the plant collection is a long-term project specimens should be mounted on sheets of archival (permanent) cardboard or paper with archival-quality fixing media These include stitching with cotton thread dental floss nickel-plated copper wire (for heavier specimens) narrow strips of archival paper linen tape or by using an archival adhesive such as methyl cellulose adhesive

One disadvantage of mounting specimens is that it can make parts of the specimen inaccessible for examination so it is essential that this be borne in mind during specimen arrangement and mounting For example easily reversible mounting media should be used specimens should be strapped to the sheet rather than glued all over and the specimen should be carefully arranged before it is attached so that it shows all features

89

Full-size herbarium mounting sheets are usually about 43 cm long x 28 cm wide The plant name and accompanying field notes should be transcribed on a permanent label stuck to one corner of the herbarium sheet (the bottom right-hand corner being the most common) or sometimes annotations may be written directly on the sheet or card

Small pieces of material which may have become separated from the specimen (eg seeds) can be placed in small plastic bags and pinned to the sheet

90

Long-term preservation and storage The long-term preservation of dry plant

specimens is largely dependent on protection from insect attack Specimens collected by Linnaeus in the eighteenth century and by Banks and Solander on the Endeavour voyage in 1788 are still excellently preserved

91

Pests and their control A range of pests attack dried plant material The

most common pests are insects and fungi though rodents and other large animals can cause damage in poor storage conditions Insects eat the material the paper surrounding the material and the adhesives and mounting media

Such insect pests range from psocids (book lice) which attack mainly the softer parts such as flowers and soft fruits to tobacco beetles and carpet beetles which can bore holes through the toughest of specimens Many insects are particularly sensitive to relative humidity levels and do not thrive at levels below 50

92

The most common and acceptable specimen treatments for insect control are Freezing Microwave Poisoning Insect deterrents Fungal pests

93

Storage

Dried and pressed plant specimens can be stored in cardboard or plastic boxes or tied in bundles in light-weight cardboard folders placed in pigeon holes

Alternatively they can be placed in protective plastic jackets and displayed in ring folders which is recommended if they are to be frequently handled such as for a reference collection

94

Filing

Specimens should be filed in a systematic order if a relatively permanent collection is being made The major groups ie ferns and fern allies cycads conifers dicotyledons and monocotyledons are best kept separately or according to some classification scheme such as that given in a flora or handbook

Similarly the genera within each family and the species within each genus may be filed alphabetically or following some such classification

95

Preservation of entire animals

Types of collection specimens of an entire animal For reference collections mammals can be prepared as a variety of specimens The condition of the specimen may determine possible ways to preserve it if for instance decomposition of the skin has loosened the hair of a carcass so much that it can easily be pulled out or removed by rubbing (ldquoslippingrdquo fur) it will be very difficult or impossible to produce a study skin or mounted specimen The most usual types of specimens (based on Nagorsen and Peterson 1980) are 1) entire fluid-preserved animals (for studying anatomy and histology fluid preservation may change the fur colour) 2) study skins with accompanying skulls partial skeletons (some bones remain in the skin) for studying pelage colour hair quality and moulting patterns 3) mounted skins with accompanying partial or entire skeleton (some bones may remain in the skin dependant on the method of preservation) or freeze-dried specimens 4) entire skeletons for instance for studying anatomy geographic variation or for age determination (entire skeletons are poorly represented in collections so Nagorsen and Peterson (1980) recommend preparation of at least one male and one female skeleton per species

96

Preservation of specimens in the field Formalin preservation Preservation in alcohol Preservation by cooling or freezing

97

Formalin preservation After weighing and measuring the animal and attaching an

adequate label very small specimens (up to 100 g) can be fixed whole by submerging them in 10 buffered formalin (tissue - formalin solution ratio of at least 1 12) the body cavity can be filled with formalin solution by injection until it is turgid and firm some formalin may also be injected under the skin into the body cavity larger muscles and organs If hypodermic needles are not available the body cavity can be opened ventrally by making a slit instead allowing the formalin to enter

Keeping the mouth open with a piece of wood or cotton may later allow examination of teeth Then the whole body can be immersed in formalin in the posture in which it is supposed to stay permanently because it will harden The ratio of formalin to carcass must be at least 12 to 1 to assure a good fixation Tissues can be left in buffered neutralized formalin for several months but formalin hardens specimens therefore after fixation longterm storage in alcohol may be better After preservation the carcass should therefore be washed in water and transferred into ethanol for permanent storage

Disadvantages for instance it discolours the fur after a longish immersion softens the bones and prevents further examination for microbiology

98

Preservation in alcohol

After weighing a whole animal can be preserved in a container of alcohol (70-90) Removal of the intestine prior to storage of the animal in alcohol is recommended

99

Preservation by cooling or freezing Removal of the skin with insulating fur

before cooling or freezing may help to cool the carcass down more quickly

Freezing is not recommended if histological examination is planned

100

THANK YOU

16

Habitat sizeAppropriate sample unit size depends on size scale

of the habitatndash Small scale habitats require smaller sized samples1048698 Ex Bouldersndash Large scale habitats require larger sized samples1048698 Ex Forests

17

Organism size and density

Depends on size and density of organisms

ndash Small dense organisms require smaller samples

1048698 Ex grassndash Large scattered organisms require

larger samples1048698 Ex Trees

18

TYPES OF SAMPLING

1048698 Systematic 1048698 Stratified 1048698 Random

19

SYSTEMATIC SAMPLING

1048698 Often used when the area being studied is varied not very large or

when time is available 1048698 Samples are taken at fixed intervals

20

How to sample systematicallySystematic samples are usually taken along a transect line marked by a tape measure

1048698 Transect- a line laid across an area

21

Sampling along gradients

Transects are setup along aenvironmentalgradientsndash down a hillsidendash across a streambedndash out from a source ofpollution

22

Types of transect sampling 1048698 Line transect 1048698 Belt transect

23

Line transect methodA measured line is laidacross the area in thedirection of theenvironmental gradientndash The species touching theline can be recordedalong the whole length ofthe line (continuoussampling) or at specificpoints along the line(systematic sampling)

24

Line Transect- useful where a transition of flora andor fauna

occurs- a string or tape is stretched out along the

ground in a straight line record the organisms touching or covering

the line all along its length or at regular intervals

- Profile transect when there is appreciable height change along the transect and thus affecting the distribution of its species

25

Belt transect method

Similar to line transect butwidens the sampling areandash Transect line is laid outndash Samples are taken bydetermining abundance or cover in an area that is adefined distance from the linendash Samples can be taken all

theway along the line at specificintervals or even randomly

26

Belt TransectIt is a strip usually a metre wide marked by putting a

second line parallel to the other The species between the lines are carefully recorded working a metre at a time

Alternatively a frame quadrat in conjunction with a single line transect could be used

Using a quadrat along a belt transect eg ladder transect (every 5m)

27

Point Frames- for grassland field study of dense vegetation

28

STRATIFIED SAMPLING1048698 Often used whenthere are smallareas within alarger habitat thatare clearly different1048698 Strata- majordifferences withincommunitiesrecognized beforesampling begins

29

RANDOM SAMPLING

1048698 Often used when the area being studied isfairly uniform very large or when there is alimited amount of time available1048698 Random = chosen by chance rather thanaccording to a plan all outcomes are

equallylikely1048698 Samples are taken from different positionswithin a habitat and those positions arechosen randomly

30

How to sample randomly

Choose individuals or Placeldquosampling unitsrdquo

haphazardlyndash This is rarely completely

random1048698 ORhellip1048698 Assign numbers to the

areasor individuals to be sampledndash Use a random number

table toselect which areas or

individualswill be sample

31

Population Attributes Density ndash size of a population in relation to a definite

unit of space Affected by

Natality ndash the reproductive output (birth rate) of a population

Mortality ndash the death rate of organisms in a population

Immigration ndash number of organisms moving into the area occupied by the population

Emigration ndash number of organisms moving out of the area occupied by the population

32

Population Density

Four primary population parameters

33

Two Types of Density Estimates

bull Absolute Density ndash a known density such as m2

bull Relative Density ndash we know when one area has more individuals than another

34

Measuring Absolute Density

Total Count ndash count the number of organisms living in an area Human census number of oak trees in a

wooded lot number of singing birds in an area

Total counts generally are not used very often

Sampling Methods ndash use a sample to estimate population size Either use the quadrat or capture-

recapture method

35

Measurement of Environmental ParametersAbiotic factors are important in determining

both the distribution of the organisms and their physical and physiological adaptations

Temperature- diurnal and seasonal temperature variations

are significant in affecting different species of plants and animals

- equipment mercury thermometer maximum-minimum thermometer

miniaturized thermistor

36

pH

-measure pH of a solution by universal indicator pH paper pH meter etc

Light

-measure its duration and intensity duration by predication from Royal Observatory intensity by photographic light meter

pH meter in use

37

Humidity

Relative humidity the water content of a given volume of air relative to the same volume of fully saturated air

- equipment whirling hygrometer

38

Wind and Water Speed- wind speed- anemometer or wind

gauges- water speed - time the movement of a

floating object over a measured distance

39

Salinity

- using a conductivity meter greater salinity has greater conductivity

Oxygen Level

- using an oxygen meter or chemical method (Winkler method)

40

Collecting MethodsCollecting all organisms within a habitat is normally

impractical and therefore small areas are selected Remember to return all material to its original position

after searching amp collecting sufficient specimens Some collecting apparatus for general use are listed

below

41

1 specimen tube

2 screwed-topped jars

3 polythene bags

4 forceps

5 paint brush

6 bulb pipette

7 pooter

42

8 widger 9 sieve 10 hand lens

11 enamel dish 12 beating tray 13 light traps

14 Tullgren funnel 15 Baermann funnel 16 mammal traps

17 pitfall traps 18 netting

43

Estimating Population Size

The exact methods used for estimation depend not only the nature of the habitat but also on the organisms involved

eg animals - population

plants - percentage cover

44

Using Quadrats

- By sampling an area using quadrats and counting the number of individuals within each quadrat it is possible to estimate the total number of individuals within the area

- confined to plants and sessile or very slow-moving animals

- fast-moving animals are disturbed and run away

45

Capture-recapture Techniques- useful for mobile animals which can be marked

- capture marked released randomly recaptured

and marked individuals recorded

no of marked individuals recaptured total no of individuals in 1st sample

-------------------------------------------- = ------------------------------------------

total no of individuals in 2nd sample estimated size of population

(the Lincoln Index)

46

Capture-recapture Techniques Factors affecting the accuracy of the estimation

deaths migration individuals become more liable to predation etc

Examples

- arthropods marked on their backs with non-toxic paint

- fish have tags attached to opercula - mammals have tags clipped to their ears

birds have their legs ringed

47

Capture-recapture Method Important tool for estimating density birth

rate and death rate for mobile animals Method

Collect a sample of individuals mark them and then release them

After a period collect more individuals from the wild and count the number that have marks

We assume that a sample if random will contain the same proportion of marked individuals as the population does

Estimate population density

48

Assumptions For All Capture-Recapture Studies Marking technique does not increase

mortality of marked animals Marked individuals are allowed to mix

with population Marking technique does not affect catch

probability Marks are not lost or overlooked No significant immigration or emigration No significant mortality or natality

49

Marked animals in second sample

Total caught in second sample

Marked animals in first sample

Total population size

=

520 N

16=

Peterson Method or Lincoln Index

N = 64N = (20)(16)5

50

Some Indices Used

Traps Number of Fecal

Pellets Vocalization

Frequency Pelt Records Catch per Unit

Fishing Effort

Number of Artifacts Questionnaires Cover Feeding Capacity Roadside Counts

51

Abundance Scales

The population size may be fairly accurately determined by making some form of frequency assessment

These are subjective and involve an experimenter making some estimate of the number of individuals in a given area or the cover of a particular species

This is especially useful where individuals are very numerous eg barnacles on a rocky shore or where it is difficult to distinguish individuals eg grass plants in a meadow

52

The assessments are usually made on an abundance scale of 5 categories

Abundance Common Frequent Occasional Rare

Barnacles exposed at low water

53

Environmental resistance are the factors which limit the growth of a particular population

eg predation disease availability of light food water oxygen and shelter the accumulation of toxic wastes and even the size of the population itself

54

Density-dependent Growth A population is a density-dependent when its size

(or density) affects its growth rate because of density-dependent factors such as food availability and toxic waste accumulation

Density-independent Growth In this type of growth a population increases until

some factor causes a sudden reduction in its size Its effect is the same regardless of the size of the

population eg temperature fires floods storms etc

55

Regulation of Population Size Fecundity is the reproductive capacity of individual

females of a species Birth rate or natality is used to measure fecundity Death rate or mortality is the number of individuals

of a species which die per unit time Immigration occurs when individuals join a

population from neighbouring ones Emigration occurs when individuals depart from a

population A cycle occurs when the size of a population

fluctuates on a regular basis

56

Ecological Sampling

57

Why Do We Sample Determine presence andor

abundance

Monitor population fluctuations

Assess lsquoecological damagersquo

Assess quality of habitat

Assess population responses

58

What Do We Sample

Physical Environment Temperature DO pH salinity clarity

flow sediment

Biotic Environment All living things

59

Physical Habitat Temperature

Mercury thermometer Electronic thermometer Long-term thermometers

Dissolved Oxygen Winkler method (titration) DO meter (electrode)

pH Litmus paper pH meter (electrode)

Salinity Salinity Meter YSI 550A DO Meter w12 cable

60

Water Clarity Secchi Disk

Disk is attached to a calibrated rope The disk is lowered into the water until the white parts can no longer be seen Secchi disk depth is then recorded and serves as the waters transparency index The clearer the water the greater the secchi disk depth

Secchi Disk

61

Current Velocity (flow) Floating-orange method

Put an orange (or something else that floats just below the water surface) and measure the time it takes it to float across a known distance

Odometer-type flow meter Number of revolutions the propeller

makes for a given time is calibrated to flow velocity

62

Sediment Sediment size is important to many

aquatic organisms Sieversquos are used to separate and

grade sediment samples Percent of each size grade can be

determined

63

Water Sample

Water and plankton from various depths can be collected

A trigger mechanism is used to close the sampler Sample is then brought back to the

surface

64

Small Mammals

Mouserat Traps Fatal

Pit Falls Bucket is placed in the ground Sometimes have lsquoleadsrsquo to the buckets

Live traps Havahart Sherman

Spot-light

Sherman trapHavahart trap

65

Birds Stick-under-the-box method Bird-trap

Works like a minnow trap Mist net

Captures birds in flight Rocket net

Uses a propellant to throw a net over birds

66

Terrestrial Insects

Sticky paper flies

Baited Traps Fire ants

Nets butterflies

Foggers Collect insects from tree canopies

67

Aquatic Insects Drift Net

Place net in flowing water Kick Net

lsquoKickrsquo sediment upstream from block net and the flow will wash them into the net

Wash bucket Serber or Hess Sampler

Stir up known area of sediment

Animals are collected by a catch net

Multi-plate Sampler Become colonized

68

Crawfish and Crab Traps

69

Fish Larvae Light Traps

Larvae are attracted to the light Ichthyoplankton nets

Can be towed at various depths Fish collect at the lsquocodrsquoend

70

Fish Lift net

Net is placed down and after a set amount of time it is quickly lifted

Pop-net Similar to a lift net but

floats are attached to a framed net

Operated by a trigger mechanism

Throw net A net attached to a heavy

frame is thrown and every thing inside is netted out Throw net

Pop-net

Lift net

71

Minnow trap

Usually use bait to attract small fish Light is used sometimes as an attractant

72

Fish Electrofishing

Electricity is put into the water Fish are temporarily stunned and usually

swim towards the electricity source Usually non-fatal but may cause some

damage

73

Fish Gill Net

Gill nets resemble tennis nets Fish can not swim completely through the

net and get caught Gill nets are size selective (based on mesh

size) Square Mesh

Bar mesh

Stretch mesh

74

Fish Trammel Net

Three panels two large mesh on the outside and a small mesh on the inside

Fish swim through the outer mesh pushes the small mesh through the other side and becomes entangled

75

Hoop nets (and other similar nets) can have bait or not

Fyke nets have leads to help guide fish to the net

76

Seine Seines are nets that are pulled

through shallow water to catch fish

77

Purse Seine Used to encircle entire schools of fish

Usually involves a spotter plane and a second boat

78

Trotline (longline) A series of baited drop lines

connected to a main line

Can be deployed by tying one end to the bank and tying the other end with a heavy weight

79

Shrimp (or fish) Trawl Net pulled behind

a boat along the bottom Either a beam or

otter boards keep the net open

80

Tagging Individuals Coded Wire Tags

Microwire that has a unique label

Magnetic wand detects the tag

Tag retention should be determined

T-Bar tags Can be individually

numbered External tag

PIT tags (Passive Integrated Transponders) Wand induces the tag to

transmit individual number is displayed

81

Other Tagging Methods

Toe clip Amphibian and reptile Clip of one or more toes

to identify individuals

Bird Band Place a metal band on a

bird leg Generally has

identification information

82

Preserving plant specimens Pressing and drying Long-term

preservation and storage

Alternative drying techniques

Special preservation and processing techniques

Mounting

83

Pressing and drying Techniques for pressing and drying specimens have been

established for many years There are minor variations in recommended methods but they are essentially the same worldwide

The best specimens are plants that are pressed as soon as possible after collection before wilting and shrivelling Most plants may be kept in sealed containers such as plastic bags for up to a day if it is inconvenient to press immediately However some plants show such rapid wilting particularly of the flowers that such delays are best avoided Flowers with a lot of nectar may go mouldy very quickly if excess nectar is not shaken off before pressing

Specimens are pressed flat and dried between sheets of absorbent blotters or semi-absorbent paper such as newspaper Papers with a glossy surface should be avoided because they are not absorbent enough to aid drying The plant should be carefully laid out between the drying sheets as their form at this stage largely determines their ultimate appearance The flowers should be spread out with the petals carefully arranged wilted leaves should be straightened and unnecessary shoots of excessively twiggy shrubs may be cut away

84

Microwave ovens Small numbers of specimens can be dried using a microwave

oven The technique recommended in the literature is to place the specimens between unprinted absorbent paper for example butchers paper not newspaper which is unsuitable because the chemicals present in the ink may cause a fire The specimens should be put in a special press which should be of a microwave-safe material (wood acrylic or polycarbonate sheeting eg plexiglass or perspex NO metal components) If such a press is not available sheets of cardboard can be placed above and below the specimens and then weighted down

Drying time depends on the power of your oven In most cases drying is accomplished by irradiating at maximum power for 1-2 minutes per specimen although it is often a case of trial and error It is best to process no more than 10-12 specimens of average thickness per batch Specimens are usually dried after the moisture that characteristically appears on the glass door has disappeared If the specimen is damp when taken out of the oven allow it to stand before re-radiating as moisture continues to evaporate from the specimen for some time Care must be taken not to irradiate the specimens for too long

It should be noted that microwave treatment damages seeds and the cellular structure of the plants which may reduce the long-term value of the specimens

85

Alternative drying techniquesSilica gelother desiccants amp freeze drying Alternative methods of drying plant specimens have been

used for some time but are mostly restricted to special purpose collections The main alternatives are freeze-drying and drying in a desiccant powder such as desiccant silica gel In general these techniques are used where it is essential to preserve the shape of a delicate plant of organ of the plant such as the flower Freeze-drying has also been used to preserve the chemical composition of a plant as accurately as possible for later study

Disadvantages and special conservation problems of specimens dried in these manners are that they are particularly susceptible to damage The dried parts are fragile lack support and often catch on packing materials They must therefore be packed especially carefully and stored in small boxes or tubes with some appropriate packing material that does not snag and break small projections Acid-free tissue paper is often used Drying in desiccant silica gel crystals or powder can also have the disadvantage that it is difficult to remove all traces of the silica gel after drying

86

Special preservation and processing techniquesWet or spirit collections

Very fleshy or delicate structures including small algae and orchid flowers are best preserved in an air-tight glass or plastic jar with a liquid preservative rather than by drying The type of preservative used should be clearly labelled in the jar Such material is often referred to as a spirit collection or wet collection

Most material can be satisfactorily preserved in 70 ethyl alcohol (or 70 methylated spirit or denatured alcohol) with 30 water Colours will fade quickly in spirit however so it is a good idea to keep comprehensive notes and photographs

87

Small algae Microscopic algae are often collected in a jar and in the

water in which they were found If the algae are to be stored for more than 2-3 days a preservative needs to be used Traditionally this has been the extremely toxic formalin - a small amount can be added to the water to make a 5 final solution and the container labelled This must not be sent through the post or by courier

There are some other equally toxic options for example propylene phenoxytol but none should be sent through the post A safer option is to add sufficient concentrated alcohol or methylated spirits to the water containing the algae to make a final solution of 70 alcohol This treatment dilutes the algae making them difficult to find so if they can be concentrated somehow first (eg by filtering) they can be stored in much less liquid Another option is to fix the algae in formalin (or something similar) first and then prepare a microscope glass slide with a permanent water-soluble mounting medium

88

Mounting Mounting specimens prevents most fragile material from

fragmenting and prevents specimens becoming separated from their labels If the plant collection is a long-term project specimens should be mounted on sheets of archival (permanent) cardboard or paper with archival-quality fixing media These include stitching with cotton thread dental floss nickel-plated copper wire (for heavier specimens) narrow strips of archival paper linen tape or by using an archival adhesive such as methyl cellulose adhesive

One disadvantage of mounting specimens is that it can make parts of the specimen inaccessible for examination so it is essential that this be borne in mind during specimen arrangement and mounting For example easily reversible mounting media should be used specimens should be strapped to the sheet rather than glued all over and the specimen should be carefully arranged before it is attached so that it shows all features

89

Full-size herbarium mounting sheets are usually about 43 cm long x 28 cm wide The plant name and accompanying field notes should be transcribed on a permanent label stuck to one corner of the herbarium sheet (the bottom right-hand corner being the most common) or sometimes annotations may be written directly on the sheet or card

Small pieces of material which may have become separated from the specimen (eg seeds) can be placed in small plastic bags and pinned to the sheet

90

Long-term preservation and storage The long-term preservation of dry plant

specimens is largely dependent on protection from insect attack Specimens collected by Linnaeus in the eighteenth century and by Banks and Solander on the Endeavour voyage in 1788 are still excellently preserved

91

Pests and their control A range of pests attack dried plant material The

most common pests are insects and fungi though rodents and other large animals can cause damage in poor storage conditions Insects eat the material the paper surrounding the material and the adhesives and mounting media

Such insect pests range from psocids (book lice) which attack mainly the softer parts such as flowers and soft fruits to tobacco beetles and carpet beetles which can bore holes through the toughest of specimens Many insects are particularly sensitive to relative humidity levels and do not thrive at levels below 50

92

The most common and acceptable specimen treatments for insect control are Freezing Microwave Poisoning Insect deterrents Fungal pests

93

Storage

Dried and pressed plant specimens can be stored in cardboard or plastic boxes or tied in bundles in light-weight cardboard folders placed in pigeon holes

Alternatively they can be placed in protective plastic jackets and displayed in ring folders which is recommended if they are to be frequently handled such as for a reference collection

94

Filing

Specimens should be filed in a systematic order if a relatively permanent collection is being made The major groups ie ferns and fern allies cycads conifers dicotyledons and monocotyledons are best kept separately or according to some classification scheme such as that given in a flora or handbook

Similarly the genera within each family and the species within each genus may be filed alphabetically or following some such classification

95

Preservation of entire animals

Types of collection specimens of an entire animal For reference collections mammals can be prepared as a variety of specimens The condition of the specimen may determine possible ways to preserve it if for instance decomposition of the skin has loosened the hair of a carcass so much that it can easily be pulled out or removed by rubbing (ldquoslippingrdquo fur) it will be very difficult or impossible to produce a study skin or mounted specimen The most usual types of specimens (based on Nagorsen and Peterson 1980) are 1) entire fluid-preserved animals (for studying anatomy and histology fluid preservation may change the fur colour) 2) study skins with accompanying skulls partial skeletons (some bones remain in the skin) for studying pelage colour hair quality and moulting patterns 3) mounted skins with accompanying partial or entire skeleton (some bones may remain in the skin dependant on the method of preservation) or freeze-dried specimens 4) entire skeletons for instance for studying anatomy geographic variation or for age determination (entire skeletons are poorly represented in collections so Nagorsen and Peterson (1980) recommend preparation of at least one male and one female skeleton per species

96

Preservation of specimens in the field Formalin preservation Preservation in alcohol Preservation by cooling or freezing

97

Formalin preservation After weighing and measuring the animal and attaching an

adequate label very small specimens (up to 100 g) can be fixed whole by submerging them in 10 buffered formalin (tissue - formalin solution ratio of at least 1 12) the body cavity can be filled with formalin solution by injection until it is turgid and firm some formalin may also be injected under the skin into the body cavity larger muscles and organs If hypodermic needles are not available the body cavity can be opened ventrally by making a slit instead allowing the formalin to enter

Keeping the mouth open with a piece of wood or cotton may later allow examination of teeth Then the whole body can be immersed in formalin in the posture in which it is supposed to stay permanently because it will harden The ratio of formalin to carcass must be at least 12 to 1 to assure a good fixation Tissues can be left in buffered neutralized formalin for several months but formalin hardens specimens therefore after fixation longterm storage in alcohol may be better After preservation the carcass should therefore be washed in water and transferred into ethanol for permanent storage

Disadvantages for instance it discolours the fur after a longish immersion softens the bones and prevents further examination for microbiology

98

Preservation in alcohol

After weighing a whole animal can be preserved in a container of alcohol (70-90) Removal of the intestine prior to storage of the animal in alcohol is recommended

99

Preservation by cooling or freezing Removal of the skin with insulating fur

before cooling or freezing may help to cool the carcass down more quickly

Freezing is not recommended if histological examination is planned

100

THANK YOU

17

Organism size and density

Depends on size and density of organisms

ndash Small dense organisms require smaller samples

1048698 Ex grassndash Large scattered organisms require

larger samples1048698 Ex Trees

18

TYPES OF SAMPLING

1048698 Systematic 1048698 Stratified 1048698 Random

19

SYSTEMATIC SAMPLING

1048698 Often used when the area being studied is varied not very large or

when time is available 1048698 Samples are taken at fixed intervals

20

How to sample systematicallySystematic samples are usually taken along a transect line marked by a tape measure

1048698 Transect- a line laid across an area

21

Sampling along gradients

Transects are setup along aenvironmentalgradientsndash down a hillsidendash across a streambedndash out from a source ofpollution

22

Types of transect sampling 1048698 Line transect 1048698 Belt transect

23

Line transect methodA measured line is laidacross the area in thedirection of theenvironmental gradientndash The species touching theline can be recordedalong the whole length ofthe line (continuoussampling) or at specificpoints along the line(systematic sampling)

24

Line Transect- useful where a transition of flora andor fauna

occurs- a string or tape is stretched out along the

ground in a straight line record the organisms touching or covering

the line all along its length or at regular intervals

- Profile transect when there is appreciable height change along the transect and thus affecting the distribution of its species

25

Belt transect method

Similar to line transect butwidens the sampling areandash Transect line is laid outndash Samples are taken bydetermining abundance or cover in an area that is adefined distance from the linendash Samples can be taken all

theway along the line at specificintervals or even randomly

26

Belt TransectIt is a strip usually a metre wide marked by putting a

second line parallel to the other The species between the lines are carefully recorded working a metre at a time

Alternatively a frame quadrat in conjunction with a single line transect could be used

Using a quadrat along a belt transect eg ladder transect (every 5m)

27

Point Frames- for grassland field study of dense vegetation

28

STRATIFIED SAMPLING1048698 Often used whenthere are smallareas within alarger habitat thatare clearly different1048698 Strata- majordifferences withincommunitiesrecognized beforesampling begins

29

RANDOM SAMPLING

1048698 Often used when the area being studied isfairly uniform very large or when there is alimited amount of time available1048698 Random = chosen by chance rather thanaccording to a plan all outcomes are

equallylikely1048698 Samples are taken from different positionswithin a habitat and those positions arechosen randomly

30

How to sample randomly

Choose individuals or Placeldquosampling unitsrdquo

haphazardlyndash This is rarely completely

random1048698 ORhellip1048698 Assign numbers to the

areasor individuals to be sampledndash Use a random number

table toselect which areas or

individualswill be sample

31

Population Attributes Density ndash size of a population in relation to a definite

unit of space Affected by

Natality ndash the reproductive output (birth rate) of a population

Mortality ndash the death rate of organisms in a population

Immigration ndash number of organisms moving into the area occupied by the population

Emigration ndash number of organisms moving out of the area occupied by the population

32

Population Density

Four primary population parameters

33

Two Types of Density Estimates

bull Absolute Density ndash a known density such as m2

bull Relative Density ndash we know when one area has more individuals than another

34

Measuring Absolute Density

Total Count ndash count the number of organisms living in an area Human census number of oak trees in a

wooded lot number of singing birds in an area

Total counts generally are not used very often

Sampling Methods ndash use a sample to estimate population size Either use the quadrat or capture-

recapture method

35

Measurement of Environmental ParametersAbiotic factors are important in determining

both the distribution of the organisms and their physical and physiological adaptations

Temperature- diurnal and seasonal temperature variations

are significant in affecting different species of plants and animals

- equipment mercury thermometer maximum-minimum thermometer

miniaturized thermistor

36

pH

-measure pH of a solution by universal indicator pH paper pH meter etc

Light

-measure its duration and intensity duration by predication from Royal Observatory intensity by photographic light meter

pH meter in use

37

Humidity

Relative humidity the water content of a given volume of air relative to the same volume of fully saturated air

- equipment whirling hygrometer

38

Wind and Water Speed- wind speed- anemometer or wind

gauges- water speed - time the movement of a

floating object over a measured distance

39

Salinity

- using a conductivity meter greater salinity has greater conductivity

Oxygen Level

- using an oxygen meter or chemical method (Winkler method)

40

Collecting MethodsCollecting all organisms within a habitat is normally

impractical and therefore small areas are selected Remember to return all material to its original position

after searching amp collecting sufficient specimens Some collecting apparatus for general use are listed

below

41

1 specimen tube

2 screwed-topped jars

3 polythene bags

4 forceps

5 paint brush

6 bulb pipette

7 pooter

42

8 widger 9 sieve 10 hand lens

11 enamel dish 12 beating tray 13 light traps

14 Tullgren funnel 15 Baermann funnel 16 mammal traps

17 pitfall traps 18 netting

43

Estimating Population Size

The exact methods used for estimation depend not only the nature of the habitat but also on the organisms involved

eg animals - population

plants - percentage cover

44

Using Quadrats

- By sampling an area using quadrats and counting the number of individuals within each quadrat it is possible to estimate the total number of individuals within the area

- confined to plants and sessile or very slow-moving animals

- fast-moving animals are disturbed and run away

45

Capture-recapture Techniques- useful for mobile animals which can be marked

- capture marked released randomly recaptured

and marked individuals recorded

no of marked individuals recaptured total no of individuals in 1st sample

-------------------------------------------- = ------------------------------------------

total no of individuals in 2nd sample estimated size of population

(the Lincoln Index)

46

Capture-recapture Techniques Factors affecting the accuracy of the estimation

deaths migration individuals become more liable to predation etc

Examples

- arthropods marked on their backs with non-toxic paint

- fish have tags attached to opercula - mammals have tags clipped to their ears

birds have their legs ringed

47

Capture-recapture Method Important tool for estimating density birth

rate and death rate for mobile animals Method

Collect a sample of individuals mark them and then release them

After a period collect more individuals from the wild and count the number that have marks

We assume that a sample if random will contain the same proportion of marked individuals as the population does

Estimate population density

48

Assumptions For All Capture-Recapture Studies Marking technique does not increase

mortality of marked animals Marked individuals are allowed to mix

with population Marking technique does not affect catch

probability Marks are not lost or overlooked No significant immigration or emigration No significant mortality or natality

49

Marked animals in second sample

Total caught in second sample

Marked animals in first sample

Total population size

=

520 N

16=

Peterson Method or Lincoln Index

N = 64N = (20)(16)5

50

Some Indices Used

Traps Number of Fecal

Pellets Vocalization

Frequency Pelt Records Catch per Unit

Fishing Effort

Number of Artifacts Questionnaires Cover Feeding Capacity Roadside Counts

51

Abundance Scales

The population size may be fairly accurately determined by making some form of frequency assessment

These are subjective and involve an experimenter making some estimate of the number of individuals in a given area or the cover of a particular species

This is especially useful where individuals are very numerous eg barnacles on a rocky shore or where it is difficult to distinguish individuals eg grass plants in a meadow

52

The assessments are usually made on an abundance scale of 5 categories

Abundance Common Frequent Occasional Rare

Barnacles exposed at low water

53

Environmental resistance are the factors which limit the growth of a particular population

eg predation disease availability of light food water oxygen and shelter the accumulation of toxic wastes and even the size of the population itself

54

Density-dependent Growth A population is a density-dependent when its size

(or density) affects its growth rate because of density-dependent factors such as food availability and toxic waste accumulation

Density-independent Growth In this type of growth a population increases until

some factor causes a sudden reduction in its size Its effect is the same regardless of the size of the

population eg temperature fires floods storms etc

55

Regulation of Population Size Fecundity is the reproductive capacity of individual

females of a species Birth rate or natality is used to measure fecundity Death rate or mortality is the number of individuals

of a species which die per unit time Immigration occurs when individuals join a

population from neighbouring ones Emigration occurs when individuals depart from a

population A cycle occurs when the size of a population

fluctuates on a regular basis

56

Ecological Sampling

57

Why Do We Sample Determine presence andor

abundance

Monitor population fluctuations

Assess lsquoecological damagersquo

Assess quality of habitat

Assess population responses

58

What Do We Sample

Physical Environment Temperature DO pH salinity clarity

flow sediment

Biotic Environment All living things

59

Physical Habitat Temperature

Mercury thermometer Electronic thermometer Long-term thermometers

Dissolved Oxygen Winkler method (titration) DO meter (electrode)

pH Litmus paper pH meter (electrode)

Salinity Salinity Meter YSI 550A DO Meter w12 cable

60

Water Clarity Secchi Disk

Disk is attached to a calibrated rope The disk is lowered into the water until the white parts can no longer be seen Secchi disk depth is then recorded and serves as the waters transparency index The clearer the water the greater the secchi disk depth

Secchi Disk

61

Current Velocity (flow) Floating-orange method

Put an orange (or something else that floats just below the water surface) and measure the time it takes it to float across a known distance

Odometer-type flow meter Number of revolutions the propeller

makes for a given time is calibrated to flow velocity

62

Sediment Sediment size is important to many

aquatic organisms Sieversquos are used to separate and

grade sediment samples Percent of each size grade can be

determined

63

Water Sample

Water and plankton from various depths can be collected

A trigger mechanism is used to close the sampler Sample is then brought back to the

surface

64

Small Mammals

Mouserat Traps Fatal

Pit Falls Bucket is placed in the ground Sometimes have lsquoleadsrsquo to the buckets

Live traps Havahart Sherman

Spot-light

Sherman trapHavahart trap

65

Birds Stick-under-the-box method Bird-trap

Works like a minnow trap Mist net

Captures birds in flight Rocket net

Uses a propellant to throw a net over birds

66

Terrestrial Insects

Sticky paper flies

Baited Traps Fire ants

Nets butterflies

Foggers Collect insects from tree canopies

67

Aquatic Insects Drift Net

Place net in flowing water Kick Net

lsquoKickrsquo sediment upstream from block net and the flow will wash them into the net

Wash bucket Serber or Hess Sampler

Stir up known area of sediment

Animals are collected by a catch net

Multi-plate Sampler Become colonized

68

Crawfish and Crab Traps

69

Fish Larvae Light Traps

Larvae are attracted to the light Ichthyoplankton nets

Can be towed at various depths Fish collect at the lsquocodrsquoend

70

Fish Lift net

Net is placed down and after a set amount of time it is quickly lifted

Pop-net Similar to a lift net but

floats are attached to a framed net

Operated by a trigger mechanism

Throw net A net attached to a heavy

frame is thrown and every thing inside is netted out Throw net

Pop-net

Lift net

71

Minnow trap

Usually use bait to attract small fish Light is used sometimes as an attractant

72

Fish Electrofishing

Electricity is put into the water Fish are temporarily stunned and usually

swim towards the electricity source Usually non-fatal but may cause some

damage

73

Fish Gill Net

Gill nets resemble tennis nets Fish can not swim completely through the

net and get caught Gill nets are size selective (based on mesh

size) Square Mesh

Bar mesh

Stretch mesh

74

Fish Trammel Net

Three panels two large mesh on the outside and a small mesh on the inside

Fish swim through the outer mesh pushes the small mesh through the other side and becomes entangled

75

Hoop nets (and other similar nets) can have bait or not

Fyke nets have leads to help guide fish to the net

76

Seine Seines are nets that are pulled

through shallow water to catch fish

77

Purse Seine Used to encircle entire schools of fish

Usually involves a spotter plane and a second boat

78

Trotline (longline) A series of baited drop lines

connected to a main line

Can be deployed by tying one end to the bank and tying the other end with a heavy weight

79

Shrimp (or fish) Trawl Net pulled behind

a boat along the bottom Either a beam or

otter boards keep the net open

80

Tagging Individuals Coded Wire Tags

Microwire that has a unique label

Magnetic wand detects the tag

Tag retention should be determined

T-Bar tags Can be individually

numbered External tag

PIT tags (Passive Integrated Transponders) Wand induces the tag to

transmit individual number is displayed

81

Other Tagging Methods

Toe clip Amphibian and reptile Clip of one or more toes

to identify individuals

Bird Band Place a metal band on a

bird leg Generally has

identification information

82

Preserving plant specimens Pressing and drying Long-term

preservation and storage

Alternative drying techniques

Special preservation and processing techniques

Mounting

83

Pressing and drying Techniques for pressing and drying specimens have been

established for many years There are minor variations in recommended methods but they are essentially the same worldwide

The best specimens are plants that are pressed as soon as possible after collection before wilting and shrivelling Most plants may be kept in sealed containers such as plastic bags for up to a day if it is inconvenient to press immediately However some plants show such rapid wilting particularly of the flowers that such delays are best avoided Flowers with a lot of nectar may go mouldy very quickly if excess nectar is not shaken off before pressing

Specimens are pressed flat and dried between sheets of absorbent blotters or semi-absorbent paper such as newspaper Papers with a glossy surface should be avoided because they are not absorbent enough to aid drying The plant should be carefully laid out between the drying sheets as their form at this stage largely determines their ultimate appearance The flowers should be spread out with the petals carefully arranged wilted leaves should be straightened and unnecessary shoots of excessively twiggy shrubs may be cut away

84

Microwave ovens Small numbers of specimens can be dried using a microwave

oven The technique recommended in the literature is to place the specimens between unprinted absorbent paper for example butchers paper not newspaper which is unsuitable because the chemicals present in the ink may cause a fire The specimens should be put in a special press which should be of a microwave-safe material (wood acrylic or polycarbonate sheeting eg plexiglass or perspex NO metal components) If such a press is not available sheets of cardboard can be placed above and below the specimens and then weighted down

Drying time depends on the power of your oven In most cases drying is accomplished by irradiating at maximum power for 1-2 minutes per specimen although it is often a case of trial and error It is best to process no more than 10-12 specimens of average thickness per batch Specimens are usually dried after the moisture that characteristically appears on the glass door has disappeared If the specimen is damp when taken out of the oven allow it to stand before re-radiating as moisture continues to evaporate from the specimen for some time Care must be taken not to irradiate the specimens for too long

It should be noted that microwave treatment damages seeds and the cellular structure of the plants which may reduce the long-term value of the specimens

85

Alternative drying techniquesSilica gelother desiccants amp freeze drying Alternative methods of drying plant specimens have been

used for some time but are mostly restricted to special purpose collections The main alternatives are freeze-drying and drying in a desiccant powder such as desiccant silica gel In general these techniques are used where it is essential to preserve the shape of a delicate plant of organ of the plant such as the flower Freeze-drying has also been used to preserve the chemical composition of a plant as accurately as possible for later study

Disadvantages and special conservation problems of specimens dried in these manners are that they are particularly susceptible to damage The dried parts are fragile lack support and often catch on packing materials They must therefore be packed especially carefully and stored in small boxes or tubes with some appropriate packing material that does not snag and break small projections Acid-free tissue paper is often used Drying in desiccant silica gel crystals or powder can also have the disadvantage that it is difficult to remove all traces of the silica gel after drying

86

Special preservation and processing techniquesWet or spirit collections

Very fleshy or delicate structures including small algae and orchid flowers are best preserved in an air-tight glass or plastic jar with a liquid preservative rather than by drying The type of preservative used should be clearly labelled in the jar Such material is often referred to as a spirit collection or wet collection

Most material can be satisfactorily preserved in 70 ethyl alcohol (or 70 methylated spirit or denatured alcohol) with 30 water Colours will fade quickly in spirit however so it is a good idea to keep comprehensive notes and photographs

87

Small algae Microscopic algae are often collected in a jar and in the

water in which they were found If the algae are to be stored for more than 2-3 days a preservative needs to be used Traditionally this has been the extremely toxic formalin - a small amount can be added to the water to make a 5 final solution and the container labelled This must not be sent through the post or by courier

There are some other equally toxic options for example propylene phenoxytol but none should be sent through the post A safer option is to add sufficient concentrated alcohol or methylated spirits to the water containing the algae to make a final solution of 70 alcohol This treatment dilutes the algae making them difficult to find so if they can be concentrated somehow first (eg by filtering) they can be stored in much less liquid Another option is to fix the algae in formalin (or something similar) first and then prepare a microscope glass slide with a permanent water-soluble mounting medium

88

Mounting Mounting specimens prevents most fragile material from

fragmenting and prevents specimens becoming separated from their labels If the plant collection is a long-term project specimens should be mounted on sheets of archival (permanent) cardboard or paper with archival-quality fixing media These include stitching with cotton thread dental floss nickel-plated copper wire (for heavier specimens) narrow strips of archival paper linen tape or by using an archival adhesive such as methyl cellulose adhesive

One disadvantage of mounting specimens is that it can make parts of the specimen inaccessible for examination so it is essential that this be borne in mind during specimen arrangement and mounting For example easily reversible mounting media should be used specimens should be strapped to the sheet rather than glued all over and the specimen should be carefully arranged before it is attached so that it shows all features

89

Full-size herbarium mounting sheets are usually about 43 cm long x 28 cm wide The plant name and accompanying field notes should be transcribed on a permanent label stuck to one corner of the herbarium sheet (the bottom right-hand corner being the most common) or sometimes annotations may be written directly on the sheet or card

Small pieces of material which may have become separated from the specimen (eg seeds) can be placed in small plastic bags and pinned to the sheet

90

Long-term preservation and storage The long-term preservation of dry plant

specimens is largely dependent on protection from insect attack Specimens collected by Linnaeus in the eighteenth century and by Banks and Solander on the Endeavour voyage in 1788 are still excellently preserved

91

Pests and their control A range of pests attack dried plant material The

most common pests are insects and fungi though rodents and other large animals can cause damage in poor storage conditions Insects eat the material the paper surrounding the material and the adhesives and mounting media

Such insect pests range from psocids (book lice) which attack mainly the softer parts such as flowers and soft fruits to tobacco beetles and carpet beetles which can bore holes through the toughest of specimens Many insects are particularly sensitive to relative humidity levels and do not thrive at levels below 50

92

The most common and acceptable specimen treatments for insect control are Freezing Microwave Poisoning Insect deterrents Fungal pests

93

Storage

Dried and pressed plant specimens can be stored in cardboard or plastic boxes or tied in bundles in light-weight cardboard folders placed in pigeon holes

Alternatively they can be placed in protective plastic jackets and displayed in ring folders which is recommended if they are to be frequently handled such as for a reference collection

94

Filing

Specimens should be filed in a systematic order if a relatively permanent collection is being made The major groups ie ferns and fern allies cycads conifers dicotyledons and monocotyledons are best kept separately or according to some classification scheme such as that given in a flora or handbook

Similarly the genera within each family and the species within each genus may be filed alphabetically or following some such classification

95

Preservation of entire animals

Types of collection specimens of an entire animal For reference collections mammals can be prepared as a variety of specimens The condition of the specimen may determine possible ways to preserve it if for instance decomposition of the skin has loosened the hair of a carcass so much that it can easily be pulled out or removed by rubbing (ldquoslippingrdquo fur) it will be very difficult or impossible to produce a study skin or mounted specimen The most usual types of specimens (based on Nagorsen and Peterson 1980) are 1) entire fluid-preserved animals (for studying anatomy and histology fluid preservation may change the fur colour) 2) study skins with accompanying skulls partial skeletons (some bones remain in the skin) for studying pelage colour hair quality and moulting patterns 3) mounted skins with accompanying partial or entire skeleton (some bones may remain in the skin dependant on the method of preservation) or freeze-dried specimens 4) entire skeletons for instance for studying anatomy geographic variation or for age determination (entire skeletons are poorly represented in collections so Nagorsen and Peterson (1980) recommend preparation of at least one male and one female skeleton per species

96

Preservation of specimens in the field Formalin preservation Preservation in alcohol Preservation by cooling or freezing

97

Formalin preservation After weighing and measuring the animal and attaching an

adequate label very small specimens (up to 100 g) can be fixed whole by submerging them in 10 buffered formalin (tissue - formalin solution ratio of at least 1 12) the body cavity can be filled with formalin solution by injection until it is turgid and firm some formalin may also be injected under the skin into the body cavity larger muscles and organs If hypodermic needles are not available the body cavity can be opened ventrally by making a slit instead allowing the formalin to enter

Keeping the mouth open with a piece of wood or cotton may later allow examination of teeth Then the whole body can be immersed in formalin in the posture in which it is supposed to stay permanently because it will harden The ratio of formalin to carcass must be at least 12 to 1 to assure a good fixation Tissues can be left in buffered neutralized formalin for several months but formalin hardens specimens therefore after fixation longterm storage in alcohol may be better After preservation the carcass should therefore be washed in water and transferred into ethanol for permanent storage

Disadvantages for instance it discolours the fur after a longish immersion softens the bones and prevents further examination for microbiology

98

Preservation in alcohol

After weighing a whole animal can be preserved in a container of alcohol (70-90) Removal of the intestine prior to storage of the animal in alcohol is recommended

99

Preservation by cooling or freezing Removal of the skin with insulating fur

before cooling or freezing may help to cool the carcass down more quickly

Freezing is not recommended if histological examination is planned

100

THANK YOU

18

TYPES OF SAMPLING

1048698 Systematic 1048698 Stratified 1048698 Random

19

SYSTEMATIC SAMPLING

1048698 Often used when the area being studied is varied not very large or

when time is available 1048698 Samples are taken at fixed intervals

20

How to sample systematicallySystematic samples are usually taken along a transect line marked by a tape measure

1048698 Transect- a line laid across an area

21

Sampling along gradients

Transects are setup along aenvironmentalgradientsndash down a hillsidendash across a streambedndash out from a source ofpollution

22

Types of transect sampling 1048698 Line transect 1048698 Belt transect

23

Line transect methodA measured line is laidacross the area in thedirection of theenvironmental gradientndash The species touching theline can be recordedalong the whole length ofthe line (continuoussampling) or at specificpoints along the line(systematic sampling)

24

Line Transect- useful where a transition of flora andor fauna

occurs- a string or tape is stretched out along the

ground in a straight line record the organisms touching or covering

the line all along its length or at regular intervals

- Profile transect when there is appreciable height change along the transect and thus affecting the distribution of its species

25

Belt transect method

Similar to line transect butwidens the sampling areandash Transect line is laid outndash Samples are taken bydetermining abundance or cover in an area that is adefined distance from the linendash Samples can be taken all

theway along the line at specificintervals or even randomly

26

Belt TransectIt is a strip usually a metre wide marked by putting a

second line parallel to the other The species between the lines are carefully recorded working a metre at a time

Alternatively a frame quadrat in conjunction with a single line transect could be used

Using a quadrat along a belt transect eg ladder transect (every 5m)

27

Point Frames- for grassland field study of dense vegetation

28

STRATIFIED SAMPLING1048698 Often used whenthere are smallareas within alarger habitat thatare clearly different1048698 Strata- majordifferences withincommunitiesrecognized beforesampling begins

29

RANDOM SAMPLING

1048698 Often used when the area being studied isfairly uniform very large or when there is alimited amount of time available1048698 Random = chosen by chance rather thanaccording to a plan all outcomes are

equallylikely1048698 Samples are taken from different positionswithin a habitat and those positions arechosen randomly

30

How to sample randomly

Choose individuals or Placeldquosampling unitsrdquo

haphazardlyndash This is rarely completely

random1048698 ORhellip1048698 Assign numbers to the

areasor individuals to be sampledndash Use a random number

table toselect which areas or

individualswill be sample

31

Population Attributes Density ndash size of a population in relation to a definite

unit of space Affected by

Natality ndash the reproductive output (birth rate) of a population

Mortality ndash the death rate of organisms in a population

Immigration ndash number of organisms moving into the area occupied by the population

Emigration ndash number of organisms moving out of the area occupied by the population

32

Population Density

Four primary population parameters

33

Two Types of Density Estimates

bull Absolute Density ndash a known density such as m2

bull Relative Density ndash we know when one area has more individuals than another

34

Measuring Absolute Density

Total Count ndash count the number of organisms living in an area Human census number of oak trees in a

wooded lot number of singing birds in an area

Total counts generally are not used very often

Sampling Methods ndash use a sample to estimate population size Either use the quadrat or capture-

recapture method

35

Measurement of Environmental ParametersAbiotic factors are important in determining

both the distribution of the organisms and their physical and physiological adaptations

Temperature- diurnal and seasonal temperature variations

are significant in affecting different species of plants and animals

- equipment mercury thermometer maximum-minimum thermometer

miniaturized thermistor

36

pH

-measure pH of a solution by universal indicator pH paper pH meter etc

Light

-measure its duration and intensity duration by predication from Royal Observatory intensity by photographic light meter

pH meter in use

37

Humidity

Relative humidity the water content of a given volume of air relative to the same volume of fully saturated air

- equipment whirling hygrometer

38

Wind and Water Speed- wind speed- anemometer or wind

gauges- water speed - time the movement of a

floating object over a measured distance

39

Salinity

- using a conductivity meter greater salinity has greater conductivity

Oxygen Level

- using an oxygen meter or chemical method (Winkler method)

40

Collecting MethodsCollecting all organisms within a habitat is normally

impractical and therefore small areas are selected Remember to return all material to its original position

after searching amp collecting sufficient specimens Some collecting apparatus for general use are listed

below

41

1 specimen tube

2 screwed-topped jars

3 polythene bags

4 forceps

5 paint brush

6 bulb pipette

7 pooter

42

8 widger 9 sieve 10 hand lens

11 enamel dish 12 beating tray 13 light traps

14 Tullgren funnel 15 Baermann funnel 16 mammal traps

17 pitfall traps 18 netting

43

Estimating Population Size

The exact methods used for estimation depend not only the nature of the habitat but also on the organisms involved

eg animals - population

plants - percentage cover

44

Using Quadrats

- By sampling an area using quadrats and counting the number of individuals within each quadrat it is possible to estimate the total number of individuals within the area

- confined to plants and sessile or very slow-moving animals

- fast-moving animals are disturbed and run away

45

Capture-recapture Techniques- useful for mobile animals which can be marked

- capture marked released randomly recaptured

and marked individuals recorded

no of marked individuals recaptured total no of individuals in 1st sample

-------------------------------------------- = ------------------------------------------

total no of individuals in 2nd sample estimated size of population

(the Lincoln Index)

46

Capture-recapture Techniques Factors affecting the accuracy of the estimation

deaths migration individuals become more liable to predation etc

Examples

- arthropods marked on their backs with non-toxic paint

- fish have tags attached to opercula - mammals have tags clipped to their ears

birds have their legs ringed

47

Capture-recapture Method Important tool for estimating density birth

rate and death rate for mobile animals Method

Collect a sample of individuals mark them and then release them

After a period collect more individuals from the wild and count the number that have marks

We assume that a sample if random will contain the same proportion of marked individuals as the population does

Estimate population density

48

Assumptions For All Capture-Recapture Studies Marking technique does not increase

mortality of marked animals Marked individuals are allowed to mix

with population Marking technique does not affect catch

probability Marks are not lost or overlooked No significant immigration or emigration No significant mortality or natality

49

Marked animals in second sample

Total caught in second sample

Marked animals in first sample

Total population size

=

520 N

16=

Peterson Method or Lincoln Index

N = 64N = (20)(16)5

50

Some Indices Used

Traps Number of Fecal

Pellets Vocalization

Frequency Pelt Records Catch per Unit

Fishing Effort

Number of Artifacts Questionnaires Cover Feeding Capacity Roadside Counts

51

Abundance Scales

The population size may be fairly accurately determined by making some form of frequency assessment

These are subjective and involve an experimenter making some estimate of the number of individuals in a given area or the cover of a particular species

This is especially useful where individuals are very numerous eg barnacles on a rocky shore or where it is difficult to distinguish individuals eg grass plants in a meadow

52

The assessments are usually made on an abundance scale of 5 categories

Abundance Common Frequent Occasional Rare

Barnacles exposed at low water

53

Environmental resistance are the factors which limit the growth of a particular population

eg predation disease availability of light food water oxygen and shelter the accumulation of toxic wastes and even the size of the population itself

54

Density-dependent Growth A population is a density-dependent when its size

(or density) affects its growth rate because of density-dependent factors such as food availability and toxic waste accumulation

Density-independent Growth In this type of growth a population increases until

some factor causes a sudden reduction in its size Its effect is the same regardless of the size of the

population eg temperature fires floods storms etc

55

Regulation of Population Size Fecundity is the reproductive capacity of individual

females of a species Birth rate or natality is used to measure fecundity Death rate or mortality is the number of individuals

of a species which die per unit time Immigration occurs when individuals join a

population from neighbouring ones Emigration occurs when individuals depart from a

population A cycle occurs when the size of a population

fluctuates on a regular basis

56

Ecological Sampling

57

Why Do We Sample Determine presence andor

abundance

Monitor population fluctuations

Assess lsquoecological damagersquo

Assess quality of habitat

Assess population responses

58

What Do We Sample

Physical Environment Temperature DO pH salinity clarity

flow sediment

Biotic Environment All living things

59

Physical Habitat Temperature

Mercury thermometer Electronic thermometer Long-term thermometers

Dissolved Oxygen Winkler method (titration) DO meter (electrode)

pH Litmus paper pH meter (electrode)

Salinity Salinity Meter YSI 550A DO Meter w12 cable

60

Water Clarity Secchi Disk

Disk is attached to a calibrated rope The disk is lowered into the water until the white parts can no longer be seen Secchi disk depth is then recorded and serves as the waters transparency index The clearer the water the greater the secchi disk depth

Secchi Disk

61

Current Velocity (flow) Floating-orange method

Put an orange (or something else that floats just below the water surface) and measure the time it takes it to float across a known distance

Odometer-type flow meter Number of revolutions the propeller

makes for a given time is calibrated to flow velocity

62

Sediment Sediment size is important to many

aquatic organisms Sieversquos are used to separate and

grade sediment samples Percent of each size grade can be

determined

63

Water Sample

Water and plankton from various depths can be collected

A trigger mechanism is used to close the sampler Sample is then brought back to the

surface

64

Small Mammals

Mouserat Traps Fatal

Pit Falls Bucket is placed in the ground Sometimes have lsquoleadsrsquo to the buckets

Live traps Havahart Sherman

Spot-light

Sherman trapHavahart trap

65

Birds Stick-under-the-box method Bird-trap

Works like a minnow trap Mist net

Captures birds in flight Rocket net

Uses a propellant to throw a net over birds

66

Terrestrial Insects

Sticky paper flies

Baited Traps Fire ants

Nets butterflies

Foggers Collect insects from tree canopies

67

Aquatic Insects Drift Net

Place net in flowing water Kick Net

lsquoKickrsquo sediment upstream from block net and the flow will wash them into the net

Wash bucket Serber or Hess Sampler

Stir up known area of sediment

Animals are collected by a catch net

Multi-plate Sampler Become colonized

68

Crawfish and Crab Traps

69

Fish Larvae Light Traps

Larvae are attracted to the light Ichthyoplankton nets

Can be towed at various depths Fish collect at the lsquocodrsquoend

70

Fish Lift net

Net is placed down and after a set amount of time it is quickly lifted

Pop-net Similar to a lift net but

floats are attached to a framed net

Operated by a trigger mechanism

Throw net A net attached to a heavy

frame is thrown and every thing inside is netted out Throw net

Pop-net

Lift net

71

Minnow trap

Usually use bait to attract small fish Light is used sometimes as an attractant

72

Fish Electrofishing

Electricity is put into the water Fish are temporarily stunned and usually

swim towards the electricity source Usually non-fatal but may cause some

damage

73

Fish Gill Net

Gill nets resemble tennis nets Fish can not swim completely through the

net and get caught Gill nets are size selective (based on mesh

size) Square Mesh

Bar mesh

Stretch mesh

74

Fish Trammel Net

Three panels two large mesh on the outside and a small mesh on the inside

Fish swim through the outer mesh pushes the small mesh through the other side and becomes entangled

75

Hoop nets (and other similar nets) can have bait or not

Fyke nets have leads to help guide fish to the net

76

Seine Seines are nets that are pulled

through shallow water to catch fish

77

Purse Seine Used to encircle entire schools of fish

Usually involves a spotter plane and a second boat

78

Trotline (longline) A series of baited drop lines

connected to a main line

Can be deployed by tying one end to the bank and tying the other end with a heavy weight

79

Shrimp (or fish) Trawl Net pulled behind

a boat along the bottom Either a beam or

otter boards keep the net open

80

Tagging Individuals Coded Wire Tags

Microwire that has a unique label

Magnetic wand detects the tag

Tag retention should be determined

T-Bar tags Can be individually

numbered External tag

PIT tags (Passive Integrated Transponders) Wand induces the tag to

transmit individual number is displayed

81

Other Tagging Methods

Toe clip Amphibian and reptile Clip of one or more toes

to identify individuals

Bird Band Place a metal band on a

bird leg Generally has

identification information

82

Preserving plant specimens Pressing and drying Long-term

preservation and storage

Alternative drying techniques

Special preservation and processing techniques

Mounting

83

Pressing and drying Techniques for pressing and drying specimens have been

established for many years There are minor variations in recommended methods but they are essentially the same worldwide

The best specimens are plants that are pressed as soon as possible after collection before wilting and shrivelling Most plants may be kept in sealed containers such as plastic bags for up to a day if it is inconvenient to press immediately However some plants show such rapid wilting particularly of the flowers that such delays are best avoided Flowers with a lot of nectar may go mouldy very quickly if excess nectar is not shaken off before pressing

Specimens are pressed flat and dried between sheets of absorbent blotters or semi-absorbent paper such as newspaper Papers with a glossy surface should be avoided because they are not absorbent enough to aid drying The plant should be carefully laid out between the drying sheets as their form at this stage largely determines their ultimate appearance The flowers should be spread out with the petals carefully arranged wilted leaves should be straightened and unnecessary shoots of excessively twiggy shrubs may be cut away

84

Microwave ovens Small numbers of specimens can be dried using a microwave

oven The technique recommended in the literature is to place the specimens between unprinted absorbent paper for example butchers paper not newspaper which is unsuitable because the chemicals present in the ink may cause a fire The specimens should be put in a special press which should be of a microwave-safe material (wood acrylic or polycarbonate sheeting eg plexiglass or perspex NO metal components) If such a press is not available sheets of cardboard can be placed above and below the specimens and then weighted down

Drying time depends on the power of your oven In most cases drying is accomplished by irradiating at maximum power for 1-2 minutes per specimen although it is often a case of trial and error It is best to process no more than 10-12 specimens of average thickness per batch Specimens are usually dried after the moisture that characteristically appears on the glass door has disappeared If the specimen is damp when taken out of the oven allow it to stand before re-radiating as moisture continues to evaporate from the specimen for some time Care must be taken not to irradiate the specimens for too long

It should be noted that microwave treatment damages seeds and the cellular structure of the plants which may reduce the long-term value of the specimens

85

Alternative drying techniquesSilica gelother desiccants amp freeze drying Alternative methods of drying plant specimens have been

used for some time but are mostly restricted to special purpose collections The main alternatives are freeze-drying and drying in a desiccant powder such as desiccant silica gel In general these techniques are used where it is essential to preserve the shape of a delicate plant of organ of the plant such as the flower Freeze-drying has also been used to preserve the chemical composition of a plant as accurately as possible for later study

Disadvantages and special conservation problems of specimens dried in these manners are that they are particularly susceptible to damage The dried parts are fragile lack support and often catch on packing materials They must therefore be packed especially carefully and stored in small boxes or tubes with some appropriate packing material that does not snag and break small projections Acid-free tissue paper is often used Drying in desiccant silica gel crystals or powder can also have the disadvantage that it is difficult to remove all traces of the silica gel after drying

86

Special preservation and processing techniquesWet or spirit collections

Very fleshy or delicate structures including small algae and orchid flowers are best preserved in an air-tight glass or plastic jar with a liquid preservative rather than by drying The type of preservative used should be clearly labelled in the jar Such material is often referred to as a spirit collection or wet collection

Most material can be satisfactorily preserved in 70 ethyl alcohol (or 70 methylated spirit or denatured alcohol) with 30 water Colours will fade quickly in spirit however so it is a good idea to keep comprehensive notes and photographs

87

Small algae Microscopic algae are often collected in a jar and in the

water in which they were found If the algae are to be stored for more than 2-3 days a preservative needs to be used Traditionally this has been the extremely toxic formalin - a small amount can be added to the water to make a 5 final solution and the container labelled This must not be sent through the post or by courier

There are some other equally toxic options for example propylene phenoxytol but none should be sent through the post A safer option is to add sufficient concentrated alcohol or methylated spirits to the water containing the algae to make a final solution of 70 alcohol This treatment dilutes the algae making them difficult to find so if they can be concentrated somehow first (eg by filtering) they can be stored in much less liquid Another option is to fix the algae in formalin (or something similar) first and then prepare a microscope glass slide with a permanent water-soluble mounting medium

88

Mounting Mounting specimens prevents most fragile material from

fragmenting and prevents specimens becoming separated from their labels If the plant collection is a long-term project specimens should be mounted on sheets of archival (permanent) cardboard or paper with archival-quality fixing media These include stitching with cotton thread dental floss nickel-plated copper wire (for heavier specimens) narrow strips of archival paper linen tape or by using an archival adhesive such as methyl cellulose adhesive

One disadvantage of mounting specimens is that it can make parts of the specimen inaccessible for examination so it is essential that this be borne in mind during specimen arrangement and mounting For example easily reversible mounting media should be used specimens should be strapped to the sheet rather than glued all over and the specimen should be carefully arranged before it is attached so that it shows all features

89

Full-size herbarium mounting sheets are usually about 43 cm long x 28 cm wide The plant name and accompanying field notes should be transcribed on a permanent label stuck to one corner of the herbarium sheet (the bottom right-hand corner being the most common) or sometimes annotations may be written directly on the sheet or card

Small pieces of material which may have become separated from the specimen (eg seeds) can be placed in small plastic bags and pinned to the sheet

90

Long-term preservation and storage The long-term preservation of dry plant

specimens is largely dependent on protection from insect attack Specimens collected by Linnaeus in the eighteenth century and by Banks and Solander on the Endeavour voyage in 1788 are still excellently preserved

91

Pests and their control A range of pests attack dried plant material The

most common pests are insects and fungi though rodents and other large animals can cause damage in poor storage conditions Insects eat the material the paper surrounding the material and the adhesives and mounting media

Such insect pests range from psocids (book lice) which attack mainly the softer parts such as flowers and soft fruits to tobacco beetles and carpet beetles which can bore holes through the toughest of specimens Many insects are particularly sensitive to relative humidity levels and do not thrive at levels below 50

92

The most common and acceptable specimen treatments for insect control are Freezing Microwave Poisoning Insect deterrents Fungal pests

93

Storage

Dried and pressed plant specimens can be stored in cardboard or plastic boxes or tied in bundles in light-weight cardboard folders placed in pigeon holes

Alternatively they can be placed in protective plastic jackets and displayed in ring folders which is recommended if they are to be frequently handled such as for a reference collection

94

Filing

Specimens should be filed in a systematic order if a relatively permanent collection is being made The major groups ie ferns and fern allies cycads conifers dicotyledons and monocotyledons are best kept separately or according to some classification scheme such as that given in a flora or handbook

Similarly the genera within each family and the species within each genus may be filed alphabetically or following some such classification

95

Preservation of entire animals

Types of collection specimens of an entire animal For reference collections mammals can be prepared as a variety of specimens The condition of the specimen may determine possible ways to preserve it if for instance decomposition of the skin has loosened the hair of a carcass so much that it can easily be pulled out or removed by rubbing (ldquoslippingrdquo fur) it will be very difficult or impossible to produce a study skin or mounted specimen The most usual types of specimens (based on Nagorsen and Peterson 1980) are 1) entire fluid-preserved animals (for studying anatomy and histology fluid preservation may change the fur colour) 2) study skins with accompanying skulls partial skeletons (some bones remain in the skin) for studying pelage colour hair quality and moulting patterns 3) mounted skins with accompanying partial or entire skeleton (some bones may remain in the skin dependant on the method of preservation) or freeze-dried specimens 4) entire skeletons for instance for studying anatomy geographic variation or for age determination (entire skeletons are poorly represented in collections so Nagorsen and Peterson (1980) recommend preparation of at least one male and one female skeleton per species

96

Preservation of specimens in the field Formalin preservation Preservation in alcohol Preservation by cooling or freezing

97

Formalin preservation After weighing and measuring the animal and attaching an

adequate label very small specimens (up to 100 g) can be fixed whole by submerging them in 10 buffered formalin (tissue - formalin solution ratio of at least 1 12) the body cavity can be filled with formalin solution by injection until it is turgid and firm some formalin may also be injected under the skin into the body cavity larger muscles and organs If hypodermic needles are not available the body cavity can be opened ventrally by making a slit instead allowing the formalin to enter

Keeping the mouth open with a piece of wood or cotton may later allow examination of teeth Then the whole body can be immersed in formalin in the posture in which it is supposed to stay permanently because it will harden The ratio of formalin to carcass must be at least 12 to 1 to assure a good fixation Tissues can be left in buffered neutralized formalin for several months but formalin hardens specimens therefore after fixation longterm storage in alcohol may be better After preservation the carcass should therefore be washed in water and transferred into ethanol for permanent storage

Disadvantages for instance it discolours the fur after a longish immersion softens the bones and prevents further examination for microbiology

98

Preservation in alcohol

After weighing a whole animal can be preserved in a container of alcohol (70-90) Removal of the intestine prior to storage of the animal in alcohol is recommended

99

Preservation by cooling or freezing Removal of the skin with insulating fur

before cooling or freezing may help to cool the carcass down more quickly

Freezing is not recommended if histological examination is planned

100

THANK YOU

19

SYSTEMATIC SAMPLING

1048698 Often used when the area being studied is varied not very large or

when time is available 1048698 Samples are taken at fixed intervals

20

How to sample systematicallySystematic samples are usually taken along a transect line marked by a tape measure

1048698 Transect- a line laid across an area

21

Sampling along gradients

Transects are setup along aenvironmentalgradientsndash down a hillsidendash across a streambedndash out from a source ofpollution

22

Types of transect sampling 1048698 Line transect 1048698 Belt transect

23

Line transect methodA measured line is laidacross the area in thedirection of theenvironmental gradientndash The species touching theline can be recordedalong the whole length ofthe line (continuoussampling) or at specificpoints along the line(systematic sampling)

24

Line Transect- useful where a transition of flora andor fauna

occurs- a string or tape is stretched out along the

ground in a straight line record the organisms touching or covering

the line all along its length or at regular intervals

- Profile transect when there is appreciable height change along the transect and thus affecting the distribution of its species

25

Belt transect method

Similar to line transect butwidens the sampling areandash Transect line is laid outndash Samples are taken bydetermining abundance or cover in an area that is adefined distance from the linendash Samples can be taken all

theway along the line at specificintervals or even randomly

26

Belt TransectIt is a strip usually a metre wide marked by putting a

second line parallel to the other The species between the lines are carefully recorded working a metre at a time

Alternatively a frame quadrat in conjunction with a single line transect could be used

Using a quadrat along a belt transect eg ladder transect (every 5m)

27

Point Frames- for grassland field study of dense vegetation

28

STRATIFIED SAMPLING1048698 Often used whenthere are smallareas within alarger habitat thatare clearly different1048698 Strata- majordifferences withincommunitiesrecognized beforesampling begins

29

RANDOM SAMPLING

1048698 Often used when the area being studied isfairly uniform very large or when there is alimited amount of time available1048698 Random = chosen by chance rather thanaccording to a plan all outcomes are

equallylikely1048698 Samples are taken from different positionswithin a habitat and those positions arechosen randomly

30

How to sample randomly

Choose individuals or Placeldquosampling unitsrdquo

haphazardlyndash This is rarely completely

random1048698 ORhellip1048698 Assign numbers to the

areasor individuals to be sampledndash Use a random number

table toselect which areas or

individualswill be sample

31

Population Attributes Density ndash size of a population in relation to a definite

unit of space Affected by

Natality ndash the reproductive output (birth rate) of a population

Mortality ndash the death rate of organisms in a population

Immigration ndash number of organisms moving into the area occupied by the population

Emigration ndash number of organisms moving out of the area occupied by the population

32

Population Density

Four primary population parameters

33

Two Types of Density Estimates

bull Absolute Density ndash a known density such as m2

bull Relative Density ndash we know when one area has more individuals than another

34

Measuring Absolute Density

Total Count ndash count the number of organisms living in an area Human census number of oak trees in a

wooded lot number of singing birds in an area

Total counts generally are not used very often

Sampling Methods ndash use a sample to estimate population size Either use the quadrat or capture-

recapture method

35

Measurement of Environmental ParametersAbiotic factors are important in determining

both the distribution of the organisms and their physical and physiological adaptations

Temperature- diurnal and seasonal temperature variations

are significant in affecting different species of plants and animals

- equipment mercury thermometer maximum-minimum thermometer

miniaturized thermistor

36

pH

-measure pH of a solution by universal indicator pH paper pH meter etc

Light

-measure its duration and intensity duration by predication from Royal Observatory intensity by photographic light meter

pH meter in use

37

Humidity

Relative humidity the water content of a given volume of air relative to the same volume of fully saturated air

- equipment whirling hygrometer

38

Wind and Water Speed- wind speed- anemometer or wind

gauges- water speed - time the movement of a

floating object over a measured distance

39

Salinity

- using a conductivity meter greater salinity has greater conductivity

Oxygen Level

- using an oxygen meter or chemical method (Winkler method)

40

Collecting MethodsCollecting all organisms within a habitat is normally

impractical and therefore small areas are selected Remember to return all material to its original position

after searching amp collecting sufficient specimens Some collecting apparatus for general use are listed

below

41

1 specimen tube

2 screwed-topped jars

3 polythene bags

4 forceps

5 paint brush

6 bulb pipette

7 pooter

42

8 widger 9 sieve 10 hand lens

11 enamel dish 12 beating tray 13 light traps

14 Tullgren funnel 15 Baermann funnel 16 mammal traps

17 pitfall traps 18 netting

43

Estimating Population Size

The exact methods used for estimation depend not only the nature of the habitat but also on the organisms involved

eg animals - population

plants - percentage cover

44

Using Quadrats

- By sampling an area using quadrats and counting the number of individuals within each quadrat it is possible to estimate the total number of individuals within the area

- confined to plants and sessile or very slow-moving animals

- fast-moving animals are disturbed and run away

45

Capture-recapture Techniques- useful for mobile animals which can be marked

- capture marked released randomly recaptured

and marked individuals recorded

no of marked individuals recaptured total no of individuals in 1st sample

-------------------------------------------- = ------------------------------------------

total no of individuals in 2nd sample estimated size of population

(the Lincoln Index)

46

Capture-recapture Techniques Factors affecting the accuracy of the estimation

deaths migration individuals become more liable to predation etc

Examples

- arthropods marked on their backs with non-toxic paint

- fish have tags attached to opercula - mammals have tags clipped to their ears

birds have their legs ringed

47

Capture-recapture Method Important tool for estimating density birth

rate and death rate for mobile animals Method

Collect a sample of individuals mark them and then release them

After a period collect more individuals from the wild and count the number that have marks

We assume that a sample if random will contain the same proportion of marked individuals as the population does

Estimate population density

48

Assumptions For All Capture-Recapture Studies Marking technique does not increase

mortality of marked animals Marked individuals are allowed to mix

with population Marking technique does not affect catch

probability Marks are not lost or overlooked No significant immigration or emigration No significant mortality or natality

49

Marked animals in second sample

Total caught in second sample

Marked animals in first sample

Total population size

=

520 N

16=

Peterson Method or Lincoln Index

N = 64N = (20)(16)5

50

Some Indices Used

Traps Number of Fecal

Pellets Vocalization

Frequency Pelt Records Catch per Unit

Fishing Effort

Number of Artifacts Questionnaires Cover Feeding Capacity Roadside Counts

51

Abundance Scales

The population size may be fairly accurately determined by making some form of frequency assessment

These are subjective and involve an experimenter making some estimate of the number of individuals in a given area or the cover of a particular species

This is especially useful where individuals are very numerous eg barnacles on a rocky shore or where it is difficult to distinguish individuals eg grass plants in a meadow

52

The assessments are usually made on an abundance scale of 5 categories

Abundance Common Frequent Occasional Rare

Barnacles exposed at low water

53

Environmental resistance are the factors which limit the growth of a particular population

eg predation disease availability of light food water oxygen and shelter the accumulation of toxic wastes and even the size of the population itself

54

Density-dependent Growth A population is a density-dependent when its size

(or density) affects its growth rate because of density-dependent factors such as food availability and toxic waste accumulation

Density-independent Growth In this type of growth a population increases until

some factor causes a sudden reduction in its size Its effect is the same regardless of the size of the

population eg temperature fires floods storms etc

55

Regulation of Population Size Fecundity is the reproductive capacity of individual

females of a species Birth rate or natality is used to measure fecundity Death rate or mortality is the number of individuals

of a species which die per unit time Immigration occurs when individuals join a

population from neighbouring ones Emigration occurs when individuals depart from a

population A cycle occurs when the size of a population

fluctuates on a regular basis

56

Ecological Sampling

57

Why Do We Sample Determine presence andor

abundance

Monitor population fluctuations

Assess lsquoecological damagersquo

Assess quality of habitat

Assess population responses

58

What Do We Sample

Physical Environment Temperature DO pH salinity clarity

flow sediment

Biotic Environment All living things

59

Physical Habitat Temperature

Mercury thermometer Electronic thermometer Long-term thermometers

Dissolved Oxygen Winkler method (titration) DO meter (electrode)

pH Litmus paper pH meter (electrode)

Salinity Salinity Meter YSI 550A DO Meter w12 cable

60

Water Clarity Secchi Disk

Disk is attached to a calibrated rope The disk is lowered into the water until the white parts can no longer be seen Secchi disk depth is then recorded and serves as the waters transparency index The clearer the water the greater the secchi disk depth

Secchi Disk

61

Current Velocity (flow) Floating-orange method

Put an orange (or something else that floats just below the water surface) and measure the time it takes it to float across a known distance

Odometer-type flow meter Number of revolutions the propeller

makes for a given time is calibrated to flow velocity

62

Sediment Sediment size is important to many

aquatic organisms Sieversquos are used to separate and

grade sediment samples Percent of each size grade can be

determined

63

Water Sample

Water and plankton from various depths can be collected

A trigger mechanism is used to close the sampler Sample is then brought back to the

surface

64

Small Mammals

Mouserat Traps Fatal

Pit Falls Bucket is placed in the ground Sometimes have lsquoleadsrsquo to the buckets

Live traps Havahart Sherman

Spot-light

Sherman trapHavahart trap

65

Birds Stick-under-the-box method Bird-trap

Works like a minnow trap Mist net

Captures birds in flight Rocket net

Uses a propellant to throw a net over birds

66

Terrestrial Insects

Sticky paper flies

Baited Traps Fire ants

Nets butterflies

Foggers Collect insects from tree canopies

67

Aquatic Insects Drift Net

Place net in flowing water Kick Net

lsquoKickrsquo sediment upstream from block net and the flow will wash them into the net

Wash bucket Serber or Hess Sampler

Stir up known area of sediment

Animals are collected by a catch net

Multi-plate Sampler Become colonized

68

Crawfish and Crab Traps

69

Fish Larvae Light Traps

Larvae are attracted to the light Ichthyoplankton nets

Can be towed at various depths Fish collect at the lsquocodrsquoend

70

Fish Lift net

Net is placed down and after a set amount of time it is quickly lifted

Pop-net Similar to a lift net but

floats are attached to a framed net

Operated by a trigger mechanism

Throw net A net attached to a heavy

frame is thrown and every thing inside is netted out Throw net

Pop-net

Lift net

71

Minnow trap

Usually use bait to attract small fish Light is used sometimes as an attractant

72

Fish Electrofishing

Electricity is put into the water Fish are temporarily stunned and usually

swim towards the electricity source Usually non-fatal but may cause some

damage

73

Fish Gill Net

Gill nets resemble tennis nets Fish can not swim completely through the

net and get caught Gill nets are size selective (based on mesh

size) Square Mesh

Bar mesh

Stretch mesh

74

Fish Trammel Net

Three panels two large mesh on the outside and a small mesh on the inside

Fish swim through the outer mesh pushes the small mesh through the other side and becomes entangled

75

Hoop nets (and other similar nets) can have bait or not

Fyke nets have leads to help guide fish to the net

76

Seine Seines are nets that are pulled

through shallow water to catch fish

77

Purse Seine Used to encircle entire schools of fish

Usually involves a spotter plane and a second boat

78

Trotline (longline) A series of baited drop lines

connected to a main line

Can be deployed by tying one end to the bank and tying the other end with a heavy weight

79

Shrimp (or fish) Trawl Net pulled behind

a boat along the bottom Either a beam or

otter boards keep the net open

80

Tagging Individuals Coded Wire Tags

Microwire that has a unique label

Magnetic wand detects the tag

Tag retention should be determined

T-Bar tags Can be individually

numbered External tag

PIT tags (Passive Integrated Transponders) Wand induces the tag to

transmit individual number is displayed

81

Other Tagging Methods

Toe clip Amphibian and reptile Clip of one or more toes

to identify individuals

Bird Band Place a metal band on a

bird leg Generally has

identification information

82

Preserving plant specimens Pressing and drying Long-term

preservation and storage

Alternative drying techniques

Special preservation and processing techniques

Mounting

83

Pressing and drying Techniques for pressing and drying specimens have been

established for many years There are minor variations in recommended methods but they are essentially the same worldwide

The best specimens are plants that are pressed as soon as possible after collection before wilting and shrivelling Most plants may be kept in sealed containers such as plastic bags for up to a day if it is inconvenient to press immediately However some plants show such rapid wilting particularly of the flowers that such delays are best avoided Flowers with a lot of nectar may go mouldy very quickly if excess nectar is not shaken off before pressing

Specimens are pressed flat and dried between sheets of absorbent blotters or semi-absorbent paper such as newspaper Papers with a glossy surface should be avoided because they are not absorbent enough to aid drying The plant should be carefully laid out between the drying sheets as their form at this stage largely determines their ultimate appearance The flowers should be spread out with the petals carefully arranged wilted leaves should be straightened and unnecessary shoots of excessively twiggy shrubs may be cut away

84

Microwave ovens Small numbers of specimens can be dried using a microwave

oven The technique recommended in the literature is to place the specimens between unprinted absorbent paper for example butchers paper not newspaper which is unsuitable because the chemicals present in the ink may cause a fire The specimens should be put in a special press which should be of a microwave-safe material (wood acrylic or polycarbonate sheeting eg plexiglass or perspex NO metal components) If such a press is not available sheets of cardboard can be placed above and below the specimens and then weighted down

Drying time depends on the power of your oven In most cases drying is accomplished by irradiating at maximum power for 1-2 minutes per specimen although it is often a case of trial and error It is best to process no more than 10-12 specimens of average thickness per batch Specimens are usually dried after the moisture that characteristically appears on the glass door has disappeared If the specimen is damp when taken out of the oven allow it to stand before re-radiating as moisture continues to evaporate from the specimen for some time Care must be taken not to irradiate the specimens for too long

It should be noted that microwave treatment damages seeds and the cellular structure of the plants which may reduce the long-term value of the specimens

85

Alternative drying techniquesSilica gelother desiccants amp freeze drying Alternative methods of drying plant specimens have been

used for some time but are mostly restricted to special purpose collections The main alternatives are freeze-drying and drying in a desiccant powder such as desiccant silica gel In general these techniques are used where it is essential to preserve the shape of a delicate plant of organ of the plant such as the flower Freeze-drying has also been used to preserve the chemical composition of a plant as accurately as possible for later study

Disadvantages and special conservation problems of specimens dried in these manners are that they are particularly susceptible to damage The dried parts are fragile lack support and often catch on packing materials They must therefore be packed especially carefully and stored in small boxes or tubes with some appropriate packing material that does not snag and break small projections Acid-free tissue paper is often used Drying in desiccant silica gel crystals or powder can also have the disadvantage that it is difficult to remove all traces of the silica gel after drying

86

Special preservation and processing techniquesWet or spirit collections

Very fleshy or delicate structures including small algae and orchid flowers are best preserved in an air-tight glass or plastic jar with a liquid preservative rather than by drying The type of preservative used should be clearly labelled in the jar Such material is often referred to as a spirit collection or wet collection

Most material can be satisfactorily preserved in 70 ethyl alcohol (or 70 methylated spirit or denatured alcohol) with 30 water Colours will fade quickly in spirit however so it is a good idea to keep comprehensive notes and photographs

87

Small algae Microscopic algae are often collected in a jar and in the

water in which they were found If the algae are to be stored for more than 2-3 days a preservative needs to be used Traditionally this has been the extremely toxic formalin - a small amount can be added to the water to make a 5 final solution and the container labelled This must not be sent through the post or by courier

There are some other equally toxic options for example propylene phenoxytol but none should be sent through the post A safer option is to add sufficient concentrated alcohol or methylated spirits to the water containing the algae to make a final solution of 70 alcohol This treatment dilutes the algae making them difficult to find so if they can be concentrated somehow first (eg by filtering) they can be stored in much less liquid Another option is to fix the algae in formalin (or something similar) first and then prepare a microscope glass slide with a permanent water-soluble mounting medium

88

Mounting Mounting specimens prevents most fragile material from

fragmenting and prevents specimens becoming separated from their labels If the plant collection is a long-term project specimens should be mounted on sheets of archival (permanent) cardboard or paper with archival-quality fixing media These include stitching with cotton thread dental floss nickel-plated copper wire (for heavier specimens) narrow strips of archival paper linen tape or by using an archival adhesive such as methyl cellulose adhesive

One disadvantage of mounting specimens is that it can make parts of the specimen inaccessible for examination so it is essential that this be borne in mind during specimen arrangement and mounting For example easily reversible mounting media should be used specimens should be strapped to the sheet rather than glued all over and the specimen should be carefully arranged before it is attached so that it shows all features

89

Full-size herbarium mounting sheets are usually about 43 cm long x 28 cm wide The plant name and accompanying field notes should be transcribed on a permanent label stuck to one corner of the herbarium sheet (the bottom right-hand corner being the most common) or sometimes annotations may be written directly on the sheet or card

Small pieces of material which may have become separated from the specimen (eg seeds) can be placed in small plastic bags and pinned to the sheet

90

Long-term preservation and storage The long-term preservation of dry plant

specimens is largely dependent on protection from insect attack Specimens collected by Linnaeus in the eighteenth century and by Banks and Solander on the Endeavour voyage in 1788 are still excellently preserved

91

Pests and their control A range of pests attack dried plant material The

most common pests are insects and fungi though rodents and other large animals can cause damage in poor storage conditions Insects eat the material the paper surrounding the material and the adhesives and mounting media

Such insect pests range from psocids (book lice) which attack mainly the softer parts such as flowers and soft fruits to tobacco beetles and carpet beetles which can bore holes through the toughest of specimens Many insects are particularly sensitive to relative humidity levels and do not thrive at levels below 50

92

The most common and acceptable specimen treatments for insect control are Freezing Microwave Poisoning Insect deterrents Fungal pests

93

Storage

Dried and pressed plant specimens can be stored in cardboard or plastic boxes or tied in bundles in light-weight cardboard folders placed in pigeon holes

Alternatively they can be placed in protective plastic jackets and displayed in ring folders which is recommended if they are to be frequently handled such as for a reference collection

94

Filing

Specimens should be filed in a systematic order if a relatively permanent collection is being made The major groups ie ferns and fern allies cycads conifers dicotyledons and monocotyledons are best kept separately or according to some classification scheme such as that given in a flora or handbook

Similarly the genera within each family and the species within each genus may be filed alphabetically or following some such classification

95

Preservation of entire animals

Types of collection specimens of an entire animal For reference collections mammals can be prepared as a variety of specimens The condition of the specimen may determine possible ways to preserve it if for instance decomposition of the skin has loosened the hair of a carcass so much that it can easily be pulled out or removed by rubbing (ldquoslippingrdquo fur) it will be very difficult or impossible to produce a study skin or mounted specimen The most usual types of specimens (based on Nagorsen and Peterson 1980) are 1) entire fluid-preserved animals (for studying anatomy and histology fluid preservation may change the fur colour) 2) study skins with accompanying skulls partial skeletons (some bones remain in the skin) for studying pelage colour hair quality and moulting patterns 3) mounted skins with accompanying partial or entire skeleton (some bones may remain in the skin dependant on the method of preservation) or freeze-dried specimens 4) entire skeletons for instance for studying anatomy geographic variation or for age determination (entire skeletons are poorly represented in collections so Nagorsen and Peterson (1980) recommend preparation of at least one male and one female skeleton per species

96

Preservation of specimens in the field Formalin preservation Preservation in alcohol Preservation by cooling or freezing

97

Formalin preservation After weighing and measuring the animal and attaching an

adequate label very small specimens (up to 100 g) can be fixed whole by submerging them in 10 buffered formalin (tissue - formalin solution ratio of at least 1 12) the body cavity can be filled with formalin solution by injection until it is turgid and firm some formalin may also be injected under the skin into the body cavity larger muscles and organs If hypodermic needles are not available the body cavity can be opened ventrally by making a slit instead allowing the formalin to enter

Keeping the mouth open with a piece of wood or cotton may later allow examination of teeth Then the whole body can be immersed in formalin in the posture in which it is supposed to stay permanently because it will harden The ratio of formalin to carcass must be at least 12 to 1 to assure a good fixation Tissues can be left in buffered neutralized formalin for several months but formalin hardens specimens therefore after fixation longterm storage in alcohol may be better After preservation the carcass should therefore be washed in water and transferred into ethanol for permanent storage

Disadvantages for instance it discolours the fur after a longish immersion softens the bones and prevents further examination for microbiology

98

Preservation in alcohol

After weighing a whole animal can be preserved in a container of alcohol (70-90) Removal of the intestine prior to storage of the animal in alcohol is recommended

99

Preservation by cooling or freezing Removal of the skin with insulating fur

before cooling or freezing may help to cool the carcass down more quickly

Freezing is not recommended if histological examination is planned

100

THANK YOU

20

How to sample systematicallySystematic samples are usually taken along a transect line marked by a tape measure

1048698 Transect- a line laid across an area

21

Sampling along gradients

Transects are setup along aenvironmentalgradientsndash down a hillsidendash across a streambedndash out from a source ofpollution

22

Types of transect sampling 1048698 Line transect 1048698 Belt transect

23

Line transect methodA measured line is laidacross the area in thedirection of theenvironmental gradientndash The species touching theline can be recordedalong the whole length ofthe line (continuoussampling) or at specificpoints along the line(systematic sampling)

24

Line Transect- useful where a transition of flora andor fauna

occurs- a string or tape is stretched out along the

ground in a straight line record the organisms touching or covering

the line all along its length or at regular intervals

- Profile transect when there is appreciable height change along the transect and thus affecting the distribution of its species

25

Belt transect method

Similar to line transect butwidens the sampling areandash Transect line is laid outndash Samples are taken bydetermining abundance or cover in an area that is adefined distance from the linendash Samples can be taken all

theway along the line at specificintervals or even randomly

26

Belt TransectIt is a strip usually a metre wide marked by putting a

second line parallel to the other The species between the lines are carefully recorded working a metre at a time

Alternatively a frame quadrat in conjunction with a single line transect could be used

Using a quadrat along a belt transect eg ladder transect (every 5m)

27

Point Frames- for grassland field study of dense vegetation

28

STRATIFIED SAMPLING1048698 Often used whenthere are smallareas within alarger habitat thatare clearly different1048698 Strata- majordifferences withincommunitiesrecognized beforesampling begins

29

RANDOM SAMPLING

1048698 Often used when the area being studied isfairly uniform very large or when there is alimited amount of time available1048698 Random = chosen by chance rather thanaccording to a plan all outcomes are

equallylikely1048698 Samples are taken from different positionswithin a habitat and those positions arechosen randomly

30

How to sample randomly

Choose individuals or Placeldquosampling unitsrdquo

haphazardlyndash This is rarely completely

random1048698 ORhellip1048698 Assign numbers to the

areasor individuals to be sampledndash Use a random number

table toselect which areas or

individualswill be sample

31

Population Attributes Density ndash size of a population in relation to a definite

unit of space Affected by

Natality ndash the reproductive output (birth rate) of a population

Mortality ndash the death rate of organisms in a population

Immigration ndash number of organisms moving into the area occupied by the population

Emigration ndash number of organisms moving out of the area occupied by the population

32

Population Density

Four primary population parameters

33

Two Types of Density Estimates

bull Absolute Density ndash a known density such as m2

bull Relative Density ndash we know when one area has more individuals than another

34

Measuring Absolute Density

Total Count ndash count the number of organisms living in an area Human census number of oak trees in a

wooded lot number of singing birds in an area

Total counts generally are not used very often

Sampling Methods ndash use a sample to estimate population size Either use the quadrat or capture-

recapture method

35

Measurement of Environmental ParametersAbiotic factors are important in determining

both the distribution of the organisms and their physical and physiological adaptations

Temperature- diurnal and seasonal temperature variations

are significant in affecting different species of plants and animals

- equipment mercury thermometer maximum-minimum thermometer

miniaturized thermistor

36

pH

-measure pH of a solution by universal indicator pH paper pH meter etc

Light

-measure its duration and intensity duration by predication from Royal Observatory intensity by photographic light meter

pH meter in use

37

Humidity

Relative humidity the water content of a given volume of air relative to the same volume of fully saturated air

- equipment whirling hygrometer

38

Wind and Water Speed- wind speed- anemometer or wind

gauges- water speed - time the movement of a

floating object over a measured distance

39

Salinity

- using a conductivity meter greater salinity has greater conductivity

Oxygen Level

- using an oxygen meter or chemical method (Winkler method)

40

Collecting MethodsCollecting all organisms within a habitat is normally

impractical and therefore small areas are selected Remember to return all material to its original position

after searching amp collecting sufficient specimens Some collecting apparatus for general use are listed

below

41

1 specimen tube

2 screwed-topped jars

3 polythene bags

4 forceps

5 paint brush

6 bulb pipette

7 pooter

42

8 widger 9 sieve 10 hand lens

11 enamel dish 12 beating tray 13 light traps

14 Tullgren funnel 15 Baermann funnel 16 mammal traps

17 pitfall traps 18 netting

43

Estimating Population Size

The exact methods used for estimation depend not only the nature of the habitat but also on the organisms involved

eg animals - population

plants - percentage cover

44

Using Quadrats

- By sampling an area using quadrats and counting the number of individuals within each quadrat it is possible to estimate the total number of individuals within the area

- confined to plants and sessile or very slow-moving animals

- fast-moving animals are disturbed and run away

45

Capture-recapture Techniques- useful for mobile animals which can be marked

- capture marked released randomly recaptured

and marked individuals recorded

no of marked individuals recaptured total no of individuals in 1st sample

-------------------------------------------- = ------------------------------------------

total no of individuals in 2nd sample estimated size of population

(the Lincoln Index)

46

Capture-recapture Techniques Factors affecting the accuracy of the estimation

deaths migration individuals become more liable to predation etc

Examples

- arthropods marked on their backs with non-toxic paint

- fish have tags attached to opercula - mammals have tags clipped to their ears

birds have their legs ringed

47

Capture-recapture Method Important tool for estimating density birth

rate and death rate for mobile animals Method

Collect a sample of individuals mark them and then release them

After a period collect more individuals from the wild and count the number that have marks

We assume that a sample if random will contain the same proportion of marked individuals as the population does

Estimate population density

48

Assumptions For All Capture-Recapture Studies Marking technique does not increase

mortality of marked animals Marked individuals are allowed to mix

with population Marking technique does not affect catch

probability Marks are not lost or overlooked No significant immigration or emigration No significant mortality or natality

49

Marked animals in second sample

Total caught in second sample

Marked animals in first sample

Total population size

=

520 N

16=

Peterson Method or Lincoln Index

N = 64N = (20)(16)5

50

Some Indices Used

Traps Number of Fecal

Pellets Vocalization

Frequency Pelt Records Catch per Unit

Fishing Effort

Number of Artifacts Questionnaires Cover Feeding Capacity Roadside Counts

51

Abundance Scales

The population size may be fairly accurately determined by making some form of frequency assessment

These are subjective and involve an experimenter making some estimate of the number of individuals in a given area or the cover of a particular species

This is especially useful where individuals are very numerous eg barnacles on a rocky shore or where it is difficult to distinguish individuals eg grass plants in a meadow

52

The assessments are usually made on an abundance scale of 5 categories

Abundance Common Frequent Occasional Rare

Barnacles exposed at low water

53

Environmental resistance are the factors which limit the growth of a particular population

eg predation disease availability of light food water oxygen and shelter the accumulation of toxic wastes and even the size of the population itself

54

Density-dependent Growth A population is a density-dependent when its size

(or density) affects its growth rate because of density-dependent factors such as food availability and toxic waste accumulation

Density-independent Growth In this type of growth a population increases until

some factor causes a sudden reduction in its size Its effect is the same regardless of the size of the

population eg temperature fires floods storms etc

55

Regulation of Population Size Fecundity is the reproductive capacity of individual

females of a species Birth rate or natality is used to measure fecundity Death rate or mortality is the number of individuals

of a species which die per unit time Immigration occurs when individuals join a

population from neighbouring ones Emigration occurs when individuals depart from a

population A cycle occurs when the size of a population

fluctuates on a regular basis

56

Ecological Sampling

57

Why Do We Sample Determine presence andor

abundance

Monitor population fluctuations

Assess lsquoecological damagersquo

Assess quality of habitat

Assess population responses

58

What Do We Sample

Physical Environment Temperature DO pH salinity clarity

flow sediment

Biotic Environment All living things

59

Physical Habitat Temperature

Mercury thermometer Electronic thermometer Long-term thermometers

Dissolved Oxygen Winkler method (titration) DO meter (electrode)

pH Litmus paper pH meter (electrode)

Salinity Salinity Meter YSI 550A DO Meter w12 cable

60

Water Clarity Secchi Disk

Disk is attached to a calibrated rope The disk is lowered into the water until the white parts can no longer be seen Secchi disk depth is then recorded and serves as the waters transparency index The clearer the water the greater the secchi disk depth

Secchi Disk

61

Current Velocity (flow) Floating-orange method

Put an orange (or something else that floats just below the water surface) and measure the time it takes it to float across a known distance

Odometer-type flow meter Number of revolutions the propeller

makes for a given time is calibrated to flow velocity

62

Sediment Sediment size is important to many

aquatic organisms Sieversquos are used to separate and

grade sediment samples Percent of each size grade can be

determined

63

Water Sample

Water and plankton from various depths can be collected

A trigger mechanism is used to close the sampler Sample is then brought back to the

surface

64

Small Mammals

Mouserat Traps Fatal

Pit Falls Bucket is placed in the ground Sometimes have lsquoleadsrsquo to the buckets

Live traps Havahart Sherman

Spot-light

Sherman trapHavahart trap

65

Birds Stick-under-the-box method Bird-trap

Works like a minnow trap Mist net

Captures birds in flight Rocket net

Uses a propellant to throw a net over birds

66

Terrestrial Insects

Sticky paper flies

Baited Traps Fire ants

Nets butterflies

Foggers Collect insects from tree canopies

67

Aquatic Insects Drift Net

Place net in flowing water Kick Net

lsquoKickrsquo sediment upstream from block net and the flow will wash them into the net

Wash bucket Serber or Hess Sampler

Stir up known area of sediment

Animals are collected by a catch net

Multi-plate Sampler Become colonized

68

Crawfish and Crab Traps

69

Fish Larvae Light Traps

Larvae are attracted to the light Ichthyoplankton nets

Can be towed at various depths Fish collect at the lsquocodrsquoend

70

Fish Lift net

Net is placed down and after a set amount of time it is quickly lifted

Pop-net Similar to a lift net but

floats are attached to a framed net

Operated by a trigger mechanism

Throw net A net attached to a heavy

frame is thrown and every thing inside is netted out Throw net

Pop-net

Lift net

71

Minnow trap

Usually use bait to attract small fish Light is used sometimes as an attractant

72

Fish Electrofishing

Electricity is put into the water Fish are temporarily stunned and usually

swim towards the electricity source Usually non-fatal but may cause some

damage

73

Fish Gill Net

Gill nets resemble tennis nets Fish can not swim completely through the

net and get caught Gill nets are size selective (based on mesh

size) Square Mesh

Bar mesh

Stretch mesh

74

Fish Trammel Net

Three panels two large mesh on the outside and a small mesh on the inside

Fish swim through the outer mesh pushes the small mesh through the other side and becomes entangled

75

Hoop nets (and other similar nets) can have bait or not

Fyke nets have leads to help guide fish to the net

76

Seine Seines are nets that are pulled

through shallow water to catch fish

77

Purse Seine Used to encircle entire schools of fish

Usually involves a spotter plane and a second boat

78

Trotline (longline) A series of baited drop lines

connected to a main line

Can be deployed by tying one end to the bank and tying the other end with a heavy weight

79

Shrimp (or fish) Trawl Net pulled behind

a boat along the bottom Either a beam or

otter boards keep the net open

80

Tagging Individuals Coded Wire Tags

Microwire that has a unique label

Magnetic wand detects the tag

Tag retention should be determined

T-Bar tags Can be individually

numbered External tag

PIT tags (Passive Integrated Transponders) Wand induces the tag to

transmit individual number is displayed

81

Other Tagging Methods

Toe clip Amphibian and reptile Clip of one or more toes

to identify individuals

Bird Band Place a metal band on a

bird leg Generally has

identification information

82

Preserving plant specimens Pressing and drying Long-term

preservation and storage

Alternative drying techniques

Special preservation and processing techniques

Mounting

83

Pressing and drying Techniques for pressing and drying specimens have been

established for many years There are minor variations in recommended methods but they are essentially the same worldwide

The best specimens are plants that are pressed as soon as possible after collection before wilting and shrivelling Most plants may be kept in sealed containers such as plastic bags for up to a day if it is inconvenient to press immediately However some plants show such rapid wilting particularly of the flowers that such delays are best avoided Flowers with a lot of nectar may go mouldy very quickly if excess nectar is not shaken off before pressing

Specimens are pressed flat and dried between sheets of absorbent blotters or semi-absorbent paper such as newspaper Papers with a glossy surface should be avoided because they are not absorbent enough to aid drying The plant should be carefully laid out between the drying sheets as their form at this stage largely determines their ultimate appearance The flowers should be spread out with the petals carefully arranged wilted leaves should be straightened and unnecessary shoots of excessively twiggy shrubs may be cut away

84

Microwave ovens Small numbers of specimens can be dried using a microwave

oven The technique recommended in the literature is to place the specimens between unprinted absorbent paper for example butchers paper not newspaper which is unsuitable because the chemicals present in the ink may cause a fire The specimens should be put in a special press which should be of a microwave-safe material (wood acrylic or polycarbonate sheeting eg plexiglass or perspex NO metal components) If such a press is not available sheets of cardboard can be placed above and below the specimens and then weighted down

Drying time depends on the power of your oven In most cases drying is accomplished by irradiating at maximum power for 1-2 minutes per specimen although it is often a case of trial and error It is best to process no more than 10-12 specimens of average thickness per batch Specimens are usually dried after the moisture that characteristically appears on the glass door has disappeared If the specimen is damp when taken out of the oven allow it to stand before re-radiating as moisture continues to evaporate from the specimen for some time Care must be taken not to irradiate the specimens for too long

It should be noted that microwave treatment damages seeds and the cellular structure of the plants which may reduce the long-term value of the specimens

85

Alternative drying techniquesSilica gelother desiccants amp freeze drying Alternative methods of drying plant specimens have been

used for some time but are mostly restricted to special purpose collections The main alternatives are freeze-drying and drying in a desiccant powder such as desiccant silica gel In general these techniques are used where it is essential to preserve the shape of a delicate plant of organ of the plant such as the flower Freeze-drying has also been used to preserve the chemical composition of a plant as accurately as possible for later study

Disadvantages and special conservation problems of specimens dried in these manners are that they are particularly susceptible to damage The dried parts are fragile lack support and often catch on packing materials They must therefore be packed especially carefully and stored in small boxes or tubes with some appropriate packing material that does not snag and break small projections Acid-free tissue paper is often used Drying in desiccant silica gel crystals or powder can also have the disadvantage that it is difficult to remove all traces of the silica gel after drying

86

Special preservation and processing techniquesWet or spirit collections

Very fleshy or delicate structures including small algae and orchid flowers are best preserved in an air-tight glass or plastic jar with a liquid preservative rather than by drying The type of preservative used should be clearly labelled in the jar Such material is often referred to as a spirit collection or wet collection

Most material can be satisfactorily preserved in 70 ethyl alcohol (or 70 methylated spirit or denatured alcohol) with 30 water Colours will fade quickly in spirit however so it is a good idea to keep comprehensive notes and photographs

87

Small algae Microscopic algae are often collected in a jar and in the

water in which they were found If the algae are to be stored for more than 2-3 days a preservative needs to be used Traditionally this has been the extremely toxic formalin - a small amount can be added to the water to make a 5 final solution and the container labelled This must not be sent through the post or by courier

There are some other equally toxic options for example propylene phenoxytol but none should be sent through the post A safer option is to add sufficient concentrated alcohol or methylated spirits to the water containing the algae to make a final solution of 70 alcohol This treatment dilutes the algae making them difficult to find so if they can be concentrated somehow first (eg by filtering) they can be stored in much less liquid Another option is to fix the algae in formalin (or something similar) first and then prepare a microscope glass slide with a permanent water-soluble mounting medium

88

Mounting Mounting specimens prevents most fragile material from

fragmenting and prevents specimens becoming separated from their labels If the plant collection is a long-term project specimens should be mounted on sheets of archival (permanent) cardboard or paper with archival-quality fixing media These include stitching with cotton thread dental floss nickel-plated copper wire (for heavier specimens) narrow strips of archival paper linen tape or by using an archival adhesive such as methyl cellulose adhesive

One disadvantage of mounting specimens is that it can make parts of the specimen inaccessible for examination so it is essential that this be borne in mind during specimen arrangement and mounting For example easily reversible mounting media should be used specimens should be strapped to the sheet rather than glued all over and the specimen should be carefully arranged before it is attached so that it shows all features

89

Full-size herbarium mounting sheets are usually about 43 cm long x 28 cm wide The plant name and accompanying field notes should be transcribed on a permanent label stuck to one corner of the herbarium sheet (the bottom right-hand corner being the most common) or sometimes annotations may be written directly on the sheet or card

Small pieces of material which may have become separated from the specimen (eg seeds) can be placed in small plastic bags and pinned to the sheet

90

Long-term preservation and storage The long-term preservation of dry plant

specimens is largely dependent on protection from insect attack Specimens collected by Linnaeus in the eighteenth century and by Banks and Solander on the Endeavour voyage in 1788 are still excellently preserved

91

Pests and their control A range of pests attack dried plant material The

most common pests are insects and fungi though rodents and other large animals can cause damage in poor storage conditions Insects eat the material the paper surrounding the material and the adhesives and mounting media

Such insect pests range from psocids (book lice) which attack mainly the softer parts such as flowers and soft fruits to tobacco beetles and carpet beetles which can bore holes through the toughest of specimens Many insects are particularly sensitive to relative humidity levels and do not thrive at levels below 50

92

The most common and acceptable specimen treatments for insect control are Freezing Microwave Poisoning Insect deterrents Fungal pests

93

Storage

Dried and pressed plant specimens can be stored in cardboard or plastic boxes or tied in bundles in light-weight cardboard folders placed in pigeon holes

Alternatively they can be placed in protective plastic jackets and displayed in ring folders which is recommended if they are to be frequently handled such as for a reference collection

94

Filing

Specimens should be filed in a systematic order if a relatively permanent collection is being made The major groups ie ferns and fern allies cycads conifers dicotyledons and monocotyledons are best kept separately or according to some classification scheme such as that given in a flora or handbook

Similarly the genera within each family and the species within each genus may be filed alphabetically or following some such classification

95

Preservation of entire animals

Types of collection specimens of an entire animal For reference collections mammals can be prepared as a variety of specimens The condition of the specimen may determine possible ways to preserve it if for instance decomposition of the skin has loosened the hair of a carcass so much that it can easily be pulled out or removed by rubbing (ldquoslippingrdquo fur) it will be very difficult or impossible to produce a study skin or mounted specimen The most usual types of specimens (based on Nagorsen and Peterson 1980) are 1) entire fluid-preserved animals (for studying anatomy and histology fluid preservation may change the fur colour) 2) study skins with accompanying skulls partial skeletons (some bones remain in the skin) for studying pelage colour hair quality and moulting patterns 3) mounted skins with accompanying partial or entire skeleton (some bones may remain in the skin dependant on the method of preservation) or freeze-dried specimens 4) entire skeletons for instance for studying anatomy geographic variation or for age determination (entire skeletons are poorly represented in collections so Nagorsen and Peterson (1980) recommend preparation of at least one male and one female skeleton per species

96

Preservation of specimens in the field Formalin preservation Preservation in alcohol Preservation by cooling or freezing

97

Formalin preservation After weighing and measuring the animal and attaching an

adequate label very small specimens (up to 100 g) can be fixed whole by submerging them in 10 buffered formalin (tissue - formalin solution ratio of at least 1 12) the body cavity can be filled with formalin solution by injection until it is turgid and firm some formalin may also be injected under the skin into the body cavity larger muscles and organs If hypodermic needles are not available the body cavity can be opened ventrally by making a slit instead allowing the formalin to enter

Keeping the mouth open with a piece of wood or cotton may later allow examination of teeth Then the whole body can be immersed in formalin in the posture in which it is supposed to stay permanently because it will harden The ratio of formalin to carcass must be at least 12 to 1 to assure a good fixation Tissues can be left in buffered neutralized formalin for several months but formalin hardens specimens therefore after fixation longterm storage in alcohol may be better After preservation the carcass should therefore be washed in water and transferred into ethanol for permanent storage

Disadvantages for instance it discolours the fur after a longish immersion softens the bones and prevents further examination for microbiology

98

Preservation in alcohol

After weighing a whole animal can be preserved in a container of alcohol (70-90) Removal of the intestine prior to storage of the animal in alcohol is recommended

99

Preservation by cooling or freezing Removal of the skin with insulating fur

before cooling or freezing may help to cool the carcass down more quickly

Freezing is not recommended if histological examination is planned

100

THANK YOU

21

Sampling along gradients

Transects are setup along aenvironmentalgradientsndash down a hillsidendash across a streambedndash out from a source ofpollution

22

Types of transect sampling 1048698 Line transect 1048698 Belt transect

23

Line transect methodA measured line is laidacross the area in thedirection of theenvironmental gradientndash The species touching theline can be recordedalong the whole length ofthe line (continuoussampling) or at specificpoints along the line(systematic sampling)

24

Line Transect- useful where a transition of flora andor fauna

occurs- a string or tape is stretched out along the

ground in a straight line record the organisms touching or covering

the line all along its length or at regular intervals

- Profile transect when there is appreciable height change along the transect and thus affecting the distribution of its species

25

Belt transect method

Similar to line transect butwidens the sampling areandash Transect line is laid outndash Samples are taken bydetermining abundance or cover in an area that is adefined distance from the linendash Samples can be taken all

theway along the line at specificintervals or even randomly

26

Belt TransectIt is a strip usually a metre wide marked by putting a

second line parallel to the other The species between the lines are carefully recorded working a metre at a time

Alternatively a frame quadrat in conjunction with a single line transect could be used

Using a quadrat along a belt transect eg ladder transect (every 5m)

27

Point Frames- for grassland field study of dense vegetation

28

STRATIFIED SAMPLING1048698 Often used whenthere are smallareas within alarger habitat thatare clearly different1048698 Strata- majordifferences withincommunitiesrecognized beforesampling begins

29

RANDOM SAMPLING

1048698 Often used when the area being studied isfairly uniform very large or when there is alimited amount of time available1048698 Random = chosen by chance rather thanaccording to a plan all outcomes are

equallylikely1048698 Samples are taken from different positionswithin a habitat and those positions arechosen randomly

30

How to sample randomly

Choose individuals or Placeldquosampling unitsrdquo

haphazardlyndash This is rarely completely

random1048698 ORhellip1048698 Assign numbers to the

areasor individuals to be sampledndash Use a random number

table toselect which areas or

individualswill be sample

31

Population Attributes Density ndash size of a population in relation to a definite

unit of space Affected by

Natality ndash the reproductive output (birth rate) of a population

Mortality ndash the death rate of organisms in a population

Immigration ndash number of organisms moving into the area occupied by the population

Emigration ndash number of organisms moving out of the area occupied by the population

32

Population Density

Four primary population parameters

33

Two Types of Density Estimates

bull Absolute Density ndash a known density such as m2

bull Relative Density ndash we know when one area has more individuals than another

34

Measuring Absolute Density

Total Count ndash count the number of organisms living in an area Human census number of oak trees in a

wooded lot number of singing birds in an area

Total counts generally are not used very often

Sampling Methods ndash use a sample to estimate population size Either use the quadrat or capture-

recapture method

35

Measurement of Environmental ParametersAbiotic factors are important in determining

both the distribution of the organisms and their physical and physiological adaptations

Temperature- diurnal and seasonal temperature variations

are significant in affecting different species of plants and animals

- equipment mercury thermometer maximum-minimum thermometer

miniaturized thermistor

36

pH

-measure pH of a solution by universal indicator pH paper pH meter etc

Light

-measure its duration and intensity duration by predication from Royal Observatory intensity by photographic light meter

pH meter in use

37

Humidity

Relative humidity the water content of a given volume of air relative to the same volume of fully saturated air

- equipment whirling hygrometer

38

Wind and Water Speed- wind speed- anemometer or wind

gauges- water speed - time the movement of a

floating object over a measured distance

39

Salinity

- using a conductivity meter greater salinity has greater conductivity

Oxygen Level

- using an oxygen meter or chemical method (Winkler method)

40

Collecting MethodsCollecting all organisms within a habitat is normally

impractical and therefore small areas are selected Remember to return all material to its original position

after searching amp collecting sufficient specimens Some collecting apparatus for general use are listed

below

41

1 specimen tube

2 screwed-topped jars

3 polythene bags

4 forceps

5 paint brush

6 bulb pipette

7 pooter

42

8 widger 9 sieve 10 hand lens

11 enamel dish 12 beating tray 13 light traps

14 Tullgren funnel 15 Baermann funnel 16 mammal traps

17 pitfall traps 18 netting

43

Estimating Population Size

The exact methods used for estimation depend not only the nature of the habitat but also on the organisms involved

eg animals - population

plants - percentage cover

44

Using Quadrats

- By sampling an area using quadrats and counting the number of individuals within each quadrat it is possible to estimate the total number of individuals within the area

- confined to plants and sessile or very slow-moving animals

- fast-moving animals are disturbed and run away

45

Capture-recapture Techniques- useful for mobile animals which can be marked

- capture marked released randomly recaptured

and marked individuals recorded

no of marked individuals recaptured total no of individuals in 1st sample

-------------------------------------------- = ------------------------------------------

total no of individuals in 2nd sample estimated size of population

(the Lincoln Index)

46

Capture-recapture Techniques Factors affecting the accuracy of the estimation

deaths migration individuals become more liable to predation etc

Examples

- arthropods marked on their backs with non-toxic paint

- fish have tags attached to opercula - mammals have tags clipped to their ears

birds have their legs ringed

47

Capture-recapture Method Important tool for estimating density birth

rate and death rate for mobile animals Method

Collect a sample of individuals mark them and then release them

After a period collect more individuals from the wild and count the number that have marks

We assume that a sample if random will contain the same proportion of marked individuals as the population does

Estimate population density

48

Assumptions For All Capture-Recapture Studies Marking technique does not increase

mortality of marked animals Marked individuals are allowed to mix

with population Marking technique does not affect catch

probability Marks are not lost or overlooked No significant immigration or emigration No significant mortality or natality

49

Marked animals in second sample

Total caught in second sample

Marked animals in first sample

Total population size

=

520 N

16=

Peterson Method or Lincoln Index

N = 64N = (20)(16)5

50

Some Indices Used

Traps Number of Fecal

Pellets Vocalization

Frequency Pelt Records Catch per Unit

Fishing Effort

Number of Artifacts Questionnaires Cover Feeding Capacity Roadside Counts

51

Abundance Scales

The population size may be fairly accurately determined by making some form of frequency assessment

These are subjective and involve an experimenter making some estimate of the number of individuals in a given area or the cover of a particular species

This is especially useful where individuals are very numerous eg barnacles on a rocky shore or where it is difficult to distinguish individuals eg grass plants in a meadow

52

The assessments are usually made on an abundance scale of 5 categories

Abundance Common Frequent Occasional Rare

Barnacles exposed at low water

53

Environmental resistance are the factors which limit the growth of a particular population

eg predation disease availability of light food water oxygen and shelter the accumulation of toxic wastes and even the size of the population itself

54

Density-dependent Growth A population is a density-dependent when its size

(or density) affects its growth rate because of density-dependent factors such as food availability and toxic waste accumulation

Density-independent Growth In this type of growth a population increases until

some factor causes a sudden reduction in its size Its effect is the same regardless of the size of the

population eg temperature fires floods storms etc

55

Regulation of Population Size Fecundity is the reproductive capacity of individual

females of a species Birth rate or natality is used to measure fecundity Death rate or mortality is the number of individuals

of a species which die per unit time Immigration occurs when individuals join a

population from neighbouring ones Emigration occurs when individuals depart from a

population A cycle occurs when the size of a population

fluctuates on a regular basis

56

Ecological Sampling

57

Why Do We Sample Determine presence andor

abundance

Monitor population fluctuations

Assess lsquoecological damagersquo

Assess quality of habitat

Assess population responses

58

What Do We Sample

Physical Environment Temperature DO pH salinity clarity

flow sediment

Biotic Environment All living things

59

Physical Habitat Temperature

Mercury thermometer Electronic thermometer Long-term thermometers

Dissolved Oxygen Winkler method (titration) DO meter (electrode)

pH Litmus paper pH meter (electrode)

Salinity Salinity Meter YSI 550A DO Meter w12 cable

60

Water Clarity Secchi Disk

Disk is attached to a calibrated rope The disk is lowered into the water until the white parts can no longer be seen Secchi disk depth is then recorded and serves as the waters transparency index The clearer the water the greater the secchi disk depth

Secchi Disk

61

Current Velocity (flow) Floating-orange method

Put an orange (or something else that floats just below the water surface) and measure the time it takes it to float across a known distance

Odometer-type flow meter Number of revolutions the propeller

makes for a given time is calibrated to flow velocity

62

Sediment Sediment size is important to many

aquatic organisms Sieversquos are used to separate and

grade sediment samples Percent of each size grade can be

determined

63

Water Sample

Water and plankton from various depths can be collected

A trigger mechanism is used to close the sampler Sample is then brought back to the

surface

64

Small Mammals

Mouserat Traps Fatal

Pit Falls Bucket is placed in the ground Sometimes have lsquoleadsrsquo to the buckets

Live traps Havahart Sherman

Spot-light

Sherman trapHavahart trap

65

Birds Stick-under-the-box method Bird-trap

Works like a minnow trap Mist net

Captures birds in flight Rocket net

Uses a propellant to throw a net over birds

66

Terrestrial Insects

Sticky paper flies

Baited Traps Fire ants

Nets butterflies

Foggers Collect insects from tree canopies

67

Aquatic Insects Drift Net

Place net in flowing water Kick Net

lsquoKickrsquo sediment upstream from block net and the flow will wash them into the net

Wash bucket Serber or Hess Sampler

Stir up known area of sediment

Animals are collected by a catch net

Multi-plate Sampler Become colonized

68

Crawfish and Crab Traps

69

Fish Larvae Light Traps

Larvae are attracted to the light Ichthyoplankton nets

Can be towed at various depths Fish collect at the lsquocodrsquoend

70

Fish Lift net

Net is placed down and after a set amount of time it is quickly lifted

Pop-net Similar to a lift net but

floats are attached to a framed net

Operated by a trigger mechanism

Throw net A net attached to a heavy

frame is thrown and every thing inside is netted out Throw net

Pop-net

Lift net

71

Minnow trap

Usually use bait to attract small fish Light is used sometimes as an attractant

72

Fish Electrofishing

Electricity is put into the water Fish are temporarily stunned and usually

swim towards the electricity source Usually non-fatal but may cause some

damage

73

Fish Gill Net

Gill nets resemble tennis nets Fish can not swim completely through the

net and get caught Gill nets are size selective (based on mesh

size) Square Mesh

Bar mesh

Stretch mesh

74

Fish Trammel Net

Three panels two large mesh on the outside and a small mesh on the inside

Fish swim through the outer mesh pushes the small mesh through the other side and becomes entangled

75

Hoop nets (and other similar nets) can have bait or not

Fyke nets have leads to help guide fish to the net

76

Seine Seines are nets that are pulled

through shallow water to catch fish

77

Purse Seine Used to encircle entire schools of fish

Usually involves a spotter plane and a second boat

78

Trotline (longline) A series of baited drop lines

connected to a main line

Can be deployed by tying one end to the bank and tying the other end with a heavy weight

79

Shrimp (or fish) Trawl Net pulled behind

a boat along the bottom Either a beam or

otter boards keep the net open

80

Tagging Individuals Coded Wire Tags

Microwire that has a unique label

Magnetic wand detects the tag

Tag retention should be determined

T-Bar tags Can be individually

numbered External tag

PIT tags (Passive Integrated Transponders) Wand induces the tag to

transmit individual number is displayed

81

Other Tagging Methods

Toe clip Amphibian and reptile Clip of one or more toes

to identify individuals

Bird Band Place a metal band on a

bird leg Generally has

identification information

82

Preserving plant specimens Pressing and drying Long-term

preservation and storage

Alternative drying techniques

Special preservation and processing techniques

Mounting

83

Pressing and drying Techniques for pressing and drying specimens have been

established for many years There are minor variations in recommended methods but they are essentially the same worldwide

The best specimens are plants that are pressed as soon as possible after collection before wilting and shrivelling Most plants may be kept in sealed containers such as plastic bags for up to a day if it is inconvenient to press immediately However some plants show such rapid wilting particularly of the flowers that such delays are best avoided Flowers with a lot of nectar may go mouldy very quickly if excess nectar is not shaken off before pressing

Specimens are pressed flat and dried between sheets of absorbent blotters or semi-absorbent paper such as newspaper Papers with a glossy surface should be avoided because they are not absorbent enough to aid drying The plant should be carefully laid out between the drying sheets as their form at this stage largely determines their ultimate appearance The flowers should be spread out with the petals carefully arranged wilted leaves should be straightened and unnecessary shoots of excessively twiggy shrubs may be cut away

84

Microwave ovens Small numbers of specimens can be dried using a microwave

oven The technique recommended in the literature is to place the specimens between unprinted absorbent paper for example butchers paper not newspaper which is unsuitable because the chemicals present in the ink may cause a fire The specimens should be put in a special press which should be of a microwave-safe material (wood acrylic or polycarbonate sheeting eg plexiglass or perspex NO metal components) If such a press is not available sheets of cardboard can be placed above and below the specimens and then weighted down

Drying time depends on the power of your oven In most cases drying is accomplished by irradiating at maximum power for 1-2 minutes per specimen although it is often a case of trial and error It is best to process no more than 10-12 specimens of average thickness per batch Specimens are usually dried after the moisture that characteristically appears on the glass door has disappeared If the specimen is damp when taken out of the oven allow it to stand before re-radiating as moisture continues to evaporate from the specimen for some time Care must be taken not to irradiate the specimens for too long

It should be noted that microwave treatment damages seeds and the cellular structure of the plants which may reduce the long-term value of the specimens

85

Alternative drying techniquesSilica gelother desiccants amp freeze drying Alternative methods of drying plant specimens have been

used for some time but are mostly restricted to special purpose collections The main alternatives are freeze-drying and drying in a desiccant powder such as desiccant silica gel In general these techniques are used where it is essential to preserve the shape of a delicate plant of organ of the plant such as the flower Freeze-drying has also been used to preserve the chemical composition of a plant as accurately as possible for later study

Disadvantages and special conservation problems of specimens dried in these manners are that they are particularly susceptible to damage The dried parts are fragile lack support and often catch on packing materials They must therefore be packed especially carefully and stored in small boxes or tubes with some appropriate packing material that does not snag and break small projections Acid-free tissue paper is often used Drying in desiccant silica gel crystals or powder can also have the disadvantage that it is difficult to remove all traces of the silica gel after drying

86

Special preservation and processing techniquesWet or spirit collections

Very fleshy or delicate structures including small algae and orchid flowers are best preserved in an air-tight glass or plastic jar with a liquid preservative rather than by drying The type of preservative used should be clearly labelled in the jar Such material is often referred to as a spirit collection or wet collection

Most material can be satisfactorily preserved in 70 ethyl alcohol (or 70 methylated spirit or denatured alcohol) with 30 water Colours will fade quickly in spirit however so it is a good idea to keep comprehensive notes and photographs

87

Small algae Microscopic algae are often collected in a jar and in the

water in which they were found If the algae are to be stored for more than 2-3 days a preservative needs to be used Traditionally this has been the extremely toxic formalin - a small amount can be added to the water to make a 5 final solution and the container labelled This must not be sent through the post or by courier

There are some other equally toxic options for example propylene phenoxytol but none should be sent through the post A safer option is to add sufficient concentrated alcohol or methylated spirits to the water containing the algae to make a final solution of 70 alcohol This treatment dilutes the algae making them difficult to find so if they can be concentrated somehow first (eg by filtering) they can be stored in much less liquid Another option is to fix the algae in formalin (or something similar) first and then prepare a microscope glass slide with a permanent water-soluble mounting medium

88

Mounting Mounting specimens prevents most fragile material from

fragmenting and prevents specimens becoming separated from their labels If the plant collection is a long-term project specimens should be mounted on sheets of archival (permanent) cardboard or paper with archival-quality fixing media These include stitching with cotton thread dental floss nickel-plated copper wire (for heavier specimens) narrow strips of archival paper linen tape or by using an archival adhesive such as methyl cellulose adhesive

One disadvantage of mounting specimens is that it can make parts of the specimen inaccessible for examination so it is essential that this be borne in mind during specimen arrangement and mounting For example easily reversible mounting media should be used specimens should be strapped to the sheet rather than glued all over and the specimen should be carefully arranged before it is attached so that it shows all features

89

Full-size herbarium mounting sheets are usually about 43 cm long x 28 cm wide The plant name and accompanying field notes should be transcribed on a permanent label stuck to one corner of the herbarium sheet (the bottom right-hand corner being the most common) or sometimes annotations may be written directly on the sheet or card

Small pieces of material which may have become separated from the specimen (eg seeds) can be placed in small plastic bags and pinned to the sheet

90

Long-term preservation and storage The long-term preservation of dry plant

specimens is largely dependent on protection from insect attack Specimens collected by Linnaeus in the eighteenth century and by Banks and Solander on the Endeavour voyage in 1788 are still excellently preserved

91

Pests and their control A range of pests attack dried plant material The

most common pests are insects and fungi though rodents and other large animals can cause damage in poor storage conditions Insects eat the material the paper surrounding the material and the adhesives and mounting media

Such insect pests range from psocids (book lice) which attack mainly the softer parts such as flowers and soft fruits to tobacco beetles and carpet beetles which can bore holes through the toughest of specimens Many insects are particularly sensitive to relative humidity levels and do not thrive at levels below 50

92

The most common and acceptable specimen treatments for insect control are Freezing Microwave Poisoning Insect deterrents Fungal pests

93

Storage

Dried and pressed plant specimens can be stored in cardboard or plastic boxes or tied in bundles in light-weight cardboard folders placed in pigeon holes

Alternatively they can be placed in protective plastic jackets and displayed in ring folders which is recommended if they are to be frequently handled such as for a reference collection

94

Filing

Specimens should be filed in a systematic order if a relatively permanent collection is being made The major groups ie ferns and fern allies cycads conifers dicotyledons and monocotyledons are best kept separately or according to some classification scheme such as that given in a flora or handbook

Similarly the genera within each family and the species within each genus may be filed alphabetically or following some such classification

95

Preservation of entire animals

Types of collection specimens of an entire animal For reference collections mammals can be prepared as a variety of specimens The condition of the specimen may determine possible ways to preserve it if for instance decomposition of the skin has loosened the hair of a carcass so much that it can easily be pulled out or removed by rubbing (ldquoslippingrdquo fur) it will be very difficult or impossible to produce a study skin or mounted specimen The most usual types of specimens (based on Nagorsen and Peterson 1980) are 1) entire fluid-preserved animals (for studying anatomy and histology fluid preservation may change the fur colour) 2) study skins with accompanying skulls partial skeletons (some bones remain in the skin) for studying pelage colour hair quality and moulting patterns 3) mounted skins with accompanying partial or entire skeleton (some bones may remain in the skin dependant on the method of preservation) or freeze-dried specimens 4) entire skeletons for instance for studying anatomy geographic variation or for age determination (entire skeletons are poorly represented in collections so Nagorsen and Peterson (1980) recommend preparation of at least one male and one female skeleton per species

96

Preservation of specimens in the field Formalin preservation Preservation in alcohol Preservation by cooling or freezing

97

Formalin preservation After weighing and measuring the animal and attaching an

adequate label very small specimens (up to 100 g) can be fixed whole by submerging them in 10 buffered formalin (tissue - formalin solution ratio of at least 1 12) the body cavity can be filled with formalin solution by injection until it is turgid and firm some formalin may also be injected under the skin into the body cavity larger muscles and organs If hypodermic needles are not available the body cavity can be opened ventrally by making a slit instead allowing the formalin to enter

Keeping the mouth open with a piece of wood or cotton may later allow examination of teeth Then the whole body can be immersed in formalin in the posture in which it is supposed to stay permanently because it will harden The ratio of formalin to carcass must be at least 12 to 1 to assure a good fixation Tissues can be left in buffered neutralized formalin for several months but formalin hardens specimens therefore after fixation longterm storage in alcohol may be better After preservation the carcass should therefore be washed in water and transferred into ethanol for permanent storage

Disadvantages for instance it discolours the fur after a longish immersion softens the bones and prevents further examination for microbiology

98

Preservation in alcohol

After weighing a whole animal can be preserved in a container of alcohol (70-90) Removal of the intestine prior to storage of the animal in alcohol is recommended

99

Preservation by cooling or freezing Removal of the skin with insulating fur

before cooling or freezing may help to cool the carcass down more quickly

Freezing is not recommended if histological examination is planned

100

THANK YOU

22

Types of transect sampling 1048698 Line transect 1048698 Belt transect

23

Line transect methodA measured line is laidacross the area in thedirection of theenvironmental gradientndash The species touching theline can be recordedalong the whole length ofthe line (continuoussampling) or at specificpoints along the line(systematic sampling)

24

Line Transect- useful where a transition of flora andor fauna

occurs- a string or tape is stretched out along the

ground in a straight line record the organisms touching or covering

the line all along its length or at regular intervals

- Profile transect when there is appreciable height change along the transect and thus affecting the distribution of its species

25

Belt transect method

Similar to line transect butwidens the sampling areandash Transect line is laid outndash Samples are taken bydetermining abundance or cover in an area that is adefined distance from the linendash Samples can be taken all

theway along the line at specificintervals or even randomly

26

Belt TransectIt is a strip usually a metre wide marked by putting a

second line parallel to the other The species between the lines are carefully recorded working a metre at a time

Alternatively a frame quadrat in conjunction with a single line transect could be used

Using a quadrat along a belt transect eg ladder transect (every 5m)

27

Point Frames- for grassland field study of dense vegetation

28

STRATIFIED SAMPLING1048698 Often used whenthere are smallareas within alarger habitat thatare clearly different1048698 Strata- majordifferences withincommunitiesrecognized beforesampling begins

29

RANDOM SAMPLING

1048698 Often used when the area being studied isfairly uniform very large or when there is alimited amount of time available1048698 Random = chosen by chance rather thanaccording to a plan all outcomes are

equallylikely1048698 Samples are taken from different positionswithin a habitat and those positions arechosen randomly

30

How to sample randomly

Choose individuals or Placeldquosampling unitsrdquo

haphazardlyndash This is rarely completely

random1048698 ORhellip1048698 Assign numbers to the

areasor individuals to be sampledndash Use a random number

table toselect which areas or

individualswill be sample

31

Population Attributes Density ndash size of a population in relation to a definite

unit of space Affected by

Natality ndash the reproductive output (birth rate) of a population

Mortality ndash the death rate of organisms in a population

Immigration ndash number of organisms moving into the area occupied by the population

Emigration ndash number of organisms moving out of the area occupied by the population

32

Population Density

Four primary population parameters

33

Two Types of Density Estimates

bull Absolute Density ndash a known density such as m2

bull Relative Density ndash we know when one area has more individuals than another

34

Measuring Absolute Density

Total Count ndash count the number of organisms living in an area Human census number of oak trees in a

wooded lot number of singing birds in an area

Total counts generally are not used very often

Sampling Methods ndash use a sample to estimate population size Either use the quadrat or capture-

recapture method

35

Measurement of Environmental ParametersAbiotic factors are important in determining

both the distribution of the organisms and their physical and physiological adaptations

Temperature- diurnal and seasonal temperature variations

are significant in affecting different species of plants and animals

- equipment mercury thermometer maximum-minimum thermometer

miniaturized thermistor

36

pH

-measure pH of a solution by universal indicator pH paper pH meter etc

Light

-measure its duration and intensity duration by predication from Royal Observatory intensity by photographic light meter

pH meter in use

37

Humidity

Relative humidity the water content of a given volume of air relative to the same volume of fully saturated air

- equipment whirling hygrometer

38

Wind and Water Speed- wind speed- anemometer or wind

gauges- water speed - time the movement of a

floating object over a measured distance

39

Salinity

- using a conductivity meter greater salinity has greater conductivity

Oxygen Level

- using an oxygen meter or chemical method (Winkler method)

40

Collecting MethodsCollecting all organisms within a habitat is normally

impractical and therefore small areas are selected Remember to return all material to its original position

after searching amp collecting sufficient specimens Some collecting apparatus for general use are listed

below

41

1 specimen tube

2 screwed-topped jars

3 polythene bags

4 forceps

5 paint brush

6 bulb pipette

7 pooter

42

8 widger 9 sieve 10 hand lens

11 enamel dish 12 beating tray 13 light traps

14 Tullgren funnel 15 Baermann funnel 16 mammal traps

17 pitfall traps 18 netting

43

Estimating Population Size

The exact methods used for estimation depend not only the nature of the habitat but also on the organisms involved

eg animals - population

plants - percentage cover

44

Using Quadrats

- By sampling an area using quadrats and counting the number of individuals within each quadrat it is possible to estimate the total number of individuals within the area

- confined to plants and sessile or very slow-moving animals

- fast-moving animals are disturbed and run away

45

Capture-recapture Techniques- useful for mobile animals which can be marked

- capture marked released randomly recaptured

and marked individuals recorded

no of marked individuals recaptured total no of individuals in 1st sample

-------------------------------------------- = ------------------------------------------

total no of individuals in 2nd sample estimated size of population

(the Lincoln Index)

46

Capture-recapture Techniques Factors affecting the accuracy of the estimation

deaths migration individuals become more liable to predation etc

Examples

- arthropods marked on their backs with non-toxic paint

- fish have tags attached to opercula - mammals have tags clipped to their ears

birds have their legs ringed

47

Capture-recapture Method Important tool for estimating density birth

rate and death rate for mobile animals Method

Collect a sample of individuals mark them and then release them

After a period collect more individuals from the wild and count the number that have marks

We assume that a sample if random will contain the same proportion of marked individuals as the population does

Estimate population density

48

Assumptions For All Capture-Recapture Studies Marking technique does not increase

mortality of marked animals Marked individuals are allowed to mix

with population Marking technique does not affect catch

probability Marks are not lost or overlooked No significant immigration or emigration No significant mortality or natality

49

Marked animals in second sample

Total caught in second sample

Marked animals in first sample

Total population size

=

520 N

16=

Peterson Method or Lincoln Index

N = 64N = (20)(16)5

50

Some Indices Used

Traps Number of Fecal

Pellets Vocalization

Frequency Pelt Records Catch per Unit

Fishing Effort

Number of Artifacts Questionnaires Cover Feeding Capacity Roadside Counts

51

Abundance Scales

The population size may be fairly accurately determined by making some form of frequency assessment

These are subjective and involve an experimenter making some estimate of the number of individuals in a given area or the cover of a particular species

This is especially useful where individuals are very numerous eg barnacles on a rocky shore or where it is difficult to distinguish individuals eg grass plants in a meadow

52

The assessments are usually made on an abundance scale of 5 categories

Abundance Common Frequent Occasional Rare

Barnacles exposed at low water

53

Environmental resistance are the factors which limit the growth of a particular population

eg predation disease availability of light food water oxygen and shelter the accumulation of toxic wastes and even the size of the population itself

54

Density-dependent Growth A population is a density-dependent when its size

(or density) affects its growth rate because of density-dependent factors such as food availability and toxic waste accumulation

Density-independent Growth In this type of growth a population increases until

some factor causes a sudden reduction in its size Its effect is the same regardless of the size of the

population eg temperature fires floods storms etc

55

Regulation of Population Size Fecundity is the reproductive capacity of individual

females of a species Birth rate or natality is used to measure fecundity Death rate or mortality is the number of individuals

of a species which die per unit time Immigration occurs when individuals join a

population from neighbouring ones Emigration occurs when individuals depart from a

population A cycle occurs when the size of a population

fluctuates on a regular basis

56

Ecological Sampling

57

Why Do We Sample Determine presence andor

abundance

Monitor population fluctuations

Assess lsquoecological damagersquo

Assess quality of habitat

Assess population responses

58

What Do We Sample

Physical Environment Temperature DO pH salinity clarity

flow sediment

Biotic Environment All living things

59

Physical Habitat Temperature

Mercury thermometer Electronic thermometer Long-term thermometers

Dissolved Oxygen Winkler method (titration) DO meter (electrode)

pH Litmus paper pH meter (electrode)

Salinity Salinity Meter YSI 550A DO Meter w12 cable

60

Water Clarity Secchi Disk

Disk is attached to a calibrated rope The disk is lowered into the water until the white parts can no longer be seen Secchi disk depth is then recorded and serves as the waters transparency index The clearer the water the greater the secchi disk depth

Secchi Disk

61

Current Velocity (flow) Floating-orange method

Put an orange (or something else that floats just below the water surface) and measure the time it takes it to float across a known distance

Odometer-type flow meter Number of revolutions the propeller

makes for a given time is calibrated to flow velocity

62

Sediment Sediment size is important to many

aquatic organisms Sieversquos are used to separate and

grade sediment samples Percent of each size grade can be

determined

63

Water Sample

Water and plankton from various depths can be collected

A trigger mechanism is used to close the sampler Sample is then brought back to the

surface

64

Small Mammals

Mouserat Traps Fatal

Pit Falls Bucket is placed in the ground Sometimes have lsquoleadsrsquo to the buckets

Live traps Havahart Sherman

Spot-light

Sherman trapHavahart trap

65

Birds Stick-under-the-box method Bird-trap

Works like a minnow trap Mist net

Captures birds in flight Rocket net

Uses a propellant to throw a net over birds

66

Terrestrial Insects

Sticky paper flies

Baited Traps Fire ants

Nets butterflies

Foggers Collect insects from tree canopies

67

Aquatic Insects Drift Net

Place net in flowing water Kick Net

lsquoKickrsquo sediment upstream from block net and the flow will wash them into the net

Wash bucket Serber or Hess Sampler

Stir up known area of sediment

Animals are collected by a catch net

Multi-plate Sampler Become colonized

68

Crawfish and Crab Traps

69

Fish Larvae Light Traps

Larvae are attracted to the light Ichthyoplankton nets

Can be towed at various depths Fish collect at the lsquocodrsquoend

70

Fish Lift net

Net is placed down and after a set amount of time it is quickly lifted

Pop-net Similar to a lift net but

floats are attached to a framed net

Operated by a trigger mechanism

Throw net A net attached to a heavy

frame is thrown and every thing inside is netted out Throw net

Pop-net

Lift net

71

Minnow trap

Usually use bait to attract small fish Light is used sometimes as an attractant

72

Fish Electrofishing

Electricity is put into the water Fish are temporarily stunned and usually

swim towards the electricity source Usually non-fatal but may cause some

damage

73

Fish Gill Net

Gill nets resemble tennis nets Fish can not swim completely through the

net and get caught Gill nets are size selective (based on mesh

size) Square Mesh

Bar mesh

Stretch mesh

74

Fish Trammel Net

Three panels two large mesh on the outside and a small mesh on the inside

Fish swim through the outer mesh pushes the small mesh through the other side and becomes entangled

75

Hoop nets (and other similar nets) can have bait or not

Fyke nets have leads to help guide fish to the net

76

Seine Seines are nets that are pulled

through shallow water to catch fish

77

Purse Seine Used to encircle entire schools of fish

Usually involves a spotter plane and a second boat

78

Trotline (longline) A series of baited drop lines

connected to a main line

Can be deployed by tying one end to the bank and tying the other end with a heavy weight

79

Shrimp (or fish) Trawl Net pulled behind

a boat along the bottom Either a beam or

otter boards keep the net open

80

Tagging Individuals Coded Wire Tags

Microwire that has a unique label

Magnetic wand detects the tag

Tag retention should be determined

T-Bar tags Can be individually

numbered External tag

PIT tags (Passive Integrated Transponders) Wand induces the tag to

transmit individual number is displayed

81

Other Tagging Methods

Toe clip Amphibian and reptile Clip of one or more toes

to identify individuals

Bird Band Place a metal band on a

bird leg Generally has

identification information

82

Preserving plant specimens Pressing and drying Long-term

preservation and storage

Alternative drying techniques

Special preservation and processing techniques

Mounting

83

Pressing and drying Techniques for pressing and drying specimens have been

established for many years There are minor variations in recommended methods but they are essentially the same worldwide

The best specimens are plants that are pressed as soon as possible after collection before wilting and shrivelling Most plants may be kept in sealed containers such as plastic bags for up to a day if it is inconvenient to press immediately However some plants show such rapid wilting particularly of the flowers that such delays are best avoided Flowers with a lot of nectar may go mouldy very quickly if excess nectar is not shaken off before pressing

Specimens are pressed flat and dried between sheets of absorbent blotters or semi-absorbent paper such as newspaper Papers with a glossy surface should be avoided because they are not absorbent enough to aid drying The plant should be carefully laid out between the drying sheets as their form at this stage largely determines their ultimate appearance The flowers should be spread out with the petals carefully arranged wilted leaves should be straightened and unnecessary shoots of excessively twiggy shrubs may be cut away

84

Microwave ovens Small numbers of specimens can be dried using a microwave

oven The technique recommended in the literature is to place the specimens between unprinted absorbent paper for example butchers paper not newspaper which is unsuitable because the chemicals present in the ink may cause a fire The specimens should be put in a special press which should be of a microwave-safe material (wood acrylic or polycarbonate sheeting eg plexiglass or perspex NO metal components) If such a press is not available sheets of cardboard can be placed above and below the specimens and then weighted down

Drying time depends on the power of your oven In most cases drying is accomplished by irradiating at maximum power for 1-2 minutes per specimen although it is often a case of trial and error It is best to process no more than 10-12 specimens of average thickness per batch Specimens are usually dried after the moisture that characteristically appears on the glass door has disappeared If the specimen is damp when taken out of the oven allow it to stand before re-radiating as moisture continues to evaporate from the specimen for some time Care must be taken not to irradiate the specimens for too long

It should be noted that microwave treatment damages seeds and the cellular structure of the plants which may reduce the long-term value of the specimens

85

Alternative drying techniquesSilica gelother desiccants amp freeze drying Alternative methods of drying plant specimens have been

used for some time but are mostly restricted to special purpose collections The main alternatives are freeze-drying and drying in a desiccant powder such as desiccant silica gel In general these techniques are used where it is essential to preserve the shape of a delicate plant of organ of the plant such as the flower Freeze-drying has also been used to preserve the chemical composition of a plant as accurately as possible for later study

Disadvantages and special conservation problems of specimens dried in these manners are that they are particularly susceptible to damage The dried parts are fragile lack support and often catch on packing materials They must therefore be packed especially carefully and stored in small boxes or tubes with some appropriate packing material that does not snag and break small projections Acid-free tissue paper is often used Drying in desiccant silica gel crystals or powder can also have the disadvantage that it is difficult to remove all traces of the silica gel after drying

86

Special preservation and processing techniquesWet or spirit collections

Very fleshy or delicate structures including small algae and orchid flowers are best preserved in an air-tight glass or plastic jar with a liquid preservative rather than by drying The type of preservative used should be clearly labelled in the jar Such material is often referred to as a spirit collection or wet collection

Most material can be satisfactorily preserved in 70 ethyl alcohol (or 70 methylated spirit or denatured alcohol) with 30 water Colours will fade quickly in spirit however so it is a good idea to keep comprehensive notes and photographs

87

Small algae Microscopic algae are often collected in a jar and in the

water in which they were found If the algae are to be stored for more than 2-3 days a preservative needs to be used Traditionally this has been the extremely toxic formalin - a small amount can be added to the water to make a 5 final solution and the container labelled This must not be sent through the post or by courier

There are some other equally toxic options for example propylene phenoxytol but none should be sent through the post A safer option is to add sufficient concentrated alcohol or methylated spirits to the water containing the algae to make a final solution of 70 alcohol This treatment dilutes the algae making them difficult to find so if they can be concentrated somehow first (eg by filtering) they can be stored in much less liquid Another option is to fix the algae in formalin (or something similar) first and then prepare a microscope glass slide with a permanent water-soluble mounting medium

88

Mounting Mounting specimens prevents most fragile material from

fragmenting and prevents specimens becoming separated from their labels If the plant collection is a long-term project specimens should be mounted on sheets of archival (permanent) cardboard or paper with archival-quality fixing media These include stitching with cotton thread dental floss nickel-plated copper wire (for heavier specimens) narrow strips of archival paper linen tape or by using an archival adhesive such as methyl cellulose adhesive

One disadvantage of mounting specimens is that it can make parts of the specimen inaccessible for examination so it is essential that this be borne in mind during specimen arrangement and mounting For example easily reversible mounting media should be used specimens should be strapped to the sheet rather than glued all over and the specimen should be carefully arranged before it is attached so that it shows all features

89

Full-size herbarium mounting sheets are usually about 43 cm long x 28 cm wide The plant name and accompanying field notes should be transcribed on a permanent label stuck to one corner of the herbarium sheet (the bottom right-hand corner being the most common) or sometimes annotations may be written directly on the sheet or card

Small pieces of material which may have become separated from the specimen (eg seeds) can be placed in small plastic bags and pinned to the sheet

90

Long-term preservation and storage The long-term preservation of dry plant

specimens is largely dependent on protection from insect attack Specimens collected by Linnaeus in the eighteenth century and by Banks and Solander on the Endeavour voyage in 1788 are still excellently preserved

91

Pests and their control A range of pests attack dried plant material The

most common pests are insects and fungi though rodents and other large animals can cause damage in poor storage conditions Insects eat the material the paper surrounding the material and the adhesives and mounting media

Such insect pests range from psocids (book lice) which attack mainly the softer parts such as flowers and soft fruits to tobacco beetles and carpet beetles which can bore holes through the toughest of specimens Many insects are particularly sensitive to relative humidity levels and do not thrive at levels below 50

92

The most common and acceptable specimen treatments for insect control are Freezing Microwave Poisoning Insect deterrents Fungal pests

93

Storage

Dried and pressed plant specimens can be stored in cardboard or plastic boxes or tied in bundles in light-weight cardboard folders placed in pigeon holes

Alternatively they can be placed in protective plastic jackets and displayed in ring folders which is recommended if they are to be frequently handled such as for a reference collection

94

Filing

Specimens should be filed in a systematic order if a relatively permanent collection is being made The major groups ie ferns and fern allies cycads conifers dicotyledons and monocotyledons are best kept separately or according to some classification scheme such as that given in a flora or handbook

Similarly the genera within each family and the species within each genus may be filed alphabetically or following some such classification

95

Preservation of entire animals

Types of collection specimens of an entire animal For reference collections mammals can be prepared as a variety of specimens The condition of the specimen may determine possible ways to preserve it if for instance decomposition of the skin has loosened the hair of a carcass so much that it can easily be pulled out or removed by rubbing (ldquoslippingrdquo fur) it will be very difficult or impossible to produce a study skin or mounted specimen The most usual types of specimens (based on Nagorsen and Peterson 1980) are 1) entire fluid-preserved animals (for studying anatomy and histology fluid preservation may change the fur colour) 2) study skins with accompanying skulls partial skeletons (some bones remain in the skin) for studying pelage colour hair quality and moulting patterns 3) mounted skins with accompanying partial or entire skeleton (some bones may remain in the skin dependant on the method of preservation) or freeze-dried specimens 4) entire skeletons for instance for studying anatomy geographic variation or for age determination (entire skeletons are poorly represented in collections so Nagorsen and Peterson (1980) recommend preparation of at least one male and one female skeleton per species

96

Preservation of specimens in the field Formalin preservation Preservation in alcohol Preservation by cooling or freezing

97

Formalin preservation After weighing and measuring the animal and attaching an

adequate label very small specimens (up to 100 g) can be fixed whole by submerging them in 10 buffered formalin (tissue - formalin solution ratio of at least 1 12) the body cavity can be filled with formalin solution by injection until it is turgid and firm some formalin may also be injected under the skin into the body cavity larger muscles and organs If hypodermic needles are not available the body cavity can be opened ventrally by making a slit instead allowing the formalin to enter

Keeping the mouth open with a piece of wood or cotton may later allow examination of teeth Then the whole body can be immersed in formalin in the posture in which it is supposed to stay permanently because it will harden The ratio of formalin to carcass must be at least 12 to 1 to assure a good fixation Tissues can be left in buffered neutralized formalin for several months but formalin hardens specimens therefore after fixation longterm storage in alcohol may be better After preservation the carcass should therefore be washed in water and transferred into ethanol for permanent storage

Disadvantages for instance it discolours the fur after a longish immersion softens the bones and prevents further examination for microbiology

98

Preservation in alcohol

After weighing a whole animal can be preserved in a container of alcohol (70-90) Removal of the intestine prior to storage of the animal in alcohol is recommended

99

Preservation by cooling or freezing Removal of the skin with insulating fur

before cooling or freezing may help to cool the carcass down more quickly

Freezing is not recommended if histological examination is planned

100

THANK YOU

23

Line transect methodA measured line is laidacross the area in thedirection of theenvironmental gradientndash The species touching theline can be recordedalong the whole length ofthe line (continuoussampling) or at specificpoints along the line(systematic sampling)

24

Line Transect- useful where a transition of flora andor fauna

occurs- a string or tape is stretched out along the

ground in a straight line record the organisms touching or covering

the line all along its length or at regular intervals

- Profile transect when there is appreciable height change along the transect and thus affecting the distribution of its species

25

Belt transect method

Similar to line transect butwidens the sampling areandash Transect line is laid outndash Samples are taken bydetermining abundance or cover in an area that is adefined distance from the linendash Samples can be taken all

theway along the line at specificintervals or even randomly

26

Belt TransectIt is a strip usually a metre wide marked by putting a

second line parallel to the other The species between the lines are carefully recorded working a metre at a time

Alternatively a frame quadrat in conjunction with a single line transect could be used

Using a quadrat along a belt transect eg ladder transect (every 5m)

27

Point Frames- for grassland field study of dense vegetation

28

STRATIFIED SAMPLING1048698 Often used whenthere are smallareas within alarger habitat thatare clearly different1048698 Strata- majordifferences withincommunitiesrecognized beforesampling begins

29

RANDOM SAMPLING

1048698 Often used when the area being studied isfairly uniform very large or when there is alimited amount of time available1048698 Random = chosen by chance rather thanaccording to a plan all outcomes are

equallylikely1048698 Samples are taken from different positionswithin a habitat and those positions arechosen randomly

30

How to sample randomly

Choose individuals or Placeldquosampling unitsrdquo

haphazardlyndash This is rarely completely

random1048698 ORhellip1048698 Assign numbers to the

areasor individuals to be sampledndash Use a random number

table toselect which areas or

individualswill be sample

31

Population Attributes Density ndash size of a population in relation to a definite

unit of space Affected by

Natality ndash the reproductive output (birth rate) of a population

Mortality ndash the death rate of organisms in a population

Immigration ndash number of organisms moving into the area occupied by the population

Emigration ndash number of organisms moving out of the area occupied by the population

32

Population Density

Four primary population parameters

33

Two Types of Density Estimates

bull Absolute Density ndash a known density such as m2

bull Relative Density ndash we know when one area has more individuals than another

34

Measuring Absolute Density

Total Count ndash count the number of organisms living in an area Human census number of oak trees in a

wooded lot number of singing birds in an area

Total counts generally are not used very often

Sampling Methods ndash use a sample to estimate population size Either use the quadrat or capture-

recapture method

35

Measurement of Environmental ParametersAbiotic factors are important in determining

both the distribution of the organisms and their physical and physiological adaptations

Temperature- diurnal and seasonal temperature variations

are significant in affecting different species of plants and animals

- equipment mercury thermometer maximum-minimum thermometer

miniaturized thermistor

36

pH

-measure pH of a solution by universal indicator pH paper pH meter etc

Light

-measure its duration and intensity duration by predication from Royal Observatory intensity by photographic light meter

pH meter in use

37

Humidity

Relative humidity the water content of a given volume of air relative to the same volume of fully saturated air

- equipment whirling hygrometer

38

Wind and Water Speed- wind speed- anemometer or wind

gauges- water speed - time the movement of a

floating object over a measured distance

39

Salinity

- using a conductivity meter greater salinity has greater conductivity

Oxygen Level

- using an oxygen meter or chemical method (Winkler method)

40

Collecting MethodsCollecting all organisms within a habitat is normally

impractical and therefore small areas are selected Remember to return all material to its original position

after searching amp collecting sufficient specimens Some collecting apparatus for general use are listed

below

41

1 specimen tube

2 screwed-topped jars

3 polythene bags

4 forceps

5 paint brush

6 bulb pipette

7 pooter

42

8 widger 9 sieve 10 hand lens

11 enamel dish 12 beating tray 13 light traps

14 Tullgren funnel 15 Baermann funnel 16 mammal traps

17 pitfall traps 18 netting

43

Estimating Population Size

The exact methods used for estimation depend not only the nature of the habitat but also on the organisms involved

eg animals - population

plants - percentage cover

44

Using Quadrats

- By sampling an area using quadrats and counting the number of individuals within each quadrat it is possible to estimate the total number of individuals within the area

- confined to plants and sessile or very slow-moving animals

- fast-moving animals are disturbed and run away

45

Capture-recapture Techniques- useful for mobile animals which can be marked

- capture marked released randomly recaptured

and marked individuals recorded

no of marked individuals recaptured total no of individuals in 1st sample

-------------------------------------------- = ------------------------------------------

total no of individuals in 2nd sample estimated size of population

(the Lincoln Index)

46

Capture-recapture Techniques Factors affecting the accuracy of the estimation

deaths migration individuals become more liable to predation etc

Examples

- arthropods marked on their backs with non-toxic paint

- fish have tags attached to opercula - mammals have tags clipped to their ears

birds have their legs ringed

47

Capture-recapture Method Important tool for estimating density birth

rate and death rate for mobile animals Method

Collect a sample of individuals mark them and then release them

After a period collect more individuals from the wild and count the number that have marks

We assume that a sample if random will contain the same proportion of marked individuals as the population does

Estimate population density

48

Assumptions For All Capture-Recapture Studies Marking technique does not increase

mortality of marked animals Marked individuals are allowed to mix

with population Marking technique does not affect catch

probability Marks are not lost or overlooked No significant immigration or emigration No significant mortality or natality

49

Marked animals in second sample

Total caught in second sample

Marked animals in first sample

Total population size

=

520 N

16=

Peterson Method or Lincoln Index

N = 64N = (20)(16)5

50

Some Indices Used

Traps Number of Fecal

Pellets Vocalization

Frequency Pelt Records Catch per Unit

Fishing Effort

Number of Artifacts Questionnaires Cover Feeding Capacity Roadside Counts

51

Abundance Scales

The population size may be fairly accurately determined by making some form of frequency assessment

These are subjective and involve an experimenter making some estimate of the number of individuals in a given area or the cover of a particular species

This is especially useful where individuals are very numerous eg barnacles on a rocky shore or where it is difficult to distinguish individuals eg grass plants in a meadow

52

The assessments are usually made on an abundance scale of 5 categories

Abundance Common Frequent Occasional Rare

Barnacles exposed at low water

53

Environmental resistance are the factors which limit the growth of a particular population

eg predation disease availability of light food water oxygen and shelter the accumulation of toxic wastes and even the size of the population itself

54

Density-dependent Growth A population is a density-dependent when its size

(or density) affects its growth rate because of density-dependent factors such as food availability and toxic waste accumulation

Density-independent Growth In this type of growth a population increases until

some factor causes a sudden reduction in its size Its effect is the same regardless of the size of the

population eg temperature fires floods storms etc

55

Regulation of Population Size Fecundity is the reproductive capacity of individual

females of a species Birth rate or natality is used to measure fecundity Death rate or mortality is the number of individuals

of a species which die per unit time Immigration occurs when individuals join a

population from neighbouring ones Emigration occurs when individuals depart from a

population A cycle occurs when the size of a population

fluctuates on a regular basis

56

Ecological Sampling

57

Why Do We Sample Determine presence andor

abundance

Monitor population fluctuations

Assess lsquoecological damagersquo

Assess quality of habitat

Assess population responses

58

What Do We Sample

Physical Environment Temperature DO pH salinity clarity

flow sediment

Biotic Environment All living things

59

Physical Habitat Temperature

Mercury thermometer Electronic thermometer Long-term thermometers

Dissolved Oxygen Winkler method (titration) DO meter (electrode)

pH Litmus paper pH meter (electrode)

Salinity Salinity Meter YSI 550A DO Meter w12 cable

60

Water Clarity Secchi Disk

Disk is attached to a calibrated rope The disk is lowered into the water until the white parts can no longer be seen Secchi disk depth is then recorded and serves as the waters transparency index The clearer the water the greater the secchi disk depth

Secchi Disk

61

Current Velocity (flow) Floating-orange method

Put an orange (or something else that floats just below the water surface) and measure the time it takes it to float across a known distance

Odometer-type flow meter Number of revolutions the propeller

makes for a given time is calibrated to flow velocity

62

Sediment Sediment size is important to many

aquatic organisms Sieversquos are used to separate and

grade sediment samples Percent of each size grade can be

determined

63

Water Sample

Water and plankton from various depths can be collected

A trigger mechanism is used to close the sampler Sample is then brought back to the

surface

64

Small Mammals

Mouserat Traps Fatal

Pit Falls Bucket is placed in the ground Sometimes have lsquoleadsrsquo to the buckets

Live traps Havahart Sherman

Spot-light

Sherman trapHavahart trap

65

Birds Stick-under-the-box method Bird-trap

Works like a minnow trap Mist net

Captures birds in flight Rocket net

Uses a propellant to throw a net over birds

66

Terrestrial Insects

Sticky paper flies

Baited Traps Fire ants

Nets butterflies

Foggers Collect insects from tree canopies

67

Aquatic Insects Drift Net

Place net in flowing water Kick Net

lsquoKickrsquo sediment upstream from block net and the flow will wash them into the net

Wash bucket Serber or Hess Sampler

Stir up known area of sediment

Animals are collected by a catch net

Multi-plate Sampler Become colonized

68

Crawfish and Crab Traps

69

Fish Larvae Light Traps

Larvae are attracted to the light Ichthyoplankton nets

Can be towed at various depths Fish collect at the lsquocodrsquoend

70

Fish Lift net

Net is placed down and after a set amount of time it is quickly lifted

Pop-net Similar to a lift net but

floats are attached to a framed net

Operated by a trigger mechanism

Throw net A net attached to a heavy

frame is thrown and every thing inside is netted out Throw net

Pop-net

Lift net

71

Minnow trap

Usually use bait to attract small fish Light is used sometimes as an attractant

72

Fish Electrofishing

Electricity is put into the water Fish are temporarily stunned and usually

swim towards the electricity source Usually non-fatal but may cause some

damage

73

Fish Gill Net

Gill nets resemble tennis nets Fish can not swim completely through the

net and get caught Gill nets are size selective (based on mesh

size) Square Mesh

Bar mesh

Stretch mesh

74

Fish Trammel Net

Three panels two large mesh on the outside and a small mesh on the inside

Fish swim through the outer mesh pushes the small mesh through the other side and becomes entangled

75

Hoop nets (and other similar nets) can have bait or not

Fyke nets have leads to help guide fish to the net

76

Seine Seines are nets that are pulled

through shallow water to catch fish

77

Purse Seine Used to encircle entire schools of fish

Usually involves a spotter plane and a second boat

78

Trotline (longline) A series of baited drop lines

connected to a main line

Can be deployed by tying one end to the bank and tying the other end with a heavy weight

79

Shrimp (or fish) Trawl Net pulled behind

a boat along the bottom Either a beam or

otter boards keep the net open

80

Tagging Individuals Coded Wire Tags

Microwire that has a unique label

Magnetic wand detects the tag

Tag retention should be determined

T-Bar tags Can be individually

numbered External tag

PIT tags (Passive Integrated Transponders) Wand induces the tag to

transmit individual number is displayed

81

Other Tagging Methods

Toe clip Amphibian and reptile Clip of one or more toes

to identify individuals

Bird Band Place a metal band on a

bird leg Generally has

identification information

82

Preserving plant specimens Pressing and drying Long-term

preservation and storage

Alternative drying techniques

Special preservation and processing techniques

Mounting

83

Pressing and drying Techniques for pressing and drying specimens have been

established for many years There are minor variations in recommended methods but they are essentially the same worldwide

The best specimens are plants that are pressed as soon as possible after collection before wilting and shrivelling Most plants may be kept in sealed containers such as plastic bags for up to a day if it is inconvenient to press immediately However some plants show such rapid wilting particularly of the flowers that such delays are best avoided Flowers with a lot of nectar may go mouldy very quickly if excess nectar is not shaken off before pressing

Specimens are pressed flat and dried between sheets of absorbent blotters or semi-absorbent paper such as newspaper Papers with a glossy surface should be avoided because they are not absorbent enough to aid drying The plant should be carefully laid out between the drying sheets as their form at this stage largely determines their ultimate appearance The flowers should be spread out with the petals carefully arranged wilted leaves should be straightened and unnecessary shoots of excessively twiggy shrubs may be cut away

84

Microwave ovens Small numbers of specimens can be dried using a microwave

oven The technique recommended in the literature is to place the specimens between unprinted absorbent paper for example butchers paper not newspaper which is unsuitable because the chemicals present in the ink may cause a fire The specimens should be put in a special press which should be of a microwave-safe material (wood acrylic or polycarbonate sheeting eg plexiglass or perspex NO metal components) If such a press is not available sheets of cardboard can be placed above and below the specimens and then weighted down

Drying time depends on the power of your oven In most cases drying is accomplished by irradiating at maximum power for 1-2 minutes per specimen although it is often a case of trial and error It is best to process no more than 10-12 specimens of average thickness per batch Specimens are usually dried after the moisture that characteristically appears on the glass door has disappeared If the specimen is damp when taken out of the oven allow it to stand before re-radiating as moisture continues to evaporate from the specimen for some time Care must be taken not to irradiate the specimens for too long

It should be noted that microwave treatment damages seeds and the cellular structure of the plants which may reduce the long-term value of the specimens

85

Alternative drying techniquesSilica gelother desiccants amp freeze drying Alternative methods of drying plant specimens have been

used for some time but are mostly restricted to special purpose collections The main alternatives are freeze-drying and drying in a desiccant powder such as desiccant silica gel In general these techniques are used where it is essential to preserve the shape of a delicate plant of organ of the plant such as the flower Freeze-drying has also been used to preserve the chemical composition of a plant as accurately as possible for later study

Disadvantages and special conservation problems of specimens dried in these manners are that they are particularly susceptible to damage The dried parts are fragile lack support and often catch on packing materials They must therefore be packed especially carefully and stored in small boxes or tubes with some appropriate packing material that does not snag and break small projections Acid-free tissue paper is often used Drying in desiccant silica gel crystals or powder can also have the disadvantage that it is difficult to remove all traces of the silica gel after drying

86

Special preservation and processing techniquesWet or spirit collections

Very fleshy or delicate structures including small algae and orchid flowers are best preserved in an air-tight glass or plastic jar with a liquid preservative rather than by drying The type of preservative used should be clearly labelled in the jar Such material is often referred to as a spirit collection or wet collection

Most material can be satisfactorily preserved in 70 ethyl alcohol (or 70 methylated spirit or denatured alcohol) with 30 water Colours will fade quickly in spirit however so it is a good idea to keep comprehensive notes and photographs

87

Small algae Microscopic algae are often collected in a jar and in the

water in which they were found If the algae are to be stored for more than 2-3 days a preservative needs to be used Traditionally this has been the extremely toxic formalin - a small amount can be added to the water to make a 5 final solution and the container labelled This must not be sent through the post or by courier

There are some other equally toxic options for example propylene phenoxytol but none should be sent through the post A safer option is to add sufficient concentrated alcohol or methylated spirits to the water containing the algae to make a final solution of 70 alcohol This treatment dilutes the algae making them difficult to find so if they can be concentrated somehow first (eg by filtering) they can be stored in much less liquid Another option is to fix the algae in formalin (or something similar) first and then prepare a microscope glass slide with a permanent water-soluble mounting medium

88

Mounting Mounting specimens prevents most fragile material from

fragmenting and prevents specimens becoming separated from their labels If the plant collection is a long-term project specimens should be mounted on sheets of archival (permanent) cardboard or paper with archival-quality fixing media These include stitching with cotton thread dental floss nickel-plated copper wire (for heavier specimens) narrow strips of archival paper linen tape or by using an archival adhesive such as methyl cellulose adhesive

One disadvantage of mounting specimens is that it can make parts of the specimen inaccessible for examination so it is essential that this be borne in mind during specimen arrangement and mounting For example easily reversible mounting media should be used specimens should be strapped to the sheet rather than glued all over and the specimen should be carefully arranged before it is attached so that it shows all features

89

Full-size herbarium mounting sheets are usually about 43 cm long x 28 cm wide The plant name and accompanying field notes should be transcribed on a permanent label stuck to one corner of the herbarium sheet (the bottom right-hand corner being the most common) or sometimes annotations may be written directly on the sheet or card

Small pieces of material which may have become separated from the specimen (eg seeds) can be placed in small plastic bags and pinned to the sheet

90

Long-term preservation and storage The long-term preservation of dry plant

specimens is largely dependent on protection from insect attack Specimens collected by Linnaeus in the eighteenth century and by Banks and Solander on the Endeavour voyage in 1788 are still excellently preserved

91

Pests and their control A range of pests attack dried plant material The

most common pests are insects and fungi though rodents and other large animals can cause damage in poor storage conditions Insects eat the material the paper surrounding the material and the adhesives and mounting media

Such insect pests range from psocids (book lice) which attack mainly the softer parts such as flowers and soft fruits to tobacco beetles and carpet beetles which can bore holes through the toughest of specimens Many insects are particularly sensitive to relative humidity levels and do not thrive at levels below 50

92

The most common and acceptable specimen treatments for insect control are Freezing Microwave Poisoning Insect deterrents Fungal pests

93

Storage

Dried and pressed plant specimens can be stored in cardboard or plastic boxes or tied in bundles in light-weight cardboard folders placed in pigeon holes

Alternatively they can be placed in protective plastic jackets and displayed in ring folders which is recommended if they are to be frequently handled such as for a reference collection

94

Filing

Specimens should be filed in a systematic order if a relatively permanent collection is being made The major groups ie ferns and fern allies cycads conifers dicotyledons and monocotyledons are best kept separately or according to some classification scheme such as that given in a flora or handbook

Similarly the genera within each family and the species within each genus may be filed alphabetically or following some such classification

95

Preservation of entire animals

Types of collection specimens of an entire animal For reference collections mammals can be prepared as a variety of specimens The condition of the specimen may determine possible ways to preserve it if for instance decomposition of the skin has loosened the hair of a carcass so much that it can easily be pulled out or removed by rubbing (ldquoslippingrdquo fur) it will be very difficult or impossible to produce a study skin or mounted specimen The most usual types of specimens (based on Nagorsen and Peterson 1980) are 1) entire fluid-preserved animals (for studying anatomy and histology fluid preservation may change the fur colour) 2) study skins with accompanying skulls partial skeletons (some bones remain in the skin) for studying pelage colour hair quality and moulting patterns 3) mounted skins with accompanying partial or entire skeleton (some bones may remain in the skin dependant on the method of preservation) or freeze-dried specimens 4) entire skeletons for instance for studying anatomy geographic variation or for age determination (entire skeletons are poorly represented in collections so Nagorsen and Peterson (1980) recommend preparation of at least one male and one female skeleton per species

96

Preservation of specimens in the field Formalin preservation Preservation in alcohol Preservation by cooling or freezing

97

Formalin preservation After weighing and measuring the animal and attaching an

adequate label very small specimens (up to 100 g) can be fixed whole by submerging them in 10 buffered formalin (tissue - formalin solution ratio of at least 1 12) the body cavity can be filled with formalin solution by injection until it is turgid and firm some formalin may also be injected under the skin into the body cavity larger muscles and organs If hypodermic needles are not available the body cavity can be opened ventrally by making a slit instead allowing the formalin to enter

Keeping the mouth open with a piece of wood or cotton may later allow examination of teeth Then the whole body can be immersed in formalin in the posture in which it is supposed to stay permanently because it will harden The ratio of formalin to carcass must be at least 12 to 1 to assure a good fixation Tissues can be left in buffered neutralized formalin for several months but formalin hardens specimens therefore after fixation longterm storage in alcohol may be better After preservation the carcass should therefore be washed in water and transferred into ethanol for permanent storage

Disadvantages for instance it discolours the fur after a longish immersion softens the bones and prevents further examination for microbiology

98

Preservation in alcohol

After weighing a whole animal can be preserved in a container of alcohol (70-90) Removal of the intestine prior to storage of the animal in alcohol is recommended

99

Preservation by cooling or freezing Removal of the skin with insulating fur

before cooling or freezing may help to cool the carcass down more quickly

Freezing is not recommended if histological examination is planned

100

THANK YOU

24

Line Transect- useful where a transition of flora andor fauna

occurs- a string or tape is stretched out along the

ground in a straight line record the organisms touching or covering

the line all along its length or at regular intervals

- Profile transect when there is appreciable height change along the transect and thus affecting the distribution of its species

25

Belt transect method

Similar to line transect butwidens the sampling areandash Transect line is laid outndash Samples are taken bydetermining abundance or cover in an area that is adefined distance from the linendash Samples can be taken all

theway along the line at specificintervals or even randomly

26

Belt TransectIt is a strip usually a metre wide marked by putting a

second line parallel to the other The species between the lines are carefully recorded working a metre at a time

Alternatively a frame quadrat in conjunction with a single line transect could be used

Using a quadrat along a belt transect eg ladder transect (every 5m)

27

Point Frames- for grassland field study of dense vegetation

28

STRATIFIED SAMPLING1048698 Often used whenthere are smallareas within alarger habitat thatare clearly different1048698 Strata- majordifferences withincommunitiesrecognized beforesampling begins

29

RANDOM SAMPLING

1048698 Often used when the area being studied isfairly uniform very large or when there is alimited amount of time available1048698 Random = chosen by chance rather thanaccording to a plan all outcomes are

equallylikely1048698 Samples are taken from different positionswithin a habitat and those positions arechosen randomly

30

How to sample randomly

Choose individuals or Placeldquosampling unitsrdquo

haphazardlyndash This is rarely completely

random1048698 ORhellip1048698 Assign numbers to the

areasor individuals to be sampledndash Use a random number

table toselect which areas or

individualswill be sample

31

Population Attributes Density ndash size of a population in relation to a definite

unit of space Affected by

Natality ndash the reproductive output (birth rate) of a population

Mortality ndash the death rate of organisms in a population

Immigration ndash number of organisms moving into the area occupied by the population

Emigration ndash number of organisms moving out of the area occupied by the population

32

Population Density

Four primary population parameters

33

Two Types of Density Estimates

bull Absolute Density ndash a known density such as m2

bull Relative Density ndash we know when one area has more individuals than another

34

Measuring Absolute Density

Total Count ndash count the number of organisms living in an area Human census number of oak trees in a

wooded lot number of singing birds in an area

Total counts generally are not used very often

Sampling Methods ndash use a sample to estimate population size Either use the quadrat or capture-

recapture method

35

Measurement of Environmental ParametersAbiotic factors are important in determining

both the distribution of the organisms and their physical and physiological adaptations

Temperature- diurnal and seasonal temperature variations

are significant in affecting different species of plants and animals

- equipment mercury thermometer maximum-minimum thermometer

miniaturized thermistor

36

pH

-measure pH of a solution by universal indicator pH paper pH meter etc

Light

-measure its duration and intensity duration by predication from Royal Observatory intensity by photographic light meter

pH meter in use

37

Humidity

Relative humidity the water content of a given volume of air relative to the same volume of fully saturated air

- equipment whirling hygrometer

38

Wind and Water Speed- wind speed- anemometer or wind

gauges- water speed - time the movement of a

floating object over a measured distance

39

Salinity

- using a conductivity meter greater salinity has greater conductivity

Oxygen Level

- using an oxygen meter or chemical method (Winkler method)

40

Collecting MethodsCollecting all organisms within a habitat is normally

impractical and therefore small areas are selected Remember to return all material to its original position

after searching amp collecting sufficient specimens Some collecting apparatus for general use are listed

below

41

1 specimen tube

2 screwed-topped jars

3 polythene bags

4 forceps

5 paint brush

6 bulb pipette

7 pooter

42

8 widger 9 sieve 10 hand lens

11 enamel dish 12 beating tray 13 light traps

14 Tullgren funnel 15 Baermann funnel 16 mammal traps

17 pitfall traps 18 netting

43

Estimating Population Size

The exact methods used for estimation depend not only the nature of the habitat but also on the organisms involved

eg animals - population

plants - percentage cover

44

Using Quadrats

- By sampling an area using quadrats and counting the number of individuals within each quadrat it is possible to estimate the total number of individuals within the area

- confined to plants and sessile or very slow-moving animals

- fast-moving animals are disturbed and run away

45

Capture-recapture Techniques- useful for mobile animals which can be marked

- capture marked released randomly recaptured

and marked individuals recorded

no of marked individuals recaptured total no of individuals in 1st sample

-------------------------------------------- = ------------------------------------------

total no of individuals in 2nd sample estimated size of population

(the Lincoln Index)

46

Capture-recapture Techniques Factors affecting the accuracy of the estimation

deaths migration individuals become more liable to predation etc

Examples

- arthropods marked on their backs with non-toxic paint

- fish have tags attached to opercula - mammals have tags clipped to their ears

birds have their legs ringed

47

Capture-recapture Method Important tool for estimating density birth

rate and death rate for mobile animals Method

Collect a sample of individuals mark them and then release them

After a period collect more individuals from the wild and count the number that have marks

We assume that a sample if random will contain the same proportion of marked individuals as the population does

Estimate population density

48

Assumptions For All Capture-Recapture Studies Marking technique does not increase

mortality of marked animals Marked individuals are allowed to mix

with population Marking technique does not affect catch

probability Marks are not lost or overlooked No significant immigration or emigration No significant mortality or natality

49

Marked animals in second sample

Total caught in second sample

Marked animals in first sample

Total population size

=

520 N

16=

Peterson Method or Lincoln Index

N = 64N = (20)(16)5

50

Some Indices Used

Traps Number of Fecal

Pellets Vocalization

Frequency Pelt Records Catch per Unit

Fishing Effort

Number of Artifacts Questionnaires Cover Feeding Capacity Roadside Counts

51

Abundance Scales

The population size may be fairly accurately determined by making some form of frequency assessment

These are subjective and involve an experimenter making some estimate of the number of individuals in a given area or the cover of a particular species

This is especially useful where individuals are very numerous eg barnacles on a rocky shore or where it is difficult to distinguish individuals eg grass plants in a meadow

52

The assessments are usually made on an abundance scale of 5 categories

Abundance Common Frequent Occasional Rare

Barnacles exposed at low water

53

Environmental resistance are the factors which limit the growth of a particular population

eg predation disease availability of light food water oxygen and shelter the accumulation of toxic wastes and even the size of the population itself

54

Density-dependent Growth A population is a density-dependent when its size

(or density) affects its growth rate because of density-dependent factors such as food availability and toxic waste accumulation

Density-independent Growth In this type of growth a population increases until

some factor causes a sudden reduction in its size Its effect is the same regardless of the size of the

population eg temperature fires floods storms etc

55

Regulation of Population Size Fecundity is the reproductive capacity of individual

females of a species Birth rate or natality is used to measure fecundity Death rate or mortality is the number of individuals

of a species which die per unit time Immigration occurs when individuals join a

population from neighbouring ones Emigration occurs when individuals depart from a

population A cycle occurs when the size of a population

fluctuates on a regular basis

56

Ecological Sampling

57

Why Do We Sample Determine presence andor

abundance

Monitor population fluctuations

Assess lsquoecological damagersquo

Assess quality of habitat

Assess population responses

58

What Do We Sample

Physical Environment Temperature DO pH salinity clarity

flow sediment

Biotic Environment All living things

59

Physical Habitat Temperature

Mercury thermometer Electronic thermometer Long-term thermometers

Dissolved Oxygen Winkler method (titration) DO meter (electrode)

pH Litmus paper pH meter (electrode)

Salinity Salinity Meter YSI 550A DO Meter w12 cable

60

Water Clarity Secchi Disk

Disk is attached to a calibrated rope The disk is lowered into the water until the white parts can no longer be seen Secchi disk depth is then recorded and serves as the waters transparency index The clearer the water the greater the secchi disk depth

Secchi Disk

61

Current Velocity (flow) Floating-orange method

Put an orange (or something else that floats just below the water surface) and measure the time it takes it to float across a known distance

Odometer-type flow meter Number of revolutions the propeller

makes for a given time is calibrated to flow velocity

62

Sediment Sediment size is important to many

aquatic organisms Sieversquos are used to separate and

grade sediment samples Percent of each size grade can be

determined

63

Water Sample

Water and plankton from various depths can be collected

A trigger mechanism is used to close the sampler Sample is then brought back to the

surface

64

Small Mammals

Mouserat Traps Fatal

Pit Falls Bucket is placed in the ground Sometimes have lsquoleadsrsquo to the buckets

Live traps Havahart Sherman

Spot-light

Sherman trapHavahart trap

65

Birds Stick-under-the-box method Bird-trap

Works like a minnow trap Mist net

Captures birds in flight Rocket net

Uses a propellant to throw a net over birds

66

Terrestrial Insects

Sticky paper flies

Baited Traps Fire ants

Nets butterflies

Foggers Collect insects from tree canopies

67

Aquatic Insects Drift Net

Place net in flowing water Kick Net

lsquoKickrsquo sediment upstream from block net and the flow will wash them into the net

Wash bucket Serber or Hess Sampler

Stir up known area of sediment

Animals are collected by a catch net

Multi-plate Sampler Become colonized

68

Crawfish and Crab Traps

69

Fish Larvae Light Traps

Larvae are attracted to the light Ichthyoplankton nets

Can be towed at various depths Fish collect at the lsquocodrsquoend

70

Fish Lift net

Net is placed down and after a set amount of time it is quickly lifted

Pop-net Similar to a lift net but

floats are attached to a framed net

Operated by a trigger mechanism

Throw net A net attached to a heavy

frame is thrown and every thing inside is netted out Throw net

Pop-net

Lift net

71

Minnow trap

Usually use bait to attract small fish Light is used sometimes as an attractant

72

Fish Electrofishing

Electricity is put into the water Fish are temporarily stunned and usually

swim towards the electricity source Usually non-fatal but may cause some

damage

73

Fish Gill Net

Gill nets resemble tennis nets Fish can not swim completely through the

net and get caught Gill nets are size selective (based on mesh

size) Square Mesh

Bar mesh

Stretch mesh

74

Fish Trammel Net

Three panels two large mesh on the outside and a small mesh on the inside

Fish swim through the outer mesh pushes the small mesh through the other side and becomes entangled

75

Hoop nets (and other similar nets) can have bait or not

Fyke nets have leads to help guide fish to the net

76

Seine Seines are nets that are pulled

through shallow water to catch fish

77

Purse Seine Used to encircle entire schools of fish

Usually involves a spotter plane and a second boat

78

Trotline (longline) A series of baited drop lines

connected to a main line

Can be deployed by tying one end to the bank and tying the other end with a heavy weight

79

Shrimp (or fish) Trawl Net pulled behind

a boat along the bottom Either a beam or

otter boards keep the net open

80

Tagging Individuals Coded Wire Tags

Microwire that has a unique label

Magnetic wand detects the tag

Tag retention should be determined

T-Bar tags Can be individually

numbered External tag

PIT tags (Passive Integrated Transponders) Wand induces the tag to

transmit individual number is displayed

81

Other Tagging Methods

Toe clip Amphibian and reptile Clip of one or more toes

to identify individuals

Bird Band Place a metal band on a

bird leg Generally has

identification information

82

Preserving plant specimens Pressing and drying Long-term

preservation and storage

Alternative drying techniques

Special preservation and processing techniques

Mounting

83

Pressing and drying Techniques for pressing and drying specimens have been

established for many years There are minor variations in recommended methods but they are essentially the same worldwide

The best specimens are plants that are pressed as soon as possible after collection before wilting and shrivelling Most plants may be kept in sealed containers such as plastic bags for up to a day if it is inconvenient to press immediately However some plants show such rapid wilting particularly of the flowers that such delays are best avoided Flowers with a lot of nectar may go mouldy very quickly if excess nectar is not shaken off before pressing

Specimens are pressed flat and dried between sheets of absorbent blotters or semi-absorbent paper such as newspaper Papers with a glossy surface should be avoided because they are not absorbent enough to aid drying The plant should be carefully laid out between the drying sheets as their form at this stage largely determines their ultimate appearance The flowers should be spread out with the petals carefully arranged wilted leaves should be straightened and unnecessary shoots of excessively twiggy shrubs may be cut away

84

Microwave ovens Small numbers of specimens can be dried using a microwave

oven The technique recommended in the literature is to place the specimens between unprinted absorbent paper for example butchers paper not newspaper which is unsuitable because the chemicals present in the ink may cause a fire The specimens should be put in a special press which should be of a microwave-safe material (wood acrylic or polycarbonate sheeting eg plexiglass or perspex NO metal components) If such a press is not available sheets of cardboard can be placed above and below the specimens and then weighted down

Drying time depends on the power of your oven In most cases drying is accomplished by irradiating at maximum power for 1-2 minutes per specimen although it is often a case of trial and error It is best to process no more than 10-12 specimens of average thickness per batch Specimens are usually dried after the moisture that characteristically appears on the glass door has disappeared If the specimen is damp when taken out of the oven allow it to stand before re-radiating as moisture continues to evaporate from the specimen for some time Care must be taken not to irradiate the specimens for too long

It should be noted that microwave treatment damages seeds and the cellular structure of the plants which may reduce the long-term value of the specimens

85

Alternative drying techniquesSilica gelother desiccants amp freeze drying Alternative methods of drying plant specimens have been

used for some time but are mostly restricted to special purpose collections The main alternatives are freeze-drying and drying in a desiccant powder such as desiccant silica gel In general these techniques are used where it is essential to preserve the shape of a delicate plant of organ of the plant such as the flower Freeze-drying has also been used to preserve the chemical composition of a plant as accurately as possible for later study

Disadvantages and special conservation problems of specimens dried in these manners are that they are particularly susceptible to damage The dried parts are fragile lack support and often catch on packing materials They must therefore be packed especially carefully and stored in small boxes or tubes with some appropriate packing material that does not snag and break small projections Acid-free tissue paper is often used Drying in desiccant silica gel crystals or powder can also have the disadvantage that it is difficult to remove all traces of the silica gel after drying

86

Special preservation and processing techniquesWet or spirit collections

Very fleshy or delicate structures including small algae and orchid flowers are best preserved in an air-tight glass or plastic jar with a liquid preservative rather than by drying The type of preservative used should be clearly labelled in the jar Such material is often referred to as a spirit collection or wet collection

Most material can be satisfactorily preserved in 70 ethyl alcohol (or 70 methylated spirit or denatured alcohol) with 30 water Colours will fade quickly in spirit however so it is a good idea to keep comprehensive notes and photographs

87

Small algae Microscopic algae are often collected in a jar and in the

water in which they were found If the algae are to be stored for more than 2-3 days a preservative needs to be used Traditionally this has been the extremely toxic formalin - a small amount can be added to the water to make a 5 final solution and the container labelled This must not be sent through the post or by courier

There are some other equally toxic options for example propylene phenoxytol but none should be sent through the post A safer option is to add sufficient concentrated alcohol or methylated spirits to the water containing the algae to make a final solution of 70 alcohol This treatment dilutes the algae making them difficult to find so if they can be concentrated somehow first (eg by filtering) they can be stored in much less liquid Another option is to fix the algae in formalin (or something similar) first and then prepare a microscope glass slide with a permanent water-soluble mounting medium

88

Mounting Mounting specimens prevents most fragile material from

fragmenting and prevents specimens becoming separated from their labels If the plant collection is a long-term project specimens should be mounted on sheets of archival (permanent) cardboard or paper with archival-quality fixing media These include stitching with cotton thread dental floss nickel-plated copper wire (for heavier specimens) narrow strips of archival paper linen tape or by using an archival adhesive such as methyl cellulose adhesive

One disadvantage of mounting specimens is that it can make parts of the specimen inaccessible for examination so it is essential that this be borne in mind during specimen arrangement and mounting For example easily reversible mounting media should be used specimens should be strapped to the sheet rather than glued all over and the specimen should be carefully arranged before it is attached so that it shows all features

89

Full-size herbarium mounting sheets are usually about 43 cm long x 28 cm wide The plant name and accompanying field notes should be transcribed on a permanent label stuck to one corner of the herbarium sheet (the bottom right-hand corner being the most common) or sometimes annotations may be written directly on the sheet or card

Small pieces of material which may have become separated from the specimen (eg seeds) can be placed in small plastic bags and pinned to the sheet

90

Long-term preservation and storage The long-term preservation of dry plant

specimens is largely dependent on protection from insect attack Specimens collected by Linnaeus in the eighteenth century and by Banks and Solander on the Endeavour voyage in 1788 are still excellently preserved

91

Pests and their control A range of pests attack dried plant material The

most common pests are insects and fungi though rodents and other large animals can cause damage in poor storage conditions Insects eat the material the paper surrounding the material and the adhesives and mounting media

Such insect pests range from psocids (book lice) which attack mainly the softer parts such as flowers and soft fruits to tobacco beetles and carpet beetles which can bore holes through the toughest of specimens Many insects are particularly sensitive to relative humidity levels and do not thrive at levels below 50

92

The most common and acceptable specimen treatments for insect control are Freezing Microwave Poisoning Insect deterrents Fungal pests

93

Storage

Dried and pressed plant specimens can be stored in cardboard or plastic boxes or tied in bundles in light-weight cardboard folders placed in pigeon holes

Alternatively they can be placed in protective plastic jackets and displayed in ring folders which is recommended if they are to be frequently handled such as for a reference collection

94

Filing

Specimens should be filed in a systematic order if a relatively permanent collection is being made The major groups ie ferns and fern allies cycads conifers dicotyledons and monocotyledons are best kept separately or according to some classification scheme such as that given in a flora or handbook

Similarly the genera within each family and the species within each genus may be filed alphabetically or following some such classification

95

Preservation of entire animals

Types of collection specimens of an entire animal For reference collections mammals can be prepared as a variety of specimens The condition of the specimen may determine possible ways to preserve it if for instance decomposition of the skin has loosened the hair of a carcass so much that it can easily be pulled out or removed by rubbing (ldquoslippingrdquo fur) it will be very difficult or impossible to produce a study skin or mounted specimen The most usual types of specimens (based on Nagorsen and Peterson 1980) are 1) entire fluid-preserved animals (for studying anatomy and histology fluid preservation may change the fur colour) 2) study skins with accompanying skulls partial skeletons (some bones remain in the skin) for studying pelage colour hair quality and moulting patterns 3) mounted skins with accompanying partial or entire skeleton (some bones may remain in the skin dependant on the method of preservation) or freeze-dried specimens 4) entire skeletons for instance for studying anatomy geographic variation or for age determination (entire skeletons are poorly represented in collections so Nagorsen and Peterson (1980) recommend preparation of at least one male and one female skeleton per species

96

Preservation of specimens in the field Formalin preservation Preservation in alcohol Preservation by cooling or freezing

97

Formalin preservation After weighing and measuring the animal and attaching an

adequate label very small specimens (up to 100 g) can be fixed whole by submerging them in 10 buffered formalin (tissue - formalin solution ratio of at least 1 12) the body cavity can be filled with formalin solution by injection until it is turgid and firm some formalin may also be injected under the skin into the body cavity larger muscles and organs If hypodermic needles are not available the body cavity can be opened ventrally by making a slit instead allowing the formalin to enter

Keeping the mouth open with a piece of wood or cotton may later allow examination of teeth Then the whole body can be immersed in formalin in the posture in which it is supposed to stay permanently because it will harden The ratio of formalin to carcass must be at least 12 to 1 to assure a good fixation Tissues can be left in buffered neutralized formalin for several months but formalin hardens specimens therefore after fixation longterm storage in alcohol may be better After preservation the carcass should therefore be washed in water and transferred into ethanol for permanent storage

Disadvantages for instance it discolours the fur after a longish immersion softens the bones and prevents further examination for microbiology

98

Preservation in alcohol

After weighing a whole animal can be preserved in a container of alcohol (70-90) Removal of the intestine prior to storage of the animal in alcohol is recommended

99

Preservation by cooling or freezing Removal of the skin with insulating fur

before cooling or freezing may help to cool the carcass down more quickly

Freezing is not recommended if histological examination is planned

100

THANK YOU

25

Belt transect method

Similar to line transect butwidens the sampling areandash Transect line is laid outndash Samples are taken bydetermining abundance or cover in an area that is adefined distance from the linendash Samples can be taken all

theway along the line at specificintervals or even randomly

26

Belt TransectIt is a strip usually a metre wide marked by putting a

second line parallel to the other The species between the lines are carefully recorded working a metre at a time

Alternatively a frame quadrat in conjunction with a single line transect could be used

Using a quadrat along a belt transect eg ladder transect (every 5m)

27

Point Frames- for grassland field study of dense vegetation

28

STRATIFIED SAMPLING1048698 Often used whenthere are smallareas within alarger habitat thatare clearly different1048698 Strata- majordifferences withincommunitiesrecognized beforesampling begins

29

RANDOM SAMPLING

1048698 Often used when the area being studied isfairly uniform very large or when there is alimited amount of time available1048698 Random = chosen by chance rather thanaccording to a plan all outcomes are

equallylikely1048698 Samples are taken from different positionswithin a habitat and those positions arechosen randomly

30

How to sample randomly

Choose individuals or Placeldquosampling unitsrdquo

haphazardlyndash This is rarely completely

random1048698 ORhellip1048698 Assign numbers to the

areasor individuals to be sampledndash Use a random number

table toselect which areas or

individualswill be sample

31

Population Attributes Density ndash size of a population in relation to a definite

unit of space Affected by

Natality ndash the reproductive output (birth rate) of a population

Mortality ndash the death rate of organisms in a population

Immigration ndash number of organisms moving into the area occupied by the population

Emigration ndash number of organisms moving out of the area occupied by the population

32

Population Density

Four primary population parameters

33

Two Types of Density Estimates

bull Absolute Density ndash a known density such as m2

bull Relative Density ndash we know when one area has more individuals than another

34

Measuring Absolute Density

Total Count ndash count the number of organisms living in an area Human census number of oak trees in a

wooded lot number of singing birds in an area

Total counts generally are not used very often

Sampling Methods ndash use a sample to estimate population size Either use the quadrat or capture-

recapture method

35

Measurement of Environmental ParametersAbiotic factors are important in determining

both the distribution of the organisms and their physical and physiological adaptations

Temperature- diurnal and seasonal temperature variations

are significant in affecting different species of plants and animals

- equipment mercury thermometer maximum-minimum thermometer

miniaturized thermistor

36

pH

-measure pH of a solution by universal indicator pH paper pH meter etc

Light

-measure its duration and intensity duration by predication from Royal Observatory intensity by photographic light meter

pH meter in use

37

Humidity

Relative humidity the water content of a given volume of air relative to the same volume of fully saturated air

- equipment whirling hygrometer

38

Wind and Water Speed- wind speed- anemometer or wind

gauges- water speed - time the movement of a

floating object over a measured distance

39

Salinity

- using a conductivity meter greater salinity has greater conductivity

Oxygen Level

- using an oxygen meter or chemical method (Winkler method)

40

Collecting MethodsCollecting all organisms within a habitat is normally

impractical and therefore small areas are selected Remember to return all material to its original position

after searching amp collecting sufficient specimens Some collecting apparatus for general use are listed

below

41

1 specimen tube

2 screwed-topped jars

3 polythene bags

4 forceps

5 paint brush

6 bulb pipette

7 pooter

42

8 widger 9 sieve 10 hand lens

11 enamel dish 12 beating tray 13 light traps

14 Tullgren funnel 15 Baermann funnel 16 mammal traps

17 pitfall traps 18 netting

43

Estimating Population Size

The exact methods used for estimation depend not only the nature of the habitat but also on the organisms involved

eg animals - population

plants - percentage cover

44

Using Quadrats

- By sampling an area using quadrats and counting the number of individuals within each quadrat it is possible to estimate the total number of individuals within the area

- confined to plants and sessile or very slow-moving animals

- fast-moving animals are disturbed and run away

45

Capture-recapture Techniques- useful for mobile animals which can be marked

- capture marked released randomly recaptured

and marked individuals recorded

no of marked individuals recaptured total no of individuals in 1st sample

-------------------------------------------- = ------------------------------------------

total no of individuals in 2nd sample estimated size of population

(the Lincoln Index)

46

Capture-recapture Techniques Factors affecting the accuracy of the estimation

deaths migration individuals become more liable to predation etc

Examples

- arthropods marked on their backs with non-toxic paint

- fish have tags attached to opercula - mammals have tags clipped to their ears

birds have their legs ringed

47

Capture-recapture Method Important tool for estimating density birth

rate and death rate for mobile animals Method

Collect a sample of individuals mark them and then release them

After a period collect more individuals from the wild and count the number that have marks

We assume that a sample if random will contain the same proportion of marked individuals as the population does

Estimate population density

48

Assumptions For All Capture-Recapture Studies Marking technique does not increase

mortality of marked animals Marked individuals are allowed to mix

with population Marking technique does not affect catch

probability Marks are not lost or overlooked No significant immigration or emigration No significant mortality or natality

49

Marked animals in second sample

Total caught in second sample

Marked animals in first sample

Total population size

=

520 N

16=

Peterson Method or Lincoln Index

N = 64N = (20)(16)5

50

Some Indices Used

Traps Number of Fecal

Pellets Vocalization

Frequency Pelt Records Catch per Unit

Fishing Effort

Number of Artifacts Questionnaires Cover Feeding Capacity Roadside Counts

51

Abundance Scales

The population size may be fairly accurately determined by making some form of frequency assessment

These are subjective and involve an experimenter making some estimate of the number of individuals in a given area or the cover of a particular species

This is especially useful where individuals are very numerous eg barnacles on a rocky shore or where it is difficult to distinguish individuals eg grass plants in a meadow

52

The assessments are usually made on an abundance scale of 5 categories

Abundance Common Frequent Occasional Rare

Barnacles exposed at low water

53

Environmental resistance are the factors which limit the growth of a particular population

eg predation disease availability of light food water oxygen and shelter the accumulation of toxic wastes and even the size of the population itself

54

Density-dependent Growth A population is a density-dependent when its size

(or density) affects its growth rate because of density-dependent factors such as food availability and toxic waste accumulation

Density-independent Growth In this type of growth a population increases until

some factor causes a sudden reduction in its size Its effect is the same regardless of the size of the

population eg temperature fires floods storms etc

55

Regulation of Population Size Fecundity is the reproductive capacity of individual

females of a species Birth rate or natality is used to measure fecundity Death rate or mortality is the number of individuals

of a species which die per unit time Immigration occurs when individuals join a

population from neighbouring ones Emigration occurs when individuals depart from a

population A cycle occurs when the size of a population

fluctuates on a regular basis

56

Ecological Sampling

57

Why Do We Sample Determine presence andor

abundance

Monitor population fluctuations

Assess lsquoecological damagersquo

Assess quality of habitat

Assess population responses

58

What Do We Sample

Physical Environment Temperature DO pH salinity clarity

flow sediment

Biotic Environment All living things

59

Physical Habitat Temperature

Mercury thermometer Electronic thermometer Long-term thermometers

Dissolved Oxygen Winkler method (titration) DO meter (electrode)

pH Litmus paper pH meter (electrode)

Salinity Salinity Meter YSI 550A DO Meter w12 cable

60

Water Clarity Secchi Disk

Disk is attached to a calibrated rope The disk is lowered into the water until the white parts can no longer be seen Secchi disk depth is then recorded and serves as the waters transparency index The clearer the water the greater the secchi disk depth

Secchi Disk

61

Current Velocity (flow) Floating-orange method

Put an orange (or something else that floats just below the water surface) and measure the time it takes it to float across a known distance

Odometer-type flow meter Number of revolutions the propeller

makes for a given time is calibrated to flow velocity

62

Sediment Sediment size is important to many

aquatic organisms Sieversquos are used to separate and

grade sediment samples Percent of each size grade can be

determined

63

Water Sample

Water and plankton from various depths can be collected

A trigger mechanism is used to close the sampler Sample is then brought back to the

surface

64

Small Mammals

Mouserat Traps Fatal

Pit Falls Bucket is placed in the ground Sometimes have lsquoleadsrsquo to the buckets

Live traps Havahart Sherman

Spot-light

Sherman trapHavahart trap

65

Birds Stick-under-the-box method Bird-trap

Works like a minnow trap Mist net

Captures birds in flight Rocket net

Uses a propellant to throw a net over birds

66

Terrestrial Insects

Sticky paper flies

Baited Traps Fire ants

Nets butterflies

Foggers Collect insects from tree canopies

67

Aquatic Insects Drift Net

Place net in flowing water Kick Net

lsquoKickrsquo sediment upstream from block net and the flow will wash them into the net

Wash bucket Serber or Hess Sampler

Stir up known area of sediment

Animals are collected by a catch net

Multi-plate Sampler Become colonized

68

Crawfish and Crab Traps

69

Fish Larvae Light Traps

Larvae are attracted to the light Ichthyoplankton nets

Can be towed at various depths Fish collect at the lsquocodrsquoend

70

Fish Lift net

Net is placed down and after a set amount of time it is quickly lifted

Pop-net Similar to a lift net but

floats are attached to a framed net

Operated by a trigger mechanism

Throw net A net attached to a heavy

frame is thrown and every thing inside is netted out Throw net

Pop-net

Lift net

71

Minnow trap

Usually use bait to attract small fish Light is used sometimes as an attractant

72

Fish Electrofishing

Electricity is put into the water Fish are temporarily stunned and usually

swim towards the electricity source Usually non-fatal but may cause some

damage

73

Fish Gill Net

Gill nets resemble tennis nets Fish can not swim completely through the

net and get caught Gill nets are size selective (based on mesh

size) Square Mesh

Bar mesh

Stretch mesh

74

Fish Trammel Net

Three panels two large mesh on the outside and a small mesh on the inside

Fish swim through the outer mesh pushes the small mesh through the other side and becomes entangled

75

Hoop nets (and other similar nets) can have bait or not

Fyke nets have leads to help guide fish to the net

76

Seine Seines are nets that are pulled

through shallow water to catch fish

77

Purse Seine Used to encircle entire schools of fish

Usually involves a spotter plane and a second boat

78

Trotline (longline) A series of baited drop lines

connected to a main line

Can be deployed by tying one end to the bank and tying the other end with a heavy weight

79

Shrimp (or fish) Trawl Net pulled behind

a boat along the bottom Either a beam or

otter boards keep the net open

80

Tagging Individuals Coded Wire Tags

Microwire that has a unique label

Magnetic wand detects the tag

Tag retention should be determined

T-Bar tags Can be individually

numbered External tag

PIT tags (Passive Integrated Transponders) Wand induces the tag to

transmit individual number is displayed

81

Other Tagging Methods

Toe clip Amphibian and reptile Clip of one or more toes

to identify individuals

Bird Band Place a metal band on a

bird leg Generally has

identification information

82

Preserving plant specimens Pressing and drying Long-term

preservation and storage

Alternative drying techniques

Special preservation and processing techniques

Mounting

83

Pressing and drying Techniques for pressing and drying specimens have been

established for many years There are minor variations in recommended methods but they are essentially the same worldwide

The best specimens are plants that are pressed as soon as possible after collection before wilting and shrivelling Most plants may be kept in sealed containers such as plastic bags for up to a day if it is inconvenient to press immediately However some plants show such rapid wilting particularly of the flowers that such delays are best avoided Flowers with a lot of nectar may go mouldy very quickly if excess nectar is not shaken off before pressing

Specimens are pressed flat and dried between sheets of absorbent blotters or semi-absorbent paper such as newspaper Papers with a glossy surface should be avoided because they are not absorbent enough to aid drying The plant should be carefully laid out between the drying sheets as their form at this stage largely determines their ultimate appearance The flowers should be spread out with the petals carefully arranged wilted leaves should be straightened and unnecessary shoots of excessively twiggy shrubs may be cut away

84

Microwave ovens Small numbers of specimens can be dried using a microwave

oven The technique recommended in the literature is to place the specimens between unprinted absorbent paper for example butchers paper not newspaper which is unsuitable because the chemicals present in the ink may cause a fire The specimens should be put in a special press which should be of a microwave-safe material (wood acrylic or polycarbonate sheeting eg plexiglass or perspex NO metal components) If such a press is not available sheets of cardboard can be placed above and below the specimens and then weighted down

Drying time depends on the power of your oven In most cases drying is accomplished by irradiating at maximum power for 1-2 minutes per specimen although it is often a case of trial and error It is best to process no more than 10-12 specimens of average thickness per batch Specimens are usually dried after the moisture that characteristically appears on the glass door has disappeared If the specimen is damp when taken out of the oven allow it to stand before re-radiating as moisture continues to evaporate from the specimen for some time Care must be taken not to irradiate the specimens for too long

It should be noted that microwave treatment damages seeds and the cellular structure of the plants which may reduce the long-term value of the specimens

85

Alternative drying techniquesSilica gelother desiccants amp freeze drying Alternative methods of drying plant specimens have been

used for some time but are mostly restricted to special purpose collections The main alternatives are freeze-drying and drying in a desiccant powder such as desiccant silica gel In general these techniques are used where it is essential to preserve the shape of a delicate plant of organ of the plant such as the flower Freeze-drying has also been used to preserve the chemical composition of a plant as accurately as possible for later study

Disadvantages and special conservation problems of specimens dried in these manners are that they are particularly susceptible to damage The dried parts are fragile lack support and often catch on packing materials They must therefore be packed especially carefully and stored in small boxes or tubes with some appropriate packing material that does not snag and break small projections Acid-free tissue paper is often used Drying in desiccant silica gel crystals or powder can also have the disadvantage that it is difficult to remove all traces of the silica gel after drying

86

Special preservation and processing techniquesWet or spirit collections

Very fleshy or delicate structures including small algae and orchid flowers are best preserved in an air-tight glass or plastic jar with a liquid preservative rather than by drying The type of preservative used should be clearly labelled in the jar Such material is often referred to as a spirit collection or wet collection

Most material can be satisfactorily preserved in 70 ethyl alcohol (or 70 methylated spirit or denatured alcohol) with 30 water Colours will fade quickly in spirit however so it is a good idea to keep comprehensive notes and photographs

87

Small algae Microscopic algae are often collected in a jar and in the

water in which they were found If the algae are to be stored for more than 2-3 days a preservative needs to be used Traditionally this has been the extremely toxic formalin - a small amount can be added to the water to make a 5 final solution and the container labelled This must not be sent through the post or by courier

There are some other equally toxic options for example propylene phenoxytol but none should be sent through the post A safer option is to add sufficient concentrated alcohol or methylated spirits to the water containing the algae to make a final solution of 70 alcohol This treatment dilutes the algae making them difficult to find so if they can be concentrated somehow first (eg by filtering) they can be stored in much less liquid Another option is to fix the algae in formalin (or something similar) first and then prepare a microscope glass slide with a permanent water-soluble mounting medium

88

Mounting Mounting specimens prevents most fragile material from

fragmenting and prevents specimens becoming separated from their labels If the plant collection is a long-term project specimens should be mounted on sheets of archival (permanent) cardboard or paper with archival-quality fixing media These include stitching with cotton thread dental floss nickel-plated copper wire (for heavier specimens) narrow strips of archival paper linen tape or by using an archival adhesive such as methyl cellulose adhesive

One disadvantage of mounting specimens is that it can make parts of the specimen inaccessible for examination so it is essential that this be borne in mind during specimen arrangement and mounting For example easily reversible mounting media should be used specimens should be strapped to the sheet rather than glued all over and the specimen should be carefully arranged before it is attached so that it shows all features

89

Full-size herbarium mounting sheets are usually about 43 cm long x 28 cm wide The plant name and accompanying field notes should be transcribed on a permanent label stuck to one corner of the herbarium sheet (the bottom right-hand corner being the most common) or sometimes annotations may be written directly on the sheet or card

Small pieces of material which may have become separated from the specimen (eg seeds) can be placed in small plastic bags and pinned to the sheet

90

Long-term preservation and storage The long-term preservation of dry plant

specimens is largely dependent on protection from insect attack Specimens collected by Linnaeus in the eighteenth century and by Banks and Solander on the Endeavour voyage in 1788 are still excellently preserved

91

Pests and their control A range of pests attack dried plant material The

most common pests are insects and fungi though rodents and other large animals can cause damage in poor storage conditions Insects eat the material the paper surrounding the material and the adhesives and mounting media

Such insect pests range from psocids (book lice) which attack mainly the softer parts such as flowers and soft fruits to tobacco beetles and carpet beetles which can bore holes through the toughest of specimens Many insects are particularly sensitive to relative humidity levels and do not thrive at levels below 50

92

The most common and acceptable specimen treatments for insect control are Freezing Microwave Poisoning Insect deterrents Fungal pests

93

Storage

Dried and pressed plant specimens can be stored in cardboard or plastic boxes or tied in bundles in light-weight cardboard folders placed in pigeon holes

Alternatively they can be placed in protective plastic jackets and displayed in ring folders which is recommended if they are to be frequently handled such as for a reference collection

94

Filing

Specimens should be filed in a systematic order if a relatively permanent collection is being made The major groups ie ferns and fern allies cycads conifers dicotyledons and monocotyledons are best kept separately or according to some classification scheme such as that given in a flora or handbook

Similarly the genera within each family and the species within each genus may be filed alphabetically or following some such classification

95

Preservation of entire animals

Types of collection specimens of an entire animal For reference collections mammals can be prepared as a variety of specimens The condition of the specimen may determine possible ways to preserve it if for instance decomposition of the skin has loosened the hair of a carcass so much that it can easily be pulled out or removed by rubbing (ldquoslippingrdquo fur) it will be very difficult or impossible to produce a study skin or mounted specimen The most usual types of specimens (based on Nagorsen and Peterson 1980) are 1) entire fluid-preserved animals (for studying anatomy and histology fluid preservation may change the fur colour) 2) study skins with accompanying skulls partial skeletons (some bones remain in the skin) for studying pelage colour hair quality and moulting patterns 3) mounted skins with accompanying partial or entire skeleton (some bones may remain in the skin dependant on the method of preservation) or freeze-dried specimens 4) entire skeletons for instance for studying anatomy geographic variation or for age determination (entire skeletons are poorly represented in collections so Nagorsen and Peterson (1980) recommend preparation of at least one male and one female skeleton per species

96

Preservation of specimens in the field Formalin preservation Preservation in alcohol Preservation by cooling or freezing

97

Formalin preservation After weighing and measuring the animal and attaching an

adequate label very small specimens (up to 100 g) can be fixed whole by submerging them in 10 buffered formalin (tissue - formalin solution ratio of at least 1 12) the body cavity can be filled with formalin solution by injection until it is turgid and firm some formalin may also be injected under the skin into the body cavity larger muscles and organs If hypodermic needles are not available the body cavity can be opened ventrally by making a slit instead allowing the formalin to enter

Keeping the mouth open with a piece of wood or cotton may later allow examination of teeth Then the whole body can be immersed in formalin in the posture in which it is supposed to stay permanently because it will harden The ratio of formalin to carcass must be at least 12 to 1 to assure a good fixation Tissues can be left in buffered neutralized formalin for several months but formalin hardens specimens therefore after fixation longterm storage in alcohol may be better After preservation the carcass should therefore be washed in water and transferred into ethanol for permanent storage

Disadvantages for instance it discolours the fur after a longish immersion softens the bones and prevents further examination for microbiology

98

Preservation in alcohol

After weighing a whole animal can be preserved in a container of alcohol (70-90) Removal of the intestine prior to storage of the animal in alcohol is recommended

99

Preservation by cooling or freezing Removal of the skin with insulating fur

before cooling or freezing may help to cool the carcass down more quickly

Freezing is not recommended if histological examination is planned

100

THANK YOU

26

Belt TransectIt is a strip usually a metre wide marked by putting a

second line parallel to the other The species between the lines are carefully recorded working a metre at a time

Alternatively a frame quadrat in conjunction with a single line transect could be used

Using a quadrat along a belt transect eg ladder transect (every 5m)

27

Point Frames- for grassland field study of dense vegetation

28

STRATIFIED SAMPLING1048698 Often used whenthere are smallareas within alarger habitat thatare clearly different1048698 Strata- majordifferences withincommunitiesrecognized beforesampling begins

29

RANDOM SAMPLING

1048698 Often used when the area being studied isfairly uniform very large or when there is alimited amount of time available1048698 Random = chosen by chance rather thanaccording to a plan all outcomes are

equallylikely1048698 Samples are taken from different positionswithin a habitat and those positions arechosen randomly

30

How to sample randomly

Choose individuals or Placeldquosampling unitsrdquo

haphazardlyndash This is rarely completely

random1048698 ORhellip1048698 Assign numbers to the

areasor individuals to be sampledndash Use a random number

table toselect which areas or

individualswill be sample

31

Population Attributes Density ndash size of a population in relation to a definite

unit of space Affected by

Natality ndash the reproductive output (birth rate) of a population

Mortality ndash the death rate of organisms in a population

Immigration ndash number of organisms moving into the area occupied by the population

Emigration ndash number of organisms moving out of the area occupied by the population

32

Population Density

Four primary population parameters

33

Two Types of Density Estimates

bull Absolute Density ndash a known density such as m2

bull Relative Density ndash we know when one area has more individuals than another

34

Measuring Absolute Density

Total Count ndash count the number of organisms living in an area Human census number of oak trees in a

wooded lot number of singing birds in an area

Total counts generally are not used very often

Sampling Methods ndash use a sample to estimate population size Either use the quadrat or capture-

recapture method

35

Measurement of Environmental ParametersAbiotic factors are important in determining

both the distribution of the organisms and their physical and physiological adaptations

Temperature- diurnal and seasonal temperature variations

are significant in affecting different species of plants and animals

- equipment mercury thermometer maximum-minimum thermometer

miniaturized thermistor

36

pH

-measure pH of a solution by universal indicator pH paper pH meter etc

Light

-measure its duration and intensity duration by predication from Royal Observatory intensity by photographic light meter

pH meter in use

37

Humidity

Relative humidity the water content of a given volume of air relative to the same volume of fully saturated air

- equipment whirling hygrometer

38

Wind and Water Speed- wind speed- anemometer or wind

gauges- water speed - time the movement of a

floating object over a measured distance

39

Salinity

- using a conductivity meter greater salinity has greater conductivity

Oxygen Level

- using an oxygen meter or chemical method (Winkler method)

40

Collecting MethodsCollecting all organisms within a habitat is normally

impractical and therefore small areas are selected Remember to return all material to its original position

after searching amp collecting sufficient specimens Some collecting apparatus for general use are listed

below

41

1 specimen tube

2 screwed-topped jars

3 polythene bags

4 forceps

5 paint brush

6 bulb pipette

7 pooter

42

8 widger 9 sieve 10 hand lens

11 enamel dish 12 beating tray 13 light traps

14 Tullgren funnel 15 Baermann funnel 16 mammal traps

17 pitfall traps 18 netting

43

Estimating Population Size

The exact methods used for estimation depend not only the nature of the habitat but also on the organisms involved

eg animals - population

plants - percentage cover

44

Using Quadrats

- By sampling an area using quadrats and counting the number of individuals within each quadrat it is possible to estimate the total number of individuals within the area

- confined to plants and sessile or very slow-moving animals

- fast-moving animals are disturbed and run away

45

Capture-recapture Techniques- useful for mobile animals which can be marked

- capture marked released randomly recaptured

and marked individuals recorded

no of marked individuals recaptured total no of individuals in 1st sample

-------------------------------------------- = ------------------------------------------

total no of individuals in 2nd sample estimated size of population

(the Lincoln Index)

46

Capture-recapture Techniques Factors affecting the accuracy of the estimation

deaths migration individuals become more liable to predation etc

Examples

- arthropods marked on their backs with non-toxic paint

- fish have tags attached to opercula - mammals have tags clipped to their ears

birds have their legs ringed

47

Capture-recapture Method Important tool for estimating density birth

rate and death rate for mobile animals Method

Collect a sample of individuals mark them and then release them

After a period collect more individuals from the wild and count the number that have marks

We assume that a sample if random will contain the same proportion of marked individuals as the population does

Estimate population density

48

Assumptions For All Capture-Recapture Studies Marking technique does not increase

mortality of marked animals Marked individuals are allowed to mix

with population Marking technique does not affect catch

probability Marks are not lost or overlooked No significant immigration or emigration No significant mortality or natality

49

Marked animals in second sample

Total caught in second sample

Marked animals in first sample

Total population size

=

520 N

16=

Peterson Method or Lincoln Index

N = 64N = (20)(16)5

50

Some Indices Used

Traps Number of Fecal

Pellets Vocalization

Frequency Pelt Records Catch per Unit

Fishing Effort

Number of Artifacts Questionnaires Cover Feeding Capacity Roadside Counts

51

Abundance Scales

The population size may be fairly accurately determined by making some form of frequency assessment

These are subjective and involve an experimenter making some estimate of the number of individuals in a given area or the cover of a particular species

This is especially useful where individuals are very numerous eg barnacles on a rocky shore or where it is difficult to distinguish individuals eg grass plants in a meadow

52

The assessments are usually made on an abundance scale of 5 categories

Abundance Common Frequent Occasional Rare

Barnacles exposed at low water

53

Environmental resistance are the factors which limit the growth of a particular population

eg predation disease availability of light food water oxygen and shelter the accumulation of toxic wastes and even the size of the population itself

54

Density-dependent Growth A population is a density-dependent when its size

(or density) affects its growth rate because of density-dependent factors such as food availability and toxic waste accumulation

Density-independent Growth In this type of growth a population increases until

some factor causes a sudden reduction in its size Its effect is the same regardless of the size of the

population eg temperature fires floods storms etc

55

Regulation of Population Size Fecundity is the reproductive capacity of individual

females of a species Birth rate or natality is used to measure fecundity Death rate or mortality is the number of individuals

of a species which die per unit time Immigration occurs when individuals join a

population from neighbouring ones Emigration occurs when individuals depart from a

population A cycle occurs when the size of a population

fluctuates on a regular basis

56

Ecological Sampling

57

Why Do We Sample Determine presence andor

abundance

Monitor population fluctuations

Assess lsquoecological damagersquo

Assess quality of habitat

Assess population responses

58

What Do We Sample

Physical Environment Temperature DO pH salinity clarity

flow sediment

Biotic Environment All living things

59

Physical Habitat Temperature

Mercury thermometer Electronic thermometer Long-term thermometers

Dissolved Oxygen Winkler method (titration) DO meter (electrode)

pH Litmus paper pH meter (electrode)

Salinity Salinity Meter YSI 550A DO Meter w12 cable

60

Water Clarity Secchi Disk

Disk is attached to a calibrated rope The disk is lowered into the water until the white parts can no longer be seen Secchi disk depth is then recorded and serves as the waters transparency index The clearer the water the greater the secchi disk depth

Secchi Disk

61

Current Velocity (flow) Floating-orange method

Put an orange (or something else that floats just below the water surface) and measure the time it takes it to float across a known distance

Odometer-type flow meter Number of revolutions the propeller

makes for a given time is calibrated to flow velocity

62

Sediment Sediment size is important to many

aquatic organisms Sieversquos are used to separate and

grade sediment samples Percent of each size grade can be

determined

63

Water Sample

Water and plankton from various depths can be collected

A trigger mechanism is used to close the sampler Sample is then brought back to the

surface

64

Small Mammals

Mouserat Traps Fatal

Pit Falls Bucket is placed in the ground Sometimes have lsquoleadsrsquo to the buckets

Live traps Havahart Sherman

Spot-light

Sherman trapHavahart trap

65

Birds Stick-under-the-box method Bird-trap

Works like a minnow trap Mist net

Captures birds in flight Rocket net

Uses a propellant to throw a net over birds

66

Terrestrial Insects

Sticky paper flies

Baited Traps Fire ants

Nets butterflies

Foggers Collect insects from tree canopies

67

Aquatic Insects Drift Net

Place net in flowing water Kick Net

lsquoKickrsquo sediment upstream from block net and the flow will wash them into the net

Wash bucket Serber or Hess Sampler

Stir up known area of sediment

Animals are collected by a catch net

Multi-plate Sampler Become colonized

68

Crawfish and Crab Traps

69

Fish Larvae Light Traps

Larvae are attracted to the light Ichthyoplankton nets

Can be towed at various depths Fish collect at the lsquocodrsquoend

70

Fish Lift net

Net is placed down and after a set amount of time it is quickly lifted

Pop-net Similar to a lift net but

floats are attached to a framed net

Operated by a trigger mechanism

Throw net A net attached to a heavy

frame is thrown and every thing inside is netted out Throw net

Pop-net

Lift net

71

Minnow trap

Usually use bait to attract small fish Light is used sometimes as an attractant

72

Fish Electrofishing

Electricity is put into the water Fish are temporarily stunned and usually

swim towards the electricity source Usually non-fatal but may cause some

damage

73

Fish Gill Net

Gill nets resemble tennis nets Fish can not swim completely through the

net and get caught Gill nets are size selective (based on mesh

size) Square Mesh

Bar mesh

Stretch mesh

74

Fish Trammel Net

Three panels two large mesh on the outside and a small mesh on the inside

Fish swim through the outer mesh pushes the small mesh through the other side and becomes entangled

75

Hoop nets (and other similar nets) can have bait or not

Fyke nets have leads to help guide fish to the net

76

Seine Seines are nets that are pulled

through shallow water to catch fish

77

Purse Seine Used to encircle entire schools of fish

Usually involves a spotter plane and a second boat

78

Trotline (longline) A series of baited drop lines

connected to a main line

Can be deployed by tying one end to the bank and tying the other end with a heavy weight

79

Shrimp (or fish) Trawl Net pulled behind

a boat along the bottom Either a beam or

otter boards keep the net open

80

Tagging Individuals Coded Wire Tags

Microwire that has a unique label

Magnetic wand detects the tag

Tag retention should be determined

T-Bar tags Can be individually

numbered External tag

PIT tags (Passive Integrated Transponders) Wand induces the tag to

transmit individual number is displayed

81

Other Tagging Methods

Toe clip Amphibian and reptile Clip of one or more toes

to identify individuals

Bird Band Place a metal band on a

bird leg Generally has

identification information

82

Preserving plant specimens Pressing and drying Long-term

preservation and storage

Alternative drying techniques

Special preservation and processing techniques

Mounting

83

Pressing and drying Techniques for pressing and drying specimens have been

established for many years There are minor variations in recommended methods but they are essentially the same worldwide

The best specimens are plants that are pressed as soon as possible after collection before wilting and shrivelling Most plants may be kept in sealed containers such as plastic bags for up to a day if it is inconvenient to press immediately However some plants show such rapid wilting particularly of the flowers that such delays are best avoided Flowers with a lot of nectar may go mouldy very quickly if excess nectar is not shaken off before pressing

Specimens are pressed flat and dried between sheets of absorbent blotters or semi-absorbent paper such as newspaper Papers with a glossy surface should be avoided because they are not absorbent enough to aid drying The plant should be carefully laid out between the drying sheets as their form at this stage largely determines their ultimate appearance The flowers should be spread out with the petals carefully arranged wilted leaves should be straightened and unnecessary shoots of excessively twiggy shrubs may be cut away

84

Microwave ovens Small numbers of specimens can be dried using a microwave

oven The technique recommended in the literature is to place the specimens between unprinted absorbent paper for example butchers paper not newspaper which is unsuitable because the chemicals present in the ink may cause a fire The specimens should be put in a special press which should be of a microwave-safe material (wood acrylic or polycarbonate sheeting eg plexiglass or perspex NO metal components) If such a press is not available sheets of cardboard can be placed above and below the specimens and then weighted down

Drying time depends on the power of your oven In most cases drying is accomplished by irradiating at maximum power for 1-2 minutes per specimen although it is often a case of trial and error It is best to process no more than 10-12 specimens of average thickness per batch Specimens are usually dried after the moisture that characteristically appears on the glass door has disappeared If the specimen is damp when taken out of the oven allow it to stand before re-radiating as moisture continues to evaporate from the specimen for some time Care must be taken not to irradiate the specimens for too long

It should be noted that microwave treatment damages seeds and the cellular structure of the plants which may reduce the long-term value of the specimens

85

Alternative drying techniquesSilica gelother desiccants amp freeze drying Alternative methods of drying plant specimens have been

used for some time but are mostly restricted to special purpose collections The main alternatives are freeze-drying and drying in a desiccant powder such as desiccant silica gel In general these techniques are used where it is essential to preserve the shape of a delicate plant of organ of the plant such as the flower Freeze-drying has also been used to preserve the chemical composition of a plant as accurately as possible for later study

Disadvantages and special conservation problems of specimens dried in these manners are that they are particularly susceptible to damage The dried parts are fragile lack support and often catch on packing materials They must therefore be packed especially carefully and stored in small boxes or tubes with some appropriate packing material that does not snag and break small projections Acid-free tissue paper is often used Drying in desiccant silica gel crystals or powder can also have the disadvantage that it is difficult to remove all traces of the silica gel after drying

86

Special preservation and processing techniquesWet or spirit collections

Very fleshy or delicate structures including small algae and orchid flowers are best preserved in an air-tight glass or plastic jar with a liquid preservative rather than by drying The type of preservative used should be clearly labelled in the jar Such material is often referred to as a spirit collection or wet collection

Most material can be satisfactorily preserved in 70 ethyl alcohol (or 70 methylated spirit or denatured alcohol) with 30 water Colours will fade quickly in spirit however so it is a good idea to keep comprehensive notes and photographs

87

Small algae Microscopic algae are often collected in a jar and in the

water in which they were found If the algae are to be stored for more than 2-3 days a preservative needs to be used Traditionally this has been the extremely toxic formalin - a small amount can be added to the water to make a 5 final solution and the container labelled This must not be sent through the post or by courier

There are some other equally toxic options for example propylene phenoxytol but none should be sent through the post A safer option is to add sufficient concentrated alcohol or methylated spirits to the water containing the algae to make a final solution of 70 alcohol This treatment dilutes the algae making them difficult to find so if they can be concentrated somehow first (eg by filtering) they can be stored in much less liquid Another option is to fix the algae in formalin (or something similar) first and then prepare a microscope glass slide with a permanent water-soluble mounting medium

88

Mounting Mounting specimens prevents most fragile material from

fragmenting and prevents specimens becoming separated from their labels If the plant collection is a long-term project specimens should be mounted on sheets of archival (permanent) cardboard or paper with archival-quality fixing media These include stitching with cotton thread dental floss nickel-plated copper wire (for heavier specimens) narrow strips of archival paper linen tape or by using an archival adhesive such as methyl cellulose adhesive

One disadvantage of mounting specimens is that it can make parts of the specimen inaccessible for examination so it is essential that this be borne in mind during specimen arrangement and mounting For example easily reversible mounting media should be used specimens should be strapped to the sheet rather than glued all over and the specimen should be carefully arranged before it is attached so that it shows all features

89

Full-size herbarium mounting sheets are usually about 43 cm long x 28 cm wide The plant name and accompanying field notes should be transcribed on a permanent label stuck to one corner of the herbarium sheet (the bottom right-hand corner being the most common) or sometimes annotations may be written directly on the sheet or card

Small pieces of material which may have become separated from the specimen (eg seeds) can be placed in small plastic bags and pinned to the sheet

90

Long-term preservation and storage The long-term preservation of dry plant

specimens is largely dependent on protection from insect attack Specimens collected by Linnaeus in the eighteenth century and by Banks and Solander on the Endeavour voyage in 1788 are still excellently preserved

91

Pests and their control A range of pests attack dried plant material The

most common pests are insects and fungi though rodents and other large animals can cause damage in poor storage conditions Insects eat the material the paper surrounding the material and the adhesives and mounting media

Such insect pests range from psocids (book lice) which attack mainly the softer parts such as flowers and soft fruits to tobacco beetles and carpet beetles which can bore holes through the toughest of specimens Many insects are particularly sensitive to relative humidity levels and do not thrive at levels below 50

92

The most common and acceptable specimen treatments for insect control are Freezing Microwave Poisoning Insect deterrents Fungal pests

93

Storage

Dried and pressed plant specimens can be stored in cardboard or plastic boxes or tied in bundles in light-weight cardboard folders placed in pigeon holes

Alternatively they can be placed in protective plastic jackets and displayed in ring folders which is recommended if they are to be frequently handled such as for a reference collection

94

Filing

Specimens should be filed in a systematic order if a relatively permanent collection is being made The major groups ie ferns and fern allies cycads conifers dicotyledons and monocotyledons are best kept separately or according to some classification scheme such as that given in a flora or handbook

Similarly the genera within each family and the species within each genus may be filed alphabetically or following some such classification

95

Preservation of entire animals

Types of collection specimens of an entire animal For reference collections mammals can be prepared as a variety of specimens The condition of the specimen may determine possible ways to preserve it if for instance decomposition of the skin has loosened the hair of a carcass so much that it can easily be pulled out or removed by rubbing (ldquoslippingrdquo fur) it will be very difficult or impossible to produce a study skin or mounted specimen The most usual types of specimens (based on Nagorsen and Peterson 1980) are 1) entire fluid-preserved animals (for studying anatomy and histology fluid preservation may change the fur colour) 2) study skins with accompanying skulls partial skeletons (some bones remain in the skin) for studying pelage colour hair quality and moulting patterns 3) mounted skins with accompanying partial or entire skeleton (some bones may remain in the skin dependant on the method of preservation) or freeze-dried specimens 4) entire skeletons for instance for studying anatomy geographic variation or for age determination (entire skeletons are poorly represented in collections so Nagorsen and Peterson (1980) recommend preparation of at least one male and one female skeleton per species

96

Preservation of specimens in the field Formalin preservation Preservation in alcohol Preservation by cooling or freezing

97

Formalin preservation After weighing and measuring the animal and attaching an

adequate label very small specimens (up to 100 g) can be fixed whole by submerging them in 10 buffered formalin (tissue - formalin solution ratio of at least 1 12) the body cavity can be filled with formalin solution by injection until it is turgid and firm some formalin may also be injected under the skin into the body cavity larger muscles and organs If hypodermic needles are not available the body cavity can be opened ventrally by making a slit instead allowing the formalin to enter

Keeping the mouth open with a piece of wood or cotton may later allow examination of teeth Then the whole body can be immersed in formalin in the posture in which it is supposed to stay permanently because it will harden The ratio of formalin to carcass must be at least 12 to 1 to assure a good fixation Tissues can be left in buffered neutralized formalin for several months but formalin hardens specimens therefore after fixation longterm storage in alcohol may be better After preservation the carcass should therefore be washed in water and transferred into ethanol for permanent storage

Disadvantages for instance it discolours the fur after a longish immersion softens the bones and prevents further examination for microbiology

98

Preservation in alcohol

After weighing a whole animal can be preserved in a container of alcohol (70-90) Removal of the intestine prior to storage of the animal in alcohol is recommended

99

Preservation by cooling or freezing Removal of the skin with insulating fur

before cooling or freezing may help to cool the carcass down more quickly

Freezing is not recommended if histological examination is planned

100

THANK YOU

27

Point Frames- for grassland field study of dense vegetation

28

STRATIFIED SAMPLING1048698 Often used whenthere are smallareas within alarger habitat thatare clearly different1048698 Strata- majordifferences withincommunitiesrecognized beforesampling begins

29

RANDOM SAMPLING

1048698 Often used when the area being studied isfairly uniform very large or when there is alimited amount of time available1048698 Random = chosen by chance rather thanaccording to a plan all outcomes are

equallylikely1048698 Samples are taken from different positionswithin a habitat and those positions arechosen randomly

30

How to sample randomly

Choose individuals or Placeldquosampling unitsrdquo

haphazardlyndash This is rarely completely

random1048698 ORhellip1048698 Assign numbers to the

areasor individuals to be sampledndash Use a random number

table toselect which areas or

individualswill be sample

31

Population Attributes Density ndash size of a population in relation to a definite

unit of space Affected by

Natality ndash the reproductive output (birth rate) of a population

Mortality ndash the death rate of organisms in a population

Immigration ndash number of organisms moving into the area occupied by the population

Emigration ndash number of organisms moving out of the area occupied by the population

32

Population Density

Four primary population parameters

33

Two Types of Density Estimates

bull Absolute Density ndash a known density such as m2

bull Relative Density ndash we know when one area has more individuals than another

34

Measuring Absolute Density

Total Count ndash count the number of organisms living in an area Human census number of oak trees in a

wooded lot number of singing birds in an area

Total counts generally are not used very often

Sampling Methods ndash use a sample to estimate population size Either use the quadrat or capture-

recapture method

35

Measurement of Environmental ParametersAbiotic factors are important in determining

both the distribution of the organisms and their physical and physiological adaptations

Temperature- diurnal and seasonal temperature variations

are significant in affecting different species of plants and animals

- equipment mercury thermometer maximum-minimum thermometer

miniaturized thermistor

36

pH

-measure pH of a solution by universal indicator pH paper pH meter etc

Light

-measure its duration and intensity duration by predication from Royal Observatory intensity by photographic light meter

pH meter in use

37

Humidity

Relative humidity the water content of a given volume of air relative to the same volume of fully saturated air

- equipment whirling hygrometer

38

Wind and Water Speed- wind speed- anemometer or wind

gauges- water speed - time the movement of a

floating object over a measured distance

39

Salinity

- using a conductivity meter greater salinity has greater conductivity

Oxygen Level

- using an oxygen meter or chemical method (Winkler method)

40

Collecting MethodsCollecting all organisms within a habitat is normally

impractical and therefore small areas are selected Remember to return all material to its original position

after searching amp collecting sufficient specimens Some collecting apparatus for general use are listed

below

41

1 specimen tube

2 screwed-topped jars

3 polythene bags

4 forceps

5 paint brush

6 bulb pipette

7 pooter

42

8 widger 9 sieve 10 hand lens

11 enamel dish 12 beating tray 13 light traps

14 Tullgren funnel 15 Baermann funnel 16 mammal traps

17 pitfall traps 18 netting

43

Estimating Population Size

The exact methods used for estimation depend not only the nature of the habitat but also on the organisms involved

eg animals - population

plants - percentage cover

44

Using Quadrats

- By sampling an area using quadrats and counting the number of individuals within each quadrat it is possible to estimate the total number of individuals within the area

- confined to plants and sessile or very slow-moving animals

- fast-moving animals are disturbed and run away

45

Capture-recapture Techniques- useful for mobile animals which can be marked

- capture marked released randomly recaptured

and marked individuals recorded

no of marked individuals recaptured total no of individuals in 1st sample

-------------------------------------------- = ------------------------------------------

total no of individuals in 2nd sample estimated size of population

(the Lincoln Index)

46

Capture-recapture Techniques Factors affecting the accuracy of the estimation

deaths migration individuals become more liable to predation etc

Examples

- arthropods marked on their backs with non-toxic paint

- fish have tags attached to opercula - mammals have tags clipped to their ears

birds have their legs ringed

47

Capture-recapture Method Important tool for estimating density birth

rate and death rate for mobile animals Method

Collect a sample of individuals mark them and then release them

After a period collect more individuals from the wild and count the number that have marks

We assume that a sample if random will contain the same proportion of marked individuals as the population does

Estimate population density

48

Assumptions For All Capture-Recapture Studies Marking technique does not increase

mortality of marked animals Marked individuals are allowed to mix

with population Marking technique does not affect catch

probability Marks are not lost or overlooked No significant immigration or emigration No significant mortality or natality

49

Marked animals in second sample

Total caught in second sample

Marked animals in first sample

Total population size

=

520 N

16=

Peterson Method or Lincoln Index

N = 64N = (20)(16)5

50

Some Indices Used

Traps Number of Fecal

Pellets Vocalization

Frequency Pelt Records Catch per Unit

Fishing Effort

Number of Artifacts Questionnaires Cover Feeding Capacity Roadside Counts

51

Abundance Scales

The population size may be fairly accurately determined by making some form of frequency assessment

These are subjective and involve an experimenter making some estimate of the number of individuals in a given area or the cover of a particular species

This is especially useful where individuals are very numerous eg barnacles on a rocky shore or where it is difficult to distinguish individuals eg grass plants in a meadow

52

The assessments are usually made on an abundance scale of 5 categories

Abundance Common Frequent Occasional Rare

Barnacles exposed at low water

53

Environmental resistance are the factors which limit the growth of a particular population

eg predation disease availability of light food water oxygen and shelter the accumulation of toxic wastes and even the size of the population itself

54

Density-dependent Growth A population is a density-dependent when its size

(or density) affects its growth rate because of density-dependent factors such as food availability and toxic waste accumulation

Density-independent Growth In this type of growth a population increases until

some factor causes a sudden reduction in its size Its effect is the same regardless of the size of the

population eg temperature fires floods storms etc

55

Regulation of Population Size Fecundity is the reproductive capacity of individual

females of a species Birth rate or natality is used to measure fecundity Death rate or mortality is the number of individuals

of a species which die per unit time Immigration occurs when individuals join a

population from neighbouring ones Emigration occurs when individuals depart from a

population A cycle occurs when the size of a population

fluctuates on a regular basis

56

Ecological Sampling

57

Why Do We Sample Determine presence andor

abundance

Monitor population fluctuations

Assess lsquoecological damagersquo

Assess quality of habitat

Assess population responses

58

What Do We Sample

Physical Environment Temperature DO pH salinity clarity

flow sediment

Biotic Environment All living things

59

Physical Habitat Temperature

Mercury thermometer Electronic thermometer Long-term thermometers

Dissolved Oxygen Winkler method (titration) DO meter (electrode)

pH Litmus paper pH meter (electrode)

Salinity Salinity Meter YSI 550A DO Meter w12 cable

60

Water Clarity Secchi Disk

Disk is attached to a calibrated rope The disk is lowered into the water until the white parts can no longer be seen Secchi disk depth is then recorded and serves as the waters transparency index The clearer the water the greater the secchi disk depth

Secchi Disk

61

Current Velocity (flow) Floating-orange method

Put an orange (or something else that floats just below the water surface) and measure the time it takes it to float across a known distance

Odometer-type flow meter Number of revolutions the propeller

makes for a given time is calibrated to flow velocity

62

Sediment Sediment size is important to many

aquatic organisms Sieversquos are used to separate and

grade sediment samples Percent of each size grade can be

determined

63

Water Sample

Water and plankton from various depths can be collected

A trigger mechanism is used to close the sampler Sample is then brought back to the

surface

64

Small Mammals

Mouserat Traps Fatal

Pit Falls Bucket is placed in the ground Sometimes have lsquoleadsrsquo to the buckets

Live traps Havahart Sherman

Spot-light

Sherman trapHavahart trap

65

Birds Stick-under-the-box method Bird-trap

Works like a minnow trap Mist net

Captures birds in flight Rocket net

Uses a propellant to throw a net over birds

66

Terrestrial Insects

Sticky paper flies

Baited Traps Fire ants

Nets butterflies

Foggers Collect insects from tree canopies

67

Aquatic Insects Drift Net

Place net in flowing water Kick Net

lsquoKickrsquo sediment upstream from block net and the flow will wash them into the net

Wash bucket Serber or Hess Sampler

Stir up known area of sediment

Animals are collected by a catch net

Multi-plate Sampler Become colonized

68

Crawfish and Crab Traps

69

Fish Larvae Light Traps

Larvae are attracted to the light Ichthyoplankton nets

Can be towed at various depths Fish collect at the lsquocodrsquoend

70

Fish Lift net

Net is placed down and after a set amount of time it is quickly lifted

Pop-net Similar to a lift net but

floats are attached to a framed net

Operated by a trigger mechanism

Throw net A net attached to a heavy

frame is thrown and every thing inside is netted out Throw net

Pop-net

Lift net

71

Minnow trap

Usually use bait to attract small fish Light is used sometimes as an attractant

72

Fish Electrofishing

Electricity is put into the water Fish are temporarily stunned and usually

swim towards the electricity source Usually non-fatal but may cause some

damage

73

Fish Gill Net

Gill nets resemble tennis nets Fish can not swim completely through the

net and get caught Gill nets are size selective (based on mesh

size) Square Mesh

Bar mesh

Stretch mesh

74

Fish Trammel Net

Three panels two large mesh on the outside and a small mesh on the inside

Fish swim through the outer mesh pushes the small mesh through the other side and becomes entangled

75

Hoop nets (and other similar nets) can have bait or not

Fyke nets have leads to help guide fish to the net

76

Seine Seines are nets that are pulled

through shallow water to catch fish

77

Purse Seine Used to encircle entire schools of fish

Usually involves a spotter plane and a second boat

78

Trotline (longline) A series of baited drop lines

connected to a main line

Can be deployed by tying one end to the bank and tying the other end with a heavy weight

79

Shrimp (or fish) Trawl Net pulled behind

a boat along the bottom Either a beam or

otter boards keep the net open

80

Tagging Individuals Coded Wire Tags

Microwire that has a unique label

Magnetic wand detects the tag

Tag retention should be determined

T-Bar tags Can be individually

numbered External tag

PIT tags (Passive Integrated Transponders) Wand induces the tag to

transmit individual number is displayed

81

Other Tagging Methods

Toe clip Amphibian and reptile Clip of one or more toes

to identify individuals

Bird Band Place a metal band on a

bird leg Generally has

identification information

82

Preserving plant specimens Pressing and drying Long-term

preservation and storage

Alternative drying techniques

Special preservation and processing techniques

Mounting

83

Pressing and drying Techniques for pressing and drying specimens have been

established for many years There are minor variations in recommended methods but they are essentially the same worldwide

The best specimens are plants that are pressed as soon as possible after collection before wilting and shrivelling Most plants may be kept in sealed containers such as plastic bags for up to a day if it is inconvenient to press immediately However some plants show such rapid wilting particularly of the flowers that such delays are best avoided Flowers with a lot of nectar may go mouldy very quickly if excess nectar is not shaken off before pressing

Specimens are pressed flat and dried between sheets of absorbent blotters or semi-absorbent paper such as newspaper Papers with a glossy surface should be avoided because they are not absorbent enough to aid drying The plant should be carefully laid out between the drying sheets as their form at this stage largely determines their ultimate appearance The flowers should be spread out with the petals carefully arranged wilted leaves should be straightened and unnecessary shoots of excessively twiggy shrubs may be cut away

84

Microwave ovens Small numbers of specimens can be dried using a microwave

oven The technique recommended in the literature is to place the specimens between unprinted absorbent paper for example butchers paper not newspaper which is unsuitable because the chemicals present in the ink may cause a fire The specimens should be put in a special press which should be of a microwave-safe material (wood acrylic or polycarbonate sheeting eg plexiglass or perspex NO metal components) If such a press is not available sheets of cardboard can be placed above and below the specimens and then weighted down

Drying time depends on the power of your oven In most cases drying is accomplished by irradiating at maximum power for 1-2 minutes per specimen although it is often a case of trial and error It is best to process no more than 10-12 specimens of average thickness per batch Specimens are usually dried after the moisture that characteristically appears on the glass door has disappeared If the specimen is damp when taken out of the oven allow it to stand before re-radiating as moisture continues to evaporate from the specimen for some time Care must be taken not to irradiate the specimens for too long

It should be noted that microwave treatment damages seeds and the cellular structure of the plants which may reduce the long-term value of the specimens

85

Alternative drying techniquesSilica gelother desiccants amp freeze drying Alternative methods of drying plant specimens have been

used for some time but are mostly restricted to special purpose collections The main alternatives are freeze-drying and drying in a desiccant powder such as desiccant silica gel In general these techniques are used where it is essential to preserve the shape of a delicate plant of organ of the plant such as the flower Freeze-drying has also been used to preserve the chemical composition of a plant as accurately as possible for later study

Disadvantages and special conservation problems of specimens dried in these manners are that they are particularly susceptible to damage The dried parts are fragile lack support and often catch on packing materials They must therefore be packed especially carefully and stored in small boxes or tubes with some appropriate packing material that does not snag and break small projections Acid-free tissue paper is often used Drying in desiccant silica gel crystals or powder can also have the disadvantage that it is difficult to remove all traces of the silica gel after drying

86

Special preservation and processing techniquesWet or spirit collections

Very fleshy or delicate structures including small algae and orchid flowers are best preserved in an air-tight glass or plastic jar with a liquid preservative rather than by drying The type of preservative used should be clearly labelled in the jar Such material is often referred to as a spirit collection or wet collection

Most material can be satisfactorily preserved in 70 ethyl alcohol (or 70 methylated spirit or denatured alcohol) with 30 water Colours will fade quickly in spirit however so it is a good idea to keep comprehensive notes and photographs

87

Small algae Microscopic algae are often collected in a jar and in the

water in which they were found If the algae are to be stored for more than 2-3 days a preservative needs to be used Traditionally this has been the extremely toxic formalin - a small amount can be added to the water to make a 5 final solution and the container labelled This must not be sent through the post or by courier

There are some other equally toxic options for example propylene phenoxytol but none should be sent through the post A safer option is to add sufficient concentrated alcohol or methylated spirits to the water containing the algae to make a final solution of 70 alcohol This treatment dilutes the algae making them difficult to find so if they can be concentrated somehow first (eg by filtering) they can be stored in much less liquid Another option is to fix the algae in formalin (or something similar) first and then prepare a microscope glass slide with a permanent water-soluble mounting medium

88

Mounting Mounting specimens prevents most fragile material from

fragmenting and prevents specimens becoming separated from their labels If the plant collection is a long-term project specimens should be mounted on sheets of archival (permanent) cardboard or paper with archival-quality fixing media These include stitching with cotton thread dental floss nickel-plated copper wire (for heavier specimens) narrow strips of archival paper linen tape or by using an archival adhesive such as methyl cellulose adhesive

One disadvantage of mounting specimens is that it can make parts of the specimen inaccessible for examination so it is essential that this be borne in mind during specimen arrangement and mounting For example easily reversible mounting media should be used specimens should be strapped to the sheet rather than glued all over and the specimen should be carefully arranged before it is attached so that it shows all features

89

Full-size herbarium mounting sheets are usually about 43 cm long x 28 cm wide The plant name and accompanying field notes should be transcribed on a permanent label stuck to one corner of the herbarium sheet (the bottom right-hand corner being the most common) or sometimes annotations may be written directly on the sheet or card

Small pieces of material which may have become separated from the specimen (eg seeds) can be placed in small plastic bags and pinned to the sheet

90

Long-term preservation and storage The long-term preservation of dry plant

specimens is largely dependent on protection from insect attack Specimens collected by Linnaeus in the eighteenth century and by Banks and Solander on the Endeavour voyage in 1788 are still excellently preserved

91

Pests and their control A range of pests attack dried plant material The

most common pests are insects and fungi though rodents and other large animals can cause damage in poor storage conditions Insects eat the material the paper surrounding the material and the adhesives and mounting media

Such insect pests range from psocids (book lice) which attack mainly the softer parts such as flowers and soft fruits to tobacco beetles and carpet beetles which can bore holes through the toughest of specimens Many insects are particularly sensitive to relative humidity levels and do not thrive at levels below 50

92

The most common and acceptable specimen treatments for insect control are Freezing Microwave Poisoning Insect deterrents Fungal pests

93

Storage

Dried and pressed plant specimens can be stored in cardboard or plastic boxes or tied in bundles in light-weight cardboard folders placed in pigeon holes

Alternatively they can be placed in protective plastic jackets and displayed in ring folders which is recommended if they are to be frequently handled such as for a reference collection

94

Filing

Specimens should be filed in a systematic order if a relatively permanent collection is being made The major groups ie ferns and fern allies cycads conifers dicotyledons and monocotyledons are best kept separately or according to some classification scheme such as that given in a flora or handbook

Similarly the genera within each family and the species within each genus may be filed alphabetically or following some such classification

95

Preservation of entire animals

Types of collection specimens of an entire animal For reference collections mammals can be prepared as a variety of specimens The condition of the specimen may determine possible ways to preserve it if for instance decomposition of the skin has loosened the hair of a carcass so much that it can easily be pulled out or removed by rubbing (ldquoslippingrdquo fur) it will be very difficult or impossible to produce a study skin or mounted specimen The most usual types of specimens (based on Nagorsen and Peterson 1980) are 1) entire fluid-preserved animals (for studying anatomy and histology fluid preservation may change the fur colour) 2) study skins with accompanying skulls partial skeletons (some bones remain in the skin) for studying pelage colour hair quality and moulting patterns 3) mounted skins with accompanying partial or entire skeleton (some bones may remain in the skin dependant on the method of preservation) or freeze-dried specimens 4) entire skeletons for instance for studying anatomy geographic variation or for age determination (entire skeletons are poorly represented in collections so Nagorsen and Peterson (1980) recommend preparation of at least one male and one female skeleton per species

96

Preservation of specimens in the field Formalin preservation Preservation in alcohol Preservation by cooling or freezing

97

Formalin preservation After weighing and measuring the animal and attaching an

adequate label very small specimens (up to 100 g) can be fixed whole by submerging them in 10 buffered formalin (tissue - formalin solution ratio of at least 1 12) the body cavity can be filled with formalin solution by injection until it is turgid and firm some formalin may also be injected under the skin into the body cavity larger muscles and organs If hypodermic needles are not available the body cavity can be opened ventrally by making a slit instead allowing the formalin to enter

Keeping the mouth open with a piece of wood or cotton may later allow examination of teeth Then the whole body can be immersed in formalin in the posture in which it is supposed to stay permanently because it will harden The ratio of formalin to carcass must be at least 12 to 1 to assure a good fixation Tissues can be left in buffered neutralized formalin for several months but formalin hardens specimens therefore after fixation longterm storage in alcohol may be better After preservation the carcass should therefore be washed in water and transferred into ethanol for permanent storage

Disadvantages for instance it discolours the fur after a longish immersion softens the bones and prevents further examination for microbiology

98

Preservation in alcohol

After weighing a whole animal can be preserved in a container of alcohol (70-90) Removal of the intestine prior to storage of the animal in alcohol is recommended

99

Preservation by cooling or freezing Removal of the skin with insulating fur

before cooling or freezing may help to cool the carcass down more quickly

Freezing is not recommended if histological examination is planned

100

THANK YOU

28

STRATIFIED SAMPLING1048698 Often used whenthere are smallareas within alarger habitat thatare clearly different1048698 Strata- majordifferences withincommunitiesrecognized beforesampling begins

29

RANDOM SAMPLING

1048698 Often used when the area being studied isfairly uniform very large or when there is alimited amount of time available1048698 Random = chosen by chance rather thanaccording to a plan all outcomes are

equallylikely1048698 Samples are taken from different positionswithin a habitat and those positions arechosen randomly

30

How to sample randomly

Choose individuals or Placeldquosampling unitsrdquo

haphazardlyndash This is rarely completely

random1048698 ORhellip1048698 Assign numbers to the

areasor individuals to be sampledndash Use a random number

table toselect which areas or

individualswill be sample

31

Population Attributes Density ndash size of a population in relation to a definite

unit of space Affected by

Natality ndash the reproductive output (birth rate) of a population

Mortality ndash the death rate of organisms in a population

Immigration ndash number of organisms moving into the area occupied by the population

Emigration ndash number of organisms moving out of the area occupied by the population

32

Population Density

Four primary population parameters

33

Two Types of Density Estimates

bull Absolute Density ndash a known density such as m2

bull Relative Density ndash we know when one area has more individuals than another

34

Measuring Absolute Density

Total Count ndash count the number of organisms living in an area Human census number of oak trees in a

wooded lot number of singing birds in an area

Total counts generally are not used very often

Sampling Methods ndash use a sample to estimate population size Either use the quadrat or capture-

recapture method

35

Measurement of Environmental ParametersAbiotic factors are important in determining

both the distribution of the organisms and their physical and physiological adaptations

Temperature- diurnal and seasonal temperature variations

are significant in affecting different species of plants and animals

- equipment mercury thermometer maximum-minimum thermometer

miniaturized thermistor

36

pH

-measure pH of a solution by universal indicator pH paper pH meter etc

Light

-measure its duration and intensity duration by predication from Royal Observatory intensity by photographic light meter

pH meter in use

37

Humidity

Relative humidity the water content of a given volume of air relative to the same volume of fully saturated air

- equipment whirling hygrometer

38

Wind and Water Speed- wind speed- anemometer or wind

gauges- water speed - time the movement of a

floating object over a measured distance

39

Salinity

- using a conductivity meter greater salinity has greater conductivity

Oxygen Level

- using an oxygen meter or chemical method (Winkler method)

40

Collecting MethodsCollecting all organisms within a habitat is normally

impractical and therefore small areas are selected Remember to return all material to its original position

after searching amp collecting sufficient specimens Some collecting apparatus for general use are listed

below

41

1 specimen tube

2 screwed-topped jars

3 polythene bags

4 forceps

5 paint brush

6 bulb pipette

7 pooter

42

8 widger 9 sieve 10 hand lens

11 enamel dish 12 beating tray 13 light traps

14 Tullgren funnel 15 Baermann funnel 16 mammal traps

17 pitfall traps 18 netting

43

Estimating Population Size

The exact methods used for estimation depend not only the nature of the habitat but also on the organisms involved

eg animals - population

plants - percentage cover

44

Using Quadrats

- By sampling an area using quadrats and counting the number of individuals within each quadrat it is possible to estimate the total number of individuals within the area

- confined to plants and sessile or very slow-moving animals

- fast-moving animals are disturbed and run away

45

Capture-recapture Techniques- useful for mobile animals which can be marked

- capture marked released randomly recaptured

and marked individuals recorded

no of marked individuals recaptured total no of individuals in 1st sample

-------------------------------------------- = ------------------------------------------

total no of individuals in 2nd sample estimated size of population

(the Lincoln Index)

46

Capture-recapture Techniques Factors affecting the accuracy of the estimation

deaths migration individuals become more liable to predation etc

Examples

- arthropods marked on their backs with non-toxic paint

- fish have tags attached to opercula - mammals have tags clipped to their ears

birds have their legs ringed

47

Capture-recapture Method Important tool for estimating density birth

rate and death rate for mobile animals Method

Collect a sample of individuals mark them and then release them

After a period collect more individuals from the wild and count the number that have marks

We assume that a sample if random will contain the same proportion of marked individuals as the population does

Estimate population density

48

Assumptions For All Capture-Recapture Studies Marking technique does not increase

mortality of marked animals Marked individuals are allowed to mix

with population Marking technique does not affect catch

probability Marks are not lost or overlooked No significant immigration or emigration No significant mortality or natality

49

Marked animals in second sample

Total caught in second sample

Marked animals in first sample

Total population size

=

520 N

16=

Peterson Method or Lincoln Index

N = 64N = (20)(16)5

50

Some Indices Used

Traps Number of Fecal

Pellets Vocalization

Frequency Pelt Records Catch per Unit

Fishing Effort

Number of Artifacts Questionnaires Cover Feeding Capacity Roadside Counts

51

Abundance Scales

The population size may be fairly accurately determined by making some form of frequency assessment

These are subjective and involve an experimenter making some estimate of the number of individuals in a given area or the cover of a particular species

This is especially useful where individuals are very numerous eg barnacles on a rocky shore or where it is difficult to distinguish individuals eg grass plants in a meadow

52

The assessments are usually made on an abundance scale of 5 categories

Abundance Common Frequent Occasional Rare

Barnacles exposed at low water

53

Environmental resistance are the factors which limit the growth of a particular population

eg predation disease availability of light food water oxygen and shelter the accumulation of toxic wastes and even the size of the population itself

54

Density-dependent Growth A population is a density-dependent when its size

(or density) affects its growth rate because of density-dependent factors such as food availability and toxic waste accumulation

Density-independent Growth In this type of growth a population increases until

some factor causes a sudden reduction in its size Its effect is the same regardless of the size of the

population eg temperature fires floods storms etc

55

Regulation of Population Size Fecundity is the reproductive capacity of individual

females of a species Birth rate or natality is used to measure fecundity Death rate or mortality is the number of individuals

of a species which die per unit time Immigration occurs when individuals join a

population from neighbouring ones Emigration occurs when individuals depart from a

population A cycle occurs when the size of a population

fluctuates on a regular basis

56

Ecological Sampling

57

Why Do We Sample Determine presence andor

abundance

Monitor population fluctuations

Assess lsquoecological damagersquo

Assess quality of habitat

Assess population responses

58

What Do We Sample

Physical Environment Temperature DO pH salinity clarity

flow sediment

Biotic Environment All living things

59

Physical Habitat Temperature

Mercury thermometer Electronic thermometer Long-term thermometers

Dissolved Oxygen Winkler method (titration) DO meter (electrode)

pH Litmus paper pH meter (electrode)

Salinity Salinity Meter YSI 550A DO Meter w12 cable

60

Water Clarity Secchi Disk

Disk is attached to a calibrated rope The disk is lowered into the water until the white parts can no longer be seen Secchi disk depth is then recorded and serves as the waters transparency index The clearer the water the greater the secchi disk depth

Secchi Disk

61

Current Velocity (flow) Floating-orange method

Put an orange (or something else that floats just below the water surface) and measure the time it takes it to float across a known distance

Odometer-type flow meter Number of revolutions the propeller

makes for a given time is calibrated to flow velocity

62

Sediment Sediment size is important to many

aquatic organisms Sieversquos are used to separate and

grade sediment samples Percent of each size grade can be

determined

63

Water Sample

Water and plankton from various depths can be collected

A trigger mechanism is used to close the sampler Sample is then brought back to the

surface

64

Small Mammals

Mouserat Traps Fatal

Pit Falls Bucket is placed in the ground Sometimes have lsquoleadsrsquo to the buckets

Live traps Havahart Sherman

Spot-light

Sherman trapHavahart trap

65

Birds Stick-under-the-box method Bird-trap

Works like a minnow trap Mist net

Captures birds in flight Rocket net

Uses a propellant to throw a net over birds

66

Terrestrial Insects

Sticky paper flies

Baited Traps Fire ants

Nets butterflies

Foggers Collect insects from tree canopies

67

Aquatic Insects Drift Net

Place net in flowing water Kick Net

lsquoKickrsquo sediment upstream from block net and the flow will wash them into the net

Wash bucket Serber or Hess Sampler

Stir up known area of sediment

Animals are collected by a catch net

Multi-plate Sampler Become colonized

68

Crawfish and Crab Traps

69

Fish Larvae Light Traps

Larvae are attracted to the light Ichthyoplankton nets

Can be towed at various depths Fish collect at the lsquocodrsquoend

70

Fish Lift net

Net is placed down and after a set amount of time it is quickly lifted

Pop-net Similar to a lift net but

floats are attached to a framed net

Operated by a trigger mechanism

Throw net A net attached to a heavy

frame is thrown and every thing inside is netted out Throw net

Pop-net

Lift net

71

Minnow trap

Usually use bait to attract small fish Light is used sometimes as an attractant

72

Fish Electrofishing

Electricity is put into the water Fish are temporarily stunned and usually

swim towards the electricity source Usually non-fatal but may cause some

damage

73

Fish Gill Net

Gill nets resemble tennis nets Fish can not swim completely through the

net and get caught Gill nets are size selective (based on mesh

size) Square Mesh

Bar mesh

Stretch mesh

74

Fish Trammel Net

Three panels two large mesh on the outside and a small mesh on the inside

Fish swim through the outer mesh pushes the small mesh through the other side and becomes entangled

75

Hoop nets (and other similar nets) can have bait or not

Fyke nets have leads to help guide fish to the net

76

Seine Seines are nets that are pulled

through shallow water to catch fish

77

Purse Seine Used to encircle entire schools of fish

Usually involves a spotter plane and a second boat

78

Trotline (longline) A series of baited drop lines

connected to a main line

Can be deployed by tying one end to the bank and tying the other end with a heavy weight

79

Shrimp (or fish) Trawl Net pulled behind

a boat along the bottom Either a beam or

otter boards keep the net open

80

Tagging Individuals Coded Wire Tags

Microwire that has a unique label

Magnetic wand detects the tag

Tag retention should be determined

T-Bar tags Can be individually

numbered External tag

PIT tags (Passive Integrated Transponders) Wand induces the tag to

transmit individual number is displayed

81

Other Tagging Methods

Toe clip Amphibian and reptile Clip of one or more toes

to identify individuals

Bird Band Place a metal band on a

bird leg Generally has

identification information

82

Preserving plant specimens Pressing and drying Long-term

preservation and storage

Alternative drying techniques

Special preservation and processing techniques

Mounting

83

Pressing and drying Techniques for pressing and drying specimens have been

established for many years There are minor variations in recommended methods but they are essentially the same worldwide

The best specimens are plants that are pressed as soon as possible after collection before wilting and shrivelling Most plants may be kept in sealed containers such as plastic bags for up to a day if it is inconvenient to press immediately However some plants show such rapid wilting particularly of the flowers that such delays are best avoided Flowers with a lot of nectar may go mouldy very quickly if excess nectar is not shaken off before pressing

Specimens are pressed flat and dried between sheets of absorbent blotters or semi-absorbent paper such as newspaper Papers with a glossy surface should be avoided because they are not absorbent enough to aid drying The plant should be carefully laid out between the drying sheets as their form at this stage largely determines their ultimate appearance The flowers should be spread out with the petals carefully arranged wilted leaves should be straightened and unnecessary shoots of excessively twiggy shrubs may be cut away

84

Microwave ovens Small numbers of specimens can be dried using a microwave

oven The technique recommended in the literature is to place the specimens between unprinted absorbent paper for example butchers paper not newspaper which is unsuitable because the chemicals present in the ink may cause a fire The specimens should be put in a special press which should be of a microwave-safe material (wood acrylic or polycarbonate sheeting eg plexiglass or perspex NO metal components) If such a press is not available sheets of cardboard can be placed above and below the specimens and then weighted down

Drying time depends on the power of your oven In most cases drying is accomplished by irradiating at maximum power for 1-2 minutes per specimen although it is often a case of trial and error It is best to process no more than 10-12 specimens of average thickness per batch Specimens are usually dried after the moisture that characteristically appears on the glass door has disappeared If the specimen is damp when taken out of the oven allow it to stand before re-radiating as moisture continues to evaporate from the specimen for some time Care must be taken not to irradiate the specimens for too long

It should be noted that microwave treatment damages seeds and the cellular structure of the plants which may reduce the long-term value of the specimens

85

Alternative drying techniquesSilica gelother desiccants amp freeze drying Alternative methods of drying plant specimens have been

used for some time but are mostly restricted to special purpose collections The main alternatives are freeze-drying and drying in a desiccant powder such as desiccant silica gel In general these techniques are used where it is essential to preserve the shape of a delicate plant of organ of the plant such as the flower Freeze-drying has also been used to preserve the chemical composition of a plant as accurately as possible for later study

Disadvantages and special conservation problems of specimens dried in these manners are that they are particularly susceptible to damage The dried parts are fragile lack support and often catch on packing materials They must therefore be packed especially carefully and stored in small boxes or tubes with some appropriate packing material that does not snag and break small projections Acid-free tissue paper is often used Drying in desiccant silica gel crystals or powder can also have the disadvantage that it is difficult to remove all traces of the silica gel after drying

86

Special preservation and processing techniquesWet or spirit collections

Very fleshy or delicate structures including small algae and orchid flowers are best preserved in an air-tight glass or plastic jar with a liquid preservative rather than by drying The type of preservative used should be clearly labelled in the jar Such material is often referred to as a spirit collection or wet collection

Most material can be satisfactorily preserved in 70 ethyl alcohol (or 70 methylated spirit or denatured alcohol) with 30 water Colours will fade quickly in spirit however so it is a good idea to keep comprehensive notes and photographs

87

Small algae Microscopic algae are often collected in a jar and in the

water in which they were found If the algae are to be stored for more than 2-3 days a preservative needs to be used Traditionally this has been the extremely toxic formalin - a small amount can be added to the water to make a 5 final solution and the container labelled This must not be sent through the post or by courier

There are some other equally toxic options for example propylene phenoxytol but none should be sent through the post A safer option is to add sufficient concentrated alcohol or methylated spirits to the water containing the algae to make a final solution of 70 alcohol This treatment dilutes the algae making them difficult to find so if they can be concentrated somehow first (eg by filtering) they can be stored in much less liquid Another option is to fix the algae in formalin (or something similar) first and then prepare a microscope glass slide with a permanent water-soluble mounting medium

88

Mounting Mounting specimens prevents most fragile material from

fragmenting and prevents specimens becoming separated from their labels If the plant collection is a long-term project specimens should be mounted on sheets of archival (permanent) cardboard or paper with archival-quality fixing media These include stitching with cotton thread dental floss nickel-plated copper wire (for heavier specimens) narrow strips of archival paper linen tape or by using an archival adhesive such as methyl cellulose adhesive

One disadvantage of mounting specimens is that it can make parts of the specimen inaccessible for examination so it is essential that this be borne in mind during specimen arrangement and mounting For example easily reversible mounting media should be used specimens should be strapped to the sheet rather than glued all over and the specimen should be carefully arranged before it is attached so that it shows all features

89

Full-size herbarium mounting sheets are usually about 43 cm long x 28 cm wide The plant name and accompanying field notes should be transcribed on a permanent label stuck to one corner of the herbarium sheet (the bottom right-hand corner being the most common) or sometimes annotations may be written directly on the sheet or card

Small pieces of material which may have become separated from the specimen (eg seeds) can be placed in small plastic bags and pinned to the sheet

90

Long-term preservation and storage The long-term preservation of dry plant

specimens is largely dependent on protection from insect attack Specimens collected by Linnaeus in the eighteenth century and by Banks and Solander on the Endeavour voyage in 1788 are still excellently preserved

91

Pests and their control A range of pests attack dried plant material The

most common pests are insects and fungi though rodents and other large animals can cause damage in poor storage conditions Insects eat the material the paper surrounding the material and the adhesives and mounting media

Such insect pests range from psocids (book lice) which attack mainly the softer parts such as flowers and soft fruits to tobacco beetles and carpet beetles which can bore holes through the toughest of specimens Many insects are particularly sensitive to relative humidity levels and do not thrive at levels below 50

92

The most common and acceptable specimen treatments for insect control are Freezing Microwave Poisoning Insect deterrents Fungal pests

93

Storage

Dried and pressed plant specimens can be stored in cardboard or plastic boxes or tied in bundles in light-weight cardboard folders placed in pigeon holes

Alternatively they can be placed in protective plastic jackets and displayed in ring folders which is recommended if they are to be frequently handled such as for a reference collection

94

Filing

Specimens should be filed in a systematic order if a relatively permanent collection is being made The major groups ie ferns and fern allies cycads conifers dicotyledons and monocotyledons are best kept separately or according to some classification scheme such as that given in a flora or handbook

Similarly the genera within each family and the species within each genus may be filed alphabetically or following some such classification

95

Preservation of entire animals

Types of collection specimens of an entire animal For reference collections mammals can be prepared as a variety of specimens The condition of the specimen may determine possible ways to preserve it if for instance decomposition of the skin has loosened the hair of a carcass so much that it can easily be pulled out or removed by rubbing (ldquoslippingrdquo fur) it will be very difficult or impossible to produce a study skin or mounted specimen The most usual types of specimens (based on Nagorsen and Peterson 1980) are 1) entire fluid-preserved animals (for studying anatomy and histology fluid preservation may change the fur colour) 2) study skins with accompanying skulls partial skeletons (some bones remain in the skin) for studying pelage colour hair quality and moulting patterns 3) mounted skins with accompanying partial or entire skeleton (some bones may remain in the skin dependant on the method of preservation) or freeze-dried specimens 4) entire skeletons for instance for studying anatomy geographic variation or for age determination (entire skeletons are poorly represented in collections so Nagorsen and Peterson (1980) recommend preparation of at least one male and one female skeleton per species

96

Preservation of specimens in the field Formalin preservation Preservation in alcohol Preservation by cooling or freezing

97

Formalin preservation After weighing and measuring the animal and attaching an

adequate label very small specimens (up to 100 g) can be fixed whole by submerging them in 10 buffered formalin (tissue - formalin solution ratio of at least 1 12) the body cavity can be filled with formalin solution by injection until it is turgid and firm some formalin may also be injected under the skin into the body cavity larger muscles and organs If hypodermic needles are not available the body cavity can be opened ventrally by making a slit instead allowing the formalin to enter

Keeping the mouth open with a piece of wood or cotton may later allow examination of teeth Then the whole body can be immersed in formalin in the posture in which it is supposed to stay permanently because it will harden The ratio of formalin to carcass must be at least 12 to 1 to assure a good fixation Tissues can be left in buffered neutralized formalin for several months but formalin hardens specimens therefore after fixation longterm storage in alcohol may be better After preservation the carcass should therefore be washed in water and transferred into ethanol for permanent storage

Disadvantages for instance it discolours the fur after a longish immersion softens the bones and prevents further examination for microbiology

98

Preservation in alcohol

After weighing a whole animal can be preserved in a container of alcohol (70-90) Removal of the intestine prior to storage of the animal in alcohol is recommended

99

Preservation by cooling or freezing Removal of the skin with insulating fur

before cooling or freezing may help to cool the carcass down more quickly

Freezing is not recommended if histological examination is planned

100

THANK YOU

29

RANDOM SAMPLING

1048698 Often used when the area being studied isfairly uniform very large or when there is alimited amount of time available1048698 Random = chosen by chance rather thanaccording to a plan all outcomes are

equallylikely1048698 Samples are taken from different positionswithin a habitat and those positions arechosen randomly

30

How to sample randomly

Choose individuals or Placeldquosampling unitsrdquo

haphazardlyndash This is rarely completely

random1048698 ORhellip1048698 Assign numbers to the

areasor individuals to be sampledndash Use a random number

table toselect which areas or

individualswill be sample

31

Population Attributes Density ndash size of a population in relation to a definite

unit of space Affected by

Natality ndash the reproductive output (birth rate) of a population

Mortality ndash the death rate of organisms in a population

Immigration ndash number of organisms moving into the area occupied by the population

Emigration ndash number of organisms moving out of the area occupied by the population

32

Population Density

Four primary population parameters

33

Two Types of Density Estimates

bull Absolute Density ndash a known density such as m2

bull Relative Density ndash we know when one area has more individuals than another

34

Measuring Absolute Density

Total Count ndash count the number of organisms living in an area Human census number of oak trees in a

wooded lot number of singing birds in an area

Total counts generally are not used very often

Sampling Methods ndash use a sample to estimate population size Either use the quadrat or capture-

recapture method

35

Measurement of Environmental ParametersAbiotic factors are important in determining

both the distribution of the organisms and their physical and physiological adaptations

Temperature- diurnal and seasonal temperature variations

are significant in affecting different species of plants and animals

- equipment mercury thermometer maximum-minimum thermometer

miniaturized thermistor

36

pH

-measure pH of a solution by universal indicator pH paper pH meter etc

Light

-measure its duration and intensity duration by predication from Royal Observatory intensity by photographic light meter

pH meter in use

37

Humidity

Relative humidity the water content of a given volume of air relative to the same volume of fully saturated air

- equipment whirling hygrometer

38

Wind and Water Speed- wind speed- anemometer or wind

gauges- water speed - time the movement of a

floating object over a measured distance

39

Salinity

- using a conductivity meter greater salinity has greater conductivity

Oxygen Level

- using an oxygen meter or chemical method (Winkler method)

40

Collecting MethodsCollecting all organisms within a habitat is normally

impractical and therefore small areas are selected Remember to return all material to its original position

after searching amp collecting sufficient specimens Some collecting apparatus for general use are listed

below

41

1 specimen tube

2 screwed-topped jars

3 polythene bags

4 forceps

5 paint brush

6 bulb pipette

7 pooter

42

8 widger 9 sieve 10 hand lens

11 enamel dish 12 beating tray 13 light traps

14 Tullgren funnel 15 Baermann funnel 16 mammal traps

17 pitfall traps 18 netting

43

Estimating Population Size

The exact methods used for estimation depend not only the nature of the habitat but also on the organisms involved

eg animals - population

plants - percentage cover

44

Using Quadrats

- By sampling an area using quadrats and counting the number of individuals within each quadrat it is possible to estimate the total number of individuals within the area

- confined to plants and sessile or very slow-moving animals

- fast-moving animals are disturbed and run away

45

Capture-recapture Techniques- useful for mobile animals which can be marked

- capture marked released randomly recaptured

and marked individuals recorded

no of marked individuals recaptured total no of individuals in 1st sample

-------------------------------------------- = ------------------------------------------

total no of individuals in 2nd sample estimated size of population

(the Lincoln Index)

46

Capture-recapture Techniques Factors affecting the accuracy of the estimation

deaths migration individuals become more liable to predation etc

Examples

- arthropods marked on their backs with non-toxic paint

- fish have tags attached to opercula - mammals have tags clipped to their ears

birds have their legs ringed

47

Capture-recapture Method Important tool for estimating density birth

rate and death rate for mobile animals Method

Collect a sample of individuals mark them and then release them

After a period collect more individuals from the wild and count the number that have marks

We assume that a sample if random will contain the same proportion of marked individuals as the population does

Estimate population density

48

Assumptions For All Capture-Recapture Studies Marking technique does not increase

mortality of marked animals Marked individuals are allowed to mix

with population Marking technique does not affect catch

probability Marks are not lost or overlooked No significant immigration or emigration No significant mortality or natality

49

Marked animals in second sample

Total caught in second sample

Marked animals in first sample

Total population size

=

520 N

16=

Peterson Method or Lincoln Index

N = 64N = (20)(16)5

50

Some Indices Used

Traps Number of Fecal

Pellets Vocalization

Frequency Pelt Records Catch per Unit

Fishing Effort

Number of Artifacts Questionnaires Cover Feeding Capacity Roadside Counts

51

Abundance Scales

The population size may be fairly accurately determined by making some form of frequency assessment

These are subjective and involve an experimenter making some estimate of the number of individuals in a given area or the cover of a particular species

This is especially useful where individuals are very numerous eg barnacles on a rocky shore or where it is difficult to distinguish individuals eg grass plants in a meadow

52

The assessments are usually made on an abundance scale of 5 categories

Abundance Common Frequent Occasional Rare

Barnacles exposed at low water

53

Environmental resistance are the factors which limit the growth of a particular population

eg predation disease availability of light food water oxygen and shelter the accumulation of toxic wastes and even the size of the population itself

54

Density-dependent Growth A population is a density-dependent when its size

(or density) affects its growth rate because of density-dependent factors such as food availability and toxic waste accumulation

Density-independent Growth In this type of growth a population increases until

some factor causes a sudden reduction in its size Its effect is the same regardless of the size of the

population eg temperature fires floods storms etc

55

Regulation of Population Size Fecundity is the reproductive capacity of individual

females of a species Birth rate or natality is used to measure fecundity Death rate or mortality is the number of individuals

of a species which die per unit time Immigration occurs when individuals join a

population from neighbouring ones Emigration occurs when individuals depart from a

population A cycle occurs when the size of a population

fluctuates on a regular basis

56

Ecological Sampling

57

Why Do We Sample Determine presence andor

abundance

Monitor population fluctuations

Assess lsquoecological damagersquo

Assess quality of habitat

Assess population responses

58

What Do We Sample

Physical Environment Temperature DO pH salinity clarity

flow sediment

Biotic Environment All living things

59

Physical Habitat Temperature

Mercury thermometer Electronic thermometer Long-term thermometers

Dissolved Oxygen Winkler method (titration) DO meter (electrode)

pH Litmus paper pH meter (electrode)

Salinity Salinity Meter YSI 550A DO Meter w12 cable

60

Water Clarity Secchi Disk

Disk is attached to a calibrated rope The disk is lowered into the water until the white parts can no longer be seen Secchi disk depth is then recorded and serves as the waters transparency index The clearer the water the greater the secchi disk depth

Secchi Disk

61

Current Velocity (flow) Floating-orange method

Put an orange (or something else that floats just below the water surface) and measure the time it takes it to float across a known distance

Odometer-type flow meter Number of revolutions the propeller

makes for a given time is calibrated to flow velocity

62

Sediment Sediment size is important to many

aquatic organisms Sieversquos are used to separate and

grade sediment samples Percent of each size grade can be

determined

63

Water Sample

Water and plankton from various depths can be collected

A trigger mechanism is used to close the sampler Sample is then brought back to the

surface

64

Small Mammals

Mouserat Traps Fatal

Pit Falls Bucket is placed in the ground Sometimes have lsquoleadsrsquo to the buckets

Live traps Havahart Sherman

Spot-light

Sherman trapHavahart trap

65

Birds Stick-under-the-box method Bird-trap

Works like a minnow trap Mist net

Captures birds in flight Rocket net

Uses a propellant to throw a net over birds

66

Terrestrial Insects

Sticky paper flies

Baited Traps Fire ants

Nets butterflies

Foggers Collect insects from tree canopies

67

Aquatic Insects Drift Net

Place net in flowing water Kick Net

lsquoKickrsquo sediment upstream from block net and the flow will wash them into the net

Wash bucket Serber or Hess Sampler

Stir up known area of sediment

Animals are collected by a catch net

Multi-plate Sampler Become colonized

68

Crawfish and Crab Traps

69

Fish Larvae Light Traps

Larvae are attracted to the light Ichthyoplankton nets

Can be towed at various depths Fish collect at the lsquocodrsquoend

70

Fish Lift net

Net is placed down and after a set amount of time it is quickly lifted

Pop-net Similar to a lift net but

floats are attached to a framed net

Operated by a trigger mechanism

Throw net A net attached to a heavy

frame is thrown and every thing inside is netted out Throw net

Pop-net

Lift net

71

Minnow trap

Usually use bait to attract small fish Light is used sometimes as an attractant

72

Fish Electrofishing

Electricity is put into the water Fish are temporarily stunned and usually

swim towards the electricity source Usually non-fatal but may cause some

damage

73

Fish Gill Net

Gill nets resemble tennis nets Fish can not swim completely through the

net and get caught Gill nets are size selective (based on mesh

size) Square Mesh

Bar mesh

Stretch mesh

74

Fish Trammel Net

Three panels two large mesh on the outside and a small mesh on the inside

Fish swim through the outer mesh pushes the small mesh through the other side and becomes entangled

75

Hoop nets (and other similar nets) can have bait or not

Fyke nets have leads to help guide fish to the net

76

Seine Seines are nets that are pulled

through shallow water to catch fish

77

Purse Seine Used to encircle entire schools of fish

Usually involves a spotter plane and a second boat

78

Trotline (longline) A series of baited drop lines

connected to a main line

Can be deployed by tying one end to the bank and tying the other end with a heavy weight

79

Shrimp (or fish) Trawl Net pulled behind

a boat along the bottom Either a beam or

otter boards keep the net open

80

Tagging Individuals Coded Wire Tags

Microwire that has a unique label

Magnetic wand detects the tag

Tag retention should be determined

T-Bar tags Can be individually

numbered External tag

PIT tags (Passive Integrated Transponders) Wand induces the tag to

transmit individual number is displayed

81

Other Tagging Methods

Toe clip Amphibian and reptile Clip of one or more toes

to identify individuals

Bird Band Place a metal band on a

bird leg Generally has

identification information

82

Preserving plant specimens Pressing and drying Long-term

preservation and storage

Alternative drying techniques

Special preservation and processing techniques

Mounting

83

Pressing and drying Techniques for pressing and drying specimens have been

established for many years There are minor variations in recommended methods but they are essentially the same worldwide

The best specimens are plants that are pressed as soon as possible after collection before wilting and shrivelling Most plants may be kept in sealed containers such as plastic bags for up to a day if it is inconvenient to press immediately However some plants show such rapid wilting particularly of the flowers that such delays are best avoided Flowers with a lot of nectar may go mouldy very quickly if excess nectar is not shaken off before pressing

Specimens are pressed flat and dried between sheets of absorbent blotters or semi-absorbent paper such as newspaper Papers with a glossy surface should be avoided because they are not absorbent enough to aid drying The plant should be carefully laid out between the drying sheets as their form at this stage largely determines their ultimate appearance The flowers should be spread out with the petals carefully arranged wilted leaves should be straightened and unnecessary shoots of excessively twiggy shrubs may be cut away

84

Microwave ovens Small numbers of specimens can be dried using a microwave

oven The technique recommended in the literature is to place the specimens between unprinted absorbent paper for example butchers paper not newspaper which is unsuitable because the chemicals present in the ink may cause a fire The specimens should be put in a special press which should be of a microwave-safe material (wood acrylic or polycarbonate sheeting eg plexiglass or perspex NO metal components) If such a press is not available sheets of cardboard can be placed above and below the specimens and then weighted down

Drying time depends on the power of your oven In most cases drying is accomplished by irradiating at maximum power for 1-2 minutes per specimen although it is often a case of trial and error It is best to process no more than 10-12 specimens of average thickness per batch Specimens are usually dried after the moisture that characteristically appears on the glass door has disappeared If the specimen is damp when taken out of the oven allow it to stand before re-radiating as moisture continues to evaporate from the specimen for some time Care must be taken not to irradiate the specimens for too long

It should be noted that microwave treatment damages seeds and the cellular structure of the plants which may reduce the long-term value of the specimens

85

Alternative drying techniquesSilica gelother desiccants amp freeze drying Alternative methods of drying plant specimens have been

used for some time but are mostly restricted to special purpose collections The main alternatives are freeze-drying and drying in a desiccant powder such as desiccant silica gel In general these techniques are used where it is essential to preserve the shape of a delicate plant of organ of the plant such as the flower Freeze-drying has also been used to preserve the chemical composition of a plant as accurately as possible for later study

Disadvantages and special conservation problems of specimens dried in these manners are that they are particularly susceptible to damage The dried parts are fragile lack support and often catch on packing materials They must therefore be packed especially carefully and stored in small boxes or tubes with some appropriate packing material that does not snag and break small projections Acid-free tissue paper is often used Drying in desiccant silica gel crystals or powder can also have the disadvantage that it is difficult to remove all traces of the silica gel after drying

86

Special preservation and processing techniquesWet or spirit collections

Very fleshy or delicate structures including small algae and orchid flowers are best preserved in an air-tight glass or plastic jar with a liquid preservative rather than by drying The type of preservative used should be clearly labelled in the jar Such material is often referred to as a spirit collection or wet collection

Most material can be satisfactorily preserved in 70 ethyl alcohol (or 70 methylated spirit or denatured alcohol) with 30 water Colours will fade quickly in spirit however so it is a good idea to keep comprehensive notes and photographs

87

Small algae Microscopic algae are often collected in a jar and in the

water in which they were found If the algae are to be stored for more than 2-3 days a preservative needs to be used Traditionally this has been the extremely toxic formalin - a small amount can be added to the water to make a 5 final solution and the container labelled This must not be sent through the post or by courier

There are some other equally toxic options for example propylene phenoxytol but none should be sent through the post A safer option is to add sufficient concentrated alcohol or methylated spirits to the water containing the algae to make a final solution of 70 alcohol This treatment dilutes the algae making them difficult to find so if they can be concentrated somehow first (eg by filtering) they can be stored in much less liquid Another option is to fix the algae in formalin (or something similar) first and then prepare a microscope glass slide with a permanent water-soluble mounting medium

88

Mounting Mounting specimens prevents most fragile material from

fragmenting and prevents specimens becoming separated from their labels If the plant collection is a long-term project specimens should be mounted on sheets of archival (permanent) cardboard or paper with archival-quality fixing media These include stitching with cotton thread dental floss nickel-plated copper wire (for heavier specimens) narrow strips of archival paper linen tape or by using an archival adhesive such as methyl cellulose adhesive

One disadvantage of mounting specimens is that it can make parts of the specimen inaccessible for examination so it is essential that this be borne in mind during specimen arrangement and mounting For example easily reversible mounting media should be used specimens should be strapped to the sheet rather than glued all over and the specimen should be carefully arranged before it is attached so that it shows all features

89

Full-size herbarium mounting sheets are usually about 43 cm long x 28 cm wide The plant name and accompanying field notes should be transcribed on a permanent label stuck to one corner of the herbarium sheet (the bottom right-hand corner being the most common) or sometimes annotations may be written directly on the sheet or card

Small pieces of material which may have become separated from the specimen (eg seeds) can be placed in small plastic bags and pinned to the sheet

90

Long-term preservation and storage The long-term preservation of dry plant

specimens is largely dependent on protection from insect attack Specimens collected by Linnaeus in the eighteenth century and by Banks and Solander on the Endeavour voyage in 1788 are still excellently preserved

91

Pests and their control A range of pests attack dried plant material The

most common pests are insects and fungi though rodents and other large animals can cause damage in poor storage conditions Insects eat the material the paper surrounding the material and the adhesives and mounting media

Such insect pests range from psocids (book lice) which attack mainly the softer parts such as flowers and soft fruits to tobacco beetles and carpet beetles which can bore holes through the toughest of specimens Many insects are particularly sensitive to relative humidity levels and do not thrive at levels below 50

92

The most common and acceptable specimen treatments for insect control are Freezing Microwave Poisoning Insect deterrents Fungal pests

93

Storage

Dried and pressed plant specimens can be stored in cardboard or plastic boxes or tied in bundles in light-weight cardboard folders placed in pigeon holes

Alternatively they can be placed in protective plastic jackets and displayed in ring folders which is recommended if they are to be frequently handled such as for a reference collection

94

Filing

Specimens should be filed in a systematic order if a relatively permanent collection is being made The major groups ie ferns and fern allies cycads conifers dicotyledons and monocotyledons are best kept separately or according to some classification scheme such as that given in a flora or handbook

Similarly the genera within each family and the species within each genus may be filed alphabetically or following some such classification

95

Preservation of entire animals

Types of collection specimens of an entire animal For reference collections mammals can be prepared as a variety of specimens The condition of the specimen may determine possible ways to preserve it if for instance decomposition of the skin has loosened the hair of a carcass so much that it can easily be pulled out or removed by rubbing (ldquoslippingrdquo fur) it will be very difficult or impossible to produce a study skin or mounted specimen The most usual types of specimens (based on Nagorsen and Peterson 1980) are 1) entire fluid-preserved animals (for studying anatomy and histology fluid preservation may change the fur colour) 2) study skins with accompanying skulls partial skeletons (some bones remain in the skin) for studying pelage colour hair quality and moulting patterns 3) mounted skins with accompanying partial or entire skeleton (some bones may remain in the skin dependant on the method of preservation) or freeze-dried specimens 4) entire skeletons for instance for studying anatomy geographic variation or for age determination (entire skeletons are poorly represented in collections so Nagorsen and Peterson (1980) recommend preparation of at least one male and one female skeleton per species

96

Preservation of specimens in the field Formalin preservation Preservation in alcohol Preservation by cooling or freezing

97

Formalin preservation After weighing and measuring the animal and attaching an

adequate label very small specimens (up to 100 g) can be fixed whole by submerging them in 10 buffered formalin (tissue - formalin solution ratio of at least 1 12) the body cavity can be filled with formalin solution by injection until it is turgid and firm some formalin may also be injected under the skin into the body cavity larger muscles and organs If hypodermic needles are not available the body cavity can be opened ventrally by making a slit instead allowing the formalin to enter

Keeping the mouth open with a piece of wood or cotton may later allow examination of teeth Then the whole body can be immersed in formalin in the posture in which it is supposed to stay permanently because it will harden The ratio of formalin to carcass must be at least 12 to 1 to assure a good fixation Tissues can be left in buffered neutralized formalin for several months but formalin hardens specimens therefore after fixation longterm storage in alcohol may be better After preservation the carcass should therefore be washed in water and transferred into ethanol for permanent storage

Disadvantages for instance it discolours the fur after a longish immersion softens the bones and prevents further examination for microbiology

98

Preservation in alcohol

After weighing a whole animal can be preserved in a container of alcohol (70-90) Removal of the intestine prior to storage of the animal in alcohol is recommended

99

Preservation by cooling or freezing Removal of the skin with insulating fur

before cooling or freezing may help to cool the carcass down more quickly

Freezing is not recommended if histological examination is planned

100

THANK YOU

30

How to sample randomly

Choose individuals or Placeldquosampling unitsrdquo

haphazardlyndash This is rarely completely

random1048698 ORhellip1048698 Assign numbers to the

areasor individuals to be sampledndash Use a random number

table toselect which areas or

individualswill be sample

31

Population Attributes Density ndash size of a population in relation to a definite

unit of space Affected by

Natality ndash the reproductive output (birth rate) of a population

Mortality ndash the death rate of organisms in a population

Immigration ndash number of organisms moving into the area occupied by the population

Emigration ndash number of organisms moving out of the area occupied by the population

32

Population Density

Four primary population parameters

33

Two Types of Density Estimates

bull Absolute Density ndash a known density such as m2

bull Relative Density ndash we know when one area has more individuals than another

34

Measuring Absolute Density

Total Count ndash count the number of organisms living in an area Human census number of oak trees in a

wooded lot number of singing birds in an area

Total counts generally are not used very often

Sampling Methods ndash use a sample to estimate population size Either use the quadrat or capture-

recapture method

35

Measurement of Environmental ParametersAbiotic factors are important in determining

both the distribution of the organisms and their physical and physiological adaptations

Temperature- diurnal and seasonal temperature variations

are significant in affecting different species of plants and animals

- equipment mercury thermometer maximum-minimum thermometer

miniaturized thermistor

36

pH

-measure pH of a solution by universal indicator pH paper pH meter etc

Light

-measure its duration and intensity duration by predication from Royal Observatory intensity by photographic light meter

pH meter in use

37

Humidity

Relative humidity the water content of a given volume of air relative to the same volume of fully saturated air

- equipment whirling hygrometer

38

Wind and Water Speed- wind speed- anemometer or wind

gauges- water speed - time the movement of a

floating object over a measured distance

39

Salinity

- using a conductivity meter greater salinity has greater conductivity

Oxygen Level

- using an oxygen meter or chemical method (Winkler method)

40

Collecting MethodsCollecting all organisms within a habitat is normally

impractical and therefore small areas are selected Remember to return all material to its original position

after searching amp collecting sufficient specimens Some collecting apparatus for general use are listed

below

41

1 specimen tube

2 screwed-topped jars

3 polythene bags

4 forceps

5 paint brush

6 bulb pipette

7 pooter

42

8 widger 9 sieve 10 hand lens

11 enamel dish 12 beating tray 13 light traps

14 Tullgren funnel 15 Baermann funnel 16 mammal traps

17 pitfall traps 18 netting

43

Estimating Population Size

The exact methods used for estimation depend not only the nature of the habitat but also on the organisms involved

eg animals - population

plants - percentage cover

44

Using Quadrats

- By sampling an area using quadrats and counting the number of individuals within each quadrat it is possible to estimate the total number of individuals within the area

- confined to plants and sessile or very slow-moving animals

- fast-moving animals are disturbed and run away

45

Capture-recapture Techniques- useful for mobile animals which can be marked

- capture marked released randomly recaptured

and marked individuals recorded

no of marked individuals recaptured total no of individuals in 1st sample

-------------------------------------------- = ------------------------------------------

total no of individuals in 2nd sample estimated size of population

(the Lincoln Index)

46

Capture-recapture Techniques Factors affecting the accuracy of the estimation

deaths migration individuals become more liable to predation etc

Examples

- arthropods marked on their backs with non-toxic paint

- fish have tags attached to opercula - mammals have tags clipped to their ears

birds have their legs ringed

47

Capture-recapture Method Important tool for estimating density birth

rate and death rate for mobile animals Method

Collect a sample of individuals mark them and then release them

After a period collect more individuals from the wild and count the number that have marks

We assume that a sample if random will contain the same proportion of marked individuals as the population does

Estimate population density

48

Assumptions For All Capture-Recapture Studies Marking technique does not increase

mortality of marked animals Marked individuals are allowed to mix

with population Marking technique does not affect catch

probability Marks are not lost or overlooked No significant immigration or emigration No significant mortality or natality

49

Marked animals in second sample

Total caught in second sample

Marked animals in first sample

Total population size

=

520 N

16=

Peterson Method or Lincoln Index

N = 64N = (20)(16)5

50

Some Indices Used

Traps Number of Fecal

Pellets Vocalization

Frequency Pelt Records Catch per Unit

Fishing Effort

Number of Artifacts Questionnaires Cover Feeding Capacity Roadside Counts

51

Abundance Scales

The population size may be fairly accurately determined by making some form of frequency assessment

These are subjective and involve an experimenter making some estimate of the number of individuals in a given area or the cover of a particular species

This is especially useful where individuals are very numerous eg barnacles on a rocky shore or where it is difficult to distinguish individuals eg grass plants in a meadow

52

The assessments are usually made on an abundance scale of 5 categories

Abundance Common Frequent Occasional Rare

Barnacles exposed at low water

53

Environmental resistance are the factors which limit the growth of a particular population

eg predation disease availability of light food water oxygen and shelter the accumulation of toxic wastes and even the size of the population itself

54

Density-dependent Growth A population is a density-dependent when its size

(or density) affects its growth rate because of density-dependent factors such as food availability and toxic waste accumulation

Density-independent Growth In this type of growth a population increases until

some factor causes a sudden reduction in its size Its effect is the same regardless of the size of the

population eg temperature fires floods storms etc

55

Regulation of Population Size Fecundity is the reproductive capacity of individual

females of a species Birth rate or natality is used to measure fecundity Death rate or mortality is the number of individuals

of a species which die per unit time Immigration occurs when individuals join a

population from neighbouring ones Emigration occurs when individuals depart from a

population A cycle occurs when the size of a population

fluctuates on a regular basis

56

Ecological Sampling

57

Why Do We Sample Determine presence andor

abundance

Monitor population fluctuations

Assess lsquoecological damagersquo

Assess quality of habitat

Assess population responses

58

What Do We Sample

Physical Environment Temperature DO pH salinity clarity

flow sediment

Biotic Environment All living things

59

Physical Habitat Temperature

Mercury thermometer Electronic thermometer Long-term thermometers

Dissolved Oxygen Winkler method (titration) DO meter (electrode)

pH Litmus paper pH meter (electrode)

Salinity Salinity Meter YSI 550A DO Meter w12 cable

60

Water Clarity Secchi Disk

Disk is attached to a calibrated rope The disk is lowered into the water until the white parts can no longer be seen Secchi disk depth is then recorded and serves as the waters transparency index The clearer the water the greater the secchi disk depth

Secchi Disk

61

Current Velocity (flow) Floating-orange method

Put an orange (or something else that floats just below the water surface) and measure the time it takes it to float across a known distance

Odometer-type flow meter Number of revolutions the propeller

makes for a given time is calibrated to flow velocity

62

Sediment Sediment size is important to many

aquatic organisms Sieversquos are used to separate and

grade sediment samples Percent of each size grade can be

determined

63

Water Sample

Water and plankton from various depths can be collected

A trigger mechanism is used to close the sampler Sample is then brought back to the

surface

64

Small Mammals

Mouserat Traps Fatal

Pit Falls Bucket is placed in the ground Sometimes have lsquoleadsrsquo to the buckets

Live traps Havahart Sherman

Spot-light

Sherman trapHavahart trap

65

Birds Stick-under-the-box method Bird-trap

Works like a minnow trap Mist net

Captures birds in flight Rocket net

Uses a propellant to throw a net over birds

66

Terrestrial Insects

Sticky paper flies

Baited Traps Fire ants

Nets butterflies

Foggers Collect insects from tree canopies

67

Aquatic Insects Drift Net

Place net in flowing water Kick Net

lsquoKickrsquo sediment upstream from block net and the flow will wash them into the net

Wash bucket Serber or Hess Sampler

Stir up known area of sediment

Animals are collected by a catch net

Multi-plate Sampler Become colonized

68

Crawfish and Crab Traps

69

Fish Larvae Light Traps

Larvae are attracted to the light Ichthyoplankton nets

Can be towed at various depths Fish collect at the lsquocodrsquoend

70

Fish Lift net

Net is placed down and after a set amount of time it is quickly lifted

Pop-net Similar to a lift net but

floats are attached to a framed net

Operated by a trigger mechanism

Throw net A net attached to a heavy

frame is thrown and every thing inside is netted out Throw net

Pop-net

Lift net

71

Minnow trap

Usually use bait to attract small fish Light is used sometimes as an attractant

72

Fish Electrofishing

Electricity is put into the water Fish are temporarily stunned and usually

swim towards the electricity source Usually non-fatal but may cause some

damage

73

Fish Gill Net

Gill nets resemble tennis nets Fish can not swim completely through the

net and get caught Gill nets are size selective (based on mesh

size) Square Mesh

Bar mesh

Stretch mesh

74

Fish Trammel Net

Three panels two large mesh on the outside and a small mesh on the inside

Fish swim through the outer mesh pushes the small mesh through the other side and becomes entangled

75

Hoop nets (and other similar nets) can have bait or not

Fyke nets have leads to help guide fish to the net

76

Seine Seines are nets that are pulled

through shallow water to catch fish

77

Purse Seine Used to encircle entire schools of fish

Usually involves a spotter plane and a second boat

78

Trotline (longline) A series of baited drop lines

connected to a main line

Can be deployed by tying one end to the bank and tying the other end with a heavy weight

79

Shrimp (or fish) Trawl Net pulled behind

a boat along the bottom Either a beam or

otter boards keep the net open

80

Tagging Individuals Coded Wire Tags

Microwire that has a unique label

Magnetic wand detects the tag

Tag retention should be determined

T-Bar tags Can be individually

numbered External tag

PIT tags (Passive Integrated Transponders) Wand induces the tag to

transmit individual number is displayed

81

Other Tagging Methods

Toe clip Amphibian and reptile Clip of one or more toes

to identify individuals

Bird Band Place a metal band on a

bird leg Generally has

identification information

82

Preserving plant specimens Pressing and drying Long-term

preservation and storage

Alternative drying techniques

Special preservation and processing techniques

Mounting

83

Pressing and drying Techniques for pressing and drying specimens have been

established for many years There are minor variations in recommended methods but they are essentially the same worldwide

The best specimens are plants that are pressed as soon as possible after collection before wilting and shrivelling Most plants may be kept in sealed containers such as plastic bags for up to a day if it is inconvenient to press immediately However some plants show such rapid wilting particularly of the flowers that such delays are best avoided Flowers with a lot of nectar may go mouldy very quickly if excess nectar is not shaken off before pressing

Specimens are pressed flat and dried between sheets of absorbent blotters or semi-absorbent paper such as newspaper Papers with a glossy surface should be avoided because they are not absorbent enough to aid drying The plant should be carefully laid out between the drying sheets as their form at this stage largely determines their ultimate appearance The flowers should be spread out with the petals carefully arranged wilted leaves should be straightened and unnecessary shoots of excessively twiggy shrubs may be cut away

84

Microwave ovens Small numbers of specimens can be dried using a microwave

oven The technique recommended in the literature is to place the specimens between unprinted absorbent paper for example butchers paper not newspaper which is unsuitable because the chemicals present in the ink may cause a fire The specimens should be put in a special press which should be of a microwave-safe material (wood acrylic or polycarbonate sheeting eg plexiglass or perspex NO metal components) If such a press is not available sheets of cardboard can be placed above and below the specimens and then weighted down

Drying time depends on the power of your oven In most cases drying is accomplished by irradiating at maximum power for 1-2 minutes per specimen although it is often a case of trial and error It is best to process no more than 10-12 specimens of average thickness per batch Specimens are usually dried after the moisture that characteristically appears on the glass door has disappeared If the specimen is damp when taken out of the oven allow it to stand before re-radiating as moisture continues to evaporate from the specimen for some time Care must be taken not to irradiate the specimens for too long

It should be noted that microwave treatment damages seeds and the cellular structure of the plants which may reduce the long-term value of the specimens

85

Alternative drying techniquesSilica gelother desiccants amp freeze drying Alternative methods of drying plant specimens have been

used for some time but are mostly restricted to special purpose collections The main alternatives are freeze-drying and drying in a desiccant powder such as desiccant silica gel In general these techniques are used where it is essential to preserve the shape of a delicate plant of organ of the plant such as the flower Freeze-drying has also been used to preserve the chemical composition of a plant as accurately as possible for later study

Disadvantages and special conservation problems of specimens dried in these manners are that they are particularly susceptible to damage The dried parts are fragile lack support and often catch on packing materials They must therefore be packed especially carefully and stored in small boxes or tubes with some appropriate packing material that does not snag and break small projections Acid-free tissue paper is often used Drying in desiccant silica gel crystals or powder can also have the disadvantage that it is difficult to remove all traces of the silica gel after drying

86

Special preservation and processing techniquesWet or spirit collections

Very fleshy or delicate structures including small algae and orchid flowers are best preserved in an air-tight glass or plastic jar with a liquid preservative rather than by drying The type of preservative used should be clearly labelled in the jar Such material is often referred to as a spirit collection or wet collection

Most material can be satisfactorily preserved in 70 ethyl alcohol (or 70 methylated spirit or denatured alcohol) with 30 water Colours will fade quickly in spirit however so it is a good idea to keep comprehensive notes and photographs

87

Small algae Microscopic algae are often collected in a jar and in the

water in which they were found If the algae are to be stored for more than 2-3 days a preservative needs to be used Traditionally this has been the extremely toxic formalin - a small amount can be added to the water to make a 5 final solution and the container labelled This must not be sent through the post or by courier

There are some other equally toxic options for example propylene phenoxytol but none should be sent through the post A safer option is to add sufficient concentrated alcohol or methylated spirits to the water containing the algae to make a final solution of 70 alcohol This treatment dilutes the algae making them difficult to find so if they can be concentrated somehow first (eg by filtering) they can be stored in much less liquid Another option is to fix the algae in formalin (or something similar) first and then prepare a microscope glass slide with a permanent water-soluble mounting medium

88

Mounting Mounting specimens prevents most fragile material from

fragmenting and prevents specimens becoming separated from their labels If the plant collection is a long-term project specimens should be mounted on sheets of archival (permanent) cardboard or paper with archival-quality fixing media These include stitching with cotton thread dental floss nickel-plated copper wire (for heavier specimens) narrow strips of archival paper linen tape or by using an archival adhesive such as methyl cellulose adhesive

One disadvantage of mounting specimens is that it can make parts of the specimen inaccessible for examination so it is essential that this be borne in mind during specimen arrangement and mounting For example easily reversible mounting media should be used specimens should be strapped to the sheet rather than glued all over and the specimen should be carefully arranged before it is attached so that it shows all features

89

Full-size herbarium mounting sheets are usually about 43 cm long x 28 cm wide The plant name and accompanying field notes should be transcribed on a permanent label stuck to one corner of the herbarium sheet (the bottom right-hand corner being the most common) or sometimes annotations may be written directly on the sheet or card

Small pieces of material which may have become separated from the specimen (eg seeds) can be placed in small plastic bags and pinned to the sheet

90

Long-term preservation and storage The long-term preservation of dry plant

specimens is largely dependent on protection from insect attack Specimens collected by Linnaeus in the eighteenth century and by Banks and Solander on the Endeavour voyage in 1788 are still excellently preserved

91

Pests and their control A range of pests attack dried plant material The

most common pests are insects and fungi though rodents and other large animals can cause damage in poor storage conditions Insects eat the material the paper surrounding the material and the adhesives and mounting media

Such insect pests range from psocids (book lice) which attack mainly the softer parts such as flowers and soft fruits to tobacco beetles and carpet beetles which can bore holes through the toughest of specimens Many insects are particularly sensitive to relative humidity levels and do not thrive at levels below 50

92

The most common and acceptable specimen treatments for insect control are Freezing Microwave Poisoning Insect deterrents Fungal pests

93

Storage

Dried and pressed plant specimens can be stored in cardboard or plastic boxes or tied in bundles in light-weight cardboard folders placed in pigeon holes

Alternatively they can be placed in protective plastic jackets and displayed in ring folders which is recommended if they are to be frequently handled such as for a reference collection

94

Filing

Specimens should be filed in a systematic order if a relatively permanent collection is being made The major groups ie ferns and fern allies cycads conifers dicotyledons and monocotyledons are best kept separately or according to some classification scheme such as that given in a flora or handbook

Similarly the genera within each family and the species within each genus may be filed alphabetically or following some such classification

95

Preservation of entire animals

Types of collection specimens of an entire animal For reference collections mammals can be prepared as a variety of specimens The condition of the specimen may determine possible ways to preserve it if for instance decomposition of the skin has loosened the hair of a carcass so much that it can easily be pulled out or removed by rubbing (ldquoslippingrdquo fur) it will be very difficult or impossible to produce a study skin or mounted specimen The most usual types of specimens (based on Nagorsen and Peterson 1980) are 1) entire fluid-preserved animals (for studying anatomy and histology fluid preservation may change the fur colour) 2) study skins with accompanying skulls partial skeletons (some bones remain in the skin) for studying pelage colour hair quality and moulting patterns 3) mounted skins with accompanying partial or entire skeleton (some bones may remain in the skin dependant on the method of preservation) or freeze-dried specimens 4) entire skeletons for instance for studying anatomy geographic variation or for age determination (entire skeletons are poorly represented in collections so Nagorsen and Peterson (1980) recommend preparation of at least one male and one female skeleton per species

96

Preservation of specimens in the field Formalin preservation Preservation in alcohol Preservation by cooling or freezing

97

Formalin preservation After weighing and measuring the animal and attaching an

adequate label very small specimens (up to 100 g) can be fixed whole by submerging them in 10 buffered formalin (tissue - formalin solution ratio of at least 1 12) the body cavity can be filled with formalin solution by injection until it is turgid and firm some formalin may also be injected under the skin into the body cavity larger muscles and organs If hypodermic needles are not available the body cavity can be opened ventrally by making a slit instead allowing the formalin to enter

Keeping the mouth open with a piece of wood or cotton may later allow examination of teeth Then the whole body can be immersed in formalin in the posture in which it is supposed to stay permanently because it will harden The ratio of formalin to carcass must be at least 12 to 1 to assure a good fixation Tissues can be left in buffered neutralized formalin for several months but formalin hardens specimens therefore after fixation longterm storage in alcohol may be better After preservation the carcass should therefore be washed in water and transferred into ethanol for permanent storage

Disadvantages for instance it discolours the fur after a longish immersion softens the bones and prevents further examination for microbiology

98

Preservation in alcohol

After weighing a whole animal can be preserved in a container of alcohol (70-90) Removal of the intestine prior to storage of the animal in alcohol is recommended

99

Preservation by cooling or freezing Removal of the skin with insulating fur

before cooling or freezing may help to cool the carcass down more quickly

Freezing is not recommended if histological examination is planned

100

THANK YOU

31

Population Attributes Density ndash size of a population in relation to a definite

unit of space Affected by

Natality ndash the reproductive output (birth rate) of a population

Mortality ndash the death rate of organisms in a population

Immigration ndash number of organisms moving into the area occupied by the population

Emigration ndash number of organisms moving out of the area occupied by the population

32

Population Density

Four primary population parameters

33

Two Types of Density Estimates

bull Absolute Density ndash a known density such as m2

bull Relative Density ndash we know when one area has more individuals than another

34

Measuring Absolute Density

Total Count ndash count the number of organisms living in an area Human census number of oak trees in a

wooded lot number of singing birds in an area

Total counts generally are not used very often

Sampling Methods ndash use a sample to estimate population size Either use the quadrat or capture-

recapture method

35

Measurement of Environmental ParametersAbiotic factors are important in determining

both the distribution of the organisms and their physical and physiological adaptations

Temperature- diurnal and seasonal temperature variations

are significant in affecting different species of plants and animals

- equipment mercury thermometer maximum-minimum thermometer

miniaturized thermistor

36

pH

-measure pH of a solution by universal indicator pH paper pH meter etc

Light

-measure its duration and intensity duration by predication from Royal Observatory intensity by photographic light meter

pH meter in use

37

Humidity

Relative humidity the water content of a given volume of air relative to the same volume of fully saturated air

- equipment whirling hygrometer

38

Wind and Water Speed- wind speed- anemometer or wind

gauges- water speed - time the movement of a

floating object over a measured distance

39

Salinity

- using a conductivity meter greater salinity has greater conductivity

Oxygen Level

- using an oxygen meter or chemical method (Winkler method)

40

Collecting MethodsCollecting all organisms within a habitat is normally

impractical and therefore small areas are selected Remember to return all material to its original position

after searching amp collecting sufficient specimens Some collecting apparatus for general use are listed

below

41

1 specimen tube

2 screwed-topped jars

3 polythene bags

4 forceps

5 paint brush

6 bulb pipette

7 pooter

42

8 widger 9 sieve 10 hand lens

11 enamel dish 12 beating tray 13 light traps

14 Tullgren funnel 15 Baermann funnel 16 mammal traps

17 pitfall traps 18 netting

43

Estimating Population Size

The exact methods used for estimation depend not only the nature of the habitat but also on the organisms involved

eg animals - population

plants - percentage cover

44

Using Quadrats

- By sampling an area using quadrats and counting the number of individuals within each quadrat it is possible to estimate the total number of individuals within the area

- confined to plants and sessile or very slow-moving animals

- fast-moving animals are disturbed and run away

45

Capture-recapture Techniques- useful for mobile animals which can be marked

- capture marked released randomly recaptured

and marked individuals recorded

no of marked individuals recaptured total no of individuals in 1st sample

-------------------------------------------- = ------------------------------------------

total no of individuals in 2nd sample estimated size of population

(the Lincoln Index)

46

Capture-recapture Techniques Factors affecting the accuracy of the estimation

deaths migration individuals become more liable to predation etc

Examples

- arthropods marked on their backs with non-toxic paint

- fish have tags attached to opercula - mammals have tags clipped to their ears

birds have their legs ringed

47

Capture-recapture Method Important tool for estimating density birth

rate and death rate for mobile animals Method

Collect a sample of individuals mark them and then release them

After a period collect more individuals from the wild and count the number that have marks

We assume that a sample if random will contain the same proportion of marked individuals as the population does

Estimate population density

48

Assumptions For All Capture-Recapture Studies Marking technique does not increase

mortality of marked animals Marked individuals are allowed to mix

with population Marking technique does not affect catch

probability Marks are not lost or overlooked No significant immigration or emigration No significant mortality or natality

49

Marked animals in second sample

Total caught in second sample

Marked animals in first sample

Total population size

=

520 N

16=

Peterson Method or Lincoln Index

N = 64N = (20)(16)5

50

Some Indices Used

Traps Number of Fecal

Pellets Vocalization

Frequency Pelt Records Catch per Unit

Fishing Effort

Number of Artifacts Questionnaires Cover Feeding Capacity Roadside Counts

51

Abundance Scales

The population size may be fairly accurately determined by making some form of frequency assessment

These are subjective and involve an experimenter making some estimate of the number of individuals in a given area or the cover of a particular species

This is especially useful where individuals are very numerous eg barnacles on a rocky shore or where it is difficult to distinguish individuals eg grass plants in a meadow

52

The assessments are usually made on an abundance scale of 5 categories

Abundance Common Frequent Occasional Rare

Barnacles exposed at low water

53

Environmental resistance are the factors which limit the growth of a particular population

eg predation disease availability of light food water oxygen and shelter the accumulation of toxic wastes and even the size of the population itself

54

Density-dependent Growth A population is a density-dependent when its size

(or density) affects its growth rate because of density-dependent factors such as food availability and toxic waste accumulation

Density-independent Growth In this type of growth a population increases until

some factor causes a sudden reduction in its size Its effect is the same regardless of the size of the

population eg temperature fires floods storms etc

55

Regulation of Population Size Fecundity is the reproductive capacity of individual

females of a species Birth rate or natality is used to measure fecundity Death rate or mortality is the number of individuals

of a species which die per unit time Immigration occurs when individuals join a

population from neighbouring ones Emigration occurs when individuals depart from a

population A cycle occurs when the size of a population

fluctuates on a regular basis

56

Ecological Sampling

57

Why Do We Sample Determine presence andor

abundance

Monitor population fluctuations

Assess lsquoecological damagersquo

Assess quality of habitat

Assess population responses

58

What Do We Sample

Physical Environment Temperature DO pH salinity clarity

flow sediment

Biotic Environment All living things

59

Physical Habitat Temperature

Mercury thermometer Electronic thermometer Long-term thermometers

Dissolved Oxygen Winkler method (titration) DO meter (electrode)

pH Litmus paper pH meter (electrode)

Salinity Salinity Meter YSI 550A DO Meter w12 cable

60

Water Clarity Secchi Disk

Disk is attached to a calibrated rope The disk is lowered into the water until the white parts can no longer be seen Secchi disk depth is then recorded and serves as the waters transparency index The clearer the water the greater the secchi disk depth

Secchi Disk

61

Current Velocity (flow) Floating-orange method

Put an orange (or something else that floats just below the water surface) and measure the time it takes it to float across a known distance

Odometer-type flow meter Number of revolutions the propeller

makes for a given time is calibrated to flow velocity

62

Sediment Sediment size is important to many

aquatic organisms Sieversquos are used to separate and

grade sediment samples Percent of each size grade can be

determined

63

Water Sample

Water and plankton from various depths can be collected

A trigger mechanism is used to close the sampler Sample is then brought back to the

surface

64

Small Mammals

Mouserat Traps Fatal

Pit Falls Bucket is placed in the ground Sometimes have lsquoleadsrsquo to the buckets

Live traps Havahart Sherman

Spot-light

Sherman trapHavahart trap

65

Birds Stick-under-the-box method Bird-trap

Works like a minnow trap Mist net

Captures birds in flight Rocket net

Uses a propellant to throw a net over birds

66

Terrestrial Insects

Sticky paper flies

Baited Traps Fire ants

Nets butterflies

Foggers Collect insects from tree canopies

67

Aquatic Insects Drift Net

Place net in flowing water Kick Net

lsquoKickrsquo sediment upstream from block net and the flow will wash them into the net

Wash bucket Serber or Hess Sampler

Stir up known area of sediment

Animals are collected by a catch net

Multi-plate Sampler Become colonized

68

Crawfish and Crab Traps

69

Fish Larvae Light Traps

Larvae are attracted to the light Ichthyoplankton nets

Can be towed at various depths Fish collect at the lsquocodrsquoend

70

Fish Lift net

Net is placed down and after a set amount of time it is quickly lifted

Pop-net Similar to a lift net but

floats are attached to a framed net

Operated by a trigger mechanism

Throw net A net attached to a heavy

frame is thrown and every thing inside is netted out Throw net

Pop-net

Lift net

71

Minnow trap

Usually use bait to attract small fish Light is used sometimes as an attractant

72

Fish Electrofishing

Electricity is put into the water Fish are temporarily stunned and usually

swim towards the electricity source Usually non-fatal but may cause some

damage

73

Fish Gill Net

Gill nets resemble tennis nets Fish can not swim completely through the

net and get caught Gill nets are size selective (based on mesh

size) Square Mesh

Bar mesh

Stretch mesh

74

Fish Trammel Net

Three panels two large mesh on the outside and a small mesh on the inside

Fish swim through the outer mesh pushes the small mesh through the other side and becomes entangled

75

Hoop nets (and other similar nets) can have bait or not

Fyke nets have leads to help guide fish to the net

76

Seine Seines are nets that are pulled

through shallow water to catch fish

77

Purse Seine Used to encircle entire schools of fish

Usually involves a spotter plane and a second boat

78

Trotline (longline) A series of baited drop lines

connected to a main line

Can be deployed by tying one end to the bank and tying the other end with a heavy weight

79

Shrimp (or fish) Trawl Net pulled behind

a boat along the bottom Either a beam or

otter boards keep the net open

80

Tagging Individuals Coded Wire Tags

Microwire that has a unique label

Magnetic wand detects the tag

Tag retention should be determined

T-Bar tags Can be individually

numbered External tag

PIT tags (Passive Integrated Transponders) Wand induces the tag to

transmit individual number is displayed

81

Other Tagging Methods

Toe clip Amphibian and reptile Clip of one or more toes

to identify individuals

Bird Band Place a metal band on a

bird leg Generally has

identification information

82

Preserving plant specimens Pressing and drying Long-term

preservation and storage

Alternative drying techniques

Special preservation and processing techniques

Mounting

83

Pressing and drying Techniques for pressing and drying specimens have been

established for many years There are minor variations in recommended methods but they are essentially the same worldwide

The best specimens are plants that are pressed as soon as possible after collection before wilting and shrivelling Most plants may be kept in sealed containers such as plastic bags for up to a day if it is inconvenient to press immediately However some plants show such rapid wilting particularly of the flowers that such delays are best avoided Flowers with a lot of nectar may go mouldy very quickly if excess nectar is not shaken off before pressing

Specimens are pressed flat and dried between sheets of absorbent blotters or semi-absorbent paper such as newspaper Papers with a glossy surface should be avoided because they are not absorbent enough to aid drying The plant should be carefully laid out between the drying sheets as their form at this stage largely determines their ultimate appearance The flowers should be spread out with the petals carefully arranged wilted leaves should be straightened and unnecessary shoots of excessively twiggy shrubs may be cut away

84

Microwave ovens Small numbers of specimens can be dried using a microwave

oven The technique recommended in the literature is to place the specimens between unprinted absorbent paper for example butchers paper not newspaper which is unsuitable because the chemicals present in the ink may cause a fire The specimens should be put in a special press which should be of a microwave-safe material (wood acrylic or polycarbonate sheeting eg plexiglass or perspex NO metal components) If such a press is not available sheets of cardboard can be placed above and below the specimens and then weighted down

Drying time depends on the power of your oven In most cases drying is accomplished by irradiating at maximum power for 1-2 minutes per specimen although it is often a case of trial and error It is best to process no more than 10-12 specimens of average thickness per batch Specimens are usually dried after the moisture that characteristically appears on the glass door has disappeared If the specimen is damp when taken out of the oven allow it to stand before re-radiating as moisture continues to evaporate from the specimen for some time Care must be taken not to irradiate the specimens for too long

It should be noted that microwave treatment damages seeds and the cellular structure of the plants which may reduce the long-term value of the specimens

85

Alternative drying techniquesSilica gelother desiccants amp freeze drying Alternative methods of drying plant specimens have been

used for some time but are mostly restricted to special purpose collections The main alternatives are freeze-drying and drying in a desiccant powder such as desiccant silica gel In general these techniques are used where it is essential to preserve the shape of a delicate plant of organ of the plant such as the flower Freeze-drying has also been used to preserve the chemical composition of a plant as accurately as possible for later study

Disadvantages and special conservation problems of specimens dried in these manners are that they are particularly susceptible to damage The dried parts are fragile lack support and often catch on packing materials They must therefore be packed especially carefully and stored in small boxes or tubes with some appropriate packing material that does not snag and break small projections Acid-free tissue paper is often used Drying in desiccant silica gel crystals or powder can also have the disadvantage that it is difficult to remove all traces of the silica gel after drying

86

Special preservation and processing techniquesWet or spirit collections

Very fleshy or delicate structures including small algae and orchid flowers are best preserved in an air-tight glass or plastic jar with a liquid preservative rather than by drying The type of preservative used should be clearly labelled in the jar Such material is often referred to as a spirit collection or wet collection

Most material can be satisfactorily preserved in 70 ethyl alcohol (or 70 methylated spirit or denatured alcohol) with 30 water Colours will fade quickly in spirit however so it is a good idea to keep comprehensive notes and photographs

87

Small algae Microscopic algae are often collected in a jar and in the

water in which they were found If the algae are to be stored for more than 2-3 days a preservative needs to be used Traditionally this has been the extremely toxic formalin - a small amount can be added to the water to make a 5 final solution and the container labelled This must not be sent through the post or by courier

There are some other equally toxic options for example propylene phenoxytol but none should be sent through the post A safer option is to add sufficient concentrated alcohol or methylated spirits to the water containing the algae to make a final solution of 70 alcohol This treatment dilutes the algae making them difficult to find so if they can be concentrated somehow first (eg by filtering) they can be stored in much less liquid Another option is to fix the algae in formalin (or something similar) first and then prepare a microscope glass slide with a permanent water-soluble mounting medium

88

Mounting Mounting specimens prevents most fragile material from

fragmenting and prevents specimens becoming separated from their labels If the plant collection is a long-term project specimens should be mounted on sheets of archival (permanent) cardboard or paper with archival-quality fixing media These include stitching with cotton thread dental floss nickel-plated copper wire (for heavier specimens) narrow strips of archival paper linen tape or by using an archival adhesive such as methyl cellulose adhesive

One disadvantage of mounting specimens is that it can make parts of the specimen inaccessible for examination so it is essential that this be borne in mind during specimen arrangement and mounting For example easily reversible mounting media should be used specimens should be strapped to the sheet rather than glued all over and the specimen should be carefully arranged before it is attached so that it shows all features

89

Full-size herbarium mounting sheets are usually about 43 cm long x 28 cm wide The plant name and accompanying field notes should be transcribed on a permanent label stuck to one corner of the herbarium sheet (the bottom right-hand corner being the most common) or sometimes annotations may be written directly on the sheet or card

Small pieces of material which may have become separated from the specimen (eg seeds) can be placed in small plastic bags and pinned to the sheet

90

Long-term preservation and storage The long-term preservation of dry plant

specimens is largely dependent on protection from insect attack Specimens collected by Linnaeus in the eighteenth century and by Banks and Solander on the Endeavour voyage in 1788 are still excellently preserved

91

Pests and their control A range of pests attack dried plant material The

most common pests are insects and fungi though rodents and other large animals can cause damage in poor storage conditions Insects eat the material the paper surrounding the material and the adhesives and mounting media

Such insect pests range from psocids (book lice) which attack mainly the softer parts such as flowers and soft fruits to tobacco beetles and carpet beetles which can bore holes through the toughest of specimens Many insects are particularly sensitive to relative humidity levels and do not thrive at levels below 50

92

The most common and acceptable specimen treatments for insect control are Freezing Microwave Poisoning Insect deterrents Fungal pests

93

Storage

Dried and pressed plant specimens can be stored in cardboard or plastic boxes or tied in bundles in light-weight cardboard folders placed in pigeon holes

Alternatively they can be placed in protective plastic jackets and displayed in ring folders which is recommended if they are to be frequently handled such as for a reference collection

94

Filing

Specimens should be filed in a systematic order if a relatively permanent collection is being made The major groups ie ferns and fern allies cycads conifers dicotyledons and monocotyledons are best kept separately or according to some classification scheme such as that given in a flora or handbook

Similarly the genera within each family and the species within each genus may be filed alphabetically or following some such classification

95

Preservation of entire animals

Types of collection specimens of an entire animal For reference collections mammals can be prepared as a variety of specimens The condition of the specimen may determine possible ways to preserve it if for instance decomposition of the skin has loosened the hair of a carcass so much that it can easily be pulled out or removed by rubbing (ldquoslippingrdquo fur) it will be very difficult or impossible to produce a study skin or mounted specimen The most usual types of specimens (based on Nagorsen and Peterson 1980) are 1) entire fluid-preserved animals (for studying anatomy and histology fluid preservation may change the fur colour) 2) study skins with accompanying skulls partial skeletons (some bones remain in the skin) for studying pelage colour hair quality and moulting patterns 3) mounted skins with accompanying partial or entire skeleton (some bones may remain in the skin dependant on the method of preservation) or freeze-dried specimens 4) entire skeletons for instance for studying anatomy geographic variation or for age determination (entire skeletons are poorly represented in collections so Nagorsen and Peterson (1980) recommend preparation of at least one male and one female skeleton per species

96

Preservation of specimens in the field Formalin preservation Preservation in alcohol Preservation by cooling or freezing

97

Formalin preservation After weighing and measuring the animal and attaching an

adequate label very small specimens (up to 100 g) can be fixed whole by submerging them in 10 buffered formalin (tissue - formalin solution ratio of at least 1 12) the body cavity can be filled with formalin solution by injection until it is turgid and firm some formalin may also be injected under the skin into the body cavity larger muscles and organs If hypodermic needles are not available the body cavity can be opened ventrally by making a slit instead allowing the formalin to enter

Keeping the mouth open with a piece of wood or cotton may later allow examination of teeth Then the whole body can be immersed in formalin in the posture in which it is supposed to stay permanently because it will harden The ratio of formalin to carcass must be at least 12 to 1 to assure a good fixation Tissues can be left in buffered neutralized formalin for several months but formalin hardens specimens therefore after fixation longterm storage in alcohol may be better After preservation the carcass should therefore be washed in water and transferred into ethanol for permanent storage

Disadvantages for instance it discolours the fur after a longish immersion softens the bones and prevents further examination for microbiology

98

Preservation in alcohol

After weighing a whole animal can be preserved in a container of alcohol (70-90) Removal of the intestine prior to storage of the animal in alcohol is recommended

99

Preservation by cooling or freezing Removal of the skin with insulating fur

before cooling or freezing may help to cool the carcass down more quickly

Freezing is not recommended if histological examination is planned

100

THANK YOU

32

Population Density

Four primary population parameters

33

Two Types of Density Estimates

bull Absolute Density ndash a known density such as m2

bull Relative Density ndash we know when one area has more individuals than another

34

Measuring Absolute Density

Total Count ndash count the number of organisms living in an area Human census number of oak trees in a

wooded lot number of singing birds in an area

Total counts generally are not used very often

Sampling Methods ndash use a sample to estimate population size Either use the quadrat or capture-

recapture method

35

Measurement of Environmental ParametersAbiotic factors are important in determining

both the distribution of the organisms and their physical and physiological adaptations

Temperature- diurnal and seasonal temperature variations

are significant in affecting different species of plants and animals

- equipment mercury thermometer maximum-minimum thermometer

miniaturized thermistor

36

pH

-measure pH of a solution by universal indicator pH paper pH meter etc

Light

-measure its duration and intensity duration by predication from Royal Observatory intensity by photographic light meter

pH meter in use

37

Humidity

Relative humidity the water content of a given volume of air relative to the same volume of fully saturated air

- equipment whirling hygrometer

38

Wind and Water Speed- wind speed- anemometer or wind

gauges- water speed - time the movement of a

floating object over a measured distance

39

Salinity

- using a conductivity meter greater salinity has greater conductivity

Oxygen Level

- using an oxygen meter or chemical method (Winkler method)

40

Collecting MethodsCollecting all organisms within a habitat is normally

impractical and therefore small areas are selected Remember to return all material to its original position

after searching amp collecting sufficient specimens Some collecting apparatus for general use are listed

below

41

1 specimen tube

2 screwed-topped jars

3 polythene bags

4 forceps

5 paint brush

6 bulb pipette

7 pooter

42

8 widger 9 sieve 10 hand lens

11 enamel dish 12 beating tray 13 light traps

14 Tullgren funnel 15 Baermann funnel 16 mammal traps

17 pitfall traps 18 netting

43

Estimating Population Size

The exact methods used for estimation depend not only the nature of the habitat but also on the organisms involved

eg animals - population

plants - percentage cover

44

Using Quadrats

- By sampling an area using quadrats and counting the number of individuals within each quadrat it is possible to estimate the total number of individuals within the area

- confined to plants and sessile or very slow-moving animals

- fast-moving animals are disturbed and run away

45

Capture-recapture Techniques- useful for mobile animals which can be marked

- capture marked released randomly recaptured

and marked individuals recorded

no of marked individuals recaptured total no of individuals in 1st sample

-------------------------------------------- = ------------------------------------------

total no of individuals in 2nd sample estimated size of population

(the Lincoln Index)

46

Capture-recapture Techniques Factors affecting the accuracy of the estimation

deaths migration individuals become more liable to predation etc

Examples

- arthropods marked on their backs with non-toxic paint

- fish have tags attached to opercula - mammals have tags clipped to their ears

birds have their legs ringed

47

Capture-recapture Method Important tool for estimating density birth

rate and death rate for mobile animals Method

Collect a sample of individuals mark them and then release them

After a period collect more individuals from the wild and count the number that have marks

We assume that a sample if random will contain the same proportion of marked individuals as the population does

Estimate population density

48

Assumptions For All Capture-Recapture Studies Marking technique does not increase

mortality of marked animals Marked individuals are allowed to mix

with population Marking technique does not affect catch

probability Marks are not lost or overlooked No significant immigration or emigration No significant mortality or natality

49

Marked animals in second sample

Total caught in second sample

Marked animals in first sample

Total population size

=

520 N

16=

Peterson Method or Lincoln Index

N = 64N = (20)(16)5

50

Some Indices Used

Traps Number of Fecal

Pellets Vocalization

Frequency Pelt Records Catch per Unit

Fishing Effort

Number of Artifacts Questionnaires Cover Feeding Capacity Roadside Counts

51

Abundance Scales

The population size may be fairly accurately determined by making some form of frequency assessment

These are subjective and involve an experimenter making some estimate of the number of individuals in a given area or the cover of a particular species

This is especially useful where individuals are very numerous eg barnacles on a rocky shore or where it is difficult to distinguish individuals eg grass plants in a meadow

52

The assessments are usually made on an abundance scale of 5 categories

Abundance Common Frequent Occasional Rare

Barnacles exposed at low water

53

Environmental resistance are the factors which limit the growth of a particular population

eg predation disease availability of light food water oxygen and shelter the accumulation of toxic wastes and even the size of the population itself

54

Density-dependent Growth A population is a density-dependent when its size

(or density) affects its growth rate because of density-dependent factors such as food availability and toxic waste accumulation

Density-independent Growth In this type of growth a population increases until

some factor causes a sudden reduction in its size Its effect is the same regardless of the size of the

population eg temperature fires floods storms etc

55

Regulation of Population Size Fecundity is the reproductive capacity of individual

females of a species Birth rate or natality is used to measure fecundity Death rate or mortality is the number of individuals

of a species which die per unit time Immigration occurs when individuals join a

population from neighbouring ones Emigration occurs when individuals depart from a

population A cycle occurs when the size of a population

fluctuates on a regular basis

56

Ecological Sampling

57

Why Do We Sample Determine presence andor

abundance

Monitor population fluctuations

Assess lsquoecological damagersquo

Assess quality of habitat

Assess population responses

58

What Do We Sample

Physical Environment Temperature DO pH salinity clarity

flow sediment

Biotic Environment All living things

59

Physical Habitat Temperature

Mercury thermometer Electronic thermometer Long-term thermometers

Dissolved Oxygen Winkler method (titration) DO meter (electrode)

pH Litmus paper pH meter (electrode)

Salinity Salinity Meter YSI 550A DO Meter w12 cable

60

Water Clarity Secchi Disk

Disk is attached to a calibrated rope The disk is lowered into the water until the white parts can no longer be seen Secchi disk depth is then recorded and serves as the waters transparency index The clearer the water the greater the secchi disk depth

Secchi Disk

61

Current Velocity (flow) Floating-orange method

Put an orange (or something else that floats just below the water surface) and measure the time it takes it to float across a known distance

Odometer-type flow meter Number of revolutions the propeller

makes for a given time is calibrated to flow velocity

62

Sediment Sediment size is important to many

aquatic organisms Sieversquos are used to separate and

grade sediment samples Percent of each size grade can be

determined

63

Water Sample

Water and plankton from various depths can be collected

A trigger mechanism is used to close the sampler Sample is then brought back to the

surface

64

Small Mammals

Mouserat Traps Fatal

Pit Falls Bucket is placed in the ground Sometimes have lsquoleadsrsquo to the buckets

Live traps Havahart Sherman

Spot-light

Sherman trapHavahart trap

65

Birds Stick-under-the-box method Bird-trap

Works like a minnow trap Mist net

Captures birds in flight Rocket net

Uses a propellant to throw a net over birds

66

Terrestrial Insects

Sticky paper flies

Baited Traps Fire ants

Nets butterflies

Foggers Collect insects from tree canopies

67

Aquatic Insects Drift Net

Place net in flowing water Kick Net

lsquoKickrsquo sediment upstream from block net and the flow will wash them into the net

Wash bucket Serber or Hess Sampler

Stir up known area of sediment

Animals are collected by a catch net

Multi-plate Sampler Become colonized

68

Crawfish and Crab Traps

69

Fish Larvae Light Traps

Larvae are attracted to the light Ichthyoplankton nets

Can be towed at various depths Fish collect at the lsquocodrsquoend

70

Fish Lift net

Net is placed down and after a set amount of time it is quickly lifted

Pop-net Similar to a lift net but

floats are attached to a framed net

Operated by a trigger mechanism

Throw net A net attached to a heavy

frame is thrown and every thing inside is netted out Throw net

Pop-net

Lift net

71

Minnow trap

Usually use bait to attract small fish Light is used sometimes as an attractant

72

Fish Electrofishing

Electricity is put into the water Fish are temporarily stunned and usually

swim towards the electricity source Usually non-fatal but may cause some

damage

73

Fish Gill Net

Gill nets resemble tennis nets Fish can not swim completely through the

net and get caught Gill nets are size selective (based on mesh

size) Square Mesh

Bar mesh

Stretch mesh

74

Fish Trammel Net

Three panels two large mesh on the outside and a small mesh on the inside

Fish swim through the outer mesh pushes the small mesh through the other side and becomes entangled

75

Hoop nets (and other similar nets) can have bait or not

Fyke nets have leads to help guide fish to the net

76

Seine Seines are nets that are pulled

through shallow water to catch fish

77

Purse Seine Used to encircle entire schools of fish

Usually involves a spotter plane and a second boat

78

Trotline (longline) A series of baited drop lines

connected to a main line

Can be deployed by tying one end to the bank and tying the other end with a heavy weight

79

Shrimp (or fish) Trawl Net pulled behind

a boat along the bottom Either a beam or

otter boards keep the net open

80

Tagging Individuals Coded Wire Tags

Microwire that has a unique label

Magnetic wand detects the tag

Tag retention should be determined

T-Bar tags Can be individually

numbered External tag

PIT tags (Passive Integrated Transponders) Wand induces the tag to

transmit individual number is displayed

81

Other Tagging Methods

Toe clip Amphibian and reptile Clip of one or more toes

to identify individuals

Bird Band Place a metal band on a

bird leg Generally has

identification information

82

Preserving plant specimens Pressing and drying Long-term

preservation and storage

Alternative drying techniques

Special preservation and processing techniques

Mounting

83

Pressing and drying Techniques for pressing and drying specimens have been

established for many years There are minor variations in recommended methods but they are essentially the same worldwide

The best specimens are plants that are pressed as soon as possible after collection before wilting and shrivelling Most plants may be kept in sealed containers such as plastic bags for up to a day if it is inconvenient to press immediately However some plants show such rapid wilting particularly of the flowers that such delays are best avoided Flowers with a lot of nectar may go mouldy very quickly if excess nectar is not shaken off before pressing

Specimens are pressed flat and dried between sheets of absorbent blotters or semi-absorbent paper such as newspaper Papers with a glossy surface should be avoided because they are not absorbent enough to aid drying The plant should be carefully laid out between the drying sheets as their form at this stage largely determines their ultimate appearance The flowers should be spread out with the petals carefully arranged wilted leaves should be straightened and unnecessary shoots of excessively twiggy shrubs may be cut away

84

Microwave ovens Small numbers of specimens can be dried using a microwave

oven The technique recommended in the literature is to place the specimens between unprinted absorbent paper for example butchers paper not newspaper which is unsuitable because the chemicals present in the ink may cause a fire The specimens should be put in a special press which should be of a microwave-safe material (wood acrylic or polycarbonate sheeting eg plexiglass or perspex NO metal components) If such a press is not available sheets of cardboard can be placed above and below the specimens and then weighted down

Drying time depends on the power of your oven In most cases drying is accomplished by irradiating at maximum power for 1-2 minutes per specimen although it is often a case of trial and error It is best to process no more than 10-12 specimens of average thickness per batch Specimens are usually dried after the moisture that characteristically appears on the glass door has disappeared If the specimen is damp when taken out of the oven allow it to stand before re-radiating as moisture continues to evaporate from the specimen for some time Care must be taken not to irradiate the specimens for too long

It should be noted that microwave treatment damages seeds and the cellular structure of the plants which may reduce the long-term value of the specimens

85

Alternative drying techniquesSilica gelother desiccants amp freeze drying Alternative methods of drying plant specimens have been

used for some time but are mostly restricted to special purpose collections The main alternatives are freeze-drying and drying in a desiccant powder such as desiccant silica gel In general these techniques are used where it is essential to preserve the shape of a delicate plant of organ of the plant such as the flower Freeze-drying has also been used to preserve the chemical composition of a plant as accurately as possible for later study

Disadvantages and special conservation problems of specimens dried in these manners are that they are particularly susceptible to damage The dried parts are fragile lack support and often catch on packing materials They must therefore be packed especially carefully and stored in small boxes or tubes with some appropriate packing material that does not snag and break small projections Acid-free tissue paper is often used Drying in desiccant silica gel crystals or powder can also have the disadvantage that it is difficult to remove all traces of the silica gel after drying

86

Special preservation and processing techniquesWet or spirit collections

Very fleshy or delicate structures including small algae and orchid flowers are best preserved in an air-tight glass or plastic jar with a liquid preservative rather than by drying The type of preservative used should be clearly labelled in the jar Such material is often referred to as a spirit collection or wet collection

Most material can be satisfactorily preserved in 70 ethyl alcohol (or 70 methylated spirit or denatured alcohol) with 30 water Colours will fade quickly in spirit however so it is a good idea to keep comprehensive notes and photographs

87

Small algae Microscopic algae are often collected in a jar and in the

water in which they were found If the algae are to be stored for more than 2-3 days a preservative needs to be used Traditionally this has been the extremely toxic formalin - a small amount can be added to the water to make a 5 final solution and the container labelled This must not be sent through the post or by courier

There are some other equally toxic options for example propylene phenoxytol but none should be sent through the post A safer option is to add sufficient concentrated alcohol or methylated spirits to the water containing the algae to make a final solution of 70 alcohol This treatment dilutes the algae making them difficult to find so if they can be concentrated somehow first (eg by filtering) they can be stored in much less liquid Another option is to fix the algae in formalin (or something similar) first and then prepare a microscope glass slide with a permanent water-soluble mounting medium

88

Mounting Mounting specimens prevents most fragile material from

fragmenting and prevents specimens becoming separated from their labels If the plant collection is a long-term project specimens should be mounted on sheets of archival (permanent) cardboard or paper with archival-quality fixing media These include stitching with cotton thread dental floss nickel-plated copper wire (for heavier specimens) narrow strips of archival paper linen tape or by using an archival adhesive such as methyl cellulose adhesive

One disadvantage of mounting specimens is that it can make parts of the specimen inaccessible for examination so it is essential that this be borne in mind during specimen arrangement and mounting For example easily reversible mounting media should be used specimens should be strapped to the sheet rather than glued all over and the specimen should be carefully arranged before it is attached so that it shows all features

89

Full-size herbarium mounting sheets are usually about 43 cm long x 28 cm wide The plant name and accompanying field notes should be transcribed on a permanent label stuck to one corner of the herbarium sheet (the bottom right-hand corner being the most common) or sometimes annotations may be written directly on the sheet or card

Small pieces of material which may have become separated from the specimen (eg seeds) can be placed in small plastic bags and pinned to the sheet

90

Long-term preservation and storage The long-term preservation of dry plant

specimens is largely dependent on protection from insect attack Specimens collected by Linnaeus in the eighteenth century and by Banks and Solander on the Endeavour voyage in 1788 are still excellently preserved

91

Pests and their control A range of pests attack dried plant material The

most common pests are insects and fungi though rodents and other large animals can cause damage in poor storage conditions Insects eat the material the paper surrounding the material and the adhesives and mounting media

Such insect pests range from psocids (book lice) which attack mainly the softer parts such as flowers and soft fruits to tobacco beetles and carpet beetles which can bore holes through the toughest of specimens Many insects are particularly sensitive to relative humidity levels and do not thrive at levels below 50

92

The most common and acceptable specimen treatments for insect control are Freezing Microwave Poisoning Insect deterrents Fungal pests

93

Storage

Dried and pressed plant specimens can be stored in cardboard or plastic boxes or tied in bundles in light-weight cardboard folders placed in pigeon holes

Alternatively they can be placed in protective plastic jackets and displayed in ring folders which is recommended if they are to be frequently handled such as for a reference collection

94

Filing

Specimens should be filed in a systematic order if a relatively permanent collection is being made The major groups ie ferns and fern allies cycads conifers dicotyledons and monocotyledons are best kept separately or according to some classification scheme such as that given in a flora or handbook

Similarly the genera within each family and the species within each genus may be filed alphabetically or following some such classification

95

Preservation of entire animals

Types of collection specimens of an entire animal For reference collections mammals can be prepared as a variety of specimens The condition of the specimen may determine possible ways to preserve it if for instance decomposition of the skin has loosened the hair of a carcass so much that it can easily be pulled out or removed by rubbing (ldquoslippingrdquo fur) it will be very difficult or impossible to produce a study skin or mounted specimen The most usual types of specimens (based on Nagorsen and Peterson 1980) are 1) entire fluid-preserved animals (for studying anatomy and histology fluid preservation may change the fur colour) 2) study skins with accompanying skulls partial skeletons (some bones remain in the skin) for studying pelage colour hair quality and moulting patterns 3) mounted skins with accompanying partial or entire skeleton (some bones may remain in the skin dependant on the method of preservation) or freeze-dried specimens 4) entire skeletons for instance for studying anatomy geographic variation or for age determination (entire skeletons are poorly represented in collections so Nagorsen and Peterson (1980) recommend preparation of at least one male and one female skeleton per species

96

Preservation of specimens in the field Formalin preservation Preservation in alcohol Preservation by cooling or freezing

97

Formalin preservation After weighing and measuring the animal and attaching an

adequate label very small specimens (up to 100 g) can be fixed whole by submerging them in 10 buffered formalin (tissue - formalin solution ratio of at least 1 12) the body cavity can be filled with formalin solution by injection until it is turgid and firm some formalin may also be injected under the skin into the body cavity larger muscles and organs If hypodermic needles are not available the body cavity can be opened ventrally by making a slit instead allowing the formalin to enter

Keeping the mouth open with a piece of wood or cotton may later allow examination of teeth Then the whole body can be immersed in formalin in the posture in which it is supposed to stay permanently because it will harden The ratio of formalin to carcass must be at least 12 to 1 to assure a good fixation Tissues can be left in buffered neutralized formalin for several months but formalin hardens specimens therefore after fixation longterm storage in alcohol may be better After preservation the carcass should therefore be washed in water and transferred into ethanol for permanent storage

Disadvantages for instance it discolours the fur after a longish immersion softens the bones and prevents further examination for microbiology

98

Preservation in alcohol

After weighing a whole animal can be preserved in a container of alcohol (70-90) Removal of the intestine prior to storage of the animal in alcohol is recommended

99

Preservation by cooling or freezing Removal of the skin with insulating fur

before cooling or freezing may help to cool the carcass down more quickly

Freezing is not recommended if histological examination is planned

100

THANK YOU

33

Two Types of Density Estimates

bull Absolute Density ndash a known density such as m2

bull Relative Density ndash we know when one area has more individuals than another

34

Measuring Absolute Density

Total Count ndash count the number of organisms living in an area Human census number of oak trees in a

wooded lot number of singing birds in an area

Total counts generally are not used very often

Sampling Methods ndash use a sample to estimate population size Either use the quadrat or capture-

recapture method

35

Measurement of Environmental ParametersAbiotic factors are important in determining

both the distribution of the organisms and their physical and physiological adaptations

Temperature- diurnal and seasonal temperature variations

are significant in affecting different species of plants and animals

- equipment mercury thermometer maximum-minimum thermometer

miniaturized thermistor

36

pH

-measure pH of a solution by universal indicator pH paper pH meter etc

Light

-measure its duration and intensity duration by predication from Royal Observatory intensity by photographic light meter

pH meter in use

37

Humidity

Relative humidity the water content of a given volume of air relative to the same volume of fully saturated air

- equipment whirling hygrometer

38

Wind and Water Speed- wind speed- anemometer or wind

gauges- water speed - time the movement of a

floating object over a measured distance

39

Salinity

- using a conductivity meter greater salinity has greater conductivity

Oxygen Level

- using an oxygen meter or chemical method (Winkler method)

40

Collecting MethodsCollecting all organisms within a habitat is normally

impractical and therefore small areas are selected Remember to return all material to its original position

after searching amp collecting sufficient specimens Some collecting apparatus for general use are listed

below

41

1 specimen tube

2 screwed-topped jars

3 polythene bags

4 forceps

5 paint brush

6 bulb pipette

7 pooter

42

8 widger 9 sieve 10 hand lens

11 enamel dish 12 beating tray 13 light traps

14 Tullgren funnel 15 Baermann funnel 16 mammal traps

17 pitfall traps 18 netting

43

Estimating Population Size

The exact methods used for estimation depend not only the nature of the habitat but also on the organisms involved

eg animals - population

plants - percentage cover

44

Using Quadrats

- By sampling an area using quadrats and counting the number of individuals within each quadrat it is possible to estimate the total number of individuals within the area

- confined to plants and sessile or very slow-moving animals

- fast-moving animals are disturbed and run away

45

Capture-recapture Techniques- useful for mobile animals which can be marked

- capture marked released randomly recaptured

and marked individuals recorded

no of marked individuals recaptured total no of individuals in 1st sample

-------------------------------------------- = ------------------------------------------

total no of individuals in 2nd sample estimated size of population

(the Lincoln Index)

46

Capture-recapture Techniques Factors affecting the accuracy of the estimation

deaths migration individuals become more liable to predation etc

Examples

- arthropods marked on their backs with non-toxic paint

- fish have tags attached to opercula - mammals have tags clipped to their ears

birds have their legs ringed

47

Capture-recapture Method Important tool for estimating density birth

rate and death rate for mobile animals Method

Collect a sample of individuals mark them and then release them

After a period collect more individuals from the wild and count the number that have marks

We assume that a sample if random will contain the same proportion of marked individuals as the population does

Estimate population density

48

Assumptions For All Capture-Recapture Studies Marking technique does not increase

mortality of marked animals Marked individuals are allowed to mix

with population Marking technique does not affect catch

probability Marks are not lost or overlooked No significant immigration or emigration No significant mortality or natality

49

Marked animals in second sample

Total caught in second sample

Marked animals in first sample

Total population size

=

520 N

16=

Peterson Method or Lincoln Index

N = 64N = (20)(16)5

50

Some Indices Used

Traps Number of Fecal

Pellets Vocalization

Frequency Pelt Records Catch per Unit

Fishing Effort

Number of Artifacts Questionnaires Cover Feeding Capacity Roadside Counts

51

Abundance Scales

The population size may be fairly accurately determined by making some form of frequency assessment

These are subjective and involve an experimenter making some estimate of the number of individuals in a given area or the cover of a particular species

This is especially useful where individuals are very numerous eg barnacles on a rocky shore or where it is difficult to distinguish individuals eg grass plants in a meadow

52

The assessments are usually made on an abundance scale of 5 categories

Abundance Common Frequent Occasional Rare

Barnacles exposed at low water

53

Environmental resistance are the factors which limit the growth of a particular population

eg predation disease availability of light food water oxygen and shelter the accumulation of toxic wastes and even the size of the population itself

54

Density-dependent Growth A population is a density-dependent when its size

(or density) affects its growth rate because of density-dependent factors such as food availability and toxic waste accumulation

Density-independent Growth In this type of growth a population increases until

some factor causes a sudden reduction in its size Its effect is the same regardless of the size of the

population eg temperature fires floods storms etc

55

Regulation of Population Size Fecundity is the reproductive capacity of individual

females of a species Birth rate or natality is used to measure fecundity Death rate or mortality is the number of individuals

of a species which die per unit time Immigration occurs when individuals join a

population from neighbouring ones Emigration occurs when individuals depart from a

population A cycle occurs when the size of a population

fluctuates on a regular basis

56

Ecological Sampling

57

Why Do We Sample Determine presence andor

abundance

Monitor population fluctuations

Assess lsquoecological damagersquo

Assess quality of habitat

Assess population responses

58

What Do We Sample

Physical Environment Temperature DO pH salinity clarity

flow sediment

Biotic Environment All living things

59

Physical Habitat Temperature

Mercury thermometer Electronic thermometer Long-term thermometers

Dissolved Oxygen Winkler method (titration) DO meter (electrode)

pH Litmus paper pH meter (electrode)

Salinity Salinity Meter YSI 550A DO Meter w12 cable

60

Water Clarity Secchi Disk

Disk is attached to a calibrated rope The disk is lowered into the water until the white parts can no longer be seen Secchi disk depth is then recorded and serves as the waters transparency index The clearer the water the greater the secchi disk depth

Secchi Disk

61

Current Velocity (flow) Floating-orange method

Put an orange (or something else that floats just below the water surface) and measure the time it takes it to float across a known distance

Odometer-type flow meter Number of revolutions the propeller

makes for a given time is calibrated to flow velocity

62

Sediment Sediment size is important to many

aquatic organisms Sieversquos are used to separate and

grade sediment samples Percent of each size grade can be

determined

63

Water Sample

Water and plankton from various depths can be collected

A trigger mechanism is used to close the sampler Sample is then brought back to the

surface

64

Small Mammals

Mouserat Traps Fatal

Pit Falls Bucket is placed in the ground Sometimes have lsquoleadsrsquo to the buckets

Live traps Havahart Sherman

Spot-light

Sherman trapHavahart trap

65

Birds Stick-under-the-box method Bird-trap

Works like a minnow trap Mist net

Captures birds in flight Rocket net

Uses a propellant to throw a net over birds

66

Terrestrial Insects

Sticky paper flies

Baited Traps Fire ants

Nets butterflies

Foggers Collect insects from tree canopies

67

Aquatic Insects Drift Net

Place net in flowing water Kick Net

lsquoKickrsquo sediment upstream from block net and the flow will wash them into the net

Wash bucket Serber or Hess Sampler

Stir up known area of sediment

Animals are collected by a catch net

Multi-plate Sampler Become colonized

68

Crawfish and Crab Traps

69

Fish Larvae Light Traps

Larvae are attracted to the light Ichthyoplankton nets

Can be towed at various depths Fish collect at the lsquocodrsquoend

70

Fish Lift net

Net is placed down and after a set amount of time it is quickly lifted

Pop-net Similar to a lift net but

floats are attached to a framed net

Operated by a trigger mechanism

Throw net A net attached to a heavy

frame is thrown and every thing inside is netted out Throw net

Pop-net

Lift net

71

Minnow trap

Usually use bait to attract small fish Light is used sometimes as an attractant

72

Fish Electrofishing

Electricity is put into the water Fish are temporarily stunned and usually

swim towards the electricity source Usually non-fatal but may cause some

damage

73

Fish Gill Net

Gill nets resemble tennis nets Fish can not swim completely through the

net and get caught Gill nets are size selective (based on mesh

size) Square Mesh

Bar mesh

Stretch mesh

74

Fish Trammel Net

Three panels two large mesh on the outside and a small mesh on the inside

Fish swim through the outer mesh pushes the small mesh through the other side and becomes entangled

75

Hoop nets (and other similar nets) can have bait or not

Fyke nets have leads to help guide fish to the net

76

Seine Seines are nets that are pulled

through shallow water to catch fish

77

Purse Seine Used to encircle entire schools of fish

Usually involves a spotter plane and a second boat

78

Trotline (longline) A series of baited drop lines

connected to a main line

Can be deployed by tying one end to the bank and tying the other end with a heavy weight

79

Shrimp (or fish) Trawl Net pulled behind

a boat along the bottom Either a beam or

otter boards keep the net open

80

Tagging Individuals Coded Wire Tags

Microwire that has a unique label

Magnetic wand detects the tag

Tag retention should be determined

T-Bar tags Can be individually

numbered External tag

PIT tags (Passive Integrated Transponders) Wand induces the tag to

transmit individual number is displayed

81

Other Tagging Methods

Toe clip Amphibian and reptile Clip of one or more toes

to identify individuals

Bird Band Place a metal band on a

bird leg Generally has

identification information

82

Preserving plant specimens Pressing and drying Long-term

preservation and storage

Alternative drying techniques

Special preservation and processing techniques

Mounting

83

Pressing and drying Techniques for pressing and drying specimens have been

established for many years There are minor variations in recommended methods but they are essentially the same worldwide

The best specimens are plants that are pressed as soon as possible after collection before wilting and shrivelling Most plants may be kept in sealed containers such as plastic bags for up to a day if it is inconvenient to press immediately However some plants show such rapid wilting particularly of the flowers that such delays are best avoided Flowers with a lot of nectar may go mouldy very quickly if excess nectar is not shaken off before pressing

Specimens are pressed flat and dried between sheets of absorbent blotters or semi-absorbent paper such as newspaper Papers with a glossy surface should be avoided because they are not absorbent enough to aid drying The plant should be carefully laid out between the drying sheets as their form at this stage largely determines their ultimate appearance The flowers should be spread out with the petals carefully arranged wilted leaves should be straightened and unnecessary shoots of excessively twiggy shrubs may be cut away

84

Microwave ovens Small numbers of specimens can be dried using a microwave

oven The technique recommended in the literature is to place the specimens between unprinted absorbent paper for example butchers paper not newspaper which is unsuitable because the chemicals present in the ink may cause a fire The specimens should be put in a special press which should be of a microwave-safe material (wood acrylic or polycarbonate sheeting eg plexiglass or perspex NO metal components) If such a press is not available sheets of cardboard can be placed above and below the specimens and then weighted down

Drying time depends on the power of your oven In most cases drying is accomplished by irradiating at maximum power for 1-2 minutes per specimen although it is often a case of trial and error It is best to process no more than 10-12 specimens of average thickness per batch Specimens are usually dried after the moisture that characteristically appears on the glass door has disappeared If the specimen is damp when taken out of the oven allow it to stand before re-radiating as moisture continues to evaporate from the specimen for some time Care must be taken not to irradiate the specimens for too long

It should be noted that microwave treatment damages seeds and the cellular structure of the plants which may reduce the long-term value of the specimens

85

Alternative drying techniquesSilica gelother desiccants amp freeze drying Alternative methods of drying plant specimens have been

used for some time but are mostly restricted to special purpose collections The main alternatives are freeze-drying and drying in a desiccant powder such as desiccant silica gel In general these techniques are used where it is essential to preserve the shape of a delicate plant of organ of the plant such as the flower Freeze-drying has also been used to preserve the chemical composition of a plant as accurately as possible for later study

Disadvantages and special conservation problems of specimens dried in these manners are that they are particularly susceptible to damage The dried parts are fragile lack support and often catch on packing materials They must therefore be packed especially carefully and stored in small boxes or tubes with some appropriate packing material that does not snag and break small projections Acid-free tissue paper is often used Drying in desiccant silica gel crystals or powder can also have the disadvantage that it is difficult to remove all traces of the silica gel after drying

86

Special preservation and processing techniquesWet or spirit collections

Very fleshy or delicate structures including small algae and orchid flowers are best preserved in an air-tight glass or plastic jar with a liquid preservative rather than by drying The type of preservative used should be clearly labelled in the jar Such material is often referred to as a spirit collection or wet collection

Most material can be satisfactorily preserved in 70 ethyl alcohol (or 70 methylated spirit or denatured alcohol) with 30 water Colours will fade quickly in spirit however so it is a good idea to keep comprehensive notes and photographs

87

Small algae Microscopic algae are often collected in a jar and in the

water in which they were found If the algae are to be stored for more than 2-3 days a preservative needs to be used Traditionally this has been the extremely toxic formalin - a small amount can be added to the water to make a 5 final solution and the container labelled This must not be sent through the post or by courier

There are some other equally toxic options for example propylene phenoxytol but none should be sent through the post A safer option is to add sufficient concentrated alcohol or methylated spirits to the water containing the algae to make a final solution of 70 alcohol This treatment dilutes the algae making them difficult to find so if they can be concentrated somehow first (eg by filtering) they can be stored in much less liquid Another option is to fix the algae in formalin (or something similar) first and then prepare a microscope glass slide with a permanent water-soluble mounting medium

88

Mounting Mounting specimens prevents most fragile material from

fragmenting and prevents specimens becoming separated from their labels If the plant collection is a long-term project specimens should be mounted on sheets of archival (permanent) cardboard or paper with archival-quality fixing media These include stitching with cotton thread dental floss nickel-plated copper wire (for heavier specimens) narrow strips of archival paper linen tape or by using an archival adhesive such as methyl cellulose adhesive

One disadvantage of mounting specimens is that it can make parts of the specimen inaccessible for examination so it is essential that this be borne in mind during specimen arrangement and mounting For example easily reversible mounting media should be used specimens should be strapped to the sheet rather than glued all over and the specimen should be carefully arranged before it is attached so that it shows all features

89

Full-size herbarium mounting sheets are usually about 43 cm long x 28 cm wide The plant name and accompanying field notes should be transcribed on a permanent label stuck to one corner of the herbarium sheet (the bottom right-hand corner being the most common) or sometimes annotations may be written directly on the sheet or card

Small pieces of material which may have become separated from the specimen (eg seeds) can be placed in small plastic bags and pinned to the sheet

90

Long-term preservation and storage The long-term preservation of dry plant

specimens is largely dependent on protection from insect attack Specimens collected by Linnaeus in the eighteenth century and by Banks and Solander on the Endeavour voyage in 1788 are still excellently preserved

91

Pests and their control A range of pests attack dried plant material The

most common pests are insects and fungi though rodents and other large animals can cause damage in poor storage conditions Insects eat the material the paper surrounding the material and the adhesives and mounting media

Such insect pests range from psocids (book lice) which attack mainly the softer parts such as flowers and soft fruits to tobacco beetles and carpet beetles which can bore holes through the toughest of specimens Many insects are particularly sensitive to relative humidity levels and do not thrive at levels below 50

92

The most common and acceptable specimen treatments for insect control are Freezing Microwave Poisoning Insect deterrents Fungal pests

93

Storage

Dried and pressed plant specimens can be stored in cardboard or plastic boxes or tied in bundles in light-weight cardboard folders placed in pigeon holes

Alternatively they can be placed in protective plastic jackets and displayed in ring folders which is recommended if they are to be frequently handled such as for a reference collection

94

Filing

Specimens should be filed in a systematic order if a relatively permanent collection is being made The major groups ie ferns and fern allies cycads conifers dicotyledons and monocotyledons are best kept separately or according to some classification scheme such as that given in a flora or handbook

Similarly the genera within each family and the species within each genus may be filed alphabetically or following some such classification

95

Preservation of entire animals

Types of collection specimens of an entire animal For reference collections mammals can be prepared as a variety of specimens The condition of the specimen may determine possible ways to preserve it if for instance decomposition of the skin has loosened the hair of a carcass so much that it can easily be pulled out or removed by rubbing (ldquoslippingrdquo fur) it will be very difficult or impossible to produce a study skin or mounted specimen The most usual types of specimens (based on Nagorsen and Peterson 1980) are 1) entire fluid-preserved animals (for studying anatomy and histology fluid preservation may change the fur colour) 2) study skins with accompanying skulls partial skeletons (some bones remain in the skin) for studying pelage colour hair quality and moulting patterns 3) mounted skins with accompanying partial or entire skeleton (some bones may remain in the skin dependant on the method of preservation) or freeze-dried specimens 4) entire skeletons for instance for studying anatomy geographic variation or for age determination (entire skeletons are poorly represented in collections so Nagorsen and Peterson (1980) recommend preparation of at least one male and one female skeleton per species

96

Preservation of specimens in the field Formalin preservation Preservation in alcohol Preservation by cooling or freezing

97

Formalin preservation After weighing and measuring the animal and attaching an

adequate label very small specimens (up to 100 g) can be fixed whole by submerging them in 10 buffered formalin (tissue - formalin solution ratio of at least 1 12) the body cavity can be filled with formalin solution by injection until it is turgid and firm some formalin may also be injected under the skin into the body cavity larger muscles and organs If hypodermic needles are not available the body cavity can be opened ventrally by making a slit instead allowing the formalin to enter

Keeping the mouth open with a piece of wood or cotton may later allow examination of teeth Then the whole body can be immersed in formalin in the posture in which it is supposed to stay permanently because it will harden The ratio of formalin to carcass must be at least 12 to 1 to assure a good fixation Tissues can be left in buffered neutralized formalin for several months but formalin hardens specimens therefore after fixation longterm storage in alcohol may be better After preservation the carcass should therefore be washed in water and transferred into ethanol for permanent storage

Disadvantages for instance it discolours the fur after a longish immersion softens the bones and prevents further examination for microbiology

98

Preservation in alcohol

After weighing a whole animal can be preserved in a container of alcohol (70-90) Removal of the intestine prior to storage of the animal in alcohol is recommended

99

Preservation by cooling or freezing Removal of the skin with insulating fur

before cooling or freezing may help to cool the carcass down more quickly

Freezing is not recommended if histological examination is planned

100

THANK YOU

34

Measuring Absolute Density

Total Count ndash count the number of organisms living in an area Human census number of oak trees in a

wooded lot number of singing birds in an area

Total counts generally are not used very often

Sampling Methods ndash use a sample to estimate population size Either use the quadrat or capture-

recapture method

35

Measurement of Environmental ParametersAbiotic factors are important in determining

both the distribution of the organisms and their physical and physiological adaptations

Temperature- diurnal and seasonal temperature variations

are significant in affecting different species of plants and animals

- equipment mercury thermometer maximum-minimum thermometer

miniaturized thermistor

36

pH

-measure pH of a solution by universal indicator pH paper pH meter etc

Light

-measure its duration and intensity duration by predication from Royal Observatory intensity by photographic light meter

pH meter in use

37

Humidity

Relative humidity the water content of a given volume of air relative to the same volume of fully saturated air

- equipment whirling hygrometer

38

Wind and Water Speed- wind speed- anemometer or wind

gauges- water speed - time the movement of a

floating object over a measured distance

39

Salinity

- using a conductivity meter greater salinity has greater conductivity

Oxygen Level

- using an oxygen meter or chemical method (Winkler method)

40

Collecting MethodsCollecting all organisms within a habitat is normally

impractical and therefore small areas are selected Remember to return all material to its original position

after searching amp collecting sufficient specimens Some collecting apparatus for general use are listed

below

41

1 specimen tube

2 screwed-topped jars

3 polythene bags

4 forceps

5 paint brush

6 bulb pipette

7 pooter

42

8 widger 9 sieve 10 hand lens

11 enamel dish 12 beating tray 13 light traps

14 Tullgren funnel 15 Baermann funnel 16 mammal traps

17 pitfall traps 18 netting

43

Estimating Population Size

The exact methods used for estimation depend not only the nature of the habitat but also on the organisms involved

eg animals - population

plants - percentage cover

44

Using Quadrats

- By sampling an area using quadrats and counting the number of individuals within each quadrat it is possible to estimate the total number of individuals within the area

- confined to plants and sessile or very slow-moving animals

- fast-moving animals are disturbed and run away

45

Capture-recapture Techniques- useful for mobile animals which can be marked

- capture marked released randomly recaptured

and marked individuals recorded

no of marked individuals recaptured total no of individuals in 1st sample

-------------------------------------------- = ------------------------------------------

total no of individuals in 2nd sample estimated size of population

(the Lincoln Index)

46

Capture-recapture Techniques Factors affecting the accuracy of the estimation

deaths migration individuals become more liable to predation etc

Examples

- arthropods marked on their backs with non-toxic paint

- fish have tags attached to opercula - mammals have tags clipped to their ears

birds have their legs ringed

47

Capture-recapture Method Important tool for estimating density birth

rate and death rate for mobile animals Method

Collect a sample of individuals mark them and then release them

After a period collect more individuals from the wild and count the number that have marks

We assume that a sample if random will contain the same proportion of marked individuals as the population does

Estimate population density

48

Assumptions For All Capture-Recapture Studies Marking technique does not increase

mortality of marked animals Marked individuals are allowed to mix

with population Marking technique does not affect catch

probability Marks are not lost or overlooked No significant immigration or emigration No significant mortality or natality

49

Marked animals in second sample

Total caught in second sample

Marked animals in first sample

Total population size

=

520 N

16=

Peterson Method or Lincoln Index

N = 64N = (20)(16)5

50

Some Indices Used

Traps Number of Fecal

Pellets Vocalization

Frequency Pelt Records Catch per Unit

Fishing Effort

Number of Artifacts Questionnaires Cover Feeding Capacity Roadside Counts

51

Abundance Scales

The population size may be fairly accurately determined by making some form of frequency assessment

These are subjective and involve an experimenter making some estimate of the number of individuals in a given area or the cover of a particular species

This is especially useful where individuals are very numerous eg barnacles on a rocky shore or where it is difficult to distinguish individuals eg grass plants in a meadow

52

The assessments are usually made on an abundance scale of 5 categories

Abundance Common Frequent Occasional Rare

Barnacles exposed at low water

53

Environmental resistance are the factors which limit the growth of a particular population

eg predation disease availability of light food water oxygen and shelter the accumulation of toxic wastes and even the size of the population itself

54

Density-dependent Growth A population is a density-dependent when its size

(or density) affects its growth rate because of density-dependent factors such as food availability and toxic waste accumulation

Density-independent Growth In this type of growth a population increases until

some factor causes a sudden reduction in its size Its effect is the same regardless of the size of the

population eg temperature fires floods storms etc

55

Regulation of Population Size Fecundity is the reproductive capacity of individual

females of a species Birth rate or natality is used to measure fecundity Death rate or mortality is the number of individuals

of a species which die per unit time Immigration occurs when individuals join a

population from neighbouring ones Emigration occurs when individuals depart from a

population A cycle occurs when the size of a population

fluctuates on a regular basis

56

Ecological Sampling

57

Why Do We Sample Determine presence andor

abundance

Monitor population fluctuations

Assess lsquoecological damagersquo

Assess quality of habitat

Assess population responses

58

What Do We Sample

Physical Environment Temperature DO pH salinity clarity

flow sediment

Biotic Environment All living things

59

Physical Habitat Temperature

Mercury thermometer Electronic thermometer Long-term thermometers

Dissolved Oxygen Winkler method (titration) DO meter (electrode)

pH Litmus paper pH meter (electrode)

Salinity Salinity Meter YSI 550A DO Meter w12 cable

60

Water Clarity Secchi Disk

Disk is attached to a calibrated rope The disk is lowered into the water until the white parts can no longer be seen Secchi disk depth is then recorded and serves as the waters transparency index The clearer the water the greater the secchi disk depth

Secchi Disk

61

Current Velocity (flow) Floating-orange method

Put an orange (or something else that floats just below the water surface) and measure the time it takes it to float across a known distance

Odometer-type flow meter Number of revolutions the propeller

makes for a given time is calibrated to flow velocity

62

Sediment Sediment size is important to many

aquatic organisms Sieversquos are used to separate and

grade sediment samples Percent of each size grade can be

determined

63

Water Sample

Water and plankton from various depths can be collected

A trigger mechanism is used to close the sampler Sample is then brought back to the

surface

64

Small Mammals

Mouserat Traps Fatal

Pit Falls Bucket is placed in the ground Sometimes have lsquoleadsrsquo to the buckets

Live traps Havahart Sherman

Spot-light

Sherman trapHavahart trap

65

Birds Stick-under-the-box method Bird-trap

Works like a minnow trap Mist net

Captures birds in flight Rocket net

Uses a propellant to throw a net over birds

66

Terrestrial Insects

Sticky paper flies

Baited Traps Fire ants

Nets butterflies

Foggers Collect insects from tree canopies

67

Aquatic Insects Drift Net

Place net in flowing water Kick Net

lsquoKickrsquo sediment upstream from block net and the flow will wash them into the net

Wash bucket Serber or Hess Sampler

Stir up known area of sediment

Animals are collected by a catch net

Multi-plate Sampler Become colonized

68

Crawfish and Crab Traps

69

Fish Larvae Light Traps

Larvae are attracted to the light Ichthyoplankton nets

Can be towed at various depths Fish collect at the lsquocodrsquoend

70

Fish Lift net

Net is placed down and after a set amount of time it is quickly lifted

Pop-net Similar to a lift net but

floats are attached to a framed net

Operated by a trigger mechanism

Throw net A net attached to a heavy

frame is thrown and every thing inside is netted out Throw net

Pop-net

Lift net

71

Minnow trap

Usually use bait to attract small fish Light is used sometimes as an attractant

72

Fish Electrofishing

Electricity is put into the water Fish are temporarily stunned and usually

swim towards the electricity source Usually non-fatal but may cause some

damage

73

Fish Gill Net

Gill nets resemble tennis nets Fish can not swim completely through the

net and get caught Gill nets are size selective (based on mesh

size) Square Mesh

Bar mesh

Stretch mesh

74

Fish Trammel Net

Three panels two large mesh on the outside and a small mesh on the inside

Fish swim through the outer mesh pushes the small mesh through the other side and becomes entangled

75

Hoop nets (and other similar nets) can have bait or not

Fyke nets have leads to help guide fish to the net

76

Seine Seines are nets that are pulled

through shallow water to catch fish

77

Purse Seine Used to encircle entire schools of fish

Usually involves a spotter plane and a second boat

78

Trotline (longline) A series of baited drop lines

connected to a main line

Can be deployed by tying one end to the bank and tying the other end with a heavy weight

79

Shrimp (or fish) Trawl Net pulled behind

a boat along the bottom Either a beam or

otter boards keep the net open

80

Tagging Individuals Coded Wire Tags

Microwire that has a unique label

Magnetic wand detects the tag

Tag retention should be determined

T-Bar tags Can be individually

numbered External tag

PIT tags (Passive Integrated Transponders) Wand induces the tag to

transmit individual number is displayed

81

Other Tagging Methods

Toe clip Amphibian and reptile Clip of one or more toes

to identify individuals

Bird Band Place a metal band on a

bird leg Generally has

identification information

82

Preserving plant specimens Pressing and drying Long-term

preservation and storage

Alternative drying techniques

Special preservation and processing techniques

Mounting

83

Pressing and drying Techniques for pressing and drying specimens have been

established for many years There are minor variations in recommended methods but they are essentially the same worldwide

The best specimens are plants that are pressed as soon as possible after collection before wilting and shrivelling Most plants may be kept in sealed containers such as plastic bags for up to a day if it is inconvenient to press immediately However some plants show such rapid wilting particularly of the flowers that such delays are best avoided Flowers with a lot of nectar may go mouldy very quickly if excess nectar is not shaken off before pressing

Specimens are pressed flat and dried between sheets of absorbent blotters or semi-absorbent paper such as newspaper Papers with a glossy surface should be avoided because they are not absorbent enough to aid drying The plant should be carefully laid out between the drying sheets as their form at this stage largely determines their ultimate appearance The flowers should be spread out with the petals carefully arranged wilted leaves should be straightened and unnecessary shoots of excessively twiggy shrubs may be cut away

84

Microwave ovens Small numbers of specimens can be dried using a microwave

oven The technique recommended in the literature is to place the specimens between unprinted absorbent paper for example butchers paper not newspaper which is unsuitable because the chemicals present in the ink may cause a fire The specimens should be put in a special press which should be of a microwave-safe material (wood acrylic or polycarbonate sheeting eg plexiglass or perspex NO metal components) If such a press is not available sheets of cardboard can be placed above and below the specimens and then weighted down

Drying time depends on the power of your oven In most cases drying is accomplished by irradiating at maximum power for 1-2 minutes per specimen although it is often a case of trial and error It is best to process no more than 10-12 specimens of average thickness per batch Specimens are usually dried after the moisture that characteristically appears on the glass door has disappeared If the specimen is damp when taken out of the oven allow it to stand before re-radiating as moisture continues to evaporate from the specimen for some time Care must be taken not to irradiate the specimens for too long

It should be noted that microwave treatment damages seeds and the cellular structure of the plants which may reduce the long-term value of the specimens

85

Alternative drying techniquesSilica gelother desiccants amp freeze drying Alternative methods of drying plant specimens have been

used for some time but are mostly restricted to special purpose collections The main alternatives are freeze-drying and drying in a desiccant powder such as desiccant silica gel In general these techniques are used where it is essential to preserve the shape of a delicate plant of organ of the plant such as the flower Freeze-drying has also been used to preserve the chemical composition of a plant as accurately as possible for later study

Disadvantages and special conservation problems of specimens dried in these manners are that they are particularly susceptible to damage The dried parts are fragile lack support and often catch on packing materials They must therefore be packed especially carefully and stored in small boxes or tubes with some appropriate packing material that does not snag and break small projections Acid-free tissue paper is often used Drying in desiccant silica gel crystals or powder can also have the disadvantage that it is difficult to remove all traces of the silica gel after drying

86

Special preservation and processing techniquesWet or spirit collections

Very fleshy or delicate structures including small algae and orchid flowers are best preserved in an air-tight glass or plastic jar with a liquid preservative rather than by drying The type of preservative used should be clearly labelled in the jar Such material is often referred to as a spirit collection or wet collection

Most material can be satisfactorily preserved in 70 ethyl alcohol (or 70 methylated spirit or denatured alcohol) with 30 water Colours will fade quickly in spirit however so it is a good idea to keep comprehensive notes and photographs

87

Small algae Microscopic algae are often collected in a jar and in the

water in which they were found If the algae are to be stored for more than 2-3 days a preservative needs to be used Traditionally this has been the extremely toxic formalin - a small amount can be added to the water to make a 5 final solution and the container labelled This must not be sent through the post or by courier

There are some other equally toxic options for example propylene phenoxytol but none should be sent through the post A safer option is to add sufficient concentrated alcohol or methylated spirits to the water containing the algae to make a final solution of 70 alcohol This treatment dilutes the algae making them difficult to find so if they can be concentrated somehow first (eg by filtering) they can be stored in much less liquid Another option is to fix the algae in formalin (or something similar) first and then prepare a microscope glass slide with a permanent water-soluble mounting medium

88

Mounting Mounting specimens prevents most fragile material from

fragmenting and prevents specimens becoming separated from their labels If the plant collection is a long-term project specimens should be mounted on sheets of archival (permanent) cardboard or paper with archival-quality fixing media These include stitching with cotton thread dental floss nickel-plated copper wire (for heavier specimens) narrow strips of archival paper linen tape or by using an archival adhesive such as methyl cellulose adhesive

One disadvantage of mounting specimens is that it can make parts of the specimen inaccessible for examination so it is essential that this be borne in mind during specimen arrangement and mounting For example easily reversible mounting media should be used specimens should be strapped to the sheet rather than glued all over and the specimen should be carefully arranged before it is attached so that it shows all features

89

Full-size herbarium mounting sheets are usually about 43 cm long x 28 cm wide The plant name and accompanying field notes should be transcribed on a permanent label stuck to one corner of the herbarium sheet (the bottom right-hand corner being the most common) or sometimes annotations may be written directly on the sheet or card

Small pieces of material which may have become separated from the specimen (eg seeds) can be placed in small plastic bags and pinned to the sheet

90

Long-term preservation and storage The long-term preservation of dry plant

specimens is largely dependent on protection from insect attack Specimens collected by Linnaeus in the eighteenth century and by Banks and Solander on the Endeavour voyage in 1788 are still excellently preserved

91

Pests and their control A range of pests attack dried plant material The

most common pests are insects and fungi though rodents and other large animals can cause damage in poor storage conditions Insects eat the material the paper surrounding the material and the adhesives and mounting media

Such insect pests range from psocids (book lice) which attack mainly the softer parts such as flowers and soft fruits to tobacco beetles and carpet beetles which can bore holes through the toughest of specimens Many insects are particularly sensitive to relative humidity levels and do not thrive at levels below 50

92

The most common and acceptable specimen treatments for insect control are Freezing Microwave Poisoning Insect deterrents Fungal pests

93

Storage

Dried and pressed plant specimens can be stored in cardboard or plastic boxes or tied in bundles in light-weight cardboard folders placed in pigeon holes

Alternatively they can be placed in protective plastic jackets and displayed in ring folders which is recommended if they are to be frequently handled such as for a reference collection

94

Filing

Specimens should be filed in a systematic order if a relatively permanent collection is being made The major groups ie ferns and fern allies cycads conifers dicotyledons and monocotyledons are best kept separately or according to some classification scheme such as that given in a flora or handbook

Similarly the genera within each family and the species within each genus may be filed alphabetically or following some such classification

95

Preservation of entire animals

Types of collection specimens of an entire animal For reference collections mammals can be prepared as a variety of specimens The condition of the specimen may determine possible ways to preserve it if for instance decomposition of the skin has loosened the hair of a carcass so much that it can easily be pulled out or removed by rubbing (ldquoslippingrdquo fur) it will be very difficult or impossible to produce a study skin or mounted specimen The most usual types of specimens (based on Nagorsen and Peterson 1980) are 1) entire fluid-preserved animals (for studying anatomy and histology fluid preservation may change the fur colour) 2) study skins with accompanying skulls partial skeletons (some bones remain in the skin) for studying pelage colour hair quality and moulting patterns 3) mounted skins with accompanying partial or entire skeleton (some bones may remain in the skin dependant on the method of preservation) or freeze-dried specimens 4) entire skeletons for instance for studying anatomy geographic variation or for age determination (entire skeletons are poorly represented in collections so Nagorsen and Peterson (1980) recommend preparation of at least one male and one female skeleton per species

96

Preservation of specimens in the field Formalin preservation Preservation in alcohol Preservation by cooling or freezing

97

Formalin preservation After weighing and measuring the animal and attaching an

adequate label very small specimens (up to 100 g) can be fixed whole by submerging them in 10 buffered formalin (tissue - formalin solution ratio of at least 1 12) the body cavity can be filled with formalin solution by injection until it is turgid and firm some formalin may also be injected under the skin into the body cavity larger muscles and organs If hypodermic needles are not available the body cavity can be opened ventrally by making a slit instead allowing the formalin to enter

Keeping the mouth open with a piece of wood or cotton may later allow examination of teeth Then the whole body can be immersed in formalin in the posture in which it is supposed to stay permanently because it will harden The ratio of formalin to carcass must be at least 12 to 1 to assure a good fixation Tissues can be left in buffered neutralized formalin for several months but formalin hardens specimens therefore after fixation longterm storage in alcohol may be better After preservation the carcass should therefore be washed in water and transferred into ethanol for permanent storage

Disadvantages for instance it discolours the fur after a longish immersion softens the bones and prevents further examination for microbiology

98

Preservation in alcohol

After weighing a whole animal can be preserved in a container of alcohol (70-90) Removal of the intestine prior to storage of the animal in alcohol is recommended

99

Preservation by cooling or freezing Removal of the skin with insulating fur

before cooling or freezing may help to cool the carcass down more quickly

Freezing is not recommended if histological examination is planned

100

THANK YOU

35

Measurement of Environmental ParametersAbiotic factors are important in determining

both the distribution of the organisms and their physical and physiological adaptations

Temperature- diurnal and seasonal temperature variations

are significant in affecting different species of plants and animals

- equipment mercury thermometer maximum-minimum thermometer

miniaturized thermistor

36

pH

-measure pH of a solution by universal indicator pH paper pH meter etc

Light

-measure its duration and intensity duration by predication from Royal Observatory intensity by photographic light meter

pH meter in use

37

Humidity

Relative humidity the water content of a given volume of air relative to the same volume of fully saturated air

- equipment whirling hygrometer

38

Wind and Water Speed- wind speed- anemometer or wind

gauges- water speed - time the movement of a

floating object over a measured distance

39

Salinity

- using a conductivity meter greater salinity has greater conductivity

Oxygen Level

- using an oxygen meter or chemical method (Winkler method)

40

Collecting MethodsCollecting all organisms within a habitat is normally

impractical and therefore small areas are selected Remember to return all material to its original position

after searching amp collecting sufficient specimens Some collecting apparatus for general use are listed

below

41

1 specimen tube

2 screwed-topped jars

3 polythene bags

4 forceps

5 paint brush

6 bulb pipette

7 pooter

42

8 widger 9 sieve 10 hand lens

11 enamel dish 12 beating tray 13 light traps

14 Tullgren funnel 15 Baermann funnel 16 mammal traps

17 pitfall traps 18 netting

43

Estimating Population Size

The exact methods used for estimation depend not only the nature of the habitat but also on the organisms involved

eg animals - population

plants - percentage cover

44

Using Quadrats

- By sampling an area using quadrats and counting the number of individuals within each quadrat it is possible to estimate the total number of individuals within the area

- confined to plants and sessile or very slow-moving animals

- fast-moving animals are disturbed and run away

45

Capture-recapture Techniques- useful for mobile animals which can be marked

- capture marked released randomly recaptured

and marked individuals recorded

no of marked individuals recaptured total no of individuals in 1st sample

-------------------------------------------- = ------------------------------------------

total no of individuals in 2nd sample estimated size of population

(the Lincoln Index)

46

Capture-recapture Techniques Factors affecting the accuracy of the estimation

deaths migration individuals become more liable to predation etc

Examples

- arthropods marked on their backs with non-toxic paint

- fish have tags attached to opercula - mammals have tags clipped to their ears

birds have their legs ringed

47

Capture-recapture Method Important tool for estimating density birth

rate and death rate for mobile animals Method

Collect a sample of individuals mark them and then release them

After a period collect more individuals from the wild and count the number that have marks

We assume that a sample if random will contain the same proportion of marked individuals as the population does

Estimate population density

48

Assumptions For All Capture-Recapture Studies Marking technique does not increase

mortality of marked animals Marked individuals are allowed to mix

with population Marking technique does not affect catch

probability Marks are not lost or overlooked No significant immigration or emigration No significant mortality or natality

49

Marked animals in second sample

Total caught in second sample

Marked animals in first sample

Total population size

=

520 N

16=

Peterson Method or Lincoln Index

N = 64N = (20)(16)5

50

Some Indices Used

Traps Number of Fecal

Pellets Vocalization

Frequency Pelt Records Catch per Unit

Fishing Effort

Number of Artifacts Questionnaires Cover Feeding Capacity Roadside Counts

51

Abundance Scales

The population size may be fairly accurately determined by making some form of frequency assessment

These are subjective and involve an experimenter making some estimate of the number of individuals in a given area or the cover of a particular species

This is especially useful where individuals are very numerous eg barnacles on a rocky shore or where it is difficult to distinguish individuals eg grass plants in a meadow

52

The assessments are usually made on an abundance scale of 5 categories

Abundance Common Frequent Occasional Rare

Barnacles exposed at low water

53

Environmental resistance are the factors which limit the growth of a particular population

eg predation disease availability of light food water oxygen and shelter the accumulation of toxic wastes and even the size of the population itself

54

Density-dependent Growth A population is a density-dependent when its size

(or density) affects its growth rate because of density-dependent factors such as food availability and toxic waste accumulation

Density-independent Growth In this type of growth a population increases until

some factor causes a sudden reduction in its size Its effect is the same regardless of the size of the

population eg temperature fires floods storms etc

55

Regulation of Population Size Fecundity is the reproductive capacity of individual

females of a species Birth rate or natality is used to measure fecundity Death rate or mortality is the number of individuals

of a species which die per unit time Immigration occurs when individuals join a

population from neighbouring ones Emigration occurs when individuals depart from a

population A cycle occurs when the size of a population

fluctuates on a regular basis

56

Ecological Sampling

57

Why Do We Sample Determine presence andor

abundance

Monitor population fluctuations

Assess lsquoecological damagersquo

Assess quality of habitat

Assess population responses

58

What Do We Sample

Physical Environment Temperature DO pH salinity clarity

flow sediment

Biotic Environment All living things

59

Physical Habitat Temperature

Mercury thermometer Electronic thermometer Long-term thermometers

Dissolved Oxygen Winkler method (titration) DO meter (electrode)

pH Litmus paper pH meter (electrode)

Salinity Salinity Meter YSI 550A DO Meter w12 cable

60

Water Clarity Secchi Disk

Disk is attached to a calibrated rope The disk is lowered into the water until the white parts can no longer be seen Secchi disk depth is then recorded and serves as the waters transparency index The clearer the water the greater the secchi disk depth

Secchi Disk

61

Current Velocity (flow) Floating-orange method

Put an orange (or something else that floats just below the water surface) and measure the time it takes it to float across a known distance

Odometer-type flow meter Number of revolutions the propeller

makes for a given time is calibrated to flow velocity

62

Sediment Sediment size is important to many

aquatic organisms Sieversquos are used to separate and

grade sediment samples Percent of each size grade can be

determined

63

Water Sample

Water and plankton from various depths can be collected

A trigger mechanism is used to close the sampler Sample is then brought back to the

surface

64

Small Mammals

Mouserat Traps Fatal

Pit Falls Bucket is placed in the ground Sometimes have lsquoleadsrsquo to the buckets

Live traps Havahart Sherman

Spot-light

Sherman trapHavahart trap

65

Birds Stick-under-the-box method Bird-trap

Works like a minnow trap Mist net

Captures birds in flight Rocket net

Uses a propellant to throw a net over birds

66

Terrestrial Insects

Sticky paper flies

Baited Traps Fire ants

Nets butterflies

Foggers Collect insects from tree canopies

67

Aquatic Insects Drift Net

Place net in flowing water Kick Net

lsquoKickrsquo sediment upstream from block net and the flow will wash them into the net

Wash bucket Serber or Hess Sampler

Stir up known area of sediment

Animals are collected by a catch net

Multi-plate Sampler Become colonized

68

Crawfish and Crab Traps

69

Fish Larvae Light Traps

Larvae are attracted to the light Ichthyoplankton nets

Can be towed at various depths Fish collect at the lsquocodrsquoend

70

Fish Lift net

Net is placed down and after a set amount of time it is quickly lifted

Pop-net Similar to a lift net but

floats are attached to a framed net

Operated by a trigger mechanism

Throw net A net attached to a heavy

frame is thrown and every thing inside is netted out Throw net

Pop-net

Lift net

71

Minnow trap

Usually use bait to attract small fish Light is used sometimes as an attractant

72

Fish Electrofishing

Electricity is put into the water Fish are temporarily stunned and usually

swim towards the electricity source Usually non-fatal but may cause some

damage

73

Fish Gill Net

Gill nets resemble tennis nets Fish can not swim completely through the

net and get caught Gill nets are size selective (based on mesh

size) Square Mesh

Bar mesh

Stretch mesh

74

Fish Trammel Net

Three panels two large mesh on the outside and a small mesh on the inside

Fish swim through the outer mesh pushes the small mesh through the other side and becomes entangled

75

Hoop nets (and other similar nets) can have bait or not

Fyke nets have leads to help guide fish to the net

76

Seine Seines are nets that are pulled

through shallow water to catch fish

77

Purse Seine Used to encircle entire schools of fish

Usually involves a spotter plane and a second boat

78

Trotline (longline) A series of baited drop lines

connected to a main line

Can be deployed by tying one end to the bank and tying the other end with a heavy weight

79

Shrimp (or fish) Trawl Net pulled behind

a boat along the bottom Either a beam or

otter boards keep the net open

80

Tagging Individuals Coded Wire Tags

Microwire that has a unique label

Magnetic wand detects the tag

Tag retention should be determined

T-Bar tags Can be individually

numbered External tag

PIT tags (Passive Integrated Transponders) Wand induces the tag to

transmit individual number is displayed

81

Other Tagging Methods

Toe clip Amphibian and reptile Clip of one or more toes

to identify individuals

Bird Band Place a metal band on a

bird leg Generally has

identification information

82

Preserving plant specimens Pressing and drying Long-term

preservation and storage

Alternative drying techniques

Special preservation and processing techniques

Mounting

83

Pressing and drying Techniques for pressing and drying specimens have been

established for many years There are minor variations in recommended methods but they are essentially the same worldwide

The best specimens are plants that are pressed as soon as possible after collection before wilting and shrivelling Most plants may be kept in sealed containers such as plastic bags for up to a day if it is inconvenient to press immediately However some plants show such rapid wilting particularly of the flowers that such delays are best avoided Flowers with a lot of nectar may go mouldy very quickly if excess nectar is not shaken off before pressing

Specimens are pressed flat and dried between sheets of absorbent blotters or semi-absorbent paper such as newspaper Papers with a glossy surface should be avoided because they are not absorbent enough to aid drying The plant should be carefully laid out between the drying sheets as their form at this stage largely determines their ultimate appearance The flowers should be spread out with the petals carefully arranged wilted leaves should be straightened and unnecessary shoots of excessively twiggy shrubs may be cut away

84

Microwave ovens Small numbers of specimens can be dried using a microwave

oven The technique recommended in the literature is to place the specimens between unprinted absorbent paper for example butchers paper not newspaper which is unsuitable because the chemicals present in the ink may cause a fire The specimens should be put in a special press which should be of a microwave-safe material (wood acrylic or polycarbonate sheeting eg plexiglass or perspex NO metal components) If such a press is not available sheets of cardboard can be placed above and below the specimens and then weighted down

Drying time depends on the power of your oven In most cases drying is accomplished by irradiating at maximum power for 1-2 minutes per specimen although it is often a case of trial and error It is best to process no more than 10-12 specimens of average thickness per batch Specimens are usually dried after the moisture that characteristically appears on the glass door has disappeared If the specimen is damp when taken out of the oven allow it to stand before re-radiating as moisture continues to evaporate from the specimen for some time Care must be taken not to irradiate the specimens for too long

It should be noted that microwave treatment damages seeds and the cellular structure of the plants which may reduce the long-term value of the specimens

85

Alternative drying techniquesSilica gelother desiccants amp freeze drying Alternative methods of drying plant specimens have been

used for some time but are mostly restricted to special purpose collections The main alternatives are freeze-drying and drying in a desiccant powder such as desiccant silica gel In general these techniques are used where it is essential to preserve the shape of a delicate plant of organ of the plant such as the flower Freeze-drying has also been used to preserve the chemical composition of a plant as accurately as possible for later study

Disadvantages and special conservation problems of specimens dried in these manners are that they are particularly susceptible to damage The dried parts are fragile lack support and often catch on packing materials They must therefore be packed especially carefully and stored in small boxes or tubes with some appropriate packing material that does not snag and break small projections Acid-free tissue paper is often used Drying in desiccant silica gel crystals or powder can also have the disadvantage that it is difficult to remove all traces of the silica gel after drying

86

Special preservation and processing techniquesWet or spirit collections

Very fleshy or delicate structures including small algae and orchid flowers are best preserved in an air-tight glass or plastic jar with a liquid preservative rather than by drying The type of preservative used should be clearly labelled in the jar Such material is often referred to as a spirit collection or wet collection

Most material can be satisfactorily preserved in 70 ethyl alcohol (or 70 methylated spirit or denatured alcohol) with 30 water Colours will fade quickly in spirit however so it is a good idea to keep comprehensive notes and photographs

87

Small algae Microscopic algae are often collected in a jar and in the

water in which they were found If the algae are to be stored for more than 2-3 days a preservative needs to be used Traditionally this has been the extremely toxic formalin - a small amount can be added to the water to make a 5 final solution and the container labelled This must not be sent through the post or by courier

There are some other equally toxic options for example propylene phenoxytol but none should be sent through the post A safer option is to add sufficient concentrated alcohol or methylated spirits to the water containing the algae to make a final solution of 70 alcohol This treatment dilutes the algae making them difficult to find so if they can be concentrated somehow first (eg by filtering) they can be stored in much less liquid Another option is to fix the algae in formalin (or something similar) first and then prepare a microscope glass slide with a permanent water-soluble mounting medium

88

Mounting Mounting specimens prevents most fragile material from

fragmenting and prevents specimens becoming separated from their labels If the plant collection is a long-term project specimens should be mounted on sheets of archival (permanent) cardboard or paper with archival-quality fixing media These include stitching with cotton thread dental floss nickel-plated copper wire (for heavier specimens) narrow strips of archival paper linen tape or by using an archival adhesive such as methyl cellulose adhesive

One disadvantage of mounting specimens is that it can make parts of the specimen inaccessible for examination so it is essential that this be borne in mind during specimen arrangement and mounting For example easily reversible mounting media should be used specimens should be strapped to the sheet rather than glued all over and the specimen should be carefully arranged before it is attached so that it shows all features

89

Full-size herbarium mounting sheets are usually about 43 cm long x 28 cm wide The plant name and accompanying field notes should be transcribed on a permanent label stuck to one corner of the herbarium sheet (the bottom right-hand corner being the most common) or sometimes annotations may be written directly on the sheet or card

Small pieces of material which may have become separated from the specimen (eg seeds) can be placed in small plastic bags and pinned to the sheet

90

Long-term preservation and storage The long-term preservation of dry plant

specimens is largely dependent on protection from insect attack Specimens collected by Linnaeus in the eighteenth century and by Banks and Solander on the Endeavour voyage in 1788 are still excellently preserved

91

Pests and their control A range of pests attack dried plant material The

most common pests are insects and fungi though rodents and other large animals can cause damage in poor storage conditions Insects eat the material the paper surrounding the material and the adhesives and mounting media

Such insect pests range from psocids (book lice) which attack mainly the softer parts such as flowers and soft fruits to tobacco beetles and carpet beetles which can bore holes through the toughest of specimens Many insects are particularly sensitive to relative humidity levels and do not thrive at levels below 50

92

The most common and acceptable specimen treatments for insect control are Freezing Microwave Poisoning Insect deterrents Fungal pests

93

Storage

Dried and pressed plant specimens can be stored in cardboard or plastic boxes or tied in bundles in light-weight cardboard folders placed in pigeon holes

Alternatively they can be placed in protective plastic jackets and displayed in ring folders which is recommended if they are to be frequently handled such as for a reference collection

94

Filing

Specimens should be filed in a systematic order if a relatively permanent collection is being made The major groups ie ferns and fern allies cycads conifers dicotyledons and monocotyledons are best kept separately or according to some classification scheme such as that given in a flora or handbook

Similarly the genera within each family and the species within each genus may be filed alphabetically or following some such classification

95

Preservation of entire animals

Types of collection specimens of an entire animal For reference collections mammals can be prepared as a variety of specimens The condition of the specimen may determine possible ways to preserve it if for instance decomposition of the skin has loosened the hair of a carcass so much that it can easily be pulled out or removed by rubbing (ldquoslippingrdquo fur) it will be very difficult or impossible to produce a study skin or mounted specimen The most usual types of specimens (based on Nagorsen and Peterson 1980) are 1) entire fluid-preserved animals (for studying anatomy and histology fluid preservation may change the fur colour) 2) study skins with accompanying skulls partial skeletons (some bones remain in the skin) for studying pelage colour hair quality and moulting patterns 3) mounted skins with accompanying partial or entire skeleton (some bones may remain in the skin dependant on the method of preservation) or freeze-dried specimens 4) entire skeletons for instance for studying anatomy geographic variation or for age determination (entire skeletons are poorly represented in collections so Nagorsen and Peterson (1980) recommend preparation of at least one male and one female skeleton per species

96

Preservation of specimens in the field Formalin preservation Preservation in alcohol Preservation by cooling or freezing

97

Formalin preservation After weighing and measuring the animal and attaching an

adequate label very small specimens (up to 100 g) can be fixed whole by submerging them in 10 buffered formalin (tissue - formalin solution ratio of at least 1 12) the body cavity can be filled with formalin solution by injection until it is turgid and firm some formalin may also be injected under the skin into the body cavity larger muscles and organs If hypodermic needles are not available the body cavity can be opened ventrally by making a slit instead allowing the formalin to enter

Keeping the mouth open with a piece of wood or cotton may later allow examination of teeth Then the whole body can be immersed in formalin in the posture in which it is supposed to stay permanently because it will harden The ratio of formalin to carcass must be at least 12 to 1 to assure a good fixation Tissues can be left in buffered neutralized formalin for several months but formalin hardens specimens therefore after fixation longterm storage in alcohol may be better After preservation the carcass should therefore be washed in water and transferred into ethanol for permanent storage

Disadvantages for instance it discolours the fur after a longish immersion softens the bones and prevents further examination for microbiology

98

Preservation in alcohol

After weighing a whole animal can be preserved in a container of alcohol (70-90) Removal of the intestine prior to storage of the animal in alcohol is recommended

99

Preservation by cooling or freezing Removal of the skin with insulating fur

before cooling or freezing may help to cool the carcass down more quickly

Freezing is not recommended if histological examination is planned

100

THANK YOU

36

pH

-measure pH of a solution by universal indicator pH paper pH meter etc

Light

-measure its duration and intensity duration by predication from Royal Observatory intensity by photographic light meter

pH meter in use

37

Humidity

Relative humidity the water content of a given volume of air relative to the same volume of fully saturated air

- equipment whirling hygrometer

38

Wind and Water Speed- wind speed- anemometer or wind

gauges- water speed - time the movement of a

floating object over a measured distance

39

Salinity

- using a conductivity meter greater salinity has greater conductivity

Oxygen Level

- using an oxygen meter or chemical method (Winkler method)

40

Collecting MethodsCollecting all organisms within a habitat is normally

impractical and therefore small areas are selected Remember to return all material to its original position

after searching amp collecting sufficient specimens Some collecting apparatus for general use are listed

below

41

1 specimen tube

2 screwed-topped jars

3 polythene bags

4 forceps

5 paint brush

6 bulb pipette

7 pooter

42

8 widger 9 sieve 10 hand lens

11 enamel dish 12 beating tray 13 light traps

14 Tullgren funnel 15 Baermann funnel 16 mammal traps

17 pitfall traps 18 netting

43

Estimating Population Size

The exact methods used for estimation depend not only the nature of the habitat but also on the organisms involved

eg animals - population

plants - percentage cover

44

Using Quadrats

- By sampling an area using quadrats and counting the number of individuals within each quadrat it is possible to estimate the total number of individuals within the area

- confined to plants and sessile or very slow-moving animals

- fast-moving animals are disturbed and run away

45

Capture-recapture Techniques- useful for mobile animals which can be marked

- capture marked released randomly recaptured

and marked individuals recorded

no of marked individuals recaptured total no of individuals in 1st sample

-------------------------------------------- = ------------------------------------------

total no of individuals in 2nd sample estimated size of population

(the Lincoln Index)

46

Capture-recapture Techniques Factors affecting the accuracy of the estimation

deaths migration individuals become more liable to predation etc

Examples

- arthropods marked on their backs with non-toxic paint

- fish have tags attached to opercula - mammals have tags clipped to their ears

birds have their legs ringed

47

Capture-recapture Method Important tool for estimating density birth

rate and death rate for mobile animals Method

Collect a sample of individuals mark them and then release them

After a period collect more individuals from the wild and count the number that have marks

We assume that a sample if random will contain the same proportion of marked individuals as the population does

Estimate population density

48

Assumptions For All Capture-Recapture Studies Marking technique does not increase

mortality of marked animals Marked individuals are allowed to mix

with population Marking technique does not affect catch

probability Marks are not lost or overlooked No significant immigration or emigration No significant mortality or natality

49

Marked animals in second sample

Total caught in second sample

Marked animals in first sample

Total population size

=

520 N

16=

Peterson Method or Lincoln Index

N = 64N = (20)(16)5

50

Some Indices Used

Traps Number of Fecal

Pellets Vocalization

Frequency Pelt Records Catch per Unit

Fishing Effort

Number of Artifacts Questionnaires Cover Feeding Capacity Roadside Counts

51

Abundance Scales

The population size may be fairly accurately determined by making some form of frequency assessment

These are subjective and involve an experimenter making some estimate of the number of individuals in a given area or the cover of a particular species

This is especially useful where individuals are very numerous eg barnacles on a rocky shore or where it is difficult to distinguish individuals eg grass plants in a meadow

52

The assessments are usually made on an abundance scale of 5 categories

Abundance Common Frequent Occasional Rare

Barnacles exposed at low water

53

Environmental resistance are the factors which limit the growth of a particular population

eg predation disease availability of light food water oxygen and shelter the accumulation of toxic wastes and even the size of the population itself

54

Density-dependent Growth A population is a density-dependent when its size

(or density) affects its growth rate because of density-dependent factors such as food availability and toxic waste accumulation

Density-independent Growth In this type of growth a population increases until

some factor causes a sudden reduction in its size Its effect is the same regardless of the size of the

population eg temperature fires floods storms etc

55

Regulation of Population Size Fecundity is the reproductive capacity of individual

females of a species Birth rate or natality is used to measure fecundity Death rate or mortality is the number of individuals

of a species which die per unit time Immigration occurs when individuals join a

population from neighbouring ones Emigration occurs when individuals depart from a

population A cycle occurs when the size of a population

fluctuates on a regular basis

56

Ecological Sampling

57

Why Do We Sample Determine presence andor

abundance

Monitor population fluctuations

Assess lsquoecological damagersquo

Assess quality of habitat

Assess population responses

58

What Do We Sample

Physical Environment Temperature DO pH salinity clarity

flow sediment

Biotic Environment All living things

59

Physical Habitat Temperature

Mercury thermometer Electronic thermometer Long-term thermometers

Dissolved Oxygen Winkler method (titration) DO meter (electrode)

pH Litmus paper pH meter (electrode)

Salinity Salinity Meter YSI 550A DO Meter w12 cable

60

Water Clarity Secchi Disk

Disk is attached to a calibrated rope The disk is lowered into the water until the white parts can no longer be seen Secchi disk depth is then recorded and serves as the waters transparency index The clearer the water the greater the secchi disk depth

Secchi Disk

61

Current Velocity (flow) Floating-orange method

Put an orange (or something else that floats just below the water surface) and measure the time it takes it to float across a known distance

Odometer-type flow meter Number of revolutions the propeller

makes for a given time is calibrated to flow velocity

62

Sediment Sediment size is important to many

aquatic organisms Sieversquos are used to separate and

grade sediment samples Percent of each size grade can be

determined

63

Water Sample

Water and plankton from various depths can be collected

A trigger mechanism is used to close the sampler Sample is then brought back to the

surface

64

Small Mammals

Mouserat Traps Fatal

Pit Falls Bucket is placed in the ground Sometimes have lsquoleadsrsquo to the buckets

Live traps Havahart Sherman

Spot-light

Sherman trapHavahart trap

65

Birds Stick-under-the-box method Bird-trap

Works like a minnow trap Mist net

Captures birds in flight Rocket net

Uses a propellant to throw a net over birds

66

Terrestrial Insects

Sticky paper flies

Baited Traps Fire ants

Nets butterflies

Foggers Collect insects from tree canopies

67

Aquatic Insects Drift Net

Place net in flowing water Kick Net

lsquoKickrsquo sediment upstream from block net and the flow will wash them into the net

Wash bucket Serber or Hess Sampler

Stir up known area of sediment

Animals are collected by a catch net

Multi-plate Sampler Become colonized

68

Crawfish and Crab Traps

69

Fish Larvae Light Traps

Larvae are attracted to the light Ichthyoplankton nets

Can be towed at various depths Fish collect at the lsquocodrsquoend

70

Fish Lift net

Net is placed down and after a set amount of time it is quickly lifted

Pop-net Similar to a lift net but

floats are attached to a framed net

Operated by a trigger mechanism

Throw net A net attached to a heavy

frame is thrown and every thing inside is netted out Throw net

Pop-net

Lift net

71

Minnow trap

Usually use bait to attract small fish Light is used sometimes as an attractant

72

Fish Electrofishing

Electricity is put into the water Fish are temporarily stunned and usually

swim towards the electricity source Usually non-fatal but may cause some

damage

73

Fish Gill Net

Gill nets resemble tennis nets Fish can not swim completely through the

net and get caught Gill nets are size selective (based on mesh

size) Square Mesh

Bar mesh

Stretch mesh

74

Fish Trammel Net

Three panels two large mesh on the outside and a small mesh on the inside

Fish swim through the outer mesh pushes the small mesh through the other side and becomes entangled

75

Hoop nets (and other similar nets) can have bait or not

Fyke nets have leads to help guide fish to the net

76

Seine Seines are nets that are pulled

through shallow water to catch fish

77

Purse Seine Used to encircle entire schools of fish

Usually involves a spotter plane and a second boat

78

Trotline (longline) A series of baited drop lines

connected to a main line

Can be deployed by tying one end to the bank and tying the other end with a heavy weight

79

Shrimp (or fish) Trawl Net pulled behind

a boat along the bottom Either a beam or

otter boards keep the net open

80

Tagging Individuals Coded Wire Tags

Microwire that has a unique label

Magnetic wand detects the tag

Tag retention should be determined

T-Bar tags Can be individually

numbered External tag

PIT tags (Passive Integrated Transponders) Wand induces the tag to

transmit individual number is displayed

81

Other Tagging Methods

Toe clip Amphibian and reptile Clip of one or more toes

to identify individuals

Bird Band Place a metal band on a

bird leg Generally has

identification information

82

Preserving plant specimens Pressing and drying Long-term

preservation and storage

Alternative drying techniques

Special preservation and processing techniques

Mounting

83

Pressing and drying Techniques for pressing and drying specimens have been

established for many years There are minor variations in recommended methods but they are essentially the same worldwide

The best specimens are plants that are pressed as soon as possible after collection before wilting and shrivelling Most plants may be kept in sealed containers such as plastic bags for up to a day if it is inconvenient to press immediately However some plants show such rapid wilting particularly of the flowers that such delays are best avoided Flowers with a lot of nectar may go mouldy very quickly if excess nectar is not shaken off before pressing

Specimens are pressed flat and dried between sheets of absorbent blotters or semi-absorbent paper such as newspaper Papers with a glossy surface should be avoided because they are not absorbent enough to aid drying The plant should be carefully laid out between the drying sheets as their form at this stage largely determines their ultimate appearance The flowers should be spread out with the petals carefully arranged wilted leaves should be straightened and unnecessary shoots of excessively twiggy shrubs may be cut away

84

Microwave ovens Small numbers of specimens can be dried using a microwave

oven The technique recommended in the literature is to place the specimens between unprinted absorbent paper for example butchers paper not newspaper which is unsuitable because the chemicals present in the ink may cause a fire The specimens should be put in a special press which should be of a microwave-safe material (wood acrylic or polycarbonate sheeting eg plexiglass or perspex NO metal components) If such a press is not available sheets of cardboard can be placed above and below the specimens and then weighted down

Drying time depends on the power of your oven In most cases drying is accomplished by irradiating at maximum power for 1-2 minutes per specimen although it is often a case of trial and error It is best to process no more than 10-12 specimens of average thickness per batch Specimens are usually dried after the moisture that characteristically appears on the glass door has disappeared If the specimen is damp when taken out of the oven allow it to stand before re-radiating as moisture continues to evaporate from the specimen for some time Care must be taken not to irradiate the specimens for too long

It should be noted that microwave treatment damages seeds and the cellular structure of the plants which may reduce the long-term value of the specimens

85

Alternative drying techniquesSilica gelother desiccants amp freeze drying Alternative methods of drying plant specimens have been

used for some time but are mostly restricted to special purpose collections The main alternatives are freeze-drying and drying in a desiccant powder such as desiccant silica gel In general these techniques are used where it is essential to preserve the shape of a delicate plant of organ of the plant such as the flower Freeze-drying has also been used to preserve the chemical composition of a plant as accurately as possible for later study

Disadvantages and special conservation problems of specimens dried in these manners are that they are particularly susceptible to damage The dried parts are fragile lack support and often catch on packing materials They must therefore be packed especially carefully and stored in small boxes or tubes with some appropriate packing material that does not snag and break small projections Acid-free tissue paper is often used Drying in desiccant silica gel crystals or powder can also have the disadvantage that it is difficult to remove all traces of the silica gel after drying

86

Special preservation and processing techniquesWet or spirit collections

Very fleshy or delicate structures including small algae and orchid flowers are best preserved in an air-tight glass or plastic jar with a liquid preservative rather than by drying The type of preservative used should be clearly labelled in the jar Such material is often referred to as a spirit collection or wet collection

Most material can be satisfactorily preserved in 70 ethyl alcohol (or 70 methylated spirit or denatured alcohol) with 30 water Colours will fade quickly in spirit however so it is a good idea to keep comprehensive notes and photographs

87

Small algae Microscopic algae are often collected in a jar and in the

water in which they were found If the algae are to be stored for more than 2-3 days a preservative needs to be used Traditionally this has been the extremely toxic formalin - a small amount can be added to the water to make a 5 final solution and the container labelled This must not be sent through the post or by courier

There are some other equally toxic options for example propylene phenoxytol but none should be sent through the post A safer option is to add sufficient concentrated alcohol or methylated spirits to the water containing the algae to make a final solution of 70 alcohol This treatment dilutes the algae making them difficult to find so if they can be concentrated somehow first (eg by filtering) they can be stored in much less liquid Another option is to fix the algae in formalin (or something similar) first and then prepare a microscope glass slide with a permanent water-soluble mounting medium

88

Mounting Mounting specimens prevents most fragile material from

fragmenting and prevents specimens becoming separated from their labels If the plant collection is a long-term project specimens should be mounted on sheets of archival (permanent) cardboard or paper with archival-quality fixing media These include stitching with cotton thread dental floss nickel-plated copper wire (for heavier specimens) narrow strips of archival paper linen tape or by using an archival adhesive such as methyl cellulose adhesive

One disadvantage of mounting specimens is that it can make parts of the specimen inaccessible for examination so it is essential that this be borne in mind during specimen arrangement and mounting For example easily reversible mounting media should be used specimens should be strapped to the sheet rather than glued all over and the specimen should be carefully arranged before it is attached so that it shows all features

89

Full-size herbarium mounting sheets are usually about 43 cm long x 28 cm wide The plant name and accompanying field notes should be transcribed on a permanent label stuck to one corner of the herbarium sheet (the bottom right-hand corner being the most common) or sometimes annotations may be written directly on the sheet or card

Small pieces of material which may have become separated from the specimen (eg seeds) can be placed in small plastic bags and pinned to the sheet

90

Long-term preservation and storage The long-term preservation of dry plant

specimens is largely dependent on protection from insect attack Specimens collected by Linnaeus in the eighteenth century and by Banks and Solander on the Endeavour voyage in 1788 are still excellently preserved

91

Pests and their control A range of pests attack dried plant material The

most common pests are insects and fungi though rodents and other large animals can cause damage in poor storage conditions Insects eat the material the paper surrounding the material and the adhesives and mounting media

Such insect pests range from psocids (book lice) which attack mainly the softer parts such as flowers and soft fruits to tobacco beetles and carpet beetles which can bore holes through the toughest of specimens Many insects are particularly sensitive to relative humidity levels and do not thrive at levels below 50

92

The most common and acceptable specimen treatments for insect control are Freezing Microwave Poisoning Insect deterrents Fungal pests

93

Storage

Dried and pressed plant specimens can be stored in cardboard or plastic boxes or tied in bundles in light-weight cardboard folders placed in pigeon holes

Alternatively they can be placed in protective plastic jackets and displayed in ring folders which is recommended if they are to be frequently handled such as for a reference collection

94

Filing

Specimens should be filed in a systematic order if a relatively permanent collection is being made The major groups ie ferns and fern allies cycads conifers dicotyledons and monocotyledons are best kept separately or according to some classification scheme such as that given in a flora or handbook

Similarly the genera within each family and the species within each genus may be filed alphabetically or following some such classification

95

Preservation of entire animals

Types of collection specimens of an entire animal For reference collections mammals can be prepared as a variety of specimens The condition of the specimen may determine possible ways to preserve it if for instance decomposition of the skin has loosened the hair of a carcass so much that it can easily be pulled out or removed by rubbing (ldquoslippingrdquo fur) it will be very difficult or impossible to produce a study skin or mounted specimen The most usual types of specimens (based on Nagorsen and Peterson 1980) are 1) entire fluid-preserved animals (for studying anatomy and histology fluid preservation may change the fur colour) 2) study skins with accompanying skulls partial skeletons (some bones remain in the skin) for studying pelage colour hair quality and moulting patterns 3) mounted skins with accompanying partial or entire skeleton (some bones may remain in the skin dependant on the method of preservation) or freeze-dried specimens 4) entire skeletons for instance for studying anatomy geographic variation or for age determination (entire skeletons are poorly represented in collections so Nagorsen and Peterson (1980) recommend preparation of at least one male and one female skeleton per species

96

Preservation of specimens in the field Formalin preservation Preservation in alcohol Preservation by cooling or freezing

97

Formalin preservation After weighing and measuring the animal and attaching an

adequate label very small specimens (up to 100 g) can be fixed whole by submerging them in 10 buffered formalin (tissue - formalin solution ratio of at least 1 12) the body cavity can be filled with formalin solution by injection until it is turgid and firm some formalin may also be injected under the skin into the body cavity larger muscles and organs If hypodermic needles are not available the body cavity can be opened ventrally by making a slit instead allowing the formalin to enter

Keeping the mouth open with a piece of wood or cotton may later allow examination of teeth Then the whole body can be immersed in formalin in the posture in which it is supposed to stay permanently because it will harden The ratio of formalin to carcass must be at least 12 to 1 to assure a good fixation Tissues can be left in buffered neutralized formalin for several months but formalin hardens specimens therefore after fixation longterm storage in alcohol may be better After preservation the carcass should therefore be washed in water and transferred into ethanol for permanent storage

Disadvantages for instance it discolours the fur after a longish immersion softens the bones and prevents further examination for microbiology

98

Preservation in alcohol

After weighing a whole animal can be preserved in a container of alcohol (70-90) Removal of the intestine prior to storage of the animal in alcohol is recommended

99

Preservation by cooling or freezing Removal of the skin with insulating fur

before cooling or freezing may help to cool the carcass down more quickly

Freezing is not recommended if histological examination is planned

100

THANK YOU

37

Humidity

Relative humidity the water content of a given volume of air relative to the same volume of fully saturated air

- equipment whirling hygrometer

38

Wind and Water Speed- wind speed- anemometer or wind

gauges- water speed - time the movement of a

floating object over a measured distance

39

Salinity

- using a conductivity meter greater salinity has greater conductivity

Oxygen Level

- using an oxygen meter or chemical method (Winkler method)

40

Collecting MethodsCollecting all organisms within a habitat is normally

impractical and therefore small areas are selected Remember to return all material to its original position

after searching amp collecting sufficient specimens Some collecting apparatus for general use are listed

below

41

1 specimen tube

2 screwed-topped jars

3 polythene bags

4 forceps

5 paint brush

6 bulb pipette

7 pooter

42

8 widger 9 sieve 10 hand lens

11 enamel dish 12 beating tray 13 light traps

14 Tullgren funnel 15 Baermann funnel 16 mammal traps

17 pitfall traps 18 netting

43

Estimating Population Size

The exact methods used for estimation depend not only the nature of the habitat but also on the organisms involved

eg animals - population

plants - percentage cover

44

Using Quadrats

- By sampling an area using quadrats and counting the number of individuals within each quadrat it is possible to estimate the total number of individuals within the area

- confined to plants and sessile or very slow-moving animals

- fast-moving animals are disturbed and run away

45

Capture-recapture Techniques- useful for mobile animals which can be marked

- capture marked released randomly recaptured

and marked individuals recorded

no of marked individuals recaptured total no of individuals in 1st sample

-------------------------------------------- = ------------------------------------------

total no of individuals in 2nd sample estimated size of population

(the Lincoln Index)

46

Capture-recapture Techniques Factors affecting the accuracy of the estimation

deaths migration individuals become more liable to predation etc

Examples

- arthropods marked on their backs with non-toxic paint

- fish have tags attached to opercula - mammals have tags clipped to their ears

birds have their legs ringed

47

Capture-recapture Method Important tool for estimating density birth

rate and death rate for mobile animals Method

Collect a sample of individuals mark them and then release them

After a period collect more individuals from the wild and count the number that have marks

We assume that a sample if random will contain the same proportion of marked individuals as the population does

Estimate population density

48

Assumptions For All Capture-Recapture Studies Marking technique does not increase

mortality of marked animals Marked individuals are allowed to mix

with population Marking technique does not affect catch

probability Marks are not lost or overlooked No significant immigration or emigration No significant mortality or natality

49

Marked animals in second sample

Total caught in second sample

Marked animals in first sample

Total population size

=

520 N

16=

Peterson Method or Lincoln Index

N = 64N = (20)(16)5

50

Some Indices Used

Traps Number of Fecal

Pellets Vocalization

Frequency Pelt Records Catch per Unit

Fishing Effort

Number of Artifacts Questionnaires Cover Feeding Capacity Roadside Counts

51

Abundance Scales

The population size may be fairly accurately determined by making some form of frequency assessment

These are subjective and involve an experimenter making some estimate of the number of individuals in a given area or the cover of a particular species

This is especially useful where individuals are very numerous eg barnacles on a rocky shore or where it is difficult to distinguish individuals eg grass plants in a meadow

52

The assessments are usually made on an abundance scale of 5 categories

Abundance Common Frequent Occasional Rare

Barnacles exposed at low water

53

Environmental resistance are the factors which limit the growth of a particular population

eg predation disease availability of light food water oxygen and shelter the accumulation of toxic wastes and even the size of the population itself

54

Density-dependent Growth A population is a density-dependent when its size

(or density) affects its growth rate because of density-dependent factors such as food availability and toxic waste accumulation

Density-independent Growth In this type of growth a population increases until

some factor causes a sudden reduction in its size Its effect is the same regardless of the size of the

population eg temperature fires floods storms etc

55

Regulation of Population Size Fecundity is the reproductive capacity of individual

females of a species Birth rate or natality is used to measure fecundity Death rate or mortality is the number of individuals

of a species which die per unit time Immigration occurs when individuals join a

population from neighbouring ones Emigration occurs when individuals depart from a

population A cycle occurs when the size of a population

fluctuates on a regular basis

56

Ecological Sampling

57

Why Do We Sample Determine presence andor

abundance

Monitor population fluctuations

Assess lsquoecological damagersquo

Assess quality of habitat

Assess population responses

58

What Do We Sample

Physical Environment Temperature DO pH salinity clarity

flow sediment

Biotic Environment All living things

59

Physical Habitat Temperature

Mercury thermometer Electronic thermometer Long-term thermometers

Dissolved Oxygen Winkler method (titration) DO meter (electrode)

pH Litmus paper pH meter (electrode)

Salinity Salinity Meter YSI 550A DO Meter w12 cable

60

Water Clarity Secchi Disk

Disk is attached to a calibrated rope The disk is lowered into the water until the white parts can no longer be seen Secchi disk depth is then recorded and serves as the waters transparency index The clearer the water the greater the secchi disk depth

Secchi Disk

61

Current Velocity (flow) Floating-orange method

Put an orange (or something else that floats just below the water surface) and measure the time it takes it to float across a known distance

Odometer-type flow meter Number of revolutions the propeller

makes for a given time is calibrated to flow velocity

62

Sediment Sediment size is important to many

aquatic organisms Sieversquos are used to separate and

grade sediment samples Percent of each size grade can be

determined

63

Water Sample

Water and plankton from various depths can be collected

A trigger mechanism is used to close the sampler Sample is then brought back to the

surface

64

Small Mammals

Mouserat Traps Fatal

Pit Falls Bucket is placed in the ground Sometimes have lsquoleadsrsquo to the buckets

Live traps Havahart Sherman

Spot-light

Sherman trapHavahart trap

65

Birds Stick-under-the-box method Bird-trap

Works like a minnow trap Mist net

Captures birds in flight Rocket net

Uses a propellant to throw a net over birds

66

Terrestrial Insects

Sticky paper flies

Baited Traps Fire ants

Nets butterflies

Foggers Collect insects from tree canopies

67

Aquatic Insects Drift Net

Place net in flowing water Kick Net

lsquoKickrsquo sediment upstream from block net and the flow will wash them into the net

Wash bucket Serber or Hess Sampler

Stir up known area of sediment

Animals are collected by a catch net

Multi-plate Sampler Become colonized

68

Crawfish and Crab Traps

69

Fish Larvae Light Traps

Larvae are attracted to the light Ichthyoplankton nets

Can be towed at various depths Fish collect at the lsquocodrsquoend

70

Fish Lift net

Net is placed down and after a set amount of time it is quickly lifted

Pop-net Similar to a lift net but

floats are attached to a framed net

Operated by a trigger mechanism

Throw net A net attached to a heavy

frame is thrown and every thing inside is netted out Throw net

Pop-net

Lift net

71

Minnow trap

Usually use bait to attract small fish Light is used sometimes as an attractant

72

Fish Electrofishing

Electricity is put into the water Fish are temporarily stunned and usually

swim towards the electricity source Usually non-fatal but may cause some

damage

73

Fish Gill Net

Gill nets resemble tennis nets Fish can not swim completely through the

net and get caught Gill nets are size selective (based on mesh

size) Square Mesh

Bar mesh

Stretch mesh

74

Fish Trammel Net

Three panels two large mesh on the outside and a small mesh on the inside

Fish swim through the outer mesh pushes the small mesh through the other side and becomes entangled

75

Hoop nets (and other similar nets) can have bait or not

Fyke nets have leads to help guide fish to the net

76

Seine Seines are nets that are pulled

through shallow water to catch fish

77

Purse Seine Used to encircle entire schools of fish

Usually involves a spotter plane and a second boat

78

Trotline (longline) A series of baited drop lines

connected to a main line

Can be deployed by tying one end to the bank and tying the other end with a heavy weight

79

Shrimp (or fish) Trawl Net pulled behind

a boat along the bottom Either a beam or

otter boards keep the net open

80

Tagging Individuals Coded Wire Tags

Microwire that has a unique label

Magnetic wand detects the tag

Tag retention should be determined

T-Bar tags Can be individually

numbered External tag

PIT tags (Passive Integrated Transponders) Wand induces the tag to

transmit individual number is displayed

81

Other Tagging Methods

Toe clip Amphibian and reptile Clip of one or more toes

to identify individuals

Bird Band Place a metal band on a

bird leg Generally has

identification information

82

Preserving plant specimens Pressing and drying Long-term

preservation and storage

Alternative drying techniques

Special preservation and processing techniques

Mounting

83

Pressing and drying Techniques for pressing and drying specimens have been

established for many years There are minor variations in recommended methods but they are essentially the same worldwide

The best specimens are plants that are pressed as soon as possible after collection before wilting and shrivelling Most plants may be kept in sealed containers such as plastic bags for up to a day if it is inconvenient to press immediately However some plants show such rapid wilting particularly of the flowers that such delays are best avoided Flowers with a lot of nectar may go mouldy very quickly if excess nectar is not shaken off before pressing

Specimens are pressed flat and dried between sheets of absorbent blotters or semi-absorbent paper such as newspaper Papers with a glossy surface should be avoided because they are not absorbent enough to aid drying The plant should be carefully laid out between the drying sheets as their form at this stage largely determines their ultimate appearance The flowers should be spread out with the petals carefully arranged wilted leaves should be straightened and unnecessary shoots of excessively twiggy shrubs may be cut away

84

Microwave ovens Small numbers of specimens can be dried using a microwave

oven The technique recommended in the literature is to place the specimens between unprinted absorbent paper for example butchers paper not newspaper which is unsuitable because the chemicals present in the ink may cause a fire The specimens should be put in a special press which should be of a microwave-safe material (wood acrylic or polycarbonate sheeting eg plexiglass or perspex NO metal components) If such a press is not available sheets of cardboard can be placed above and below the specimens and then weighted down

Drying time depends on the power of your oven In most cases drying is accomplished by irradiating at maximum power for 1-2 minutes per specimen although it is often a case of trial and error It is best to process no more than 10-12 specimens of average thickness per batch Specimens are usually dried after the moisture that characteristically appears on the glass door has disappeared If the specimen is damp when taken out of the oven allow it to stand before re-radiating as moisture continues to evaporate from the specimen for some time Care must be taken not to irradiate the specimens for too long

It should be noted that microwave treatment damages seeds and the cellular structure of the plants which may reduce the long-term value of the specimens

85

Alternative drying techniquesSilica gelother desiccants amp freeze drying Alternative methods of drying plant specimens have been

used for some time but are mostly restricted to special purpose collections The main alternatives are freeze-drying and drying in a desiccant powder such as desiccant silica gel In general these techniques are used where it is essential to preserve the shape of a delicate plant of organ of the plant such as the flower Freeze-drying has also been used to preserve the chemical composition of a plant as accurately as possible for later study

Disadvantages and special conservation problems of specimens dried in these manners are that they are particularly susceptible to damage The dried parts are fragile lack support and often catch on packing materials They must therefore be packed especially carefully and stored in small boxes or tubes with some appropriate packing material that does not snag and break small projections Acid-free tissue paper is often used Drying in desiccant silica gel crystals or powder can also have the disadvantage that it is difficult to remove all traces of the silica gel after drying

86

Special preservation and processing techniquesWet or spirit collections

Very fleshy or delicate structures including small algae and orchid flowers are best preserved in an air-tight glass or plastic jar with a liquid preservative rather than by drying The type of preservative used should be clearly labelled in the jar Such material is often referred to as a spirit collection or wet collection

Most material can be satisfactorily preserved in 70 ethyl alcohol (or 70 methylated spirit or denatured alcohol) with 30 water Colours will fade quickly in spirit however so it is a good idea to keep comprehensive notes and photographs

87

Small algae Microscopic algae are often collected in a jar and in the

water in which they were found If the algae are to be stored for more than 2-3 days a preservative needs to be used Traditionally this has been the extremely toxic formalin - a small amount can be added to the water to make a 5 final solution and the container labelled This must not be sent through the post or by courier

There are some other equally toxic options for example propylene phenoxytol but none should be sent through the post A safer option is to add sufficient concentrated alcohol or methylated spirits to the water containing the algae to make a final solution of 70 alcohol This treatment dilutes the algae making them difficult to find so if they can be concentrated somehow first (eg by filtering) they can be stored in much less liquid Another option is to fix the algae in formalin (or something similar) first and then prepare a microscope glass slide with a permanent water-soluble mounting medium

88

Mounting Mounting specimens prevents most fragile material from

fragmenting and prevents specimens becoming separated from their labels If the plant collection is a long-term project specimens should be mounted on sheets of archival (permanent) cardboard or paper with archival-quality fixing media These include stitching with cotton thread dental floss nickel-plated copper wire (for heavier specimens) narrow strips of archival paper linen tape or by using an archival adhesive such as methyl cellulose adhesive

One disadvantage of mounting specimens is that it can make parts of the specimen inaccessible for examination so it is essential that this be borne in mind during specimen arrangement and mounting For example easily reversible mounting media should be used specimens should be strapped to the sheet rather than glued all over and the specimen should be carefully arranged before it is attached so that it shows all features

89

Full-size herbarium mounting sheets are usually about 43 cm long x 28 cm wide The plant name and accompanying field notes should be transcribed on a permanent label stuck to one corner of the herbarium sheet (the bottom right-hand corner being the most common) or sometimes annotations may be written directly on the sheet or card

Small pieces of material which may have become separated from the specimen (eg seeds) can be placed in small plastic bags and pinned to the sheet

90

Long-term preservation and storage The long-term preservation of dry plant

specimens is largely dependent on protection from insect attack Specimens collected by Linnaeus in the eighteenth century and by Banks and Solander on the Endeavour voyage in 1788 are still excellently preserved

91

Pests and their control A range of pests attack dried plant material The

most common pests are insects and fungi though rodents and other large animals can cause damage in poor storage conditions Insects eat the material the paper surrounding the material and the adhesives and mounting media

Such insect pests range from psocids (book lice) which attack mainly the softer parts such as flowers and soft fruits to tobacco beetles and carpet beetles which can bore holes through the toughest of specimens Many insects are particularly sensitive to relative humidity levels and do not thrive at levels below 50

92

The most common and acceptable specimen treatments for insect control are Freezing Microwave Poisoning Insect deterrents Fungal pests

93

Storage

Dried and pressed plant specimens can be stored in cardboard or plastic boxes or tied in bundles in light-weight cardboard folders placed in pigeon holes

Alternatively they can be placed in protective plastic jackets and displayed in ring folders which is recommended if they are to be frequently handled such as for a reference collection

94

Filing

Specimens should be filed in a systematic order if a relatively permanent collection is being made The major groups ie ferns and fern allies cycads conifers dicotyledons and monocotyledons are best kept separately or according to some classification scheme such as that given in a flora or handbook

Similarly the genera within each family and the species within each genus may be filed alphabetically or following some such classification

95

Preservation of entire animals

Types of collection specimens of an entire animal For reference collections mammals can be prepared as a variety of specimens The condition of the specimen may determine possible ways to preserve it if for instance decomposition of the skin has loosened the hair of a carcass so much that it can easily be pulled out or removed by rubbing (ldquoslippingrdquo fur) it will be very difficult or impossible to produce a study skin or mounted specimen The most usual types of specimens (based on Nagorsen and Peterson 1980) are 1) entire fluid-preserved animals (for studying anatomy and histology fluid preservation may change the fur colour) 2) study skins with accompanying skulls partial skeletons (some bones remain in the skin) for studying pelage colour hair quality and moulting patterns 3) mounted skins with accompanying partial or entire skeleton (some bones may remain in the skin dependant on the method of preservation) or freeze-dried specimens 4) entire skeletons for instance for studying anatomy geographic variation or for age determination (entire skeletons are poorly represented in collections so Nagorsen and Peterson (1980) recommend preparation of at least one male and one female skeleton per species

96

Preservation of specimens in the field Formalin preservation Preservation in alcohol Preservation by cooling or freezing

97

Formalin preservation After weighing and measuring the animal and attaching an

adequate label very small specimens (up to 100 g) can be fixed whole by submerging them in 10 buffered formalin (tissue - formalin solution ratio of at least 1 12) the body cavity can be filled with formalin solution by injection until it is turgid and firm some formalin may also be injected under the skin into the body cavity larger muscles and organs If hypodermic needles are not available the body cavity can be opened ventrally by making a slit instead allowing the formalin to enter

Keeping the mouth open with a piece of wood or cotton may later allow examination of teeth Then the whole body can be immersed in formalin in the posture in which it is supposed to stay permanently because it will harden The ratio of formalin to carcass must be at least 12 to 1 to assure a good fixation Tissues can be left in buffered neutralized formalin for several months but formalin hardens specimens therefore after fixation longterm storage in alcohol may be better After preservation the carcass should therefore be washed in water and transferred into ethanol for permanent storage

Disadvantages for instance it discolours the fur after a longish immersion softens the bones and prevents further examination for microbiology

98

Preservation in alcohol

After weighing a whole animal can be preserved in a container of alcohol (70-90) Removal of the intestine prior to storage of the animal in alcohol is recommended

99

Preservation by cooling or freezing Removal of the skin with insulating fur

before cooling or freezing may help to cool the carcass down more quickly

Freezing is not recommended if histological examination is planned

100

THANK YOU

38

Wind and Water Speed- wind speed- anemometer or wind

gauges- water speed - time the movement of a

floating object over a measured distance

39

Salinity

- using a conductivity meter greater salinity has greater conductivity

Oxygen Level

- using an oxygen meter or chemical method (Winkler method)

40

Collecting MethodsCollecting all organisms within a habitat is normally

impractical and therefore small areas are selected Remember to return all material to its original position

after searching amp collecting sufficient specimens Some collecting apparatus for general use are listed

below

41

1 specimen tube

2 screwed-topped jars

3 polythene bags

4 forceps

5 paint brush

6 bulb pipette

7 pooter

42

8 widger 9 sieve 10 hand lens

11 enamel dish 12 beating tray 13 light traps

14 Tullgren funnel 15 Baermann funnel 16 mammal traps

17 pitfall traps 18 netting

43

Estimating Population Size

The exact methods used for estimation depend not only the nature of the habitat but also on the organisms involved

eg animals - population

plants - percentage cover

44

Using Quadrats

- By sampling an area using quadrats and counting the number of individuals within each quadrat it is possible to estimate the total number of individuals within the area

- confined to plants and sessile or very slow-moving animals

- fast-moving animals are disturbed and run away

45

Capture-recapture Techniques- useful for mobile animals which can be marked

- capture marked released randomly recaptured

and marked individuals recorded

no of marked individuals recaptured total no of individuals in 1st sample

-------------------------------------------- = ------------------------------------------

total no of individuals in 2nd sample estimated size of population

(the Lincoln Index)

46

Capture-recapture Techniques Factors affecting the accuracy of the estimation

deaths migration individuals become more liable to predation etc

Examples

- arthropods marked on their backs with non-toxic paint

- fish have tags attached to opercula - mammals have tags clipped to their ears

birds have their legs ringed

47

Capture-recapture Method Important tool for estimating density birth

rate and death rate for mobile animals Method

Collect a sample of individuals mark them and then release them

After a period collect more individuals from the wild and count the number that have marks

We assume that a sample if random will contain the same proportion of marked individuals as the population does

Estimate population density

48

Assumptions For All Capture-Recapture Studies Marking technique does not increase

mortality of marked animals Marked individuals are allowed to mix

with population Marking technique does not affect catch

probability Marks are not lost or overlooked No significant immigration or emigration No significant mortality or natality

49

Marked animals in second sample

Total caught in second sample

Marked animals in first sample

Total population size

=

520 N

16=

Peterson Method or Lincoln Index

N = 64N = (20)(16)5

50

Some Indices Used

Traps Number of Fecal

Pellets Vocalization

Frequency Pelt Records Catch per Unit

Fishing Effort

Number of Artifacts Questionnaires Cover Feeding Capacity Roadside Counts

51

Abundance Scales

The population size may be fairly accurately determined by making some form of frequency assessment

These are subjective and involve an experimenter making some estimate of the number of individuals in a given area or the cover of a particular species

This is especially useful where individuals are very numerous eg barnacles on a rocky shore or where it is difficult to distinguish individuals eg grass plants in a meadow

52

The assessments are usually made on an abundance scale of 5 categories

Abundance Common Frequent Occasional Rare

Barnacles exposed at low water

53

Environmental resistance are the factors which limit the growth of a particular population

eg predation disease availability of light food water oxygen and shelter the accumulation of toxic wastes and even the size of the population itself

54

Density-dependent Growth A population is a density-dependent when its size

(or density) affects its growth rate because of density-dependent factors such as food availability and toxic waste accumulation

Density-independent Growth In this type of growth a population increases until

some factor causes a sudden reduction in its size Its effect is the same regardless of the size of the

population eg temperature fires floods storms etc

55

Regulation of Population Size Fecundity is the reproductive capacity of individual

females of a species Birth rate or natality is used to measure fecundity Death rate or mortality is the number of individuals

of a species which die per unit time Immigration occurs when individuals join a

population from neighbouring ones Emigration occurs when individuals depart from a

population A cycle occurs when the size of a population

fluctuates on a regular basis

56

Ecological Sampling

57

Why Do We Sample Determine presence andor

abundance

Monitor population fluctuations

Assess lsquoecological damagersquo

Assess quality of habitat

Assess population responses

58

What Do We Sample

Physical Environment Temperature DO pH salinity clarity

flow sediment

Biotic Environment All living things

59

Physical Habitat Temperature

Mercury thermometer Electronic thermometer Long-term thermometers

Dissolved Oxygen Winkler method (titration) DO meter (electrode)

pH Litmus paper pH meter (electrode)

Salinity Salinity Meter YSI 550A DO Meter w12 cable

60

Water Clarity Secchi Disk

Disk is attached to a calibrated rope The disk is lowered into the water until the white parts can no longer be seen Secchi disk depth is then recorded and serves as the waters transparency index The clearer the water the greater the secchi disk depth

Secchi Disk

61

Current Velocity (flow) Floating-orange method

Put an orange (or something else that floats just below the water surface) and measure the time it takes it to float across a known distance

Odometer-type flow meter Number of revolutions the propeller

makes for a given time is calibrated to flow velocity

62

Sediment Sediment size is important to many

aquatic organisms Sieversquos are used to separate and

grade sediment samples Percent of each size grade can be

determined

63

Water Sample

Water and plankton from various depths can be collected

A trigger mechanism is used to close the sampler Sample is then brought back to the

surface

64

Small Mammals

Mouserat Traps Fatal

Pit Falls Bucket is placed in the ground Sometimes have lsquoleadsrsquo to the buckets

Live traps Havahart Sherman

Spot-light

Sherman trapHavahart trap

65

Birds Stick-under-the-box method Bird-trap

Works like a minnow trap Mist net

Captures birds in flight Rocket net

Uses a propellant to throw a net over birds

66

Terrestrial Insects

Sticky paper flies

Baited Traps Fire ants

Nets butterflies

Foggers Collect insects from tree canopies

67

Aquatic Insects Drift Net

Place net in flowing water Kick Net

lsquoKickrsquo sediment upstream from block net and the flow will wash them into the net

Wash bucket Serber or Hess Sampler

Stir up known area of sediment

Animals are collected by a catch net

Multi-plate Sampler Become colonized

68

Crawfish and Crab Traps

69

Fish Larvae Light Traps

Larvae are attracted to the light Ichthyoplankton nets

Can be towed at various depths Fish collect at the lsquocodrsquoend

70

Fish Lift net

Net is placed down and after a set amount of time it is quickly lifted

Pop-net Similar to a lift net but

floats are attached to a framed net

Operated by a trigger mechanism

Throw net A net attached to a heavy

frame is thrown and every thing inside is netted out Throw net

Pop-net

Lift net

71

Minnow trap

Usually use bait to attract small fish Light is used sometimes as an attractant

72

Fish Electrofishing

Electricity is put into the water Fish are temporarily stunned and usually

swim towards the electricity source Usually non-fatal but may cause some

damage

73

Fish Gill Net

Gill nets resemble tennis nets Fish can not swim completely through the

net and get caught Gill nets are size selective (based on mesh

size) Square Mesh

Bar mesh

Stretch mesh

74

Fish Trammel Net

Three panels two large mesh on the outside and a small mesh on the inside

Fish swim through the outer mesh pushes the small mesh through the other side and becomes entangled

75

Hoop nets (and other similar nets) can have bait or not

Fyke nets have leads to help guide fish to the net

76

Seine Seines are nets that are pulled

through shallow water to catch fish

77

Purse Seine Used to encircle entire schools of fish

Usually involves a spotter plane and a second boat

78

Trotline (longline) A series of baited drop lines

connected to a main line

Can be deployed by tying one end to the bank and tying the other end with a heavy weight

79

Shrimp (or fish) Trawl Net pulled behind

a boat along the bottom Either a beam or

otter boards keep the net open

80

Tagging Individuals Coded Wire Tags

Microwire that has a unique label

Magnetic wand detects the tag

Tag retention should be determined

T-Bar tags Can be individually

numbered External tag

PIT tags (Passive Integrated Transponders) Wand induces the tag to

transmit individual number is displayed

81

Other Tagging Methods

Toe clip Amphibian and reptile Clip of one or more toes

to identify individuals

Bird Band Place a metal band on a

bird leg Generally has

identification information

82

Preserving plant specimens Pressing and drying Long-term

preservation and storage

Alternative drying techniques

Special preservation and processing techniques

Mounting

83

Pressing and drying Techniques for pressing and drying specimens have been

established for many years There are minor variations in recommended methods but they are essentially the same worldwide

The best specimens are plants that are pressed as soon as possible after collection before wilting and shrivelling Most plants may be kept in sealed containers such as plastic bags for up to a day if it is inconvenient to press immediately However some plants show such rapid wilting particularly of the flowers that such delays are best avoided Flowers with a lot of nectar may go mouldy very quickly if excess nectar is not shaken off before pressing

Specimens are pressed flat and dried between sheets of absorbent blotters or semi-absorbent paper such as newspaper Papers with a glossy surface should be avoided because they are not absorbent enough to aid drying The plant should be carefully laid out between the drying sheets as their form at this stage largely determines their ultimate appearance The flowers should be spread out with the petals carefully arranged wilted leaves should be straightened and unnecessary shoots of excessively twiggy shrubs may be cut away

84

Microwave ovens Small numbers of specimens can be dried using a microwave

oven The technique recommended in the literature is to place the specimens between unprinted absorbent paper for example butchers paper not newspaper which is unsuitable because the chemicals present in the ink may cause a fire The specimens should be put in a special press which should be of a microwave-safe material (wood acrylic or polycarbonate sheeting eg plexiglass or perspex NO metal components) If such a press is not available sheets of cardboard can be placed above and below the specimens and then weighted down

Drying time depends on the power of your oven In most cases drying is accomplished by irradiating at maximum power for 1-2 minutes per specimen although it is often a case of trial and error It is best to process no more than 10-12 specimens of average thickness per batch Specimens are usually dried after the moisture that characteristically appears on the glass door has disappeared If the specimen is damp when taken out of the oven allow it to stand before re-radiating as moisture continues to evaporate from the specimen for some time Care must be taken not to irradiate the specimens for too long

It should be noted that microwave treatment damages seeds and the cellular structure of the plants which may reduce the long-term value of the specimens

85

Alternative drying techniquesSilica gelother desiccants amp freeze drying Alternative methods of drying plant specimens have been

used for some time but are mostly restricted to special purpose collections The main alternatives are freeze-drying and drying in a desiccant powder such as desiccant silica gel In general these techniques are used where it is essential to preserve the shape of a delicate plant of organ of the plant such as the flower Freeze-drying has also been used to preserve the chemical composition of a plant as accurately as possible for later study

Disadvantages and special conservation problems of specimens dried in these manners are that they are particularly susceptible to damage The dried parts are fragile lack support and often catch on packing materials They must therefore be packed especially carefully and stored in small boxes or tubes with some appropriate packing material that does not snag and break small projections Acid-free tissue paper is often used Drying in desiccant silica gel crystals or powder can also have the disadvantage that it is difficult to remove all traces of the silica gel after drying

86

Special preservation and processing techniquesWet or spirit collections

Very fleshy or delicate structures including small algae and orchid flowers are best preserved in an air-tight glass or plastic jar with a liquid preservative rather than by drying The type of preservative used should be clearly labelled in the jar Such material is often referred to as a spirit collection or wet collection

Most material can be satisfactorily preserved in 70 ethyl alcohol (or 70 methylated spirit or denatured alcohol) with 30 water Colours will fade quickly in spirit however so it is a good idea to keep comprehensive notes and photographs

87

Small algae Microscopic algae are often collected in a jar and in the

water in which they were found If the algae are to be stored for more than 2-3 days a preservative needs to be used Traditionally this has been the extremely toxic formalin - a small amount can be added to the water to make a 5 final solution and the container labelled This must not be sent through the post or by courier

There are some other equally toxic options for example propylene phenoxytol but none should be sent through the post A safer option is to add sufficient concentrated alcohol or methylated spirits to the water containing the algae to make a final solution of 70 alcohol This treatment dilutes the algae making them difficult to find so if they can be concentrated somehow first (eg by filtering) they can be stored in much less liquid Another option is to fix the algae in formalin (or something similar) first and then prepare a microscope glass slide with a permanent water-soluble mounting medium

88

Mounting Mounting specimens prevents most fragile material from

fragmenting and prevents specimens becoming separated from their labels If the plant collection is a long-term project specimens should be mounted on sheets of archival (permanent) cardboard or paper with archival-quality fixing media These include stitching with cotton thread dental floss nickel-plated copper wire (for heavier specimens) narrow strips of archival paper linen tape or by using an archival adhesive such as methyl cellulose adhesive

One disadvantage of mounting specimens is that it can make parts of the specimen inaccessible for examination so it is essential that this be borne in mind during specimen arrangement and mounting For example easily reversible mounting media should be used specimens should be strapped to the sheet rather than glued all over and the specimen should be carefully arranged before it is attached so that it shows all features

89

Full-size herbarium mounting sheets are usually about 43 cm long x 28 cm wide The plant name and accompanying field notes should be transcribed on a permanent label stuck to one corner of the herbarium sheet (the bottom right-hand corner being the most common) or sometimes annotations may be written directly on the sheet or card

Small pieces of material which may have become separated from the specimen (eg seeds) can be placed in small plastic bags and pinned to the sheet

90

Long-term preservation and storage The long-term preservation of dry plant

specimens is largely dependent on protection from insect attack Specimens collected by Linnaeus in the eighteenth century and by Banks and Solander on the Endeavour voyage in 1788 are still excellently preserved

91

Pests and their control A range of pests attack dried plant material The

most common pests are insects and fungi though rodents and other large animals can cause damage in poor storage conditions Insects eat the material the paper surrounding the material and the adhesives and mounting media

Such insect pests range from psocids (book lice) which attack mainly the softer parts such as flowers and soft fruits to tobacco beetles and carpet beetles which can bore holes through the toughest of specimens Many insects are particularly sensitive to relative humidity levels and do not thrive at levels below 50

92

The most common and acceptable specimen treatments for insect control are Freezing Microwave Poisoning Insect deterrents Fungal pests

93

Storage

Dried and pressed plant specimens can be stored in cardboard or plastic boxes or tied in bundles in light-weight cardboard folders placed in pigeon holes

Alternatively they can be placed in protective plastic jackets and displayed in ring folders which is recommended if they are to be frequently handled such as for a reference collection

94

Filing

Specimens should be filed in a systematic order if a relatively permanent collection is being made The major groups ie ferns and fern allies cycads conifers dicotyledons and monocotyledons are best kept separately or according to some classification scheme such as that given in a flora or handbook

Similarly the genera within each family and the species within each genus may be filed alphabetically or following some such classification

95

Preservation of entire animals

Types of collection specimens of an entire animal For reference collections mammals can be prepared as a variety of specimens The condition of the specimen may determine possible ways to preserve it if for instance decomposition of the skin has loosened the hair of a carcass so much that it can easily be pulled out or removed by rubbing (ldquoslippingrdquo fur) it will be very difficult or impossible to produce a study skin or mounted specimen The most usual types of specimens (based on Nagorsen and Peterson 1980) are 1) entire fluid-preserved animals (for studying anatomy and histology fluid preservation may change the fur colour) 2) study skins with accompanying skulls partial skeletons (some bones remain in the skin) for studying pelage colour hair quality and moulting patterns 3) mounted skins with accompanying partial or entire skeleton (some bones may remain in the skin dependant on the method of preservation) or freeze-dried specimens 4) entire skeletons for instance for studying anatomy geographic variation or for age determination (entire skeletons are poorly represented in collections so Nagorsen and Peterson (1980) recommend preparation of at least one male and one female skeleton per species

96

Preservation of specimens in the field Formalin preservation Preservation in alcohol Preservation by cooling or freezing

97

Formalin preservation After weighing and measuring the animal and attaching an

adequate label very small specimens (up to 100 g) can be fixed whole by submerging them in 10 buffered formalin (tissue - formalin solution ratio of at least 1 12) the body cavity can be filled with formalin solution by injection until it is turgid and firm some formalin may also be injected under the skin into the body cavity larger muscles and organs If hypodermic needles are not available the body cavity can be opened ventrally by making a slit instead allowing the formalin to enter

Keeping the mouth open with a piece of wood or cotton may later allow examination of teeth Then the whole body can be immersed in formalin in the posture in which it is supposed to stay permanently because it will harden The ratio of formalin to carcass must be at least 12 to 1 to assure a good fixation Tissues can be left in buffered neutralized formalin for several months but formalin hardens specimens therefore after fixation longterm storage in alcohol may be better After preservation the carcass should therefore be washed in water and transferred into ethanol for permanent storage

Disadvantages for instance it discolours the fur after a longish immersion softens the bones and prevents further examination for microbiology

98

Preservation in alcohol

After weighing a whole animal can be preserved in a container of alcohol (70-90) Removal of the intestine prior to storage of the animal in alcohol is recommended

99

Preservation by cooling or freezing Removal of the skin with insulating fur

before cooling or freezing may help to cool the carcass down more quickly

Freezing is not recommended if histological examination is planned

100

THANK YOU

39

Salinity

- using a conductivity meter greater salinity has greater conductivity

Oxygen Level

- using an oxygen meter or chemical method (Winkler method)

40

Collecting MethodsCollecting all organisms within a habitat is normally

impractical and therefore small areas are selected Remember to return all material to its original position

after searching amp collecting sufficient specimens Some collecting apparatus for general use are listed

below

41

1 specimen tube

2 screwed-topped jars

3 polythene bags

4 forceps

5 paint brush

6 bulb pipette

7 pooter

42

8 widger 9 sieve 10 hand lens

11 enamel dish 12 beating tray 13 light traps

14 Tullgren funnel 15 Baermann funnel 16 mammal traps

17 pitfall traps 18 netting

43

Estimating Population Size

The exact methods used for estimation depend not only the nature of the habitat but also on the organisms involved

eg animals - population

plants - percentage cover

44

Using Quadrats

- By sampling an area using quadrats and counting the number of individuals within each quadrat it is possible to estimate the total number of individuals within the area

- confined to plants and sessile or very slow-moving animals

- fast-moving animals are disturbed and run away

45

Capture-recapture Techniques- useful for mobile animals which can be marked

- capture marked released randomly recaptured

and marked individuals recorded

no of marked individuals recaptured total no of individuals in 1st sample

-------------------------------------------- = ------------------------------------------

total no of individuals in 2nd sample estimated size of population

(the Lincoln Index)

46

Capture-recapture Techniques Factors affecting the accuracy of the estimation

deaths migration individuals become more liable to predation etc

Examples

- arthropods marked on their backs with non-toxic paint

- fish have tags attached to opercula - mammals have tags clipped to their ears

birds have their legs ringed

47

Capture-recapture Method Important tool for estimating density birth

rate and death rate for mobile animals Method

Collect a sample of individuals mark them and then release them

After a period collect more individuals from the wild and count the number that have marks

We assume that a sample if random will contain the same proportion of marked individuals as the population does

Estimate population density

48

Assumptions For All Capture-Recapture Studies Marking technique does not increase

mortality of marked animals Marked individuals are allowed to mix

with population Marking technique does not affect catch

probability Marks are not lost or overlooked No significant immigration or emigration No significant mortality or natality

49

Marked animals in second sample

Total caught in second sample

Marked animals in first sample

Total population size

=

520 N

16=

Peterson Method or Lincoln Index

N = 64N = (20)(16)5

50

Some Indices Used

Traps Number of Fecal

Pellets Vocalization

Frequency Pelt Records Catch per Unit

Fishing Effort

Number of Artifacts Questionnaires Cover Feeding Capacity Roadside Counts

51

Abundance Scales

The population size may be fairly accurately determined by making some form of frequency assessment

These are subjective and involve an experimenter making some estimate of the number of individuals in a given area or the cover of a particular species

This is especially useful where individuals are very numerous eg barnacles on a rocky shore or where it is difficult to distinguish individuals eg grass plants in a meadow

52

The assessments are usually made on an abundance scale of 5 categories

Abundance Common Frequent Occasional Rare

Barnacles exposed at low water

53

Environmental resistance are the factors which limit the growth of a particular population

eg predation disease availability of light food water oxygen and shelter the accumulation of toxic wastes and even the size of the population itself

54

Density-dependent Growth A population is a density-dependent when its size

(or density) affects its growth rate because of density-dependent factors such as food availability and toxic waste accumulation

Density-independent Growth In this type of growth a population increases until

some factor causes a sudden reduction in its size Its effect is the same regardless of the size of the

population eg temperature fires floods storms etc

55

Regulation of Population Size Fecundity is the reproductive capacity of individual

females of a species Birth rate or natality is used to measure fecundity Death rate or mortality is the number of individuals

of a species which die per unit time Immigration occurs when individuals join a

population from neighbouring ones Emigration occurs when individuals depart from a

population A cycle occurs when the size of a population

fluctuates on a regular basis

56

Ecological Sampling

57

Why Do We Sample Determine presence andor

abundance

Monitor population fluctuations

Assess lsquoecological damagersquo

Assess quality of habitat

Assess population responses

58

What Do We Sample

Physical Environment Temperature DO pH salinity clarity

flow sediment

Biotic Environment All living things

59

Physical Habitat Temperature

Mercury thermometer Electronic thermometer Long-term thermometers

Dissolved Oxygen Winkler method (titration) DO meter (electrode)

pH Litmus paper pH meter (electrode)

Salinity Salinity Meter YSI 550A DO Meter w12 cable

60

Water Clarity Secchi Disk

Disk is attached to a calibrated rope The disk is lowered into the water until the white parts can no longer be seen Secchi disk depth is then recorded and serves as the waters transparency index The clearer the water the greater the secchi disk depth

Secchi Disk

61

Current Velocity (flow) Floating-orange method

Put an orange (or something else that floats just below the water surface) and measure the time it takes it to float across a known distance

Odometer-type flow meter Number of revolutions the propeller

makes for a given time is calibrated to flow velocity

62

Sediment Sediment size is important to many

aquatic organisms Sieversquos are used to separate and

grade sediment samples Percent of each size grade can be

determined

63

Water Sample

Water and plankton from various depths can be collected

A trigger mechanism is used to close the sampler Sample is then brought back to the

surface

64

Small Mammals

Mouserat Traps Fatal

Pit Falls Bucket is placed in the ground Sometimes have lsquoleadsrsquo to the buckets

Live traps Havahart Sherman

Spot-light

Sherman trapHavahart trap

65

Birds Stick-under-the-box method Bird-trap

Works like a minnow trap Mist net

Captures birds in flight Rocket net

Uses a propellant to throw a net over birds

66

Terrestrial Insects

Sticky paper flies

Baited Traps Fire ants

Nets butterflies

Foggers Collect insects from tree canopies

67

Aquatic Insects Drift Net

Place net in flowing water Kick Net

lsquoKickrsquo sediment upstream from block net and the flow will wash them into the net

Wash bucket Serber or Hess Sampler

Stir up known area of sediment

Animals are collected by a catch net

Multi-plate Sampler Become colonized

68

Crawfish and Crab Traps

69

Fish Larvae Light Traps

Larvae are attracted to the light Ichthyoplankton nets

Can be towed at various depths Fish collect at the lsquocodrsquoend

70

Fish Lift net

Net is placed down and after a set amount of time it is quickly lifted

Pop-net Similar to a lift net but

floats are attached to a framed net

Operated by a trigger mechanism

Throw net A net attached to a heavy

frame is thrown and every thing inside is netted out Throw net

Pop-net

Lift net

71

Minnow trap

Usually use bait to attract small fish Light is used sometimes as an attractant

72

Fish Electrofishing

Electricity is put into the water Fish are temporarily stunned and usually

swim towards the electricity source Usually non-fatal but may cause some

damage

73

Fish Gill Net

Gill nets resemble tennis nets Fish can not swim completely through the

net and get caught Gill nets are size selective (based on mesh

size) Square Mesh

Bar mesh

Stretch mesh

74

Fish Trammel Net

Three panels two large mesh on the outside and a small mesh on the inside

Fish swim through the outer mesh pushes the small mesh through the other side and becomes entangled

75

Hoop nets (and other similar nets) can have bait or not

Fyke nets have leads to help guide fish to the net

76

Seine Seines are nets that are pulled

through shallow water to catch fish

77

Purse Seine Used to encircle entire schools of fish

Usually involves a spotter plane and a second boat

78

Trotline (longline) A series of baited drop lines

connected to a main line

Can be deployed by tying one end to the bank and tying the other end with a heavy weight

79

Shrimp (or fish) Trawl Net pulled behind

a boat along the bottom Either a beam or

otter boards keep the net open

80

Tagging Individuals Coded Wire Tags

Microwire that has a unique label

Magnetic wand detects the tag

Tag retention should be determined

T-Bar tags Can be individually

numbered External tag

PIT tags (Passive Integrated Transponders) Wand induces the tag to

transmit individual number is displayed

81

Other Tagging Methods

Toe clip Amphibian and reptile Clip of one or more toes

to identify individuals

Bird Band Place a metal band on a

bird leg Generally has

identification information

82

Preserving plant specimens Pressing and drying Long-term

preservation and storage

Alternative drying techniques

Special preservation and processing techniques

Mounting

83

Pressing and drying Techniques for pressing and drying specimens have been

established for many years There are minor variations in recommended methods but they are essentially the same worldwide

The best specimens are plants that are pressed as soon as possible after collection before wilting and shrivelling Most plants may be kept in sealed containers such as plastic bags for up to a day if it is inconvenient to press immediately However some plants show such rapid wilting particularly of the flowers that such delays are best avoided Flowers with a lot of nectar may go mouldy very quickly if excess nectar is not shaken off before pressing

Specimens are pressed flat and dried between sheets of absorbent blotters or semi-absorbent paper such as newspaper Papers with a glossy surface should be avoided because they are not absorbent enough to aid drying The plant should be carefully laid out between the drying sheets as their form at this stage largely determines their ultimate appearance The flowers should be spread out with the petals carefully arranged wilted leaves should be straightened and unnecessary shoots of excessively twiggy shrubs may be cut away

84

Microwave ovens Small numbers of specimens can be dried using a microwave

oven The technique recommended in the literature is to place the specimens between unprinted absorbent paper for example butchers paper not newspaper which is unsuitable because the chemicals present in the ink may cause a fire The specimens should be put in a special press which should be of a microwave-safe material (wood acrylic or polycarbonate sheeting eg plexiglass or perspex NO metal components) If such a press is not available sheets of cardboard can be placed above and below the specimens and then weighted down

Drying time depends on the power of your oven In most cases drying is accomplished by irradiating at maximum power for 1-2 minutes per specimen although it is often a case of trial and error It is best to process no more than 10-12 specimens of average thickness per batch Specimens are usually dried after the moisture that characteristically appears on the glass door has disappeared If the specimen is damp when taken out of the oven allow it to stand before re-radiating as moisture continues to evaporate from the specimen for some time Care must be taken not to irradiate the specimens for too long

It should be noted that microwave treatment damages seeds and the cellular structure of the plants which may reduce the long-term value of the specimens

85

Alternative drying techniquesSilica gelother desiccants amp freeze drying Alternative methods of drying plant specimens have been

used for some time but are mostly restricted to special purpose collections The main alternatives are freeze-drying and drying in a desiccant powder such as desiccant silica gel In general these techniques are used where it is essential to preserve the shape of a delicate plant of organ of the plant such as the flower Freeze-drying has also been used to preserve the chemical composition of a plant as accurately as possible for later study

Disadvantages and special conservation problems of specimens dried in these manners are that they are particularly susceptible to damage The dried parts are fragile lack support and often catch on packing materials They must therefore be packed especially carefully and stored in small boxes or tubes with some appropriate packing material that does not snag and break small projections Acid-free tissue paper is often used Drying in desiccant silica gel crystals or powder can also have the disadvantage that it is difficult to remove all traces of the silica gel after drying

86

Special preservation and processing techniquesWet or spirit collections

Very fleshy or delicate structures including small algae and orchid flowers are best preserved in an air-tight glass or plastic jar with a liquid preservative rather than by drying The type of preservative used should be clearly labelled in the jar Such material is often referred to as a spirit collection or wet collection

Most material can be satisfactorily preserved in 70 ethyl alcohol (or 70 methylated spirit or denatured alcohol) with 30 water Colours will fade quickly in spirit however so it is a good idea to keep comprehensive notes and photographs

87

Small algae Microscopic algae are often collected in a jar and in the

water in which they were found If the algae are to be stored for more than 2-3 days a preservative needs to be used Traditionally this has been the extremely toxic formalin - a small amount can be added to the water to make a 5 final solution and the container labelled This must not be sent through the post or by courier

There are some other equally toxic options for example propylene phenoxytol but none should be sent through the post A safer option is to add sufficient concentrated alcohol or methylated spirits to the water containing the algae to make a final solution of 70 alcohol This treatment dilutes the algae making them difficult to find so if they can be concentrated somehow first (eg by filtering) they can be stored in much less liquid Another option is to fix the algae in formalin (or something similar) first and then prepare a microscope glass slide with a permanent water-soluble mounting medium

88

Mounting Mounting specimens prevents most fragile material from

fragmenting and prevents specimens becoming separated from their labels If the plant collection is a long-term project specimens should be mounted on sheets of archival (permanent) cardboard or paper with archival-quality fixing media These include stitching with cotton thread dental floss nickel-plated copper wire (for heavier specimens) narrow strips of archival paper linen tape or by using an archival adhesive such as methyl cellulose adhesive

One disadvantage of mounting specimens is that it can make parts of the specimen inaccessible for examination so it is essential that this be borne in mind during specimen arrangement and mounting For example easily reversible mounting media should be used specimens should be strapped to the sheet rather than glued all over and the specimen should be carefully arranged before it is attached so that it shows all features

89

Full-size herbarium mounting sheets are usually about 43 cm long x 28 cm wide The plant name and accompanying field notes should be transcribed on a permanent label stuck to one corner of the herbarium sheet (the bottom right-hand corner being the most common) or sometimes annotations may be written directly on the sheet or card

Small pieces of material which may have become separated from the specimen (eg seeds) can be placed in small plastic bags and pinned to the sheet

90

Long-term preservation and storage The long-term preservation of dry plant

specimens is largely dependent on protection from insect attack Specimens collected by Linnaeus in the eighteenth century and by Banks and Solander on the Endeavour voyage in 1788 are still excellently preserved

91

Pests and their control A range of pests attack dried plant material The

most common pests are insects and fungi though rodents and other large animals can cause damage in poor storage conditions Insects eat the material the paper surrounding the material and the adhesives and mounting media

Such insect pests range from psocids (book lice) which attack mainly the softer parts such as flowers and soft fruits to tobacco beetles and carpet beetles which can bore holes through the toughest of specimens Many insects are particularly sensitive to relative humidity levels and do not thrive at levels below 50

92

The most common and acceptable specimen treatments for insect control are Freezing Microwave Poisoning Insect deterrents Fungal pests

93

Storage

Dried and pressed plant specimens can be stored in cardboard or plastic boxes or tied in bundles in light-weight cardboard folders placed in pigeon holes

Alternatively they can be placed in protective plastic jackets and displayed in ring folders which is recommended if they are to be frequently handled such as for a reference collection

94

Filing

Specimens should be filed in a systematic order if a relatively permanent collection is being made The major groups ie ferns and fern allies cycads conifers dicotyledons and monocotyledons are best kept separately or according to some classification scheme such as that given in a flora or handbook

Similarly the genera within each family and the species within each genus may be filed alphabetically or following some such classification

95

Preservation of entire animals

Types of collection specimens of an entire animal For reference collections mammals can be prepared as a variety of specimens The condition of the specimen may determine possible ways to preserve it if for instance decomposition of the skin has loosened the hair of a carcass so much that it can easily be pulled out or removed by rubbing (ldquoslippingrdquo fur) it will be very difficult or impossible to produce a study skin or mounted specimen The most usual types of specimens (based on Nagorsen and Peterson 1980) are 1) entire fluid-preserved animals (for studying anatomy and histology fluid preservation may change the fur colour) 2) study skins with accompanying skulls partial skeletons (some bones remain in the skin) for studying pelage colour hair quality and moulting patterns 3) mounted skins with accompanying partial or entire skeleton (some bones may remain in the skin dependant on the method of preservation) or freeze-dried specimens 4) entire skeletons for instance for studying anatomy geographic variation or for age determination (entire skeletons are poorly represented in collections so Nagorsen and Peterson (1980) recommend preparation of at least one male and one female skeleton per species

96

Preservation of specimens in the field Formalin preservation Preservation in alcohol Preservation by cooling or freezing

97

Formalin preservation After weighing and measuring the animal and attaching an

adequate label very small specimens (up to 100 g) can be fixed whole by submerging them in 10 buffered formalin (tissue - formalin solution ratio of at least 1 12) the body cavity can be filled with formalin solution by injection until it is turgid and firm some formalin may also be injected under the skin into the body cavity larger muscles and organs If hypodermic needles are not available the body cavity can be opened ventrally by making a slit instead allowing the formalin to enter

Keeping the mouth open with a piece of wood or cotton may later allow examination of teeth Then the whole body can be immersed in formalin in the posture in which it is supposed to stay permanently because it will harden The ratio of formalin to carcass must be at least 12 to 1 to assure a good fixation Tissues can be left in buffered neutralized formalin for several months but formalin hardens specimens therefore after fixation longterm storage in alcohol may be better After preservation the carcass should therefore be washed in water and transferred into ethanol for permanent storage

Disadvantages for instance it discolours the fur after a longish immersion softens the bones and prevents further examination for microbiology

98

Preservation in alcohol

After weighing a whole animal can be preserved in a container of alcohol (70-90) Removal of the intestine prior to storage of the animal in alcohol is recommended

99

Preservation by cooling or freezing Removal of the skin with insulating fur

before cooling or freezing may help to cool the carcass down more quickly

Freezing is not recommended if histological examination is planned

100

THANK YOU

40

Collecting MethodsCollecting all organisms within a habitat is normally

impractical and therefore small areas are selected Remember to return all material to its original position

after searching amp collecting sufficient specimens Some collecting apparatus for general use are listed

below

41

1 specimen tube

2 screwed-topped jars

3 polythene bags

4 forceps

5 paint brush

6 bulb pipette

7 pooter

42

8 widger 9 sieve 10 hand lens

11 enamel dish 12 beating tray 13 light traps

14 Tullgren funnel 15 Baermann funnel 16 mammal traps

17 pitfall traps 18 netting

43

Estimating Population Size

The exact methods used for estimation depend not only the nature of the habitat but also on the organisms involved

eg animals - population

plants - percentage cover

44

Using Quadrats

- By sampling an area using quadrats and counting the number of individuals within each quadrat it is possible to estimate the total number of individuals within the area

- confined to plants and sessile or very slow-moving animals

- fast-moving animals are disturbed and run away

45

Capture-recapture Techniques- useful for mobile animals which can be marked

- capture marked released randomly recaptured

and marked individuals recorded

no of marked individuals recaptured total no of individuals in 1st sample

-------------------------------------------- = ------------------------------------------

total no of individuals in 2nd sample estimated size of population

(the Lincoln Index)

46

Capture-recapture Techniques Factors affecting the accuracy of the estimation

deaths migration individuals become more liable to predation etc

Examples

- arthropods marked on their backs with non-toxic paint

- fish have tags attached to opercula - mammals have tags clipped to their ears

birds have their legs ringed

47

Capture-recapture Method Important tool for estimating density birth

rate and death rate for mobile animals Method

Collect a sample of individuals mark them and then release them

After a period collect more individuals from the wild and count the number that have marks

We assume that a sample if random will contain the same proportion of marked individuals as the population does

Estimate population density

48

Assumptions For All Capture-Recapture Studies Marking technique does not increase

mortality of marked animals Marked individuals are allowed to mix

with population Marking technique does not affect catch

probability Marks are not lost or overlooked No significant immigration or emigration No significant mortality or natality

49

Marked animals in second sample

Total caught in second sample

Marked animals in first sample

Total population size

=

520 N

16=

Peterson Method or Lincoln Index

N = 64N = (20)(16)5

50

Some Indices Used

Traps Number of Fecal

Pellets Vocalization

Frequency Pelt Records Catch per Unit

Fishing Effort

Number of Artifacts Questionnaires Cover Feeding Capacity Roadside Counts

51

Abundance Scales

The population size may be fairly accurately determined by making some form of frequency assessment

These are subjective and involve an experimenter making some estimate of the number of individuals in a given area or the cover of a particular species

This is especially useful where individuals are very numerous eg barnacles on a rocky shore or where it is difficult to distinguish individuals eg grass plants in a meadow

52

The assessments are usually made on an abundance scale of 5 categories

Abundance Common Frequent Occasional Rare

Barnacles exposed at low water

53

Environmental resistance are the factors which limit the growth of a particular population

eg predation disease availability of light food water oxygen and shelter the accumulation of toxic wastes and even the size of the population itself

54

Density-dependent Growth A population is a density-dependent when its size

(or density) affects its growth rate because of density-dependent factors such as food availability and toxic waste accumulation

Density-independent Growth In this type of growth a population increases until

some factor causes a sudden reduction in its size Its effect is the same regardless of the size of the

population eg temperature fires floods storms etc

55

Regulation of Population Size Fecundity is the reproductive capacity of individual

females of a species Birth rate or natality is used to measure fecundity Death rate or mortality is the number of individuals

of a species which die per unit time Immigration occurs when individuals join a

population from neighbouring ones Emigration occurs when individuals depart from a

population A cycle occurs when the size of a population

fluctuates on a regular basis

56

Ecological Sampling

57

Why Do We Sample Determine presence andor

abundance

Monitor population fluctuations

Assess lsquoecological damagersquo

Assess quality of habitat

Assess population responses

58

What Do We Sample

Physical Environment Temperature DO pH salinity clarity

flow sediment

Biotic Environment All living things

59

Physical Habitat Temperature

Mercury thermometer Electronic thermometer Long-term thermometers

Dissolved Oxygen Winkler method (titration) DO meter (electrode)

pH Litmus paper pH meter (electrode)

Salinity Salinity Meter YSI 550A DO Meter w12 cable

60

Water Clarity Secchi Disk

Disk is attached to a calibrated rope The disk is lowered into the water until the white parts can no longer be seen Secchi disk depth is then recorded and serves as the waters transparency index The clearer the water the greater the secchi disk depth

Secchi Disk

61

Current Velocity (flow) Floating-orange method

Put an orange (or something else that floats just below the water surface) and measure the time it takes it to float across a known distance

Odometer-type flow meter Number of revolutions the propeller

makes for a given time is calibrated to flow velocity

62

Sediment Sediment size is important to many

aquatic organisms Sieversquos are used to separate and

grade sediment samples Percent of each size grade can be

determined

63

Water Sample

Water and plankton from various depths can be collected

A trigger mechanism is used to close the sampler Sample is then brought back to the

surface

64

Small Mammals

Mouserat Traps Fatal

Pit Falls Bucket is placed in the ground Sometimes have lsquoleadsrsquo to the buckets

Live traps Havahart Sherman

Spot-light

Sherman trapHavahart trap

65

Birds Stick-under-the-box method Bird-trap

Works like a minnow trap Mist net

Captures birds in flight Rocket net

Uses a propellant to throw a net over birds

66

Terrestrial Insects

Sticky paper flies

Baited Traps Fire ants

Nets butterflies

Foggers Collect insects from tree canopies

67

Aquatic Insects Drift Net

Place net in flowing water Kick Net

lsquoKickrsquo sediment upstream from block net and the flow will wash them into the net

Wash bucket Serber or Hess Sampler

Stir up known area of sediment

Animals are collected by a catch net

Multi-plate Sampler Become colonized

68

Crawfish and Crab Traps

69

Fish Larvae Light Traps

Larvae are attracted to the light Ichthyoplankton nets

Can be towed at various depths Fish collect at the lsquocodrsquoend

70

Fish Lift net

Net is placed down and after a set amount of time it is quickly lifted

Pop-net Similar to a lift net but

floats are attached to a framed net

Operated by a trigger mechanism

Throw net A net attached to a heavy

frame is thrown and every thing inside is netted out Throw net

Pop-net

Lift net

71

Minnow trap

Usually use bait to attract small fish Light is used sometimes as an attractant

72

Fish Electrofishing

Electricity is put into the water Fish are temporarily stunned and usually

swim towards the electricity source Usually non-fatal but may cause some

damage

73

Fish Gill Net

Gill nets resemble tennis nets Fish can not swim completely through the

net and get caught Gill nets are size selective (based on mesh

size) Square Mesh

Bar mesh

Stretch mesh

74

Fish Trammel Net

Three panels two large mesh on the outside and a small mesh on the inside

Fish swim through the outer mesh pushes the small mesh through the other side and becomes entangled

75

Hoop nets (and other similar nets) can have bait or not

Fyke nets have leads to help guide fish to the net

76

Seine Seines are nets that are pulled

through shallow water to catch fish

77

Purse Seine Used to encircle entire schools of fish

Usually involves a spotter plane and a second boat

78

Trotline (longline) A series of baited drop lines

connected to a main line

Can be deployed by tying one end to the bank and tying the other end with a heavy weight

79

Shrimp (or fish) Trawl Net pulled behind

a boat along the bottom Either a beam or

otter boards keep the net open

80

Tagging Individuals Coded Wire Tags

Microwire that has a unique label

Magnetic wand detects the tag

Tag retention should be determined

T-Bar tags Can be individually

numbered External tag

PIT tags (Passive Integrated Transponders) Wand induces the tag to

transmit individual number is displayed

81

Other Tagging Methods

Toe clip Amphibian and reptile Clip of one or more toes

to identify individuals

Bird Band Place a metal band on a

bird leg Generally has

identification information

82

Preserving plant specimens Pressing and drying Long-term

preservation and storage

Alternative drying techniques

Special preservation and processing techniques

Mounting

83

Pressing and drying Techniques for pressing and drying specimens have been

established for many years There are minor variations in recommended methods but they are essentially the same worldwide

The best specimens are plants that are pressed as soon as possible after collection before wilting and shrivelling Most plants may be kept in sealed containers such as plastic bags for up to a day if it is inconvenient to press immediately However some plants show such rapid wilting particularly of the flowers that such delays are best avoided Flowers with a lot of nectar may go mouldy very quickly if excess nectar is not shaken off before pressing

Specimens are pressed flat and dried between sheets of absorbent blotters or semi-absorbent paper such as newspaper Papers with a glossy surface should be avoided because they are not absorbent enough to aid drying The plant should be carefully laid out between the drying sheets as their form at this stage largely determines their ultimate appearance The flowers should be spread out with the petals carefully arranged wilted leaves should be straightened and unnecessary shoots of excessively twiggy shrubs may be cut away

84

Microwave ovens Small numbers of specimens can be dried using a microwave

oven The technique recommended in the literature is to place the specimens between unprinted absorbent paper for example butchers paper not newspaper which is unsuitable because the chemicals present in the ink may cause a fire The specimens should be put in a special press which should be of a microwave-safe material (wood acrylic or polycarbonate sheeting eg plexiglass or perspex NO metal components) If such a press is not available sheets of cardboard can be placed above and below the specimens and then weighted down

Drying time depends on the power of your oven In most cases drying is accomplished by irradiating at maximum power for 1-2 minutes per specimen although it is often a case of trial and error It is best to process no more than 10-12 specimens of average thickness per batch Specimens are usually dried after the moisture that characteristically appears on the glass door has disappeared If the specimen is damp when taken out of the oven allow it to stand before re-radiating as moisture continues to evaporate from the specimen for some time Care must be taken not to irradiate the specimens for too long

It should be noted that microwave treatment damages seeds and the cellular structure of the plants which may reduce the long-term value of the specimens

85

Alternative drying techniquesSilica gelother desiccants amp freeze drying Alternative methods of drying plant specimens have been

used for some time but are mostly restricted to special purpose collections The main alternatives are freeze-drying and drying in a desiccant powder such as desiccant silica gel In general these techniques are used where it is essential to preserve the shape of a delicate plant of organ of the plant such as the flower Freeze-drying has also been used to preserve the chemical composition of a plant as accurately as possible for later study

Disadvantages and special conservation problems of specimens dried in these manners are that they are particularly susceptible to damage The dried parts are fragile lack support and often catch on packing materials They must therefore be packed especially carefully and stored in small boxes or tubes with some appropriate packing material that does not snag and break small projections Acid-free tissue paper is often used Drying in desiccant silica gel crystals or powder can also have the disadvantage that it is difficult to remove all traces of the silica gel after drying

86

Special preservation and processing techniquesWet or spirit collections

Very fleshy or delicate structures including small algae and orchid flowers are best preserved in an air-tight glass or plastic jar with a liquid preservative rather than by drying The type of preservative used should be clearly labelled in the jar Such material is often referred to as a spirit collection or wet collection

Most material can be satisfactorily preserved in 70 ethyl alcohol (or 70 methylated spirit or denatured alcohol) with 30 water Colours will fade quickly in spirit however so it is a good idea to keep comprehensive notes and photographs

87

Small algae Microscopic algae are often collected in a jar and in the

water in which they were found If the algae are to be stored for more than 2-3 days a preservative needs to be used Traditionally this has been the extremely toxic formalin - a small amount can be added to the water to make a 5 final solution and the container labelled This must not be sent through the post or by courier

There are some other equally toxic options for example propylene phenoxytol but none should be sent through the post A safer option is to add sufficient concentrated alcohol or methylated spirits to the water containing the algae to make a final solution of 70 alcohol This treatment dilutes the algae making them difficult to find so if they can be concentrated somehow first (eg by filtering) they can be stored in much less liquid Another option is to fix the algae in formalin (or something similar) first and then prepare a microscope glass slide with a permanent water-soluble mounting medium

88

Mounting Mounting specimens prevents most fragile material from

fragmenting and prevents specimens becoming separated from their labels If the plant collection is a long-term project specimens should be mounted on sheets of archival (permanent) cardboard or paper with archival-quality fixing media These include stitching with cotton thread dental floss nickel-plated copper wire (for heavier specimens) narrow strips of archival paper linen tape or by using an archival adhesive such as methyl cellulose adhesive

One disadvantage of mounting specimens is that it can make parts of the specimen inaccessible for examination so it is essential that this be borne in mind during specimen arrangement and mounting For example easily reversible mounting media should be used specimens should be strapped to the sheet rather than glued all over and the specimen should be carefully arranged before it is attached so that it shows all features

89

Full-size herbarium mounting sheets are usually about 43 cm long x 28 cm wide The plant name and accompanying field notes should be transcribed on a permanent label stuck to one corner of the herbarium sheet (the bottom right-hand corner being the most common) or sometimes annotations may be written directly on the sheet or card

Small pieces of material which may have become separated from the specimen (eg seeds) can be placed in small plastic bags and pinned to the sheet

90

Long-term preservation and storage The long-term preservation of dry plant

specimens is largely dependent on protection from insect attack Specimens collected by Linnaeus in the eighteenth century and by Banks and Solander on the Endeavour voyage in 1788 are still excellently preserved

91

Pests and their control A range of pests attack dried plant material The

most common pests are insects and fungi though rodents and other large animals can cause damage in poor storage conditions Insects eat the material the paper surrounding the material and the adhesives and mounting media

Such insect pests range from psocids (book lice) which attack mainly the softer parts such as flowers and soft fruits to tobacco beetles and carpet beetles which can bore holes through the toughest of specimens Many insects are particularly sensitive to relative humidity levels and do not thrive at levels below 50

92

The most common and acceptable specimen treatments for insect control are Freezing Microwave Poisoning Insect deterrents Fungal pests

93

Storage

Dried and pressed plant specimens can be stored in cardboard or plastic boxes or tied in bundles in light-weight cardboard folders placed in pigeon holes

Alternatively they can be placed in protective plastic jackets and displayed in ring folders which is recommended if they are to be frequently handled such as for a reference collection

94

Filing

Specimens should be filed in a systematic order if a relatively permanent collection is being made The major groups ie ferns and fern allies cycads conifers dicotyledons and monocotyledons are best kept separately or according to some classification scheme such as that given in a flora or handbook

Similarly the genera within each family and the species within each genus may be filed alphabetically or following some such classification

95

Preservation of entire animals

Types of collection specimens of an entire animal For reference collections mammals can be prepared as a variety of specimens The condition of the specimen may determine possible ways to preserve it if for instance decomposition of the skin has loosened the hair of a carcass so much that it can easily be pulled out or removed by rubbing (ldquoslippingrdquo fur) it will be very difficult or impossible to produce a study skin or mounted specimen The most usual types of specimens (based on Nagorsen and Peterson 1980) are 1) entire fluid-preserved animals (for studying anatomy and histology fluid preservation may change the fur colour) 2) study skins with accompanying skulls partial skeletons (some bones remain in the skin) for studying pelage colour hair quality and moulting patterns 3) mounted skins with accompanying partial or entire skeleton (some bones may remain in the skin dependant on the method of preservation) or freeze-dried specimens 4) entire skeletons for instance for studying anatomy geographic variation or for age determination (entire skeletons are poorly represented in collections so Nagorsen and Peterson (1980) recommend preparation of at least one male and one female skeleton per species

96

Preservation of specimens in the field Formalin preservation Preservation in alcohol Preservation by cooling or freezing

97

Formalin preservation After weighing and measuring the animal and attaching an

adequate label very small specimens (up to 100 g) can be fixed whole by submerging them in 10 buffered formalin (tissue - formalin solution ratio of at least 1 12) the body cavity can be filled with formalin solution by injection until it is turgid and firm some formalin may also be injected under the skin into the body cavity larger muscles and organs If hypodermic needles are not available the body cavity can be opened ventrally by making a slit instead allowing the formalin to enter

Keeping the mouth open with a piece of wood or cotton may later allow examination of teeth Then the whole body can be immersed in formalin in the posture in which it is supposed to stay permanently because it will harden The ratio of formalin to carcass must be at least 12 to 1 to assure a good fixation Tissues can be left in buffered neutralized formalin for several months but formalin hardens specimens therefore after fixation longterm storage in alcohol may be better After preservation the carcass should therefore be washed in water and transferred into ethanol for permanent storage

Disadvantages for instance it discolours the fur after a longish immersion softens the bones and prevents further examination for microbiology

98

Preservation in alcohol

After weighing a whole animal can be preserved in a container of alcohol (70-90) Removal of the intestine prior to storage of the animal in alcohol is recommended

99

Preservation by cooling or freezing Removal of the skin with insulating fur

before cooling or freezing may help to cool the carcass down more quickly

Freezing is not recommended if histological examination is planned

100

THANK YOU

41

1 specimen tube

2 screwed-topped jars

3 polythene bags

4 forceps

5 paint brush

6 bulb pipette

7 pooter

42

8 widger 9 sieve 10 hand lens

11 enamel dish 12 beating tray 13 light traps

14 Tullgren funnel 15 Baermann funnel 16 mammal traps

17 pitfall traps 18 netting

43

Estimating Population Size

The exact methods used for estimation depend not only the nature of the habitat but also on the organisms involved

eg animals - population

plants - percentage cover

44

Using Quadrats

- By sampling an area using quadrats and counting the number of individuals within each quadrat it is possible to estimate the total number of individuals within the area

- confined to plants and sessile or very slow-moving animals

- fast-moving animals are disturbed and run away

45

Capture-recapture Techniques- useful for mobile animals which can be marked

- capture marked released randomly recaptured

and marked individuals recorded

no of marked individuals recaptured total no of individuals in 1st sample

-------------------------------------------- = ------------------------------------------

total no of individuals in 2nd sample estimated size of population

(the Lincoln Index)

46

Capture-recapture Techniques Factors affecting the accuracy of the estimation

deaths migration individuals become more liable to predation etc

Examples

- arthropods marked on their backs with non-toxic paint

- fish have tags attached to opercula - mammals have tags clipped to their ears

birds have their legs ringed

47

Capture-recapture Method Important tool for estimating density birth

rate and death rate for mobile animals Method

Collect a sample of individuals mark them and then release them

After a period collect more individuals from the wild and count the number that have marks

We assume that a sample if random will contain the same proportion of marked individuals as the population does

Estimate population density

48

Assumptions For All Capture-Recapture Studies Marking technique does not increase

mortality of marked animals Marked individuals are allowed to mix

with population Marking technique does not affect catch

probability Marks are not lost or overlooked No significant immigration or emigration No significant mortality or natality

49

Marked animals in second sample

Total caught in second sample

Marked animals in first sample

Total population size

=

520 N

16=

Peterson Method or Lincoln Index

N = 64N = (20)(16)5

50

Some Indices Used

Traps Number of Fecal

Pellets Vocalization

Frequency Pelt Records Catch per Unit

Fishing Effort

Number of Artifacts Questionnaires Cover Feeding Capacity Roadside Counts

51

Abundance Scales

The population size may be fairly accurately determined by making some form of frequency assessment

These are subjective and involve an experimenter making some estimate of the number of individuals in a given area or the cover of a particular species

This is especially useful where individuals are very numerous eg barnacles on a rocky shore or where it is difficult to distinguish individuals eg grass plants in a meadow

52

The assessments are usually made on an abundance scale of 5 categories

Abundance Common Frequent Occasional Rare

Barnacles exposed at low water

53

Environmental resistance are the factors which limit the growth of a particular population

eg predation disease availability of light food water oxygen and shelter the accumulation of toxic wastes and even the size of the population itself

54

Density-dependent Growth A population is a density-dependent when its size

(or density) affects its growth rate because of density-dependent factors such as food availability and toxic waste accumulation

Density-independent Growth In this type of growth a population increases until

some factor causes a sudden reduction in its size Its effect is the same regardless of the size of the

population eg temperature fires floods storms etc

55

Regulation of Population Size Fecundity is the reproductive capacity of individual

females of a species Birth rate or natality is used to measure fecundity Death rate or mortality is the number of individuals

of a species which die per unit time Immigration occurs when individuals join a

population from neighbouring ones Emigration occurs when individuals depart from a

population A cycle occurs when the size of a population

fluctuates on a regular basis

56

Ecological Sampling

57

Why Do We Sample Determine presence andor

abundance

Monitor population fluctuations

Assess lsquoecological damagersquo

Assess quality of habitat

Assess population responses

58

What Do We Sample

Physical Environment Temperature DO pH salinity clarity

flow sediment

Biotic Environment All living things

59

Physical Habitat Temperature

Mercury thermometer Electronic thermometer Long-term thermometers

Dissolved Oxygen Winkler method (titration) DO meter (electrode)

pH Litmus paper pH meter (electrode)

Salinity Salinity Meter YSI 550A DO Meter w12 cable

60

Water Clarity Secchi Disk

Disk is attached to a calibrated rope The disk is lowered into the water until the white parts can no longer be seen Secchi disk depth is then recorded and serves as the waters transparency index The clearer the water the greater the secchi disk depth

Secchi Disk

61

Current Velocity (flow) Floating-orange method

Put an orange (or something else that floats just below the water surface) and measure the time it takes it to float across a known distance

Odometer-type flow meter Number of revolutions the propeller

makes for a given time is calibrated to flow velocity

62

Sediment Sediment size is important to many

aquatic organisms Sieversquos are used to separate and

grade sediment samples Percent of each size grade can be

determined

63

Water Sample

Water and plankton from various depths can be collected

A trigger mechanism is used to close the sampler Sample is then brought back to the

surface

64

Small Mammals

Mouserat Traps Fatal

Pit Falls Bucket is placed in the ground Sometimes have lsquoleadsrsquo to the buckets

Live traps Havahart Sherman

Spot-light

Sherman trapHavahart trap

65

Birds Stick-under-the-box method Bird-trap

Works like a minnow trap Mist net

Captures birds in flight Rocket net

Uses a propellant to throw a net over birds

66

Terrestrial Insects

Sticky paper flies

Baited Traps Fire ants

Nets butterflies

Foggers Collect insects from tree canopies

67

Aquatic Insects Drift Net

Place net in flowing water Kick Net

lsquoKickrsquo sediment upstream from block net and the flow will wash them into the net

Wash bucket Serber or Hess Sampler

Stir up known area of sediment

Animals are collected by a catch net

Multi-plate Sampler Become colonized

68

Crawfish and Crab Traps

69

Fish Larvae Light Traps

Larvae are attracted to the light Ichthyoplankton nets

Can be towed at various depths Fish collect at the lsquocodrsquoend

70

Fish Lift net

Net is placed down and after a set amount of time it is quickly lifted

Pop-net Similar to a lift net but

floats are attached to a framed net

Operated by a trigger mechanism

Throw net A net attached to a heavy

frame is thrown and every thing inside is netted out Throw net

Pop-net

Lift net

71

Minnow trap

Usually use bait to attract small fish Light is used sometimes as an attractant

72

Fish Electrofishing

Electricity is put into the water Fish are temporarily stunned and usually

swim towards the electricity source Usually non-fatal but may cause some

damage

73

Fish Gill Net

Gill nets resemble tennis nets Fish can not swim completely through the

net and get caught Gill nets are size selective (based on mesh

size) Square Mesh

Bar mesh

Stretch mesh

74

Fish Trammel Net

Three panels two large mesh on the outside and a small mesh on the inside

Fish swim through the outer mesh pushes the small mesh through the other side and becomes entangled

75

Hoop nets (and other similar nets) can have bait or not

Fyke nets have leads to help guide fish to the net

76

Seine Seines are nets that are pulled

through shallow water to catch fish

77

Purse Seine Used to encircle entire schools of fish

Usually involves a spotter plane and a second boat

78

Trotline (longline) A series of baited drop lines

connected to a main line

Can be deployed by tying one end to the bank and tying the other end with a heavy weight

79

Shrimp (or fish) Trawl Net pulled behind

a boat along the bottom Either a beam or

otter boards keep the net open

80

Tagging Individuals Coded Wire Tags

Microwire that has a unique label

Magnetic wand detects the tag

Tag retention should be determined

T-Bar tags Can be individually

numbered External tag

PIT tags (Passive Integrated Transponders) Wand induces the tag to

transmit individual number is displayed

81

Other Tagging Methods

Toe clip Amphibian and reptile Clip of one or more toes

to identify individuals

Bird Band Place a metal band on a

bird leg Generally has

identification information

82

Preserving plant specimens Pressing and drying Long-term

preservation and storage

Alternative drying techniques

Special preservation and processing techniques

Mounting

83

Pressing and drying Techniques for pressing and drying specimens have been

established for many years There are minor variations in recommended methods but they are essentially the same worldwide

The best specimens are plants that are pressed as soon as possible after collection before wilting and shrivelling Most plants may be kept in sealed containers such as plastic bags for up to a day if it is inconvenient to press immediately However some plants show such rapid wilting particularly of the flowers that such delays are best avoided Flowers with a lot of nectar may go mouldy very quickly if excess nectar is not shaken off before pressing

Specimens are pressed flat and dried between sheets of absorbent blotters or semi-absorbent paper such as newspaper Papers with a glossy surface should be avoided because they are not absorbent enough to aid drying The plant should be carefully laid out between the drying sheets as their form at this stage largely determines their ultimate appearance The flowers should be spread out with the petals carefully arranged wilted leaves should be straightened and unnecessary shoots of excessively twiggy shrubs may be cut away

84

Microwave ovens Small numbers of specimens can be dried using a microwave

oven The technique recommended in the literature is to place the specimens between unprinted absorbent paper for example butchers paper not newspaper which is unsuitable because the chemicals present in the ink may cause a fire The specimens should be put in a special press which should be of a microwave-safe material (wood acrylic or polycarbonate sheeting eg plexiglass or perspex NO metal components) If such a press is not available sheets of cardboard can be placed above and below the specimens and then weighted down

Drying time depends on the power of your oven In most cases drying is accomplished by irradiating at maximum power for 1-2 minutes per specimen although it is often a case of trial and error It is best to process no more than 10-12 specimens of average thickness per batch Specimens are usually dried after the moisture that characteristically appears on the glass door has disappeared If the specimen is damp when taken out of the oven allow it to stand before re-radiating as moisture continues to evaporate from the specimen for some time Care must be taken not to irradiate the specimens for too long

It should be noted that microwave treatment damages seeds and the cellular structure of the plants which may reduce the long-term value of the specimens

85

Alternative drying techniquesSilica gelother desiccants amp freeze drying Alternative methods of drying plant specimens have been

used for some time but are mostly restricted to special purpose collections The main alternatives are freeze-drying and drying in a desiccant powder such as desiccant silica gel In general these techniques are used where it is essential to preserve the shape of a delicate plant of organ of the plant such as the flower Freeze-drying has also been used to preserve the chemical composition of a plant as accurately as possible for later study

Disadvantages and special conservation problems of specimens dried in these manners are that they are particularly susceptible to damage The dried parts are fragile lack support and often catch on packing materials They must therefore be packed especially carefully and stored in small boxes or tubes with some appropriate packing material that does not snag and break small projections Acid-free tissue paper is often used Drying in desiccant silica gel crystals or powder can also have the disadvantage that it is difficult to remove all traces of the silica gel after drying

86

Special preservation and processing techniquesWet or spirit collections

Very fleshy or delicate structures including small algae and orchid flowers are best preserved in an air-tight glass or plastic jar with a liquid preservative rather than by drying The type of preservative used should be clearly labelled in the jar Such material is often referred to as a spirit collection or wet collection

Most material can be satisfactorily preserved in 70 ethyl alcohol (or 70 methylated spirit or denatured alcohol) with 30 water Colours will fade quickly in spirit however so it is a good idea to keep comprehensive notes and photographs

87

Small algae Microscopic algae are often collected in a jar and in the

water in which they were found If the algae are to be stored for more than 2-3 days a preservative needs to be used Traditionally this has been the extremely toxic formalin - a small amount can be added to the water to make a 5 final solution and the container labelled This must not be sent through the post or by courier

There are some other equally toxic options for example propylene phenoxytol but none should be sent through the post A safer option is to add sufficient concentrated alcohol or methylated spirits to the water containing the algae to make a final solution of 70 alcohol This treatment dilutes the algae making them difficult to find so if they can be concentrated somehow first (eg by filtering) they can be stored in much less liquid Another option is to fix the algae in formalin (or something similar) first and then prepare a microscope glass slide with a permanent water-soluble mounting medium

88

Mounting Mounting specimens prevents most fragile material from

fragmenting and prevents specimens becoming separated from their labels If the plant collection is a long-term project specimens should be mounted on sheets of archival (permanent) cardboard or paper with archival-quality fixing media These include stitching with cotton thread dental floss nickel-plated copper wire (for heavier specimens) narrow strips of archival paper linen tape or by using an archival adhesive such as methyl cellulose adhesive

One disadvantage of mounting specimens is that it can make parts of the specimen inaccessible for examination so it is essential that this be borne in mind during specimen arrangement and mounting For example easily reversible mounting media should be used specimens should be strapped to the sheet rather than glued all over and the specimen should be carefully arranged before it is attached so that it shows all features

89

Full-size herbarium mounting sheets are usually about 43 cm long x 28 cm wide The plant name and accompanying field notes should be transcribed on a permanent label stuck to one corner of the herbarium sheet (the bottom right-hand corner being the most common) or sometimes annotations may be written directly on the sheet or card

Small pieces of material which may have become separated from the specimen (eg seeds) can be placed in small plastic bags and pinned to the sheet

90

Long-term preservation and storage The long-term preservation of dry plant

specimens is largely dependent on protection from insect attack Specimens collected by Linnaeus in the eighteenth century and by Banks and Solander on the Endeavour voyage in 1788 are still excellently preserved

91

Pests and their control A range of pests attack dried plant material The

most common pests are insects and fungi though rodents and other large animals can cause damage in poor storage conditions Insects eat the material the paper surrounding the material and the adhesives and mounting media

Such insect pests range from psocids (book lice) which attack mainly the softer parts such as flowers and soft fruits to tobacco beetles and carpet beetles which can bore holes through the toughest of specimens Many insects are particularly sensitive to relative humidity levels and do not thrive at levels below 50

92

The most common and acceptable specimen treatments for insect control are Freezing Microwave Poisoning Insect deterrents Fungal pests

93

Storage

Dried and pressed plant specimens can be stored in cardboard or plastic boxes or tied in bundles in light-weight cardboard folders placed in pigeon holes

Alternatively they can be placed in protective plastic jackets and displayed in ring folders which is recommended if they are to be frequently handled such as for a reference collection

94

Filing

Specimens should be filed in a systematic order if a relatively permanent collection is being made The major groups ie ferns and fern allies cycads conifers dicotyledons and monocotyledons are best kept separately or according to some classification scheme such as that given in a flora or handbook

Similarly the genera within each family and the species within each genus may be filed alphabetically or following some such classification

95

Preservation of entire animals

Types of collection specimens of an entire animal For reference collections mammals can be prepared as a variety of specimens The condition of the specimen may determine possible ways to preserve it if for instance decomposition of the skin has loosened the hair of a carcass so much that it can easily be pulled out or removed by rubbing (ldquoslippingrdquo fur) it will be very difficult or impossible to produce a study skin or mounted specimen The most usual types of specimens (based on Nagorsen and Peterson 1980) are 1) entire fluid-preserved animals (for studying anatomy and histology fluid preservation may change the fur colour) 2) study skins with accompanying skulls partial skeletons (some bones remain in the skin) for studying pelage colour hair quality and moulting patterns 3) mounted skins with accompanying partial or entire skeleton (some bones may remain in the skin dependant on the method of preservation) or freeze-dried specimens 4) entire skeletons for instance for studying anatomy geographic variation or for age determination (entire skeletons are poorly represented in collections so Nagorsen and Peterson (1980) recommend preparation of at least one male and one female skeleton per species

96

Preservation of specimens in the field Formalin preservation Preservation in alcohol Preservation by cooling or freezing

97

Formalin preservation After weighing and measuring the animal and attaching an

adequate label very small specimens (up to 100 g) can be fixed whole by submerging them in 10 buffered formalin (tissue - formalin solution ratio of at least 1 12) the body cavity can be filled with formalin solution by injection until it is turgid and firm some formalin may also be injected under the skin into the body cavity larger muscles and organs If hypodermic needles are not available the body cavity can be opened ventrally by making a slit instead allowing the formalin to enter

Keeping the mouth open with a piece of wood or cotton may later allow examination of teeth Then the whole body can be immersed in formalin in the posture in which it is supposed to stay permanently because it will harden The ratio of formalin to carcass must be at least 12 to 1 to assure a good fixation Tissues can be left in buffered neutralized formalin for several months but formalin hardens specimens therefore after fixation longterm storage in alcohol may be better After preservation the carcass should therefore be washed in water and transferred into ethanol for permanent storage

Disadvantages for instance it discolours the fur after a longish immersion softens the bones and prevents further examination for microbiology

98

Preservation in alcohol

After weighing a whole animal can be preserved in a container of alcohol (70-90) Removal of the intestine prior to storage of the animal in alcohol is recommended

99

Preservation by cooling or freezing Removal of the skin with insulating fur

before cooling or freezing may help to cool the carcass down more quickly

Freezing is not recommended if histological examination is planned

100

THANK YOU

42

8 widger 9 sieve 10 hand lens

11 enamel dish 12 beating tray 13 light traps

14 Tullgren funnel 15 Baermann funnel 16 mammal traps

17 pitfall traps 18 netting

43

Estimating Population Size

The exact methods used for estimation depend not only the nature of the habitat but also on the organisms involved

eg animals - population

plants - percentage cover

44

Using Quadrats

- By sampling an area using quadrats and counting the number of individuals within each quadrat it is possible to estimate the total number of individuals within the area

- confined to plants and sessile or very slow-moving animals

- fast-moving animals are disturbed and run away

45

Capture-recapture Techniques- useful for mobile animals which can be marked

- capture marked released randomly recaptured

and marked individuals recorded

no of marked individuals recaptured total no of individuals in 1st sample

-------------------------------------------- = ------------------------------------------

total no of individuals in 2nd sample estimated size of population

(the Lincoln Index)

46

Capture-recapture Techniques Factors affecting the accuracy of the estimation

deaths migration individuals become more liable to predation etc

Examples

- arthropods marked on their backs with non-toxic paint

- fish have tags attached to opercula - mammals have tags clipped to their ears

birds have their legs ringed

47

Capture-recapture Method Important tool for estimating density birth

rate and death rate for mobile animals Method

Collect a sample of individuals mark them and then release them

After a period collect more individuals from the wild and count the number that have marks

We assume that a sample if random will contain the same proportion of marked individuals as the population does

Estimate population density

48

Assumptions For All Capture-Recapture Studies Marking technique does not increase

mortality of marked animals Marked individuals are allowed to mix

with population Marking technique does not affect catch

probability Marks are not lost or overlooked No significant immigration or emigration No significant mortality or natality

49

Marked animals in second sample

Total caught in second sample

Marked animals in first sample

Total population size

=

520 N

16=

Peterson Method or Lincoln Index

N = 64N = (20)(16)5

50

Some Indices Used

Traps Number of Fecal

Pellets Vocalization

Frequency Pelt Records Catch per Unit

Fishing Effort

Number of Artifacts Questionnaires Cover Feeding Capacity Roadside Counts

51

Abundance Scales

The population size may be fairly accurately determined by making some form of frequency assessment

These are subjective and involve an experimenter making some estimate of the number of individuals in a given area or the cover of a particular species

This is especially useful where individuals are very numerous eg barnacles on a rocky shore or where it is difficult to distinguish individuals eg grass plants in a meadow

52

The assessments are usually made on an abundance scale of 5 categories

Abundance Common Frequent Occasional Rare

Barnacles exposed at low water

53

Environmental resistance are the factors which limit the growth of a particular population

eg predation disease availability of light food water oxygen and shelter the accumulation of toxic wastes and even the size of the population itself

54

Density-dependent Growth A population is a density-dependent when its size

(or density) affects its growth rate because of density-dependent factors such as food availability and toxic waste accumulation

Density-independent Growth In this type of growth a population increases until

some factor causes a sudden reduction in its size Its effect is the same regardless of the size of the

population eg temperature fires floods storms etc

55

Regulation of Population Size Fecundity is the reproductive capacity of individual

females of a species Birth rate or natality is used to measure fecundity Death rate or mortality is the number of individuals

of a species which die per unit time Immigration occurs when individuals join a

population from neighbouring ones Emigration occurs when individuals depart from a

population A cycle occurs when the size of a population

fluctuates on a regular basis

56

Ecological Sampling

57

Why Do We Sample Determine presence andor

abundance

Monitor population fluctuations

Assess lsquoecological damagersquo

Assess quality of habitat

Assess population responses

58

What Do We Sample

Physical Environment Temperature DO pH salinity clarity

flow sediment

Biotic Environment All living things

59

Physical Habitat Temperature

Mercury thermometer Electronic thermometer Long-term thermometers

Dissolved Oxygen Winkler method (titration) DO meter (electrode)

pH Litmus paper pH meter (electrode)

Salinity Salinity Meter YSI 550A DO Meter w12 cable

60

Water Clarity Secchi Disk

Disk is attached to a calibrated rope The disk is lowered into the water until the white parts can no longer be seen Secchi disk depth is then recorded and serves as the waters transparency index The clearer the water the greater the secchi disk depth

Secchi Disk

61

Current Velocity (flow) Floating-orange method

Put an orange (or something else that floats just below the water surface) and measure the time it takes it to float across a known distance

Odometer-type flow meter Number of revolutions the propeller

makes for a given time is calibrated to flow velocity

62

Sediment Sediment size is important to many

aquatic organisms Sieversquos are used to separate and

grade sediment samples Percent of each size grade can be

determined

63

Water Sample

Water and plankton from various depths can be collected

A trigger mechanism is used to close the sampler Sample is then brought back to the

surface

64

Small Mammals

Mouserat Traps Fatal

Pit Falls Bucket is placed in the ground Sometimes have lsquoleadsrsquo to the buckets

Live traps Havahart Sherman

Spot-light

Sherman trapHavahart trap

65

Birds Stick-under-the-box method Bird-trap

Works like a minnow trap Mist net

Captures birds in flight Rocket net

Uses a propellant to throw a net over birds

66

Terrestrial Insects

Sticky paper flies

Baited Traps Fire ants

Nets butterflies

Foggers Collect insects from tree canopies

67

Aquatic Insects Drift Net

Place net in flowing water Kick Net

lsquoKickrsquo sediment upstream from block net and the flow will wash them into the net

Wash bucket Serber or Hess Sampler

Stir up known area of sediment

Animals are collected by a catch net

Multi-plate Sampler Become colonized

68

Crawfish and Crab Traps

69

Fish Larvae Light Traps

Larvae are attracted to the light Ichthyoplankton nets

Can be towed at various depths Fish collect at the lsquocodrsquoend

70

Fish Lift net

Net is placed down and after a set amount of time it is quickly lifted

Pop-net Similar to a lift net but

floats are attached to a framed net

Operated by a trigger mechanism

Throw net A net attached to a heavy

frame is thrown and every thing inside is netted out Throw net

Pop-net

Lift net

71

Minnow trap

Usually use bait to attract small fish Light is used sometimes as an attractant

72

Fish Electrofishing

Electricity is put into the water Fish are temporarily stunned and usually

swim towards the electricity source Usually non-fatal but may cause some

damage

73

Fish Gill Net

Gill nets resemble tennis nets Fish can not swim completely through the

net and get caught Gill nets are size selective (based on mesh

size) Square Mesh

Bar mesh

Stretch mesh

74

Fish Trammel Net

Three panels two large mesh on the outside and a small mesh on the inside

Fish swim through the outer mesh pushes the small mesh through the other side and becomes entangled

75

Hoop nets (and other similar nets) can have bait or not

Fyke nets have leads to help guide fish to the net

76

Seine Seines are nets that are pulled

through shallow water to catch fish

77

Purse Seine Used to encircle entire schools of fish

Usually involves a spotter plane and a second boat

78

Trotline (longline) A series of baited drop lines

connected to a main line

Can be deployed by tying one end to the bank and tying the other end with a heavy weight

79

Shrimp (or fish) Trawl Net pulled behind

a boat along the bottom Either a beam or

otter boards keep the net open

80

Tagging Individuals Coded Wire Tags

Microwire that has a unique label

Magnetic wand detects the tag

Tag retention should be determined

T-Bar tags Can be individually

numbered External tag

PIT tags (Passive Integrated Transponders) Wand induces the tag to

transmit individual number is displayed

81

Other Tagging Methods

Toe clip Amphibian and reptile Clip of one or more toes

to identify individuals

Bird Band Place a metal band on a

bird leg Generally has

identification information

82

Preserving plant specimens Pressing and drying Long-term

preservation and storage

Alternative drying techniques

Special preservation and processing techniques

Mounting

83

Pressing and drying Techniques for pressing and drying specimens have been

established for many years There are minor variations in recommended methods but they are essentially the same worldwide

The best specimens are plants that are pressed as soon as possible after collection before wilting and shrivelling Most plants may be kept in sealed containers such as plastic bags for up to a day if it is inconvenient to press immediately However some plants show such rapid wilting particularly of the flowers that such delays are best avoided Flowers with a lot of nectar may go mouldy very quickly if excess nectar is not shaken off before pressing

Specimens are pressed flat and dried between sheets of absorbent blotters or semi-absorbent paper such as newspaper Papers with a glossy surface should be avoided because they are not absorbent enough to aid drying The plant should be carefully laid out between the drying sheets as their form at this stage largely determines their ultimate appearance The flowers should be spread out with the petals carefully arranged wilted leaves should be straightened and unnecessary shoots of excessively twiggy shrubs may be cut away

84

Microwave ovens Small numbers of specimens can be dried using a microwave

oven The technique recommended in the literature is to place the specimens between unprinted absorbent paper for example butchers paper not newspaper which is unsuitable because the chemicals present in the ink may cause a fire The specimens should be put in a special press which should be of a microwave-safe material (wood acrylic or polycarbonate sheeting eg plexiglass or perspex NO metal components) If such a press is not available sheets of cardboard can be placed above and below the specimens and then weighted down

Drying time depends on the power of your oven In most cases drying is accomplished by irradiating at maximum power for 1-2 minutes per specimen although it is often a case of trial and error It is best to process no more than 10-12 specimens of average thickness per batch Specimens are usually dried after the moisture that characteristically appears on the glass door has disappeared If the specimen is damp when taken out of the oven allow it to stand before re-radiating as moisture continues to evaporate from the specimen for some time Care must be taken not to irradiate the specimens for too long

It should be noted that microwave treatment damages seeds and the cellular structure of the plants which may reduce the long-term value of the specimens

85

Alternative drying techniquesSilica gelother desiccants amp freeze drying Alternative methods of drying plant specimens have been

used for some time but are mostly restricted to special purpose collections The main alternatives are freeze-drying and drying in a desiccant powder such as desiccant silica gel In general these techniques are used where it is essential to preserve the shape of a delicate plant of organ of the plant such as the flower Freeze-drying has also been used to preserve the chemical composition of a plant as accurately as possible for later study

Disadvantages and special conservation problems of specimens dried in these manners are that they are particularly susceptible to damage The dried parts are fragile lack support and often catch on packing materials They must therefore be packed especially carefully and stored in small boxes or tubes with some appropriate packing material that does not snag and break small projections Acid-free tissue paper is often used Drying in desiccant silica gel crystals or powder can also have the disadvantage that it is difficult to remove all traces of the silica gel after drying

86

Special preservation and processing techniquesWet or spirit collections

Very fleshy or delicate structures including small algae and orchid flowers are best preserved in an air-tight glass or plastic jar with a liquid preservative rather than by drying The type of preservative used should be clearly labelled in the jar Such material is often referred to as a spirit collection or wet collection

Most material can be satisfactorily preserved in 70 ethyl alcohol (or 70 methylated spirit or denatured alcohol) with 30 water Colours will fade quickly in spirit however so it is a good idea to keep comprehensive notes and photographs

87

Small algae Microscopic algae are often collected in a jar and in the

water in which they were found If the algae are to be stored for more than 2-3 days a preservative needs to be used Traditionally this has been the extremely toxic formalin - a small amount can be added to the water to make a 5 final solution and the container labelled This must not be sent through the post or by courier

There are some other equally toxic options for example propylene phenoxytol but none should be sent through the post A safer option is to add sufficient concentrated alcohol or methylated spirits to the water containing the algae to make a final solution of 70 alcohol This treatment dilutes the algae making them difficult to find so if they can be concentrated somehow first (eg by filtering) they can be stored in much less liquid Another option is to fix the algae in formalin (or something similar) first and then prepare a microscope glass slide with a permanent water-soluble mounting medium

88

Mounting Mounting specimens prevents most fragile material from

fragmenting and prevents specimens becoming separated from their labels If the plant collection is a long-term project specimens should be mounted on sheets of archival (permanent) cardboard or paper with archival-quality fixing media These include stitching with cotton thread dental floss nickel-plated copper wire (for heavier specimens) narrow strips of archival paper linen tape or by using an archival adhesive such as methyl cellulose adhesive

One disadvantage of mounting specimens is that it can make parts of the specimen inaccessible for examination so it is essential that this be borne in mind during specimen arrangement and mounting For example easily reversible mounting media should be used specimens should be strapped to the sheet rather than glued all over and the specimen should be carefully arranged before it is attached so that it shows all features

89

Full-size herbarium mounting sheets are usually about 43 cm long x 28 cm wide The plant name and accompanying field notes should be transcribed on a permanent label stuck to one corner of the herbarium sheet (the bottom right-hand corner being the most common) or sometimes annotations may be written directly on the sheet or card

Small pieces of material which may have become separated from the specimen (eg seeds) can be placed in small plastic bags and pinned to the sheet

90

Long-term preservation and storage The long-term preservation of dry plant

specimens is largely dependent on protection from insect attack Specimens collected by Linnaeus in the eighteenth century and by Banks and Solander on the Endeavour voyage in 1788 are still excellently preserved

91

Pests and their control A range of pests attack dried plant material The

most common pests are insects and fungi though rodents and other large animals can cause damage in poor storage conditions Insects eat the material the paper surrounding the material and the adhesives and mounting media

Such insect pests range from psocids (book lice) which attack mainly the softer parts such as flowers and soft fruits to tobacco beetles and carpet beetles which can bore holes through the toughest of specimens Many insects are particularly sensitive to relative humidity levels and do not thrive at levels below 50

92

The most common and acceptable specimen treatments for insect control are Freezing Microwave Poisoning Insect deterrents Fungal pests

93

Storage

Dried and pressed plant specimens can be stored in cardboard or plastic boxes or tied in bundles in light-weight cardboard folders placed in pigeon holes

Alternatively they can be placed in protective plastic jackets and displayed in ring folders which is recommended if they are to be frequently handled such as for a reference collection

94

Filing

Specimens should be filed in a systematic order if a relatively permanent collection is being made The major groups ie ferns and fern allies cycads conifers dicotyledons and monocotyledons are best kept separately or according to some classification scheme such as that given in a flora or handbook

Similarly the genera within each family and the species within each genus may be filed alphabetically or following some such classification

95

Preservation of entire animals

Types of collection specimens of an entire animal For reference collections mammals can be prepared as a variety of specimens The condition of the specimen may determine possible ways to preserve it if for instance decomposition of the skin has loosened the hair of a carcass so much that it can easily be pulled out or removed by rubbing (ldquoslippingrdquo fur) it will be very difficult or impossible to produce a study skin or mounted specimen The most usual types of specimens (based on Nagorsen and Peterson 1980) are 1) entire fluid-preserved animals (for studying anatomy and histology fluid preservation may change the fur colour) 2) study skins with accompanying skulls partial skeletons (some bones remain in the skin) for studying pelage colour hair quality and moulting patterns 3) mounted skins with accompanying partial or entire skeleton (some bones may remain in the skin dependant on the method of preservation) or freeze-dried specimens 4) entire skeletons for instance for studying anatomy geographic variation or for age determination (entire skeletons are poorly represented in collections so Nagorsen and Peterson (1980) recommend preparation of at least one male and one female skeleton per species

96

Preservation of specimens in the field Formalin preservation Preservation in alcohol Preservation by cooling or freezing

97

Formalin preservation After weighing and measuring the animal and attaching an

adequate label very small specimens (up to 100 g) can be fixed whole by submerging them in 10 buffered formalin (tissue - formalin solution ratio of at least 1 12) the body cavity can be filled with formalin solution by injection until it is turgid and firm some formalin may also be injected under the skin into the body cavity larger muscles and organs If hypodermic needles are not available the body cavity can be opened ventrally by making a slit instead allowing the formalin to enter

Keeping the mouth open with a piece of wood or cotton may later allow examination of teeth Then the whole body can be immersed in formalin in the posture in which it is supposed to stay permanently because it will harden The ratio of formalin to carcass must be at least 12 to 1 to assure a good fixation Tissues can be left in buffered neutralized formalin for several months but formalin hardens specimens therefore after fixation longterm storage in alcohol may be better After preservation the carcass should therefore be washed in water and transferred into ethanol for permanent storage

Disadvantages for instance it discolours the fur after a longish immersion softens the bones and prevents further examination for microbiology

98

Preservation in alcohol

After weighing a whole animal can be preserved in a container of alcohol (70-90) Removal of the intestine prior to storage of the animal in alcohol is recommended

99

Preservation by cooling or freezing Removal of the skin with insulating fur

before cooling or freezing may help to cool the carcass down more quickly

Freezing is not recommended if histological examination is planned

100

THANK YOU

43

Estimating Population Size

The exact methods used for estimation depend not only the nature of the habitat but also on the organisms involved

eg animals - population

plants - percentage cover

44

Using Quadrats

- By sampling an area using quadrats and counting the number of individuals within each quadrat it is possible to estimate the total number of individuals within the area

- confined to plants and sessile or very slow-moving animals

- fast-moving animals are disturbed and run away

45

Capture-recapture Techniques- useful for mobile animals which can be marked

- capture marked released randomly recaptured

and marked individuals recorded

no of marked individuals recaptured total no of individuals in 1st sample

-------------------------------------------- = ------------------------------------------

total no of individuals in 2nd sample estimated size of population

(the Lincoln Index)

46

Capture-recapture Techniques Factors affecting the accuracy of the estimation

deaths migration individuals become more liable to predation etc

Examples

- arthropods marked on their backs with non-toxic paint

- fish have tags attached to opercula - mammals have tags clipped to their ears

birds have their legs ringed

47

Capture-recapture Method Important tool for estimating density birth

rate and death rate for mobile animals Method

Collect a sample of individuals mark them and then release them

After a period collect more individuals from the wild and count the number that have marks

We assume that a sample if random will contain the same proportion of marked individuals as the population does

Estimate population density

48

Assumptions For All Capture-Recapture Studies Marking technique does not increase

mortality of marked animals Marked individuals are allowed to mix

with population Marking technique does not affect catch

probability Marks are not lost or overlooked No significant immigration or emigration No significant mortality or natality

49

Marked animals in second sample

Total caught in second sample

Marked animals in first sample

Total population size

=

520 N

16=

Peterson Method or Lincoln Index

N = 64N = (20)(16)5

50

Some Indices Used

Traps Number of Fecal

Pellets Vocalization

Frequency Pelt Records Catch per Unit

Fishing Effort

Number of Artifacts Questionnaires Cover Feeding Capacity Roadside Counts

51

Abundance Scales

The population size may be fairly accurately determined by making some form of frequency assessment

These are subjective and involve an experimenter making some estimate of the number of individuals in a given area or the cover of a particular species

This is especially useful where individuals are very numerous eg barnacles on a rocky shore or where it is difficult to distinguish individuals eg grass plants in a meadow

52

The assessments are usually made on an abundance scale of 5 categories

Abundance Common Frequent Occasional Rare

Barnacles exposed at low water

53

Environmental resistance are the factors which limit the growth of a particular population

eg predation disease availability of light food water oxygen and shelter the accumulation of toxic wastes and even the size of the population itself

54

Density-dependent Growth A population is a density-dependent when its size

(or density) affects its growth rate because of density-dependent factors such as food availability and toxic waste accumulation

Density-independent Growth In this type of growth a population increases until

some factor causes a sudden reduction in its size Its effect is the same regardless of the size of the

population eg temperature fires floods storms etc

55

Regulation of Population Size Fecundity is the reproductive capacity of individual

females of a species Birth rate or natality is used to measure fecundity Death rate or mortality is the number of individuals

of a species which die per unit time Immigration occurs when individuals join a

population from neighbouring ones Emigration occurs when individuals depart from a

population A cycle occurs when the size of a population

fluctuates on a regular basis

56

Ecological Sampling

57

Why Do We Sample Determine presence andor

abundance

Monitor population fluctuations

Assess lsquoecological damagersquo

Assess quality of habitat

Assess population responses

58

What Do We Sample

Physical Environment Temperature DO pH salinity clarity

flow sediment

Biotic Environment All living things

59

Physical Habitat Temperature

Mercury thermometer Electronic thermometer Long-term thermometers

Dissolved Oxygen Winkler method (titration) DO meter (electrode)

pH Litmus paper pH meter (electrode)

Salinity Salinity Meter YSI 550A DO Meter w12 cable

60

Water Clarity Secchi Disk

Disk is attached to a calibrated rope The disk is lowered into the water until the white parts can no longer be seen Secchi disk depth is then recorded and serves as the waters transparency index The clearer the water the greater the secchi disk depth

Secchi Disk

61

Current Velocity (flow) Floating-orange method

Put an orange (or something else that floats just below the water surface) and measure the time it takes it to float across a known distance

Odometer-type flow meter Number of revolutions the propeller

makes for a given time is calibrated to flow velocity

62

Sediment Sediment size is important to many

aquatic organisms Sieversquos are used to separate and

grade sediment samples Percent of each size grade can be

determined

63

Water Sample

Water and plankton from various depths can be collected

A trigger mechanism is used to close the sampler Sample is then brought back to the

surface

64

Small Mammals

Mouserat Traps Fatal

Pit Falls Bucket is placed in the ground Sometimes have lsquoleadsrsquo to the buckets

Live traps Havahart Sherman

Spot-light

Sherman trapHavahart trap

65

Birds Stick-under-the-box method Bird-trap

Works like a minnow trap Mist net

Captures birds in flight Rocket net

Uses a propellant to throw a net over birds

66

Terrestrial Insects

Sticky paper flies

Baited Traps Fire ants

Nets butterflies

Foggers Collect insects from tree canopies

67

Aquatic Insects Drift Net

Place net in flowing water Kick Net

lsquoKickrsquo sediment upstream from block net and the flow will wash them into the net

Wash bucket Serber or Hess Sampler

Stir up known area of sediment

Animals are collected by a catch net

Multi-plate Sampler Become colonized

68

Crawfish and Crab Traps

69

Fish Larvae Light Traps

Larvae are attracted to the light Ichthyoplankton nets

Can be towed at various depths Fish collect at the lsquocodrsquoend

70

Fish Lift net

Net is placed down and after a set amount of time it is quickly lifted

Pop-net Similar to a lift net but

floats are attached to a framed net

Operated by a trigger mechanism

Throw net A net attached to a heavy

frame is thrown and every thing inside is netted out Throw net

Pop-net

Lift net

71

Minnow trap

Usually use bait to attract small fish Light is used sometimes as an attractant

72

Fish Electrofishing

Electricity is put into the water Fish are temporarily stunned and usually

swim towards the electricity source Usually non-fatal but may cause some

damage

73

Fish Gill Net

Gill nets resemble tennis nets Fish can not swim completely through the

net and get caught Gill nets are size selective (based on mesh

size) Square Mesh

Bar mesh

Stretch mesh

74

Fish Trammel Net

Three panels two large mesh on the outside and a small mesh on the inside

Fish swim through the outer mesh pushes the small mesh through the other side and becomes entangled

75

Hoop nets (and other similar nets) can have bait or not

Fyke nets have leads to help guide fish to the net

76

Seine Seines are nets that are pulled

through shallow water to catch fish

77

Purse Seine Used to encircle entire schools of fish

Usually involves a spotter plane and a second boat

78

Trotline (longline) A series of baited drop lines

connected to a main line

Can be deployed by tying one end to the bank and tying the other end with a heavy weight

79

Shrimp (or fish) Trawl Net pulled behind

a boat along the bottom Either a beam or

otter boards keep the net open

80

Tagging Individuals Coded Wire Tags

Microwire that has a unique label

Magnetic wand detects the tag

Tag retention should be determined

T-Bar tags Can be individually

numbered External tag

PIT tags (Passive Integrated Transponders) Wand induces the tag to

transmit individual number is displayed

81

Other Tagging Methods

Toe clip Amphibian and reptile Clip of one or more toes

to identify individuals

Bird Band Place a metal band on a

bird leg Generally has

identification information

82

Preserving plant specimens Pressing and drying Long-term

preservation and storage

Alternative drying techniques

Special preservation and processing techniques

Mounting

83

Pressing and drying Techniques for pressing and drying specimens have been

established for many years There are minor variations in recommended methods but they are essentially the same worldwide

The best specimens are plants that are pressed as soon as possible after collection before wilting and shrivelling Most plants may be kept in sealed containers such as plastic bags for up to a day if it is inconvenient to press immediately However some plants show such rapid wilting particularly of the flowers that such delays are best avoided Flowers with a lot of nectar may go mouldy very quickly if excess nectar is not shaken off before pressing

Specimens are pressed flat and dried between sheets of absorbent blotters or semi-absorbent paper such as newspaper Papers with a glossy surface should be avoided because they are not absorbent enough to aid drying The plant should be carefully laid out between the drying sheets as their form at this stage largely determines their ultimate appearance The flowers should be spread out with the petals carefully arranged wilted leaves should be straightened and unnecessary shoots of excessively twiggy shrubs may be cut away

84

Microwave ovens Small numbers of specimens can be dried using a microwave

oven The technique recommended in the literature is to place the specimens between unprinted absorbent paper for example butchers paper not newspaper which is unsuitable because the chemicals present in the ink may cause a fire The specimens should be put in a special press which should be of a microwave-safe material (wood acrylic or polycarbonate sheeting eg plexiglass or perspex NO metal components) If such a press is not available sheets of cardboard can be placed above and below the specimens and then weighted down

Drying time depends on the power of your oven In most cases drying is accomplished by irradiating at maximum power for 1-2 minutes per specimen although it is often a case of trial and error It is best to process no more than 10-12 specimens of average thickness per batch Specimens are usually dried after the moisture that characteristically appears on the glass door has disappeared If the specimen is damp when taken out of the oven allow it to stand before re-radiating as moisture continues to evaporate from the specimen for some time Care must be taken not to irradiate the specimens for too long

It should be noted that microwave treatment damages seeds and the cellular structure of the plants which may reduce the long-term value of the specimens

85

Alternative drying techniquesSilica gelother desiccants amp freeze drying Alternative methods of drying plant specimens have been

used for some time but are mostly restricted to special purpose collections The main alternatives are freeze-drying and drying in a desiccant powder such as desiccant silica gel In general these techniques are used where it is essential to preserve the shape of a delicate plant of organ of the plant such as the flower Freeze-drying has also been used to preserve the chemical composition of a plant as accurately as possible for later study

Disadvantages and special conservation problems of specimens dried in these manners are that they are particularly susceptible to damage The dried parts are fragile lack support and often catch on packing materials They must therefore be packed especially carefully and stored in small boxes or tubes with some appropriate packing material that does not snag and break small projections Acid-free tissue paper is often used Drying in desiccant silica gel crystals or powder can also have the disadvantage that it is difficult to remove all traces of the silica gel after drying

86

Special preservation and processing techniquesWet or spirit collections

Very fleshy or delicate structures including small algae and orchid flowers are best preserved in an air-tight glass or plastic jar with a liquid preservative rather than by drying The type of preservative used should be clearly labelled in the jar Such material is often referred to as a spirit collection or wet collection

Most material can be satisfactorily preserved in 70 ethyl alcohol (or 70 methylated spirit or denatured alcohol) with 30 water Colours will fade quickly in spirit however so it is a good idea to keep comprehensive notes and photographs

87

Small algae Microscopic algae are often collected in a jar and in the

water in which they were found If the algae are to be stored for more than 2-3 days a preservative needs to be used Traditionally this has been the extremely toxic formalin - a small amount can be added to the water to make a 5 final solution and the container labelled This must not be sent through the post or by courier

There are some other equally toxic options for example propylene phenoxytol but none should be sent through the post A safer option is to add sufficient concentrated alcohol or methylated spirits to the water containing the algae to make a final solution of 70 alcohol This treatment dilutes the algae making them difficult to find so if they can be concentrated somehow first (eg by filtering) they can be stored in much less liquid Another option is to fix the algae in formalin (or something similar) first and then prepare a microscope glass slide with a permanent water-soluble mounting medium

88

Mounting Mounting specimens prevents most fragile material from

fragmenting and prevents specimens becoming separated from their labels If the plant collection is a long-term project specimens should be mounted on sheets of archival (permanent) cardboard or paper with archival-quality fixing media These include stitching with cotton thread dental floss nickel-plated copper wire (for heavier specimens) narrow strips of archival paper linen tape or by using an archival adhesive such as methyl cellulose adhesive

One disadvantage of mounting specimens is that it can make parts of the specimen inaccessible for examination so it is essential that this be borne in mind during specimen arrangement and mounting For example easily reversible mounting media should be used specimens should be strapped to the sheet rather than glued all over and the specimen should be carefully arranged before it is attached so that it shows all features

89

Full-size herbarium mounting sheets are usually about 43 cm long x 28 cm wide The plant name and accompanying field notes should be transcribed on a permanent label stuck to one corner of the herbarium sheet (the bottom right-hand corner being the most common) or sometimes annotations may be written directly on the sheet or card

Small pieces of material which may have become separated from the specimen (eg seeds) can be placed in small plastic bags and pinned to the sheet

90

Long-term preservation and storage The long-term preservation of dry plant

specimens is largely dependent on protection from insect attack Specimens collected by Linnaeus in the eighteenth century and by Banks and Solander on the Endeavour voyage in 1788 are still excellently preserved

91

Pests and their control A range of pests attack dried plant material The

most common pests are insects and fungi though rodents and other large animals can cause damage in poor storage conditions Insects eat the material the paper surrounding the material and the adhesives and mounting media

Such insect pests range from psocids (book lice) which attack mainly the softer parts such as flowers and soft fruits to tobacco beetles and carpet beetles which can bore holes through the toughest of specimens Many insects are particularly sensitive to relative humidity levels and do not thrive at levels below 50

92

The most common and acceptable specimen treatments for insect control are Freezing Microwave Poisoning Insect deterrents Fungal pests

93

Storage

Dried and pressed plant specimens can be stored in cardboard or plastic boxes or tied in bundles in light-weight cardboard folders placed in pigeon holes

Alternatively they can be placed in protective plastic jackets and displayed in ring folders which is recommended if they are to be frequently handled such as for a reference collection

94

Filing

Specimens should be filed in a systematic order if a relatively permanent collection is being made The major groups ie ferns and fern allies cycads conifers dicotyledons and monocotyledons are best kept separately or according to some classification scheme such as that given in a flora or handbook

Similarly the genera within each family and the species within each genus may be filed alphabetically or following some such classification

95

Preservation of entire animals

Types of collection specimens of an entire animal For reference collections mammals can be prepared as a variety of specimens The condition of the specimen may determine possible ways to preserve it if for instance decomposition of the skin has loosened the hair of a carcass so much that it can easily be pulled out or removed by rubbing (ldquoslippingrdquo fur) it will be very difficult or impossible to produce a study skin or mounted specimen The most usual types of specimens (based on Nagorsen and Peterson 1980) are 1) entire fluid-preserved animals (for studying anatomy and histology fluid preservation may change the fur colour) 2) study skins with accompanying skulls partial skeletons (some bones remain in the skin) for studying pelage colour hair quality and moulting patterns 3) mounted skins with accompanying partial or entire skeleton (some bones may remain in the skin dependant on the method of preservation) or freeze-dried specimens 4) entire skeletons for instance for studying anatomy geographic variation or for age determination (entire skeletons are poorly represented in collections so Nagorsen and Peterson (1980) recommend preparation of at least one male and one female skeleton per species

96

Preservation of specimens in the field Formalin preservation Preservation in alcohol Preservation by cooling or freezing

97

Formalin preservation After weighing and measuring the animal and attaching an

adequate label very small specimens (up to 100 g) can be fixed whole by submerging them in 10 buffered formalin (tissue - formalin solution ratio of at least 1 12) the body cavity can be filled with formalin solution by injection until it is turgid and firm some formalin may also be injected under the skin into the body cavity larger muscles and organs If hypodermic needles are not available the body cavity can be opened ventrally by making a slit instead allowing the formalin to enter

Keeping the mouth open with a piece of wood or cotton may later allow examination of teeth Then the whole body can be immersed in formalin in the posture in which it is supposed to stay permanently because it will harden The ratio of formalin to carcass must be at least 12 to 1 to assure a good fixation Tissues can be left in buffered neutralized formalin for several months but formalin hardens specimens therefore after fixation longterm storage in alcohol may be better After preservation the carcass should therefore be washed in water and transferred into ethanol for permanent storage

Disadvantages for instance it discolours the fur after a longish immersion softens the bones and prevents further examination for microbiology

98

Preservation in alcohol

After weighing a whole animal can be preserved in a container of alcohol (70-90) Removal of the intestine prior to storage of the animal in alcohol is recommended

99

Preservation by cooling or freezing Removal of the skin with insulating fur

before cooling or freezing may help to cool the carcass down more quickly

Freezing is not recommended if histological examination is planned

100

THANK YOU

44

Using Quadrats

- By sampling an area using quadrats and counting the number of individuals within each quadrat it is possible to estimate the total number of individuals within the area

- confined to plants and sessile or very slow-moving animals

- fast-moving animals are disturbed and run away

45

Capture-recapture Techniques- useful for mobile animals which can be marked

- capture marked released randomly recaptured

and marked individuals recorded

no of marked individuals recaptured total no of individuals in 1st sample

-------------------------------------------- = ------------------------------------------

total no of individuals in 2nd sample estimated size of population

(the Lincoln Index)

46

Capture-recapture Techniques Factors affecting the accuracy of the estimation

deaths migration individuals become more liable to predation etc

Examples

- arthropods marked on their backs with non-toxic paint

- fish have tags attached to opercula - mammals have tags clipped to their ears

birds have their legs ringed

47

Capture-recapture Method Important tool for estimating density birth

rate and death rate for mobile animals Method

Collect a sample of individuals mark them and then release them

After a period collect more individuals from the wild and count the number that have marks

We assume that a sample if random will contain the same proportion of marked individuals as the population does

Estimate population density

48

Assumptions For All Capture-Recapture Studies Marking technique does not increase

mortality of marked animals Marked individuals are allowed to mix

with population Marking technique does not affect catch

probability Marks are not lost or overlooked No significant immigration or emigration No significant mortality or natality

49

Marked animals in second sample

Total caught in second sample

Marked animals in first sample

Total population size

=

520 N

16=

Peterson Method or Lincoln Index

N = 64N = (20)(16)5

50

Some Indices Used

Traps Number of Fecal

Pellets Vocalization

Frequency Pelt Records Catch per Unit

Fishing Effort

Number of Artifacts Questionnaires Cover Feeding Capacity Roadside Counts

51

Abundance Scales

The population size may be fairly accurately determined by making some form of frequency assessment

These are subjective and involve an experimenter making some estimate of the number of individuals in a given area or the cover of a particular species

This is especially useful where individuals are very numerous eg barnacles on a rocky shore or where it is difficult to distinguish individuals eg grass plants in a meadow

52

The assessments are usually made on an abundance scale of 5 categories

Abundance Common Frequent Occasional Rare

Barnacles exposed at low water

53

Environmental resistance are the factors which limit the growth of a particular population

eg predation disease availability of light food water oxygen and shelter the accumulation of toxic wastes and even the size of the population itself

54

Density-dependent Growth A population is a density-dependent when its size

(or density) affects its growth rate because of density-dependent factors such as food availability and toxic waste accumulation

Density-independent Growth In this type of growth a population increases until

some factor causes a sudden reduction in its size Its effect is the same regardless of the size of the

population eg temperature fires floods storms etc

55

Regulation of Population Size Fecundity is the reproductive capacity of individual

females of a species Birth rate or natality is used to measure fecundity Death rate or mortality is the number of individuals

of a species which die per unit time Immigration occurs when individuals join a

population from neighbouring ones Emigration occurs when individuals depart from a

population A cycle occurs when the size of a population

fluctuates on a regular basis

56

Ecological Sampling

57

Why Do We Sample Determine presence andor

abundance

Monitor population fluctuations

Assess lsquoecological damagersquo

Assess quality of habitat

Assess population responses

58

What Do We Sample

Physical Environment Temperature DO pH salinity clarity

flow sediment

Biotic Environment All living things

59

Physical Habitat Temperature

Mercury thermometer Electronic thermometer Long-term thermometers

Dissolved Oxygen Winkler method (titration) DO meter (electrode)

pH Litmus paper pH meter (electrode)

Salinity Salinity Meter YSI 550A DO Meter w12 cable

60

Water Clarity Secchi Disk

Disk is attached to a calibrated rope The disk is lowered into the water until the white parts can no longer be seen Secchi disk depth is then recorded and serves as the waters transparency index The clearer the water the greater the secchi disk depth

Secchi Disk

61

Current Velocity (flow) Floating-orange method

Put an orange (or something else that floats just below the water surface) and measure the time it takes it to float across a known distance

Odometer-type flow meter Number of revolutions the propeller

makes for a given time is calibrated to flow velocity

62

Sediment Sediment size is important to many

aquatic organisms Sieversquos are used to separate and

grade sediment samples Percent of each size grade can be

determined

63

Water Sample

Water and plankton from various depths can be collected

A trigger mechanism is used to close the sampler Sample is then brought back to the

surface

64

Small Mammals

Mouserat Traps Fatal

Pit Falls Bucket is placed in the ground Sometimes have lsquoleadsrsquo to the buckets

Live traps Havahart Sherman

Spot-light

Sherman trapHavahart trap

65

Birds Stick-under-the-box method Bird-trap

Works like a minnow trap Mist net

Captures birds in flight Rocket net

Uses a propellant to throw a net over birds

66

Terrestrial Insects

Sticky paper flies

Baited Traps Fire ants

Nets butterflies

Foggers Collect insects from tree canopies

67

Aquatic Insects Drift Net

Place net in flowing water Kick Net

lsquoKickrsquo sediment upstream from block net and the flow will wash them into the net

Wash bucket Serber or Hess Sampler

Stir up known area of sediment

Animals are collected by a catch net

Multi-plate Sampler Become colonized

68

Crawfish and Crab Traps

69

Fish Larvae Light Traps

Larvae are attracted to the light Ichthyoplankton nets

Can be towed at various depths Fish collect at the lsquocodrsquoend

70

Fish Lift net

Net is placed down and after a set amount of time it is quickly lifted

Pop-net Similar to a lift net but

floats are attached to a framed net

Operated by a trigger mechanism

Throw net A net attached to a heavy

frame is thrown and every thing inside is netted out Throw net

Pop-net

Lift net

71

Minnow trap

Usually use bait to attract small fish Light is used sometimes as an attractant

72

Fish Electrofishing

Electricity is put into the water Fish are temporarily stunned and usually

swim towards the electricity source Usually non-fatal but may cause some

damage

73

Fish Gill Net

Gill nets resemble tennis nets Fish can not swim completely through the

net and get caught Gill nets are size selective (based on mesh

size) Square Mesh

Bar mesh

Stretch mesh

74

Fish Trammel Net

Three panels two large mesh on the outside and a small mesh on the inside

Fish swim through the outer mesh pushes the small mesh through the other side and becomes entangled

75

Hoop nets (and other similar nets) can have bait or not

Fyke nets have leads to help guide fish to the net

76

Seine Seines are nets that are pulled

through shallow water to catch fish

77

Purse Seine Used to encircle entire schools of fish

Usually involves a spotter plane and a second boat

78

Trotline (longline) A series of baited drop lines

connected to a main line

Can be deployed by tying one end to the bank and tying the other end with a heavy weight

79

Shrimp (or fish) Trawl Net pulled behind

a boat along the bottom Either a beam or

otter boards keep the net open

80

Tagging Individuals Coded Wire Tags

Microwire that has a unique label

Magnetic wand detects the tag

Tag retention should be determined

T-Bar tags Can be individually

numbered External tag

PIT tags (Passive Integrated Transponders) Wand induces the tag to

transmit individual number is displayed

81

Other Tagging Methods

Toe clip Amphibian and reptile Clip of one or more toes

to identify individuals

Bird Band Place a metal band on a

bird leg Generally has

identification information

82

Preserving plant specimens Pressing and drying Long-term

preservation and storage

Alternative drying techniques

Special preservation and processing techniques

Mounting

83

Pressing and drying Techniques for pressing and drying specimens have been

established for many years There are minor variations in recommended methods but they are essentially the same worldwide

The best specimens are plants that are pressed as soon as possible after collection before wilting and shrivelling Most plants may be kept in sealed containers such as plastic bags for up to a day if it is inconvenient to press immediately However some plants show such rapid wilting particularly of the flowers that such delays are best avoided Flowers with a lot of nectar may go mouldy very quickly if excess nectar is not shaken off before pressing

Specimens are pressed flat and dried between sheets of absorbent blotters or semi-absorbent paper such as newspaper Papers with a glossy surface should be avoided because they are not absorbent enough to aid drying The plant should be carefully laid out between the drying sheets as their form at this stage largely determines their ultimate appearance The flowers should be spread out with the petals carefully arranged wilted leaves should be straightened and unnecessary shoots of excessively twiggy shrubs may be cut away

84

Microwave ovens Small numbers of specimens can be dried using a microwave

oven The technique recommended in the literature is to place the specimens between unprinted absorbent paper for example butchers paper not newspaper which is unsuitable because the chemicals present in the ink may cause a fire The specimens should be put in a special press which should be of a microwave-safe material (wood acrylic or polycarbonate sheeting eg plexiglass or perspex NO metal components) If such a press is not available sheets of cardboard can be placed above and below the specimens and then weighted down

Drying time depends on the power of your oven In most cases drying is accomplished by irradiating at maximum power for 1-2 minutes per specimen although it is often a case of trial and error It is best to process no more than 10-12 specimens of average thickness per batch Specimens are usually dried after the moisture that characteristically appears on the glass door has disappeared If the specimen is damp when taken out of the oven allow it to stand before re-radiating as moisture continues to evaporate from the specimen for some time Care must be taken not to irradiate the specimens for too long

It should be noted that microwave treatment damages seeds and the cellular structure of the plants which may reduce the long-term value of the specimens

85

Alternative drying techniquesSilica gelother desiccants amp freeze drying Alternative methods of drying plant specimens have been

used for some time but are mostly restricted to special purpose collections The main alternatives are freeze-drying and drying in a desiccant powder such as desiccant silica gel In general these techniques are used where it is essential to preserve the shape of a delicate plant of organ of the plant such as the flower Freeze-drying has also been used to preserve the chemical composition of a plant as accurately as possible for later study

Disadvantages and special conservation problems of specimens dried in these manners are that they are particularly susceptible to damage The dried parts are fragile lack support and often catch on packing materials They must therefore be packed especially carefully and stored in small boxes or tubes with some appropriate packing material that does not snag and break small projections Acid-free tissue paper is often used Drying in desiccant silica gel crystals or powder can also have the disadvantage that it is difficult to remove all traces of the silica gel after drying

86

Special preservation and processing techniquesWet or spirit collections

Very fleshy or delicate structures including small algae and orchid flowers are best preserved in an air-tight glass or plastic jar with a liquid preservative rather than by drying The type of preservative used should be clearly labelled in the jar Such material is often referred to as a spirit collection or wet collection

Most material can be satisfactorily preserved in 70 ethyl alcohol (or 70 methylated spirit or denatured alcohol) with 30 water Colours will fade quickly in spirit however so it is a good idea to keep comprehensive notes and photographs

87

Small algae Microscopic algae are often collected in a jar and in the

water in which they were found If the algae are to be stored for more than 2-3 days a preservative needs to be used Traditionally this has been the extremely toxic formalin - a small amount can be added to the water to make a 5 final solution and the container labelled This must not be sent through the post or by courier

There are some other equally toxic options for example propylene phenoxytol but none should be sent through the post A safer option is to add sufficient concentrated alcohol or methylated spirits to the water containing the algae to make a final solution of 70 alcohol This treatment dilutes the algae making them difficult to find so if they can be concentrated somehow first (eg by filtering) they can be stored in much less liquid Another option is to fix the algae in formalin (or something similar) first and then prepare a microscope glass slide with a permanent water-soluble mounting medium

88

Mounting Mounting specimens prevents most fragile material from

fragmenting and prevents specimens becoming separated from their labels If the plant collection is a long-term project specimens should be mounted on sheets of archival (permanent) cardboard or paper with archival-quality fixing media These include stitching with cotton thread dental floss nickel-plated copper wire (for heavier specimens) narrow strips of archival paper linen tape or by using an archival adhesive such as methyl cellulose adhesive

One disadvantage of mounting specimens is that it can make parts of the specimen inaccessible for examination so it is essential that this be borne in mind during specimen arrangement and mounting For example easily reversible mounting media should be used specimens should be strapped to the sheet rather than glued all over and the specimen should be carefully arranged before it is attached so that it shows all features

89

Full-size herbarium mounting sheets are usually about 43 cm long x 28 cm wide The plant name and accompanying field notes should be transcribed on a permanent label stuck to one corner of the herbarium sheet (the bottom right-hand corner being the most common) or sometimes annotations may be written directly on the sheet or card

Small pieces of material which may have become separated from the specimen (eg seeds) can be placed in small plastic bags and pinned to the sheet

90

Long-term preservation and storage The long-term preservation of dry plant

specimens is largely dependent on protection from insect attack Specimens collected by Linnaeus in the eighteenth century and by Banks and Solander on the Endeavour voyage in 1788 are still excellently preserved

91

Pests and their control A range of pests attack dried plant material The

most common pests are insects and fungi though rodents and other large animals can cause damage in poor storage conditions Insects eat the material the paper surrounding the material and the adhesives and mounting media

Such insect pests range from psocids (book lice) which attack mainly the softer parts such as flowers and soft fruits to tobacco beetles and carpet beetles which can bore holes through the toughest of specimens Many insects are particularly sensitive to relative humidity levels and do not thrive at levels below 50

92

The most common and acceptable specimen treatments for insect control are Freezing Microwave Poisoning Insect deterrents Fungal pests

93

Storage

Dried and pressed plant specimens can be stored in cardboard or plastic boxes or tied in bundles in light-weight cardboard folders placed in pigeon holes

Alternatively they can be placed in protective plastic jackets and displayed in ring folders which is recommended if they are to be frequently handled such as for a reference collection

94

Filing

Specimens should be filed in a systematic order if a relatively permanent collection is being made The major groups ie ferns and fern allies cycads conifers dicotyledons and monocotyledons are best kept separately or according to some classification scheme such as that given in a flora or handbook

Similarly the genera within each family and the species within each genus may be filed alphabetically or following some such classification

95

Preservation of entire animals

Types of collection specimens of an entire animal For reference collections mammals can be prepared as a variety of specimens The condition of the specimen may determine possible ways to preserve it if for instance decomposition of the skin has loosened the hair of a carcass so much that it can easily be pulled out or removed by rubbing (ldquoslippingrdquo fur) it will be very difficult or impossible to produce a study skin or mounted specimen The most usual types of specimens (based on Nagorsen and Peterson 1980) are 1) entire fluid-preserved animals (for studying anatomy and histology fluid preservation may change the fur colour) 2) study skins with accompanying skulls partial skeletons (some bones remain in the skin) for studying pelage colour hair quality and moulting patterns 3) mounted skins with accompanying partial or entire skeleton (some bones may remain in the skin dependant on the method of preservation) or freeze-dried specimens 4) entire skeletons for instance for studying anatomy geographic variation or for age determination (entire skeletons are poorly represented in collections so Nagorsen and Peterson (1980) recommend preparation of at least one male and one female skeleton per species

96

Preservation of specimens in the field Formalin preservation Preservation in alcohol Preservation by cooling or freezing

97

Formalin preservation After weighing and measuring the animal and attaching an

adequate label very small specimens (up to 100 g) can be fixed whole by submerging them in 10 buffered formalin (tissue - formalin solution ratio of at least 1 12) the body cavity can be filled with formalin solution by injection until it is turgid and firm some formalin may also be injected under the skin into the body cavity larger muscles and organs If hypodermic needles are not available the body cavity can be opened ventrally by making a slit instead allowing the formalin to enter

Keeping the mouth open with a piece of wood or cotton may later allow examination of teeth Then the whole body can be immersed in formalin in the posture in which it is supposed to stay permanently because it will harden The ratio of formalin to carcass must be at least 12 to 1 to assure a good fixation Tissues can be left in buffered neutralized formalin for several months but formalin hardens specimens therefore after fixation longterm storage in alcohol may be better After preservation the carcass should therefore be washed in water and transferred into ethanol for permanent storage

Disadvantages for instance it discolours the fur after a longish immersion softens the bones and prevents further examination for microbiology

98

Preservation in alcohol

After weighing a whole animal can be preserved in a container of alcohol (70-90) Removal of the intestine prior to storage of the animal in alcohol is recommended

99

Preservation by cooling or freezing Removal of the skin with insulating fur

before cooling or freezing may help to cool the carcass down more quickly

Freezing is not recommended if histological examination is planned

100

THANK YOU

45

Capture-recapture Techniques- useful for mobile animals which can be marked

- capture marked released randomly recaptured

and marked individuals recorded

no of marked individuals recaptured total no of individuals in 1st sample

-------------------------------------------- = ------------------------------------------

total no of individuals in 2nd sample estimated size of population

(the Lincoln Index)

46

Capture-recapture Techniques Factors affecting the accuracy of the estimation

deaths migration individuals become more liable to predation etc

Examples

- arthropods marked on their backs with non-toxic paint

- fish have tags attached to opercula - mammals have tags clipped to their ears

birds have their legs ringed

47

Capture-recapture Method Important tool for estimating density birth

rate and death rate for mobile animals Method

Collect a sample of individuals mark them and then release them

After a period collect more individuals from the wild and count the number that have marks

We assume that a sample if random will contain the same proportion of marked individuals as the population does

Estimate population density

48

Assumptions For All Capture-Recapture Studies Marking technique does not increase

mortality of marked animals Marked individuals are allowed to mix

with population Marking technique does not affect catch

probability Marks are not lost or overlooked No significant immigration or emigration No significant mortality or natality

49

Marked animals in second sample

Total caught in second sample

Marked animals in first sample

Total population size

=

520 N

16=

Peterson Method or Lincoln Index

N = 64N = (20)(16)5

50

Some Indices Used

Traps Number of Fecal

Pellets Vocalization

Frequency Pelt Records Catch per Unit

Fishing Effort

Number of Artifacts Questionnaires Cover Feeding Capacity Roadside Counts

51

Abundance Scales

The population size may be fairly accurately determined by making some form of frequency assessment

These are subjective and involve an experimenter making some estimate of the number of individuals in a given area or the cover of a particular species

This is especially useful where individuals are very numerous eg barnacles on a rocky shore or where it is difficult to distinguish individuals eg grass plants in a meadow

52

The assessments are usually made on an abundance scale of 5 categories

Abundance Common Frequent Occasional Rare

Barnacles exposed at low water

53

Environmental resistance are the factors which limit the growth of a particular population

eg predation disease availability of light food water oxygen and shelter the accumulation of toxic wastes and even the size of the population itself

54

Density-dependent Growth A population is a density-dependent when its size

(or density) affects its growth rate because of density-dependent factors such as food availability and toxic waste accumulation

Density-independent Growth In this type of growth a population increases until

some factor causes a sudden reduction in its size Its effect is the same regardless of the size of the

population eg temperature fires floods storms etc

55

Regulation of Population Size Fecundity is the reproductive capacity of individual

females of a species Birth rate or natality is used to measure fecundity Death rate or mortality is the number of individuals

of a species which die per unit time Immigration occurs when individuals join a

population from neighbouring ones Emigration occurs when individuals depart from a

population A cycle occurs when the size of a population

fluctuates on a regular basis

56

Ecological Sampling

57

Why Do We Sample Determine presence andor

abundance

Monitor population fluctuations

Assess lsquoecological damagersquo

Assess quality of habitat

Assess population responses

58

What Do We Sample

Physical Environment Temperature DO pH salinity clarity

flow sediment

Biotic Environment All living things

59

Physical Habitat Temperature

Mercury thermometer Electronic thermometer Long-term thermometers

Dissolved Oxygen Winkler method (titration) DO meter (electrode)

pH Litmus paper pH meter (electrode)

Salinity Salinity Meter YSI 550A DO Meter w12 cable

60

Water Clarity Secchi Disk

Disk is attached to a calibrated rope The disk is lowered into the water until the white parts can no longer be seen Secchi disk depth is then recorded and serves as the waters transparency index The clearer the water the greater the secchi disk depth

Secchi Disk

61

Current Velocity (flow) Floating-orange method

Put an orange (or something else that floats just below the water surface) and measure the time it takes it to float across a known distance

Odometer-type flow meter Number of revolutions the propeller

makes for a given time is calibrated to flow velocity

62

Sediment Sediment size is important to many

aquatic organisms Sieversquos are used to separate and

grade sediment samples Percent of each size grade can be

determined

63

Water Sample

Water and plankton from various depths can be collected

A trigger mechanism is used to close the sampler Sample is then brought back to the

surface

64

Small Mammals

Mouserat Traps Fatal

Pit Falls Bucket is placed in the ground Sometimes have lsquoleadsrsquo to the buckets

Live traps Havahart Sherman

Spot-light

Sherman trapHavahart trap

65

Birds Stick-under-the-box method Bird-trap

Works like a minnow trap Mist net

Captures birds in flight Rocket net

Uses a propellant to throw a net over birds

66

Terrestrial Insects

Sticky paper flies

Baited Traps Fire ants

Nets butterflies

Foggers Collect insects from tree canopies

67

Aquatic Insects Drift Net

Place net in flowing water Kick Net

lsquoKickrsquo sediment upstream from block net and the flow will wash them into the net

Wash bucket Serber or Hess Sampler

Stir up known area of sediment

Animals are collected by a catch net

Multi-plate Sampler Become colonized

68

Crawfish and Crab Traps

69

Fish Larvae Light Traps

Larvae are attracted to the light Ichthyoplankton nets

Can be towed at various depths Fish collect at the lsquocodrsquoend

70

Fish Lift net

Net is placed down and after a set amount of time it is quickly lifted

Pop-net Similar to a lift net but

floats are attached to a framed net

Operated by a trigger mechanism

Throw net A net attached to a heavy

frame is thrown and every thing inside is netted out Throw net

Pop-net

Lift net

71

Minnow trap

Usually use bait to attract small fish Light is used sometimes as an attractant

72

Fish Electrofishing

Electricity is put into the water Fish are temporarily stunned and usually

swim towards the electricity source Usually non-fatal but may cause some

damage

73

Fish Gill Net

Gill nets resemble tennis nets Fish can not swim completely through the

net and get caught Gill nets are size selective (based on mesh

size) Square Mesh

Bar mesh

Stretch mesh

74

Fish Trammel Net

Three panels two large mesh on the outside and a small mesh on the inside

Fish swim through the outer mesh pushes the small mesh through the other side and becomes entangled

75

Hoop nets (and other similar nets) can have bait or not

Fyke nets have leads to help guide fish to the net

76

Seine Seines are nets that are pulled

through shallow water to catch fish

77

Purse Seine Used to encircle entire schools of fish

Usually involves a spotter plane and a second boat

78

Trotline (longline) A series of baited drop lines

connected to a main line

Can be deployed by tying one end to the bank and tying the other end with a heavy weight

79

Shrimp (or fish) Trawl Net pulled behind

a boat along the bottom Either a beam or

otter boards keep the net open

80

Tagging Individuals Coded Wire Tags

Microwire that has a unique label

Magnetic wand detects the tag

Tag retention should be determined

T-Bar tags Can be individually

numbered External tag

PIT tags (Passive Integrated Transponders) Wand induces the tag to

transmit individual number is displayed

81

Other Tagging Methods

Toe clip Amphibian and reptile Clip of one or more toes

to identify individuals

Bird Band Place a metal band on a

bird leg Generally has

identification information

82

Preserving plant specimens Pressing and drying Long-term

preservation and storage

Alternative drying techniques

Special preservation and processing techniques

Mounting

83

Pressing and drying Techniques for pressing and drying specimens have been

established for many years There are minor variations in recommended methods but they are essentially the same worldwide

The best specimens are plants that are pressed as soon as possible after collection before wilting and shrivelling Most plants may be kept in sealed containers such as plastic bags for up to a day if it is inconvenient to press immediately However some plants show such rapid wilting particularly of the flowers that such delays are best avoided Flowers with a lot of nectar may go mouldy very quickly if excess nectar is not shaken off before pressing

Specimens are pressed flat and dried between sheets of absorbent blotters or semi-absorbent paper such as newspaper Papers with a glossy surface should be avoided because they are not absorbent enough to aid drying The plant should be carefully laid out between the drying sheets as their form at this stage largely determines their ultimate appearance The flowers should be spread out with the petals carefully arranged wilted leaves should be straightened and unnecessary shoots of excessively twiggy shrubs may be cut away

84

Microwave ovens Small numbers of specimens can be dried using a microwave

oven The technique recommended in the literature is to place the specimens between unprinted absorbent paper for example butchers paper not newspaper which is unsuitable because the chemicals present in the ink may cause a fire The specimens should be put in a special press which should be of a microwave-safe material (wood acrylic or polycarbonate sheeting eg plexiglass or perspex NO metal components) If such a press is not available sheets of cardboard can be placed above and below the specimens and then weighted down

Drying time depends on the power of your oven In most cases drying is accomplished by irradiating at maximum power for 1-2 minutes per specimen although it is often a case of trial and error It is best to process no more than 10-12 specimens of average thickness per batch Specimens are usually dried after the moisture that characteristically appears on the glass door has disappeared If the specimen is damp when taken out of the oven allow it to stand before re-radiating as moisture continues to evaporate from the specimen for some time Care must be taken not to irradiate the specimens for too long

It should be noted that microwave treatment damages seeds and the cellular structure of the plants which may reduce the long-term value of the specimens

85

Alternative drying techniquesSilica gelother desiccants amp freeze drying Alternative methods of drying plant specimens have been

used for some time but are mostly restricted to special purpose collections The main alternatives are freeze-drying and drying in a desiccant powder such as desiccant silica gel In general these techniques are used where it is essential to preserve the shape of a delicate plant of organ of the plant such as the flower Freeze-drying has also been used to preserve the chemical composition of a plant as accurately as possible for later study

Disadvantages and special conservation problems of specimens dried in these manners are that they are particularly susceptible to damage The dried parts are fragile lack support and often catch on packing materials They must therefore be packed especially carefully and stored in small boxes or tubes with some appropriate packing material that does not snag and break small projections Acid-free tissue paper is often used Drying in desiccant silica gel crystals or powder can also have the disadvantage that it is difficult to remove all traces of the silica gel after drying

86

Special preservation and processing techniquesWet or spirit collections

Very fleshy or delicate structures including small algae and orchid flowers are best preserved in an air-tight glass or plastic jar with a liquid preservative rather than by drying The type of preservative used should be clearly labelled in the jar Such material is often referred to as a spirit collection or wet collection

Most material can be satisfactorily preserved in 70 ethyl alcohol (or 70 methylated spirit or denatured alcohol) with 30 water Colours will fade quickly in spirit however so it is a good idea to keep comprehensive notes and photographs

87

Small algae Microscopic algae are often collected in a jar and in the

water in which they were found If the algae are to be stored for more than 2-3 days a preservative needs to be used Traditionally this has been the extremely toxic formalin - a small amount can be added to the water to make a 5 final solution and the container labelled This must not be sent through the post or by courier

There are some other equally toxic options for example propylene phenoxytol but none should be sent through the post A safer option is to add sufficient concentrated alcohol or methylated spirits to the water containing the algae to make a final solution of 70 alcohol This treatment dilutes the algae making them difficult to find so if they can be concentrated somehow first (eg by filtering) they can be stored in much less liquid Another option is to fix the algae in formalin (or something similar) first and then prepare a microscope glass slide with a permanent water-soluble mounting medium

88

Mounting Mounting specimens prevents most fragile material from

fragmenting and prevents specimens becoming separated from their labels If the plant collection is a long-term project specimens should be mounted on sheets of archival (permanent) cardboard or paper with archival-quality fixing media These include stitching with cotton thread dental floss nickel-plated copper wire (for heavier specimens) narrow strips of archival paper linen tape or by using an archival adhesive such as methyl cellulose adhesive

One disadvantage of mounting specimens is that it can make parts of the specimen inaccessible for examination so it is essential that this be borne in mind during specimen arrangement and mounting For example easily reversible mounting media should be used specimens should be strapped to the sheet rather than glued all over and the specimen should be carefully arranged before it is attached so that it shows all features

89

Full-size herbarium mounting sheets are usually about 43 cm long x 28 cm wide The plant name and accompanying field notes should be transcribed on a permanent label stuck to one corner of the herbarium sheet (the bottom right-hand corner being the most common) or sometimes annotations may be written directly on the sheet or card

Small pieces of material which may have become separated from the specimen (eg seeds) can be placed in small plastic bags and pinned to the sheet

90

Long-term preservation and storage The long-term preservation of dry plant

specimens is largely dependent on protection from insect attack Specimens collected by Linnaeus in the eighteenth century and by Banks and Solander on the Endeavour voyage in 1788 are still excellently preserved

91

Pests and their control A range of pests attack dried plant material The

most common pests are insects and fungi though rodents and other large animals can cause damage in poor storage conditions Insects eat the material the paper surrounding the material and the adhesives and mounting media

Such insect pests range from psocids (book lice) which attack mainly the softer parts such as flowers and soft fruits to tobacco beetles and carpet beetles which can bore holes through the toughest of specimens Many insects are particularly sensitive to relative humidity levels and do not thrive at levels below 50

92

The most common and acceptable specimen treatments for insect control are Freezing Microwave Poisoning Insect deterrents Fungal pests

93

Storage

Dried and pressed plant specimens can be stored in cardboard or plastic boxes or tied in bundles in light-weight cardboard folders placed in pigeon holes

Alternatively they can be placed in protective plastic jackets and displayed in ring folders which is recommended if they are to be frequently handled such as for a reference collection

94

Filing

Specimens should be filed in a systematic order if a relatively permanent collection is being made The major groups ie ferns and fern allies cycads conifers dicotyledons and monocotyledons are best kept separately or according to some classification scheme such as that given in a flora or handbook

Similarly the genera within each family and the species within each genus may be filed alphabetically or following some such classification

95

Preservation of entire animals

Types of collection specimens of an entire animal For reference collections mammals can be prepared as a variety of specimens The condition of the specimen may determine possible ways to preserve it if for instance decomposition of the skin has loosened the hair of a carcass so much that it can easily be pulled out or removed by rubbing (ldquoslippingrdquo fur) it will be very difficult or impossible to produce a study skin or mounted specimen The most usual types of specimens (based on Nagorsen and Peterson 1980) are 1) entire fluid-preserved animals (for studying anatomy and histology fluid preservation may change the fur colour) 2) study skins with accompanying skulls partial skeletons (some bones remain in the skin) for studying pelage colour hair quality and moulting patterns 3) mounted skins with accompanying partial or entire skeleton (some bones may remain in the skin dependant on the method of preservation) or freeze-dried specimens 4) entire skeletons for instance for studying anatomy geographic variation or for age determination (entire skeletons are poorly represented in collections so Nagorsen and Peterson (1980) recommend preparation of at least one male and one female skeleton per species

96

Preservation of specimens in the field Formalin preservation Preservation in alcohol Preservation by cooling or freezing

97

Formalin preservation After weighing and measuring the animal and attaching an

adequate label very small specimens (up to 100 g) can be fixed whole by submerging them in 10 buffered formalin (tissue - formalin solution ratio of at least 1 12) the body cavity can be filled with formalin solution by injection until it is turgid and firm some formalin may also be injected under the skin into the body cavity larger muscles and organs If hypodermic needles are not available the body cavity can be opened ventrally by making a slit instead allowing the formalin to enter

Keeping the mouth open with a piece of wood or cotton may later allow examination of teeth Then the whole body can be immersed in formalin in the posture in which it is supposed to stay permanently because it will harden The ratio of formalin to carcass must be at least 12 to 1 to assure a good fixation Tissues can be left in buffered neutralized formalin for several months but formalin hardens specimens therefore after fixation longterm storage in alcohol may be better After preservation the carcass should therefore be washed in water and transferred into ethanol for permanent storage

Disadvantages for instance it discolours the fur after a longish immersion softens the bones and prevents further examination for microbiology

98

Preservation in alcohol

After weighing a whole animal can be preserved in a container of alcohol (70-90) Removal of the intestine prior to storage of the animal in alcohol is recommended

99

Preservation by cooling or freezing Removal of the skin with insulating fur

before cooling or freezing may help to cool the carcass down more quickly

Freezing is not recommended if histological examination is planned

100

THANK YOU

46

Capture-recapture Techniques Factors affecting the accuracy of the estimation

deaths migration individuals become more liable to predation etc

Examples

- arthropods marked on their backs with non-toxic paint

- fish have tags attached to opercula - mammals have tags clipped to their ears

birds have their legs ringed

47

Capture-recapture Method Important tool for estimating density birth

rate and death rate for mobile animals Method

Collect a sample of individuals mark them and then release them

After a period collect more individuals from the wild and count the number that have marks

We assume that a sample if random will contain the same proportion of marked individuals as the population does

Estimate population density

48

Assumptions For All Capture-Recapture Studies Marking technique does not increase

mortality of marked animals Marked individuals are allowed to mix

with population Marking technique does not affect catch

probability Marks are not lost or overlooked No significant immigration or emigration No significant mortality or natality

49

Marked animals in second sample

Total caught in second sample

Marked animals in first sample

Total population size

=

520 N

16=

Peterson Method or Lincoln Index

N = 64N = (20)(16)5

50

Some Indices Used

Traps Number of Fecal

Pellets Vocalization

Frequency Pelt Records Catch per Unit

Fishing Effort

Number of Artifacts Questionnaires Cover Feeding Capacity Roadside Counts

51

Abundance Scales

The population size may be fairly accurately determined by making some form of frequency assessment

These are subjective and involve an experimenter making some estimate of the number of individuals in a given area or the cover of a particular species

This is especially useful where individuals are very numerous eg barnacles on a rocky shore or where it is difficult to distinguish individuals eg grass plants in a meadow

52

The assessments are usually made on an abundance scale of 5 categories

Abundance Common Frequent Occasional Rare

Barnacles exposed at low water

53

Environmental resistance are the factors which limit the growth of a particular population

eg predation disease availability of light food water oxygen and shelter the accumulation of toxic wastes and even the size of the population itself

54

Density-dependent Growth A population is a density-dependent when its size

(or density) affects its growth rate because of density-dependent factors such as food availability and toxic waste accumulation

Density-independent Growth In this type of growth a population increases until

some factor causes a sudden reduction in its size Its effect is the same regardless of the size of the

population eg temperature fires floods storms etc

55

Regulation of Population Size Fecundity is the reproductive capacity of individual

females of a species Birth rate or natality is used to measure fecundity Death rate or mortality is the number of individuals

of a species which die per unit time Immigration occurs when individuals join a

population from neighbouring ones Emigration occurs when individuals depart from a

population A cycle occurs when the size of a population

fluctuates on a regular basis

56

Ecological Sampling

57

Why Do We Sample Determine presence andor

abundance

Monitor population fluctuations

Assess lsquoecological damagersquo

Assess quality of habitat

Assess population responses

58

What Do We Sample

Physical Environment Temperature DO pH salinity clarity

flow sediment

Biotic Environment All living things

59

Physical Habitat Temperature

Mercury thermometer Electronic thermometer Long-term thermometers

Dissolved Oxygen Winkler method (titration) DO meter (electrode)

pH Litmus paper pH meter (electrode)

Salinity Salinity Meter YSI 550A DO Meter w12 cable

60

Water Clarity Secchi Disk

Disk is attached to a calibrated rope The disk is lowered into the water until the white parts can no longer be seen Secchi disk depth is then recorded and serves as the waters transparency index The clearer the water the greater the secchi disk depth

Secchi Disk

61

Current Velocity (flow) Floating-orange method

Put an orange (or something else that floats just below the water surface) and measure the time it takes it to float across a known distance

Odometer-type flow meter Number of revolutions the propeller

makes for a given time is calibrated to flow velocity

62

Sediment Sediment size is important to many

aquatic organisms Sieversquos are used to separate and

grade sediment samples Percent of each size grade can be

determined

63

Water Sample

Water and plankton from various depths can be collected

A trigger mechanism is used to close the sampler Sample is then brought back to the

surface

64

Small Mammals

Mouserat Traps Fatal

Pit Falls Bucket is placed in the ground Sometimes have lsquoleadsrsquo to the buckets

Live traps Havahart Sherman

Spot-light

Sherman trapHavahart trap

65

Birds Stick-under-the-box method Bird-trap

Works like a minnow trap Mist net

Captures birds in flight Rocket net

Uses a propellant to throw a net over birds

66

Terrestrial Insects

Sticky paper flies

Baited Traps Fire ants

Nets butterflies

Foggers Collect insects from tree canopies

67

Aquatic Insects Drift Net

Place net in flowing water Kick Net

lsquoKickrsquo sediment upstream from block net and the flow will wash them into the net

Wash bucket Serber or Hess Sampler

Stir up known area of sediment

Animals are collected by a catch net

Multi-plate Sampler Become colonized

68

Crawfish and Crab Traps

69

Fish Larvae Light Traps

Larvae are attracted to the light Ichthyoplankton nets

Can be towed at various depths Fish collect at the lsquocodrsquoend

70

Fish Lift net

Net is placed down and after a set amount of time it is quickly lifted

Pop-net Similar to a lift net but

floats are attached to a framed net

Operated by a trigger mechanism

Throw net A net attached to a heavy

frame is thrown and every thing inside is netted out Throw net

Pop-net

Lift net

71

Minnow trap

Usually use bait to attract small fish Light is used sometimes as an attractant

72

Fish Electrofishing

Electricity is put into the water Fish are temporarily stunned and usually

swim towards the electricity source Usually non-fatal but may cause some

damage

73

Fish Gill Net

Gill nets resemble tennis nets Fish can not swim completely through the

net and get caught Gill nets are size selective (based on mesh

size) Square Mesh

Bar mesh

Stretch mesh

74

Fish Trammel Net

Three panels two large mesh on the outside and a small mesh on the inside

Fish swim through the outer mesh pushes the small mesh through the other side and becomes entangled

75

Hoop nets (and other similar nets) can have bait or not

Fyke nets have leads to help guide fish to the net

76

Seine Seines are nets that are pulled

through shallow water to catch fish

77

Purse Seine Used to encircle entire schools of fish

Usually involves a spotter plane and a second boat

78

Trotline (longline) A series of baited drop lines

connected to a main line

Can be deployed by tying one end to the bank and tying the other end with a heavy weight

79

Shrimp (or fish) Trawl Net pulled behind

a boat along the bottom Either a beam or

otter boards keep the net open

80

Tagging Individuals Coded Wire Tags

Microwire that has a unique label

Magnetic wand detects the tag

Tag retention should be determined

T-Bar tags Can be individually

numbered External tag

PIT tags (Passive Integrated Transponders) Wand induces the tag to

transmit individual number is displayed

81

Other Tagging Methods

Toe clip Amphibian and reptile Clip of one or more toes

to identify individuals

Bird Band Place a metal band on a

bird leg Generally has

identification information

82

Preserving plant specimens Pressing and drying Long-term

preservation and storage

Alternative drying techniques

Special preservation and processing techniques

Mounting

83

Pressing and drying Techniques for pressing and drying specimens have been

established for many years There are minor variations in recommended methods but they are essentially the same worldwide

The best specimens are plants that are pressed as soon as possible after collection before wilting and shrivelling Most plants may be kept in sealed containers such as plastic bags for up to a day if it is inconvenient to press immediately However some plants show such rapid wilting particularly of the flowers that such delays are best avoided Flowers with a lot of nectar may go mouldy very quickly if excess nectar is not shaken off before pressing

Specimens are pressed flat and dried between sheets of absorbent blotters or semi-absorbent paper such as newspaper Papers with a glossy surface should be avoided because they are not absorbent enough to aid drying The plant should be carefully laid out between the drying sheets as their form at this stage largely determines their ultimate appearance The flowers should be spread out with the petals carefully arranged wilted leaves should be straightened and unnecessary shoots of excessively twiggy shrubs may be cut away

84

Microwave ovens Small numbers of specimens can be dried using a microwave

oven The technique recommended in the literature is to place the specimens between unprinted absorbent paper for example butchers paper not newspaper which is unsuitable because the chemicals present in the ink may cause a fire The specimens should be put in a special press which should be of a microwave-safe material (wood acrylic or polycarbonate sheeting eg plexiglass or perspex NO metal components) If such a press is not available sheets of cardboard can be placed above and below the specimens and then weighted down

Drying time depends on the power of your oven In most cases drying is accomplished by irradiating at maximum power for 1-2 minutes per specimen although it is often a case of trial and error It is best to process no more than 10-12 specimens of average thickness per batch Specimens are usually dried after the moisture that characteristically appears on the glass door has disappeared If the specimen is damp when taken out of the oven allow it to stand before re-radiating as moisture continues to evaporate from the specimen for some time Care must be taken not to irradiate the specimens for too long

It should be noted that microwave treatment damages seeds and the cellular structure of the plants which may reduce the long-term value of the specimens

85

Alternative drying techniquesSilica gelother desiccants amp freeze drying Alternative methods of drying plant specimens have been

used for some time but are mostly restricted to special purpose collections The main alternatives are freeze-drying and drying in a desiccant powder such as desiccant silica gel In general these techniques are used where it is essential to preserve the shape of a delicate plant of organ of the plant such as the flower Freeze-drying has also been used to preserve the chemical composition of a plant as accurately as possible for later study

Disadvantages and special conservation problems of specimens dried in these manners are that they are particularly susceptible to damage The dried parts are fragile lack support and often catch on packing materials They must therefore be packed especially carefully and stored in small boxes or tubes with some appropriate packing material that does not snag and break small projections Acid-free tissue paper is often used Drying in desiccant silica gel crystals or powder can also have the disadvantage that it is difficult to remove all traces of the silica gel after drying

86

Special preservation and processing techniquesWet or spirit collections

Very fleshy or delicate structures including small algae and orchid flowers are best preserved in an air-tight glass or plastic jar with a liquid preservative rather than by drying The type of preservative used should be clearly labelled in the jar Such material is often referred to as a spirit collection or wet collection

Most material can be satisfactorily preserved in 70 ethyl alcohol (or 70 methylated spirit or denatured alcohol) with 30 water Colours will fade quickly in spirit however so it is a good idea to keep comprehensive notes and photographs

87

Small algae Microscopic algae are often collected in a jar and in the

water in which they were found If the algae are to be stored for more than 2-3 days a preservative needs to be used Traditionally this has been the extremely toxic formalin - a small amount can be added to the water to make a 5 final solution and the container labelled This must not be sent through the post or by courier

There are some other equally toxic options for example propylene phenoxytol but none should be sent through the post A safer option is to add sufficient concentrated alcohol or methylated spirits to the water containing the algae to make a final solution of 70 alcohol This treatment dilutes the algae making them difficult to find so if they can be concentrated somehow first (eg by filtering) they can be stored in much less liquid Another option is to fix the algae in formalin (or something similar) first and then prepare a microscope glass slide with a permanent water-soluble mounting medium

88

Mounting Mounting specimens prevents most fragile material from

fragmenting and prevents specimens becoming separated from their labels If the plant collection is a long-term project specimens should be mounted on sheets of archival (permanent) cardboard or paper with archival-quality fixing media These include stitching with cotton thread dental floss nickel-plated copper wire (for heavier specimens) narrow strips of archival paper linen tape or by using an archival adhesive such as methyl cellulose adhesive

One disadvantage of mounting specimens is that it can make parts of the specimen inaccessible for examination so it is essential that this be borne in mind during specimen arrangement and mounting For example easily reversible mounting media should be used specimens should be strapped to the sheet rather than glued all over and the specimen should be carefully arranged before it is attached so that it shows all features

89

Full-size herbarium mounting sheets are usually about 43 cm long x 28 cm wide The plant name and accompanying field notes should be transcribed on a permanent label stuck to one corner of the herbarium sheet (the bottom right-hand corner being the most common) or sometimes annotations may be written directly on the sheet or card

Small pieces of material which may have become separated from the specimen (eg seeds) can be placed in small plastic bags and pinned to the sheet

90

Long-term preservation and storage The long-term preservation of dry plant

specimens is largely dependent on protection from insect attack Specimens collected by Linnaeus in the eighteenth century and by Banks and Solander on the Endeavour voyage in 1788 are still excellently preserved

91

Pests and their control A range of pests attack dried plant material The

most common pests are insects and fungi though rodents and other large animals can cause damage in poor storage conditions Insects eat the material the paper surrounding the material and the adhesives and mounting media

Such insect pests range from psocids (book lice) which attack mainly the softer parts such as flowers and soft fruits to tobacco beetles and carpet beetles which can bore holes through the toughest of specimens Many insects are particularly sensitive to relative humidity levels and do not thrive at levels below 50

92

The most common and acceptable specimen treatments for insect control are Freezing Microwave Poisoning Insect deterrents Fungal pests

93

Storage

Dried and pressed plant specimens can be stored in cardboard or plastic boxes or tied in bundles in light-weight cardboard folders placed in pigeon holes

Alternatively they can be placed in protective plastic jackets and displayed in ring folders which is recommended if they are to be frequently handled such as for a reference collection

94

Filing

Specimens should be filed in a systematic order if a relatively permanent collection is being made The major groups ie ferns and fern allies cycads conifers dicotyledons and monocotyledons are best kept separately or according to some classification scheme such as that given in a flora or handbook

Similarly the genera within each family and the species within each genus may be filed alphabetically or following some such classification

95

Preservation of entire animals

Types of collection specimens of an entire animal For reference collections mammals can be prepared as a variety of specimens The condition of the specimen may determine possible ways to preserve it if for instance decomposition of the skin has loosened the hair of a carcass so much that it can easily be pulled out or removed by rubbing (ldquoslippingrdquo fur) it will be very difficult or impossible to produce a study skin or mounted specimen The most usual types of specimens (based on Nagorsen and Peterson 1980) are 1) entire fluid-preserved animals (for studying anatomy and histology fluid preservation may change the fur colour) 2) study skins with accompanying skulls partial skeletons (some bones remain in the skin) for studying pelage colour hair quality and moulting patterns 3) mounted skins with accompanying partial or entire skeleton (some bones may remain in the skin dependant on the method of preservation) or freeze-dried specimens 4) entire skeletons for instance for studying anatomy geographic variation or for age determination (entire skeletons are poorly represented in collections so Nagorsen and Peterson (1980) recommend preparation of at least one male and one female skeleton per species

96

Preservation of specimens in the field Formalin preservation Preservation in alcohol Preservation by cooling or freezing

97

Formalin preservation After weighing and measuring the animal and attaching an

adequate label very small specimens (up to 100 g) can be fixed whole by submerging them in 10 buffered formalin (tissue - formalin solution ratio of at least 1 12) the body cavity can be filled with formalin solution by injection until it is turgid and firm some formalin may also be injected under the skin into the body cavity larger muscles and organs If hypodermic needles are not available the body cavity can be opened ventrally by making a slit instead allowing the formalin to enter

Keeping the mouth open with a piece of wood or cotton may later allow examination of teeth Then the whole body can be immersed in formalin in the posture in which it is supposed to stay permanently because it will harden The ratio of formalin to carcass must be at least 12 to 1 to assure a good fixation Tissues can be left in buffered neutralized formalin for several months but formalin hardens specimens therefore after fixation longterm storage in alcohol may be better After preservation the carcass should therefore be washed in water and transferred into ethanol for permanent storage

Disadvantages for instance it discolours the fur after a longish immersion softens the bones and prevents further examination for microbiology

98

Preservation in alcohol

After weighing a whole animal can be preserved in a container of alcohol (70-90) Removal of the intestine prior to storage of the animal in alcohol is recommended

99

Preservation by cooling or freezing Removal of the skin with insulating fur

before cooling or freezing may help to cool the carcass down more quickly

Freezing is not recommended if histological examination is planned

100

THANK YOU

47

Capture-recapture Method Important tool for estimating density birth

rate and death rate for mobile animals Method

Collect a sample of individuals mark them and then release them

After a period collect more individuals from the wild and count the number that have marks

We assume that a sample if random will contain the same proportion of marked individuals as the population does

Estimate population density

48

Assumptions For All Capture-Recapture Studies Marking technique does not increase

mortality of marked animals Marked individuals are allowed to mix

with population Marking technique does not affect catch

probability Marks are not lost or overlooked No significant immigration or emigration No significant mortality or natality

49

Marked animals in second sample

Total caught in second sample

Marked animals in first sample

Total population size

=

520 N

16=

Peterson Method or Lincoln Index

N = 64N = (20)(16)5

50

Some Indices Used

Traps Number of Fecal

Pellets Vocalization

Frequency Pelt Records Catch per Unit

Fishing Effort

Number of Artifacts Questionnaires Cover Feeding Capacity Roadside Counts

51

Abundance Scales

The population size may be fairly accurately determined by making some form of frequency assessment

These are subjective and involve an experimenter making some estimate of the number of individuals in a given area or the cover of a particular species

This is especially useful where individuals are very numerous eg barnacles on a rocky shore or where it is difficult to distinguish individuals eg grass plants in a meadow

52

The assessments are usually made on an abundance scale of 5 categories

Abundance Common Frequent Occasional Rare

Barnacles exposed at low water

53

Environmental resistance are the factors which limit the growth of a particular population

eg predation disease availability of light food water oxygen and shelter the accumulation of toxic wastes and even the size of the population itself

54

Density-dependent Growth A population is a density-dependent when its size

(or density) affects its growth rate because of density-dependent factors such as food availability and toxic waste accumulation

Density-independent Growth In this type of growth a population increases until

some factor causes a sudden reduction in its size Its effect is the same regardless of the size of the

population eg temperature fires floods storms etc

55

Regulation of Population Size Fecundity is the reproductive capacity of individual

females of a species Birth rate or natality is used to measure fecundity Death rate or mortality is the number of individuals

of a species which die per unit time Immigration occurs when individuals join a

population from neighbouring ones Emigration occurs when individuals depart from a

population A cycle occurs when the size of a population

fluctuates on a regular basis

56

Ecological Sampling

57

Why Do We Sample Determine presence andor

abundance

Monitor population fluctuations

Assess lsquoecological damagersquo

Assess quality of habitat

Assess population responses

58

What Do We Sample

Physical Environment Temperature DO pH salinity clarity

flow sediment

Biotic Environment All living things

59

Physical Habitat Temperature

Mercury thermometer Electronic thermometer Long-term thermometers

Dissolved Oxygen Winkler method (titration) DO meter (electrode)

pH Litmus paper pH meter (electrode)

Salinity Salinity Meter YSI 550A DO Meter w12 cable

60

Water Clarity Secchi Disk

Disk is attached to a calibrated rope The disk is lowered into the water until the white parts can no longer be seen Secchi disk depth is then recorded and serves as the waters transparency index The clearer the water the greater the secchi disk depth

Secchi Disk

61

Current Velocity (flow) Floating-orange method

Put an orange (or something else that floats just below the water surface) and measure the time it takes it to float across a known distance

Odometer-type flow meter Number of revolutions the propeller

makes for a given time is calibrated to flow velocity

62

Sediment Sediment size is important to many

aquatic organisms Sieversquos are used to separate and

grade sediment samples Percent of each size grade can be

determined

63

Water Sample

Water and plankton from various depths can be collected

A trigger mechanism is used to close the sampler Sample is then brought back to the

surface

64

Small Mammals

Mouserat Traps Fatal

Pit Falls Bucket is placed in the ground Sometimes have lsquoleadsrsquo to the buckets

Live traps Havahart Sherman

Spot-light

Sherman trapHavahart trap

65

Birds Stick-under-the-box method Bird-trap

Works like a minnow trap Mist net

Captures birds in flight Rocket net

Uses a propellant to throw a net over birds

66

Terrestrial Insects

Sticky paper flies

Baited Traps Fire ants

Nets butterflies

Foggers Collect insects from tree canopies

67

Aquatic Insects Drift Net

Place net in flowing water Kick Net

lsquoKickrsquo sediment upstream from block net and the flow will wash them into the net

Wash bucket Serber or Hess Sampler

Stir up known area of sediment

Animals are collected by a catch net

Multi-plate Sampler Become colonized

68

Crawfish and Crab Traps

69

Fish Larvae Light Traps

Larvae are attracted to the light Ichthyoplankton nets

Can be towed at various depths Fish collect at the lsquocodrsquoend

70

Fish Lift net

Net is placed down and after a set amount of time it is quickly lifted

Pop-net Similar to a lift net but

floats are attached to a framed net

Operated by a trigger mechanism

Throw net A net attached to a heavy

frame is thrown and every thing inside is netted out Throw net

Pop-net

Lift net

71

Minnow trap

Usually use bait to attract small fish Light is used sometimes as an attractant

72

Fish Electrofishing

Electricity is put into the water Fish are temporarily stunned and usually

swim towards the electricity source Usually non-fatal but may cause some

damage

73

Fish Gill Net

Gill nets resemble tennis nets Fish can not swim completely through the

net and get caught Gill nets are size selective (based on mesh

size) Square Mesh

Bar mesh

Stretch mesh

74

Fish Trammel Net

Three panels two large mesh on the outside and a small mesh on the inside

Fish swim through the outer mesh pushes the small mesh through the other side and becomes entangled

75

Hoop nets (and other similar nets) can have bait or not

Fyke nets have leads to help guide fish to the net

76

Seine Seines are nets that are pulled

through shallow water to catch fish

77

Purse Seine Used to encircle entire schools of fish

Usually involves a spotter plane and a second boat

78

Trotline (longline) A series of baited drop lines

connected to a main line

Can be deployed by tying one end to the bank and tying the other end with a heavy weight

79

Shrimp (or fish) Trawl Net pulled behind

a boat along the bottom Either a beam or

otter boards keep the net open

80

Tagging Individuals Coded Wire Tags

Microwire that has a unique label

Magnetic wand detects the tag

Tag retention should be determined

T-Bar tags Can be individually

numbered External tag

PIT tags (Passive Integrated Transponders) Wand induces the tag to

transmit individual number is displayed

81

Other Tagging Methods

Toe clip Amphibian and reptile Clip of one or more toes

to identify individuals

Bird Band Place a metal band on a

bird leg Generally has

identification information

82

Preserving plant specimens Pressing and drying Long-term

preservation and storage

Alternative drying techniques

Special preservation and processing techniques

Mounting

83

Pressing and drying Techniques for pressing and drying specimens have been

established for many years There are minor variations in recommended methods but they are essentially the same worldwide

The best specimens are plants that are pressed as soon as possible after collection before wilting and shrivelling Most plants may be kept in sealed containers such as plastic bags for up to a day if it is inconvenient to press immediately However some plants show such rapid wilting particularly of the flowers that such delays are best avoided Flowers with a lot of nectar may go mouldy very quickly if excess nectar is not shaken off before pressing

Specimens are pressed flat and dried between sheets of absorbent blotters or semi-absorbent paper such as newspaper Papers with a glossy surface should be avoided because they are not absorbent enough to aid drying The plant should be carefully laid out between the drying sheets as their form at this stage largely determines their ultimate appearance The flowers should be spread out with the petals carefully arranged wilted leaves should be straightened and unnecessary shoots of excessively twiggy shrubs may be cut away

84

Microwave ovens Small numbers of specimens can be dried using a microwave

oven The technique recommended in the literature is to place the specimens between unprinted absorbent paper for example butchers paper not newspaper which is unsuitable because the chemicals present in the ink may cause a fire The specimens should be put in a special press which should be of a microwave-safe material (wood acrylic or polycarbonate sheeting eg plexiglass or perspex NO metal components) If such a press is not available sheets of cardboard can be placed above and below the specimens and then weighted down

Drying time depends on the power of your oven In most cases drying is accomplished by irradiating at maximum power for 1-2 minutes per specimen although it is often a case of trial and error It is best to process no more than 10-12 specimens of average thickness per batch Specimens are usually dried after the moisture that characteristically appears on the glass door has disappeared If the specimen is damp when taken out of the oven allow it to stand before re-radiating as moisture continues to evaporate from the specimen for some time Care must be taken not to irradiate the specimens for too long

It should be noted that microwave treatment damages seeds and the cellular structure of the plants which may reduce the long-term value of the specimens

85

Alternative drying techniquesSilica gelother desiccants amp freeze drying Alternative methods of drying plant specimens have been

used for some time but are mostly restricted to special purpose collections The main alternatives are freeze-drying and drying in a desiccant powder such as desiccant silica gel In general these techniques are used where it is essential to preserve the shape of a delicate plant of organ of the plant such as the flower Freeze-drying has also been used to preserve the chemical composition of a plant as accurately as possible for later study

Disadvantages and special conservation problems of specimens dried in these manners are that they are particularly susceptible to damage The dried parts are fragile lack support and often catch on packing materials They must therefore be packed especially carefully and stored in small boxes or tubes with some appropriate packing material that does not snag and break small projections Acid-free tissue paper is often used Drying in desiccant silica gel crystals or powder can also have the disadvantage that it is difficult to remove all traces of the silica gel after drying

86

Special preservation and processing techniquesWet or spirit collections

Very fleshy or delicate structures including small algae and orchid flowers are best preserved in an air-tight glass or plastic jar with a liquid preservative rather than by drying The type of preservative used should be clearly labelled in the jar Such material is often referred to as a spirit collection or wet collection

Most material can be satisfactorily preserved in 70 ethyl alcohol (or 70 methylated spirit or denatured alcohol) with 30 water Colours will fade quickly in spirit however so it is a good idea to keep comprehensive notes and photographs

87

Small algae Microscopic algae are often collected in a jar and in the

water in which they were found If the algae are to be stored for more than 2-3 days a preservative needs to be used Traditionally this has been the extremely toxic formalin - a small amount can be added to the water to make a 5 final solution and the container labelled This must not be sent through the post or by courier

There are some other equally toxic options for example propylene phenoxytol but none should be sent through the post A safer option is to add sufficient concentrated alcohol or methylated spirits to the water containing the algae to make a final solution of 70 alcohol This treatment dilutes the algae making them difficult to find so if they can be concentrated somehow first (eg by filtering) they can be stored in much less liquid Another option is to fix the algae in formalin (or something similar) first and then prepare a microscope glass slide with a permanent water-soluble mounting medium

88

Mounting Mounting specimens prevents most fragile material from

fragmenting and prevents specimens becoming separated from their labels If the plant collection is a long-term project specimens should be mounted on sheets of archival (permanent) cardboard or paper with archival-quality fixing media These include stitching with cotton thread dental floss nickel-plated copper wire (for heavier specimens) narrow strips of archival paper linen tape or by using an archival adhesive such as methyl cellulose adhesive

One disadvantage of mounting specimens is that it can make parts of the specimen inaccessible for examination so it is essential that this be borne in mind during specimen arrangement and mounting For example easily reversible mounting media should be used specimens should be strapped to the sheet rather than glued all over and the specimen should be carefully arranged before it is attached so that it shows all features

89

Full-size herbarium mounting sheets are usually about 43 cm long x 28 cm wide The plant name and accompanying field notes should be transcribed on a permanent label stuck to one corner of the herbarium sheet (the bottom right-hand corner being the most common) or sometimes annotations may be written directly on the sheet or card

Small pieces of material which may have become separated from the specimen (eg seeds) can be placed in small plastic bags and pinned to the sheet

90

Long-term preservation and storage The long-term preservation of dry plant

specimens is largely dependent on protection from insect attack Specimens collected by Linnaeus in the eighteenth century and by Banks and Solander on the Endeavour voyage in 1788 are still excellently preserved

91

Pests and their control A range of pests attack dried plant material The

most common pests are insects and fungi though rodents and other large animals can cause damage in poor storage conditions Insects eat the material the paper surrounding the material and the adhesives and mounting media

Such insect pests range from psocids (book lice) which attack mainly the softer parts such as flowers and soft fruits to tobacco beetles and carpet beetles which can bore holes through the toughest of specimens Many insects are particularly sensitive to relative humidity levels and do not thrive at levels below 50

92

The most common and acceptable specimen treatments for insect control are Freezing Microwave Poisoning Insect deterrents Fungal pests

93

Storage

Dried and pressed plant specimens can be stored in cardboard or plastic boxes or tied in bundles in light-weight cardboard folders placed in pigeon holes

Alternatively they can be placed in protective plastic jackets and displayed in ring folders which is recommended if they are to be frequently handled such as for a reference collection

94

Filing

Specimens should be filed in a systematic order if a relatively permanent collection is being made The major groups ie ferns and fern allies cycads conifers dicotyledons and monocotyledons are best kept separately or according to some classification scheme such as that given in a flora or handbook

Similarly the genera within each family and the species within each genus may be filed alphabetically or following some such classification

95

Preservation of entire animals

Types of collection specimens of an entire animal For reference collections mammals can be prepared as a variety of specimens The condition of the specimen may determine possible ways to preserve it if for instance decomposition of the skin has loosened the hair of a carcass so much that it can easily be pulled out or removed by rubbing (ldquoslippingrdquo fur) it will be very difficult or impossible to produce a study skin or mounted specimen The most usual types of specimens (based on Nagorsen and Peterson 1980) are 1) entire fluid-preserved animals (for studying anatomy and histology fluid preservation may change the fur colour) 2) study skins with accompanying skulls partial skeletons (some bones remain in the skin) for studying pelage colour hair quality and moulting patterns 3) mounted skins with accompanying partial or entire skeleton (some bones may remain in the skin dependant on the method of preservation) or freeze-dried specimens 4) entire skeletons for instance for studying anatomy geographic variation or for age determination (entire skeletons are poorly represented in collections so Nagorsen and Peterson (1980) recommend preparation of at least one male and one female skeleton per species

96

Preservation of specimens in the field Formalin preservation Preservation in alcohol Preservation by cooling or freezing

97

Formalin preservation After weighing and measuring the animal and attaching an

adequate label very small specimens (up to 100 g) can be fixed whole by submerging them in 10 buffered formalin (tissue - formalin solution ratio of at least 1 12) the body cavity can be filled with formalin solution by injection until it is turgid and firm some formalin may also be injected under the skin into the body cavity larger muscles and organs If hypodermic needles are not available the body cavity can be opened ventrally by making a slit instead allowing the formalin to enter

Keeping the mouth open with a piece of wood or cotton may later allow examination of teeth Then the whole body can be immersed in formalin in the posture in which it is supposed to stay permanently because it will harden The ratio of formalin to carcass must be at least 12 to 1 to assure a good fixation Tissues can be left in buffered neutralized formalin for several months but formalin hardens specimens therefore after fixation longterm storage in alcohol may be better After preservation the carcass should therefore be washed in water and transferred into ethanol for permanent storage

Disadvantages for instance it discolours the fur after a longish immersion softens the bones and prevents further examination for microbiology

98

Preservation in alcohol

After weighing a whole animal can be preserved in a container of alcohol (70-90) Removal of the intestine prior to storage of the animal in alcohol is recommended

99

Preservation by cooling or freezing Removal of the skin with insulating fur

before cooling or freezing may help to cool the carcass down more quickly

Freezing is not recommended if histological examination is planned

100

THANK YOU

48

Assumptions For All Capture-Recapture Studies Marking technique does not increase

mortality of marked animals Marked individuals are allowed to mix

with population Marking technique does not affect catch

probability Marks are not lost or overlooked No significant immigration or emigration No significant mortality or natality

49

Marked animals in second sample

Total caught in second sample

Marked animals in first sample

Total population size

=

520 N

16=

Peterson Method or Lincoln Index

N = 64N = (20)(16)5

50

Some Indices Used

Traps Number of Fecal

Pellets Vocalization

Frequency Pelt Records Catch per Unit

Fishing Effort

Number of Artifacts Questionnaires Cover Feeding Capacity Roadside Counts

51

Abundance Scales

The population size may be fairly accurately determined by making some form of frequency assessment

These are subjective and involve an experimenter making some estimate of the number of individuals in a given area or the cover of a particular species

This is especially useful where individuals are very numerous eg barnacles on a rocky shore or where it is difficult to distinguish individuals eg grass plants in a meadow

52

The assessments are usually made on an abundance scale of 5 categories

Abundance Common Frequent Occasional Rare

Barnacles exposed at low water

53

Environmental resistance are the factors which limit the growth of a particular population

eg predation disease availability of light food water oxygen and shelter the accumulation of toxic wastes and even the size of the population itself

54

Density-dependent Growth A population is a density-dependent when its size

(or density) affects its growth rate because of density-dependent factors such as food availability and toxic waste accumulation

Density-independent Growth In this type of growth a population increases until

some factor causes a sudden reduction in its size Its effect is the same regardless of the size of the

population eg temperature fires floods storms etc

55

Regulation of Population Size Fecundity is the reproductive capacity of individual

females of a species Birth rate or natality is used to measure fecundity Death rate or mortality is the number of individuals

of a species which die per unit time Immigration occurs when individuals join a

population from neighbouring ones Emigration occurs when individuals depart from a

population A cycle occurs when the size of a population

fluctuates on a regular basis

56

Ecological Sampling

57

Why Do We Sample Determine presence andor

abundance

Monitor population fluctuations

Assess lsquoecological damagersquo

Assess quality of habitat

Assess population responses

58

What Do We Sample

Physical Environment Temperature DO pH salinity clarity

flow sediment

Biotic Environment All living things

59

Physical Habitat Temperature

Mercury thermometer Electronic thermometer Long-term thermometers

Dissolved Oxygen Winkler method (titration) DO meter (electrode)

pH Litmus paper pH meter (electrode)

Salinity Salinity Meter YSI 550A DO Meter w12 cable

60

Water Clarity Secchi Disk

Disk is attached to a calibrated rope The disk is lowered into the water until the white parts can no longer be seen Secchi disk depth is then recorded and serves as the waters transparency index The clearer the water the greater the secchi disk depth

Secchi Disk

61

Current Velocity (flow) Floating-orange method

Put an orange (or something else that floats just below the water surface) and measure the time it takes it to float across a known distance

Odometer-type flow meter Number of revolutions the propeller

makes for a given time is calibrated to flow velocity

62

Sediment Sediment size is important to many

aquatic organisms Sieversquos are used to separate and

grade sediment samples Percent of each size grade can be

determined

63

Water Sample

Water and plankton from various depths can be collected

A trigger mechanism is used to close the sampler Sample is then brought back to the

surface

64

Small Mammals

Mouserat Traps Fatal

Pit Falls Bucket is placed in the ground Sometimes have lsquoleadsrsquo to the buckets

Live traps Havahart Sherman

Spot-light

Sherman trapHavahart trap

65

Birds Stick-under-the-box method Bird-trap

Works like a minnow trap Mist net

Captures birds in flight Rocket net

Uses a propellant to throw a net over birds

66

Terrestrial Insects

Sticky paper flies

Baited Traps Fire ants

Nets butterflies

Foggers Collect insects from tree canopies

67

Aquatic Insects Drift Net

Place net in flowing water Kick Net

lsquoKickrsquo sediment upstream from block net and the flow will wash them into the net

Wash bucket Serber or Hess Sampler

Stir up known area of sediment

Animals are collected by a catch net

Multi-plate Sampler Become colonized

68

Crawfish and Crab Traps

69

Fish Larvae Light Traps

Larvae are attracted to the light Ichthyoplankton nets

Can be towed at various depths Fish collect at the lsquocodrsquoend

70

Fish Lift net

Net is placed down and after a set amount of time it is quickly lifted

Pop-net Similar to a lift net but

floats are attached to a framed net

Operated by a trigger mechanism

Throw net A net attached to a heavy

frame is thrown and every thing inside is netted out Throw net

Pop-net

Lift net

71

Minnow trap

Usually use bait to attract small fish Light is used sometimes as an attractant

72

Fish Electrofishing

Electricity is put into the water Fish are temporarily stunned and usually

swim towards the electricity source Usually non-fatal but may cause some

damage

73

Fish Gill Net

Gill nets resemble tennis nets Fish can not swim completely through the

net and get caught Gill nets are size selective (based on mesh

size) Square Mesh

Bar mesh

Stretch mesh

74

Fish Trammel Net

Three panels two large mesh on the outside and a small mesh on the inside

Fish swim through the outer mesh pushes the small mesh through the other side and becomes entangled

75

Hoop nets (and other similar nets) can have bait or not

Fyke nets have leads to help guide fish to the net

76

Seine Seines are nets that are pulled

through shallow water to catch fish

77

Purse Seine Used to encircle entire schools of fish

Usually involves a spotter plane and a second boat

78

Trotline (longline) A series of baited drop lines

connected to a main line

Can be deployed by tying one end to the bank and tying the other end with a heavy weight

79

Shrimp (or fish) Trawl Net pulled behind

a boat along the bottom Either a beam or

otter boards keep the net open

80

Tagging Individuals Coded Wire Tags

Microwire that has a unique label

Magnetic wand detects the tag

Tag retention should be determined

T-Bar tags Can be individually

numbered External tag

PIT tags (Passive Integrated Transponders) Wand induces the tag to

transmit individual number is displayed

81

Other Tagging Methods

Toe clip Amphibian and reptile Clip of one or more toes

to identify individuals

Bird Band Place a metal band on a

bird leg Generally has

identification information

82

Preserving plant specimens Pressing and drying Long-term

preservation and storage

Alternative drying techniques

Special preservation and processing techniques

Mounting

83

Pressing and drying Techniques for pressing and drying specimens have been

established for many years There are minor variations in recommended methods but they are essentially the same worldwide

The best specimens are plants that are pressed as soon as possible after collection before wilting and shrivelling Most plants may be kept in sealed containers such as plastic bags for up to a day if it is inconvenient to press immediately However some plants show such rapid wilting particularly of the flowers that such delays are best avoided Flowers with a lot of nectar may go mouldy very quickly if excess nectar is not shaken off before pressing

Specimens are pressed flat and dried between sheets of absorbent blotters or semi-absorbent paper such as newspaper Papers with a glossy surface should be avoided because they are not absorbent enough to aid drying The plant should be carefully laid out between the drying sheets as their form at this stage largely determines their ultimate appearance The flowers should be spread out with the petals carefully arranged wilted leaves should be straightened and unnecessary shoots of excessively twiggy shrubs may be cut away

84

Microwave ovens Small numbers of specimens can be dried using a microwave

oven The technique recommended in the literature is to place the specimens between unprinted absorbent paper for example butchers paper not newspaper which is unsuitable because the chemicals present in the ink may cause a fire The specimens should be put in a special press which should be of a microwave-safe material (wood acrylic or polycarbonate sheeting eg plexiglass or perspex NO metal components) If such a press is not available sheets of cardboard can be placed above and below the specimens and then weighted down

Drying time depends on the power of your oven In most cases drying is accomplished by irradiating at maximum power for 1-2 minutes per specimen although it is often a case of trial and error It is best to process no more than 10-12 specimens of average thickness per batch Specimens are usually dried after the moisture that characteristically appears on the glass door has disappeared If the specimen is damp when taken out of the oven allow it to stand before re-radiating as moisture continues to evaporate from the specimen for some time Care must be taken not to irradiate the specimens for too long

It should be noted that microwave treatment damages seeds and the cellular structure of the plants which may reduce the long-term value of the specimens

85

Alternative drying techniquesSilica gelother desiccants amp freeze drying Alternative methods of drying plant specimens have been

used for some time but are mostly restricted to special purpose collections The main alternatives are freeze-drying and drying in a desiccant powder such as desiccant silica gel In general these techniques are used where it is essential to preserve the shape of a delicate plant of organ of the plant such as the flower Freeze-drying has also been used to preserve the chemical composition of a plant as accurately as possible for later study

Disadvantages and special conservation problems of specimens dried in these manners are that they are particularly susceptible to damage The dried parts are fragile lack support and often catch on packing materials They must therefore be packed especially carefully and stored in small boxes or tubes with some appropriate packing material that does not snag and break small projections Acid-free tissue paper is often used Drying in desiccant silica gel crystals or powder can also have the disadvantage that it is difficult to remove all traces of the silica gel after drying

86

Special preservation and processing techniquesWet or spirit collections

Very fleshy or delicate structures including small algae and orchid flowers are best preserved in an air-tight glass or plastic jar with a liquid preservative rather than by drying The type of preservative used should be clearly labelled in the jar Such material is often referred to as a spirit collection or wet collection

Most material can be satisfactorily preserved in 70 ethyl alcohol (or 70 methylated spirit or denatured alcohol) with 30 water Colours will fade quickly in spirit however so it is a good idea to keep comprehensive notes and photographs

87

Small algae Microscopic algae are often collected in a jar and in the

water in which they were found If the algae are to be stored for more than 2-3 days a preservative needs to be used Traditionally this has been the extremely toxic formalin - a small amount can be added to the water to make a 5 final solution and the container labelled This must not be sent through the post or by courier

There are some other equally toxic options for example propylene phenoxytol but none should be sent through the post A safer option is to add sufficient concentrated alcohol or methylated spirits to the water containing the algae to make a final solution of 70 alcohol This treatment dilutes the algae making them difficult to find so if they can be concentrated somehow first (eg by filtering) they can be stored in much less liquid Another option is to fix the algae in formalin (or something similar) first and then prepare a microscope glass slide with a permanent water-soluble mounting medium

88

Mounting Mounting specimens prevents most fragile material from

fragmenting and prevents specimens becoming separated from their labels If the plant collection is a long-term project specimens should be mounted on sheets of archival (permanent) cardboard or paper with archival-quality fixing media These include stitching with cotton thread dental floss nickel-plated copper wire (for heavier specimens) narrow strips of archival paper linen tape or by using an archival adhesive such as methyl cellulose adhesive

One disadvantage of mounting specimens is that it can make parts of the specimen inaccessible for examination so it is essential that this be borne in mind during specimen arrangement and mounting For example easily reversible mounting media should be used specimens should be strapped to the sheet rather than glued all over and the specimen should be carefully arranged before it is attached so that it shows all features

89

Full-size herbarium mounting sheets are usually about 43 cm long x 28 cm wide The plant name and accompanying field notes should be transcribed on a permanent label stuck to one corner of the herbarium sheet (the bottom right-hand corner being the most common) or sometimes annotations may be written directly on the sheet or card

Small pieces of material which may have become separated from the specimen (eg seeds) can be placed in small plastic bags and pinned to the sheet

90

Long-term preservation and storage The long-term preservation of dry plant

specimens is largely dependent on protection from insect attack Specimens collected by Linnaeus in the eighteenth century and by Banks and Solander on the Endeavour voyage in 1788 are still excellently preserved

91

Pests and their control A range of pests attack dried plant material The

most common pests are insects and fungi though rodents and other large animals can cause damage in poor storage conditions Insects eat the material the paper surrounding the material and the adhesives and mounting media

Such insect pests range from psocids (book lice) which attack mainly the softer parts such as flowers and soft fruits to tobacco beetles and carpet beetles which can bore holes through the toughest of specimens Many insects are particularly sensitive to relative humidity levels and do not thrive at levels below 50

92

The most common and acceptable specimen treatments for insect control are Freezing Microwave Poisoning Insect deterrents Fungal pests

93

Storage

Dried and pressed plant specimens can be stored in cardboard or plastic boxes or tied in bundles in light-weight cardboard folders placed in pigeon holes

Alternatively they can be placed in protective plastic jackets and displayed in ring folders which is recommended if they are to be frequently handled such as for a reference collection

94

Filing

Specimens should be filed in a systematic order if a relatively permanent collection is being made The major groups ie ferns and fern allies cycads conifers dicotyledons and monocotyledons are best kept separately or according to some classification scheme such as that given in a flora or handbook

Similarly the genera within each family and the species within each genus may be filed alphabetically or following some such classification

95

Preservation of entire animals

Types of collection specimens of an entire animal For reference collections mammals can be prepared as a variety of specimens The condition of the specimen may determine possible ways to preserve it if for instance decomposition of the skin has loosened the hair of a carcass so much that it can easily be pulled out or removed by rubbing (ldquoslippingrdquo fur) it will be very difficult or impossible to produce a study skin or mounted specimen The most usual types of specimens (based on Nagorsen and Peterson 1980) are 1) entire fluid-preserved animals (for studying anatomy and histology fluid preservation may change the fur colour) 2) study skins with accompanying skulls partial skeletons (some bones remain in the skin) for studying pelage colour hair quality and moulting patterns 3) mounted skins with accompanying partial or entire skeleton (some bones may remain in the skin dependant on the method of preservation) or freeze-dried specimens 4) entire skeletons for instance for studying anatomy geographic variation or for age determination (entire skeletons are poorly represented in collections so Nagorsen and Peterson (1980) recommend preparation of at least one male and one female skeleton per species

96

Preservation of specimens in the field Formalin preservation Preservation in alcohol Preservation by cooling or freezing

97

Formalin preservation After weighing and measuring the animal and attaching an

adequate label very small specimens (up to 100 g) can be fixed whole by submerging them in 10 buffered formalin (tissue - formalin solution ratio of at least 1 12) the body cavity can be filled with formalin solution by injection until it is turgid and firm some formalin may also be injected under the skin into the body cavity larger muscles and organs If hypodermic needles are not available the body cavity can be opened ventrally by making a slit instead allowing the formalin to enter

Keeping the mouth open with a piece of wood or cotton may later allow examination of teeth Then the whole body can be immersed in formalin in the posture in which it is supposed to stay permanently because it will harden The ratio of formalin to carcass must be at least 12 to 1 to assure a good fixation Tissues can be left in buffered neutralized formalin for several months but formalin hardens specimens therefore after fixation longterm storage in alcohol may be better After preservation the carcass should therefore be washed in water and transferred into ethanol for permanent storage

Disadvantages for instance it discolours the fur after a longish immersion softens the bones and prevents further examination for microbiology

98

Preservation in alcohol

After weighing a whole animal can be preserved in a container of alcohol (70-90) Removal of the intestine prior to storage of the animal in alcohol is recommended

99

Preservation by cooling or freezing Removal of the skin with insulating fur

before cooling or freezing may help to cool the carcass down more quickly

Freezing is not recommended if histological examination is planned

100

THANK YOU

49

Marked animals in second sample

Total caught in second sample

Marked animals in first sample

Total population size

=

520 N

16=

Peterson Method or Lincoln Index

N = 64N = (20)(16)5

50

Some Indices Used

Traps Number of Fecal

Pellets Vocalization

Frequency Pelt Records Catch per Unit

Fishing Effort

Number of Artifacts Questionnaires Cover Feeding Capacity Roadside Counts

51

Abundance Scales

The population size may be fairly accurately determined by making some form of frequency assessment

These are subjective and involve an experimenter making some estimate of the number of individuals in a given area or the cover of a particular species

This is especially useful where individuals are very numerous eg barnacles on a rocky shore or where it is difficult to distinguish individuals eg grass plants in a meadow

52

The assessments are usually made on an abundance scale of 5 categories

Abundance Common Frequent Occasional Rare

Barnacles exposed at low water

53

Environmental resistance are the factors which limit the growth of a particular population

eg predation disease availability of light food water oxygen and shelter the accumulation of toxic wastes and even the size of the population itself

54

Density-dependent Growth A population is a density-dependent when its size

(or density) affects its growth rate because of density-dependent factors such as food availability and toxic waste accumulation

Density-independent Growth In this type of growth a population increases until

some factor causes a sudden reduction in its size Its effect is the same regardless of the size of the

population eg temperature fires floods storms etc

55

Regulation of Population Size Fecundity is the reproductive capacity of individual

females of a species Birth rate or natality is used to measure fecundity Death rate or mortality is the number of individuals

of a species which die per unit time Immigration occurs when individuals join a

population from neighbouring ones Emigration occurs when individuals depart from a

population A cycle occurs when the size of a population

fluctuates on a regular basis

56

Ecological Sampling

57

Why Do We Sample Determine presence andor

abundance

Monitor population fluctuations

Assess lsquoecological damagersquo

Assess quality of habitat

Assess population responses

58

What Do We Sample

Physical Environment Temperature DO pH salinity clarity

flow sediment

Biotic Environment All living things

59

Physical Habitat Temperature

Mercury thermometer Electronic thermometer Long-term thermometers

Dissolved Oxygen Winkler method (titration) DO meter (electrode)

pH Litmus paper pH meter (electrode)

Salinity Salinity Meter YSI 550A DO Meter w12 cable

60

Water Clarity Secchi Disk

Disk is attached to a calibrated rope The disk is lowered into the water until the white parts can no longer be seen Secchi disk depth is then recorded and serves as the waters transparency index The clearer the water the greater the secchi disk depth

Secchi Disk

61

Current Velocity (flow) Floating-orange method

Put an orange (or something else that floats just below the water surface) and measure the time it takes it to float across a known distance

Odometer-type flow meter Number of revolutions the propeller

makes for a given time is calibrated to flow velocity

62

Sediment Sediment size is important to many

aquatic organisms Sieversquos are used to separate and

grade sediment samples Percent of each size grade can be

determined

63

Water Sample

Water and plankton from various depths can be collected

A trigger mechanism is used to close the sampler Sample is then brought back to the

surface

64

Small Mammals

Mouserat Traps Fatal

Pit Falls Bucket is placed in the ground Sometimes have lsquoleadsrsquo to the buckets

Live traps Havahart Sherman

Spot-light

Sherman trapHavahart trap

65

Birds Stick-under-the-box method Bird-trap

Works like a minnow trap Mist net

Captures birds in flight Rocket net

Uses a propellant to throw a net over birds

66

Terrestrial Insects

Sticky paper flies

Baited Traps Fire ants

Nets butterflies

Foggers Collect insects from tree canopies

67

Aquatic Insects Drift Net

Place net in flowing water Kick Net

lsquoKickrsquo sediment upstream from block net and the flow will wash them into the net

Wash bucket Serber or Hess Sampler

Stir up known area of sediment

Animals are collected by a catch net

Multi-plate Sampler Become colonized

68

Crawfish and Crab Traps

69

Fish Larvae Light Traps

Larvae are attracted to the light Ichthyoplankton nets

Can be towed at various depths Fish collect at the lsquocodrsquoend

70

Fish Lift net

Net is placed down and after a set amount of time it is quickly lifted

Pop-net Similar to a lift net but

floats are attached to a framed net

Operated by a trigger mechanism

Throw net A net attached to a heavy

frame is thrown and every thing inside is netted out Throw net

Pop-net

Lift net

71

Minnow trap

Usually use bait to attract small fish Light is used sometimes as an attractant

72

Fish Electrofishing

Electricity is put into the water Fish are temporarily stunned and usually

swim towards the electricity source Usually non-fatal but may cause some

damage

73

Fish Gill Net

Gill nets resemble tennis nets Fish can not swim completely through the

net and get caught Gill nets are size selective (based on mesh

size) Square Mesh

Bar mesh

Stretch mesh

74

Fish Trammel Net

Three panels two large mesh on the outside and a small mesh on the inside

Fish swim through the outer mesh pushes the small mesh through the other side and becomes entangled

75

Hoop nets (and other similar nets) can have bait or not

Fyke nets have leads to help guide fish to the net

76

Seine Seines are nets that are pulled

through shallow water to catch fish

77

Purse Seine Used to encircle entire schools of fish

Usually involves a spotter plane and a second boat

78

Trotline (longline) A series of baited drop lines

connected to a main line

Can be deployed by tying one end to the bank and tying the other end with a heavy weight

79

Shrimp (or fish) Trawl Net pulled behind

a boat along the bottom Either a beam or

otter boards keep the net open

80

Tagging Individuals Coded Wire Tags

Microwire that has a unique label

Magnetic wand detects the tag

Tag retention should be determined

T-Bar tags Can be individually

numbered External tag

PIT tags (Passive Integrated Transponders) Wand induces the tag to

transmit individual number is displayed

81

Other Tagging Methods

Toe clip Amphibian and reptile Clip of one or more toes

to identify individuals

Bird Band Place a metal band on a

bird leg Generally has

identification information

82

Preserving plant specimens Pressing and drying Long-term

preservation and storage

Alternative drying techniques

Special preservation and processing techniques

Mounting

83

Pressing and drying Techniques for pressing and drying specimens have been

established for many years There are minor variations in recommended methods but they are essentially the same worldwide

The best specimens are plants that are pressed as soon as possible after collection before wilting and shrivelling Most plants may be kept in sealed containers such as plastic bags for up to a day if it is inconvenient to press immediately However some plants show such rapid wilting particularly of the flowers that such delays are best avoided Flowers with a lot of nectar may go mouldy very quickly if excess nectar is not shaken off before pressing

Specimens are pressed flat and dried between sheets of absorbent blotters or semi-absorbent paper such as newspaper Papers with a glossy surface should be avoided because they are not absorbent enough to aid drying The plant should be carefully laid out between the drying sheets as their form at this stage largely determines their ultimate appearance The flowers should be spread out with the petals carefully arranged wilted leaves should be straightened and unnecessary shoots of excessively twiggy shrubs may be cut away

84

Microwave ovens Small numbers of specimens can be dried using a microwave

oven The technique recommended in the literature is to place the specimens between unprinted absorbent paper for example butchers paper not newspaper which is unsuitable because the chemicals present in the ink may cause a fire The specimens should be put in a special press which should be of a microwave-safe material (wood acrylic or polycarbonate sheeting eg plexiglass or perspex NO metal components) If such a press is not available sheets of cardboard can be placed above and below the specimens and then weighted down

Drying time depends on the power of your oven In most cases drying is accomplished by irradiating at maximum power for 1-2 minutes per specimen although it is often a case of trial and error It is best to process no more than 10-12 specimens of average thickness per batch Specimens are usually dried after the moisture that characteristically appears on the glass door has disappeared If the specimen is damp when taken out of the oven allow it to stand before re-radiating as moisture continues to evaporate from the specimen for some time Care must be taken not to irradiate the specimens for too long

It should be noted that microwave treatment damages seeds and the cellular structure of the plants which may reduce the long-term value of the specimens

85

Alternative drying techniquesSilica gelother desiccants amp freeze drying Alternative methods of drying plant specimens have been

used for some time but are mostly restricted to special purpose collections The main alternatives are freeze-drying and drying in a desiccant powder such as desiccant silica gel In general these techniques are used where it is essential to preserve the shape of a delicate plant of organ of the plant such as the flower Freeze-drying has also been used to preserve the chemical composition of a plant as accurately as possible for later study

Disadvantages and special conservation problems of specimens dried in these manners are that they are particularly susceptible to damage The dried parts are fragile lack support and often catch on packing materials They must therefore be packed especially carefully and stored in small boxes or tubes with some appropriate packing material that does not snag and break small projections Acid-free tissue paper is often used Drying in desiccant silica gel crystals or powder can also have the disadvantage that it is difficult to remove all traces of the silica gel after drying

86

Special preservation and processing techniquesWet or spirit collections

Very fleshy or delicate structures including small algae and orchid flowers are best preserved in an air-tight glass or plastic jar with a liquid preservative rather than by drying The type of preservative used should be clearly labelled in the jar Such material is often referred to as a spirit collection or wet collection

Most material can be satisfactorily preserved in 70 ethyl alcohol (or 70 methylated spirit or denatured alcohol) with 30 water Colours will fade quickly in spirit however so it is a good idea to keep comprehensive notes and photographs

87

Small algae Microscopic algae are often collected in a jar and in the

water in which they were found If the algae are to be stored for more than 2-3 days a preservative needs to be used Traditionally this has been the extremely toxic formalin - a small amount can be added to the water to make a 5 final solution and the container labelled This must not be sent through the post or by courier

There are some other equally toxic options for example propylene phenoxytol but none should be sent through the post A safer option is to add sufficient concentrated alcohol or methylated spirits to the water containing the algae to make a final solution of 70 alcohol This treatment dilutes the algae making them difficult to find so if they can be concentrated somehow first (eg by filtering) they can be stored in much less liquid Another option is to fix the algae in formalin (or something similar) first and then prepare a microscope glass slide with a permanent water-soluble mounting medium

88

Mounting Mounting specimens prevents most fragile material from

fragmenting and prevents specimens becoming separated from their labels If the plant collection is a long-term project specimens should be mounted on sheets of archival (permanent) cardboard or paper with archival-quality fixing media These include stitching with cotton thread dental floss nickel-plated copper wire (for heavier specimens) narrow strips of archival paper linen tape or by using an archival adhesive such as methyl cellulose adhesive

One disadvantage of mounting specimens is that it can make parts of the specimen inaccessible for examination so it is essential that this be borne in mind during specimen arrangement and mounting For example easily reversible mounting media should be used specimens should be strapped to the sheet rather than glued all over and the specimen should be carefully arranged before it is attached so that it shows all features

89

Full-size herbarium mounting sheets are usually about 43 cm long x 28 cm wide The plant name and accompanying field notes should be transcribed on a permanent label stuck to one corner of the herbarium sheet (the bottom right-hand corner being the most common) or sometimes annotations may be written directly on the sheet or card

Small pieces of material which may have become separated from the specimen (eg seeds) can be placed in small plastic bags and pinned to the sheet

90

Long-term preservation and storage The long-term preservation of dry plant

specimens is largely dependent on protection from insect attack Specimens collected by Linnaeus in the eighteenth century and by Banks and Solander on the Endeavour voyage in 1788 are still excellently preserved

91

Pests and their control A range of pests attack dried plant material The

most common pests are insects and fungi though rodents and other large animals can cause damage in poor storage conditions Insects eat the material the paper surrounding the material and the adhesives and mounting media

Such insect pests range from psocids (book lice) which attack mainly the softer parts such as flowers and soft fruits to tobacco beetles and carpet beetles which can bore holes through the toughest of specimens Many insects are particularly sensitive to relative humidity levels and do not thrive at levels below 50

92

The most common and acceptable specimen treatments for insect control are Freezing Microwave Poisoning Insect deterrents Fungal pests

93

Storage

Dried and pressed plant specimens can be stored in cardboard or plastic boxes or tied in bundles in light-weight cardboard folders placed in pigeon holes

Alternatively they can be placed in protective plastic jackets and displayed in ring folders which is recommended if they are to be frequently handled such as for a reference collection

94

Filing

Specimens should be filed in a systematic order if a relatively permanent collection is being made The major groups ie ferns and fern allies cycads conifers dicotyledons and monocotyledons are best kept separately or according to some classification scheme such as that given in a flora or handbook

Similarly the genera within each family and the species within each genus may be filed alphabetically or following some such classification

95

Preservation of entire animals

Types of collection specimens of an entire animal For reference collections mammals can be prepared as a variety of specimens The condition of the specimen may determine possible ways to preserve it if for instance decomposition of the skin has loosened the hair of a carcass so much that it can easily be pulled out or removed by rubbing (ldquoslippingrdquo fur) it will be very difficult or impossible to produce a study skin or mounted specimen The most usual types of specimens (based on Nagorsen and Peterson 1980) are 1) entire fluid-preserved animals (for studying anatomy and histology fluid preservation may change the fur colour) 2) study skins with accompanying skulls partial skeletons (some bones remain in the skin) for studying pelage colour hair quality and moulting patterns 3) mounted skins with accompanying partial or entire skeleton (some bones may remain in the skin dependant on the method of preservation) or freeze-dried specimens 4) entire skeletons for instance for studying anatomy geographic variation or for age determination (entire skeletons are poorly represented in collections so Nagorsen and Peterson (1980) recommend preparation of at least one male and one female skeleton per species

96

Preservation of specimens in the field Formalin preservation Preservation in alcohol Preservation by cooling or freezing

97

Formalin preservation After weighing and measuring the animal and attaching an

adequate label very small specimens (up to 100 g) can be fixed whole by submerging them in 10 buffered formalin (tissue - formalin solution ratio of at least 1 12) the body cavity can be filled with formalin solution by injection until it is turgid and firm some formalin may also be injected under the skin into the body cavity larger muscles and organs If hypodermic needles are not available the body cavity can be opened ventrally by making a slit instead allowing the formalin to enter

Keeping the mouth open with a piece of wood or cotton may later allow examination of teeth Then the whole body can be immersed in formalin in the posture in which it is supposed to stay permanently because it will harden The ratio of formalin to carcass must be at least 12 to 1 to assure a good fixation Tissues can be left in buffered neutralized formalin for several months but formalin hardens specimens therefore after fixation longterm storage in alcohol may be better After preservation the carcass should therefore be washed in water and transferred into ethanol for permanent storage

Disadvantages for instance it discolours the fur after a longish immersion softens the bones and prevents further examination for microbiology

98

Preservation in alcohol

After weighing a whole animal can be preserved in a container of alcohol (70-90) Removal of the intestine prior to storage of the animal in alcohol is recommended

99

Preservation by cooling or freezing Removal of the skin with insulating fur

before cooling or freezing may help to cool the carcass down more quickly

Freezing is not recommended if histological examination is planned

100

THANK YOU

50

Some Indices Used

Traps Number of Fecal

Pellets Vocalization

Frequency Pelt Records Catch per Unit

Fishing Effort

Number of Artifacts Questionnaires Cover Feeding Capacity Roadside Counts

51

Abundance Scales

The population size may be fairly accurately determined by making some form of frequency assessment

These are subjective and involve an experimenter making some estimate of the number of individuals in a given area or the cover of a particular species

This is especially useful where individuals are very numerous eg barnacles on a rocky shore or where it is difficult to distinguish individuals eg grass plants in a meadow

52

The assessments are usually made on an abundance scale of 5 categories

Abundance Common Frequent Occasional Rare

Barnacles exposed at low water

53

Environmental resistance are the factors which limit the growth of a particular population

eg predation disease availability of light food water oxygen and shelter the accumulation of toxic wastes and even the size of the population itself

54

Density-dependent Growth A population is a density-dependent when its size

(or density) affects its growth rate because of density-dependent factors such as food availability and toxic waste accumulation

Density-independent Growth In this type of growth a population increases until

some factor causes a sudden reduction in its size Its effect is the same regardless of the size of the

population eg temperature fires floods storms etc

55

Regulation of Population Size Fecundity is the reproductive capacity of individual

females of a species Birth rate or natality is used to measure fecundity Death rate or mortality is the number of individuals

of a species which die per unit time Immigration occurs when individuals join a

population from neighbouring ones Emigration occurs when individuals depart from a

population A cycle occurs when the size of a population

fluctuates on a regular basis

56

Ecological Sampling

57

Why Do We Sample Determine presence andor

abundance

Monitor population fluctuations

Assess lsquoecological damagersquo

Assess quality of habitat

Assess population responses

58

What Do We Sample

Physical Environment Temperature DO pH salinity clarity

flow sediment

Biotic Environment All living things

59

Physical Habitat Temperature

Mercury thermometer Electronic thermometer Long-term thermometers

Dissolved Oxygen Winkler method (titration) DO meter (electrode)

pH Litmus paper pH meter (electrode)

Salinity Salinity Meter YSI 550A DO Meter w12 cable

60

Water Clarity Secchi Disk

Disk is attached to a calibrated rope The disk is lowered into the water until the white parts can no longer be seen Secchi disk depth is then recorded and serves as the waters transparency index The clearer the water the greater the secchi disk depth

Secchi Disk

61

Current Velocity (flow) Floating-orange method

Put an orange (or something else that floats just below the water surface) and measure the time it takes it to float across a known distance

Odometer-type flow meter Number of revolutions the propeller

makes for a given time is calibrated to flow velocity

62

Sediment Sediment size is important to many

aquatic organisms Sieversquos are used to separate and

grade sediment samples Percent of each size grade can be

determined

63

Water Sample

Water and plankton from various depths can be collected

A trigger mechanism is used to close the sampler Sample is then brought back to the

surface

64

Small Mammals

Mouserat Traps Fatal

Pit Falls Bucket is placed in the ground Sometimes have lsquoleadsrsquo to the buckets

Live traps Havahart Sherman

Spot-light

Sherman trapHavahart trap

65

Birds Stick-under-the-box method Bird-trap

Works like a minnow trap Mist net

Captures birds in flight Rocket net

Uses a propellant to throw a net over birds

66

Terrestrial Insects

Sticky paper flies

Baited Traps Fire ants

Nets butterflies

Foggers Collect insects from tree canopies

67

Aquatic Insects Drift Net

Place net in flowing water Kick Net

lsquoKickrsquo sediment upstream from block net and the flow will wash them into the net

Wash bucket Serber or Hess Sampler

Stir up known area of sediment

Animals are collected by a catch net

Multi-plate Sampler Become colonized

68

Crawfish and Crab Traps

69

Fish Larvae Light Traps

Larvae are attracted to the light Ichthyoplankton nets

Can be towed at various depths Fish collect at the lsquocodrsquoend

70

Fish Lift net

Net is placed down and after a set amount of time it is quickly lifted

Pop-net Similar to a lift net but

floats are attached to a framed net

Operated by a trigger mechanism

Throw net A net attached to a heavy

frame is thrown and every thing inside is netted out Throw net

Pop-net

Lift net

71

Minnow trap

Usually use bait to attract small fish Light is used sometimes as an attractant

72

Fish Electrofishing

Electricity is put into the water Fish are temporarily stunned and usually

swim towards the electricity source Usually non-fatal but may cause some

damage

73

Fish Gill Net

Gill nets resemble tennis nets Fish can not swim completely through the

net and get caught Gill nets are size selective (based on mesh

size) Square Mesh

Bar mesh

Stretch mesh

74

Fish Trammel Net

Three panels two large mesh on the outside and a small mesh on the inside

Fish swim through the outer mesh pushes the small mesh through the other side and becomes entangled

75

Hoop nets (and other similar nets) can have bait or not

Fyke nets have leads to help guide fish to the net

76

Seine Seines are nets that are pulled

through shallow water to catch fish

77

Purse Seine Used to encircle entire schools of fish

Usually involves a spotter plane and a second boat

78

Trotline (longline) A series of baited drop lines

connected to a main line

Can be deployed by tying one end to the bank and tying the other end with a heavy weight

79

Shrimp (or fish) Trawl Net pulled behind

a boat along the bottom Either a beam or

otter boards keep the net open

80

Tagging Individuals Coded Wire Tags

Microwire that has a unique label

Magnetic wand detects the tag

Tag retention should be determined

T-Bar tags Can be individually

numbered External tag

PIT tags (Passive Integrated Transponders) Wand induces the tag to

transmit individual number is displayed

81

Other Tagging Methods

Toe clip Amphibian and reptile Clip of one or more toes

to identify individuals

Bird Band Place a metal band on a

bird leg Generally has

identification information

82

Preserving plant specimens Pressing and drying Long-term

preservation and storage

Alternative drying techniques

Special preservation and processing techniques

Mounting

83

Pressing and drying Techniques for pressing and drying specimens have been

established for many years There are minor variations in recommended methods but they are essentially the same worldwide

The best specimens are plants that are pressed as soon as possible after collection before wilting and shrivelling Most plants may be kept in sealed containers such as plastic bags for up to a day if it is inconvenient to press immediately However some plants show such rapid wilting particularly of the flowers that such delays are best avoided Flowers with a lot of nectar may go mouldy very quickly if excess nectar is not shaken off before pressing

Specimens are pressed flat and dried between sheets of absorbent blotters or semi-absorbent paper such as newspaper Papers with a glossy surface should be avoided because they are not absorbent enough to aid drying The plant should be carefully laid out between the drying sheets as their form at this stage largely determines their ultimate appearance The flowers should be spread out with the petals carefully arranged wilted leaves should be straightened and unnecessary shoots of excessively twiggy shrubs may be cut away

84

Microwave ovens Small numbers of specimens can be dried using a microwave

oven The technique recommended in the literature is to place the specimens between unprinted absorbent paper for example butchers paper not newspaper which is unsuitable because the chemicals present in the ink may cause a fire The specimens should be put in a special press which should be of a microwave-safe material (wood acrylic or polycarbonate sheeting eg plexiglass or perspex NO metal components) If such a press is not available sheets of cardboard can be placed above and below the specimens and then weighted down

Drying time depends on the power of your oven In most cases drying is accomplished by irradiating at maximum power for 1-2 minutes per specimen although it is often a case of trial and error It is best to process no more than 10-12 specimens of average thickness per batch Specimens are usually dried after the moisture that characteristically appears on the glass door has disappeared If the specimen is damp when taken out of the oven allow it to stand before re-radiating as moisture continues to evaporate from the specimen for some time Care must be taken not to irradiate the specimens for too long

It should be noted that microwave treatment damages seeds and the cellular structure of the plants which may reduce the long-term value of the specimens

85

Alternative drying techniquesSilica gelother desiccants amp freeze drying Alternative methods of drying plant specimens have been

used for some time but are mostly restricted to special purpose collections The main alternatives are freeze-drying and drying in a desiccant powder such as desiccant silica gel In general these techniques are used where it is essential to preserve the shape of a delicate plant of organ of the plant such as the flower Freeze-drying has also been used to preserve the chemical composition of a plant as accurately as possible for later study

Disadvantages and special conservation problems of specimens dried in these manners are that they are particularly susceptible to damage The dried parts are fragile lack support and often catch on packing materials They must therefore be packed especially carefully and stored in small boxes or tubes with some appropriate packing material that does not snag and break small projections Acid-free tissue paper is often used Drying in desiccant silica gel crystals or powder can also have the disadvantage that it is difficult to remove all traces of the silica gel after drying

86

Special preservation and processing techniquesWet or spirit collections

Very fleshy or delicate structures including small algae and orchid flowers are best preserved in an air-tight glass or plastic jar with a liquid preservative rather than by drying The type of preservative used should be clearly labelled in the jar Such material is often referred to as a spirit collection or wet collection

Most material can be satisfactorily preserved in 70 ethyl alcohol (or 70 methylated spirit or denatured alcohol) with 30 water Colours will fade quickly in spirit however so it is a good idea to keep comprehensive notes and photographs

87

Small algae Microscopic algae are often collected in a jar and in the

water in which they were found If the algae are to be stored for more than 2-3 days a preservative needs to be used Traditionally this has been the extremely toxic formalin - a small amount can be added to the water to make a 5 final solution and the container labelled This must not be sent through the post or by courier

There are some other equally toxic options for example propylene phenoxytol but none should be sent through the post A safer option is to add sufficient concentrated alcohol or methylated spirits to the water containing the algae to make a final solution of 70 alcohol This treatment dilutes the algae making them difficult to find so if they can be concentrated somehow first (eg by filtering) they can be stored in much less liquid Another option is to fix the algae in formalin (or something similar) first and then prepare a microscope glass slide with a permanent water-soluble mounting medium

88

Mounting Mounting specimens prevents most fragile material from

fragmenting and prevents specimens becoming separated from their labels If the plant collection is a long-term project specimens should be mounted on sheets of archival (permanent) cardboard or paper with archival-quality fixing media These include stitching with cotton thread dental floss nickel-plated copper wire (for heavier specimens) narrow strips of archival paper linen tape or by using an archival adhesive such as methyl cellulose adhesive

One disadvantage of mounting specimens is that it can make parts of the specimen inaccessible for examination so it is essential that this be borne in mind during specimen arrangement and mounting For example easily reversible mounting media should be used specimens should be strapped to the sheet rather than glued all over and the specimen should be carefully arranged before it is attached so that it shows all features

89

Full-size herbarium mounting sheets are usually about 43 cm long x 28 cm wide The plant name and accompanying field notes should be transcribed on a permanent label stuck to one corner of the herbarium sheet (the bottom right-hand corner being the most common) or sometimes annotations may be written directly on the sheet or card

Small pieces of material which may have become separated from the specimen (eg seeds) can be placed in small plastic bags and pinned to the sheet

90

Long-term preservation and storage The long-term preservation of dry plant

specimens is largely dependent on protection from insect attack Specimens collected by Linnaeus in the eighteenth century and by Banks and Solander on the Endeavour voyage in 1788 are still excellently preserved

91

Pests and their control A range of pests attack dried plant material The

most common pests are insects and fungi though rodents and other large animals can cause damage in poor storage conditions Insects eat the material the paper surrounding the material and the adhesives and mounting media

Such insect pests range from psocids (book lice) which attack mainly the softer parts such as flowers and soft fruits to tobacco beetles and carpet beetles which can bore holes through the toughest of specimens Many insects are particularly sensitive to relative humidity levels and do not thrive at levels below 50

92

The most common and acceptable specimen treatments for insect control are Freezing Microwave Poisoning Insect deterrents Fungal pests

93

Storage

Dried and pressed plant specimens can be stored in cardboard or plastic boxes or tied in bundles in light-weight cardboard folders placed in pigeon holes

Alternatively they can be placed in protective plastic jackets and displayed in ring folders which is recommended if they are to be frequently handled such as for a reference collection

94

Filing

Specimens should be filed in a systematic order if a relatively permanent collection is being made The major groups ie ferns and fern allies cycads conifers dicotyledons and monocotyledons are best kept separately or according to some classification scheme such as that given in a flora or handbook

Similarly the genera within each family and the species within each genus may be filed alphabetically or following some such classification

95

Preservation of entire animals

Types of collection specimens of an entire animal For reference collections mammals can be prepared as a variety of specimens The condition of the specimen may determine possible ways to preserve it if for instance decomposition of the skin has loosened the hair of a carcass so much that it can easily be pulled out or removed by rubbing (ldquoslippingrdquo fur) it will be very difficult or impossible to produce a study skin or mounted specimen The most usual types of specimens (based on Nagorsen and Peterson 1980) are 1) entire fluid-preserved animals (for studying anatomy and histology fluid preservation may change the fur colour) 2) study skins with accompanying skulls partial skeletons (some bones remain in the skin) for studying pelage colour hair quality and moulting patterns 3) mounted skins with accompanying partial or entire skeleton (some bones may remain in the skin dependant on the method of preservation) or freeze-dried specimens 4) entire skeletons for instance for studying anatomy geographic variation or for age determination (entire skeletons are poorly represented in collections so Nagorsen and Peterson (1980) recommend preparation of at least one male and one female skeleton per species

96

Preservation of specimens in the field Formalin preservation Preservation in alcohol Preservation by cooling or freezing

97

Formalin preservation After weighing and measuring the animal and attaching an

adequate label very small specimens (up to 100 g) can be fixed whole by submerging them in 10 buffered formalin (tissue - formalin solution ratio of at least 1 12) the body cavity can be filled with formalin solution by injection until it is turgid and firm some formalin may also be injected under the skin into the body cavity larger muscles and organs If hypodermic needles are not available the body cavity can be opened ventrally by making a slit instead allowing the formalin to enter

Keeping the mouth open with a piece of wood or cotton may later allow examination of teeth Then the whole body can be immersed in formalin in the posture in which it is supposed to stay permanently because it will harden The ratio of formalin to carcass must be at least 12 to 1 to assure a good fixation Tissues can be left in buffered neutralized formalin for several months but formalin hardens specimens therefore after fixation longterm storage in alcohol may be better After preservation the carcass should therefore be washed in water and transferred into ethanol for permanent storage

Disadvantages for instance it discolours the fur after a longish immersion softens the bones and prevents further examination for microbiology

98

Preservation in alcohol

After weighing a whole animal can be preserved in a container of alcohol (70-90) Removal of the intestine prior to storage of the animal in alcohol is recommended

99

Preservation by cooling or freezing Removal of the skin with insulating fur

before cooling or freezing may help to cool the carcass down more quickly

Freezing is not recommended if histological examination is planned

100

THANK YOU

51

Abundance Scales

The population size may be fairly accurately determined by making some form of frequency assessment

These are subjective and involve an experimenter making some estimate of the number of individuals in a given area or the cover of a particular species

This is especially useful where individuals are very numerous eg barnacles on a rocky shore or where it is difficult to distinguish individuals eg grass plants in a meadow

52

The assessments are usually made on an abundance scale of 5 categories

Abundance Common Frequent Occasional Rare

Barnacles exposed at low water

53

Environmental resistance are the factors which limit the growth of a particular population

eg predation disease availability of light food water oxygen and shelter the accumulation of toxic wastes and even the size of the population itself

54

Density-dependent Growth A population is a density-dependent when its size

(or density) affects its growth rate because of density-dependent factors such as food availability and toxic waste accumulation

Density-independent Growth In this type of growth a population increases until

some factor causes a sudden reduction in its size Its effect is the same regardless of the size of the

population eg temperature fires floods storms etc

55

Regulation of Population Size Fecundity is the reproductive capacity of individual

females of a species Birth rate or natality is used to measure fecundity Death rate or mortality is the number of individuals

of a species which die per unit time Immigration occurs when individuals join a

population from neighbouring ones Emigration occurs when individuals depart from a

population A cycle occurs when the size of a population

fluctuates on a regular basis

56

Ecological Sampling

57

Why Do We Sample Determine presence andor

abundance

Monitor population fluctuations

Assess lsquoecological damagersquo

Assess quality of habitat

Assess population responses

58

What Do We Sample

Physical Environment Temperature DO pH salinity clarity

flow sediment

Biotic Environment All living things

59

Physical Habitat Temperature

Mercury thermometer Electronic thermometer Long-term thermometers

Dissolved Oxygen Winkler method (titration) DO meter (electrode)

pH Litmus paper pH meter (electrode)

Salinity Salinity Meter YSI 550A DO Meter w12 cable

60

Water Clarity Secchi Disk

Disk is attached to a calibrated rope The disk is lowered into the water until the white parts can no longer be seen Secchi disk depth is then recorded and serves as the waters transparency index The clearer the water the greater the secchi disk depth

Secchi Disk

61

Current Velocity (flow) Floating-orange method

Put an orange (or something else that floats just below the water surface) and measure the time it takes it to float across a known distance

Odometer-type flow meter Number of revolutions the propeller

makes for a given time is calibrated to flow velocity

62

Sediment Sediment size is important to many

aquatic organisms Sieversquos are used to separate and

grade sediment samples Percent of each size grade can be

determined

63

Water Sample

Water and plankton from various depths can be collected

A trigger mechanism is used to close the sampler Sample is then brought back to the

surface

64

Small Mammals

Mouserat Traps Fatal

Pit Falls Bucket is placed in the ground Sometimes have lsquoleadsrsquo to the buckets

Live traps Havahart Sherman

Spot-light

Sherman trapHavahart trap

65

Birds Stick-under-the-box method Bird-trap

Works like a minnow trap Mist net

Captures birds in flight Rocket net

Uses a propellant to throw a net over birds

66

Terrestrial Insects

Sticky paper flies

Baited Traps Fire ants

Nets butterflies

Foggers Collect insects from tree canopies

67

Aquatic Insects Drift Net

Place net in flowing water Kick Net

lsquoKickrsquo sediment upstream from block net and the flow will wash them into the net

Wash bucket Serber or Hess Sampler

Stir up known area of sediment

Animals are collected by a catch net

Multi-plate Sampler Become colonized

68

Crawfish and Crab Traps

69

Fish Larvae Light Traps

Larvae are attracted to the light Ichthyoplankton nets

Can be towed at various depths Fish collect at the lsquocodrsquoend

70

Fish Lift net

Net is placed down and after a set amount of time it is quickly lifted

Pop-net Similar to a lift net but

floats are attached to a framed net

Operated by a trigger mechanism

Throw net A net attached to a heavy

frame is thrown and every thing inside is netted out Throw net

Pop-net

Lift net

71

Minnow trap

Usually use bait to attract small fish Light is used sometimes as an attractant

72

Fish Electrofishing

Electricity is put into the water Fish are temporarily stunned and usually

swim towards the electricity source Usually non-fatal but may cause some

damage

73

Fish Gill Net

Gill nets resemble tennis nets Fish can not swim completely through the

net and get caught Gill nets are size selective (based on mesh

size) Square Mesh

Bar mesh

Stretch mesh

74

Fish Trammel Net

Three panels two large mesh on the outside and a small mesh on the inside

Fish swim through the outer mesh pushes the small mesh through the other side and becomes entangled

75

Hoop nets (and other similar nets) can have bait or not

Fyke nets have leads to help guide fish to the net

76

Seine Seines are nets that are pulled

through shallow water to catch fish

77

Purse Seine Used to encircle entire schools of fish

Usually involves a spotter plane and a second boat

78

Trotline (longline) A series of baited drop lines

connected to a main line

Can be deployed by tying one end to the bank and tying the other end with a heavy weight

79

Shrimp (or fish) Trawl Net pulled behind

a boat along the bottom Either a beam or

otter boards keep the net open

80

Tagging Individuals Coded Wire Tags

Microwire that has a unique label

Magnetic wand detects the tag

Tag retention should be determined

T-Bar tags Can be individually

numbered External tag

PIT tags (Passive Integrated Transponders) Wand induces the tag to

transmit individual number is displayed

81

Other Tagging Methods

Toe clip Amphibian and reptile Clip of one or more toes

to identify individuals

Bird Band Place a metal band on a

bird leg Generally has

identification information

82

Preserving plant specimens Pressing and drying Long-term

preservation and storage

Alternative drying techniques

Special preservation and processing techniques

Mounting

83

Pressing and drying Techniques for pressing and drying specimens have been

established for many years There are minor variations in recommended methods but they are essentially the same worldwide

The best specimens are plants that are pressed as soon as possible after collection before wilting and shrivelling Most plants may be kept in sealed containers such as plastic bags for up to a day if it is inconvenient to press immediately However some plants show such rapid wilting particularly of the flowers that such delays are best avoided Flowers with a lot of nectar may go mouldy very quickly if excess nectar is not shaken off before pressing

Specimens are pressed flat and dried between sheets of absorbent blotters or semi-absorbent paper such as newspaper Papers with a glossy surface should be avoided because they are not absorbent enough to aid drying The plant should be carefully laid out between the drying sheets as their form at this stage largely determines their ultimate appearance The flowers should be spread out with the petals carefully arranged wilted leaves should be straightened and unnecessary shoots of excessively twiggy shrubs may be cut away

84

Microwave ovens Small numbers of specimens can be dried using a microwave

oven The technique recommended in the literature is to place the specimens between unprinted absorbent paper for example butchers paper not newspaper which is unsuitable because the chemicals present in the ink may cause a fire The specimens should be put in a special press which should be of a microwave-safe material (wood acrylic or polycarbonate sheeting eg plexiglass or perspex NO metal components) If such a press is not available sheets of cardboard can be placed above and below the specimens and then weighted down

Drying time depends on the power of your oven In most cases drying is accomplished by irradiating at maximum power for 1-2 minutes per specimen although it is often a case of trial and error It is best to process no more than 10-12 specimens of average thickness per batch Specimens are usually dried after the moisture that characteristically appears on the glass door has disappeared If the specimen is damp when taken out of the oven allow it to stand before re-radiating as moisture continues to evaporate from the specimen for some time Care must be taken not to irradiate the specimens for too long

It should be noted that microwave treatment damages seeds and the cellular structure of the plants which may reduce the long-term value of the specimens

85

Alternative drying techniquesSilica gelother desiccants amp freeze drying Alternative methods of drying plant specimens have been

used for some time but are mostly restricted to special purpose collections The main alternatives are freeze-drying and drying in a desiccant powder such as desiccant silica gel In general these techniques are used where it is essential to preserve the shape of a delicate plant of organ of the plant such as the flower Freeze-drying has also been used to preserve the chemical composition of a plant as accurately as possible for later study

Disadvantages and special conservation problems of specimens dried in these manners are that they are particularly susceptible to damage The dried parts are fragile lack support and often catch on packing materials They must therefore be packed especially carefully and stored in small boxes or tubes with some appropriate packing material that does not snag and break small projections Acid-free tissue paper is often used Drying in desiccant silica gel crystals or powder can also have the disadvantage that it is difficult to remove all traces of the silica gel after drying

86

Special preservation and processing techniquesWet or spirit collections

Very fleshy or delicate structures including small algae and orchid flowers are best preserved in an air-tight glass or plastic jar with a liquid preservative rather than by drying The type of preservative used should be clearly labelled in the jar Such material is often referred to as a spirit collection or wet collection

Most material can be satisfactorily preserved in 70 ethyl alcohol (or 70 methylated spirit or denatured alcohol) with 30 water Colours will fade quickly in spirit however so it is a good idea to keep comprehensive notes and photographs

87

Small algae Microscopic algae are often collected in a jar and in the

water in which they were found If the algae are to be stored for more than 2-3 days a preservative needs to be used Traditionally this has been the extremely toxic formalin - a small amount can be added to the water to make a 5 final solution and the container labelled This must not be sent through the post or by courier

There are some other equally toxic options for example propylene phenoxytol but none should be sent through the post A safer option is to add sufficient concentrated alcohol or methylated spirits to the water containing the algae to make a final solution of 70 alcohol This treatment dilutes the algae making them difficult to find so if they can be concentrated somehow first (eg by filtering) they can be stored in much less liquid Another option is to fix the algae in formalin (or something similar) first and then prepare a microscope glass slide with a permanent water-soluble mounting medium

88

Mounting Mounting specimens prevents most fragile material from

fragmenting and prevents specimens becoming separated from their labels If the plant collection is a long-term project specimens should be mounted on sheets of archival (permanent) cardboard or paper with archival-quality fixing media These include stitching with cotton thread dental floss nickel-plated copper wire (for heavier specimens) narrow strips of archival paper linen tape or by using an archival adhesive such as methyl cellulose adhesive

One disadvantage of mounting specimens is that it can make parts of the specimen inaccessible for examination so it is essential that this be borne in mind during specimen arrangement and mounting For example easily reversible mounting media should be used specimens should be strapped to the sheet rather than glued all over and the specimen should be carefully arranged before it is attached so that it shows all features

89

Full-size herbarium mounting sheets are usually about 43 cm long x 28 cm wide The plant name and accompanying field notes should be transcribed on a permanent label stuck to one corner of the herbarium sheet (the bottom right-hand corner being the most common) or sometimes annotations may be written directly on the sheet or card

Small pieces of material which may have become separated from the specimen (eg seeds) can be placed in small plastic bags and pinned to the sheet

90

Long-term preservation and storage The long-term preservation of dry plant

specimens is largely dependent on protection from insect attack Specimens collected by Linnaeus in the eighteenth century and by Banks and Solander on the Endeavour voyage in 1788 are still excellently preserved

91

Pests and their control A range of pests attack dried plant material The

most common pests are insects and fungi though rodents and other large animals can cause damage in poor storage conditions Insects eat the material the paper surrounding the material and the adhesives and mounting media

Such insect pests range from psocids (book lice) which attack mainly the softer parts such as flowers and soft fruits to tobacco beetles and carpet beetles which can bore holes through the toughest of specimens Many insects are particularly sensitive to relative humidity levels and do not thrive at levels below 50

92

The most common and acceptable specimen treatments for insect control are Freezing Microwave Poisoning Insect deterrents Fungal pests

93

Storage

Dried and pressed plant specimens can be stored in cardboard or plastic boxes or tied in bundles in light-weight cardboard folders placed in pigeon holes

Alternatively they can be placed in protective plastic jackets and displayed in ring folders which is recommended if they are to be frequently handled such as for a reference collection

94

Filing

Specimens should be filed in a systematic order if a relatively permanent collection is being made The major groups ie ferns and fern allies cycads conifers dicotyledons and monocotyledons are best kept separately or according to some classification scheme such as that given in a flora or handbook

Similarly the genera within each family and the species within each genus may be filed alphabetically or following some such classification

95

Preservation of entire animals

Types of collection specimens of an entire animal For reference collections mammals can be prepared as a variety of specimens The condition of the specimen may determine possible ways to preserve it if for instance decomposition of the skin has loosened the hair of a carcass so much that it can easily be pulled out or removed by rubbing (ldquoslippingrdquo fur) it will be very difficult or impossible to produce a study skin or mounted specimen The most usual types of specimens (based on Nagorsen and Peterson 1980) are 1) entire fluid-preserved animals (for studying anatomy and histology fluid preservation may change the fur colour) 2) study skins with accompanying skulls partial skeletons (some bones remain in the skin) for studying pelage colour hair quality and moulting patterns 3) mounted skins with accompanying partial or entire skeleton (some bones may remain in the skin dependant on the method of preservation) or freeze-dried specimens 4) entire skeletons for instance for studying anatomy geographic variation or for age determination (entire skeletons are poorly represented in collections so Nagorsen and Peterson (1980) recommend preparation of at least one male and one female skeleton per species

96

Preservation of specimens in the field Formalin preservation Preservation in alcohol Preservation by cooling or freezing

97

Formalin preservation After weighing and measuring the animal and attaching an

adequate label very small specimens (up to 100 g) can be fixed whole by submerging them in 10 buffered formalin (tissue - formalin solution ratio of at least 1 12) the body cavity can be filled with formalin solution by injection until it is turgid and firm some formalin may also be injected under the skin into the body cavity larger muscles and organs If hypodermic needles are not available the body cavity can be opened ventrally by making a slit instead allowing the formalin to enter

Keeping the mouth open with a piece of wood or cotton may later allow examination of teeth Then the whole body can be immersed in formalin in the posture in which it is supposed to stay permanently because it will harden The ratio of formalin to carcass must be at least 12 to 1 to assure a good fixation Tissues can be left in buffered neutralized formalin for several months but formalin hardens specimens therefore after fixation longterm storage in alcohol may be better After preservation the carcass should therefore be washed in water and transferred into ethanol for permanent storage

Disadvantages for instance it discolours the fur after a longish immersion softens the bones and prevents further examination for microbiology

98

Preservation in alcohol

After weighing a whole animal can be preserved in a container of alcohol (70-90) Removal of the intestine prior to storage of the animal in alcohol is recommended

99

Preservation by cooling or freezing Removal of the skin with insulating fur

before cooling or freezing may help to cool the carcass down more quickly

Freezing is not recommended if histological examination is planned

100

THANK YOU

52

The assessments are usually made on an abundance scale of 5 categories

Abundance Common Frequent Occasional Rare

Barnacles exposed at low water

53

Environmental resistance are the factors which limit the growth of a particular population

eg predation disease availability of light food water oxygen and shelter the accumulation of toxic wastes and even the size of the population itself

54

Density-dependent Growth A population is a density-dependent when its size

(or density) affects its growth rate because of density-dependent factors such as food availability and toxic waste accumulation

Density-independent Growth In this type of growth a population increases until

some factor causes a sudden reduction in its size Its effect is the same regardless of the size of the

population eg temperature fires floods storms etc

55

Regulation of Population Size Fecundity is the reproductive capacity of individual

females of a species Birth rate or natality is used to measure fecundity Death rate or mortality is the number of individuals

of a species which die per unit time Immigration occurs when individuals join a

population from neighbouring ones Emigration occurs when individuals depart from a

population A cycle occurs when the size of a population

fluctuates on a regular basis

56

Ecological Sampling

57

Why Do We Sample Determine presence andor

abundance

Monitor population fluctuations

Assess lsquoecological damagersquo

Assess quality of habitat

Assess population responses

58

What Do We Sample

Physical Environment Temperature DO pH salinity clarity

flow sediment

Biotic Environment All living things

59

Physical Habitat Temperature

Mercury thermometer Electronic thermometer Long-term thermometers

Dissolved Oxygen Winkler method (titration) DO meter (electrode)

pH Litmus paper pH meter (electrode)

Salinity Salinity Meter YSI 550A DO Meter w12 cable

60

Water Clarity Secchi Disk

Disk is attached to a calibrated rope The disk is lowered into the water until the white parts can no longer be seen Secchi disk depth is then recorded and serves as the waters transparency index The clearer the water the greater the secchi disk depth

Secchi Disk

61

Current Velocity (flow) Floating-orange method

Put an orange (or something else that floats just below the water surface) and measure the time it takes it to float across a known distance

Odometer-type flow meter Number of revolutions the propeller

makes for a given time is calibrated to flow velocity

62

Sediment Sediment size is important to many

aquatic organisms Sieversquos are used to separate and

grade sediment samples Percent of each size grade can be

determined

63

Water Sample

Water and plankton from various depths can be collected

A trigger mechanism is used to close the sampler Sample is then brought back to the

surface

64

Small Mammals

Mouserat Traps Fatal

Pit Falls Bucket is placed in the ground Sometimes have lsquoleadsrsquo to the buckets

Live traps Havahart Sherman

Spot-light

Sherman trapHavahart trap

65

Birds Stick-under-the-box method Bird-trap

Works like a minnow trap Mist net

Captures birds in flight Rocket net

Uses a propellant to throw a net over birds

66

Terrestrial Insects

Sticky paper flies

Baited Traps Fire ants

Nets butterflies

Foggers Collect insects from tree canopies

67

Aquatic Insects Drift Net

Place net in flowing water Kick Net

lsquoKickrsquo sediment upstream from block net and the flow will wash them into the net

Wash bucket Serber or Hess Sampler

Stir up known area of sediment

Animals are collected by a catch net

Multi-plate Sampler Become colonized

68

Crawfish and Crab Traps

69

Fish Larvae Light Traps

Larvae are attracted to the light Ichthyoplankton nets

Can be towed at various depths Fish collect at the lsquocodrsquoend

70

Fish Lift net

Net is placed down and after a set amount of time it is quickly lifted

Pop-net Similar to a lift net but

floats are attached to a framed net

Operated by a trigger mechanism

Throw net A net attached to a heavy

frame is thrown and every thing inside is netted out Throw net

Pop-net

Lift net

71

Minnow trap

Usually use bait to attract small fish Light is used sometimes as an attractant

72

Fish Electrofishing

Electricity is put into the water Fish are temporarily stunned and usually

swim towards the electricity source Usually non-fatal but may cause some

damage

73

Fish Gill Net

Gill nets resemble tennis nets Fish can not swim completely through the

net and get caught Gill nets are size selective (based on mesh

size) Square Mesh

Bar mesh

Stretch mesh

74

Fish Trammel Net

Three panels two large mesh on the outside and a small mesh on the inside

Fish swim through the outer mesh pushes the small mesh through the other side and becomes entangled

75

Hoop nets (and other similar nets) can have bait or not

Fyke nets have leads to help guide fish to the net

76

Seine Seines are nets that are pulled

through shallow water to catch fish

77

Purse Seine Used to encircle entire schools of fish

Usually involves a spotter plane and a second boat

78

Trotline (longline) A series of baited drop lines

connected to a main line

Can be deployed by tying one end to the bank and tying the other end with a heavy weight

79

Shrimp (or fish) Trawl Net pulled behind

a boat along the bottom Either a beam or

otter boards keep the net open

80

Tagging Individuals Coded Wire Tags

Microwire that has a unique label

Magnetic wand detects the tag

Tag retention should be determined

T-Bar tags Can be individually

numbered External tag

PIT tags (Passive Integrated Transponders) Wand induces the tag to

transmit individual number is displayed

81

Other Tagging Methods

Toe clip Amphibian and reptile Clip of one or more toes

to identify individuals

Bird Band Place a metal band on a

bird leg Generally has

identification information

82

Preserving plant specimens Pressing and drying Long-term

preservation and storage

Alternative drying techniques

Special preservation and processing techniques

Mounting

83

Pressing and drying Techniques for pressing and drying specimens have been

established for many years There are minor variations in recommended methods but they are essentially the same worldwide

The best specimens are plants that are pressed as soon as possible after collection before wilting and shrivelling Most plants may be kept in sealed containers such as plastic bags for up to a day if it is inconvenient to press immediately However some plants show such rapid wilting particularly of the flowers that such delays are best avoided Flowers with a lot of nectar may go mouldy very quickly if excess nectar is not shaken off before pressing

Specimens are pressed flat and dried between sheets of absorbent blotters or semi-absorbent paper such as newspaper Papers with a glossy surface should be avoided because they are not absorbent enough to aid drying The plant should be carefully laid out between the drying sheets as their form at this stage largely determines their ultimate appearance The flowers should be spread out with the petals carefully arranged wilted leaves should be straightened and unnecessary shoots of excessively twiggy shrubs may be cut away

84

Microwave ovens Small numbers of specimens can be dried using a microwave

oven The technique recommended in the literature is to place the specimens between unprinted absorbent paper for example butchers paper not newspaper which is unsuitable because the chemicals present in the ink may cause a fire The specimens should be put in a special press which should be of a microwave-safe material (wood acrylic or polycarbonate sheeting eg plexiglass or perspex NO metal components) If such a press is not available sheets of cardboard can be placed above and below the specimens and then weighted down

Drying time depends on the power of your oven In most cases drying is accomplished by irradiating at maximum power for 1-2 minutes per specimen although it is often a case of trial and error It is best to process no more than 10-12 specimens of average thickness per batch Specimens are usually dried after the moisture that characteristically appears on the glass door has disappeared If the specimen is damp when taken out of the oven allow it to stand before re-radiating as moisture continues to evaporate from the specimen for some time Care must be taken not to irradiate the specimens for too long

It should be noted that microwave treatment damages seeds and the cellular structure of the plants which may reduce the long-term value of the specimens

85

Alternative drying techniquesSilica gelother desiccants amp freeze drying Alternative methods of drying plant specimens have been

used for some time but are mostly restricted to special purpose collections The main alternatives are freeze-drying and drying in a desiccant powder such as desiccant silica gel In general these techniques are used where it is essential to preserve the shape of a delicate plant of organ of the plant such as the flower Freeze-drying has also been used to preserve the chemical composition of a plant as accurately as possible for later study

Disadvantages and special conservation problems of specimens dried in these manners are that they are particularly susceptible to damage The dried parts are fragile lack support and often catch on packing materials They must therefore be packed especially carefully and stored in small boxes or tubes with some appropriate packing material that does not snag and break small projections Acid-free tissue paper is often used Drying in desiccant silica gel crystals or powder can also have the disadvantage that it is difficult to remove all traces of the silica gel after drying

86

Special preservation and processing techniquesWet or spirit collections

Very fleshy or delicate structures including small algae and orchid flowers are best preserved in an air-tight glass or plastic jar with a liquid preservative rather than by drying The type of preservative used should be clearly labelled in the jar Such material is often referred to as a spirit collection or wet collection

Most material can be satisfactorily preserved in 70 ethyl alcohol (or 70 methylated spirit or denatured alcohol) with 30 water Colours will fade quickly in spirit however so it is a good idea to keep comprehensive notes and photographs

87

Small algae Microscopic algae are often collected in a jar and in the

water in which they were found If the algae are to be stored for more than 2-3 days a preservative needs to be used Traditionally this has been the extremely toxic formalin - a small amount can be added to the water to make a 5 final solution and the container labelled This must not be sent through the post or by courier

There are some other equally toxic options for example propylene phenoxytol but none should be sent through the post A safer option is to add sufficient concentrated alcohol or methylated spirits to the water containing the algae to make a final solution of 70 alcohol This treatment dilutes the algae making them difficult to find so if they can be concentrated somehow first (eg by filtering) they can be stored in much less liquid Another option is to fix the algae in formalin (or something similar) first and then prepare a microscope glass slide with a permanent water-soluble mounting medium

88

Mounting Mounting specimens prevents most fragile material from

fragmenting and prevents specimens becoming separated from their labels If the plant collection is a long-term project specimens should be mounted on sheets of archival (permanent) cardboard or paper with archival-quality fixing media These include stitching with cotton thread dental floss nickel-plated copper wire (for heavier specimens) narrow strips of archival paper linen tape or by using an archival adhesive such as methyl cellulose adhesive

One disadvantage of mounting specimens is that it can make parts of the specimen inaccessible for examination so it is essential that this be borne in mind during specimen arrangement and mounting For example easily reversible mounting media should be used specimens should be strapped to the sheet rather than glued all over and the specimen should be carefully arranged before it is attached so that it shows all features

89

Full-size herbarium mounting sheets are usually about 43 cm long x 28 cm wide The plant name and accompanying field notes should be transcribed on a permanent label stuck to one corner of the herbarium sheet (the bottom right-hand corner being the most common) or sometimes annotations may be written directly on the sheet or card

Small pieces of material which may have become separated from the specimen (eg seeds) can be placed in small plastic bags and pinned to the sheet

90

Long-term preservation and storage The long-term preservation of dry plant

specimens is largely dependent on protection from insect attack Specimens collected by Linnaeus in the eighteenth century and by Banks and Solander on the Endeavour voyage in 1788 are still excellently preserved

91

Pests and their control A range of pests attack dried plant material The

most common pests are insects and fungi though rodents and other large animals can cause damage in poor storage conditions Insects eat the material the paper surrounding the material and the adhesives and mounting media

Such insect pests range from psocids (book lice) which attack mainly the softer parts such as flowers and soft fruits to tobacco beetles and carpet beetles which can bore holes through the toughest of specimens Many insects are particularly sensitive to relative humidity levels and do not thrive at levels below 50

92

The most common and acceptable specimen treatments for insect control are Freezing Microwave Poisoning Insect deterrents Fungal pests

93

Storage

Dried and pressed plant specimens can be stored in cardboard or plastic boxes or tied in bundles in light-weight cardboard folders placed in pigeon holes

Alternatively they can be placed in protective plastic jackets and displayed in ring folders which is recommended if they are to be frequently handled such as for a reference collection

94

Filing

Specimens should be filed in a systematic order if a relatively permanent collection is being made The major groups ie ferns and fern allies cycads conifers dicotyledons and monocotyledons are best kept separately or according to some classification scheme such as that given in a flora or handbook

Similarly the genera within each family and the species within each genus may be filed alphabetically or following some such classification

95

Preservation of entire animals

Types of collection specimens of an entire animal For reference collections mammals can be prepared as a variety of specimens The condition of the specimen may determine possible ways to preserve it if for instance decomposition of the skin has loosened the hair of a carcass so much that it can easily be pulled out or removed by rubbing (ldquoslippingrdquo fur) it will be very difficult or impossible to produce a study skin or mounted specimen The most usual types of specimens (based on Nagorsen and Peterson 1980) are 1) entire fluid-preserved animals (for studying anatomy and histology fluid preservation may change the fur colour) 2) study skins with accompanying skulls partial skeletons (some bones remain in the skin) for studying pelage colour hair quality and moulting patterns 3) mounted skins with accompanying partial or entire skeleton (some bones may remain in the skin dependant on the method of preservation) or freeze-dried specimens 4) entire skeletons for instance for studying anatomy geographic variation or for age determination (entire skeletons are poorly represented in collections so Nagorsen and Peterson (1980) recommend preparation of at least one male and one female skeleton per species

96

Preservation of specimens in the field Formalin preservation Preservation in alcohol Preservation by cooling or freezing

97

Formalin preservation After weighing and measuring the animal and attaching an

adequate label very small specimens (up to 100 g) can be fixed whole by submerging them in 10 buffered formalin (tissue - formalin solution ratio of at least 1 12) the body cavity can be filled with formalin solution by injection until it is turgid and firm some formalin may also be injected under the skin into the body cavity larger muscles and organs If hypodermic needles are not available the body cavity can be opened ventrally by making a slit instead allowing the formalin to enter

Keeping the mouth open with a piece of wood or cotton may later allow examination of teeth Then the whole body can be immersed in formalin in the posture in which it is supposed to stay permanently because it will harden The ratio of formalin to carcass must be at least 12 to 1 to assure a good fixation Tissues can be left in buffered neutralized formalin for several months but formalin hardens specimens therefore after fixation longterm storage in alcohol may be better After preservation the carcass should therefore be washed in water and transferred into ethanol for permanent storage

Disadvantages for instance it discolours the fur after a longish immersion softens the bones and prevents further examination for microbiology

98

Preservation in alcohol

After weighing a whole animal can be preserved in a container of alcohol (70-90) Removal of the intestine prior to storage of the animal in alcohol is recommended

99

Preservation by cooling or freezing Removal of the skin with insulating fur

before cooling or freezing may help to cool the carcass down more quickly

Freezing is not recommended if histological examination is planned

100

THANK YOU

53

Environmental resistance are the factors which limit the growth of a particular population

eg predation disease availability of light food water oxygen and shelter the accumulation of toxic wastes and even the size of the population itself

54

Density-dependent Growth A population is a density-dependent when its size

(or density) affects its growth rate because of density-dependent factors such as food availability and toxic waste accumulation

Density-independent Growth In this type of growth a population increases until

some factor causes a sudden reduction in its size Its effect is the same regardless of the size of the

population eg temperature fires floods storms etc

55

Regulation of Population Size Fecundity is the reproductive capacity of individual

females of a species Birth rate or natality is used to measure fecundity Death rate or mortality is the number of individuals

of a species which die per unit time Immigration occurs when individuals join a

population from neighbouring ones Emigration occurs when individuals depart from a

population A cycle occurs when the size of a population

fluctuates on a regular basis

56

Ecological Sampling

57

Why Do We Sample Determine presence andor

abundance

Monitor population fluctuations

Assess lsquoecological damagersquo

Assess quality of habitat

Assess population responses

58

What Do We Sample

Physical Environment Temperature DO pH salinity clarity

flow sediment

Biotic Environment All living things

59

Physical Habitat Temperature

Mercury thermometer Electronic thermometer Long-term thermometers

Dissolved Oxygen Winkler method (titration) DO meter (electrode)

pH Litmus paper pH meter (electrode)

Salinity Salinity Meter YSI 550A DO Meter w12 cable

60

Water Clarity Secchi Disk

Disk is attached to a calibrated rope The disk is lowered into the water until the white parts can no longer be seen Secchi disk depth is then recorded and serves as the waters transparency index The clearer the water the greater the secchi disk depth

Secchi Disk

61

Current Velocity (flow) Floating-orange method

Put an orange (or something else that floats just below the water surface) and measure the time it takes it to float across a known distance

Odometer-type flow meter Number of revolutions the propeller

makes for a given time is calibrated to flow velocity

62

Sediment Sediment size is important to many

aquatic organisms Sieversquos are used to separate and

grade sediment samples Percent of each size grade can be

determined

63

Water Sample

Water and plankton from various depths can be collected

A trigger mechanism is used to close the sampler Sample is then brought back to the

surface

64

Small Mammals

Mouserat Traps Fatal

Pit Falls Bucket is placed in the ground Sometimes have lsquoleadsrsquo to the buckets

Live traps Havahart Sherman

Spot-light

Sherman trapHavahart trap

65

Birds Stick-under-the-box method Bird-trap

Works like a minnow trap Mist net

Captures birds in flight Rocket net

Uses a propellant to throw a net over birds

66

Terrestrial Insects

Sticky paper flies

Baited Traps Fire ants

Nets butterflies

Foggers Collect insects from tree canopies

67

Aquatic Insects Drift Net

Place net in flowing water Kick Net

lsquoKickrsquo sediment upstream from block net and the flow will wash them into the net

Wash bucket Serber or Hess Sampler

Stir up known area of sediment

Animals are collected by a catch net

Multi-plate Sampler Become colonized

68

Crawfish and Crab Traps

69

Fish Larvae Light Traps

Larvae are attracted to the light Ichthyoplankton nets

Can be towed at various depths Fish collect at the lsquocodrsquoend

70

Fish Lift net

Net is placed down and after a set amount of time it is quickly lifted

Pop-net Similar to a lift net but

floats are attached to a framed net

Operated by a trigger mechanism

Throw net A net attached to a heavy

frame is thrown and every thing inside is netted out Throw net

Pop-net

Lift net

71

Minnow trap

Usually use bait to attract small fish Light is used sometimes as an attractant

72

Fish Electrofishing

Electricity is put into the water Fish are temporarily stunned and usually

swim towards the electricity source Usually non-fatal but may cause some

damage

73

Fish Gill Net

Gill nets resemble tennis nets Fish can not swim completely through the

net and get caught Gill nets are size selective (based on mesh

size) Square Mesh

Bar mesh

Stretch mesh

74

Fish Trammel Net

Three panels two large mesh on the outside and a small mesh on the inside

Fish swim through the outer mesh pushes the small mesh through the other side and becomes entangled

75

Hoop nets (and other similar nets) can have bait or not

Fyke nets have leads to help guide fish to the net

76

Seine Seines are nets that are pulled

through shallow water to catch fish

77

Purse Seine Used to encircle entire schools of fish

Usually involves a spotter plane and a second boat

78

Trotline (longline) A series of baited drop lines

connected to a main line

Can be deployed by tying one end to the bank and tying the other end with a heavy weight

79

Shrimp (or fish) Trawl Net pulled behind

a boat along the bottom Either a beam or

otter boards keep the net open

80

Tagging Individuals Coded Wire Tags

Microwire that has a unique label

Magnetic wand detects the tag

Tag retention should be determined

T-Bar tags Can be individually

numbered External tag

PIT tags (Passive Integrated Transponders) Wand induces the tag to

transmit individual number is displayed

81

Other Tagging Methods

Toe clip Amphibian and reptile Clip of one or more toes

to identify individuals

Bird Band Place a metal band on a

bird leg Generally has

identification information

82

Preserving plant specimens Pressing and drying Long-term

preservation and storage

Alternative drying techniques

Special preservation and processing techniques

Mounting

83

Pressing and drying Techniques for pressing and drying specimens have been

established for many years There are minor variations in recommended methods but they are essentially the same worldwide

The best specimens are plants that are pressed as soon as possible after collection before wilting and shrivelling Most plants may be kept in sealed containers such as plastic bags for up to a day if it is inconvenient to press immediately However some plants show such rapid wilting particularly of the flowers that such delays are best avoided Flowers with a lot of nectar may go mouldy very quickly if excess nectar is not shaken off before pressing

Specimens are pressed flat and dried between sheets of absorbent blotters or semi-absorbent paper such as newspaper Papers with a glossy surface should be avoided because they are not absorbent enough to aid drying The plant should be carefully laid out between the drying sheets as their form at this stage largely determines their ultimate appearance The flowers should be spread out with the petals carefully arranged wilted leaves should be straightened and unnecessary shoots of excessively twiggy shrubs may be cut away

84

Microwave ovens Small numbers of specimens can be dried using a microwave

oven The technique recommended in the literature is to place the specimens between unprinted absorbent paper for example butchers paper not newspaper which is unsuitable because the chemicals present in the ink may cause a fire The specimens should be put in a special press which should be of a microwave-safe material (wood acrylic or polycarbonate sheeting eg plexiglass or perspex NO metal components) If such a press is not available sheets of cardboard can be placed above and below the specimens and then weighted down

Drying time depends on the power of your oven In most cases drying is accomplished by irradiating at maximum power for 1-2 minutes per specimen although it is often a case of trial and error It is best to process no more than 10-12 specimens of average thickness per batch Specimens are usually dried after the moisture that characteristically appears on the glass door has disappeared If the specimen is damp when taken out of the oven allow it to stand before re-radiating as moisture continues to evaporate from the specimen for some time Care must be taken not to irradiate the specimens for too long

It should be noted that microwave treatment damages seeds and the cellular structure of the plants which may reduce the long-term value of the specimens

85

Alternative drying techniquesSilica gelother desiccants amp freeze drying Alternative methods of drying plant specimens have been

used for some time but are mostly restricted to special purpose collections The main alternatives are freeze-drying and drying in a desiccant powder such as desiccant silica gel In general these techniques are used where it is essential to preserve the shape of a delicate plant of organ of the plant such as the flower Freeze-drying has also been used to preserve the chemical composition of a plant as accurately as possible for later study

Disadvantages and special conservation problems of specimens dried in these manners are that they are particularly susceptible to damage The dried parts are fragile lack support and often catch on packing materials They must therefore be packed especially carefully and stored in small boxes or tubes with some appropriate packing material that does not snag and break small projections Acid-free tissue paper is often used Drying in desiccant silica gel crystals or powder can also have the disadvantage that it is difficult to remove all traces of the silica gel after drying

86

Special preservation and processing techniquesWet or spirit collections

Very fleshy or delicate structures including small algae and orchid flowers are best preserved in an air-tight glass or plastic jar with a liquid preservative rather than by drying The type of preservative used should be clearly labelled in the jar Such material is often referred to as a spirit collection or wet collection

Most material can be satisfactorily preserved in 70 ethyl alcohol (or 70 methylated spirit or denatured alcohol) with 30 water Colours will fade quickly in spirit however so it is a good idea to keep comprehensive notes and photographs

87

Small algae Microscopic algae are often collected in a jar and in the

water in which they were found If the algae are to be stored for more than 2-3 days a preservative needs to be used Traditionally this has been the extremely toxic formalin - a small amount can be added to the water to make a 5 final solution and the container labelled This must not be sent through the post or by courier

There are some other equally toxic options for example propylene phenoxytol but none should be sent through the post A safer option is to add sufficient concentrated alcohol or methylated spirits to the water containing the algae to make a final solution of 70 alcohol This treatment dilutes the algae making them difficult to find so if they can be concentrated somehow first (eg by filtering) they can be stored in much less liquid Another option is to fix the algae in formalin (or something similar) first and then prepare a microscope glass slide with a permanent water-soluble mounting medium

88

Mounting Mounting specimens prevents most fragile material from

fragmenting and prevents specimens becoming separated from their labels If the plant collection is a long-term project specimens should be mounted on sheets of archival (permanent) cardboard or paper with archival-quality fixing media These include stitching with cotton thread dental floss nickel-plated copper wire (for heavier specimens) narrow strips of archival paper linen tape or by using an archival adhesive such as methyl cellulose adhesive

One disadvantage of mounting specimens is that it can make parts of the specimen inaccessible for examination so it is essential that this be borne in mind during specimen arrangement and mounting For example easily reversible mounting media should be used specimens should be strapped to the sheet rather than glued all over and the specimen should be carefully arranged before it is attached so that it shows all features

89

Full-size herbarium mounting sheets are usually about 43 cm long x 28 cm wide The plant name and accompanying field notes should be transcribed on a permanent label stuck to one corner of the herbarium sheet (the bottom right-hand corner being the most common) or sometimes annotations may be written directly on the sheet or card

Small pieces of material which may have become separated from the specimen (eg seeds) can be placed in small plastic bags and pinned to the sheet

90

Long-term preservation and storage The long-term preservation of dry plant

specimens is largely dependent on protection from insect attack Specimens collected by Linnaeus in the eighteenth century and by Banks and Solander on the Endeavour voyage in 1788 are still excellently preserved

91

Pests and their control A range of pests attack dried plant material The

most common pests are insects and fungi though rodents and other large animals can cause damage in poor storage conditions Insects eat the material the paper surrounding the material and the adhesives and mounting media

Such insect pests range from psocids (book lice) which attack mainly the softer parts such as flowers and soft fruits to tobacco beetles and carpet beetles which can bore holes through the toughest of specimens Many insects are particularly sensitive to relative humidity levels and do not thrive at levels below 50

92

The most common and acceptable specimen treatments for insect control are Freezing Microwave Poisoning Insect deterrents Fungal pests

93

Storage

Dried and pressed plant specimens can be stored in cardboard or plastic boxes or tied in bundles in light-weight cardboard folders placed in pigeon holes

Alternatively they can be placed in protective plastic jackets and displayed in ring folders which is recommended if they are to be frequently handled such as for a reference collection

94

Filing

Specimens should be filed in a systematic order if a relatively permanent collection is being made The major groups ie ferns and fern allies cycads conifers dicotyledons and monocotyledons are best kept separately or according to some classification scheme such as that given in a flora or handbook

Similarly the genera within each family and the species within each genus may be filed alphabetically or following some such classification

95

Preservation of entire animals

Types of collection specimens of an entire animal For reference collections mammals can be prepared as a variety of specimens The condition of the specimen may determine possible ways to preserve it if for instance decomposition of the skin has loosened the hair of a carcass so much that it can easily be pulled out or removed by rubbing (ldquoslippingrdquo fur) it will be very difficult or impossible to produce a study skin or mounted specimen The most usual types of specimens (based on Nagorsen and Peterson 1980) are 1) entire fluid-preserved animals (for studying anatomy and histology fluid preservation may change the fur colour) 2) study skins with accompanying skulls partial skeletons (some bones remain in the skin) for studying pelage colour hair quality and moulting patterns 3) mounted skins with accompanying partial or entire skeleton (some bones may remain in the skin dependant on the method of preservation) or freeze-dried specimens 4) entire skeletons for instance for studying anatomy geographic variation or for age determination (entire skeletons are poorly represented in collections so Nagorsen and Peterson (1980) recommend preparation of at least one male and one female skeleton per species

96

Preservation of specimens in the field Formalin preservation Preservation in alcohol Preservation by cooling or freezing

97

Formalin preservation After weighing and measuring the animal and attaching an

adequate label very small specimens (up to 100 g) can be fixed whole by submerging them in 10 buffered formalin (tissue - formalin solution ratio of at least 1 12) the body cavity can be filled with formalin solution by injection until it is turgid and firm some formalin may also be injected under the skin into the body cavity larger muscles and organs If hypodermic needles are not available the body cavity can be opened ventrally by making a slit instead allowing the formalin to enter

Keeping the mouth open with a piece of wood or cotton may later allow examination of teeth Then the whole body can be immersed in formalin in the posture in which it is supposed to stay permanently because it will harden The ratio of formalin to carcass must be at least 12 to 1 to assure a good fixation Tissues can be left in buffered neutralized formalin for several months but formalin hardens specimens therefore after fixation longterm storage in alcohol may be better After preservation the carcass should therefore be washed in water and transferred into ethanol for permanent storage

Disadvantages for instance it discolours the fur after a longish immersion softens the bones and prevents further examination for microbiology

98

Preservation in alcohol

After weighing a whole animal can be preserved in a container of alcohol (70-90) Removal of the intestine prior to storage of the animal in alcohol is recommended

99

Preservation by cooling or freezing Removal of the skin with insulating fur

before cooling or freezing may help to cool the carcass down more quickly

Freezing is not recommended if histological examination is planned

100

THANK YOU

54

Density-dependent Growth A population is a density-dependent when its size

(or density) affects its growth rate because of density-dependent factors such as food availability and toxic waste accumulation

Density-independent Growth In this type of growth a population increases until

some factor causes a sudden reduction in its size Its effect is the same regardless of the size of the

population eg temperature fires floods storms etc

55

Regulation of Population Size Fecundity is the reproductive capacity of individual

females of a species Birth rate or natality is used to measure fecundity Death rate or mortality is the number of individuals

of a species which die per unit time Immigration occurs when individuals join a

population from neighbouring ones Emigration occurs when individuals depart from a

population A cycle occurs when the size of a population

fluctuates on a regular basis

56

Ecological Sampling

57

Why Do We Sample Determine presence andor

abundance

Monitor population fluctuations

Assess lsquoecological damagersquo

Assess quality of habitat

Assess population responses

58

What Do We Sample

Physical Environment Temperature DO pH salinity clarity

flow sediment

Biotic Environment All living things

59

Physical Habitat Temperature

Mercury thermometer Electronic thermometer Long-term thermometers

Dissolved Oxygen Winkler method (titration) DO meter (electrode)

pH Litmus paper pH meter (electrode)

Salinity Salinity Meter YSI 550A DO Meter w12 cable

60

Water Clarity Secchi Disk

Disk is attached to a calibrated rope The disk is lowered into the water until the white parts can no longer be seen Secchi disk depth is then recorded and serves as the waters transparency index The clearer the water the greater the secchi disk depth

Secchi Disk

61

Current Velocity (flow) Floating-orange method

Put an orange (or something else that floats just below the water surface) and measure the time it takes it to float across a known distance

Odometer-type flow meter Number of revolutions the propeller

makes for a given time is calibrated to flow velocity

62

Sediment Sediment size is important to many

aquatic organisms Sieversquos are used to separate and

grade sediment samples Percent of each size grade can be

determined

63

Water Sample

Water and plankton from various depths can be collected

A trigger mechanism is used to close the sampler Sample is then brought back to the

surface

64

Small Mammals

Mouserat Traps Fatal

Pit Falls Bucket is placed in the ground Sometimes have lsquoleadsrsquo to the buckets

Live traps Havahart Sherman

Spot-light

Sherman trapHavahart trap

65

Birds Stick-under-the-box method Bird-trap

Works like a minnow trap Mist net

Captures birds in flight Rocket net

Uses a propellant to throw a net over birds

66

Terrestrial Insects

Sticky paper flies

Baited Traps Fire ants

Nets butterflies

Foggers Collect insects from tree canopies

67

Aquatic Insects Drift Net

Place net in flowing water Kick Net

lsquoKickrsquo sediment upstream from block net and the flow will wash them into the net

Wash bucket Serber or Hess Sampler

Stir up known area of sediment

Animals are collected by a catch net

Multi-plate Sampler Become colonized

68

Crawfish and Crab Traps

69

Fish Larvae Light Traps

Larvae are attracted to the light Ichthyoplankton nets

Can be towed at various depths Fish collect at the lsquocodrsquoend

70

Fish Lift net

Net is placed down and after a set amount of time it is quickly lifted

Pop-net Similar to a lift net but

floats are attached to a framed net

Operated by a trigger mechanism

Throw net A net attached to a heavy

frame is thrown and every thing inside is netted out Throw net

Pop-net

Lift net

71

Minnow trap

Usually use bait to attract small fish Light is used sometimes as an attractant

72

Fish Electrofishing

Electricity is put into the water Fish are temporarily stunned and usually

swim towards the electricity source Usually non-fatal but may cause some

damage

73

Fish Gill Net

Gill nets resemble tennis nets Fish can not swim completely through the

net and get caught Gill nets are size selective (based on mesh

size) Square Mesh

Bar mesh

Stretch mesh

74

Fish Trammel Net

Three panels two large mesh on the outside and a small mesh on the inside

Fish swim through the outer mesh pushes the small mesh through the other side and becomes entangled

75

Hoop nets (and other similar nets) can have bait or not

Fyke nets have leads to help guide fish to the net

76

Seine Seines are nets that are pulled

through shallow water to catch fish

77

Purse Seine Used to encircle entire schools of fish

Usually involves a spotter plane and a second boat

78

Trotline (longline) A series of baited drop lines

connected to a main line

Can be deployed by tying one end to the bank and tying the other end with a heavy weight

79

Shrimp (or fish) Trawl Net pulled behind

a boat along the bottom Either a beam or

otter boards keep the net open

80

Tagging Individuals Coded Wire Tags

Microwire that has a unique label

Magnetic wand detects the tag

Tag retention should be determined

T-Bar tags Can be individually

numbered External tag

PIT tags (Passive Integrated Transponders) Wand induces the tag to

transmit individual number is displayed

81

Other Tagging Methods

Toe clip Amphibian and reptile Clip of one or more toes

to identify individuals

Bird Band Place a metal band on a

bird leg Generally has

identification information

82

Preserving plant specimens Pressing and drying Long-term

preservation and storage

Alternative drying techniques

Special preservation and processing techniques

Mounting

83

Pressing and drying Techniques for pressing and drying specimens have been

established for many years There are minor variations in recommended methods but they are essentially the same worldwide

The best specimens are plants that are pressed as soon as possible after collection before wilting and shrivelling Most plants may be kept in sealed containers such as plastic bags for up to a day if it is inconvenient to press immediately However some plants show such rapid wilting particularly of the flowers that such delays are best avoided Flowers with a lot of nectar may go mouldy very quickly if excess nectar is not shaken off before pressing

Specimens are pressed flat and dried between sheets of absorbent blotters or semi-absorbent paper such as newspaper Papers with a glossy surface should be avoided because they are not absorbent enough to aid drying The plant should be carefully laid out between the drying sheets as their form at this stage largely determines their ultimate appearance The flowers should be spread out with the petals carefully arranged wilted leaves should be straightened and unnecessary shoots of excessively twiggy shrubs may be cut away

84

Microwave ovens Small numbers of specimens can be dried using a microwave

oven The technique recommended in the literature is to place the specimens between unprinted absorbent paper for example butchers paper not newspaper which is unsuitable because the chemicals present in the ink may cause a fire The specimens should be put in a special press which should be of a microwave-safe material (wood acrylic or polycarbonate sheeting eg plexiglass or perspex NO metal components) If such a press is not available sheets of cardboard can be placed above and below the specimens and then weighted down

Drying time depends on the power of your oven In most cases drying is accomplished by irradiating at maximum power for 1-2 minutes per specimen although it is often a case of trial and error It is best to process no more than 10-12 specimens of average thickness per batch Specimens are usually dried after the moisture that characteristically appears on the glass door has disappeared If the specimen is damp when taken out of the oven allow it to stand before re-radiating as moisture continues to evaporate from the specimen for some time Care must be taken not to irradiate the specimens for too long

It should be noted that microwave treatment damages seeds and the cellular structure of the plants which may reduce the long-term value of the specimens

85

Alternative drying techniquesSilica gelother desiccants amp freeze drying Alternative methods of drying plant specimens have been

used for some time but are mostly restricted to special purpose collections The main alternatives are freeze-drying and drying in a desiccant powder such as desiccant silica gel In general these techniques are used where it is essential to preserve the shape of a delicate plant of organ of the plant such as the flower Freeze-drying has also been used to preserve the chemical composition of a plant as accurately as possible for later study

Disadvantages and special conservation problems of specimens dried in these manners are that they are particularly susceptible to damage The dried parts are fragile lack support and often catch on packing materials They must therefore be packed especially carefully and stored in small boxes or tubes with some appropriate packing material that does not snag and break small projections Acid-free tissue paper is often used Drying in desiccant silica gel crystals or powder can also have the disadvantage that it is difficult to remove all traces of the silica gel after drying

86

Special preservation and processing techniquesWet or spirit collections

Very fleshy or delicate structures including small algae and orchid flowers are best preserved in an air-tight glass or plastic jar with a liquid preservative rather than by drying The type of preservative used should be clearly labelled in the jar Such material is often referred to as a spirit collection or wet collection

Most material can be satisfactorily preserved in 70 ethyl alcohol (or 70 methylated spirit or denatured alcohol) with 30 water Colours will fade quickly in spirit however so it is a good idea to keep comprehensive notes and photographs

87

Small algae Microscopic algae are often collected in a jar and in the

water in which they were found If the algae are to be stored for more than 2-3 days a preservative needs to be used Traditionally this has been the extremely toxic formalin - a small amount can be added to the water to make a 5 final solution and the container labelled This must not be sent through the post or by courier

There are some other equally toxic options for example propylene phenoxytol but none should be sent through the post A safer option is to add sufficient concentrated alcohol or methylated spirits to the water containing the algae to make a final solution of 70 alcohol This treatment dilutes the algae making them difficult to find so if they can be concentrated somehow first (eg by filtering) they can be stored in much less liquid Another option is to fix the algae in formalin (or something similar) first and then prepare a microscope glass slide with a permanent water-soluble mounting medium

88

Mounting Mounting specimens prevents most fragile material from

fragmenting and prevents specimens becoming separated from their labels If the plant collection is a long-term project specimens should be mounted on sheets of archival (permanent) cardboard or paper with archival-quality fixing media These include stitching with cotton thread dental floss nickel-plated copper wire (for heavier specimens) narrow strips of archival paper linen tape or by using an archival adhesive such as methyl cellulose adhesive

One disadvantage of mounting specimens is that it can make parts of the specimen inaccessible for examination so it is essential that this be borne in mind during specimen arrangement and mounting For example easily reversible mounting media should be used specimens should be strapped to the sheet rather than glued all over and the specimen should be carefully arranged before it is attached so that it shows all features

89

Full-size herbarium mounting sheets are usually about 43 cm long x 28 cm wide The plant name and accompanying field notes should be transcribed on a permanent label stuck to one corner of the herbarium sheet (the bottom right-hand corner being the most common) or sometimes annotations may be written directly on the sheet or card

Small pieces of material which may have become separated from the specimen (eg seeds) can be placed in small plastic bags and pinned to the sheet

90

Long-term preservation and storage The long-term preservation of dry plant

specimens is largely dependent on protection from insect attack Specimens collected by Linnaeus in the eighteenth century and by Banks and Solander on the Endeavour voyage in 1788 are still excellently preserved

91

Pests and their control A range of pests attack dried plant material The

most common pests are insects and fungi though rodents and other large animals can cause damage in poor storage conditions Insects eat the material the paper surrounding the material and the adhesives and mounting media

Such insect pests range from psocids (book lice) which attack mainly the softer parts such as flowers and soft fruits to tobacco beetles and carpet beetles which can bore holes through the toughest of specimens Many insects are particularly sensitive to relative humidity levels and do not thrive at levels below 50

92

The most common and acceptable specimen treatments for insect control are Freezing Microwave Poisoning Insect deterrents Fungal pests

93

Storage

Dried and pressed plant specimens can be stored in cardboard or plastic boxes or tied in bundles in light-weight cardboard folders placed in pigeon holes

Alternatively they can be placed in protective plastic jackets and displayed in ring folders which is recommended if they are to be frequently handled such as for a reference collection

94

Filing

Specimens should be filed in a systematic order if a relatively permanent collection is being made The major groups ie ferns and fern allies cycads conifers dicotyledons and monocotyledons are best kept separately or according to some classification scheme such as that given in a flora or handbook

Similarly the genera within each family and the species within each genus may be filed alphabetically or following some such classification

95

Preservation of entire animals

Types of collection specimens of an entire animal For reference collections mammals can be prepared as a variety of specimens The condition of the specimen may determine possible ways to preserve it if for instance decomposition of the skin has loosened the hair of a carcass so much that it can easily be pulled out or removed by rubbing (ldquoslippingrdquo fur) it will be very difficult or impossible to produce a study skin or mounted specimen The most usual types of specimens (based on Nagorsen and Peterson 1980) are 1) entire fluid-preserved animals (for studying anatomy and histology fluid preservation may change the fur colour) 2) study skins with accompanying skulls partial skeletons (some bones remain in the skin) for studying pelage colour hair quality and moulting patterns 3) mounted skins with accompanying partial or entire skeleton (some bones may remain in the skin dependant on the method of preservation) or freeze-dried specimens 4) entire skeletons for instance for studying anatomy geographic variation or for age determination (entire skeletons are poorly represented in collections so Nagorsen and Peterson (1980) recommend preparation of at least one male and one female skeleton per species

96

Preservation of specimens in the field Formalin preservation Preservation in alcohol Preservation by cooling or freezing

97

Formalin preservation After weighing and measuring the animal and attaching an

adequate label very small specimens (up to 100 g) can be fixed whole by submerging them in 10 buffered formalin (tissue - formalin solution ratio of at least 1 12) the body cavity can be filled with formalin solution by injection until it is turgid and firm some formalin may also be injected under the skin into the body cavity larger muscles and organs If hypodermic needles are not available the body cavity can be opened ventrally by making a slit instead allowing the formalin to enter

Keeping the mouth open with a piece of wood or cotton may later allow examination of teeth Then the whole body can be immersed in formalin in the posture in which it is supposed to stay permanently because it will harden The ratio of formalin to carcass must be at least 12 to 1 to assure a good fixation Tissues can be left in buffered neutralized formalin for several months but formalin hardens specimens therefore after fixation longterm storage in alcohol may be better After preservation the carcass should therefore be washed in water and transferred into ethanol for permanent storage

Disadvantages for instance it discolours the fur after a longish immersion softens the bones and prevents further examination for microbiology

98

Preservation in alcohol

After weighing a whole animal can be preserved in a container of alcohol (70-90) Removal of the intestine prior to storage of the animal in alcohol is recommended

99

Preservation by cooling or freezing Removal of the skin with insulating fur

before cooling or freezing may help to cool the carcass down more quickly

Freezing is not recommended if histological examination is planned

100

THANK YOU

55

Regulation of Population Size Fecundity is the reproductive capacity of individual

females of a species Birth rate or natality is used to measure fecundity Death rate or mortality is the number of individuals

of a species which die per unit time Immigration occurs when individuals join a

population from neighbouring ones Emigration occurs when individuals depart from a

population A cycle occurs when the size of a population

fluctuates on a regular basis

56

Ecological Sampling

57

Why Do We Sample Determine presence andor

abundance

Monitor population fluctuations

Assess lsquoecological damagersquo

Assess quality of habitat

Assess population responses

58

What Do We Sample

Physical Environment Temperature DO pH salinity clarity

flow sediment

Biotic Environment All living things

59

Physical Habitat Temperature

Mercury thermometer Electronic thermometer Long-term thermometers

Dissolved Oxygen Winkler method (titration) DO meter (electrode)

pH Litmus paper pH meter (electrode)

Salinity Salinity Meter YSI 550A DO Meter w12 cable

60

Water Clarity Secchi Disk

Disk is attached to a calibrated rope The disk is lowered into the water until the white parts can no longer be seen Secchi disk depth is then recorded and serves as the waters transparency index The clearer the water the greater the secchi disk depth

Secchi Disk

61

Current Velocity (flow) Floating-orange method

Put an orange (or something else that floats just below the water surface) and measure the time it takes it to float across a known distance

Odometer-type flow meter Number of revolutions the propeller

makes for a given time is calibrated to flow velocity

62

Sediment Sediment size is important to many

aquatic organisms Sieversquos are used to separate and

grade sediment samples Percent of each size grade can be

determined

63

Water Sample

Water and plankton from various depths can be collected

A trigger mechanism is used to close the sampler Sample is then brought back to the

surface

64

Small Mammals

Mouserat Traps Fatal

Pit Falls Bucket is placed in the ground Sometimes have lsquoleadsrsquo to the buckets

Live traps Havahart Sherman

Spot-light

Sherman trapHavahart trap

65

Birds Stick-under-the-box method Bird-trap

Works like a minnow trap Mist net

Captures birds in flight Rocket net

Uses a propellant to throw a net over birds

66

Terrestrial Insects

Sticky paper flies

Baited Traps Fire ants

Nets butterflies

Foggers Collect insects from tree canopies

67

Aquatic Insects Drift Net

Place net in flowing water Kick Net

lsquoKickrsquo sediment upstream from block net and the flow will wash them into the net

Wash bucket Serber or Hess Sampler

Stir up known area of sediment

Animals are collected by a catch net

Multi-plate Sampler Become colonized

68

Crawfish and Crab Traps

69

Fish Larvae Light Traps

Larvae are attracted to the light Ichthyoplankton nets

Can be towed at various depths Fish collect at the lsquocodrsquoend

70

Fish Lift net

Net is placed down and after a set amount of time it is quickly lifted

Pop-net Similar to a lift net but

floats are attached to a framed net

Operated by a trigger mechanism

Throw net A net attached to a heavy

frame is thrown and every thing inside is netted out Throw net

Pop-net

Lift net

71

Minnow trap

Usually use bait to attract small fish Light is used sometimes as an attractant

72

Fish Electrofishing

Electricity is put into the water Fish are temporarily stunned and usually

swim towards the electricity source Usually non-fatal but may cause some

damage

73

Fish Gill Net

Gill nets resemble tennis nets Fish can not swim completely through the

net and get caught Gill nets are size selective (based on mesh

size) Square Mesh

Bar mesh

Stretch mesh

74

Fish Trammel Net

Three panels two large mesh on the outside and a small mesh on the inside

Fish swim through the outer mesh pushes the small mesh through the other side and becomes entangled

75

Hoop nets (and other similar nets) can have bait or not

Fyke nets have leads to help guide fish to the net

76

Seine Seines are nets that are pulled

through shallow water to catch fish

77

Purse Seine Used to encircle entire schools of fish

Usually involves a spotter plane and a second boat

78

Trotline (longline) A series of baited drop lines

connected to a main line

Can be deployed by tying one end to the bank and tying the other end with a heavy weight

79

Shrimp (or fish) Trawl Net pulled behind

a boat along the bottom Either a beam or

otter boards keep the net open

80

Tagging Individuals Coded Wire Tags

Microwire that has a unique label

Magnetic wand detects the tag

Tag retention should be determined

T-Bar tags Can be individually

numbered External tag

PIT tags (Passive Integrated Transponders) Wand induces the tag to

transmit individual number is displayed

81

Other Tagging Methods

Toe clip Amphibian and reptile Clip of one or more toes

to identify individuals

Bird Band Place a metal band on a

bird leg Generally has

identification information

82

Preserving plant specimens Pressing and drying Long-term

preservation and storage

Alternative drying techniques

Special preservation and processing techniques

Mounting

83

Pressing and drying Techniques for pressing and drying specimens have been

established for many years There are minor variations in recommended methods but they are essentially the same worldwide

The best specimens are plants that are pressed as soon as possible after collection before wilting and shrivelling Most plants may be kept in sealed containers such as plastic bags for up to a day if it is inconvenient to press immediately However some plants show such rapid wilting particularly of the flowers that such delays are best avoided Flowers with a lot of nectar may go mouldy very quickly if excess nectar is not shaken off before pressing

Specimens are pressed flat and dried between sheets of absorbent blotters or semi-absorbent paper such as newspaper Papers with a glossy surface should be avoided because they are not absorbent enough to aid drying The plant should be carefully laid out between the drying sheets as their form at this stage largely determines their ultimate appearance The flowers should be spread out with the petals carefully arranged wilted leaves should be straightened and unnecessary shoots of excessively twiggy shrubs may be cut away

84

Microwave ovens Small numbers of specimens can be dried using a microwave

oven The technique recommended in the literature is to place the specimens between unprinted absorbent paper for example butchers paper not newspaper which is unsuitable because the chemicals present in the ink may cause a fire The specimens should be put in a special press which should be of a microwave-safe material (wood acrylic or polycarbonate sheeting eg plexiglass or perspex NO metal components) If such a press is not available sheets of cardboard can be placed above and below the specimens and then weighted down

Drying time depends on the power of your oven In most cases drying is accomplished by irradiating at maximum power for 1-2 minutes per specimen although it is often a case of trial and error It is best to process no more than 10-12 specimens of average thickness per batch Specimens are usually dried after the moisture that characteristically appears on the glass door has disappeared If the specimen is damp when taken out of the oven allow it to stand before re-radiating as moisture continues to evaporate from the specimen for some time Care must be taken not to irradiate the specimens for too long

It should be noted that microwave treatment damages seeds and the cellular structure of the plants which may reduce the long-term value of the specimens

85

Alternative drying techniquesSilica gelother desiccants amp freeze drying Alternative methods of drying plant specimens have been

used for some time but are mostly restricted to special purpose collections The main alternatives are freeze-drying and drying in a desiccant powder such as desiccant silica gel In general these techniques are used where it is essential to preserve the shape of a delicate plant of organ of the plant such as the flower Freeze-drying has also been used to preserve the chemical composition of a plant as accurately as possible for later study

Disadvantages and special conservation problems of specimens dried in these manners are that they are particularly susceptible to damage The dried parts are fragile lack support and often catch on packing materials They must therefore be packed especially carefully and stored in small boxes or tubes with some appropriate packing material that does not snag and break small projections Acid-free tissue paper is often used Drying in desiccant silica gel crystals or powder can also have the disadvantage that it is difficult to remove all traces of the silica gel after drying

86

Special preservation and processing techniquesWet or spirit collections

Very fleshy or delicate structures including small algae and orchid flowers are best preserved in an air-tight glass or plastic jar with a liquid preservative rather than by drying The type of preservative used should be clearly labelled in the jar Such material is often referred to as a spirit collection or wet collection

Most material can be satisfactorily preserved in 70 ethyl alcohol (or 70 methylated spirit or denatured alcohol) with 30 water Colours will fade quickly in spirit however so it is a good idea to keep comprehensive notes and photographs

87

Small algae Microscopic algae are often collected in a jar and in the

water in which they were found If the algae are to be stored for more than 2-3 days a preservative needs to be used Traditionally this has been the extremely toxic formalin - a small amount can be added to the water to make a 5 final solution and the container labelled This must not be sent through the post or by courier

There are some other equally toxic options for example propylene phenoxytol but none should be sent through the post A safer option is to add sufficient concentrated alcohol or methylated spirits to the water containing the algae to make a final solution of 70 alcohol This treatment dilutes the algae making them difficult to find so if they can be concentrated somehow first (eg by filtering) they can be stored in much less liquid Another option is to fix the algae in formalin (or something similar) first and then prepare a microscope glass slide with a permanent water-soluble mounting medium

88

Mounting Mounting specimens prevents most fragile material from

fragmenting and prevents specimens becoming separated from their labels If the plant collection is a long-term project specimens should be mounted on sheets of archival (permanent) cardboard or paper with archival-quality fixing media These include stitching with cotton thread dental floss nickel-plated copper wire (for heavier specimens) narrow strips of archival paper linen tape or by using an archival adhesive such as methyl cellulose adhesive

One disadvantage of mounting specimens is that it can make parts of the specimen inaccessible for examination so it is essential that this be borne in mind during specimen arrangement and mounting For example easily reversible mounting media should be used specimens should be strapped to the sheet rather than glued all over and the specimen should be carefully arranged before it is attached so that it shows all features

89

Full-size herbarium mounting sheets are usually about 43 cm long x 28 cm wide The plant name and accompanying field notes should be transcribed on a permanent label stuck to one corner of the herbarium sheet (the bottom right-hand corner being the most common) or sometimes annotations may be written directly on the sheet or card

Small pieces of material which may have become separated from the specimen (eg seeds) can be placed in small plastic bags and pinned to the sheet

90

Long-term preservation and storage The long-term preservation of dry plant

specimens is largely dependent on protection from insect attack Specimens collected by Linnaeus in the eighteenth century and by Banks and Solander on the Endeavour voyage in 1788 are still excellently preserved

91

Pests and their control A range of pests attack dried plant material The

most common pests are insects and fungi though rodents and other large animals can cause damage in poor storage conditions Insects eat the material the paper surrounding the material and the adhesives and mounting media

Such insect pests range from psocids (book lice) which attack mainly the softer parts such as flowers and soft fruits to tobacco beetles and carpet beetles which can bore holes through the toughest of specimens Many insects are particularly sensitive to relative humidity levels and do not thrive at levels below 50

92

The most common and acceptable specimen treatments for insect control are Freezing Microwave Poisoning Insect deterrents Fungal pests

93

Storage

Dried and pressed plant specimens can be stored in cardboard or plastic boxes or tied in bundles in light-weight cardboard folders placed in pigeon holes

Alternatively they can be placed in protective plastic jackets and displayed in ring folders which is recommended if they are to be frequently handled such as for a reference collection

94

Filing

Specimens should be filed in a systematic order if a relatively permanent collection is being made The major groups ie ferns and fern allies cycads conifers dicotyledons and monocotyledons are best kept separately or according to some classification scheme such as that given in a flora or handbook

Similarly the genera within each family and the species within each genus may be filed alphabetically or following some such classification

95

Preservation of entire animals

Types of collection specimens of an entire animal For reference collections mammals can be prepared as a variety of specimens The condition of the specimen may determine possible ways to preserve it if for instance decomposition of the skin has loosened the hair of a carcass so much that it can easily be pulled out or removed by rubbing (ldquoslippingrdquo fur) it will be very difficult or impossible to produce a study skin or mounted specimen The most usual types of specimens (based on Nagorsen and Peterson 1980) are 1) entire fluid-preserved animals (for studying anatomy and histology fluid preservation may change the fur colour) 2) study skins with accompanying skulls partial skeletons (some bones remain in the skin) for studying pelage colour hair quality and moulting patterns 3) mounted skins with accompanying partial or entire skeleton (some bones may remain in the skin dependant on the method of preservation) or freeze-dried specimens 4) entire skeletons for instance for studying anatomy geographic variation or for age determination (entire skeletons are poorly represented in collections so Nagorsen and Peterson (1980) recommend preparation of at least one male and one female skeleton per species

96

Preservation of specimens in the field Formalin preservation Preservation in alcohol Preservation by cooling or freezing

97

Formalin preservation After weighing and measuring the animal and attaching an

adequate label very small specimens (up to 100 g) can be fixed whole by submerging them in 10 buffered formalin (tissue - formalin solution ratio of at least 1 12) the body cavity can be filled with formalin solution by injection until it is turgid and firm some formalin may also be injected under the skin into the body cavity larger muscles and organs If hypodermic needles are not available the body cavity can be opened ventrally by making a slit instead allowing the formalin to enter

Keeping the mouth open with a piece of wood or cotton may later allow examination of teeth Then the whole body can be immersed in formalin in the posture in which it is supposed to stay permanently because it will harden The ratio of formalin to carcass must be at least 12 to 1 to assure a good fixation Tissues can be left in buffered neutralized formalin for several months but formalin hardens specimens therefore after fixation longterm storage in alcohol may be better After preservation the carcass should therefore be washed in water and transferred into ethanol for permanent storage

Disadvantages for instance it discolours the fur after a longish immersion softens the bones and prevents further examination for microbiology

98

Preservation in alcohol

After weighing a whole animal can be preserved in a container of alcohol (70-90) Removal of the intestine prior to storage of the animal in alcohol is recommended

99

Preservation by cooling or freezing Removal of the skin with insulating fur

before cooling or freezing may help to cool the carcass down more quickly

Freezing is not recommended if histological examination is planned

100

THANK YOU

56

Ecological Sampling

57

Why Do We Sample Determine presence andor

abundance

Monitor population fluctuations

Assess lsquoecological damagersquo

Assess quality of habitat

Assess population responses

58

What Do We Sample

Physical Environment Temperature DO pH salinity clarity

flow sediment

Biotic Environment All living things

59

Physical Habitat Temperature

Mercury thermometer Electronic thermometer Long-term thermometers

Dissolved Oxygen Winkler method (titration) DO meter (electrode)

pH Litmus paper pH meter (electrode)

Salinity Salinity Meter YSI 550A DO Meter w12 cable

60

Water Clarity Secchi Disk

Disk is attached to a calibrated rope The disk is lowered into the water until the white parts can no longer be seen Secchi disk depth is then recorded and serves as the waters transparency index The clearer the water the greater the secchi disk depth

Secchi Disk

61

Current Velocity (flow) Floating-orange method

Put an orange (or something else that floats just below the water surface) and measure the time it takes it to float across a known distance

Odometer-type flow meter Number of revolutions the propeller

makes for a given time is calibrated to flow velocity

62

Sediment Sediment size is important to many

aquatic organisms Sieversquos are used to separate and

grade sediment samples Percent of each size grade can be

determined

63

Water Sample

Water and plankton from various depths can be collected

A trigger mechanism is used to close the sampler Sample is then brought back to the

surface

64

Small Mammals

Mouserat Traps Fatal

Pit Falls Bucket is placed in the ground Sometimes have lsquoleadsrsquo to the buckets

Live traps Havahart Sherman

Spot-light

Sherman trapHavahart trap

65

Birds Stick-under-the-box method Bird-trap

Works like a minnow trap Mist net

Captures birds in flight Rocket net

Uses a propellant to throw a net over birds

66

Terrestrial Insects

Sticky paper flies

Baited Traps Fire ants

Nets butterflies

Foggers Collect insects from tree canopies

67

Aquatic Insects Drift Net

Place net in flowing water Kick Net

lsquoKickrsquo sediment upstream from block net and the flow will wash them into the net

Wash bucket Serber or Hess Sampler

Stir up known area of sediment

Animals are collected by a catch net

Multi-plate Sampler Become colonized

68

Crawfish and Crab Traps

69

Fish Larvae Light Traps

Larvae are attracted to the light Ichthyoplankton nets

Can be towed at various depths Fish collect at the lsquocodrsquoend

70

Fish Lift net

Net is placed down and after a set amount of time it is quickly lifted

Pop-net Similar to a lift net but

floats are attached to a framed net

Operated by a trigger mechanism

Throw net A net attached to a heavy

frame is thrown and every thing inside is netted out Throw net

Pop-net

Lift net

71

Minnow trap

Usually use bait to attract small fish Light is used sometimes as an attractant

72

Fish Electrofishing

Electricity is put into the water Fish are temporarily stunned and usually

swim towards the electricity source Usually non-fatal but may cause some

damage

73

Fish Gill Net

Gill nets resemble tennis nets Fish can not swim completely through the

net and get caught Gill nets are size selective (based on mesh

size) Square Mesh

Bar mesh

Stretch mesh

74

Fish Trammel Net

Three panels two large mesh on the outside and a small mesh on the inside

Fish swim through the outer mesh pushes the small mesh through the other side and becomes entangled

75

Hoop nets (and other similar nets) can have bait or not

Fyke nets have leads to help guide fish to the net

76

Seine Seines are nets that are pulled

through shallow water to catch fish

77

Purse Seine Used to encircle entire schools of fish

Usually involves a spotter plane and a second boat

78

Trotline (longline) A series of baited drop lines

connected to a main line

Can be deployed by tying one end to the bank and tying the other end with a heavy weight

79

Shrimp (or fish) Trawl Net pulled behind

a boat along the bottom Either a beam or

otter boards keep the net open

80

Tagging Individuals Coded Wire Tags

Microwire that has a unique label

Magnetic wand detects the tag

Tag retention should be determined

T-Bar tags Can be individually

numbered External tag

PIT tags (Passive Integrated Transponders) Wand induces the tag to

transmit individual number is displayed

81

Other Tagging Methods

Toe clip Amphibian and reptile Clip of one or more toes

to identify individuals

Bird Band Place a metal band on a

bird leg Generally has

identification information

82

Preserving plant specimens Pressing and drying Long-term

preservation and storage

Alternative drying techniques

Special preservation and processing techniques

Mounting

83

Pressing and drying Techniques for pressing and drying specimens have been

established for many years There are minor variations in recommended methods but they are essentially the same worldwide

The best specimens are plants that are pressed as soon as possible after collection before wilting and shrivelling Most plants may be kept in sealed containers such as plastic bags for up to a day if it is inconvenient to press immediately However some plants show such rapid wilting particularly of the flowers that such delays are best avoided Flowers with a lot of nectar may go mouldy very quickly if excess nectar is not shaken off before pressing

Specimens are pressed flat and dried between sheets of absorbent blotters or semi-absorbent paper such as newspaper Papers with a glossy surface should be avoided because they are not absorbent enough to aid drying The plant should be carefully laid out between the drying sheets as their form at this stage largely determines their ultimate appearance The flowers should be spread out with the petals carefully arranged wilted leaves should be straightened and unnecessary shoots of excessively twiggy shrubs may be cut away

84

Microwave ovens Small numbers of specimens can be dried using a microwave

oven The technique recommended in the literature is to place the specimens between unprinted absorbent paper for example butchers paper not newspaper which is unsuitable because the chemicals present in the ink may cause a fire The specimens should be put in a special press which should be of a microwave-safe material (wood acrylic or polycarbonate sheeting eg plexiglass or perspex NO metal components) If such a press is not available sheets of cardboard can be placed above and below the specimens and then weighted down

Drying time depends on the power of your oven In most cases drying is accomplished by irradiating at maximum power for 1-2 minutes per specimen although it is often a case of trial and error It is best to process no more than 10-12 specimens of average thickness per batch Specimens are usually dried after the moisture that characteristically appears on the glass door has disappeared If the specimen is damp when taken out of the oven allow it to stand before re-radiating as moisture continues to evaporate from the specimen for some time Care must be taken not to irradiate the specimens for too long

It should be noted that microwave treatment damages seeds and the cellular structure of the plants which may reduce the long-term value of the specimens

85

Alternative drying techniquesSilica gelother desiccants amp freeze drying Alternative methods of drying plant specimens have been

used for some time but are mostly restricted to special purpose collections The main alternatives are freeze-drying and drying in a desiccant powder such as desiccant silica gel In general these techniques are used where it is essential to preserve the shape of a delicate plant of organ of the plant such as the flower Freeze-drying has also been used to preserve the chemical composition of a plant as accurately as possible for later study

Disadvantages and special conservation problems of specimens dried in these manners are that they are particularly susceptible to damage The dried parts are fragile lack support and often catch on packing materials They must therefore be packed especially carefully and stored in small boxes or tubes with some appropriate packing material that does not snag and break small projections Acid-free tissue paper is often used Drying in desiccant silica gel crystals or powder can also have the disadvantage that it is difficult to remove all traces of the silica gel after drying

86

Special preservation and processing techniquesWet or spirit collections

Very fleshy or delicate structures including small algae and orchid flowers are best preserved in an air-tight glass or plastic jar with a liquid preservative rather than by drying The type of preservative used should be clearly labelled in the jar Such material is often referred to as a spirit collection or wet collection

Most material can be satisfactorily preserved in 70 ethyl alcohol (or 70 methylated spirit or denatured alcohol) with 30 water Colours will fade quickly in spirit however so it is a good idea to keep comprehensive notes and photographs

87

Small algae Microscopic algae are often collected in a jar and in the

water in which they were found If the algae are to be stored for more than 2-3 days a preservative needs to be used Traditionally this has been the extremely toxic formalin - a small amount can be added to the water to make a 5 final solution and the container labelled This must not be sent through the post or by courier

There are some other equally toxic options for example propylene phenoxytol but none should be sent through the post A safer option is to add sufficient concentrated alcohol or methylated spirits to the water containing the algae to make a final solution of 70 alcohol This treatment dilutes the algae making them difficult to find so if they can be concentrated somehow first (eg by filtering) they can be stored in much less liquid Another option is to fix the algae in formalin (or something similar) first and then prepare a microscope glass slide with a permanent water-soluble mounting medium

88

Mounting Mounting specimens prevents most fragile material from

fragmenting and prevents specimens becoming separated from their labels If the plant collection is a long-term project specimens should be mounted on sheets of archival (permanent) cardboard or paper with archival-quality fixing media These include stitching with cotton thread dental floss nickel-plated copper wire (for heavier specimens) narrow strips of archival paper linen tape or by using an archival adhesive such as methyl cellulose adhesive

One disadvantage of mounting specimens is that it can make parts of the specimen inaccessible for examination so it is essential that this be borne in mind during specimen arrangement and mounting For example easily reversible mounting media should be used specimens should be strapped to the sheet rather than glued all over and the specimen should be carefully arranged before it is attached so that it shows all features

89

Full-size herbarium mounting sheets are usually about 43 cm long x 28 cm wide The plant name and accompanying field notes should be transcribed on a permanent label stuck to one corner of the herbarium sheet (the bottom right-hand corner being the most common) or sometimes annotations may be written directly on the sheet or card

Small pieces of material which may have become separated from the specimen (eg seeds) can be placed in small plastic bags and pinned to the sheet

90

Long-term preservation and storage The long-term preservation of dry plant

specimens is largely dependent on protection from insect attack Specimens collected by Linnaeus in the eighteenth century and by Banks and Solander on the Endeavour voyage in 1788 are still excellently preserved

91

Pests and their control A range of pests attack dried plant material The

most common pests are insects and fungi though rodents and other large animals can cause damage in poor storage conditions Insects eat the material the paper surrounding the material and the adhesives and mounting media

Such insect pests range from psocids (book lice) which attack mainly the softer parts such as flowers and soft fruits to tobacco beetles and carpet beetles which can bore holes through the toughest of specimens Many insects are particularly sensitive to relative humidity levels and do not thrive at levels below 50

92

The most common and acceptable specimen treatments for insect control are Freezing Microwave Poisoning Insect deterrents Fungal pests

93

Storage

Dried and pressed plant specimens can be stored in cardboard or plastic boxes or tied in bundles in light-weight cardboard folders placed in pigeon holes

Alternatively they can be placed in protective plastic jackets and displayed in ring folders which is recommended if they are to be frequently handled such as for a reference collection

94

Filing

Specimens should be filed in a systematic order if a relatively permanent collection is being made The major groups ie ferns and fern allies cycads conifers dicotyledons and monocotyledons are best kept separately or according to some classification scheme such as that given in a flora or handbook

Similarly the genera within each family and the species within each genus may be filed alphabetically or following some such classification

95

Preservation of entire animals

Types of collection specimens of an entire animal For reference collections mammals can be prepared as a variety of specimens The condition of the specimen may determine possible ways to preserve it if for instance decomposition of the skin has loosened the hair of a carcass so much that it can easily be pulled out or removed by rubbing (ldquoslippingrdquo fur) it will be very difficult or impossible to produce a study skin or mounted specimen The most usual types of specimens (based on Nagorsen and Peterson 1980) are 1) entire fluid-preserved animals (for studying anatomy and histology fluid preservation may change the fur colour) 2) study skins with accompanying skulls partial skeletons (some bones remain in the skin) for studying pelage colour hair quality and moulting patterns 3) mounted skins with accompanying partial or entire skeleton (some bones may remain in the skin dependant on the method of preservation) or freeze-dried specimens 4) entire skeletons for instance for studying anatomy geographic variation or for age determination (entire skeletons are poorly represented in collections so Nagorsen and Peterson (1980) recommend preparation of at least one male and one female skeleton per species

96

Preservation of specimens in the field Formalin preservation Preservation in alcohol Preservation by cooling or freezing

97

Formalin preservation After weighing and measuring the animal and attaching an

adequate label very small specimens (up to 100 g) can be fixed whole by submerging them in 10 buffered formalin (tissue - formalin solution ratio of at least 1 12) the body cavity can be filled with formalin solution by injection until it is turgid and firm some formalin may also be injected under the skin into the body cavity larger muscles and organs If hypodermic needles are not available the body cavity can be opened ventrally by making a slit instead allowing the formalin to enter

Keeping the mouth open with a piece of wood or cotton may later allow examination of teeth Then the whole body can be immersed in formalin in the posture in which it is supposed to stay permanently because it will harden The ratio of formalin to carcass must be at least 12 to 1 to assure a good fixation Tissues can be left in buffered neutralized formalin for several months but formalin hardens specimens therefore after fixation longterm storage in alcohol may be better After preservation the carcass should therefore be washed in water and transferred into ethanol for permanent storage

Disadvantages for instance it discolours the fur after a longish immersion softens the bones and prevents further examination for microbiology

98

Preservation in alcohol

After weighing a whole animal can be preserved in a container of alcohol (70-90) Removal of the intestine prior to storage of the animal in alcohol is recommended

99

Preservation by cooling or freezing Removal of the skin with insulating fur

before cooling or freezing may help to cool the carcass down more quickly

Freezing is not recommended if histological examination is planned

100

THANK YOU

57

Why Do We Sample Determine presence andor

abundance

Monitor population fluctuations

Assess lsquoecological damagersquo

Assess quality of habitat

Assess population responses

58

What Do We Sample

Physical Environment Temperature DO pH salinity clarity

flow sediment

Biotic Environment All living things

59

Physical Habitat Temperature

Mercury thermometer Electronic thermometer Long-term thermometers

Dissolved Oxygen Winkler method (titration) DO meter (electrode)

pH Litmus paper pH meter (electrode)

Salinity Salinity Meter YSI 550A DO Meter w12 cable

60

Water Clarity Secchi Disk

Disk is attached to a calibrated rope The disk is lowered into the water until the white parts can no longer be seen Secchi disk depth is then recorded and serves as the waters transparency index The clearer the water the greater the secchi disk depth

Secchi Disk

61

Current Velocity (flow) Floating-orange method

Put an orange (or something else that floats just below the water surface) and measure the time it takes it to float across a known distance

Odometer-type flow meter Number of revolutions the propeller

makes for a given time is calibrated to flow velocity

62

Sediment Sediment size is important to many

aquatic organisms Sieversquos are used to separate and

grade sediment samples Percent of each size grade can be

determined

63

Water Sample

Water and plankton from various depths can be collected

A trigger mechanism is used to close the sampler Sample is then brought back to the

surface

64

Small Mammals

Mouserat Traps Fatal

Pit Falls Bucket is placed in the ground Sometimes have lsquoleadsrsquo to the buckets

Live traps Havahart Sherman

Spot-light

Sherman trapHavahart trap

65

Birds Stick-under-the-box method Bird-trap

Works like a minnow trap Mist net

Captures birds in flight Rocket net

Uses a propellant to throw a net over birds

66

Terrestrial Insects

Sticky paper flies

Baited Traps Fire ants

Nets butterflies

Foggers Collect insects from tree canopies

67

Aquatic Insects Drift Net

Place net in flowing water Kick Net

lsquoKickrsquo sediment upstream from block net and the flow will wash them into the net

Wash bucket Serber or Hess Sampler

Stir up known area of sediment

Animals are collected by a catch net

Multi-plate Sampler Become colonized

68

Crawfish and Crab Traps

69

Fish Larvae Light Traps

Larvae are attracted to the light Ichthyoplankton nets

Can be towed at various depths Fish collect at the lsquocodrsquoend

70

Fish Lift net

Net is placed down and after a set amount of time it is quickly lifted

Pop-net Similar to a lift net but

floats are attached to a framed net

Operated by a trigger mechanism

Throw net A net attached to a heavy

frame is thrown and every thing inside is netted out Throw net

Pop-net

Lift net

71

Minnow trap

Usually use bait to attract small fish Light is used sometimes as an attractant

72

Fish Electrofishing

Electricity is put into the water Fish are temporarily stunned and usually

swim towards the electricity source Usually non-fatal but may cause some

damage

73

Fish Gill Net

Gill nets resemble tennis nets Fish can not swim completely through the

net and get caught Gill nets are size selective (based on mesh

size) Square Mesh

Bar mesh

Stretch mesh

74

Fish Trammel Net

Three panels two large mesh on the outside and a small mesh on the inside

Fish swim through the outer mesh pushes the small mesh through the other side and becomes entangled

75

Hoop nets (and other similar nets) can have bait or not

Fyke nets have leads to help guide fish to the net

76

Seine Seines are nets that are pulled

through shallow water to catch fish

77

Purse Seine Used to encircle entire schools of fish

Usually involves a spotter plane and a second boat

78

Trotline (longline) A series of baited drop lines

connected to a main line

Can be deployed by tying one end to the bank and tying the other end with a heavy weight

79

Shrimp (or fish) Trawl Net pulled behind

a boat along the bottom Either a beam or

otter boards keep the net open

80

Tagging Individuals Coded Wire Tags

Microwire that has a unique label

Magnetic wand detects the tag

Tag retention should be determined

T-Bar tags Can be individually

numbered External tag

PIT tags (Passive Integrated Transponders) Wand induces the tag to

transmit individual number is displayed

81

Other Tagging Methods

Toe clip Amphibian and reptile Clip of one or more toes

to identify individuals

Bird Band Place a metal band on a

bird leg Generally has

identification information

82

Preserving plant specimens Pressing and drying Long-term

preservation and storage

Alternative drying techniques

Special preservation and processing techniques

Mounting

83

Pressing and drying Techniques for pressing and drying specimens have been

established for many years There are minor variations in recommended methods but they are essentially the same worldwide

The best specimens are plants that are pressed as soon as possible after collection before wilting and shrivelling Most plants may be kept in sealed containers such as plastic bags for up to a day if it is inconvenient to press immediately However some plants show such rapid wilting particularly of the flowers that such delays are best avoided Flowers with a lot of nectar may go mouldy very quickly if excess nectar is not shaken off before pressing

Specimens are pressed flat and dried between sheets of absorbent blotters or semi-absorbent paper such as newspaper Papers with a glossy surface should be avoided because they are not absorbent enough to aid drying The plant should be carefully laid out between the drying sheets as their form at this stage largely determines their ultimate appearance The flowers should be spread out with the petals carefully arranged wilted leaves should be straightened and unnecessary shoots of excessively twiggy shrubs may be cut away

84

Microwave ovens Small numbers of specimens can be dried using a microwave

oven The technique recommended in the literature is to place the specimens between unprinted absorbent paper for example butchers paper not newspaper which is unsuitable because the chemicals present in the ink may cause a fire The specimens should be put in a special press which should be of a microwave-safe material (wood acrylic or polycarbonate sheeting eg plexiglass or perspex NO metal components) If such a press is not available sheets of cardboard can be placed above and below the specimens and then weighted down

Drying time depends on the power of your oven In most cases drying is accomplished by irradiating at maximum power for 1-2 minutes per specimen although it is often a case of trial and error It is best to process no more than 10-12 specimens of average thickness per batch Specimens are usually dried after the moisture that characteristically appears on the glass door has disappeared If the specimen is damp when taken out of the oven allow it to stand before re-radiating as moisture continues to evaporate from the specimen for some time Care must be taken not to irradiate the specimens for too long

It should be noted that microwave treatment damages seeds and the cellular structure of the plants which may reduce the long-term value of the specimens

85

Alternative drying techniquesSilica gelother desiccants amp freeze drying Alternative methods of drying plant specimens have been

used for some time but are mostly restricted to special purpose collections The main alternatives are freeze-drying and drying in a desiccant powder such as desiccant silica gel In general these techniques are used where it is essential to preserve the shape of a delicate plant of organ of the plant such as the flower Freeze-drying has also been used to preserve the chemical composition of a plant as accurately as possible for later study

Disadvantages and special conservation problems of specimens dried in these manners are that they are particularly susceptible to damage The dried parts are fragile lack support and often catch on packing materials They must therefore be packed especially carefully and stored in small boxes or tubes with some appropriate packing material that does not snag and break small projections Acid-free tissue paper is often used Drying in desiccant silica gel crystals or powder can also have the disadvantage that it is difficult to remove all traces of the silica gel after drying

86

Special preservation and processing techniquesWet or spirit collections

Very fleshy or delicate structures including small algae and orchid flowers are best preserved in an air-tight glass or plastic jar with a liquid preservative rather than by drying The type of preservative used should be clearly labelled in the jar Such material is often referred to as a spirit collection or wet collection

Most material can be satisfactorily preserved in 70 ethyl alcohol (or 70 methylated spirit or denatured alcohol) with 30 water Colours will fade quickly in spirit however so it is a good idea to keep comprehensive notes and photographs

87

Small algae Microscopic algae are often collected in a jar and in the

water in which they were found If the algae are to be stored for more than 2-3 days a preservative needs to be used Traditionally this has been the extremely toxic formalin - a small amount can be added to the water to make a 5 final solution and the container labelled This must not be sent through the post or by courier

There are some other equally toxic options for example propylene phenoxytol but none should be sent through the post A safer option is to add sufficient concentrated alcohol or methylated spirits to the water containing the algae to make a final solution of 70 alcohol This treatment dilutes the algae making them difficult to find so if they can be concentrated somehow first (eg by filtering) they can be stored in much less liquid Another option is to fix the algae in formalin (or something similar) first and then prepare a microscope glass slide with a permanent water-soluble mounting medium

88

Mounting Mounting specimens prevents most fragile material from

fragmenting and prevents specimens becoming separated from their labels If the plant collection is a long-term project specimens should be mounted on sheets of archival (permanent) cardboard or paper with archival-quality fixing media These include stitching with cotton thread dental floss nickel-plated copper wire (for heavier specimens) narrow strips of archival paper linen tape or by using an archival adhesive such as methyl cellulose adhesive

One disadvantage of mounting specimens is that it can make parts of the specimen inaccessible for examination so it is essential that this be borne in mind during specimen arrangement and mounting For example easily reversible mounting media should be used specimens should be strapped to the sheet rather than glued all over and the specimen should be carefully arranged before it is attached so that it shows all features

89

Full-size herbarium mounting sheets are usually about 43 cm long x 28 cm wide The plant name and accompanying field notes should be transcribed on a permanent label stuck to one corner of the herbarium sheet (the bottom right-hand corner being the most common) or sometimes annotations may be written directly on the sheet or card

Small pieces of material which may have become separated from the specimen (eg seeds) can be placed in small plastic bags and pinned to the sheet

90

Long-term preservation and storage The long-term preservation of dry plant

specimens is largely dependent on protection from insect attack Specimens collected by Linnaeus in the eighteenth century and by Banks and Solander on the Endeavour voyage in 1788 are still excellently preserved

91

Pests and their control A range of pests attack dried plant material The

most common pests are insects and fungi though rodents and other large animals can cause damage in poor storage conditions Insects eat the material the paper surrounding the material and the adhesives and mounting media

Such insect pests range from psocids (book lice) which attack mainly the softer parts such as flowers and soft fruits to tobacco beetles and carpet beetles which can bore holes through the toughest of specimens Many insects are particularly sensitive to relative humidity levels and do not thrive at levels below 50

92

The most common and acceptable specimen treatments for insect control are Freezing Microwave Poisoning Insect deterrents Fungal pests

93

Storage

Dried and pressed plant specimens can be stored in cardboard or plastic boxes or tied in bundles in light-weight cardboard folders placed in pigeon holes

Alternatively they can be placed in protective plastic jackets and displayed in ring folders which is recommended if they are to be frequently handled such as for a reference collection

94

Filing

Specimens should be filed in a systematic order if a relatively permanent collection is being made The major groups ie ferns and fern allies cycads conifers dicotyledons and monocotyledons are best kept separately or according to some classification scheme such as that given in a flora or handbook

Similarly the genera within each family and the species within each genus may be filed alphabetically or following some such classification

95

Preservation of entire animals

Types of collection specimens of an entire animal For reference collections mammals can be prepared as a variety of specimens The condition of the specimen may determine possible ways to preserve it if for instance decomposition of the skin has loosened the hair of a carcass so much that it can easily be pulled out or removed by rubbing (ldquoslippingrdquo fur) it will be very difficult or impossible to produce a study skin or mounted specimen The most usual types of specimens (based on Nagorsen and Peterson 1980) are 1) entire fluid-preserved animals (for studying anatomy and histology fluid preservation may change the fur colour) 2) study skins with accompanying skulls partial skeletons (some bones remain in the skin) for studying pelage colour hair quality and moulting patterns 3) mounted skins with accompanying partial or entire skeleton (some bones may remain in the skin dependant on the method of preservation) or freeze-dried specimens 4) entire skeletons for instance for studying anatomy geographic variation or for age determination (entire skeletons are poorly represented in collections so Nagorsen and Peterson (1980) recommend preparation of at least one male and one female skeleton per species

96

Preservation of specimens in the field Formalin preservation Preservation in alcohol Preservation by cooling or freezing

97

Formalin preservation After weighing and measuring the animal and attaching an

adequate label very small specimens (up to 100 g) can be fixed whole by submerging them in 10 buffered formalin (tissue - formalin solution ratio of at least 1 12) the body cavity can be filled with formalin solution by injection until it is turgid and firm some formalin may also be injected under the skin into the body cavity larger muscles and organs If hypodermic needles are not available the body cavity can be opened ventrally by making a slit instead allowing the formalin to enter

Keeping the mouth open with a piece of wood or cotton may later allow examination of teeth Then the whole body can be immersed in formalin in the posture in which it is supposed to stay permanently because it will harden The ratio of formalin to carcass must be at least 12 to 1 to assure a good fixation Tissues can be left in buffered neutralized formalin for several months but formalin hardens specimens therefore after fixation longterm storage in alcohol may be better After preservation the carcass should therefore be washed in water and transferred into ethanol for permanent storage

Disadvantages for instance it discolours the fur after a longish immersion softens the bones and prevents further examination for microbiology

98

Preservation in alcohol

After weighing a whole animal can be preserved in a container of alcohol (70-90) Removal of the intestine prior to storage of the animal in alcohol is recommended

99

Preservation by cooling or freezing Removal of the skin with insulating fur

before cooling or freezing may help to cool the carcass down more quickly

Freezing is not recommended if histological examination is planned

100

THANK YOU

58

What Do We Sample

Physical Environment Temperature DO pH salinity clarity

flow sediment

Biotic Environment All living things

59

Physical Habitat Temperature

Mercury thermometer Electronic thermometer Long-term thermometers

Dissolved Oxygen Winkler method (titration) DO meter (electrode)

pH Litmus paper pH meter (electrode)

Salinity Salinity Meter YSI 550A DO Meter w12 cable

60

Water Clarity Secchi Disk

Disk is attached to a calibrated rope The disk is lowered into the water until the white parts can no longer be seen Secchi disk depth is then recorded and serves as the waters transparency index The clearer the water the greater the secchi disk depth

Secchi Disk

61

Current Velocity (flow) Floating-orange method

Put an orange (or something else that floats just below the water surface) and measure the time it takes it to float across a known distance

Odometer-type flow meter Number of revolutions the propeller

makes for a given time is calibrated to flow velocity

62

Sediment Sediment size is important to many

aquatic organisms Sieversquos are used to separate and

grade sediment samples Percent of each size grade can be

determined

63

Water Sample

Water and plankton from various depths can be collected

A trigger mechanism is used to close the sampler Sample is then brought back to the

surface

64

Small Mammals

Mouserat Traps Fatal

Pit Falls Bucket is placed in the ground Sometimes have lsquoleadsrsquo to the buckets

Live traps Havahart Sherman

Spot-light

Sherman trapHavahart trap

65

Birds Stick-under-the-box method Bird-trap

Works like a minnow trap Mist net

Captures birds in flight Rocket net

Uses a propellant to throw a net over birds

66

Terrestrial Insects

Sticky paper flies

Baited Traps Fire ants

Nets butterflies

Foggers Collect insects from tree canopies

67

Aquatic Insects Drift Net

Place net in flowing water Kick Net

lsquoKickrsquo sediment upstream from block net and the flow will wash them into the net

Wash bucket Serber or Hess Sampler

Stir up known area of sediment

Animals are collected by a catch net

Multi-plate Sampler Become colonized

68

Crawfish and Crab Traps

69

Fish Larvae Light Traps

Larvae are attracted to the light Ichthyoplankton nets

Can be towed at various depths Fish collect at the lsquocodrsquoend

70

Fish Lift net

Net is placed down and after a set amount of time it is quickly lifted

Pop-net Similar to a lift net but

floats are attached to a framed net

Operated by a trigger mechanism

Throw net A net attached to a heavy

frame is thrown and every thing inside is netted out Throw net

Pop-net

Lift net

71

Minnow trap

Usually use bait to attract small fish Light is used sometimes as an attractant

72

Fish Electrofishing

Electricity is put into the water Fish are temporarily stunned and usually

swim towards the electricity source Usually non-fatal but may cause some

damage

73

Fish Gill Net

Gill nets resemble tennis nets Fish can not swim completely through the

net and get caught Gill nets are size selective (based on mesh

size) Square Mesh

Bar mesh

Stretch mesh

74

Fish Trammel Net

Three panels two large mesh on the outside and a small mesh on the inside

Fish swim through the outer mesh pushes the small mesh through the other side and becomes entangled

75

Hoop nets (and other similar nets) can have bait or not

Fyke nets have leads to help guide fish to the net

76

Seine Seines are nets that are pulled

through shallow water to catch fish

77

Purse Seine Used to encircle entire schools of fish

Usually involves a spotter plane and a second boat

78

Trotline (longline) A series of baited drop lines

connected to a main line

Can be deployed by tying one end to the bank and tying the other end with a heavy weight

79

Shrimp (or fish) Trawl Net pulled behind

a boat along the bottom Either a beam or

otter boards keep the net open

80

Tagging Individuals Coded Wire Tags

Microwire that has a unique label

Magnetic wand detects the tag

Tag retention should be determined

T-Bar tags Can be individually

numbered External tag

PIT tags (Passive Integrated Transponders) Wand induces the tag to

transmit individual number is displayed

81

Other Tagging Methods

Toe clip Amphibian and reptile Clip of one or more toes

to identify individuals

Bird Band Place a metal band on a

bird leg Generally has

identification information

82

Preserving plant specimens Pressing and drying Long-term

preservation and storage

Alternative drying techniques

Special preservation and processing techniques

Mounting

83

Pressing and drying Techniques for pressing and drying specimens have been

established for many years There are minor variations in recommended methods but they are essentially the same worldwide

The best specimens are plants that are pressed as soon as possible after collection before wilting and shrivelling Most plants may be kept in sealed containers such as plastic bags for up to a day if it is inconvenient to press immediately However some plants show such rapid wilting particularly of the flowers that such delays are best avoided Flowers with a lot of nectar may go mouldy very quickly if excess nectar is not shaken off before pressing

Specimens are pressed flat and dried between sheets of absorbent blotters or semi-absorbent paper such as newspaper Papers with a glossy surface should be avoided because they are not absorbent enough to aid drying The plant should be carefully laid out between the drying sheets as their form at this stage largely determines their ultimate appearance The flowers should be spread out with the petals carefully arranged wilted leaves should be straightened and unnecessary shoots of excessively twiggy shrubs may be cut away

84

Microwave ovens Small numbers of specimens can be dried using a microwave

oven The technique recommended in the literature is to place the specimens between unprinted absorbent paper for example butchers paper not newspaper which is unsuitable because the chemicals present in the ink may cause a fire The specimens should be put in a special press which should be of a microwave-safe material (wood acrylic or polycarbonate sheeting eg plexiglass or perspex NO metal components) If such a press is not available sheets of cardboard can be placed above and below the specimens and then weighted down

Drying time depends on the power of your oven In most cases drying is accomplished by irradiating at maximum power for 1-2 minutes per specimen although it is often a case of trial and error It is best to process no more than 10-12 specimens of average thickness per batch Specimens are usually dried after the moisture that characteristically appears on the glass door has disappeared If the specimen is damp when taken out of the oven allow it to stand before re-radiating as moisture continues to evaporate from the specimen for some time Care must be taken not to irradiate the specimens for too long

It should be noted that microwave treatment damages seeds and the cellular structure of the plants which may reduce the long-term value of the specimens

85

Alternative drying techniquesSilica gelother desiccants amp freeze drying Alternative methods of drying plant specimens have been

used for some time but are mostly restricted to special purpose collections The main alternatives are freeze-drying and drying in a desiccant powder such as desiccant silica gel In general these techniques are used where it is essential to preserve the shape of a delicate plant of organ of the plant such as the flower Freeze-drying has also been used to preserve the chemical composition of a plant as accurately as possible for later study

Disadvantages and special conservation problems of specimens dried in these manners are that they are particularly susceptible to damage The dried parts are fragile lack support and often catch on packing materials They must therefore be packed especially carefully and stored in small boxes or tubes with some appropriate packing material that does not snag and break small projections Acid-free tissue paper is often used Drying in desiccant silica gel crystals or powder can also have the disadvantage that it is difficult to remove all traces of the silica gel after drying

86

Special preservation and processing techniquesWet or spirit collections

Very fleshy or delicate structures including small algae and orchid flowers are best preserved in an air-tight glass or plastic jar with a liquid preservative rather than by drying The type of preservative used should be clearly labelled in the jar Such material is often referred to as a spirit collection or wet collection

Most material can be satisfactorily preserved in 70 ethyl alcohol (or 70 methylated spirit or denatured alcohol) with 30 water Colours will fade quickly in spirit however so it is a good idea to keep comprehensive notes and photographs

87

Small algae Microscopic algae are often collected in a jar and in the

water in which they were found If the algae are to be stored for more than 2-3 days a preservative needs to be used Traditionally this has been the extremely toxic formalin - a small amount can be added to the water to make a 5 final solution and the container labelled This must not be sent through the post or by courier

There are some other equally toxic options for example propylene phenoxytol but none should be sent through the post A safer option is to add sufficient concentrated alcohol or methylated spirits to the water containing the algae to make a final solution of 70 alcohol This treatment dilutes the algae making them difficult to find so if they can be concentrated somehow first (eg by filtering) they can be stored in much less liquid Another option is to fix the algae in formalin (or something similar) first and then prepare a microscope glass slide with a permanent water-soluble mounting medium

88

Mounting Mounting specimens prevents most fragile material from

fragmenting and prevents specimens becoming separated from their labels If the plant collection is a long-term project specimens should be mounted on sheets of archival (permanent) cardboard or paper with archival-quality fixing media These include stitching with cotton thread dental floss nickel-plated copper wire (for heavier specimens) narrow strips of archival paper linen tape or by using an archival adhesive such as methyl cellulose adhesive

One disadvantage of mounting specimens is that it can make parts of the specimen inaccessible for examination so it is essential that this be borne in mind during specimen arrangement and mounting For example easily reversible mounting media should be used specimens should be strapped to the sheet rather than glued all over and the specimen should be carefully arranged before it is attached so that it shows all features

89

Full-size herbarium mounting sheets are usually about 43 cm long x 28 cm wide The plant name and accompanying field notes should be transcribed on a permanent label stuck to one corner of the herbarium sheet (the bottom right-hand corner being the most common) or sometimes annotations may be written directly on the sheet or card

Small pieces of material which may have become separated from the specimen (eg seeds) can be placed in small plastic bags and pinned to the sheet

90

Long-term preservation and storage The long-term preservation of dry plant

specimens is largely dependent on protection from insect attack Specimens collected by Linnaeus in the eighteenth century and by Banks and Solander on the Endeavour voyage in 1788 are still excellently preserved

91

Pests and their control A range of pests attack dried plant material The

most common pests are insects and fungi though rodents and other large animals can cause damage in poor storage conditions Insects eat the material the paper surrounding the material and the adhesives and mounting media

Such insect pests range from psocids (book lice) which attack mainly the softer parts such as flowers and soft fruits to tobacco beetles and carpet beetles which can bore holes through the toughest of specimens Many insects are particularly sensitive to relative humidity levels and do not thrive at levels below 50

92

The most common and acceptable specimen treatments for insect control are Freezing Microwave Poisoning Insect deterrents Fungal pests

93

Storage

Dried and pressed plant specimens can be stored in cardboard or plastic boxes or tied in bundles in light-weight cardboard folders placed in pigeon holes

Alternatively they can be placed in protective plastic jackets and displayed in ring folders which is recommended if they are to be frequently handled such as for a reference collection

94

Filing

Specimens should be filed in a systematic order if a relatively permanent collection is being made The major groups ie ferns and fern allies cycads conifers dicotyledons and monocotyledons are best kept separately or according to some classification scheme such as that given in a flora or handbook

Similarly the genera within each family and the species within each genus may be filed alphabetically or following some such classification

95

Preservation of entire animals

Types of collection specimens of an entire animal For reference collections mammals can be prepared as a variety of specimens The condition of the specimen may determine possible ways to preserve it if for instance decomposition of the skin has loosened the hair of a carcass so much that it can easily be pulled out or removed by rubbing (ldquoslippingrdquo fur) it will be very difficult or impossible to produce a study skin or mounted specimen The most usual types of specimens (based on Nagorsen and Peterson 1980) are 1) entire fluid-preserved animals (for studying anatomy and histology fluid preservation may change the fur colour) 2) study skins with accompanying skulls partial skeletons (some bones remain in the skin) for studying pelage colour hair quality and moulting patterns 3) mounted skins with accompanying partial or entire skeleton (some bones may remain in the skin dependant on the method of preservation) or freeze-dried specimens 4) entire skeletons for instance for studying anatomy geographic variation or for age determination (entire skeletons are poorly represented in collections so Nagorsen and Peterson (1980) recommend preparation of at least one male and one female skeleton per species

96

Preservation of specimens in the field Formalin preservation Preservation in alcohol Preservation by cooling or freezing

97

Formalin preservation After weighing and measuring the animal and attaching an

adequate label very small specimens (up to 100 g) can be fixed whole by submerging them in 10 buffered formalin (tissue - formalin solution ratio of at least 1 12) the body cavity can be filled with formalin solution by injection until it is turgid and firm some formalin may also be injected under the skin into the body cavity larger muscles and organs If hypodermic needles are not available the body cavity can be opened ventrally by making a slit instead allowing the formalin to enter

Keeping the mouth open with a piece of wood or cotton may later allow examination of teeth Then the whole body can be immersed in formalin in the posture in which it is supposed to stay permanently because it will harden The ratio of formalin to carcass must be at least 12 to 1 to assure a good fixation Tissues can be left in buffered neutralized formalin for several months but formalin hardens specimens therefore after fixation longterm storage in alcohol may be better After preservation the carcass should therefore be washed in water and transferred into ethanol for permanent storage

Disadvantages for instance it discolours the fur after a longish immersion softens the bones and prevents further examination for microbiology

98

Preservation in alcohol

After weighing a whole animal can be preserved in a container of alcohol (70-90) Removal of the intestine prior to storage of the animal in alcohol is recommended

99

Preservation by cooling or freezing Removal of the skin with insulating fur

before cooling or freezing may help to cool the carcass down more quickly

Freezing is not recommended if histological examination is planned

100

THANK YOU

59

Physical Habitat Temperature

Mercury thermometer Electronic thermometer Long-term thermometers

Dissolved Oxygen Winkler method (titration) DO meter (electrode)

pH Litmus paper pH meter (electrode)

Salinity Salinity Meter YSI 550A DO Meter w12 cable

60

Water Clarity Secchi Disk

Disk is attached to a calibrated rope The disk is lowered into the water until the white parts can no longer be seen Secchi disk depth is then recorded and serves as the waters transparency index The clearer the water the greater the secchi disk depth

Secchi Disk

61

Current Velocity (flow) Floating-orange method

Put an orange (or something else that floats just below the water surface) and measure the time it takes it to float across a known distance

Odometer-type flow meter Number of revolutions the propeller

makes for a given time is calibrated to flow velocity

62

Sediment Sediment size is important to many

aquatic organisms Sieversquos are used to separate and

grade sediment samples Percent of each size grade can be

determined

63

Water Sample

Water and plankton from various depths can be collected

A trigger mechanism is used to close the sampler Sample is then brought back to the

surface

64

Small Mammals

Mouserat Traps Fatal

Pit Falls Bucket is placed in the ground Sometimes have lsquoleadsrsquo to the buckets

Live traps Havahart Sherman

Spot-light

Sherman trapHavahart trap

65

Birds Stick-under-the-box method Bird-trap

Works like a minnow trap Mist net

Captures birds in flight Rocket net

Uses a propellant to throw a net over birds

66

Terrestrial Insects

Sticky paper flies

Baited Traps Fire ants

Nets butterflies

Foggers Collect insects from tree canopies

67

Aquatic Insects Drift Net

Place net in flowing water Kick Net

lsquoKickrsquo sediment upstream from block net and the flow will wash them into the net

Wash bucket Serber or Hess Sampler

Stir up known area of sediment

Animals are collected by a catch net

Multi-plate Sampler Become colonized

68

Crawfish and Crab Traps

69

Fish Larvae Light Traps

Larvae are attracted to the light Ichthyoplankton nets

Can be towed at various depths Fish collect at the lsquocodrsquoend

70

Fish Lift net

Net is placed down and after a set amount of time it is quickly lifted

Pop-net Similar to a lift net but

floats are attached to a framed net

Operated by a trigger mechanism

Throw net A net attached to a heavy

frame is thrown and every thing inside is netted out Throw net

Pop-net

Lift net

71

Minnow trap

Usually use bait to attract small fish Light is used sometimes as an attractant

72

Fish Electrofishing

Electricity is put into the water Fish are temporarily stunned and usually

swim towards the electricity source Usually non-fatal but may cause some

damage

73

Fish Gill Net

Gill nets resemble tennis nets Fish can not swim completely through the

net and get caught Gill nets are size selective (based on mesh

size) Square Mesh

Bar mesh

Stretch mesh

74

Fish Trammel Net

Three panels two large mesh on the outside and a small mesh on the inside

Fish swim through the outer mesh pushes the small mesh through the other side and becomes entangled

75

Hoop nets (and other similar nets) can have bait or not

Fyke nets have leads to help guide fish to the net

76

Seine Seines are nets that are pulled

through shallow water to catch fish

77

Purse Seine Used to encircle entire schools of fish

Usually involves a spotter plane and a second boat

78

Trotline (longline) A series of baited drop lines

connected to a main line

Can be deployed by tying one end to the bank and tying the other end with a heavy weight

79

Shrimp (or fish) Trawl Net pulled behind

a boat along the bottom Either a beam or

otter boards keep the net open

80

Tagging Individuals Coded Wire Tags

Microwire that has a unique label

Magnetic wand detects the tag

Tag retention should be determined

T-Bar tags Can be individually

numbered External tag

PIT tags (Passive Integrated Transponders) Wand induces the tag to

transmit individual number is displayed

81

Other Tagging Methods

Toe clip Amphibian and reptile Clip of one or more toes

to identify individuals

Bird Band Place a metal band on a

bird leg Generally has

identification information

82

Preserving plant specimens Pressing and drying Long-term

preservation and storage

Alternative drying techniques

Special preservation and processing techniques

Mounting

83

Pressing and drying Techniques for pressing and drying specimens have been

established for many years There are minor variations in recommended methods but they are essentially the same worldwide

The best specimens are plants that are pressed as soon as possible after collection before wilting and shrivelling Most plants may be kept in sealed containers such as plastic bags for up to a day if it is inconvenient to press immediately However some plants show such rapid wilting particularly of the flowers that such delays are best avoided Flowers with a lot of nectar may go mouldy very quickly if excess nectar is not shaken off before pressing

Specimens are pressed flat and dried between sheets of absorbent blotters or semi-absorbent paper such as newspaper Papers with a glossy surface should be avoided because they are not absorbent enough to aid drying The plant should be carefully laid out between the drying sheets as their form at this stage largely determines their ultimate appearance The flowers should be spread out with the petals carefully arranged wilted leaves should be straightened and unnecessary shoots of excessively twiggy shrubs may be cut away

84

Microwave ovens Small numbers of specimens can be dried using a microwave

oven The technique recommended in the literature is to place the specimens between unprinted absorbent paper for example butchers paper not newspaper which is unsuitable because the chemicals present in the ink may cause a fire The specimens should be put in a special press which should be of a microwave-safe material (wood acrylic or polycarbonate sheeting eg plexiglass or perspex NO metal components) If such a press is not available sheets of cardboard can be placed above and below the specimens and then weighted down

Drying time depends on the power of your oven In most cases drying is accomplished by irradiating at maximum power for 1-2 minutes per specimen although it is often a case of trial and error It is best to process no more than 10-12 specimens of average thickness per batch Specimens are usually dried after the moisture that characteristically appears on the glass door has disappeared If the specimen is damp when taken out of the oven allow it to stand before re-radiating as moisture continues to evaporate from the specimen for some time Care must be taken not to irradiate the specimens for too long

It should be noted that microwave treatment damages seeds and the cellular structure of the plants which may reduce the long-term value of the specimens

85

Alternative drying techniquesSilica gelother desiccants amp freeze drying Alternative methods of drying plant specimens have been

used for some time but are mostly restricted to special purpose collections The main alternatives are freeze-drying and drying in a desiccant powder such as desiccant silica gel In general these techniques are used where it is essential to preserve the shape of a delicate plant of organ of the plant such as the flower Freeze-drying has also been used to preserve the chemical composition of a plant as accurately as possible for later study

Disadvantages and special conservation problems of specimens dried in these manners are that they are particularly susceptible to damage The dried parts are fragile lack support and often catch on packing materials They must therefore be packed especially carefully and stored in small boxes or tubes with some appropriate packing material that does not snag and break small projections Acid-free tissue paper is often used Drying in desiccant silica gel crystals or powder can also have the disadvantage that it is difficult to remove all traces of the silica gel after drying

86

Special preservation and processing techniquesWet or spirit collections

Very fleshy or delicate structures including small algae and orchid flowers are best preserved in an air-tight glass or plastic jar with a liquid preservative rather than by drying The type of preservative used should be clearly labelled in the jar Such material is often referred to as a spirit collection or wet collection

Most material can be satisfactorily preserved in 70 ethyl alcohol (or 70 methylated spirit or denatured alcohol) with 30 water Colours will fade quickly in spirit however so it is a good idea to keep comprehensive notes and photographs

87

Small algae Microscopic algae are often collected in a jar and in the

water in which they were found If the algae are to be stored for more than 2-3 days a preservative needs to be used Traditionally this has been the extremely toxic formalin - a small amount can be added to the water to make a 5 final solution and the container labelled This must not be sent through the post or by courier

There are some other equally toxic options for example propylene phenoxytol but none should be sent through the post A safer option is to add sufficient concentrated alcohol or methylated spirits to the water containing the algae to make a final solution of 70 alcohol This treatment dilutes the algae making them difficult to find so if they can be concentrated somehow first (eg by filtering) they can be stored in much less liquid Another option is to fix the algae in formalin (or something similar) first and then prepare a microscope glass slide with a permanent water-soluble mounting medium

88

Mounting Mounting specimens prevents most fragile material from

fragmenting and prevents specimens becoming separated from their labels If the plant collection is a long-term project specimens should be mounted on sheets of archival (permanent) cardboard or paper with archival-quality fixing media These include stitching with cotton thread dental floss nickel-plated copper wire (for heavier specimens) narrow strips of archival paper linen tape or by using an archival adhesive such as methyl cellulose adhesive

One disadvantage of mounting specimens is that it can make parts of the specimen inaccessible for examination so it is essential that this be borne in mind during specimen arrangement and mounting For example easily reversible mounting media should be used specimens should be strapped to the sheet rather than glued all over and the specimen should be carefully arranged before it is attached so that it shows all features

89

Full-size herbarium mounting sheets are usually about 43 cm long x 28 cm wide The plant name and accompanying field notes should be transcribed on a permanent label stuck to one corner of the herbarium sheet (the bottom right-hand corner being the most common) or sometimes annotations may be written directly on the sheet or card

Small pieces of material which may have become separated from the specimen (eg seeds) can be placed in small plastic bags and pinned to the sheet

90

Long-term preservation and storage The long-term preservation of dry plant

specimens is largely dependent on protection from insect attack Specimens collected by Linnaeus in the eighteenth century and by Banks and Solander on the Endeavour voyage in 1788 are still excellently preserved

91

Pests and their control A range of pests attack dried plant material The

most common pests are insects and fungi though rodents and other large animals can cause damage in poor storage conditions Insects eat the material the paper surrounding the material and the adhesives and mounting media

Such insect pests range from psocids (book lice) which attack mainly the softer parts such as flowers and soft fruits to tobacco beetles and carpet beetles which can bore holes through the toughest of specimens Many insects are particularly sensitive to relative humidity levels and do not thrive at levels below 50

92

The most common and acceptable specimen treatments for insect control are Freezing Microwave Poisoning Insect deterrents Fungal pests

93

Storage

Dried and pressed plant specimens can be stored in cardboard or plastic boxes or tied in bundles in light-weight cardboard folders placed in pigeon holes

Alternatively they can be placed in protective plastic jackets and displayed in ring folders which is recommended if they are to be frequently handled such as for a reference collection

94

Filing

Specimens should be filed in a systematic order if a relatively permanent collection is being made The major groups ie ferns and fern allies cycads conifers dicotyledons and monocotyledons are best kept separately or according to some classification scheme such as that given in a flora or handbook

Similarly the genera within each family and the species within each genus may be filed alphabetically or following some such classification

95

Preservation of entire animals

Types of collection specimens of an entire animal For reference collections mammals can be prepared as a variety of specimens The condition of the specimen may determine possible ways to preserve it if for instance decomposition of the skin has loosened the hair of a carcass so much that it can easily be pulled out or removed by rubbing (ldquoslippingrdquo fur) it will be very difficult or impossible to produce a study skin or mounted specimen The most usual types of specimens (based on Nagorsen and Peterson 1980) are 1) entire fluid-preserved animals (for studying anatomy and histology fluid preservation may change the fur colour) 2) study skins with accompanying skulls partial skeletons (some bones remain in the skin) for studying pelage colour hair quality and moulting patterns 3) mounted skins with accompanying partial or entire skeleton (some bones may remain in the skin dependant on the method of preservation) or freeze-dried specimens 4) entire skeletons for instance for studying anatomy geographic variation or for age determination (entire skeletons are poorly represented in collections so Nagorsen and Peterson (1980) recommend preparation of at least one male and one female skeleton per species

96

Preservation of specimens in the field Formalin preservation Preservation in alcohol Preservation by cooling or freezing

97

Formalin preservation After weighing and measuring the animal and attaching an

adequate label very small specimens (up to 100 g) can be fixed whole by submerging them in 10 buffered formalin (tissue - formalin solution ratio of at least 1 12) the body cavity can be filled with formalin solution by injection until it is turgid and firm some formalin may also be injected under the skin into the body cavity larger muscles and organs If hypodermic needles are not available the body cavity can be opened ventrally by making a slit instead allowing the formalin to enter

Keeping the mouth open with a piece of wood or cotton may later allow examination of teeth Then the whole body can be immersed in formalin in the posture in which it is supposed to stay permanently because it will harden The ratio of formalin to carcass must be at least 12 to 1 to assure a good fixation Tissues can be left in buffered neutralized formalin for several months but formalin hardens specimens therefore after fixation longterm storage in alcohol may be better After preservation the carcass should therefore be washed in water and transferred into ethanol for permanent storage

Disadvantages for instance it discolours the fur after a longish immersion softens the bones and prevents further examination for microbiology

98

Preservation in alcohol

After weighing a whole animal can be preserved in a container of alcohol (70-90) Removal of the intestine prior to storage of the animal in alcohol is recommended

99

Preservation by cooling or freezing Removal of the skin with insulating fur

before cooling or freezing may help to cool the carcass down more quickly

Freezing is not recommended if histological examination is planned

100

THANK YOU

60

Water Clarity Secchi Disk

Disk is attached to a calibrated rope The disk is lowered into the water until the white parts can no longer be seen Secchi disk depth is then recorded and serves as the waters transparency index The clearer the water the greater the secchi disk depth

Secchi Disk

61

Current Velocity (flow) Floating-orange method

Put an orange (or something else that floats just below the water surface) and measure the time it takes it to float across a known distance

Odometer-type flow meter Number of revolutions the propeller

makes for a given time is calibrated to flow velocity

62

Sediment Sediment size is important to many

aquatic organisms Sieversquos are used to separate and

grade sediment samples Percent of each size grade can be

determined

63

Water Sample

Water and plankton from various depths can be collected

A trigger mechanism is used to close the sampler Sample is then brought back to the

surface

64

Small Mammals

Mouserat Traps Fatal

Pit Falls Bucket is placed in the ground Sometimes have lsquoleadsrsquo to the buckets

Live traps Havahart Sherman

Spot-light

Sherman trapHavahart trap

65

Birds Stick-under-the-box method Bird-trap

Works like a minnow trap Mist net

Captures birds in flight Rocket net

Uses a propellant to throw a net over birds

66

Terrestrial Insects

Sticky paper flies

Baited Traps Fire ants

Nets butterflies

Foggers Collect insects from tree canopies

67

Aquatic Insects Drift Net

Place net in flowing water Kick Net

lsquoKickrsquo sediment upstream from block net and the flow will wash them into the net

Wash bucket Serber or Hess Sampler

Stir up known area of sediment

Animals are collected by a catch net

Multi-plate Sampler Become colonized

68

Crawfish and Crab Traps

69

Fish Larvae Light Traps

Larvae are attracted to the light Ichthyoplankton nets

Can be towed at various depths Fish collect at the lsquocodrsquoend

70

Fish Lift net

Net is placed down and after a set amount of time it is quickly lifted

Pop-net Similar to a lift net but

floats are attached to a framed net

Operated by a trigger mechanism

Throw net A net attached to a heavy

frame is thrown and every thing inside is netted out Throw net

Pop-net

Lift net

71

Minnow trap

Usually use bait to attract small fish Light is used sometimes as an attractant

72

Fish Electrofishing

Electricity is put into the water Fish are temporarily stunned and usually

swim towards the electricity source Usually non-fatal but may cause some

damage

73

Fish Gill Net

Gill nets resemble tennis nets Fish can not swim completely through the

net and get caught Gill nets are size selective (based on mesh

size) Square Mesh

Bar mesh

Stretch mesh

74

Fish Trammel Net

Three panels two large mesh on the outside and a small mesh on the inside

Fish swim through the outer mesh pushes the small mesh through the other side and becomes entangled

75

Hoop nets (and other similar nets) can have bait or not

Fyke nets have leads to help guide fish to the net

76

Seine Seines are nets that are pulled

through shallow water to catch fish

77

Purse Seine Used to encircle entire schools of fish

Usually involves a spotter plane and a second boat

78

Trotline (longline) A series of baited drop lines

connected to a main line

Can be deployed by tying one end to the bank and tying the other end with a heavy weight

79

Shrimp (or fish) Trawl Net pulled behind

a boat along the bottom Either a beam or

otter boards keep the net open

80

Tagging Individuals Coded Wire Tags

Microwire that has a unique label

Magnetic wand detects the tag

Tag retention should be determined

T-Bar tags Can be individually

numbered External tag

PIT tags (Passive Integrated Transponders) Wand induces the tag to

transmit individual number is displayed

81

Other Tagging Methods

Toe clip Amphibian and reptile Clip of one or more toes

to identify individuals

Bird Band Place a metal band on a

bird leg Generally has

identification information

82

Preserving plant specimens Pressing and drying Long-term

preservation and storage

Alternative drying techniques

Special preservation and processing techniques

Mounting

83

Pressing and drying Techniques for pressing and drying specimens have been

established for many years There are minor variations in recommended methods but they are essentially the same worldwide

The best specimens are plants that are pressed as soon as possible after collection before wilting and shrivelling Most plants may be kept in sealed containers such as plastic bags for up to a day if it is inconvenient to press immediately However some plants show such rapid wilting particularly of the flowers that such delays are best avoided Flowers with a lot of nectar may go mouldy very quickly if excess nectar is not shaken off before pressing

Specimens are pressed flat and dried between sheets of absorbent blotters or semi-absorbent paper such as newspaper Papers with a glossy surface should be avoided because they are not absorbent enough to aid drying The plant should be carefully laid out between the drying sheets as their form at this stage largely determines their ultimate appearance The flowers should be spread out with the petals carefully arranged wilted leaves should be straightened and unnecessary shoots of excessively twiggy shrubs may be cut away

84

Microwave ovens Small numbers of specimens can be dried using a microwave

oven The technique recommended in the literature is to place the specimens between unprinted absorbent paper for example butchers paper not newspaper which is unsuitable because the chemicals present in the ink may cause a fire The specimens should be put in a special press which should be of a microwave-safe material (wood acrylic or polycarbonate sheeting eg plexiglass or perspex NO metal components) If such a press is not available sheets of cardboard can be placed above and below the specimens and then weighted down

Drying time depends on the power of your oven In most cases drying is accomplished by irradiating at maximum power for 1-2 minutes per specimen although it is often a case of trial and error It is best to process no more than 10-12 specimens of average thickness per batch Specimens are usually dried after the moisture that characteristically appears on the glass door has disappeared If the specimen is damp when taken out of the oven allow it to stand before re-radiating as moisture continues to evaporate from the specimen for some time Care must be taken not to irradiate the specimens for too long

It should be noted that microwave treatment damages seeds and the cellular structure of the plants which may reduce the long-term value of the specimens

85

Alternative drying techniquesSilica gelother desiccants amp freeze drying Alternative methods of drying plant specimens have been

used for some time but are mostly restricted to special purpose collections The main alternatives are freeze-drying and drying in a desiccant powder such as desiccant silica gel In general these techniques are used where it is essential to preserve the shape of a delicate plant of organ of the plant such as the flower Freeze-drying has also been used to preserve the chemical composition of a plant as accurately as possible for later study

Disadvantages and special conservation problems of specimens dried in these manners are that they are particularly susceptible to damage The dried parts are fragile lack support and often catch on packing materials They must therefore be packed especially carefully and stored in small boxes or tubes with some appropriate packing material that does not snag and break small projections Acid-free tissue paper is often used Drying in desiccant silica gel crystals or powder can also have the disadvantage that it is difficult to remove all traces of the silica gel after drying

86

Special preservation and processing techniquesWet or spirit collections

Very fleshy or delicate structures including small algae and orchid flowers are best preserved in an air-tight glass or plastic jar with a liquid preservative rather than by drying The type of preservative used should be clearly labelled in the jar Such material is often referred to as a spirit collection or wet collection

Most material can be satisfactorily preserved in 70 ethyl alcohol (or 70 methylated spirit or denatured alcohol) with 30 water Colours will fade quickly in spirit however so it is a good idea to keep comprehensive notes and photographs

87

Small algae Microscopic algae are often collected in a jar and in the

water in which they were found If the algae are to be stored for more than 2-3 days a preservative needs to be used Traditionally this has been the extremely toxic formalin - a small amount can be added to the water to make a 5 final solution and the container labelled This must not be sent through the post or by courier

There are some other equally toxic options for example propylene phenoxytol but none should be sent through the post A safer option is to add sufficient concentrated alcohol or methylated spirits to the water containing the algae to make a final solution of 70 alcohol This treatment dilutes the algae making them difficult to find so if they can be concentrated somehow first (eg by filtering) they can be stored in much less liquid Another option is to fix the algae in formalin (or something similar) first and then prepare a microscope glass slide with a permanent water-soluble mounting medium

88

Mounting Mounting specimens prevents most fragile material from

fragmenting and prevents specimens becoming separated from their labels If the plant collection is a long-term project specimens should be mounted on sheets of archival (permanent) cardboard or paper with archival-quality fixing media These include stitching with cotton thread dental floss nickel-plated copper wire (for heavier specimens) narrow strips of archival paper linen tape or by using an archival adhesive such as methyl cellulose adhesive

One disadvantage of mounting specimens is that it can make parts of the specimen inaccessible for examination so it is essential that this be borne in mind during specimen arrangement and mounting For example easily reversible mounting media should be used specimens should be strapped to the sheet rather than glued all over and the specimen should be carefully arranged before it is attached so that it shows all features

89

Full-size herbarium mounting sheets are usually about 43 cm long x 28 cm wide The plant name and accompanying field notes should be transcribed on a permanent label stuck to one corner of the herbarium sheet (the bottom right-hand corner being the most common) or sometimes annotations may be written directly on the sheet or card

Small pieces of material which may have become separated from the specimen (eg seeds) can be placed in small plastic bags and pinned to the sheet

90

Long-term preservation and storage The long-term preservation of dry plant

specimens is largely dependent on protection from insect attack Specimens collected by Linnaeus in the eighteenth century and by Banks and Solander on the Endeavour voyage in 1788 are still excellently preserved

91

Pests and their control A range of pests attack dried plant material The

most common pests are insects and fungi though rodents and other large animals can cause damage in poor storage conditions Insects eat the material the paper surrounding the material and the adhesives and mounting media

Such insect pests range from psocids (book lice) which attack mainly the softer parts such as flowers and soft fruits to tobacco beetles and carpet beetles which can bore holes through the toughest of specimens Many insects are particularly sensitive to relative humidity levels and do not thrive at levels below 50

92

The most common and acceptable specimen treatments for insect control are Freezing Microwave Poisoning Insect deterrents Fungal pests

93

Storage

Dried and pressed plant specimens can be stored in cardboard or plastic boxes or tied in bundles in light-weight cardboard folders placed in pigeon holes

Alternatively they can be placed in protective plastic jackets and displayed in ring folders which is recommended if they are to be frequently handled such as for a reference collection

94

Filing

Specimens should be filed in a systematic order if a relatively permanent collection is being made The major groups ie ferns and fern allies cycads conifers dicotyledons and monocotyledons are best kept separately or according to some classification scheme such as that given in a flora or handbook

Similarly the genera within each family and the species within each genus may be filed alphabetically or following some such classification

95

Preservation of entire animals

Types of collection specimens of an entire animal For reference collections mammals can be prepared as a variety of specimens The condition of the specimen may determine possible ways to preserve it if for instance decomposition of the skin has loosened the hair of a carcass so much that it can easily be pulled out or removed by rubbing (ldquoslippingrdquo fur) it will be very difficult or impossible to produce a study skin or mounted specimen The most usual types of specimens (based on Nagorsen and Peterson 1980) are 1) entire fluid-preserved animals (for studying anatomy and histology fluid preservation may change the fur colour) 2) study skins with accompanying skulls partial skeletons (some bones remain in the skin) for studying pelage colour hair quality and moulting patterns 3) mounted skins with accompanying partial or entire skeleton (some bones may remain in the skin dependant on the method of preservation) or freeze-dried specimens 4) entire skeletons for instance for studying anatomy geographic variation or for age determination (entire skeletons are poorly represented in collections so Nagorsen and Peterson (1980) recommend preparation of at least one male and one female skeleton per species

96

Preservation of specimens in the field Formalin preservation Preservation in alcohol Preservation by cooling or freezing

97

Formalin preservation After weighing and measuring the animal and attaching an

adequate label very small specimens (up to 100 g) can be fixed whole by submerging them in 10 buffered formalin (tissue - formalin solution ratio of at least 1 12) the body cavity can be filled with formalin solution by injection until it is turgid and firm some formalin may also be injected under the skin into the body cavity larger muscles and organs If hypodermic needles are not available the body cavity can be opened ventrally by making a slit instead allowing the formalin to enter

Keeping the mouth open with a piece of wood or cotton may later allow examination of teeth Then the whole body can be immersed in formalin in the posture in which it is supposed to stay permanently because it will harden The ratio of formalin to carcass must be at least 12 to 1 to assure a good fixation Tissues can be left in buffered neutralized formalin for several months but formalin hardens specimens therefore after fixation longterm storage in alcohol may be better After preservation the carcass should therefore be washed in water and transferred into ethanol for permanent storage

Disadvantages for instance it discolours the fur after a longish immersion softens the bones and prevents further examination for microbiology

98

Preservation in alcohol

After weighing a whole animal can be preserved in a container of alcohol (70-90) Removal of the intestine prior to storage of the animal in alcohol is recommended

99

Preservation by cooling or freezing Removal of the skin with insulating fur

before cooling or freezing may help to cool the carcass down more quickly

Freezing is not recommended if histological examination is planned

100

THANK YOU

61

Current Velocity (flow) Floating-orange method

Put an orange (or something else that floats just below the water surface) and measure the time it takes it to float across a known distance

Odometer-type flow meter Number of revolutions the propeller

makes for a given time is calibrated to flow velocity

62

Sediment Sediment size is important to many

aquatic organisms Sieversquos are used to separate and

grade sediment samples Percent of each size grade can be

determined

63

Water Sample

Water and plankton from various depths can be collected

A trigger mechanism is used to close the sampler Sample is then brought back to the

surface

64

Small Mammals

Mouserat Traps Fatal

Pit Falls Bucket is placed in the ground Sometimes have lsquoleadsrsquo to the buckets

Live traps Havahart Sherman

Spot-light

Sherman trapHavahart trap

65

Birds Stick-under-the-box method Bird-trap

Works like a minnow trap Mist net

Captures birds in flight Rocket net

Uses a propellant to throw a net over birds

66

Terrestrial Insects

Sticky paper flies

Baited Traps Fire ants

Nets butterflies

Foggers Collect insects from tree canopies

67

Aquatic Insects Drift Net

Place net in flowing water Kick Net

lsquoKickrsquo sediment upstream from block net and the flow will wash them into the net

Wash bucket Serber or Hess Sampler

Stir up known area of sediment

Animals are collected by a catch net

Multi-plate Sampler Become colonized

68

Crawfish and Crab Traps

69

Fish Larvae Light Traps

Larvae are attracted to the light Ichthyoplankton nets

Can be towed at various depths Fish collect at the lsquocodrsquoend

70

Fish Lift net

Net is placed down and after a set amount of time it is quickly lifted

Pop-net Similar to a lift net but

floats are attached to a framed net

Operated by a trigger mechanism

Throw net A net attached to a heavy

frame is thrown and every thing inside is netted out Throw net

Pop-net

Lift net

71

Minnow trap

Usually use bait to attract small fish Light is used sometimes as an attractant

72

Fish Electrofishing

Electricity is put into the water Fish are temporarily stunned and usually

swim towards the electricity source Usually non-fatal but may cause some

damage

73

Fish Gill Net

Gill nets resemble tennis nets Fish can not swim completely through the

net and get caught Gill nets are size selective (based on mesh

size) Square Mesh

Bar mesh

Stretch mesh

74

Fish Trammel Net

Three panels two large mesh on the outside and a small mesh on the inside

Fish swim through the outer mesh pushes the small mesh through the other side and becomes entangled

75

Hoop nets (and other similar nets) can have bait or not

Fyke nets have leads to help guide fish to the net

76

Seine Seines are nets that are pulled

through shallow water to catch fish

77

Purse Seine Used to encircle entire schools of fish

Usually involves a spotter plane and a second boat

78

Trotline (longline) A series of baited drop lines

connected to a main line

Can be deployed by tying one end to the bank and tying the other end with a heavy weight

79

Shrimp (or fish) Trawl Net pulled behind

a boat along the bottom Either a beam or

otter boards keep the net open

80

Tagging Individuals Coded Wire Tags

Microwire that has a unique label

Magnetic wand detects the tag

Tag retention should be determined

T-Bar tags Can be individually

numbered External tag

PIT tags (Passive Integrated Transponders) Wand induces the tag to

transmit individual number is displayed

81

Other Tagging Methods

Toe clip Amphibian and reptile Clip of one or more toes

to identify individuals

Bird Band Place a metal band on a

bird leg Generally has

identification information

82

Preserving plant specimens Pressing and drying Long-term

preservation and storage

Alternative drying techniques

Special preservation and processing techniques

Mounting

83

Pressing and drying Techniques for pressing and drying specimens have been

established for many years There are minor variations in recommended methods but they are essentially the same worldwide

The best specimens are plants that are pressed as soon as possible after collection before wilting and shrivelling Most plants may be kept in sealed containers such as plastic bags for up to a day if it is inconvenient to press immediately However some plants show such rapid wilting particularly of the flowers that such delays are best avoided Flowers with a lot of nectar may go mouldy very quickly if excess nectar is not shaken off before pressing

Specimens are pressed flat and dried between sheets of absorbent blotters or semi-absorbent paper such as newspaper Papers with a glossy surface should be avoided because they are not absorbent enough to aid drying The plant should be carefully laid out between the drying sheets as their form at this stage largely determines their ultimate appearance The flowers should be spread out with the petals carefully arranged wilted leaves should be straightened and unnecessary shoots of excessively twiggy shrubs may be cut away

84

Microwave ovens Small numbers of specimens can be dried using a microwave

oven The technique recommended in the literature is to place the specimens between unprinted absorbent paper for example butchers paper not newspaper which is unsuitable because the chemicals present in the ink may cause a fire The specimens should be put in a special press which should be of a microwave-safe material (wood acrylic or polycarbonate sheeting eg plexiglass or perspex NO metal components) If such a press is not available sheets of cardboard can be placed above and below the specimens and then weighted down

Drying time depends on the power of your oven In most cases drying is accomplished by irradiating at maximum power for 1-2 minutes per specimen although it is often a case of trial and error It is best to process no more than 10-12 specimens of average thickness per batch Specimens are usually dried after the moisture that characteristically appears on the glass door has disappeared If the specimen is damp when taken out of the oven allow it to stand before re-radiating as moisture continues to evaporate from the specimen for some time Care must be taken not to irradiate the specimens for too long

It should be noted that microwave treatment damages seeds and the cellular structure of the plants which may reduce the long-term value of the specimens

85

Alternative drying techniquesSilica gelother desiccants amp freeze drying Alternative methods of drying plant specimens have been

used for some time but are mostly restricted to special purpose collections The main alternatives are freeze-drying and drying in a desiccant powder such as desiccant silica gel In general these techniques are used where it is essential to preserve the shape of a delicate plant of organ of the plant such as the flower Freeze-drying has also been used to preserve the chemical composition of a plant as accurately as possible for later study

Disadvantages and special conservation problems of specimens dried in these manners are that they are particularly susceptible to damage The dried parts are fragile lack support and often catch on packing materials They must therefore be packed especially carefully and stored in small boxes or tubes with some appropriate packing material that does not snag and break small projections Acid-free tissue paper is often used Drying in desiccant silica gel crystals or powder can also have the disadvantage that it is difficult to remove all traces of the silica gel after drying

86

Special preservation and processing techniquesWet or spirit collections

Very fleshy or delicate structures including small algae and orchid flowers are best preserved in an air-tight glass or plastic jar with a liquid preservative rather than by drying The type of preservative used should be clearly labelled in the jar Such material is often referred to as a spirit collection or wet collection

Most material can be satisfactorily preserved in 70 ethyl alcohol (or 70 methylated spirit or denatured alcohol) with 30 water Colours will fade quickly in spirit however so it is a good idea to keep comprehensive notes and photographs

87

Small algae Microscopic algae are often collected in a jar and in the

water in which they were found If the algae are to be stored for more than 2-3 days a preservative needs to be used Traditionally this has been the extremely toxic formalin - a small amount can be added to the water to make a 5 final solution and the container labelled This must not be sent through the post or by courier

There are some other equally toxic options for example propylene phenoxytol but none should be sent through the post A safer option is to add sufficient concentrated alcohol or methylated spirits to the water containing the algae to make a final solution of 70 alcohol This treatment dilutes the algae making them difficult to find so if they can be concentrated somehow first (eg by filtering) they can be stored in much less liquid Another option is to fix the algae in formalin (or something similar) first and then prepare a microscope glass slide with a permanent water-soluble mounting medium

88

Mounting Mounting specimens prevents most fragile material from

fragmenting and prevents specimens becoming separated from their labels If the plant collection is a long-term project specimens should be mounted on sheets of archival (permanent) cardboard or paper with archival-quality fixing media These include stitching with cotton thread dental floss nickel-plated copper wire (for heavier specimens) narrow strips of archival paper linen tape or by using an archival adhesive such as methyl cellulose adhesive

One disadvantage of mounting specimens is that it can make parts of the specimen inaccessible for examination so it is essential that this be borne in mind during specimen arrangement and mounting For example easily reversible mounting media should be used specimens should be strapped to the sheet rather than glued all over and the specimen should be carefully arranged before it is attached so that it shows all features

89

Full-size herbarium mounting sheets are usually about 43 cm long x 28 cm wide The plant name and accompanying field notes should be transcribed on a permanent label stuck to one corner of the herbarium sheet (the bottom right-hand corner being the most common) or sometimes annotations may be written directly on the sheet or card

Small pieces of material which may have become separated from the specimen (eg seeds) can be placed in small plastic bags and pinned to the sheet

90

Long-term preservation and storage The long-term preservation of dry plant

specimens is largely dependent on protection from insect attack Specimens collected by Linnaeus in the eighteenth century and by Banks and Solander on the Endeavour voyage in 1788 are still excellently preserved

91

Pests and their control A range of pests attack dried plant material The

most common pests are insects and fungi though rodents and other large animals can cause damage in poor storage conditions Insects eat the material the paper surrounding the material and the adhesives and mounting media

Such insect pests range from psocids (book lice) which attack mainly the softer parts such as flowers and soft fruits to tobacco beetles and carpet beetles which can bore holes through the toughest of specimens Many insects are particularly sensitive to relative humidity levels and do not thrive at levels below 50

92

The most common and acceptable specimen treatments for insect control are Freezing Microwave Poisoning Insect deterrents Fungal pests

93

Storage

Dried and pressed plant specimens can be stored in cardboard or plastic boxes or tied in bundles in light-weight cardboard folders placed in pigeon holes

Alternatively they can be placed in protective plastic jackets and displayed in ring folders which is recommended if they are to be frequently handled such as for a reference collection

94

Filing

Specimens should be filed in a systematic order if a relatively permanent collection is being made The major groups ie ferns and fern allies cycads conifers dicotyledons and monocotyledons are best kept separately or according to some classification scheme such as that given in a flora or handbook

Similarly the genera within each family and the species within each genus may be filed alphabetically or following some such classification

95

Preservation of entire animals

Types of collection specimens of an entire animal For reference collections mammals can be prepared as a variety of specimens The condition of the specimen may determine possible ways to preserve it if for instance decomposition of the skin has loosened the hair of a carcass so much that it can easily be pulled out or removed by rubbing (ldquoslippingrdquo fur) it will be very difficult or impossible to produce a study skin or mounted specimen The most usual types of specimens (based on Nagorsen and Peterson 1980) are 1) entire fluid-preserved animals (for studying anatomy and histology fluid preservation may change the fur colour) 2) study skins with accompanying skulls partial skeletons (some bones remain in the skin) for studying pelage colour hair quality and moulting patterns 3) mounted skins with accompanying partial or entire skeleton (some bones may remain in the skin dependant on the method of preservation) or freeze-dried specimens 4) entire skeletons for instance for studying anatomy geographic variation or for age determination (entire skeletons are poorly represented in collections so Nagorsen and Peterson (1980) recommend preparation of at least one male and one female skeleton per species

96

Preservation of specimens in the field Formalin preservation Preservation in alcohol Preservation by cooling or freezing

97

Formalin preservation After weighing and measuring the animal and attaching an

adequate label very small specimens (up to 100 g) can be fixed whole by submerging them in 10 buffered formalin (tissue - formalin solution ratio of at least 1 12) the body cavity can be filled with formalin solution by injection until it is turgid and firm some formalin may also be injected under the skin into the body cavity larger muscles and organs If hypodermic needles are not available the body cavity can be opened ventrally by making a slit instead allowing the formalin to enter

Keeping the mouth open with a piece of wood or cotton may later allow examination of teeth Then the whole body can be immersed in formalin in the posture in which it is supposed to stay permanently because it will harden The ratio of formalin to carcass must be at least 12 to 1 to assure a good fixation Tissues can be left in buffered neutralized formalin for several months but formalin hardens specimens therefore after fixation longterm storage in alcohol may be better After preservation the carcass should therefore be washed in water and transferred into ethanol for permanent storage

Disadvantages for instance it discolours the fur after a longish immersion softens the bones and prevents further examination for microbiology

98

Preservation in alcohol

After weighing a whole animal can be preserved in a container of alcohol (70-90) Removal of the intestine prior to storage of the animal in alcohol is recommended

99

Preservation by cooling or freezing Removal of the skin with insulating fur

before cooling or freezing may help to cool the carcass down more quickly

Freezing is not recommended if histological examination is planned

100

THANK YOU

62

Sediment Sediment size is important to many

aquatic organisms Sieversquos are used to separate and

grade sediment samples Percent of each size grade can be

determined

63

Water Sample

Water and plankton from various depths can be collected

A trigger mechanism is used to close the sampler Sample is then brought back to the

surface

64

Small Mammals

Mouserat Traps Fatal

Pit Falls Bucket is placed in the ground Sometimes have lsquoleadsrsquo to the buckets

Live traps Havahart Sherman

Spot-light

Sherman trapHavahart trap

65

Birds Stick-under-the-box method Bird-trap

Works like a minnow trap Mist net

Captures birds in flight Rocket net

Uses a propellant to throw a net over birds

66

Terrestrial Insects

Sticky paper flies

Baited Traps Fire ants

Nets butterflies

Foggers Collect insects from tree canopies

67

Aquatic Insects Drift Net

Place net in flowing water Kick Net

lsquoKickrsquo sediment upstream from block net and the flow will wash them into the net

Wash bucket Serber or Hess Sampler

Stir up known area of sediment

Animals are collected by a catch net

Multi-plate Sampler Become colonized

68

Crawfish and Crab Traps

69

Fish Larvae Light Traps

Larvae are attracted to the light Ichthyoplankton nets

Can be towed at various depths Fish collect at the lsquocodrsquoend

70

Fish Lift net

Net is placed down and after a set amount of time it is quickly lifted

Pop-net Similar to a lift net but

floats are attached to a framed net

Operated by a trigger mechanism

Throw net A net attached to a heavy

frame is thrown and every thing inside is netted out Throw net

Pop-net

Lift net

71

Minnow trap

Usually use bait to attract small fish Light is used sometimes as an attractant

72

Fish Electrofishing

Electricity is put into the water Fish are temporarily stunned and usually

swim towards the electricity source Usually non-fatal but may cause some

damage

73

Fish Gill Net

Gill nets resemble tennis nets Fish can not swim completely through the

net and get caught Gill nets are size selective (based on mesh

size) Square Mesh

Bar mesh

Stretch mesh

74

Fish Trammel Net

Three panels two large mesh on the outside and a small mesh on the inside

Fish swim through the outer mesh pushes the small mesh through the other side and becomes entangled

75

Hoop nets (and other similar nets) can have bait or not

Fyke nets have leads to help guide fish to the net

76

Seine Seines are nets that are pulled

through shallow water to catch fish

77

Purse Seine Used to encircle entire schools of fish

Usually involves a spotter plane and a second boat

78

Trotline (longline) A series of baited drop lines

connected to a main line

Can be deployed by tying one end to the bank and tying the other end with a heavy weight

79

Shrimp (or fish) Trawl Net pulled behind

a boat along the bottom Either a beam or

otter boards keep the net open

80

Tagging Individuals Coded Wire Tags

Microwire that has a unique label

Magnetic wand detects the tag

Tag retention should be determined

T-Bar tags Can be individually

numbered External tag

PIT tags (Passive Integrated Transponders) Wand induces the tag to

transmit individual number is displayed

81

Other Tagging Methods

Toe clip Amphibian and reptile Clip of one or more toes

to identify individuals

Bird Band Place a metal band on a

bird leg Generally has

identification information

82

Preserving plant specimens Pressing and drying Long-term

preservation and storage

Alternative drying techniques

Special preservation and processing techniques

Mounting

83

Pressing and drying Techniques for pressing and drying specimens have been

established for many years There are minor variations in recommended methods but they are essentially the same worldwide

The best specimens are plants that are pressed as soon as possible after collection before wilting and shrivelling Most plants may be kept in sealed containers such as plastic bags for up to a day if it is inconvenient to press immediately However some plants show such rapid wilting particularly of the flowers that such delays are best avoided Flowers with a lot of nectar may go mouldy very quickly if excess nectar is not shaken off before pressing

Specimens are pressed flat and dried between sheets of absorbent blotters or semi-absorbent paper such as newspaper Papers with a glossy surface should be avoided because they are not absorbent enough to aid drying The plant should be carefully laid out between the drying sheets as their form at this stage largely determines their ultimate appearance The flowers should be spread out with the petals carefully arranged wilted leaves should be straightened and unnecessary shoots of excessively twiggy shrubs may be cut away

84

Microwave ovens Small numbers of specimens can be dried using a microwave

oven The technique recommended in the literature is to place the specimens between unprinted absorbent paper for example butchers paper not newspaper which is unsuitable because the chemicals present in the ink may cause a fire The specimens should be put in a special press which should be of a microwave-safe material (wood acrylic or polycarbonate sheeting eg plexiglass or perspex NO metal components) If such a press is not available sheets of cardboard can be placed above and below the specimens and then weighted down

Drying time depends on the power of your oven In most cases drying is accomplished by irradiating at maximum power for 1-2 minutes per specimen although it is often a case of trial and error It is best to process no more than 10-12 specimens of average thickness per batch Specimens are usually dried after the moisture that characteristically appears on the glass door has disappeared If the specimen is damp when taken out of the oven allow it to stand before re-radiating as moisture continues to evaporate from the specimen for some time Care must be taken not to irradiate the specimens for too long

It should be noted that microwave treatment damages seeds and the cellular structure of the plants which may reduce the long-term value of the specimens

85

Alternative drying techniquesSilica gelother desiccants amp freeze drying Alternative methods of drying plant specimens have been

used for some time but are mostly restricted to special purpose collections The main alternatives are freeze-drying and drying in a desiccant powder such as desiccant silica gel In general these techniques are used where it is essential to preserve the shape of a delicate plant of organ of the plant such as the flower Freeze-drying has also been used to preserve the chemical composition of a plant as accurately as possible for later study

Disadvantages and special conservation problems of specimens dried in these manners are that they are particularly susceptible to damage The dried parts are fragile lack support and often catch on packing materials They must therefore be packed especially carefully and stored in small boxes or tubes with some appropriate packing material that does not snag and break small projections Acid-free tissue paper is often used Drying in desiccant silica gel crystals or powder can also have the disadvantage that it is difficult to remove all traces of the silica gel after drying

86

Special preservation and processing techniquesWet or spirit collections

Very fleshy or delicate structures including small algae and orchid flowers are best preserved in an air-tight glass or plastic jar with a liquid preservative rather than by drying The type of preservative used should be clearly labelled in the jar Such material is often referred to as a spirit collection or wet collection

Most material can be satisfactorily preserved in 70 ethyl alcohol (or 70 methylated spirit or denatured alcohol) with 30 water Colours will fade quickly in spirit however so it is a good idea to keep comprehensive notes and photographs

87

Small algae Microscopic algae are often collected in a jar and in the

water in which they were found If the algae are to be stored for more than 2-3 days a preservative needs to be used Traditionally this has been the extremely toxic formalin - a small amount can be added to the water to make a 5 final solution and the container labelled This must not be sent through the post or by courier

There are some other equally toxic options for example propylene phenoxytol but none should be sent through the post A safer option is to add sufficient concentrated alcohol or methylated spirits to the water containing the algae to make a final solution of 70 alcohol This treatment dilutes the algae making them difficult to find so if they can be concentrated somehow first (eg by filtering) they can be stored in much less liquid Another option is to fix the algae in formalin (or something similar) first and then prepare a microscope glass slide with a permanent water-soluble mounting medium

88

Mounting Mounting specimens prevents most fragile material from

fragmenting and prevents specimens becoming separated from their labels If the plant collection is a long-term project specimens should be mounted on sheets of archival (permanent) cardboard or paper with archival-quality fixing media These include stitching with cotton thread dental floss nickel-plated copper wire (for heavier specimens) narrow strips of archival paper linen tape or by using an archival adhesive such as methyl cellulose adhesive

One disadvantage of mounting specimens is that it can make parts of the specimen inaccessible for examination so it is essential that this be borne in mind during specimen arrangement and mounting For example easily reversible mounting media should be used specimens should be strapped to the sheet rather than glued all over and the specimen should be carefully arranged before it is attached so that it shows all features

89

Full-size herbarium mounting sheets are usually about 43 cm long x 28 cm wide The plant name and accompanying field notes should be transcribed on a permanent label stuck to one corner of the herbarium sheet (the bottom right-hand corner being the most common) or sometimes annotations may be written directly on the sheet or card

Small pieces of material which may have become separated from the specimen (eg seeds) can be placed in small plastic bags and pinned to the sheet

90

Long-term preservation and storage The long-term preservation of dry plant

specimens is largely dependent on protection from insect attack Specimens collected by Linnaeus in the eighteenth century and by Banks and Solander on the Endeavour voyage in 1788 are still excellently preserved

91

Pests and their control A range of pests attack dried plant material The

most common pests are insects and fungi though rodents and other large animals can cause damage in poor storage conditions Insects eat the material the paper surrounding the material and the adhesives and mounting media

Such insect pests range from psocids (book lice) which attack mainly the softer parts such as flowers and soft fruits to tobacco beetles and carpet beetles which can bore holes through the toughest of specimens Many insects are particularly sensitive to relative humidity levels and do not thrive at levels below 50

92

The most common and acceptable specimen treatments for insect control are Freezing Microwave Poisoning Insect deterrents Fungal pests

93

Storage

Dried and pressed plant specimens can be stored in cardboard or plastic boxes or tied in bundles in light-weight cardboard folders placed in pigeon holes

Alternatively they can be placed in protective plastic jackets and displayed in ring folders which is recommended if they are to be frequently handled such as for a reference collection

94

Filing

Specimens should be filed in a systematic order if a relatively permanent collection is being made The major groups ie ferns and fern allies cycads conifers dicotyledons and monocotyledons are best kept separately or according to some classification scheme such as that given in a flora or handbook

Similarly the genera within each family and the species within each genus may be filed alphabetically or following some such classification

95

Preservation of entire animals

Types of collection specimens of an entire animal For reference collections mammals can be prepared as a variety of specimens The condition of the specimen may determine possible ways to preserve it if for instance decomposition of the skin has loosened the hair of a carcass so much that it can easily be pulled out or removed by rubbing (ldquoslippingrdquo fur) it will be very difficult or impossible to produce a study skin or mounted specimen The most usual types of specimens (based on Nagorsen and Peterson 1980) are 1) entire fluid-preserved animals (for studying anatomy and histology fluid preservation may change the fur colour) 2) study skins with accompanying skulls partial skeletons (some bones remain in the skin) for studying pelage colour hair quality and moulting patterns 3) mounted skins with accompanying partial or entire skeleton (some bones may remain in the skin dependant on the method of preservation) or freeze-dried specimens 4) entire skeletons for instance for studying anatomy geographic variation or for age determination (entire skeletons are poorly represented in collections so Nagorsen and Peterson (1980) recommend preparation of at least one male and one female skeleton per species

96

Preservation of specimens in the field Formalin preservation Preservation in alcohol Preservation by cooling or freezing

97

Formalin preservation After weighing and measuring the animal and attaching an

adequate label very small specimens (up to 100 g) can be fixed whole by submerging them in 10 buffered formalin (tissue - formalin solution ratio of at least 1 12) the body cavity can be filled with formalin solution by injection until it is turgid and firm some formalin may also be injected under the skin into the body cavity larger muscles and organs If hypodermic needles are not available the body cavity can be opened ventrally by making a slit instead allowing the formalin to enter

Keeping the mouth open with a piece of wood or cotton may later allow examination of teeth Then the whole body can be immersed in formalin in the posture in which it is supposed to stay permanently because it will harden The ratio of formalin to carcass must be at least 12 to 1 to assure a good fixation Tissues can be left in buffered neutralized formalin for several months but formalin hardens specimens therefore after fixation longterm storage in alcohol may be better After preservation the carcass should therefore be washed in water and transferred into ethanol for permanent storage

Disadvantages for instance it discolours the fur after a longish immersion softens the bones and prevents further examination for microbiology

98

Preservation in alcohol

After weighing a whole animal can be preserved in a container of alcohol (70-90) Removal of the intestine prior to storage of the animal in alcohol is recommended

99

Preservation by cooling or freezing Removal of the skin with insulating fur

before cooling or freezing may help to cool the carcass down more quickly

Freezing is not recommended if histological examination is planned

100

THANK YOU

63

Water Sample

Water and plankton from various depths can be collected

A trigger mechanism is used to close the sampler Sample is then brought back to the

surface

64

Small Mammals

Mouserat Traps Fatal

Pit Falls Bucket is placed in the ground Sometimes have lsquoleadsrsquo to the buckets

Live traps Havahart Sherman

Spot-light

Sherman trapHavahart trap

65

Birds Stick-under-the-box method Bird-trap

Works like a minnow trap Mist net

Captures birds in flight Rocket net

Uses a propellant to throw a net over birds

66

Terrestrial Insects

Sticky paper flies

Baited Traps Fire ants

Nets butterflies

Foggers Collect insects from tree canopies

67

Aquatic Insects Drift Net

Place net in flowing water Kick Net

lsquoKickrsquo sediment upstream from block net and the flow will wash them into the net

Wash bucket Serber or Hess Sampler

Stir up known area of sediment

Animals are collected by a catch net

Multi-plate Sampler Become colonized

68

Crawfish and Crab Traps

69

Fish Larvae Light Traps

Larvae are attracted to the light Ichthyoplankton nets

Can be towed at various depths Fish collect at the lsquocodrsquoend

70

Fish Lift net

Net is placed down and after a set amount of time it is quickly lifted

Pop-net Similar to a lift net but

floats are attached to a framed net

Operated by a trigger mechanism

Throw net A net attached to a heavy

frame is thrown and every thing inside is netted out Throw net

Pop-net

Lift net

71

Minnow trap

Usually use bait to attract small fish Light is used sometimes as an attractant

72

Fish Electrofishing

Electricity is put into the water Fish are temporarily stunned and usually

swim towards the electricity source Usually non-fatal but may cause some

damage

73

Fish Gill Net

Gill nets resemble tennis nets Fish can not swim completely through the

net and get caught Gill nets are size selective (based on mesh

size) Square Mesh

Bar mesh

Stretch mesh

74

Fish Trammel Net

Three panels two large mesh on the outside and a small mesh on the inside

Fish swim through the outer mesh pushes the small mesh through the other side and becomes entangled

75

Hoop nets (and other similar nets) can have bait or not

Fyke nets have leads to help guide fish to the net

76

Seine Seines are nets that are pulled

through shallow water to catch fish

77

Purse Seine Used to encircle entire schools of fish

Usually involves a spotter plane and a second boat

78

Trotline (longline) A series of baited drop lines

connected to a main line

Can be deployed by tying one end to the bank and tying the other end with a heavy weight

79

Shrimp (or fish) Trawl Net pulled behind

a boat along the bottom Either a beam or

otter boards keep the net open

80

Tagging Individuals Coded Wire Tags

Microwire that has a unique label

Magnetic wand detects the tag

Tag retention should be determined

T-Bar tags Can be individually

numbered External tag

PIT tags (Passive Integrated Transponders) Wand induces the tag to

transmit individual number is displayed

81

Other Tagging Methods

Toe clip Amphibian and reptile Clip of one or more toes

to identify individuals

Bird Band Place a metal band on a

bird leg Generally has

identification information

82

Preserving plant specimens Pressing and drying Long-term

preservation and storage

Alternative drying techniques

Special preservation and processing techniques

Mounting

83

Pressing and drying Techniques for pressing and drying specimens have been

established for many years There are minor variations in recommended methods but they are essentially the same worldwide

The best specimens are plants that are pressed as soon as possible after collection before wilting and shrivelling Most plants may be kept in sealed containers such as plastic bags for up to a day if it is inconvenient to press immediately However some plants show such rapid wilting particularly of the flowers that such delays are best avoided Flowers with a lot of nectar may go mouldy very quickly if excess nectar is not shaken off before pressing

Specimens are pressed flat and dried between sheets of absorbent blotters or semi-absorbent paper such as newspaper Papers with a glossy surface should be avoided because they are not absorbent enough to aid drying The plant should be carefully laid out between the drying sheets as their form at this stage largely determines their ultimate appearance The flowers should be spread out with the petals carefully arranged wilted leaves should be straightened and unnecessary shoots of excessively twiggy shrubs may be cut away

84

Microwave ovens Small numbers of specimens can be dried using a microwave

oven The technique recommended in the literature is to place the specimens between unprinted absorbent paper for example butchers paper not newspaper which is unsuitable because the chemicals present in the ink may cause a fire The specimens should be put in a special press which should be of a microwave-safe material (wood acrylic or polycarbonate sheeting eg plexiglass or perspex NO metal components) If such a press is not available sheets of cardboard can be placed above and below the specimens and then weighted down

Drying time depends on the power of your oven In most cases drying is accomplished by irradiating at maximum power for 1-2 minutes per specimen although it is often a case of trial and error It is best to process no more than 10-12 specimens of average thickness per batch Specimens are usually dried after the moisture that characteristically appears on the glass door has disappeared If the specimen is damp when taken out of the oven allow it to stand before re-radiating as moisture continues to evaporate from the specimen for some time Care must be taken not to irradiate the specimens for too long

It should be noted that microwave treatment damages seeds and the cellular structure of the plants which may reduce the long-term value of the specimens

85

Alternative drying techniquesSilica gelother desiccants amp freeze drying Alternative methods of drying plant specimens have been

used for some time but are mostly restricted to special purpose collections The main alternatives are freeze-drying and drying in a desiccant powder such as desiccant silica gel In general these techniques are used where it is essential to preserve the shape of a delicate plant of organ of the plant such as the flower Freeze-drying has also been used to preserve the chemical composition of a plant as accurately as possible for later study

Disadvantages and special conservation problems of specimens dried in these manners are that they are particularly susceptible to damage The dried parts are fragile lack support and often catch on packing materials They must therefore be packed especially carefully and stored in small boxes or tubes with some appropriate packing material that does not snag and break small projections Acid-free tissue paper is often used Drying in desiccant silica gel crystals or powder can also have the disadvantage that it is difficult to remove all traces of the silica gel after drying

86

Special preservation and processing techniquesWet or spirit collections

Very fleshy or delicate structures including small algae and orchid flowers are best preserved in an air-tight glass or plastic jar with a liquid preservative rather than by drying The type of preservative used should be clearly labelled in the jar Such material is often referred to as a spirit collection or wet collection

Most material can be satisfactorily preserved in 70 ethyl alcohol (or 70 methylated spirit or denatured alcohol) with 30 water Colours will fade quickly in spirit however so it is a good idea to keep comprehensive notes and photographs

87

Small algae Microscopic algae are often collected in a jar and in the

water in which they were found If the algae are to be stored for more than 2-3 days a preservative needs to be used Traditionally this has been the extremely toxic formalin - a small amount can be added to the water to make a 5 final solution and the container labelled This must not be sent through the post or by courier

There are some other equally toxic options for example propylene phenoxytol but none should be sent through the post A safer option is to add sufficient concentrated alcohol or methylated spirits to the water containing the algae to make a final solution of 70 alcohol This treatment dilutes the algae making them difficult to find so if they can be concentrated somehow first (eg by filtering) they can be stored in much less liquid Another option is to fix the algae in formalin (or something similar) first and then prepare a microscope glass slide with a permanent water-soluble mounting medium

88

Mounting Mounting specimens prevents most fragile material from

fragmenting and prevents specimens becoming separated from their labels If the plant collection is a long-term project specimens should be mounted on sheets of archival (permanent) cardboard or paper with archival-quality fixing media These include stitching with cotton thread dental floss nickel-plated copper wire (for heavier specimens) narrow strips of archival paper linen tape or by using an archival adhesive such as methyl cellulose adhesive

One disadvantage of mounting specimens is that it can make parts of the specimen inaccessible for examination so it is essential that this be borne in mind during specimen arrangement and mounting For example easily reversible mounting media should be used specimens should be strapped to the sheet rather than glued all over and the specimen should be carefully arranged before it is attached so that it shows all features

89

Full-size herbarium mounting sheets are usually about 43 cm long x 28 cm wide The plant name and accompanying field notes should be transcribed on a permanent label stuck to one corner of the herbarium sheet (the bottom right-hand corner being the most common) or sometimes annotations may be written directly on the sheet or card

Small pieces of material which may have become separated from the specimen (eg seeds) can be placed in small plastic bags and pinned to the sheet

90

Long-term preservation and storage The long-term preservation of dry plant

specimens is largely dependent on protection from insect attack Specimens collected by Linnaeus in the eighteenth century and by Banks and Solander on the Endeavour voyage in 1788 are still excellently preserved

91

Pests and their control A range of pests attack dried plant material The

most common pests are insects and fungi though rodents and other large animals can cause damage in poor storage conditions Insects eat the material the paper surrounding the material and the adhesives and mounting media

Such insect pests range from psocids (book lice) which attack mainly the softer parts such as flowers and soft fruits to tobacco beetles and carpet beetles which can bore holes through the toughest of specimens Many insects are particularly sensitive to relative humidity levels and do not thrive at levels below 50

92

The most common and acceptable specimen treatments for insect control are Freezing Microwave Poisoning Insect deterrents Fungal pests

93

Storage

Dried and pressed plant specimens can be stored in cardboard or plastic boxes or tied in bundles in light-weight cardboard folders placed in pigeon holes

Alternatively they can be placed in protective plastic jackets and displayed in ring folders which is recommended if they are to be frequently handled such as for a reference collection

94

Filing

Specimens should be filed in a systematic order if a relatively permanent collection is being made The major groups ie ferns and fern allies cycads conifers dicotyledons and monocotyledons are best kept separately or according to some classification scheme such as that given in a flora or handbook

Similarly the genera within each family and the species within each genus may be filed alphabetically or following some such classification

95

Preservation of entire animals

Types of collection specimens of an entire animal For reference collections mammals can be prepared as a variety of specimens The condition of the specimen may determine possible ways to preserve it if for instance decomposition of the skin has loosened the hair of a carcass so much that it can easily be pulled out or removed by rubbing (ldquoslippingrdquo fur) it will be very difficult or impossible to produce a study skin or mounted specimen The most usual types of specimens (based on Nagorsen and Peterson 1980) are 1) entire fluid-preserved animals (for studying anatomy and histology fluid preservation may change the fur colour) 2) study skins with accompanying skulls partial skeletons (some bones remain in the skin) for studying pelage colour hair quality and moulting patterns 3) mounted skins with accompanying partial or entire skeleton (some bones may remain in the skin dependant on the method of preservation) or freeze-dried specimens 4) entire skeletons for instance for studying anatomy geographic variation or for age determination (entire skeletons are poorly represented in collections so Nagorsen and Peterson (1980) recommend preparation of at least one male and one female skeleton per species

96

Preservation of specimens in the field Formalin preservation Preservation in alcohol Preservation by cooling or freezing

97

Formalin preservation After weighing and measuring the animal and attaching an

adequate label very small specimens (up to 100 g) can be fixed whole by submerging them in 10 buffered formalin (tissue - formalin solution ratio of at least 1 12) the body cavity can be filled with formalin solution by injection until it is turgid and firm some formalin may also be injected under the skin into the body cavity larger muscles and organs If hypodermic needles are not available the body cavity can be opened ventrally by making a slit instead allowing the formalin to enter

Keeping the mouth open with a piece of wood or cotton may later allow examination of teeth Then the whole body can be immersed in formalin in the posture in which it is supposed to stay permanently because it will harden The ratio of formalin to carcass must be at least 12 to 1 to assure a good fixation Tissues can be left in buffered neutralized formalin for several months but formalin hardens specimens therefore after fixation longterm storage in alcohol may be better After preservation the carcass should therefore be washed in water and transferred into ethanol for permanent storage

Disadvantages for instance it discolours the fur after a longish immersion softens the bones and prevents further examination for microbiology

98

Preservation in alcohol

After weighing a whole animal can be preserved in a container of alcohol (70-90) Removal of the intestine prior to storage of the animal in alcohol is recommended

99

Preservation by cooling or freezing Removal of the skin with insulating fur

before cooling or freezing may help to cool the carcass down more quickly

Freezing is not recommended if histological examination is planned

100

THANK YOU

64

Small Mammals

Mouserat Traps Fatal

Pit Falls Bucket is placed in the ground Sometimes have lsquoleadsrsquo to the buckets

Live traps Havahart Sherman

Spot-light

Sherman trapHavahart trap

65

Birds Stick-under-the-box method Bird-trap

Works like a minnow trap Mist net

Captures birds in flight Rocket net

Uses a propellant to throw a net over birds

66

Terrestrial Insects

Sticky paper flies

Baited Traps Fire ants

Nets butterflies

Foggers Collect insects from tree canopies

67

Aquatic Insects Drift Net

Place net in flowing water Kick Net

lsquoKickrsquo sediment upstream from block net and the flow will wash them into the net

Wash bucket Serber or Hess Sampler

Stir up known area of sediment

Animals are collected by a catch net

Multi-plate Sampler Become colonized

68

Crawfish and Crab Traps

69

Fish Larvae Light Traps

Larvae are attracted to the light Ichthyoplankton nets

Can be towed at various depths Fish collect at the lsquocodrsquoend

70

Fish Lift net

Net is placed down and after a set amount of time it is quickly lifted

Pop-net Similar to a lift net but

floats are attached to a framed net

Operated by a trigger mechanism

Throw net A net attached to a heavy

frame is thrown and every thing inside is netted out Throw net

Pop-net

Lift net

71

Minnow trap

Usually use bait to attract small fish Light is used sometimes as an attractant

72

Fish Electrofishing

Electricity is put into the water Fish are temporarily stunned and usually

swim towards the electricity source Usually non-fatal but may cause some

damage

73

Fish Gill Net

Gill nets resemble tennis nets Fish can not swim completely through the

net and get caught Gill nets are size selective (based on mesh

size) Square Mesh

Bar mesh

Stretch mesh

74

Fish Trammel Net

Three panels two large mesh on the outside and a small mesh on the inside

Fish swim through the outer mesh pushes the small mesh through the other side and becomes entangled

75

Hoop nets (and other similar nets) can have bait or not

Fyke nets have leads to help guide fish to the net

76

Seine Seines are nets that are pulled

through shallow water to catch fish

77

Purse Seine Used to encircle entire schools of fish

Usually involves a spotter plane and a second boat

78

Trotline (longline) A series of baited drop lines

connected to a main line

Can be deployed by tying one end to the bank and tying the other end with a heavy weight

79

Shrimp (or fish) Trawl Net pulled behind

a boat along the bottom Either a beam or

otter boards keep the net open

80

Tagging Individuals Coded Wire Tags

Microwire that has a unique label

Magnetic wand detects the tag

Tag retention should be determined

T-Bar tags Can be individually

numbered External tag

PIT tags (Passive Integrated Transponders) Wand induces the tag to

transmit individual number is displayed

81

Other Tagging Methods

Toe clip Amphibian and reptile Clip of one or more toes

to identify individuals

Bird Band Place a metal band on a

bird leg Generally has

identification information

82

Preserving plant specimens Pressing and drying Long-term

preservation and storage

Alternative drying techniques

Special preservation and processing techniques

Mounting

83

Pressing and drying Techniques for pressing and drying specimens have been

established for many years There are minor variations in recommended methods but they are essentially the same worldwide

The best specimens are plants that are pressed as soon as possible after collection before wilting and shrivelling Most plants may be kept in sealed containers such as plastic bags for up to a day if it is inconvenient to press immediately However some plants show such rapid wilting particularly of the flowers that such delays are best avoided Flowers with a lot of nectar may go mouldy very quickly if excess nectar is not shaken off before pressing

Specimens are pressed flat and dried between sheets of absorbent blotters or semi-absorbent paper such as newspaper Papers with a glossy surface should be avoided because they are not absorbent enough to aid drying The plant should be carefully laid out between the drying sheets as their form at this stage largely determines their ultimate appearance The flowers should be spread out with the petals carefully arranged wilted leaves should be straightened and unnecessary shoots of excessively twiggy shrubs may be cut away

84

Microwave ovens Small numbers of specimens can be dried using a microwave

oven The technique recommended in the literature is to place the specimens between unprinted absorbent paper for example butchers paper not newspaper which is unsuitable because the chemicals present in the ink may cause a fire The specimens should be put in a special press which should be of a microwave-safe material (wood acrylic or polycarbonate sheeting eg plexiglass or perspex NO metal components) If such a press is not available sheets of cardboard can be placed above and below the specimens and then weighted down

Drying time depends on the power of your oven In most cases drying is accomplished by irradiating at maximum power for 1-2 minutes per specimen although it is often a case of trial and error It is best to process no more than 10-12 specimens of average thickness per batch Specimens are usually dried after the moisture that characteristically appears on the glass door has disappeared If the specimen is damp when taken out of the oven allow it to stand before re-radiating as moisture continues to evaporate from the specimen for some time Care must be taken not to irradiate the specimens for too long

It should be noted that microwave treatment damages seeds and the cellular structure of the plants which may reduce the long-term value of the specimens

85

Alternative drying techniquesSilica gelother desiccants amp freeze drying Alternative methods of drying plant specimens have been

used for some time but are mostly restricted to special purpose collections The main alternatives are freeze-drying and drying in a desiccant powder such as desiccant silica gel In general these techniques are used where it is essential to preserve the shape of a delicate plant of organ of the plant such as the flower Freeze-drying has also been used to preserve the chemical composition of a plant as accurately as possible for later study

Disadvantages and special conservation problems of specimens dried in these manners are that they are particularly susceptible to damage The dried parts are fragile lack support and often catch on packing materials They must therefore be packed especially carefully and stored in small boxes or tubes with some appropriate packing material that does not snag and break small projections Acid-free tissue paper is often used Drying in desiccant silica gel crystals or powder can also have the disadvantage that it is difficult to remove all traces of the silica gel after drying

86

Special preservation and processing techniquesWet or spirit collections

Very fleshy or delicate structures including small algae and orchid flowers are best preserved in an air-tight glass or plastic jar with a liquid preservative rather than by drying The type of preservative used should be clearly labelled in the jar Such material is often referred to as a spirit collection or wet collection

Most material can be satisfactorily preserved in 70 ethyl alcohol (or 70 methylated spirit or denatured alcohol) with 30 water Colours will fade quickly in spirit however so it is a good idea to keep comprehensive notes and photographs

87

Small algae Microscopic algae are often collected in a jar and in the

water in which they were found If the algae are to be stored for more than 2-3 days a preservative needs to be used Traditionally this has been the extremely toxic formalin - a small amount can be added to the water to make a 5 final solution and the container labelled This must not be sent through the post or by courier

There are some other equally toxic options for example propylene phenoxytol but none should be sent through the post A safer option is to add sufficient concentrated alcohol or methylated spirits to the water containing the algae to make a final solution of 70 alcohol This treatment dilutes the algae making them difficult to find so if they can be concentrated somehow first (eg by filtering) they can be stored in much less liquid Another option is to fix the algae in formalin (or something similar) first and then prepare a microscope glass slide with a permanent water-soluble mounting medium

88

Mounting Mounting specimens prevents most fragile material from

fragmenting and prevents specimens becoming separated from their labels If the plant collection is a long-term project specimens should be mounted on sheets of archival (permanent) cardboard or paper with archival-quality fixing media These include stitching with cotton thread dental floss nickel-plated copper wire (for heavier specimens) narrow strips of archival paper linen tape or by using an archival adhesive such as methyl cellulose adhesive

One disadvantage of mounting specimens is that it can make parts of the specimen inaccessible for examination so it is essential that this be borne in mind during specimen arrangement and mounting For example easily reversible mounting media should be used specimens should be strapped to the sheet rather than glued all over and the specimen should be carefully arranged before it is attached so that it shows all features

89

Full-size herbarium mounting sheets are usually about 43 cm long x 28 cm wide The plant name and accompanying field notes should be transcribed on a permanent label stuck to one corner of the herbarium sheet (the bottom right-hand corner being the most common) or sometimes annotations may be written directly on the sheet or card

Small pieces of material which may have become separated from the specimen (eg seeds) can be placed in small plastic bags and pinned to the sheet

90

Long-term preservation and storage The long-term preservation of dry plant

specimens is largely dependent on protection from insect attack Specimens collected by Linnaeus in the eighteenth century and by Banks and Solander on the Endeavour voyage in 1788 are still excellently preserved

91

Pests and their control A range of pests attack dried plant material The

most common pests are insects and fungi though rodents and other large animals can cause damage in poor storage conditions Insects eat the material the paper surrounding the material and the adhesives and mounting media

Such insect pests range from psocids (book lice) which attack mainly the softer parts such as flowers and soft fruits to tobacco beetles and carpet beetles which can bore holes through the toughest of specimens Many insects are particularly sensitive to relative humidity levels and do not thrive at levels below 50

92

The most common and acceptable specimen treatments for insect control are Freezing Microwave Poisoning Insect deterrents Fungal pests

93

Storage

Dried and pressed plant specimens can be stored in cardboard or plastic boxes or tied in bundles in light-weight cardboard folders placed in pigeon holes

Alternatively they can be placed in protective plastic jackets and displayed in ring folders which is recommended if they are to be frequently handled such as for a reference collection

94

Filing

Specimens should be filed in a systematic order if a relatively permanent collection is being made The major groups ie ferns and fern allies cycads conifers dicotyledons and monocotyledons are best kept separately or according to some classification scheme such as that given in a flora or handbook

Similarly the genera within each family and the species within each genus may be filed alphabetically or following some such classification

95

Preservation of entire animals

Types of collection specimens of an entire animal For reference collections mammals can be prepared as a variety of specimens The condition of the specimen may determine possible ways to preserve it if for instance decomposition of the skin has loosened the hair of a carcass so much that it can easily be pulled out or removed by rubbing (ldquoslippingrdquo fur) it will be very difficult or impossible to produce a study skin or mounted specimen The most usual types of specimens (based on Nagorsen and Peterson 1980) are 1) entire fluid-preserved animals (for studying anatomy and histology fluid preservation may change the fur colour) 2) study skins with accompanying skulls partial skeletons (some bones remain in the skin) for studying pelage colour hair quality and moulting patterns 3) mounted skins with accompanying partial or entire skeleton (some bones may remain in the skin dependant on the method of preservation) or freeze-dried specimens 4) entire skeletons for instance for studying anatomy geographic variation or for age determination (entire skeletons are poorly represented in collections so Nagorsen and Peterson (1980) recommend preparation of at least one male and one female skeleton per species

96

Preservation of specimens in the field Formalin preservation Preservation in alcohol Preservation by cooling or freezing

97

Formalin preservation After weighing and measuring the animal and attaching an

adequate label very small specimens (up to 100 g) can be fixed whole by submerging them in 10 buffered formalin (tissue - formalin solution ratio of at least 1 12) the body cavity can be filled with formalin solution by injection until it is turgid and firm some formalin may also be injected under the skin into the body cavity larger muscles and organs If hypodermic needles are not available the body cavity can be opened ventrally by making a slit instead allowing the formalin to enter

Keeping the mouth open with a piece of wood or cotton may later allow examination of teeth Then the whole body can be immersed in formalin in the posture in which it is supposed to stay permanently because it will harden The ratio of formalin to carcass must be at least 12 to 1 to assure a good fixation Tissues can be left in buffered neutralized formalin for several months but formalin hardens specimens therefore after fixation longterm storage in alcohol may be better After preservation the carcass should therefore be washed in water and transferred into ethanol for permanent storage

Disadvantages for instance it discolours the fur after a longish immersion softens the bones and prevents further examination for microbiology

98

Preservation in alcohol

After weighing a whole animal can be preserved in a container of alcohol (70-90) Removal of the intestine prior to storage of the animal in alcohol is recommended

99

Preservation by cooling or freezing Removal of the skin with insulating fur

before cooling or freezing may help to cool the carcass down more quickly

Freezing is not recommended if histological examination is planned

100

THANK YOU

65

Birds Stick-under-the-box method Bird-trap

Works like a minnow trap Mist net

Captures birds in flight Rocket net

Uses a propellant to throw a net over birds

66

Terrestrial Insects

Sticky paper flies

Baited Traps Fire ants

Nets butterflies

Foggers Collect insects from tree canopies

67

Aquatic Insects Drift Net

Place net in flowing water Kick Net

lsquoKickrsquo sediment upstream from block net and the flow will wash them into the net

Wash bucket Serber or Hess Sampler

Stir up known area of sediment

Animals are collected by a catch net

Multi-plate Sampler Become colonized

68

Crawfish and Crab Traps

69

Fish Larvae Light Traps

Larvae are attracted to the light Ichthyoplankton nets

Can be towed at various depths Fish collect at the lsquocodrsquoend

70

Fish Lift net

Net is placed down and after a set amount of time it is quickly lifted

Pop-net Similar to a lift net but

floats are attached to a framed net

Operated by a trigger mechanism

Throw net A net attached to a heavy

frame is thrown and every thing inside is netted out Throw net

Pop-net

Lift net

71

Minnow trap

Usually use bait to attract small fish Light is used sometimes as an attractant

72

Fish Electrofishing

Electricity is put into the water Fish are temporarily stunned and usually

swim towards the electricity source Usually non-fatal but may cause some

damage

73

Fish Gill Net

Gill nets resemble tennis nets Fish can not swim completely through the

net and get caught Gill nets are size selective (based on mesh

size) Square Mesh

Bar mesh

Stretch mesh

74

Fish Trammel Net

Three panels two large mesh on the outside and a small mesh on the inside

Fish swim through the outer mesh pushes the small mesh through the other side and becomes entangled

75

Hoop nets (and other similar nets) can have bait or not

Fyke nets have leads to help guide fish to the net

76

Seine Seines are nets that are pulled

through shallow water to catch fish

77

Purse Seine Used to encircle entire schools of fish

Usually involves a spotter plane and a second boat

78

Trotline (longline) A series of baited drop lines

connected to a main line

Can be deployed by tying one end to the bank and tying the other end with a heavy weight

79

Shrimp (or fish) Trawl Net pulled behind

a boat along the bottom Either a beam or

otter boards keep the net open

80

Tagging Individuals Coded Wire Tags

Microwire that has a unique label

Magnetic wand detects the tag

Tag retention should be determined

T-Bar tags Can be individually

numbered External tag

PIT tags (Passive Integrated Transponders) Wand induces the tag to

transmit individual number is displayed

81

Other Tagging Methods

Toe clip Amphibian and reptile Clip of one or more toes

to identify individuals

Bird Band Place a metal band on a

bird leg Generally has

identification information

82

Preserving plant specimens Pressing and drying Long-term

preservation and storage

Alternative drying techniques

Special preservation and processing techniques

Mounting

83

Pressing and drying Techniques for pressing and drying specimens have been

established for many years There are minor variations in recommended methods but they are essentially the same worldwide

The best specimens are plants that are pressed as soon as possible after collection before wilting and shrivelling Most plants may be kept in sealed containers such as plastic bags for up to a day if it is inconvenient to press immediately However some plants show such rapid wilting particularly of the flowers that such delays are best avoided Flowers with a lot of nectar may go mouldy very quickly if excess nectar is not shaken off before pressing

Specimens are pressed flat and dried between sheets of absorbent blotters or semi-absorbent paper such as newspaper Papers with a glossy surface should be avoided because they are not absorbent enough to aid drying The plant should be carefully laid out between the drying sheets as their form at this stage largely determines their ultimate appearance The flowers should be spread out with the petals carefully arranged wilted leaves should be straightened and unnecessary shoots of excessively twiggy shrubs may be cut away

84

Microwave ovens Small numbers of specimens can be dried using a microwave

oven The technique recommended in the literature is to place the specimens between unprinted absorbent paper for example butchers paper not newspaper which is unsuitable because the chemicals present in the ink may cause a fire The specimens should be put in a special press which should be of a microwave-safe material (wood acrylic or polycarbonate sheeting eg plexiglass or perspex NO metal components) If such a press is not available sheets of cardboard can be placed above and below the specimens and then weighted down

Drying time depends on the power of your oven In most cases drying is accomplished by irradiating at maximum power for 1-2 minutes per specimen although it is often a case of trial and error It is best to process no more than 10-12 specimens of average thickness per batch Specimens are usually dried after the moisture that characteristically appears on the glass door has disappeared If the specimen is damp when taken out of the oven allow it to stand before re-radiating as moisture continues to evaporate from the specimen for some time Care must be taken not to irradiate the specimens for too long

It should be noted that microwave treatment damages seeds and the cellular structure of the plants which may reduce the long-term value of the specimens

85

Alternative drying techniquesSilica gelother desiccants amp freeze drying Alternative methods of drying plant specimens have been

used for some time but are mostly restricted to special purpose collections The main alternatives are freeze-drying and drying in a desiccant powder such as desiccant silica gel In general these techniques are used where it is essential to preserve the shape of a delicate plant of organ of the plant such as the flower Freeze-drying has also been used to preserve the chemical composition of a plant as accurately as possible for later study

Disadvantages and special conservation problems of specimens dried in these manners are that they are particularly susceptible to damage The dried parts are fragile lack support and often catch on packing materials They must therefore be packed especially carefully and stored in small boxes or tubes with some appropriate packing material that does not snag and break small projections Acid-free tissue paper is often used Drying in desiccant silica gel crystals or powder can also have the disadvantage that it is difficult to remove all traces of the silica gel after drying

86

Special preservation and processing techniquesWet or spirit collections

Very fleshy or delicate structures including small algae and orchid flowers are best preserved in an air-tight glass or plastic jar with a liquid preservative rather than by drying The type of preservative used should be clearly labelled in the jar Such material is often referred to as a spirit collection or wet collection

Most material can be satisfactorily preserved in 70 ethyl alcohol (or 70 methylated spirit or denatured alcohol) with 30 water Colours will fade quickly in spirit however so it is a good idea to keep comprehensive notes and photographs

87

Small algae Microscopic algae are often collected in a jar and in the

water in which they were found If the algae are to be stored for more than 2-3 days a preservative needs to be used Traditionally this has been the extremely toxic formalin - a small amount can be added to the water to make a 5 final solution and the container labelled This must not be sent through the post or by courier

There are some other equally toxic options for example propylene phenoxytol but none should be sent through the post A safer option is to add sufficient concentrated alcohol or methylated spirits to the water containing the algae to make a final solution of 70 alcohol This treatment dilutes the algae making them difficult to find so if they can be concentrated somehow first (eg by filtering) they can be stored in much less liquid Another option is to fix the algae in formalin (or something similar) first and then prepare a microscope glass slide with a permanent water-soluble mounting medium

88

Mounting Mounting specimens prevents most fragile material from

fragmenting and prevents specimens becoming separated from their labels If the plant collection is a long-term project specimens should be mounted on sheets of archival (permanent) cardboard or paper with archival-quality fixing media These include stitching with cotton thread dental floss nickel-plated copper wire (for heavier specimens) narrow strips of archival paper linen tape or by using an archival adhesive such as methyl cellulose adhesive

One disadvantage of mounting specimens is that it can make parts of the specimen inaccessible for examination so it is essential that this be borne in mind during specimen arrangement and mounting For example easily reversible mounting media should be used specimens should be strapped to the sheet rather than glued all over and the specimen should be carefully arranged before it is attached so that it shows all features

89

Full-size herbarium mounting sheets are usually about 43 cm long x 28 cm wide The plant name and accompanying field notes should be transcribed on a permanent label stuck to one corner of the herbarium sheet (the bottom right-hand corner being the most common) or sometimes annotations may be written directly on the sheet or card

Small pieces of material which may have become separated from the specimen (eg seeds) can be placed in small plastic bags and pinned to the sheet

90

Long-term preservation and storage The long-term preservation of dry plant

specimens is largely dependent on protection from insect attack Specimens collected by Linnaeus in the eighteenth century and by Banks and Solander on the Endeavour voyage in 1788 are still excellently preserved

91

Pests and their control A range of pests attack dried plant material The

most common pests are insects and fungi though rodents and other large animals can cause damage in poor storage conditions Insects eat the material the paper surrounding the material and the adhesives and mounting media

Such insect pests range from psocids (book lice) which attack mainly the softer parts such as flowers and soft fruits to tobacco beetles and carpet beetles which can bore holes through the toughest of specimens Many insects are particularly sensitive to relative humidity levels and do not thrive at levels below 50

92

The most common and acceptable specimen treatments for insect control are Freezing Microwave Poisoning Insect deterrents Fungal pests

93

Storage

Dried and pressed plant specimens can be stored in cardboard or plastic boxes or tied in bundles in light-weight cardboard folders placed in pigeon holes

Alternatively they can be placed in protective plastic jackets and displayed in ring folders which is recommended if they are to be frequently handled such as for a reference collection

94

Filing

Specimens should be filed in a systematic order if a relatively permanent collection is being made The major groups ie ferns and fern allies cycads conifers dicotyledons and monocotyledons are best kept separately or according to some classification scheme such as that given in a flora or handbook

Similarly the genera within each family and the species within each genus may be filed alphabetically or following some such classification

95

Preservation of entire animals

Types of collection specimens of an entire animal For reference collections mammals can be prepared as a variety of specimens The condition of the specimen may determine possible ways to preserve it if for instance decomposition of the skin has loosened the hair of a carcass so much that it can easily be pulled out or removed by rubbing (ldquoslippingrdquo fur) it will be very difficult or impossible to produce a study skin or mounted specimen The most usual types of specimens (based on Nagorsen and Peterson 1980) are 1) entire fluid-preserved animals (for studying anatomy and histology fluid preservation may change the fur colour) 2) study skins with accompanying skulls partial skeletons (some bones remain in the skin) for studying pelage colour hair quality and moulting patterns 3) mounted skins with accompanying partial or entire skeleton (some bones may remain in the skin dependant on the method of preservation) or freeze-dried specimens 4) entire skeletons for instance for studying anatomy geographic variation or for age determination (entire skeletons are poorly represented in collections so Nagorsen and Peterson (1980) recommend preparation of at least one male and one female skeleton per species

96

Preservation of specimens in the field Formalin preservation Preservation in alcohol Preservation by cooling or freezing

97

Formalin preservation After weighing and measuring the animal and attaching an

adequate label very small specimens (up to 100 g) can be fixed whole by submerging them in 10 buffered formalin (tissue - formalin solution ratio of at least 1 12) the body cavity can be filled with formalin solution by injection until it is turgid and firm some formalin may also be injected under the skin into the body cavity larger muscles and organs If hypodermic needles are not available the body cavity can be opened ventrally by making a slit instead allowing the formalin to enter

Keeping the mouth open with a piece of wood or cotton may later allow examination of teeth Then the whole body can be immersed in formalin in the posture in which it is supposed to stay permanently because it will harden The ratio of formalin to carcass must be at least 12 to 1 to assure a good fixation Tissues can be left in buffered neutralized formalin for several months but formalin hardens specimens therefore after fixation longterm storage in alcohol may be better After preservation the carcass should therefore be washed in water and transferred into ethanol for permanent storage

Disadvantages for instance it discolours the fur after a longish immersion softens the bones and prevents further examination for microbiology

98

Preservation in alcohol

After weighing a whole animal can be preserved in a container of alcohol (70-90) Removal of the intestine prior to storage of the animal in alcohol is recommended

99

Preservation by cooling or freezing Removal of the skin with insulating fur

before cooling or freezing may help to cool the carcass down more quickly

Freezing is not recommended if histological examination is planned

100

THANK YOU

66

Terrestrial Insects

Sticky paper flies

Baited Traps Fire ants

Nets butterflies

Foggers Collect insects from tree canopies

67

Aquatic Insects Drift Net

Place net in flowing water Kick Net

lsquoKickrsquo sediment upstream from block net and the flow will wash them into the net

Wash bucket Serber or Hess Sampler

Stir up known area of sediment

Animals are collected by a catch net

Multi-plate Sampler Become colonized

68

Crawfish and Crab Traps

69

Fish Larvae Light Traps

Larvae are attracted to the light Ichthyoplankton nets

Can be towed at various depths Fish collect at the lsquocodrsquoend

70

Fish Lift net

Net is placed down and after a set amount of time it is quickly lifted

Pop-net Similar to a lift net but

floats are attached to a framed net

Operated by a trigger mechanism

Throw net A net attached to a heavy

frame is thrown and every thing inside is netted out Throw net

Pop-net

Lift net

71

Minnow trap

Usually use bait to attract small fish Light is used sometimes as an attractant

72

Fish Electrofishing

Electricity is put into the water Fish are temporarily stunned and usually

swim towards the electricity source Usually non-fatal but may cause some

damage

73

Fish Gill Net

Gill nets resemble tennis nets Fish can not swim completely through the

net and get caught Gill nets are size selective (based on mesh

size) Square Mesh

Bar mesh

Stretch mesh

74

Fish Trammel Net

Three panels two large mesh on the outside and a small mesh on the inside

Fish swim through the outer mesh pushes the small mesh through the other side and becomes entangled

75

Hoop nets (and other similar nets) can have bait or not

Fyke nets have leads to help guide fish to the net

76

Seine Seines are nets that are pulled

through shallow water to catch fish

77

Purse Seine Used to encircle entire schools of fish

Usually involves a spotter plane and a second boat

78

Trotline (longline) A series of baited drop lines

connected to a main line

Can be deployed by tying one end to the bank and tying the other end with a heavy weight

79

Shrimp (or fish) Trawl Net pulled behind

a boat along the bottom Either a beam or

otter boards keep the net open

80

Tagging Individuals Coded Wire Tags

Microwire that has a unique label

Magnetic wand detects the tag

Tag retention should be determined

T-Bar tags Can be individually

numbered External tag

PIT tags (Passive Integrated Transponders) Wand induces the tag to

transmit individual number is displayed

81

Other Tagging Methods

Toe clip Amphibian and reptile Clip of one or more toes

to identify individuals

Bird Band Place a metal band on a

bird leg Generally has

identification information

82

Preserving plant specimens Pressing and drying Long-term

preservation and storage

Alternative drying techniques

Special preservation and processing techniques

Mounting

83

Pressing and drying Techniques for pressing and drying specimens have been

established for many years There are minor variations in recommended methods but they are essentially the same worldwide

The best specimens are plants that are pressed as soon as possible after collection before wilting and shrivelling Most plants may be kept in sealed containers such as plastic bags for up to a day if it is inconvenient to press immediately However some plants show such rapid wilting particularly of the flowers that such delays are best avoided Flowers with a lot of nectar may go mouldy very quickly if excess nectar is not shaken off before pressing

Specimens are pressed flat and dried between sheets of absorbent blotters or semi-absorbent paper such as newspaper Papers with a glossy surface should be avoided because they are not absorbent enough to aid drying The plant should be carefully laid out between the drying sheets as their form at this stage largely determines their ultimate appearance The flowers should be spread out with the petals carefully arranged wilted leaves should be straightened and unnecessary shoots of excessively twiggy shrubs may be cut away

84

Microwave ovens Small numbers of specimens can be dried using a microwave

oven The technique recommended in the literature is to place the specimens between unprinted absorbent paper for example butchers paper not newspaper which is unsuitable because the chemicals present in the ink may cause a fire The specimens should be put in a special press which should be of a microwave-safe material (wood acrylic or polycarbonate sheeting eg plexiglass or perspex NO metal components) If such a press is not available sheets of cardboard can be placed above and below the specimens and then weighted down

Drying time depends on the power of your oven In most cases drying is accomplished by irradiating at maximum power for 1-2 minutes per specimen although it is often a case of trial and error It is best to process no more than 10-12 specimens of average thickness per batch Specimens are usually dried after the moisture that characteristically appears on the glass door has disappeared If the specimen is damp when taken out of the oven allow it to stand before re-radiating as moisture continues to evaporate from the specimen for some time Care must be taken not to irradiate the specimens for too long

It should be noted that microwave treatment damages seeds and the cellular structure of the plants which may reduce the long-term value of the specimens

85

Alternative drying techniquesSilica gelother desiccants amp freeze drying Alternative methods of drying plant specimens have been

used for some time but are mostly restricted to special purpose collections The main alternatives are freeze-drying and drying in a desiccant powder such as desiccant silica gel In general these techniques are used where it is essential to preserve the shape of a delicate plant of organ of the plant such as the flower Freeze-drying has also been used to preserve the chemical composition of a plant as accurately as possible for later study

Disadvantages and special conservation problems of specimens dried in these manners are that they are particularly susceptible to damage The dried parts are fragile lack support and often catch on packing materials They must therefore be packed especially carefully and stored in small boxes or tubes with some appropriate packing material that does not snag and break small projections Acid-free tissue paper is often used Drying in desiccant silica gel crystals or powder can also have the disadvantage that it is difficult to remove all traces of the silica gel after drying

86

Special preservation and processing techniquesWet or spirit collections

Very fleshy or delicate structures including small algae and orchid flowers are best preserved in an air-tight glass or plastic jar with a liquid preservative rather than by drying The type of preservative used should be clearly labelled in the jar Such material is often referred to as a spirit collection or wet collection

Most material can be satisfactorily preserved in 70 ethyl alcohol (or 70 methylated spirit or denatured alcohol) with 30 water Colours will fade quickly in spirit however so it is a good idea to keep comprehensive notes and photographs

87

Small algae Microscopic algae are often collected in a jar and in the

water in which they were found If the algae are to be stored for more than 2-3 days a preservative needs to be used Traditionally this has been the extremely toxic formalin - a small amount can be added to the water to make a 5 final solution and the container labelled This must not be sent through the post or by courier

There are some other equally toxic options for example propylene phenoxytol but none should be sent through the post A safer option is to add sufficient concentrated alcohol or methylated spirits to the water containing the algae to make a final solution of 70 alcohol This treatment dilutes the algae making them difficult to find so if they can be concentrated somehow first (eg by filtering) they can be stored in much less liquid Another option is to fix the algae in formalin (or something similar) first and then prepare a microscope glass slide with a permanent water-soluble mounting medium

88

Mounting Mounting specimens prevents most fragile material from

fragmenting and prevents specimens becoming separated from their labels If the plant collection is a long-term project specimens should be mounted on sheets of archival (permanent) cardboard or paper with archival-quality fixing media These include stitching with cotton thread dental floss nickel-plated copper wire (for heavier specimens) narrow strips of archival paper linen tape or by using an archival adhesive such as methyl cellulose adhesive

One disadvantage of mounting specimens is that it can make parts of the specimen inaccessible for examination so it is essential that this be borne in mind during specimen arrangement and mounting For example easily reversible mounting media should be used specimens should be strapped to the sheet rather than glued all over and the specimen should be carefully arranged before it is attached so that it shows all features

89

Full-size herbarium mounting sheets are usually about 43 cm long x 28 cm wide The plant name and accompanying field notes should be transcribed on a permanent label stuck to one corner of the herbarium sheet (the bottom right-hand corner being the most common) or sometimes annotations may be written directly on the sheet or card

Small pieces of material which may have become separated from the specimen (eg seeds) can be placed in small plastic bags and pinned to the sheet

90

Long-term preservation and storage The long-term preservation of dry plant

specimens is largely dependent on protection from insect attack Specimens collected by Linnaeus in the eighteenth century and by Banks and Solander on the Endeavour voyage in 1788 are still excellently preserved

91

Pests and their control A range of pests attack dried plant material The

most common pests are insects and fungi though rodents and other large animals can cause damage in poor storage conditions Insects eat the material the paper surrounding the material and the adhesives and mounting media

Such insect pests range from psocids (book lice) which attack mainly the softer parts such as flowers and soft fruits to tobacco beetles and carpet beetles which can bore holes through the toughest of specimens Many insects are particularly sensitive to relative humidity levels and do not thrive at levels below 50

92

The most common and acceptable specimen treatments for insect control are Freezing Microwave Poisoning Insect deterrents Fungal pests

93

Storage

Dried and pressed plant specimens can be stored in cardboard or plastic boxes or tied in bundles in light-weight cardboard folders placed in pigeon holes

Alternatively they can be placed in protective plastic jackets and displayed in ring folders which is recommended if they are to be frequently handled such as for a reference collection

94

Filing

Specimens should be filed in a systematic order if a relatively permanent collection is being made The major groups ie ferns and fern allies cycads conifers dicotyledons and monocotyledons are best kept separately or according to some classification scheme such as that given in a flora or handbook

Similarly the genera within each family and the species within each genus may be filed alphabetically or following some such classification

95

Preservation of entire animals

Types of collection specimens of an entire animal For reference collections mammals can be prepared as a variety of specimens The condition of the specimen may determine possible ways to preserve it if for instance decomposition of the skin has loosened the hair of a carcass so much that it can easily be pulled out or removed by rubbing (ldquoslippingrdquo fur) it will be very difficult or impossible to produce a study skin or mounted specimen The most usual types of specimens (based on Nagorsen and Peterson 1980) are 1) entire fluid-preserved animals (for studying anatomy and histology fluid preservation may change the fur colour) 2) study skins with accompanying skulls partial skeletons (some bones remain in the skin) for studying pelage colour hair quality and moulting patterns 3) mounted skins with accompanying partial or entire skeleton (some bones may remain in the skin dependant on the method of preservation) or freeze-dried specimens 4) entire skeletons for instance for studying anatomy geographic variation or for age determination (entire skeletons are poorly represented in collections so Nagorsen and Peterson (1980) recommend preparation of at least one male and one female skeleton per species

96

Preservation of specimens in the field Formalin preservation Preservation in alcohol Preservation by cooling or freezing

97

Formalin preservation After weighing and measuring the animal and attaching an

adequate label very small specimens (up to 100 g) can be fixed whole by submerging them in 10 buffered formalin (tissue - formalin solution ratio of at least 1 12) the body cavity can be filled with formalin solution by injection until it is turgid and firm some formalin may also be injected under the skin into the body cavity larger muscles and organs If hypodermic needles are not available the body cavity can be opened ventrally by making a slit instead allowing the formalin to enter

Keeping the mouth open with a piece of wood or cotton may later allow examination of teeth Then the whole body can be immersed in formalin in the posture in which it is supposed to stay permanently because it will harden The ratio of formalin to carcass must be at least 12 to 1 to assure a good fixation Tissues can be left in buffered neutralized formalin for several months but formalin hardens specimens therefore after fixation longterm storage in alcohol may be better After preservation the carcass should therefore be washed in water and transferred into ethanol for permanent storage

Disadvantages for instance it discolours the fur after a longish immersion softens the bones and prevents further examination for microbiology

98

Preservation in alcohol

After weighing a whole animal can be preserved in a container of alcohol (70-90) Removal of the intestine prior to storage of the animal in alcohol is recommended

99

Preservation by cooling or freezing Removal of the skin with insulating fur

before cooling or freezing may help to cool the carcass down more quickly

Freezing is not recommended if histological examination is planned

100

THANK YOU

67

Aquatic Insects Drift Net

Place net in flowing water Kick Net

lsquoKickrsquo sediment upstream from block net and the flow will wash them into the net

Wash bucket Serber or Hess Sampler

Stir up known area of sediment

Animals are collected by a catch net

Multi-plate Sampler Become colonized

68

Crawfish and Crab Traps

69

Fish Larvae Light Traps

Larvae are attracted to the light Ichthyoplankton nets

Can be towed at various depths Fish collect at the lsquocodrsquoend

70

Fish Lift net

Net is placed down and after a set amount of time it is quickly lifted

Pop-net Similar to a lift net but

floats are attached to a framed net

Operated by a trigger mechanism

Throw net A net attached to a heavy

frame is thrown and every thing inside is netted out Throw net

Pop-net

Lift net

71

Minnow trap

Usually use bait to attract small fish Light is used sometimes as an attractant

72

Fish Electrofishing

Electricity is put into the water Fish are temporarily stunned and usually

swim towards the electricity source Usually non-fatal but may cause some

damage

73

Fish Gill Net

Gill nets resemble tennis nets Fish can not swim completely through the

net and get caught Gill nets are size selective (based on mesh

size) Square Mesh

Bar mesh

Stretch mesh

74

Fish Trammel Net

Three panels two large mesh on the outside and a small mesh on the inside

Fish swim through the outer mesh pushes the small mesh through the other side and becomes entangled

75

Hoop nets (and other similar nets) can have bait or not

Fyke nets have leads to help guide fish to the net

76

Seine Seines are nets that are pulled

through shallow water to catch fish

77

Purse Seine Used to encircle entire schools of fish

Usually involves a spotter plane and a second boat

78

Trotline (longline) A series of baited drop lines

connected to a main line

Can be deployed by tying one end to the bank and tying the other end with a heavy weight

79

Shrimp (or fish) Trawl Net pulled behind

a boat along the bottom Either a beam or

otter boards keep the net open

80

Tagging Individuals Coded Wire Tags

Microwire that has a unique label

Magnetic wand detects the tag

Tag retention should be determined

T-Bar tags Can be individually

numbered External tag

PIT tags (Passive Integrated Transponders) Wand induces the tag to

transmit individual number is displayed

81

Other Tagging Methods

Toe clip Amphibian and reptile Clip of one or more toes

to identify individuals

Bird Band Place a metal band on a

bird leg Generally has

identification information

82

Preserving plant specimens Pressing and drying Long-term

preservation and storage

Alternative drying techniques

Special preservation and processing techniques

Mounting

83

Pressing and drying Techniques for pressing and drying specimens have been

established for many years There are minor variations in recommended methods but they are essentially the same worldwide

The best specimens are plants that are pressed as soon as possible after collection before wilting and shrivelling Most plants may be kept in sealed containers such as plastic bags for up to a day if it is inconvenient to press immediately However some plants show such rapid wilting particularly of the flowers that such delays are best avoided Flowers with a lot of nectar may go mouldy very quickly if excess nectar is not shaken off before pressing

Specimens are pressed flat and dried between sheets of absorbent blotters or semi-absorbent paper such as newspaper Papers with a glossy surface should be avoided because they are not absorbent enough to aid drying The plant should be carefully laid out between the drying sheets as their form at this stage largely determines their ultimate appearance The flowers should be spread out with the petals carefully arranged wilted leaves should be straightened and unnecessary shoots of excessively twiggy shrubs may be cut away

84

Microwave ovens Small numbers of specimens can be dried using a microwave

oven The technique recommended in the literature is to place the specimens between unprinted absorbent paper for example butchers paper not newspaper which is unsuitable because the chemicals present in the ink may cause a fire The specimens should be put in a special press which should be of a microwave-safe material (wood acrylic or polycarbonate sheeting eg plexiglass or perspex NO metal components) If such a press is not available sheets of cardboard can be placed above and below the specimens and then weighted down

Drying time depends on the power of your oven In most cases drying is accomplished by irradiating at maximum power for 1-2 minutes per specimen although it is often a case of trial and error It is best to process no more than 10-12 specimens of average thickness per batch Specimens are usually dried after the moisture that characteristically appears on the glass door has disappeared If the specimen is damp when taken out of the oven allow it to stand before re-radiating as moisture continues to evaporate from the specimen for some time Care must be taken not to irradiate the specimens for too long

It should be noted that microwave treatment damages seeds and the cellular structure of the plants which may reduce the long-term value of the specimens

85

Alternative drying techniquesSilica gelother desiccants amp freeze drying Alternative methods of drying plant specimens have been

used for some time but are mostly restricted to special purpose collections The main alternatives are freeze-drying and drying in a desiccant powder such as desiccant silica gel In general these techniques are used where it is essential to preserve the shape of a delicate plant of organ of the plant such as the flower Freeze-drying has also been used to preserve the chemical composition of a plant as accurately as possible for later study

Disadvantages and special conservation problems of specimens dried in these manners are that they are particularly susceptible to damage The dried parts are fragile lack support and often catch on packing materials They must therefore be packed especially carefully and stored in small boxes or tubes with some appropriate packing material that does not snag and break small projections Acid-free tissue paper is often used Drying in desiccant silica gel crystals or powder can also have the disadvantage that it is difficult to remove all traces of the silica gel after drying

86

Special preservation and processing techniquesWet or spirit collections

Very fleshy or delicate structures including small algae and orchid flowers are best preserved in an air-tight glass or plastic jar with a liquid preservative rather than by drying The type of preservative used should be clearly labelled in the jar Such material is often referred to as a spirit collection or wet collection

Most material can be satisfactorily preserved in 70 ethyl alcohol (or 70 methylated spirit or denatured alcohol) with 30 water Colours will fade quickly in spirit however so it is a good idea to keep comprehensive notes and photographs

87

Small algae Microscopic algae are often collected in a jar and in the

water in which they were found If the algae are to be stored for more than 2-3 days a preservative needs to be used Traditionally this has been the extremely toxic formalin - a small amount can be added to the water to make a 5 final solution and the container labelled This must not be sent through the post or by courier

There are some other equally toxic options for example propylene phenoxytol but none should be sent through the post A safer option is to add sufficient concentrated alcohol or methylated spirits to the water containing the algae to make a final solution of 70 alcohol This treatment dilutes the algae making them difficult to find so if they can be concentrated somehow first (eg by filtering) they can be stored in much less liquid Another option is to fix the algae in formalin (or something similar) first and then prepare a microscope glass slide with a permanent water-soluble mounting medium

88

Mounting Mounting specimens prevents most fragile material from

fragmenting and prevents specimens becoming separated from their labels If the plant collection is a long-term project specimens should be mounted on sheets of archival (permanent) cardboard or paper with archival-quality fixing media These include stitching with cotton thread dental floss nickel-plated copper wire (for heavier specimens) narrow strips of archival paper linen tape or by using an archival adhesive such as methyl cellulose adhesive

One disadvantage of mounting specimens is that it can make parts of the specimen inaccessible for examination so it is essential that this be borne in mind during specimen arrangement and mounting For example easily reversible mounting media should be used specimens should be strapped to the sheet rather than glued all over and the specimen should be carefully arranged before it is attached so that it shows all features

89

Full-size herbarium mounting sheets are usually about 43 cm long x 28 cm wide The plant name and accompanying field notes should be transcribed on a permanent label stuck to one corner of the herbarium sheet (the bottom right-hand corner being the most common) or sometimes annotations may be written directly on the sheet or card

Small pieces of material which may have become separated from the specimen (eg seeds) can be placed in small plastic bags and pinned to the sheet

90

Long-term preservation and storage The long-term preservation of dry plant

specimens is largely dependent on protection from insect attack Specimens collected by Linnaeus in the eighteenth century and by Banks and Solander on the Endeavour voyage in 1788 are still excellently preserved

91

Pests and their control A range of pests attack dried plant material The

most common pests are insects and fungi though rodents and other large animals can cause damage in poor storage conditions Insects eat the material the paper surrounding the material and the adhesives and mounting media

Such insect pests range from psocids (book lice) which attack mainly the softer parts such as flowers and soft fruits to tobacco beetles and carpet beetles which can bore holes through the toughest of specimens Many insects are particularly sensitive to relative humidity levels and do not thrive at levels below 50

92

The most common and acceptable specimen treatments for insect control are Freezing Microwave Poisoning Insect deterrents Fungal pests

93

Storage

Dried and pressed plant specimens can be stored in cardboard or plastic boxes or tied in bundles in light-weight cardboard folders placed in pigeon holes

Alternatively they can be placed in protective plastic jackets and displayed in ring folders which is recommended if they are to be frequently handled such as for a reference collection

94

Filing

Specimens should be filed in a systematic order if a relatively permanent collection is being made The major groups ie ferns and fern allies cycads conifers dicotyledons and monocotyledons are best kept separately or according to some classification scheme such as that given in a flora or handbook

Similarly the genera within each family and the species within each genus may be filed alphabetically or following some such classification

95

Preservation of entire animals

Types of collection specimens of an entire animal For reference collections mammals can be prepared as a variety of specimens The condition of the specimen may determine possible ways to preserve it if for instance decomposition of the skin has loosened the hair of a carcass so much that it can easily be pulled out or removed by rubbing (ldquoslippingrdquo fur) it will be very difficult or impossible to produce a study skin or mounted specimen The most usual types of specimens (based on Nagorsen and Peterson 1980) are 1) entire fluid-preserved animals (for studying anatomy and histology fluid preservation may change the fur colour) 2) study skins with accompanying skulls partial skeletons (some bones remain in the skin) for studying pelage colour hair quality and moulting patterns 3) mounted skins with accompanying partial or entire skeleton (some bones may remain in the skin dependant on the method of preservation) or freeze-dried specimens 4) entire skeletons for instance for studying anatomy geographic variation or for age determination (entire skeletons are poorly represented in collections so Nagorsen and Peterson (1980) recommend preparation of at least one male and one female skeleton per species

96

Preservation of specimens in the field Formalin preservation Preservation in alcohol Preservation by cooling or freezing

97

Formalin preservation After weighing and measuring the animal and attaching an

adequate label very small specimens (up to 100 g) can be fixed whole by submerging them in 10 buffered formalin (tissue - formalin solution ratio of at least 1 12) the body cavity can be filled with formalin solution by injection until it is turgid and firm some formalin may also be injected under the skin into the body cavity larger muscles and organs If hypodermic needles are not available the body cavity can be opened ventrally by making a slit instead allowing the formalin to enter

Keeping the mouth open with a piece of wood or cotton may later allow examination of teeth Then the whole body can be immersed in formalin in the posture in which it is supposed to stay permanently because it will harden The ratio of formalin to carcass must be at least 12 to 1 to assure a good fixation Tissues can be left in buffered neutralized formalin for several months but formalin hardens specimens therefore after fixation longterm storage in alcohol may be better After preservation the carcass should therefore be washed in water and transferred into ethanol for permanent storage

Disadvantages for instance it discolours the fur after a longish immersion softens the bones and prevents further examination for microbiology

98

Preservation in alcohol

After weighing a whole animal can be preserved in a container of alcohol (70-90) Removal of the intestine prior to storage of the animal in alcohol is recommended

99

Preservation by cooling or freezing Removal of the skin with insulating fur

before cooling or freezing may help to cool the carcass down more quickly

Freezing is not recommended if histological examination is planned

100

THANK YOU

68

Crawfish and Crab Traps

69

Fish Larvae Light Traps

Larvae are attracted to the light Ichthyoplankton nets

Can be towed at various depths Fish collect at the lsquocodrsquoend

70

Fish Lift net

Net is placed down and after a set amount of time it is quickly lifted

Pop-net Similar to a lift net but

floats are attached to a framed net

Operated by a trigger mechanism

Throw net A net attached to a heavy

frame is thrown and every thing inside is netted out Throw net

Pop-net

Lift net

71

Minnow trap

Usually use bait to attract small fish Light is used sometimes as an attractant

72

Fish Electrofishing

Electricity is put into the water Fish are temporarily stunned and usually

swim towards the electricity source Usually non-fatal but may cause some

damage

73

Fish Gill Net

Gill nets resemble tennis nets Fish can not swim completely through the

net and get caught Gill nets are size selective (based on mesh

size) Square Mesh

Bar mesh

Stretch mesh

74

Fish Trammel Net

Three panels two large mesh on the outside and a small mesh on the inside

Fish swim through the outer mesh pushes the small mesh through the other side and becomes entangled

75

Hoop nets (and other similar nets) can have bait or not

Fyke nets have leads to help guide fish to the net

76

Seine Seines are nets that are pulled

through shallow water to catch fish

77

Purse Seine Used to encircle entire schools of fish

Usually involves a spotter plane and a second boat

78

Trotline (longline) A series of baited drop lines

connected to a main line

Can be deployed by tying one end to the bank and tying the other end with a heavy weight

79

Shrimp (or fish) Trawl Net pulled behind

a boat along the bottom Either a beam or

otter boards keep the net open

80

Tagging Individuals Coded Wire Tags

Microwire that has a unique label

Magnetic wand detects the tag

Tag retention should be determined

T-Bar tags Can be individually

numbered External tag

PIT tags (Passive Integrated Transponders) Wand induces the tag to

transmit individual number is displayed

81

Other Tagging Methods

Toe clip Amphibian and reptile Clip of one or more toes

to identify individuals

Bird Band Place a metal band on a

bird leg Generally has

identification information

82

Preserving plant specimens Pressing and drying Long-term

preservation and storage

Alternative drying techniques

Special preservation and processing techniques

Mounting

83

Pressing and drying Techniques for pressing and drying specimens have been

established for many years There are minor variations in recommended methods but they are essentially the same worldwide

The best specimens are plants that are pressed as soon as possible after collection before wilting and shrivelling Most plants may be kept in sealed containers such as plastic bags for up to a day if it is inconvenient to press immediately However some plants show such rapid wilting particularly of the flowers that such delays are best avoided Flowers with a lot of nectar may go mouldy very quickly if excess nectar is not shaken off before pressing

Specimens are pressed flat and dried between sheets of absorbent blotters or semi-absorbent paper such as newspaper Papers with a glossy surface should be avoided because they are not absorbent enough to aid drying The plant should be carefully laid out between the drying sheets as their form at this stage largely determines their ultimate appearance The flowers should be spread out with the petals carefully arranged wilted leaves should be straightened and unnecessary shoots of excessively twiggy shrubs may be cut away

84

Microwave ovens Small numbers of specimens can be dried using a microwave

oven The technique recommended in the literature is to place the specimens between unprinted absorbent paper for example butchers paper not newspaper which is unsuitable because the chemicals present in the ink may cause a fire The specimens should be put in a special press which should be of a microwave-safe material (wood acrylic or polycarbonate sheeting eg plexiglass or perspex NO metal components) If such a press is not available sheets of cardboard can be placed above and below the specimens and then weighted down

Drying time depends on the power of your oven In most cases drying is accomplished by irradiating at maximum power for 1-2 minutes per specimen although it is often a case of trial and error It is best to process no more than 10-12 specimens of average thickness per batch Specimens are usually dried after the moisture that characteristically appears on the glass door has disappeared If the specimen is damp when taken out of the oven allow it to stand before re-radiating as moisture continues to evaporate from the specimen for some time Care must be taken not to irradiate the specimens for too long

It should be noted that microwave treatment damages seeds and the cellular structure of the plants which may reduce the long-term value of the specimens

85

Alternative drying techniquesSilica gelother desiccants amp freeze drying Alternative methods of drying plant specimens have been

used for some time but are mostly restricted to special purpose collections The main alternatives are freeze-drying and drying in a desiccant powder such as desiccant silica gel In general these techniques are used where it is essential to preserve the shape of a delicate plant of organ of the plant such as the flower Freeze-drying has also been used to preserve the chemical composition of a plant as accurately as possible for later study

Disadvantages and special conservation problems of specimens dried in these manners are that they are particularly susceptible to damage The dried parts are fragile lack support and often catch on packing materials They must therefore be packed especially carefully and stored in small boxes or tubes with some appropriate packing material that does not snag and break small projections Acid-free tissue paper is often used Drying in desiccant silica gel crystals or powder can also have the disadvantage that it is difficult to remove all traces of the silica gel after drying

86

Special preservation and processing techniquesWet or spirit collections

Very fleshy or delicate structures including small algae and orchid flowers are best preserved in an air-tight glass or plastic jar with a liquid preservative rather than by drying The type of preservative used should be clearly labelled in the jar Such material is often referred to as a spirit collection or wet collection

Most material can be satisfactorily preserved in 70 ethyl alcohol (or 70 methylated spirit or denatured alcohol) with 30 water Colours will fade quickly in spirit however so it is a good idea to keep comprehensive notes and photographs

87

Small algae Microscopic algae are often collected in a jar and in the

water in which they were found If the algae are to be stored for more than 2-3 days a preservative needs to be used Traditionally this has been the extremely toxic formalin - a small amount can be added to the water to make a 5 final solution and the container labelled This must not be sent through the post or by courier

There are some other equally toxic options for example propylene phenoxytol but none should be sent through the post A safer option is to add sufficient concentrated alcohol or methylated spirits to the water containing the algae to make a final solution of 70 alcohol This treatment dilutes the algae making them difficult to find so if they can be concentrated somehow first (eg by filtering) they can be stored in much less liquid Another option is to fix the algae in formalin (or something similar) first and then prepare a microscope glass slide with a permanent water-soluble mounting medium

88

Mounting Mounting specimens prevents most fragile material from

fragmenting and prevents specimens becoming separated from their labels If the plant collection is a long-term project specimens should be mounted on sheets of archival (permanent) cardboard or paper with archival-quality fixing media These include stitching with cotton thread dental floss nickel-plated copper wire (for heavier specimens) narrow strips of archival paper linen tape or by using an archival adhesive such as methyl cellulose adhesive

One disadvantage of mounting specimens is that it can make parts of the specimen inaccessible for examination so it is essential that this be borne in mind during specimen arrangement and mounting For example easily reversible mounting media should be used specimens should be strapped to the sheet rather than glued all over and the specimen should be carefully arranged before it is attached so that it shows all features

89

Full-size herbarium mounting sheets are usually about 43 cm long x 28 cm wide The plant name and accompanying field notes should be transcribed on a permanent label stuck to one corner of the herbarium sheet (the bottom right-hand corner being the most common) or sometimes annotations may be written directly on the sheet or card

Small pieces of material which may have become separated from the specimen (eg seeds) can be placed in small plastic bags and pinned to the sheet

90

Long-term preservation and storage The long-term preservation of dry plant

specimens is largely dependent on protection from insect attack Specimens collected by Linnaeus in the eighteenth century and by Banks and Solander on the Endeavour voyage in 1788 are still excellently preserved

91

Pests and their control A range of pests attack dried plant material The

most common pests are insects and fungi though rodents and other large animals can cause damage in poor storage conditions Insects eat the material the paper surrounding the material and the adhesives and mounting media

Such insect pests range from psocids (book lice) which attack mainly the softer parts such as flowers and soft fruits to tobacco beetles and carpet beetles which can bore holes through the toughest of specimens Many insects are particularly sensitive to relative humidity levels and do not thrive at levels below 50

92

The most common and acceptable specimen treatments for insect control are Freezing Microwave Poisoning Insect deterrents Fungal pests

93

Storage

Dried and pressed plant specimens can be stored in cardboard or plastic boxes or tied in bundles in light-weight cardboard folders placed in pigeon holes

Alternatively they can be placed in protective plastic jackets and displayed in ring folders which is recommended if they are to be frequently handled such as for a reference collection

94

Filing

Specimens should be filed in a systematic order if a relatively permanent collection is being made The major groups ie ferns and fern allies cycads conifers dicotyledons and monocotyledons are best kept separately or according to some classification scheme such as that given in a flora or handbook

Similarly the genera within each family and the species within each genus may be filed alphabetically or following some such classification

95

Preservation of entire animals

Types of collection specimens of an entire animal For reference collections mammals can be prepared as a variety of specimens The condition of the specimen may determine possible ways to preserve it if for instance decomposition of the skin has loosened the hair of a carcass so much that it can easily be pulled out or removed by rubbing (ldquoslippingrdquo fur) it will be very difficult or impossible to produce a study skin or mounted specimen The most usual types of specimens (based on Nagorsen and Peterson 1980) are 1) entire fluid-preserved animals (for studying anatomy and histology fluid preservation may change the fur colour) 2) study skins with accompanying skulls partial skeletons (some bones remain in the skin) for studying pelage colour hair quality and moulting patterns 3) mounted skins with accompanying partial or entire skeleton (some bones may remain in the skin dependant on the method of preservation) or freeze-dried specimens 4) entire skeletons for instance for studying anatomy geographic variation or for age determination (entire skeletons are poorly represented in collections so Nagorsen and Peterson (1980) recommend preparation of at least one male and one female skeleton per species

96

Preservation of specimens in the field Formalin preservation Preservation in alcohol Preservation by cooling or freezing

97

Formalin preservation After weighing and measuring the animal and attaching an

adequate label very small specimens (up to 100 g) can be fixed whole by submerging them in 10 buffered formalin (tissue - formalin solution ratio of at least 1 12) the body cavity can be filled with formalin solution by injection until it is turgid and firm some formalin may also be injected under the skin into the body cavity larger muscles and organs If hypodermic needles are not available the body cavity can be opened ventrally by making a slit instead allowing the formalin to enter

Keeping the mouth open with a piece of wood or cotton may later allow examination of teeth Then the whole body can be immersed in formalin in the posture in which it is supposed to stay permanently because it will harden The ratio of formalin to carcass must be at least 12 to 1 to assure a good fixation Tissues can be left in buffered neutralized formalin for several months but formalin hardens specimens therefore after fixation longterm storage in alcohol may be better After preservation the carcass should therefore be washed in water and transferred into ethanol for permanent storage

Disadvantages for instance it discolours the fur after a longish immersion softens the bones and prevents further examination for microbiology

98

Preservation in alcohol

After weighing a whole animal can be preserved in a container of alcohol (70-90) Removal of the intestine prior to storage of the animal in alcohol is recommended

99

Preservation by cooling or freezing Removal of the skin with insulating fur

before cooling or freezing may help to cool the carcass down more quickly

Freezing is not recommended if histological examination is planned

100

THANK YOU

69

Fish Larvae Light Traps

Larvae are attracted to the light Ichthyoplankton nets

Can be towed at various depths Fish collect at the lsquocodrsquoend

70

Fish Lift net

Net is placed down and after a set amount of time it is quickly lifted

Pop-net Similar to a lift net but

floats are attached to a framed net

Operated by a trigger mechanism

Throw net A net attached to a heavy

frame is thrown and every thing inside is netted out Throw net

Pop-net

Lift net

71

Minnow trap

Usually use bait to attract small fish Light is used sometimes as an attractant

72

Fish Electrofishing

Electricity is put into the water Fish are temporarily stunned and usually

swim towards the electricity source Usually non-fatal but may cause some

damage

73

Fish Gill Net

Gill nets resemble tennis nets Fish can not swim completely through the

net and get caught Gill nets are size selective (based on mesh

size) Square Mesh

Bar mesh

Stretch mesh

74

Fish Trammel Net

Three panels two large mesh on the outside and a small mesh on the inside

Fish swim through the outer mesh pushes the small mesh through the other side and becomes entangled

75

Hoop nets (and other similar nets) can have bait or not

Fyke nets have leads to help guide fish to the net

76

Seine Seines are nets that are pulled

through shallow water to catch fish

77

Purse Seine Used to encircle entire schools of fish

Usually involves a spotter plane and a second boat

78

Trotline (longline) A series of baited drop lines

connected to a main line

Can be deployed by tying one end to the bank and tying the other end with a heavy weight

79

Shrimp (or fish) Trawl Net pulled behind

a boat along the bottom Either a beam or

otter boards keep the net open

80

Tagging Individuals Coded Wire Tags

Microwire that has a unique label

Magnetic wand detects the tag

Tag retention should be determined

T-Bar tags Can be individually

numbered External tag

PIT tags (Passive Integrated Transponders) Wand induces the tag to

transmit individual number is displayed

81

Other Tagging Methods

Toe clip Amphibian and reptile Clip of one or more toes

to identify individuals

Bird Band Place a metal band on a

bird leg Generally has

identification information

82

Preserving plant specimens Pressing and drying Long-term

preservation and storage

Alternative drying techniques

Special preservation and processing techniques

Mounting

83

Pressing and drying Techniques for pressing and drying specimens have been

established for many years There are minor variations in recommended methods but they are essentially the same worldwide

The best specimens are plants that are pressed as soon as possible after collection before wilting and shrivelling Most plants may be kept in sealed containers such as plastic bags for up to a day if it is inconvenient to press immediately However some plants show such rapid wilting particularly of the flowers that such delays are best avoided Flowers with a lot of nectar may go mouldy very quickly if excess nectar is not shaken off before pressing

Specimens are pressed flat and dried between sheets of absorbent blotters or semi-absorbent paper such as newspaper Papers with a glossy surface should be avoided because they are not absorbent enough to aid drying The plant should be carefully laid out between the drying sheets as their form at this stage largely determines their ultimate appearance The flowers should be spread out with the petals carefully arranged wilted leaves should be straightened and unnecessary shoots of excessively twiggy shrubs may be cut away

84

Microwave ovens Small numbers of specimens can be dried using a microwave

oven The technique recommended in the literature is to place the specimens between unprinted absorbent paper for example butchers paper not newspaper which is unsuitable because the chemicals present in the ink may cause a fire The specimens should be put in a special press which should be of a microwave-safe material (wood acrylic or polycarbonate sheeting eg plexiglass or perspex NO metal components) If such a press is not available sheets of cardboard can be placed above and below the specimens and then weighted down

Drying time depends on the power of your oven In most cases drying is accomplished by irradiating at maximum power for 1-2 minutes per specimen although it is often a case of trial and error It is best to process no more than 10-12 specimens of average thickness per batch Specimens are usually dried after the moisture that characteristically appears on the glass door has disappeared If the specimen is damp when taken out of the oven allow it to stand before re-radiating as moisture continues to evaporate from the specimen for some time Care must be taken not to irradiate the specimens for too long

It should be noted that microwave treatment damages seeds and the cellular structure of the plants which may reduce the long-term value of the specimens

85

Alternative drying techniquesSilica gelother desiccants amp freeze drying Alternative methods of drying plant specimens have been

used for some time but are mostly restricted to special purpose collections The main alternatives are freeze-drying and drying in a desiccant powder such as desiccant silica gel In general these techniques are used where it is essential to preserve the shape of a delicate plant of organ of the plant such as the flower Freeze-drying has also been used to preserve the chemical composition of a plant as accurately as possible for later study

Disadvantages and special conservation problems of specimens dried in these manners are that they are particularly susceptible to damage The dried parts are fragile lack support and often catch on packing materials They must therefore be packed especially carefully and stored in small boxes or tubes with some appropriate packing material that does not snag and break small projections Acid-free tissue paper is often used Drying in desiccant silica gel crystals or powder can also have the disadvantage that it is difficult to remove all traces of the silica gel after drying

86

Special preservation and processing techniquesWet or spirit collections

Very fleshy or delicate structures including small algae and orchid flowers are best preserved in an air-tight glass or plastic jar with a liquid preservative rather than by drying The type of preservative used should be clearly labelled in the jar Such material is often referred to as a spirit collection or wet collection

Most material can be satisfactorily preserved in 70 ethyl alcohol (or 70 methylated spirit or denatured alcohol) with 30 water Colours will fade quickly in spirit however so it is a good idea to keep comprehensive notes and photographs

87

Small algae Microscopic algae are often collected in a jar and in the

water in which they were found If the algae are to be stored for more than 2-3 days a preservative needs to be used Traditionally this has been the extremely toxic formalin - a small amount can be added to the water to make a 5 final solution and the container labelled This must not be sent through the post or by courier

There are some other equally toxic options for example propylene phenoxytol but none should be sent through the post A safer option is to add sufficient concentrated alcohol or methylated spirits to the water containing the algae to make a final solution of 70 alcohol This treatment dilutes the algae making them difficult to find so if they can be concentrated somehow first (eg by filtering) they can be stored in much less liquid Another option is to fix the algae in formalin (or something similar) first and then prepare a microscope glass slide with a permanent water-soluble mounting medium

88

Mounting Mounting specimens prevents most fragile material from

fragmenting and prevents specimens becoming separated from their labels If the plant collection is a long-term project specimens should be mounted on sheets of archival (permanent) cardboard or paper with archival-quality fixing media These include stitching with cotton thread dental floss nickel-plated copper wire (for heavier specimens) narrow strips of archival paper linen tape or by using an archival adhesive such as methyl cellulose adhesive

One disadvantage of mounting specimens is that it can make parts of the specimen inaccessible for examination so it is essential that this be borne in mind during specimen arrangement and mounting For example easily reversible mounting media should be used specimens should be strapped to the sheet rather than glued all over and the specimen should be carefully arranged before it is attached so that it shows all features

89

Full-size herbarium mounting sheets are usually about 43 cm long x 28 cm wide The plant name and accompanying field notes should be transcribed on a permanent label stuck to one corner of the herbarium sheet (the bottom right-hand corner being the most common) or sometimes annotations may be written directly on the sheet or card

Small pieces of material which may have become separated from the specimen (eg seeds) can be placed in small plastic bags and pinned to the sheet

90

Long-term preservation and storage The long-term preservation of dry plant

specimens is largely dependent on protection from insect attack Specimens collected by Linnaeus in the eighteenth century and by Banks and Solander on the Endeavour voyage in 1788 are still excellently preserved

91

Pests and their control A range of pests attack dried plant material The

most common pests are insects and fungi though rodents and other large animals can cause damage in poor storage conditions Insects eat the material the paper surrounding the material and the adhesives and mounting media

Such insect pests range from psocids (book lice) which attack mainly the softer parts such as flowers and soft fruits to tobacco beetles and carpet beetles which can bore holes through the toughest of specimens Many insects are particularly sensitive to relative humidity levels and do not thrive at levels below 50

92

The most common and acceptable specimen treatments for insect control are Freezing Microwave Poisoning Insect deterrents Fungal pests

93

Storage

Dried and pressed plant specimens can be stored in cardboard or plastic boxes or tied in bundles in light-weight cardboard folders placed in pigeon holes

Alternatively they can be placed in protective plastic jackets and displayed in ring folders which is recommended if they are to be frequently handled such as for a reference collection

94

Filing

Specimens should be filed in a systematic order if a relatively permanent collection is being made The major groups ie ferns and fern allies cycads conifers dicotyledons and monocotyledons are best kept separately or according to some classification scheme such as that given in a flora or handbook

Similarly the genera within each family and the species within each genus may be filed alphabetically or following some such classification

95

Preservation of entire animals

Types of collection specimens of an entire animal For reference collections mammals can be prepared as a variety of specimens The condition of the specimen may determine possible ways to preserve it if for instance decomposition of the skin has loosened the hair of a carcass so much that it can easily be pulled out or removed by rubbing (ldquoslippingrdquo fur) it will be very difficult or impossible to produce a study skin or mounted specimen The most usual types of specimens (based on Nagorsen and Peterson 1980) are 1) entire fluid-preserved animals (for studying anatomy and histology fluid preservation may change the fur colour) 2) study skins with accompanying skulls partial skeletons (some bones remain in the skin) for studying pelage colour hair quality and moulting patterns 3) mounted skins with accompanying partial or entire skeleton (some bones may remain in the skin dependant on the method of preservation) or freeze-dried specimens 4) entire skeletons for instance for studying anatomy geographic variation or for age determination (entire skeletons are poorly represented in collections so Nagorsen and Peterson (1980) recommend preparation of at least one male and one female skeleton per species

96

Preservation of specimens in the field Formalin preservation Preservation in alcohol Preservation by cooling or freezing

97

Formalin preservation After weighing and measuring the animal and attaching an

adequate label very small specimens (up to 100 g) can be fixed whole by submerging them in 10 buffered formalin (tissue - formalin solution ratio of at least 1 12) the body cavity can be filled with formalin solution by injection until it is turgid and firm some formalin may also be injected under the skin into the body cavity larger muscles and organs If hypodermic needles are not available the body cavity can be opened ventrally by making a slit instead allowing the formalin to enter

Keeping the mouth open with a piece of wood or cotton may later allow examination of teeth Then the whole body can be immersed in formalin in the posture in which it is supposed to stay permanently because it will harden The ratio of formalin to carcass must be at least 12 to 1 to assure a good fixation Tissues can be left in buffered neutralized formalin for several months but formalin hardens specimens therefore after fixation longterm storage in alcohol may be better After preservation the carcass should therefore be washed in water and transferred into ethanol for permanent storage

Disadvantages for instance it discolours the fur after a longish immersion softens the bones and prevents further examination for microbiology

98

Preservation in alcohol

After weighing a whole animal can be preserved in a container of alcohol (70-90) Removal of the intestine prior to storage of the animal in alcohol is recommended

99

Preservation by cooling or freezing Removal of the skin with insulating fur

before cooling or freezing may help to cool the carcass down more quickly

Freezing is not recommended if histological examination is planned

100

THANK YOU

70

Fish Lift net

Net is placed down and after a set amount of time it is quickly lifted

Pop-net Similar to a lift net but

floats are attached to a framed net

Operated by a trigger mechanism

Throw net A net attached to a heavy

frame is thrown and every thing inside is netted out Throw net

Pop-net

Lift net

71

Minnow trap

Usually use bait to attract small fish Light is used sometimes as an attractant

72

Fish Electrofishing

Electricity is put into the water Fish are temporarily stunned and usually

swim towards the electricity source Usually non-fatal but may cause some

damage

73

Fish Gill Net

Gill nets resemble tennis nets Fish can not swim completely through the

net and get caught Gill nets are size selective (based on mesh

size) Square Mesh

Bar mesh

Stretch mesh

74

Fish Trammel Net

Three panels two large mesh on the outside and a small mesh on the inside

Fish swim through the outer mesh pushes the small mesh through the other side and becomes entangled

75

Hoop nets (and other similar nets) can have bait or not

Fyke nets have leads to help guide fish to the net

76

Seine Seines are nets that are pulled

through shallow water to catch fish

77

Purse Seine Used to encircle entire schools of fish

Usually involves a spotter plane and a second boat

78

Trotline (longline) A series of baited drop lines

connected to a main line

Can be deployed by tying one end to the bank and tying the other end with a heavy weight

79

Shrimp (or fish) Trawl Net pulled behind

a boat along the bottom Either a beam or

otter boards keep the net open

80

Tagging Individuals Coded Wire Tags

Microwire that has a unique label

Magnetic wand detects the tag

Tag retention should be determined

T-Bar tags Can be individually

numbered External tag

PIT tags (Passive Integrated Transponders) Wand induces the tag to

transmit individual number is displayed

81

Other Tagging Methods

Toe clip Amphibian and reptile Clip of one or more toes

to identify individuals

Bird Band Place a metal band on a

bird leg Generally has

identification information

82

Preserving plant specimens Pressing and drying Long-term

preservation and storage

Alternative drying techniques

Special preservation and processing techniques

Mounting

83

Pressing and drying Techniques for pressing and drying specimens have been

established for many years There are minor variations in recommended methods but they are essentially the same worldwide

The best specimens are plants that are pressed as soon as possible after collection before wilting and shrivelling Most plants may be kept in sealed containers such as plastic bags for up to a day if it is inconvenient to press immediately However some plants show such rapid wilting particularly of the flowers that such delays are best avoided Flowers with a lot of nectar may go mouldy very quickly if excess nectar is not shaken off before pressing

Specimens are pressed flat and dried between sheets of absorbent blotters or semi-absorbent paper such as newspaper Papers with a glossy surface should be avoided because they are not absorbent enough to aid drying The plant should be carefully laid out between the drying sheets as their form at this stage largely determines their ultimate appearance The flowers should be spread out with the petals carefully arranged wilted leaves should be straightened and unnecessary shoots of excessively twiggy shrubs may be cut away

84

Microwave ovens Small numbers of specimens can be dried using a microwave

oven The technique recommended in the literature is to place the specimens between unprinted absorbent paper for example butchers paper not newspaper which is unsuitable because the chemicals present in the ink may cause a fire The specimens should be put in a special press which should be of a microwave-safe material (wood acrylic or polycarbonate sheeting eg plexiglass or perspex NO metal components) If such a press is not available sheets of cardboard can be placed above and below the specimens and then weighted down

Drying time depends on the power of your oven In most cases drying is accomplished by irradiating at maximum power for 1-2 minutes per specimen although it is often a case of trial and error It is best to process no more than 10-12 specimens of average thickness per batch Specimens are usually dried after the moisture that characteristically appears on the glass door has disappeared If the specimen is damp when taken out of the oven allow it to stand before re-radiating as moisture continues to evaporate from the specimen for some time Care must be taken not to irradiate the specimens for too long

It should be noted that microwave treatment damages seeds and the cellular structure of the plants which may reduce the long-term value of the specimens

85

Alternative drying techniquesSilica gelother desiccants amp freeze drying Alternative methods of drying plant specimens have been

used for some time but are mostly restricted to special purpose collections The main alternatives are freeze-drying and drying in a desiccant powder such as desiccant silica gel In general these techniques are used where it is essential to preserve the shape of a delicate plant of organ of the plant such as the flower Freeze-drying has also been used to preserve the chemical composition of a plant as accurately as possible for later study

Disadvantages and special conservation problems of specimens dried in these manners are that they are particularly susceptible to damage The dried parts are fragile lack support and often catch on packing materials They must therefore be packed especially carefully and stored in small boxes or tubes with some appropriate packing material that does not snag and break small projections Acid-free tissue paper is often used Drying in desiccant silica gel crystals or powder can also have the disadvantage that it is difficult to remove all traces of the silica gel after drying

86

Special preservation and processing techniquesWet or spirit collections

Very fleshy or delicate structures including small algae and orchid flowers are best preserved in an air-tight glass or plastic jar with a liquid preservative rather than by drying The type of preservative used should be clearly labelled in the jar Such material is often referred to as a spirit collection or wet collection

Most material can be satisfactorily preserved in 70 ethyl alcohol (or 70 methylated spirit or denatured alcohol) with 30 water Colours will fade quickly in spirit however so it is a good idea to keep comprehensive notes and photographs

87

Small algae Microscopic algae are often collected in a jar and in the

water in which they were found If the algae are to be stored for more than 2-3 days a preservative needs to be used Traditionally this has been the extremely toxic formalin - a small amount can be added to the water to make a 5 final solution and the container labelled This must not be sent through the post or by courier

There are some other equally toxic options for example propylene phenoxytol but none should be sent through the post A safer option is to add sufficient concentrated alcohol or methylated spirits to the water containing the algae to make a final solution of 70 alcohol This treatment dilutes the algae making them difficult to find so if they can be concentrated somehow first (eg by filtering) they can be stored in much less liquid Another option is to fix the algae in formalin (or something similar) first and then prepare a microscope glass slide with a permanent water-soluble mounting medium

88

Mounting Mounting specimens prevents most fragile material from

fragmenting and prevents specimens becoming separated from their labels If the plant collection is a long-term project specimens should be mounted on sheets of archival (permanent) cardboard or paper with archival-quality fixing media These include stitching with cotton thread dental floss nickel-plated copper wire (for heavier specimens) narrow strips of archival paper linen tape or by using an archival adhesive such as methyl cellulose adhesive

One disadvantage of mounting specimens is that it can make parts of the specimen inaccessible for examination so it is essential that this be borne in mind during specimen arrangement and mounting For example easily reversible mounting media should be used specimens should be strapped to the sheet rather than glued all over and the specimen should be carefully arranged before it is attached so that it shows all features

89

Full-size herbarium mounting sheets are usually about 43 cm long x 28 cm wide The plant name and accompanying field notes should be transcribed on a permanent label stuck to one corner of the herbarium sheet (the bottom right-hand corner being the most common) or sometimes annotations may be written directly on the sheet or card

Small pieces of material which may have become separated from the specimen (eg seeds) can be placed in small plastic bags and pinned to the sheet

90

Long-term preservation and storage The long-term preservation of dry plant

specimens is largely dependent on protection from insect attack Specimens collected by Linnaeus in the eighteenth century and by Banks and Solander on the Endeavour voyage in 1788 are still excellently preserved

91

Pests and their control A range of pests attack dried plant material The

most common pests are insects and fungi though rodents and other large animals can cause damage in poor storage conditions Insects eat the material the paper surrounding the material and the adhesives and mounting media

Such insect pests range from psocids (book lice) which attack mainly the softer parts such as flowers and soft fruits to tobacco beetles and carpet beetles which can bore holes through the toughest of specimens Many insects are particularly sensitive to relative humidity levels and do not thrive at levels below 50

92

The most common and acceptable specimen treatments for insect control are Freezing Microwave Poisoning Insect deterrents Fungal pests

93

Storage

Dried and pressed plant specimens can be stored in cardboard or plastic boxes or tied in bundles in light-weight cardboard folders placed in pigeon holes

Alternatively they can be placed in protective plastic jackets and displayed in ring folders which is recommended if they are to be frequently handled such as for a reference collection

94

Filing

Specimens should be filed in a systematic order if a relatively permanent collection is being made The major groups ie ferns and fern allies cycads conifers dicotyledons and monocotyledons are best kept separately or according to some classification scheme such as that given in a flora or handbook

Similarly the genera within each family and the species within each genus may be filed alphabetically or following some such classification

95

Preservation of entire animals

Types of collection specimens of an entire animal For reference collections mammals can be prepared as a variety of specimens The condition of the specimen may determine possible ways to preserve it if for instance decomposition of the skin has loosened the hair of a carcass so much that it can easily be pulled out or removed by rubbing (ldquoslippingrdquo fur) it will be very difficult or impossible to produce a study skin or mounted specimen The most usual types of specimens (based on Nagorsen and Peterson 1980) are 1) entire fluid-preserved animals (for studying anatomy and histology fluid preservation may change the fur colour) 2) study skins with accompanying skulls partial skeletons (some bones remain in the skin) for studying pelage colour hair quality and moulting patterns 3) mounted skins with accompanying partial or entire skeleton (some bones may remain in the skin dependant on the method of preservation) or freeze-dried specimens 4) entire skeletons for instance for studying anatomy geographic variation or for age determination (entire skeletons are poorly represented in collections so Nagorsen and Peterson (1980) recommend preparation of at least one male and one female skeleton per species

96

Preservation of specimens in the field Formalin preservation Preservation in alcohol Preservation by cooling or freezing

97

Formalin preservation After weighing and measuring the animal and attaching an

adequate label very small specimens (up to 100 g) can be fixed whole by submerging them in 10 buffered formalin (tissue - formalin solution ratio of at least 1 12) the body cavity can be filled with formalin solution by injection until it is turgid and firm some formalin may also be injected under the skin into the body cavity larger muscles and organs If hypodermic needles are not available the body cavity can be opened ventrally by making a slit instead allowing the formalin to enter

Keeping the mouth open with a piece of wood or cotton may later allow examination of teeth Then the whole body can be immersed in formalin in the posture in which it is supposed to stay permanently because it will harden The ratio of formalin to carcass must be at least 12 to 1 to assure a good fixation Tissues can be left in buffered neutralized formalin for several months but formalin hardens specimens therefore after fixation longterm storage in alcohol may be better After preservation the carcass should therefore be washed in water and transferred into ethanol for permanent storage

Disadvantages for instance it discolours the fur after a longish immersion softens the bones and prevents further examination for microbiology

98

Preservation in alcohol

After weighing a whole animal can be preserved in a container of alcohol (70-90) Removal of the intestine prior to storage of the animal in alcohol is recommended

99

Preservation by cooling or freezing Removal of the skin with insulating fur

before cooling or freezing may help to cool the carcass down more quickly

Freezing is not recommended if histological examination is planned

100

THANK YOU

71

Minnow trap

Usually use bait to attract small fish Light is used sometimes as an attractant

72

Fish Electrofishing

Electricity is put into the water Fish are temporarily stunned and usually

swim towards the electricity source Usually non-fatal but may cause some

damage

73

Fish Gill Net

Gill nets resemble tennis nets Fish can not swim completely through the

net and get caught Gill nets are size selective (based on mesh

size) Square Mesh

Bar mesh

Stretch mesh

74

Fish Trammel Net

Three panels two large mesh on the outside and a small mesh on the inside

Fish swim through the outer mesh pushes the small mesh through the other side and becomes entangled

75

Hoop nets (and other similar nets) can have bait or not

Fyke nets have leads to help guide fish to the net

76

Seine Seines are nets that are pulled

through shallow water to catch fish

77

Purse Seine Used to encircle entire schools of fish

Usually involves a spotter plane and a second boat

78

Trotline (longline) A series of baited drop lines

connected to a main line

Can be deployed by tying one end to the bank and tying the other end with a heavy weight

79

Shrimp (or fish) Trawl Net pulled behind

a boat along the bottom Either a beam or

otter boards keep the net open

80

Tagging Individuals Coded Wire Tags

Microwire that has a unique label

Magnetic wand detects the tag

Tag retention should be determined

T-Bar tags Can be individually

numbered External tag

PIT tags (Passive Integrated Transponders) Wand induces the tag to

transmit individual number is displayed

81

Other Tagging Methods

Toe clip Amphibian and reptile Clip of one or more toes

to identify individuals

Bird Band Place a metal band on a

bird leg Generally has

identification information

82

Preserving plant specimens Pressing and drying Long-term

preservation and storage

Alternative drying techniques

Special preservation and processing techniques

Mounting

83

Pressing and drying Techniques for pressing and drying specimens have been

established for many years There are minor variations in recommended methods but they are essentially the same worldwide

The best specimens are plants that are pressed as soon as possible after collection before wilting and shrivelling Most plants may be kept in sealed containers such as plastic bags for up to a day if it is inconvenient to press immediately However some plants show such rapid wilting particularly of the flowers that such delays are best avoided Flowers with a lot of nectar may go mouldy very quickly if excess nectar is not shaken off before pressing

Specimens are pressed flat and dried between sheets of absorbent blotters or semi-absorbent paper such as newspaper Papers with a glossy surface should be avoided because they are not absorbent enough to aid drying The plant should be carefully laid out between the drying sheets as their form at this stage largely determines their ultimate appearance The flowers should be spread out with the petals carefully arranged wilted leaves should be straightened and unnecessary shoots of excessively twiggy shrubs may be cut away

84

Microwave ovens Small numbers of specimens can be dried using a microwave

oven The technique recommended in the literature is to place the specimens between unprinted absorbent paper for example butchers paper not newspaper which is unsuitable because the chemicals present in the ink may cause a fire The specimens should be put in a special press which should be of a microwave-safe material (wood acrylic or polycarbonate sheeting eg plexiglass or perspex NO metal components) If such a press is not available sheets of cardboard can be placed above and below the specimens and then weighted down

Drying time depends on the power of your oven In most cases drying is accomplished by irradiating at maximum power for 1-2 minutes per specimen although it is often a case of trial and error It is best to process no more than 10-12 specimens of average thickness per batch Specimens are usually dried after the moisture that characteristically appears on the glass door has disappeared If the specimen is damp when taken out of the oven allow it to stand before re-radiating as moisture continues to evaporate from the specimen for some time Care must be taken not to irradiate the specimens for too long

It should be noted that microwave treatment damages seeds and the cellular structure of the plants which may reduce the long-term value of the specimens

85

Alternative drying techniquesSilica gelother desiccants amp freeze drying Alternative methods of drying plant specimens have been

used for some time but are mostly restricted to special purpose collections The main alternatives are freeze-drying and drying in a desiccant powder such as desiccant silica gel In general these techniques are used where it is essential to preserve the shape of a delicate plant of organ of the plant such as the flower Freeze-drying has also been used to preserve the chemical composition of a plant as accurately as possible for later study

Disadvantages and special conservation problems of specimens dried in these manners are that they are particularly susceptible to damage The dried parts are fragile lack support and often catch on packing materials They must therefore be packed especially carefully and stored in small boxes or tubes with some appropriate packing material that does not snag and break small projections Acid-free tissue paper is often used Drying in desiccant silica gel crystals or powder can also have the disadvantage that it is difficult to remove all traces of the silica gel after drying

86

Special preservation and processing techniquesWet or spirit collections

Very fleshy or delicate structures including small algae and orchid flowers are best preserved in an air-tight glass or plastic jar with a liquid preservative rather than by drying The type of preservative used should be clearly labelled in the jar Such material is often referred to as a spirit collection or wet collection

Most material can be satisfactorily preserved in 70 ethyl alcohol (or 70 methylated spirit or denatured alcohol) with 30 water Colours will fade quickly in spirit however so it is a good idea to keep comprehensive notes and photographs

87

Small algae Microscopic algae are often collected in a jar and in the

water in which they were found If the algae are to be stored for more than 2-3 days a preservative needs to be used Traditionally this has been the extremely toxic formalin - a small amount can be added to the water to make a 5 final solution and the container labelled This must not be sent through the post or by courier

There are some other equally toxic options for example propylene phenoxytol but none should be sent through the post A safer option is to add sufficient concentrated alcohol or methylated spirits to the water containing the algae to make a final solution of 70 alcohol This treatment dilutes the algae making them difficult to find so if they can be concentrated somehow first (eg by filtering) they can be stored in much less liquid Another option is to fix the algae in formalin (or something similar) first and then prepare a microscope glass slide with a permanent water-soluble mounting medium

88

Mounting Mounting specimens prevents most fragile material from

fragmenting and prevents specimens becoming separated from their labels If the plant collection is a long-term project specimens should be mounted on sheets of archival (permanent) cardboard or paper with archival-quality fixing media These include stitching with cotton thread dental floss nickel-plated copper wire (for heavier specimens) narrow strips of archival paper linen tape or by using an archival adhesive such as methyl cellulose adhesive

One disadvantage of mounting specimens is that it can make parts of the specimen inaccessible for examination so it is essential that this be borne in mind during specimen arrangement and mounting For example easily reversible mounting media should be used specimens should be strapped to the sheet rather than glued all over and the specimen should be carefully arranged before it is attached so that it shows all features

89

Full-size herbarium mounting sheets are usually about 43 cm long x 28 cm wide The plant name and accompanying field notes should be transcribed on a permanent label stuck to one corner of the herbarium sheet (the bottom right-hand corner being the most common) or sometimes annotations may be written directly on the sheet or card

Small pieces of material which may have become separated from the specimen (eg seeds) can be placed in small plastic bags and pinned to the sheet

90

Long-term preservation and storage The long-term preservation of dry plant

specimens is largely dependent on protection from insect attack Specimens collected by Linnaeus in the eighteenth century and by Banks and Solander on the Endeavour voyage in 1788 are still excellently preserved

91

Pests and their control A range of pests attack dried plant material The

most common pests are insects and fungi though rodents and other large animals can cause damage in poor storage conditions Insects eat the material the paper surrounding the material and the adhesives and mounting media

Such insect pests range from psocids (book lice) which attack mainly the softer parts such as flowers and soft fruits to tobacco beetles and carpet beetles which can bore holes through the toughest of specimens Many insects are particularly sensitive to relative humidity levels and do not thrive at levels below 50

92

The most common and acceptable specimen treatments for insect control are Freezing Microwave Poisoning Insect deterrents Fungal pests

93

Storage

Dried and pressed plant specimens can be stored in cardboard or plastic boxes or tied in bundles in light-weight cardboard folders placed in pigeon holes

Alternatively they can be placed in protective plastic jackets and displayed in ring folders which is recommended if they are to be frequently handled such as for a reference collection

94

Filing

Specimens should be filed in a systematic order if a relatively permanent collection is being made The major groups ie ferns and fern allies cycads conifers dicotyledons and monocotyledons are best kept separately or according to some classification scheme such as that given in a flora or handbook

Similarly the genera within each family and the species within each genus may be filed alphabetically or following some such classification

95

Preservation of entire animals

Types of collection specimens of an entire animal For reference collections mammals can be prepared as a variety of specimens The condition of the specimen may determine possible ways to preserve it if for instance decomposition of the skin has loosened the hair of a carcass so much that it can easily be pulled out or removed by rubbing (ldquoslippingrdquo fur) it will be very difficult or impossible to produce a study skin or mounted specimen The most usual types of specimens (based on Nagorsen and Peterson 1980) are 1) entire fluid-preserved animals (for studying anatomy and histology fluid preservation may change the fur colour) 2) study skins with accompanying skulls partial skeletons (some bones remain in the skin) for studying pelage colour hair quality and moulting patterns 3) mounted skins with accompanying partial or entire skeleton (some bones may remain in the skin dependant on the method of preservation) or freeze-dried specimens 4) entire skeletons for instance for studying anatomy geographic variation or for age determination (entire skeletons are poorly represented in collections so Nagorsen and Peterson (1980) recommend preparation of at least one male and one female skeleton per species

96

Preservation of specimens in the field Formalin preservation Preservation in alcohol Preservation by cooling or freezing

97

Formalin preservation After weighing and measuring the animal and attaching an

adequate label very small specimens (up to 100 g) can be fixed whole by submerging them in 10 buffered formalin (tissue - formalin solution ratio of at least 1 12) the body cavity can be filled with formalin solution by injection until it is turgid and firm some formalin may also be injected under the skin into the body cavity larger muscles and organs If hypodermic needles are not available the body cavity can be opened ventrally by making a slit instead allowing the formalin to enter

Keeping the mouth open with a piece of wood or cotton may later allow examination of teeth Then the whole body can be immersed in formalin in the posture in which it is supposed to stay permanently because it will harden The ratio of formalin to carcass must be at least 12 to 1 to assure a good fixation Tissues can be left in buffered neutralized formalin for several months but formalin hardens specimens therefore after fixation longterm storage in alcohol may be better After preservation the carcass should therefore be washed in water and transferred into ethanol for permanent storage

Disadvantages for instance it discolours the fur after a longish immersion softens the bones and prevents further examination for microbiology

98

Preservation in alcohol

After weighing a whole animal can be preserved in a container of alcohol (70-90) Removal of the intestine prior to storage of the animal in alcohol is recommended

99

Preservation by cooling or freezing Removal of the skin with insulating fur

before cooling or freezing may help to cool the carcass down more quickly

Freezing is not recommended if histological examination is planned

100

THANK YOU

72

Fish Electrofishing

Electricity is put into the water Fish are temporarily stunned and usually

swim towards the electricity source Usually non-fatal but may cause some

damage

73

Fish Gill Net

Gill nets resemble tennis nets Fish can not swim completely through the

net and get caught Gill nets are size selective (based on mesh

size) Square Mesh

Bar mesh

Stretch mesh

74

Fish Trammel Net

Three panels two large mesh on the outside and a small mesh on the inside

Fish swim through the outer mesh pushes the small mesh through the other side and becomes entangled

75

Hoop nets (and other similar nets) can have bait or not

Fyke nets have leads to help guide fish to the net

76

Seine Seines are nets that are pulled

through shallow water to catch fish

77

Purse Seine Used to encircle entire schools of fish

Usually involves a spotter plane and a second boat

78

Trotline (longline) A series of baited drop lines

connected to a main line

Can be deployed by tying one end to the bank and tying the other end with a heavy weight

79

Shrimp (or fish) Trawl Net pulled behind

a boat along the bottom Either a beam or

otter boards keep the net open

80

Tagging Individuals Coded Wire Tags

Microwire that has a unique label

Magnetic wand detects the tag

Tag retention should be determined

T-Bar tags Can be individually

numbered External tag

PIT tags (Passive Integrated Transponders) Wand induces the tag to

transmit individual number is displayed

81

Other Tagging Methods

Toe clip Amphibian and reptile Clip of one or more toes

to identify individuals

Bird Band Place a metal band on a

bird leg Generally has

identification information

82

Preserving plant specimens Pressing and drying Long-term

preservation and storage

Alternative drying techniques

Special preservation and processing techniques

Mounting

83

Pressing and drying Techniques for pressing and drying specimens have been

established for many years There are minor variations in recommended methods but they are essentially the same worldwide

The best specimens are plants that are pressed as soon as possible after collection before wilting and shrivelling Most plants may be kept in sealed containers such as plastic bags for up to a day if it is inconvenient to press immediately However some plants show such rapid wilting particularly of the flowers that such delays are best avoided Flowers with a lot of nectar may go mouldy very quickly if excess nectar is not shaken off before pressing

Specimens are pressed flat and dried between sheets of absorbent blotters or semi-absorbent paper such as newspaper Papers with a glossy surface should be avoided because they are not absorbent enough to aid drying The plant should be carefully laid out between the drying sheets as their form at this stage largely determines their ultimate appearance The flowers should be spread out with the petals carefully arranged wilted leaves should be straightened and unnecessary shoots of excessively twiggy shrubs may be cut away

84

Microwave ovens Small numbers of specimens can be dried using a microwave

oven The technique recommended in the literature is to place the specimens between unprinted absorbent paper for example butchers paper not newspaper which is unsuitable because the chemicals present in the ink may cause a fire The specimens should be put in a special press which should be of a microwave-safe material (wood acrylic or polycarbonate sheeting eg plexiglass or perspex NO metal components) If such a press is not available sheets of cardboard can be placed above and below the specimens and then weighted down

Drying time depends on the power of your oven In most cases drying is accomplished by irradiating at maximum power for 1-2 minutes per specimen although it is often a case of trial and error It is best to process no more than 10-12 specimens of average thickness per batch Specimens are usually dried after the moisture that characteristically appears on the glass door has disappeared If the specimen is damp when taken out of the oven allow it to stand before re-radiating as moisture continues to evaporate from the specimen for some time Care must be taken not to irradiate the specimens for too long

It should be noted that microwave treatment damages seeds and the cellular structure of the plants which may reduce the long-term value of the specimens

85

Alternative drying techniquesSilica gelother desiccants amp freeze drying Alternative methods of drying plant specimens have been

used for some time but are mostly restricted to special purpose collections The main alternatives are freeze-drying and drying in a desiccant powder such as desiccant silica gel In general these techniques are used where it is essential to preserve the shape of a delicate plant of organ of the plant such as the flower Freeze-drying has also been used to preserve the chemical composition of a plant as accurately as possible for later study

Disadvantages and special conservation problems of specimens dried in these manners are that they are particularly susceptible to damage The dried parts are fragile lack support and often catch on packing materials They must therefore be packed especially carefully and stored in small boxes or tubes with some appropriate packing material that does not snag and break small projections Acid-free tissue paper is often used Drying in desiccant silica gel crystals or powder can also have the disadvantage that it is difficult to remove all traces of the silica gel after drying

86

Special preservation and processing techniquesWet or spirit collections

Very fleshy or delicate structures including small algae and orchid flowers are best preserved in an air-tight glass or plastic jar with a liquid preservative rather than by drying The type of preservative used should be clearly labelled in the jar Such material is often referred to as a spirit collection or wet collection

Most material can be satisfactorily preserved in 70 ethyl alcohol (or 70 methylated spirit or denatured alcohol) with 30 water Colours will fade quickly in spirit however so it is a good idea to keep comprehensive notes and photographs

87

Small algae Microscopic algae are often collected in a jar and in the

water in which they were found If the algae are to be stored for more than 2-3 days a preservative needs to be used Traditionally this has been the extremely toxic formalin - a small amount can be added to the water to make a 5 final solution and the container labelled This must not be sent through the post or by courier

There are some other equally toxic options for example propylene phenoxytol but none should be sent through the post A safer option is to add sufficient concentrated alcohol or methylated spirits to the water containing the algae to make a final solution of 70 alcohol This treatment dilutes the algae making them difficult to find so if they can be concentrated somehow first (eg by filtering) they can be stored in much less liquid Another option is to fix the algae in formalin (or something similar) first and then prepare a microscope glass slide with a permanent water-soluble mounting medium

88

Mounting Mounting specimens prevents most fragile material from

fragmenting and prevents specimens becoming separated from their labels If the plant collection is a long-term project specimens should be mounted on sheets of archival (permanent) cardboard or paper with archival-quality fixing media These include stitching with cotton thread dental floss nickel-plated copper wire (for heavier specimens) narrow strips of archival paper linen tape or by using an archival adhesive such as methyl cellulose adhesive

One disadvantage of mounting specimens is that it can make parts of the specimen inaccessible for examination so it is essential that this be borne in mind during specimen arrangement and mounting For example easily reversible mounting media should be used specimens should be strapped to the sheet rather than glued all over and the specimen should be carefully arranged before it is attached so that it shows all features

89

Full-size herbarium mounting sheets are usually about 43 cm long x 28 cm wide The plant name and accompanying field notes should be transcribed on a permanent label stuck to one corner of the herbarium sheet (the bottom right-hand corner being the most common) or sometimes annotations may be written directly on the sheet or card

Small pieces of material which may have become separated from the specimen (eg seeds) can be placed in small plastic bags and pinned to the sheet

90

Long-term preservation and storage The long-term preservation of dry plant

specimens is largely dependent on protection from insect attack Specimens collected by Linnaeus in the eighteenth century and by Banks and Solander on the Endeavour voyage in 1788 are still excellently preserved

91

Pests and their control A range of pests attack dried plant material The

most common pests are insects and fungi though rodents and other large animals can cause damage in poor storage conditions Insects eat the material the paper surrounding the material and the adhesives and mounting media

Such insect pests range from psocids (book lice) which attack mainly the softer parts such as flowers and soft fruits to tobacco beetles and carpet beetles which can bore holes through the toughest of specimens Many insects are particularly sensitive to relative humidity levels and do not thrive at levels below 50

92

The most common and acceptable specimen treatments for insect control are Freezing Microwave Poisoning Insect deterrents Fungal pests

93

Storage

Dried and pressed plant specimens can be stored in cardboard or plastic boxes or tied in bundles in light-weight cardboard folders placed in pigeon holes

Alternatively they can be placed in protective plastic jackets and displayed in ring folders which is recommended if they are to be frequently handled such as for a reference collection

94

Filing

Specimens should be filed in a systematic order if a relatively permanent collection is being made The major groups ie ferns and fern allies cycads conifers dicotyledons and monocotyledons are best kept separately or according to some classification scheme such as that given in a flora or handbook

Similarly the genera within each family and the species within each genus may be filed alphabetically or following some such classification

95

Preservation of entire animals

Types of collection specimens of an entire animal For reference collections mammals can be prepared as a variety of specimens The condition of the specimen may determine possible ways to preserve it if for instance decomposition of the skin has loosened the hair of a carcass so much that it can easily be pulled out or removed by rubbing (ldquoslippingrdquo fur) it will be very difficult or impossible to produce a study skin or mounted specimen The most usual types of specimens (based on Nagorsen and Peterson 1980) are 1) entire fluid-preserved animals (for studying anatomy and histology fluid preservation may change the fur colour) 2) study skins with accompanying skulls partial skeletons (some bones remain in the skin) for studying pelage colour hair quality and moulting patterns 3) mounted skins with accompanying partial or entire skeleton (some bones may remain in the skin dependant on the method of preservation) or freeze-dried specimens 4) entire skeletons for instance for studying anatomy geographic variation or for age determination (entire skeletons are poorly represented in collections so Nagorsen and Peterson (1980) recommend preparation of at least one male and one female skeleton per species

96

Preservation of specimens in the field Formalin preservation Preservation in alcohol Preservation by cooling or freezing

97

Formalin preservation After weighing and measuring the animal and attaching an

adequate label very small specimens (up to 100 g) can be fixed whole by submerging them in 10 buffered formalin (tissue - formalin solution ratio of at least 1 12) the body cavity can be filled with formalin solution by injection until it is turgid and firm some formalin may also be injected under the skin into the body cavity larger muscles and organs If hypodermic needles are not available the body cavity can be opened ventrally by making a slit instead allowing the formalin to enter

Keeping the mouth open with a piece of wood or cotton may later allow examination of teeth Then the whole body can be immersed in formalin in the posture in which it is supposed to stay permanently because it will harden The ratio of formalin to carcass must be at least 12 to 1 to assure a good fixation Tissues can be left in buffered neutralized formalin for several months but formalin hardens specimens therefore after fixation longterm storage in alcohol may be better After preservation the carcass should therefore be washed in water and transferred into ethanol for permanent storage

Disadvantages for instance it discolours the fur after a longish immersion softens the bones and prevents further examination for microbiology

98

Preservation in alcohol

After weighing a whole animal can be preserved in a container of alcohol (70-90) Removal of the intestine prior to storage of the animal in alcohol is recommended

99

Preservation by cooling or freezing Removal of the skin with insulating fur

before cooling or freezing may help to cool the carcass down more quickly

Freezing is not recommended if histological examination is planned

100

THANK YOU

73

Fish Gill Net

Gill nets resemble tennis nets Fish can not swim completely through the

net and get caught Gill nets are size selective (based on mesh

size) Square Mesh

Bar mesh

Stretch mesh

74

Fish Trammel Net

Three panels two large mesh on the outside and a small mesh on the inside

Fish swim through the outer mesh pushes the small mesh through the other side and becomes entangled

75

Hoop nets (and other similar nets) can have bait or not

Fyke nets have leads to help guide fish to the net

76

Seine Seines are nets that are pulled

through shallow water to catch fish

77

Purse Seine Used to encircle entire schools of fish

Usually involves a spotter plane and a second boat

78

Trotline (longline) A series of baited drop lines

connected to a main line

Can be deployed by tying one end to the bank and tying the other end with a heavy weight

79

Shrimp (or fish) Trawl Net pulled behind

a boat along the bottom Either a beam or

otter boards keep the net open

80

Tagging Individuals Coded Wire Tags

Microwire that has a unique label

Magnetic wand detects the tag

Tag retention should be determined

T-Bar tags Can be individually

numbered External tag

PIT tags (Passive Integrated Transponders) Wand induces the tag to

transmit individual number is displayed

81

Other Tagging Methods

Toe clip Amphibian and reptile Clip of one or more toes

to identify individuals

Bird Band Place a metal band on a

bird leg Generally has

identification information

82

Preserving plant specimens Pressing and drying Long-term

preservation and storage

Alternative drying techniques

Special preservation and processing techniques

Mounting

83

Pressing and drying Techniques for pressing and drying specimens have been

established for many years There are minor variations in recommended methods but they are essentially the same worldwide

The best specimens are plants that are pressed as soon as possible after collection before wilting and shrivelling Most plants may be kept in sealed containers such as plastic bags for up to a day if it is inconvenient to press immediately However some plants show such rapid wilting particularly of the flowers that such delays are best avoided Flowers with a lot of nectar may go mouldy very quickly if excess nectar is not shaken off before pressing

Specimens are pressed flat and dried between sheets of absorbent blotters or semi-absorbent paper such as newspaper Papers with a glossy surface should be avoided because they are not absorbent enough to aid drying The plant should be carefully laid out between the drying sheets as their form at this stage largely determines their ultimate appearance The flowers should be spread out with the petals carefully arranged wilted leaves should be straightened and unnecessary shoots of excessively twiggy shrubs may be cut away

84

Microwave ovens Small numbers of specimens can be dried using a microwave

oven The technique recommended in the literature is to place the specimens between unprinted absorbent paper for example butchers paper not newspaper which is unsuitable because the chemicals present in the ink may cause a fire The specimens should be put in a special press which should be of a microwave-safe material (wood acrylic or polycarbonate sheeting eg plexiglass or perspex NO metal components) If such a press is not available sheets of cardboard can be placed above and below the specimens and then weighted down

Drying time depends on the power of your oven In most cases drying is accomplished by irradiating at maximum power for 1-2 minutes per specimen although it is often a case of trial and error It is best to process no more than 10-12 specimens of average thickness per batch Specimens are usually dried after the moisture that characteristically appears on the glass door has disappeared If the specimen is damp when taken out of the oven allow it to stand before re-radiating as moisture continues to evaporate from the specimen for some time Care must be taken not to irradiate the specimens for too long

It should be noted that microwave treatment damages seeds and the cellular structure of the plants which may reduce the long-term value of the specimens

85

Alternative drying techniquesSilica gelother desiccants amp freeze drying Alternative methods of drying plant specimens have been

used for some time but are mostly restricted to special purpose collections The main alternatives are freeze-drying and drying in a desiccant powder such as desiccant silica gel In general these techniques are used where it is essential to preserve the shape of a delicate plant of organ of the plant such as the flower Freeze-drying has also been used to preserve the chemical composition of a plant as accurately as possible for later study

Disadvantages and special conservation problems of specimens dried in these manners are that they are particularly susceptible to damage The dried parts are fragile lack support and often catch on packing materials They must therefore be packed especially carefully and stored in small boxes or tubes with some appropriate packing material that does not snag and break small projections Acid-free tissue paper is often used Drying in desiccant silica gel crystals or powder can also have the disadvantage that it is difficult to remove all traces of the silica gel after drying

86

Special preservation and processing techniquesWet or spirit collections

Very fleshy or delicate structures including small algae and orchid flowers are best preserved in an air-tight glass or plastic jar with a liquid preservative rather than by drying The type of preservative used should be clearly labelled in the jar Such material is often referred to as a spirit collection or wet collection

Most material can be satisfactorily preserved in 70 ethyl alcohol (or 70 methylated spirit or denatured alcohol) with 30 water Colours will fade quickly in spirit however so it is a good idea to keep comprehensive notes and photographs

87

Small algae Microscopic algae are often collected in a jar and in the

water in which they were found If the algae are to be stored for more than 2-3 days a preservative needs to be used Traditionally this has been the extremely toxic formalin - a small amount can be added to the water to make a 5 final solution and the container labelled This must not be sent through the post or by courier

There are some other equally toxic options for example propylene phenoxytol but none should be sent through the post A safer option is to add sufficient concentrated alcohol or methylated spirits to the water containing the algae to make a final solution of 70 alcohol This treatment dilutes the algae making them difficult to find so if they can be concentrated somehow first (eg by filtering) they can be stored in much less liquid Another option is to fix the algae in formalin (or something similar) first and then prepare a microscope glass slide with a permanent water-soluble mounting medium

88

Mounting Mounting specimens prevents most fragile material from

fragmenting and prevents specimens becoming separated from their labels If the plant collection is a long-term project specimens should be mounted on sheets of archival (permanent) cardboard or paper with archival-quality fixing media These include stitching with cotton thread dental floss nickel-plated copper wire (for heavier specimens) narrow strips of archival paper linen tape or by using an archival adhesive such as methyl cellulose adhesive

One disadvantage of mounting specimens is that it can make parts of the specimen inaccessible for examination so it is essential that this be borne in mind during specimen arrangement and mounting For example easily reversible mounting media should be used specimens should be strapped to the sheet rather than glued all over and the specimen should be carefully arranged before it is attached so that it shows all features

89

Full-size herbarium mounting sheets are usually about 43 cm long x 28 cm wide The plant name and accompanying field notes should be transcribed on a permanent label stuck to one corner of the herbarium sheet (the bottom right-hand corner being the most common) or sometimes annotations may be written directly on the sheet or card

Small pieces of material which may have become separated from the specimen (eg seeds) can be placed in small plastic bags and pinned to the sheet

90

Long-term preservation and storage The long-term preservation of dry plant

specimens is largely dependent on protection from insect attack Specimens collected by Linnaeus in the eighteenth century and by Banks and Solander on the Endeavour voyage in 1788 are still excellently preserved

91

Pests and their control A range of pests attack dried plant material The

most common pests are insects and fungi though rodents and other large animals can cause damage in poor storage conditions Insects eat the material the paper surrounding the material and the adhesives and mounting media

Such insect pests range from psocids (book lice) which attack mainly the softer parts such as flowers and soft fruits to tobacco beetles and carpet beetles which can bore holes through the toughest of specimens Many insects are particularly sensitive to relative humidity levels and do not thrive at levels below 50

92

The most common and acceptable specimen treatments for insect control are Freezing Microwave Poisoning Insect deterrents Fungal pests

93

Storage

Dried and pressed plant specimens can be stored in cardboard or plastic boxes or tied in bundles in light-weight cardboard folders placed in pigeon holes

Alternatively they can be placed in protective plastic jackets and displayed in ring folders which is recommended if they are to be frequently handled such as for a reference collection

94

Filing

Specimens should be filed in a systematic order if a relatively permanent collection is being made The major groups ie ferns and fern allies cycads conifers dicotyledons and monocotyledons are best kept separately or according to some classification scheme such as that given in a flora or handbook

Similarly the genera within each family and the species within each genus may be filed alphabetically or following some such classification

95

Preservation of entire animals

Types of collection specimens of an entire animal For reference collections mammals can be prepared as a variety of specimens The condition of the specimen may determine possible ways to preserve it if for instance decomposition of the skin has loosened the hair of a carcass so much that it can easily be pulled out or removed by rubbing (ldquoslippingrdquo fur) it will be very difficult or impossible to produce a study skin or mounted specimen The most usual types of specimens (based on Nagorsen and Peterson 1980) are 1) entire fluid-preserved animals (for studying anatomy and histology fluid preservation may change the fur colour) 2) study skins with accompanying skulls partial skeletons (some bones remain in the skin) for studying pelage colour hair quality and moulting patterns 3) mounted skins with accompanying partial or entire skeleton (some bones may remain in the skin dependant on the method of preservation) or freeze-dried specimens 4) entire skeletons for instance for studying anatomy geographic variation or for age determination (entire skeletons are poorly represented in collections so Nagorsen and Peterson (1980) recommend preparation of at least one male and one female skeleton per species

96

Preservation of specimens in the field Formalin preservation Preservation in alcohol Preservation by cooling or freezing

97

Formalin preservation After weighing and measuring the animal and attaching an

adequate label very small specimens (up to 100 g) can be fixed whole by submerging them in 10 buffered formalin (tissue - formalin solution ratio of at least 1 12) the body cavity can be filled with formalin solution by injection until it is turgid and firm some formalin may also be injected under the skin into the body cavity larger muscles and organs If hypodermic needles are not available the body cavity can be opened ventrally by making a slit instead allowing the formalin to enter

Keeping the mouth open with a piece of wood or cotton may later allow examination of teeth Then the whole body can be immersed in formalin in the posture in which it is supposed to stay permanently because it will harden The ratio of formalin to carcass must be at least 12 to 1 to assure a good fixation Tissues can be left in buffered neutralized formalin for several months but formalin hardens specimens therefore after fixation longterm storage in alcohol may be better After preservation the carcass should therefore be washed in water and transferred into ethanol for permanent storage

Disadvantages for instance it discolours the fur after a longish immersion softens the bones and prevents further examination for microbiology

98

Preservation in alcohol

After weighing a whole animal can be preserved in a container of alcohol (70-90) Removal of the intestine prior to storage of the animal in alcohol is recommended

99

Preservation by cooling or freezing Removal of the skin with insulating fur

before cooling or freezing may help to cool the carcass down more quickly

Freezing is not recommended if histological examination is planned

100

THANK YOU

74

Fish Trammel Net

Three panels two large mesh on the outside and a small mesh on the inside

Fish swim through the outer mesh pushes the small mesh through the other side and becomes entangled

75

Hoop nets (and other similar nets) can have bait or not

Fyke nets have leads to help guide fish to the net

76

Seine Seines are nets that are pulled

through shallow water to catch fish

77

Purse Seine Used to encircle entire schools of fish

Usually involves a spotter plane and a second boat

78

Trotline (longline) A series of baited drop lines

connected to a main line

Can be deployed by tying one end to the bank and tying the other end with a heavy weight

79

Shrimp (or fish) Trawl Net pulled behind

a boat along the bottom Either a beam or

otter boards keep the net open

80

Tagging Individuals Coded Wire Tags

Microwire that has a unique label

Magnetic wand detects the tag

Tag retention should be determined

T-Bar tags Can be individually

numbered External tag

PIT tags (Passive Integrated Transponders) Wand induces the tag to

transmit individual number is displayed

81

Other Tagging Methods

Toe clip Amphibian and reptile Clip of one or more toes

to identify individuals

Bird Band Place a metal band on a

bird leg Generally has

identification information

82

Preserving plant specimens Pressing and drying Long-term

preservation and storage

Alternative drying techniques

Special preservation and processing techniques

Mounting

83

Pressing and drying Techniques for pressing and drying specimens have been

established for many years There are minor variations in recommended methods but they are essentially the same worldwide

The best specimens are plants that are pressed as soon as possible after collection before wilting and shrivelling Most plants may be kept in sealed containers such as plastic bags for up to a day if it is inconvenient to press immediately However some plants show such rapid wilting particularly of the flowers that such delays are best avoided Flowers with a lot of nectar may go mouldy very quickly if excess nectar is not shaken off before pressing

Specimens are pressed flat and dried between sheets of absorbent blotters or semi-absorbent paper such as newspaper Papers with a glossy surface should be avoided because they are not absorbent enough to aid drying The plant should be carefully laid out between the drying sheets as their form at this stage largely determines their ultimate appearance The flowers should be spread out with the petals carefully arranged wilted leaves should be straightened and unnecessary shoots of excessively twiggy shrubs may be cut away

84

Microwave ovens Small numbers of specimens can be dried using a microwave

oven The technique recommended in the literature is to place the specimens between unprinted absorbent paper for example butchers paper not newspaper which is unsuitable because the chemicals present in the ink may cause a fire The specimens should be put in a special press which should be of a microwave-safe material (wood acrylic or polycarbonate sheeting eg plexiglass or perspex NO metal components) If such a press is not available sheets of cardboard can be placed above and below the specimens and then weighted down

Drying time depends on the power of your oven In most cases drying is accomplished by irradiating at maximum power for 1-2 minutes per specimen although it is often a case of trial and error It is best to process no more than 10-12 specimens of average thickness per batch Specimens are usually dried after the moisture that characteristically appears on the glass door has disappeared If the specimen is damp when taken out of the oven allow it to stand before re-radiating as moisture continues to evaporate from the specimen for some time Care must be taken not to irradiate the specimens for too long

It should be noted that microwave treatment damages seeds and the cellular structure of the plants which may reduce the long-term value of the specimens

85

Alternative drying techniquesSilica gelother desiccants amp freeze drying Alternative methods of drying plant specimens have been

used for some time but are mostly restricted to special purpose collections The main alternatives are freeze-drying and drying in a desiccant powder such as desiccant silica gel In general these techniques are used where it is essential to preserve the shape of a delicate plant of organ of the plant such as the flower Freeze-drying has also been used to preserve the chemical composition of a plant as accurately as possible for later study

Disadvantages and special conservation problems of specimens dried in these manners are that they are particularly susceptible to damage The dried parts are fragile lack support and often catch on packing materials They must therefore be packed especially carefully and stored in small boxes or tubes with some appropriate packing material that does not snag and break small projections Acid-free tissue paper is often used Drying in desiccant silica gel crystals or powder can also have the disadvantage that it is difficult to remove all traces of the silica gel after drying

86

Special preservation and processing techniquesWet or spirit collections

Very fleshy or delicate structures including small algae and orchid flowers are best preserved in an air-tight glass or plastic jar with a liquid preservative rather than by drying The type of preservative used should be clearly labelled in the jar Such material is often referred to as a spirit collection or wet collection

Most material can be satisfactorily preserved in 70 ethyl alcohol (or 70 methylated spirit or denatured alcohol) with 30 water Colours will fade quickly in spirit however so it is a good idea to keep comprehensive notes and photographs

87

Small algae Microscopic algae are often collected in a jar and in the

water in which they were found If the algae are to be stored for more than 2-3 days a preservative needs to be used Traditionally this has been the extremely toxic formalin - a small amount can be added to the water to make a 5 final solution and the container labelled This must not be sent through the post or by courier

There are some other equally toxic options for example propylene phenoxytol but none should be sent through the post A safer option is to add sufficient concentrated alcohol or methylated spirits to the water containing the algae to make a final solution of 70 alcohol This treatment dilutes the algae making them difficult to find so if they can be concentrated somehow first (eg by filtering) they can be stored in much less liquid Another option is to fix the algae in formalin (or something similar) first and then prepare a microscope glass slide with a permanent water-soluble mounting medium

88

Mounting Mounting specimens prevents most fragile material from

fragmenting and prevents specimens becoming separated from their labels If the plant collection is a long-term project specimens should be mounted on sheets of archival (permanent) cardboard or paper with archival-quality fixing media These include stitching with cotton thread dental floss nickel-plated copper wire (for heavier specimens) narrow strips of archival paper linen tape or by using an archival adhesive such as methyl cellulose adhesive

One disadvantage of mounting specimens is that it can make parts of the specimen inaccessible for examination so it is essential that this be borne in mind during specimen arrangement and mounting For example easily reversible mounting media should be used specimens should be strapped to the sheet rather than glued all over and the specimen should be carefully arranged before it is attached so that it shows all features

89

Full-size herbarium mounting sheets are usually about 43 cm long x 28 cm wide The plant name and accompanying field notes should be transcribed on a permanent label stuck to one corner of the herbarium sheet (the bottom right-hand corner being the most common) or sometimes annotations may be written directly on the sheet or card

Small pieces of material which may have become separated from the specimen (eg seeds) can be placed in small plastic bags and pinned to the sheet

90

Long-term preservation and storage The long-term preservation of dry plant

specimens is largely dependent on protection from insect attack Specimens collected by Linnaeus in the eighteenth century and by Banks and Solander on the Endeavour voyage in 1788 are still excellently preserved

91

Pests and their control A range of pests attack dried plant material The

most common pests are insects and fungi though rodents and other large animals can cause damage in poor storage conditions Insects eat the material the paper surrounding the material and the adhesives and mounting media

Such insect pests range from psocids (book lice) which attack mainly the softer parts such as flowers and soft fruits to tobacco beetles and carpet beetles which can bore holes through the toughest of specimens Many insects are particularly sensitive to relative humidity levels and do not thrive at levels below 50

92

The most common and acceptable specimen treatments for insect control are Freezing Microwave Poisoning Insect deterrents Fungal pests

93

Storage

Dried and pressed plant specimens can be stored in cardboard or plastic boxes or tied in bundles in light-weight cardboard folders placed in pigeon holes

Alternatively they can be placed in protective plastic jackets and displayed in ring folders which is recommended if they are to be frequently handled such as for a reference collection

94

Filing

Specimens should be filed in a systematic order if a relatively permanent collection is being made The major groups ie ferns and fern allies cycads conifers dicotyledons and monocotyledons are best kept separately or according to some classification scheme such as that given in a flora or handbook

Similarly the genera within each family and the species within each genus may be filed alphabetically or following some such classification

95

Preservation of entire animals

Types of collection specimens of an entire animal For reference collections mammals can be prepared as a variety of specimens The condition of the specimen may determine possible ways to preserve it if for instance decomposition of the skin has loosened the hair of a carcass so much that it can easily be pulled out or removed by rubbing (ldquoslippingrdquo fur) it will be very difficult or impossible to produce a study skin or mounted specimen The most usual types of specimens (based on Nagorsen and Peterson 1980) are 1) entire fluid-preserved animals (for studying anatomy and histology fluid preservation may change the fur colour) 2) study skins with accompanying skulls partial skeletons (some bones remain in the skin) for studying pelage colour hair quality and moulting patterns 3) mounted skins with accompanying partial or entire skeleton (some bones may remain in the skin dependant on the method of preservation) or freeze-dried specimens 4) entire skeletons for instance for studying anatomy geographic variation or for age determination (entire skeletons are poorly represented in collections so Nagorsen and Peterson (1980) recommend preparation of at least one male and one female skeleton per species

96

Preservation of specimens in the field Formalin preservation Preservation in alcohol Preservation by cooling or freezing

97

Formalin preservation After weighing and measuring the animal and attaching an

adequate label very small specimens (up to 100 g) can be fixed whole by submerging them in 10 buffered formalin (tissue - formalin solution ratio of at least 1 12) the body cavity can be filled with formalin solution by injection until it is turgid and firm some formalin may also be injected under the skin into the body cavity larger muscles and organs If hypodermic needles are not available the body cavity can be opened ventrally by making a slit instead allowing the formalin to enter

Keeping the mouth open with a piece of wood or cotton may later allow examination of teeth Then the whole body can be immersed in formalin in the posture in which it is supposed to stay permanently because it will harden The ratio of formalin to carcass must be at least 12 to 1 to assure a good fixation Tissues can be left in buffered neutralized formalin for several months but formalin hardens specimens therefore after fixation longterm storage in alcohol may be better After preservation the carcass should therefore be washed in water and transferred into ethanol for permanent storage

Disadvantages for instance it discolours the fur after a longish immersion softens the bones and prevents further examination for microbiology

98

Preservation in alcohol

After weighing a whole animal can be preserved in a container of alcohol (70-90) Removal of the intestine prior to storage of the animal in alcohol is recommended

99

Preservation by cooling or freezing Removal of the skin with insulating fur

before cooling or freezing may help to cool the carcass down more quickly

Freezing is not recommended if histological examination is planned

100

THANK YOU

75

Hoop nets (and other similar nets) can have bait or not

Fyke nets have leads to help guide fish to the net

76

Seine Seines are nets that are pulled

through shallow water to catch fish

77

Purse Seine Used to encircle entire schools of fish

Usually involves a spotter plane and a second boat

78

Trotline (longline) A series of baited drop lines

connected to a main line

Can be deployed by tying one end to the bank and tying the other end with a heavy weight

79

Shrimp (or fish) Trawl Net pulled behind

a boat along the bottom Either a beam or

otter boards keep the net open

80

Tagging Individuals Coded Wire Tags

Microwire that has a unique label

Magnetic wand detects the tag

Tag retention should be determined

T-Bar tags Can be individually

numbered External tag

PIT tags (Passive Integrated Transponders) Wand induces the tag to

transmit individual number is displayed

81

Other Tagging Methods

Toe clip Amphibian and reptile Clip of one or more toes

to identify individuals

Bird Band Place a metal band on a

bird leg Generally has

identification information

82

Preserving plant specimens Pressing and drying Long-term

preservation and storage

Alternative drying techniques

Special preservation and processing techniques

Mounting

83

Pressing and drying Techniques for pressing and drying specimens have been

established for many years There are minor variations in recommended methods but they are essentially the same worldwide

The best specimens are plants that are pressed as soon as possible after collection before wilting and shrivelling Most plants may be kept in sealed containers such as plastic bags for up to a day if it is inconvenient to press immediately However some plants show such rapid wilting particularly of the flowers that such delays are best avoided Flowers with a lot of nectar may go mouldy very quickly if excess nectar is not shaken off before pressing

Specimens are pressed flat and dried between sheets of absorbent blotters or semi-absorbent paper such as newspaper Papers with a glossy surface should be avoided because they are not absorbent enough to aid drying The plant should be carefully laid out between the drying sheets as their form at this stage largely determines their ultimate appearance The flowers should be spread out with the petals carefully arranged wilted leaves should be straightened and unnecessary shoots of excessively twiggy shrubs may be cut away

84

Microwave ovens Small numbers of specimens can be dried using a microwave

oven The technique recommended in the literature is to place the specimens between unprinted absorbent paper for example butchers paper not newspaper which is unsuitable because the chemicals present in the ink may cause a fire The specimens should be put in a special press which should be of a microwave-safe material (wood acrylic or polycarbonate sheeting eg plexiglass or perspex NO metal components) If such a press is not available sheets of cardboard can be placed above and below the specimens and then weighted down

Drying time depends on the power of your oven In most cases drying is accomplished by irradiating at maximum power for 1-2 minutes per specimen although it is often a case of trial and error It is best to process no more than 10-12 specimens of average thickness per batch Specimens are usually dried after the moisture that characteristically appears on the glass door has disappeared If the specimen is damp when taken out of the oven allow it to stand before re-radiating as moisture continues to evaporate from the specimen for some time Care must be taken not to irradiate the specimens for too long

It should be noted that microwave treatment damages seeds and the cellular structure of the plants which may reduce the long-term value of the specimens

85

Alternative drying techniquesSilica gelother desiccants amp freeze drying Alternative methods of drying plant specimens have been

used for some time but are mostly restricted to special purpose collections The main alternatives are freeze-drying and drying in a desiccant powder such as desiccant silica gel In general these techniques are used where it is essential to preserve the shape of a delicate plant of organ of the plant such as the flower Freeze-drying has also been used to preserve the chemical composition of a plant as accurately as possible for later study

Disadvantages and special conservation problems of specimens dried in these manners are that they are particularly susceptible to damage The dried parts are fragile lack support and often catch on packing materials They must therefore be packed especially carefully and stored in small boxes or tubes with some appropriate packing material that does not snag and break small projections Acid-free tissue paper is often used Drying in desiccant silica gel crystals or powder can also have the disadvantage that it is difficult to remove all traces of the silica gel after drying

86

Special preservation and processing techniquesWet or spirit collections

Very fleshy or delicate structures including small algae and orchid flowers are best preserved in an air-tight glass or plastic jar with a liquid preservative rather than by drying The type of preservative used should be clearly labelled in the jar Such material is often referred to as a spirit collection or wet collection

Most material can be satisfactorily preserved in 70 ethyl alcohol (or 70 methylated spirit or denatured alcohol) with 30 water Colours will fade quickly in spirit however so it is a good idea to keep comprehensive notes and photographs

87

Small algae Microscopic algae are often collected in a jar and in the

water in which they were found If the algae are to be stored for more than 2-3 days a preservative needs to be used Traditionally this has been the extremely toxic formalin - a small amount can be added to the water to make a 5 final solution and the container labelled This must not be sent through the post or by courier

There are some other equally toxic options for example propylene phenoxytol but none should be sent through the post A safer option is to add sufficient concentrated alcohol or methylated spirits to the water containing the algae to make a final solution of 70 alcohol This treatment dilutes the algae making them difficult to find so if they can be concentrated somehow first (eg by filtering) they can be stored in much less liquid Another option is to fix the algae in formalin (or something similar) first and then prepare a microscope glass slide with a permanent water-soluble mounting medium

88

Mounting Mounting specimens prevents most fragile material from

fragmenting and prevents specimens becoming separated from their labels If the plant collection is a long-term project specimens should be mounted on sheets of archival (permanent) cardboard or paper with archival-quality fixing media These include stitching with cotton thread dental floss nickel-plated copper wire (for heavier specimens) narrow strips of archival paper linen tape or by using an archival adhesive such as methyl cellulose adhesive

One disadvantage of mounting specimens is that it can make parts of the specimen inaccessible for examination so it is essential that this be borne in mind during specimen arrangement and mounting For example easily reversible mounting media should be used specimens should be strapped to the sheet rather than glued all over and the specimen should be carefully arranged before it is attached so that it shows all features

89

Full-size herbarium mounting sheets are usually about 43 cm long x 28 cm wide The plant name and accompanying field notes should be transcribed on a permanent label stuck to one corner of the herbarium sheet (the bottom right-hand corner being the most common) or sometimes annotations may be written directly on the sheet or card

Small pieces of material which may have become separated from the specimen (eg seeds) can be placed in small plastic bags and pinned to the sheet

90

Long-term preservation and storage The long-term preservation of dry plant

specimens is largely dependent on protection from insect attack Specimens collected by Linnaeus in the eighteenth century and by Banks and Solander on the Endeavour voyage in 1788 are still excellently preserved

91

Pests and their control A range of pests attack dried plant material The

most common pests are insects and fungi though rodents and other large animals can cause damage in poor storage conditions Insects eat the material the paper surrounding the material and the adhesives and mounting media

Such insect pests range from psocids (book lice) which attack mainly the softer parts such as flowers and soft fruits to tobacco beetles and carpet beetles which can bore holes through the toughest of specimens Many insects are particularly sensitive to relative humidity levels and do not thrive at levels below 50

92

The most common and acceptable specimen treatments for insect control are Freezing Microwave Poisoning Insect deterrents Fungal pests

93

Storage

Dried and pressed plant specimens can be stored in cardboard or plastic boxes or tied in bundles in light-weight cardboard folders placed in pigeon holes

Alternatively they can be placed in protective plastic jackets and displayed in ring folders which is recommended if they are to be frequently handled such as for a reference collection

94

Filing

Specimens should be filed in a systematic order if a relatively permanent collection is being made The major groups ie ferns and fern allies cycads conifers dicotyledons and monocotyledons are best kept separately or according to some classification scheme such as that given in a flora or handbook

Similarly the genera within each family and the species within each genus may be filed alphabetically or following some such classification

95

Preservation of entire animals

Types of collection specimens of an entire animal For reference collections mammals can be prepared as a variety of specimens The condition of the specimen may determine possible ways to preserve it if for instance decomposition of the skin has loosened the hair of a carcass so much that it can easily be pulled out or removed by rubbing (ldquoslippingrdquo fur) it will be very difficult or impossible to produce a study skin or mounted specimen The most usual types of specimens (based on Nagorsen and Peterson 1980) are 1) entire fluid-preserved animals (for studying anatomy and histology fluid preservation may change the fur colour) 2) study skins with accompanying skulls partial skeletons (some bones remain in the skin) for studying pelage colour hair quality and moulting patterns 3) mounted skins with accompanying partial or entire skeleton (some bones may remain in the skin dependant on the method of preservation) or freeze-dried specimens 4) entire skeletons for instance for studying anatomy geographic variation or for age determination (entire skeletons are poorly represented in collections so Nagorsen and Peterson (1980) recommend preparation of at least one male and one female skeleton per species

96

Preservation of specimens in the field Formalin preservation Preservation in alcohol Preservation by cooling or freezing

97

Formalin preservation After weighing and measuring the animal and attaching an

adequate label very small specimens (up to 100 g) can be fixed whole by submerging them in 10 buffered formalin (tissue - formalin solution ratio of at least 1 12) the body cavity can be filled with formalin solution by injection until it is turgid and firm some formalin may also be injected under the skin into the body cavity larger muscles and organs If hypodermic needles are not available the body cavity can be opened ventrally by making a slit instead allowing the formalin to enter

Keeping the mouth open with a piece of wood or cotton may later allow examination of teeth Then the whole body can be immersed in formalin in the posture in which it is supposed to stay permanently because it will harden The ratio of formalin to carcass must be at least 12 to 1 to assure a good fixation Tissues can be left in buffered neutralized formalin for several months but formalin hardens specimens therefore after fixation longterm storage in alcohol may be better After preservation the carcass should therefore be washed in water and transferred into ethanol for permanent storage

Disadvantages for instance it discolours the fur after a longish immersion softens the bones and prevents further examination for microbiology

98

Preservation in alcohol

After weighing a whole animal can be preserved in a container of alcohol (70-90) Removal of the intestine prior to storage of the animal in alcohol is recommended

99

Preservation by cooling or freezing Removal of the skin with insulating fur

before cooling or freezing may help to cool the carcass down more quickly

Freezing is not recommended if histological examination is planned

100

THANK YOU

76

Seine Seines are nets that are pulled

through shallow water to catch fish

77

Purse Seine Used to encircle entire schools of fish

Usually involves a spotter plane and a second boat

78

Trotline (longline) A series of baited drop lines

connected to a main line

Can be deployed by tying one end to the bank and tying the other end with a heavy weight

79

Shrimp (or fish) Trawl Net pulled behind

a boat along the bottom Either a beam or

otter boards keep the net open

80

Tagging Individuals Coded Wire Tags

Microwire that has a unique label

Magnetic wand detects the tag

Tag retention should be determined

T-Bar tags Can be individually

numbered External tag

PIT tags (Passive Integrated Transponders) Wand induces the tag to

transmit individual number is displayed

81

Other Tagging Methods

Toe clip Amphibian and reptile Clip of one or more toes

to identify individuals

Bird Band Place a metal band on a

bird leg Generally has

identification information

82

Preserving plant specimens Pressing and drying Long-term

preservation and storage

Alternative drying techniques

Special preservation and processing techniques

Mounting

83

Pressing and drying Techniques for pressing and drying specimens have been

established for many years There are minor variations in recommended methods but they are essentially the same worldwide

The best specimens are plants that are pressed as soon as possible after collection before wilting and shrivelling Most plants may be kept in sealed containers such as plastic bags for up to a day if it is inconvenient to press immediately However some plants show such rapid wilting particularly of the flowers that such delays are best avoided Flowers with a lot of nectar may go mouldy very quickly if excess nectar is not shaken off before pressing

Specimens are pressed flat and dried between sheets of absorbent blotters or semi-absorbent paper such as newspaper Papers with a glossy surface should be avoided because they are not absorbent enough to aid drying The plant should be carefully laid out between the drying sheets as their form at this stage largely determines their ultimate appearance The flowers should be spread out with the petals carefully arranged wilted leaves should be straightened and unnecessary shoots of excessively twiggy shrubs may be cut away

84

Microwave ovens Small numbers of specimens can be dried using a microwave

oven The technique recommended in the literature is to place the specimens between unprinted absorbent paper for example butchers paper not newspaper which is unsuitable because the chemicals present in the ink may cause a fire The specimens should be put in a special press which should be of a microwave-safe material (wood acrylic or polycarbonate sheeting eg plexiglass or perspex NO metal components) If such a press is not available sheets of cardboard can be placed above and below the specimens and then weighted down

Drying time depends on the power of your oven In most cases drying is accomplished by irradiating at maximum power for 1-2 minutes per specimen although it is often a case of trial and error It is best to process no more than 10-12 specimens of average thickness per batch Specimens are usually dried after the moisture that characteristically appears on the glass door has disappeared If the specimen is damp when taken out of the oven allow it to stand before re-radiating as moisture continues to evaporate from the specimen for some time Care must be taken not to irradiate the specimens for too long

It should be noted that microwave treatment damages seeds and the cellular structure of the plants which may reduce the long-term value of the specimens

85

Alternative drying techniquesSilica gelother desiccants amp freeze drying Alternative methods of drying plant specimens have been

used for some time but are mostly restricted to special purpose collections The main alternatives are freeze-drying and drying in a desiccant powder such as desiccant silica gel In general these techniques are used where it is essential to preserve the shape of a delicate plant of organ of the plant such as the flower Freeze-drying has also been used to preserve the chemical composition of a plant as accurately as possible for later study

Disadvantages and special conservation problems of specimens dried in these manners are that they are particularly susceptible to damage The dried parts are fragile lack support and often catch on packing materials They must therefore be packed especially carefully and stored in small boxes or tubes with some appropriate packing material that does not snag and break small projections Acid-free tissue paper is often used Drying in desiccant silica gel crystals or powder can also have the disadvantage that it is difficult to remove all traces of the silica gel after drying

86

Special preservation and processing techniquesWet or spirit collections

Very fleshy or delicate structures including small algae and orchid flowers are best preserved in an air-tight glass or plastic jar with a liquid preservative rather than by drying The type of preservative used should be clearly labelled in the jar Such material is often referred to as a spirit collection or wet collection

Most material can be satisfactorily preserved in 70 ethyl alcohol (or 70 methylated spirit or denatured alcohol) with 30 water Colours will fade quickly in spirit however so it is a good idea to keep comprehensive notes and photographs

87

Small algae Microscopic algae are often collected in a jar and in the

water in which they were found If the algae are to be stored for more than 2-3 days a preservative needs to be used Traditionally this has been the extremely toxic formalin - a small amount can be added to the water to make a 5 final solution and the container labelled This must not be sent through the post or by courier

There are some other equally toxic options for example propylene phenoxytol but none should be sent through the post A safer option is to add sufficient concentrated alcohol or methylated spirits to the water containing the algae to make a final solution of 70 alcohol This treatment dilutes the algae making them difficult to find so if they can be concentrated somehow first (eg by filtering) they can be stored in much less liquid Another option is to fix the algae in formalin (or something similar) first and then prepare a microscope glass slide with a permanent water-soluble mounting medium

88

Mounting Mounting specimens prevents most fragile material from

fragmenting and prevents specimens becoming separated from their labels If the plant collection is a long-term project specimens should be mounted on sheets of archival (permanent) cardboard or paper with archival-quality fixing media These include stitching with cotton thread dental floss nickel-plated copper wire (for heavier specimens) narrow strips of archival paper linen tape or by using an archival adhesive such as methyl cellulose adhesive

One disadvantage of mounting specimens is that it can make parts of the specimen inaccessible for examination so it is essential that this be borne in mind during specimen arrangement and mounting For example easily reversible mounting media should be used specimens should be strapped to the sheet rather than glued all over and the specimen should be carefully arranged before it is attached so that it shows all features

89

Full-size herbarium mounting sheets are usually about 43 cm long x 28 cm wide The plant name and accompanying field notes should be transcribed on a permanent label stuck to one corner of the herbarium sheet (the bottom right-hand corner being the most common) or sometimes annotations may be written directly on the sheet or card

Small pieces of material which may have become separated from the specimen (eg seeds) can be placed in small plastic bags and pinned to the sheet

90

Long-term preservation and storage The long-term preservation of dry plant

specimens is largely dependent on protection from insect attack Specimens collected by Linnaeus in the eighteenth century and by Banks and Solander on the Endeavour voyage in 1788 are still excellently preserved

91

Pests and their control A range of pests attack dried plant material The

most common pests are insects and fungi though rodents and other large animals can cause damage in poor storage conditions Insects eat the material the paper surrounding the material and the adhesives and mounting media

Such insect pests range from psocids (book lice) which attack mainly the softer parts such as flowers and soft fruits to tobacco beetles and carpet beetles which can bore holes through the toughest of specimens Many insects are particularly sensitive to relative humidity levels and do not thrive at levels below 50

92

The most common and acceptable specimen treatments for insect control are Freezing Microwave Poisoning Insect deterrents Fungal pests

93

Storage

Dried and pressed plant specimens can be stored in cardboard or plastic boxes or tied in bundles in light-weight cardboard folders placed in pigeon holes

Alternatively they can be placed in protective plastic jackets and displayed in ring folders which is recommended if they are to be frequently handled such as for a reference collection

94

Filing

Specimens should be filed in a systematic order if a relatively permanent collection is being made The major groups ie ferns and fern allies cycads conifers dicotyledons and monocotyledons are best kept separately or according to some classification scheme such as that given in a flora or handbook

Similarly the genera within each family and the species within each genus may be filed alphabetically or following some such classification

95

Preservation of entire animals

Types of collection specimens of an entire animal For reference collections mammals can be prepared as a variety of specimens The condition of the specimen may determine possible ways to preserve it if for instance decomposition of the skin has loosened the hair of a carcass so much that it can easily be pulled out or removed by rubbing (ldquoslippingrdquo fur) it will be very difficult or impossible to produce a study skin or mounted specimen The most usual types of specimens (based on Nagorsen and Peterson 1980) are 1) entire fluid-preserved animals (for studying anatomy and histology fluid preservation may change the fur colour) 2) study skins with accompanying skulls partial skeletons (some bones remain in the skin) for studying pelage colour hair quality and moulting patterns 3) mounted skins with accompanying partial or entire skeleton (some bones may remain in the skin dependant on the method of preservation) or freeze-dried specimens 4) entire skeletons for instance for studying anatomy geographic variation or for age determination (entire skeletons are poorly represented in collections so Nagorsen and Peterson (1980) recommend preparation of at least one male and one female skeleton per species

96

Preservation of specimens in the field Formalin preservation Preservation in alcohol Preservation by cooling or freezing

97

Formalin preservation After weighing and measuring the animal and attaching an

adequate label very small specimens (up to 100 g) can be fixed whole by submerging them in 10 buffered formalin (tissue - formalin solution ratio of at least 1 12) the body cavity can be filled with formalin solution by injection until it is turgid and firm some formalin may also be injected under the skin into the body cavity larger muscles and organs If hypodermic needles are not available the body cavity can be opened ventrally by making a slit instead allowing the formalin to enter

Keeping the mouth open with a piece of wood or cotton may later allow examination of teeth Then the whole body can be immersed in formalin in the posture in which it is supposed to stay permanently because it will harden The ratio of formalin to carcass must be at least 12 to 1 to assure a good fixation Tissues can be left in buffered neutralized formalin for several months but formalin hardens specimens therefore after fixation longterm storage in alcohol may be better After preservation the carcass should therefore be washed in water and transferred into ethanol for permanent storage

Disadvantages for instance it discolours the fur after a longish immersion softens the bones and prevents further examination for microbiology

98

Preservation in alcohol

After weighing a whole animal can be preserved in a container of alcohol (70-90) Removal of the intestine prior to storage of the animal in alcohol is recommended

99

Preservation by cooling or freezing Removal of the skin with insulating fur

before cooling or freezing may help to cool the carcass down more quickly

Freezing is not recommended if histological examination is planned

100

THANK YOU

77

Purse Seine Used to encircle entire schools of fish

Usually involves a spotter plane and a second boat

78

Trotline (longline) A series of baited drop lines

connected to a main line

Can be deployed by tying one end to the bank and tying the other end with a heavy weight

79

Shrimp (or fish) Trawl Net pulled behind

a boat along the bottom Either a beam or

otter boards keep the net open

80

Tagging Individuals Coded Wire Tags

Microwire that has a unique label

Magnetic wand detects the tag

Tag retention should be determined

T-Bar tags Can be individually

numbered External tag

PIT tags (Passive Integrated Transponders) Wand induces the tag to

transmit individual number is displayed

81

Other Tagging Methods

Toe clip Amphibian and reptile Clip of one or more toes

to identify individuals

Bird Band Place a metal band on a

bird leg Generally has

identification information

82

Preserving plant specimens Pressing and drying Long-term

preservation and storage

Alternative drying techniques

Special preservation and processing techniques

Mounting

83

Pressing and drying Techniques for pressing and drying specimens have been

established for many years There are minor variations in recommended methods but they are essentially the same worldwide

The best specimens are plants that are pressed as soon as possible after collection before wilting and shrivelling Most plants may be kept in sealed containers such as plastic bags for up to a day if it is inconvenient to press immediately However some plants show such rapid wilting particularly of the flowers that such delays are best avoided Flowers with a lot of nectar may go mouldy very quickly if excess nectar is not shaken off before pressing

Specimens are pressed flat and dried between sheets of absorbent blotters or semi-absorbent paper such as newspaper Papers with a glossy surface should be avoided because they are not absorbent enough to aid drying The plant should be carefully laid out between the drying sheets as their form at this stage largely determines their ultimate appearance The flowers should be spread out with the petals carefully arranged wilted leaves should be straightened and unnecessary shoots of excessively twiggy shrubs may be cut away

84

Microwave ovens Small numbers of specimens can be dried using a microwave

oven The technique recommended in the literature is to place the specimens between unprinted absorbent paper for example butchers paper not newspaper which is unsuitable because the chemicals present in the ink may cause a fire The specimens should be put in a special press which should be of a microwave-safe material (wood acrylic or polycarbonate sheeting eg plexiglass or perspex NO metal components) If such a press is not available sheets of cardboard can be placed above and below the specimens and then weighted down

Drying time depends on the power of your oven In most cases drying is accomplished by irradiating at maximum power for 1-2 minutes per specimen although it is often a case of trial and error It is best to process no more than 10-12 specimens of average thickness per batch Specimens are usually dried after the moisture that characteristically appears on the glass door has disappeared If the specimen is damp when taken out of the oven allow it to stand before re-radiating as moisture continues to evaporate from the specimen for some time Care must be taken not to irradiate the specimens for too long

It should be noted that microwave treatment damages seeds and the cellular structure of the plants which may reduce the long-term value of the specimens

85

Alternative drying techniquesSilica gelother desiccants amp freeze drying Alternative methods of drying plant specimens have been

used for some time but are mostly restricted to special purpose collections The main alternatives are freeze-drying and drying in a desiccant powder such as desiccant silica gel In general these techniques are used where it is essential to preserve the shape of a delicate plant of organ of the plant such as the flower Freeze-drying has also been used to preserve the chemical composition of a plant as accurately as possible for later study

Disadvantages and special conservation problems of specimens dried in these manners are that they are particularly susceptible to damage The dried parts are fragile lack support and often catch on packing materials They must therefore be packed especially carefully and stored in small boxes or tubes with some appropriate packing material that does not snag and break small projections Acid-free tissue paper is often used Drying in desiccant silica gel crystals or powder can also have the disadvantage that it is difficult to remove all traces of the silica gel after drying

86

Special preservation and processing techniquesWet or spirit collections

Very fleshy or delicate structures including small algae and orchid flowers are best preserved in an air-tight glass or plastic jar with a liquid preservative rather than by drying The type of preservative used should be clearly labelled in the jar Such material is often referred to as a spirit collection or wet collection

Most material can be satisfactorily preserved in 70 ethyl alcohol (or 70 methylated spirit or denatured alcohol) with 30 water Colours will fade quickly in spirit however so it is a good idea to keep comprehensive notes and photographs

87

Small algae Microscopic algae are often collected in a jar and in the

water in which they were found If the algae are to be stored for more than 2-3 days a preservative needs to be used Traditionally this has been the extremely toxic formalin - a small amount can be added to the water to make a 5 final solution and the container labelled This must not be sent through the post or by courier

There are some other equally toxic options for example propylene phenoxytol but none should be sent through the post A safer option is to add sufficient concentrated alcohol or methylated spirits to the water containing the algae to make a final solution of 70 alcohol This treatment dilutes the algae making them difficult to find so if they can be concentrated somehow first (eg by filtering) they can be stored in much less liquid Another option is to fix the algae in formalin (or something similar) first and then prepare a microscope glass slide with a permanent water-soluble mounting medium

88

Mounting Mounting specimens prevents most fragile material from

fragmenting and prevents specimens becoming separated from their labels If the plant collection is a long-term project specimens should be mounted on sheets of archival (permanent) cardboard or paper with archival-quality fixing media These include stitching with cotton thread dental floss nickel-plated copper wire (for heavier specimens) narrow strips of archival paper linen tape or by using an archival adhesive such as methyl cellulose adhesive

One disadvantage of mounting specimens is that it can make parts of the specimen inaccessible for examination so it is essential that this be borne in mind during specimen arrangement and mounting For example easily reversible mounting media should be used specimens should be strapped to the sheet rather than glued all over and the specimen should be carefully arranged before it is attached so that it shows all features

89

Full-size herbarium mounting sheets are usually about 43 cm long x 28 cm wide The plant name and accompanying field notes should be transcribed on a permanent label stuck to one corner of the herbarium sheet (the bottom right-hand corner being the most common) or sometimes annotations may be written directly on the sheet or card

Small pieces of material which may have become separated from the specimen (eg seeds) can be placed in small plastic bags and pinned to the sheet

90

Long-term preservation and storage The long-term preservation of dry plant

specimens is largely dependent on protection from insect attack Specimens collected by Linnaeus in the eighteenth century and by Banks and Solander on the Endeavour voyage in 1788 are still excellently preserved

91

Pests and their control A range of pests attack dried plant material The

most common pests are insects and fungi though rodents and other large animals can cause damage in poor storage conditions Insects eat the material the paper surrounding the material and the adhesives and mounting media

Such insect pests range from psocids (book lice) which attack mainly the softer parts such as flowers and soft fruits to tobacco beetles and carpet beetles which can bore holes through the toughest of specimens Many insects are particularly sensitive to relative humidity levels and do not thrive at levels below 50

92

The most common and acceptable specimen treatments for insect control are Freezing Microwave Poisoning Insect deterrents Fungal pests

93

Storage

Dried and pressed plant specimens can be stored in cardboard or plastic boxes or tied in bundles in light-weight cardboard folders placed in pigeon holes

Alternatively they can be placed in protective plastic jackets and displayed in ring folders which is recommended if they are to be frequently handled such as for a reference collection

94

Filing

Specimens should be filed in a systematic order if a relatively permanent collection is being made The major groups ie ferns and fern allies cycads conifers dicotyledons and monocotyledons are best kept separately or according to some classification scheme such as that given in a flora or handbook

Similarly the genera within each family and the species within each genus may be filed alphabetically or following some such classification

95

Preservation of entire animals

Types of collection specimens of an entire animal For reference collections mammals can be prepared as a variety of specimens The condition of the specimen may determine possible ways to preserve it if for instance decomposition of the skin has loosened the hair of a carcass so much that it can easily be pulled out or removed by rubbing (ldquoslippingrdquo fur) it will be very difficult or impossible to produce a study skin or mounted specimen The most usual types of specimens (based on Nagorsen and Peterson 1980) are 1) entire fluid-preserved animals (for studying anatomy and histology fluid preservation may change the fur colour) 2) study skins with accompanying skulls partial skeletons (some bones remain in the skin) for studying pelage colour hair quality and moulting patterns 3) mounted skins with accompanying partial or entire skeleton (some bones may remain in the skin dependant on the method of preservation) or freeze-dried specimens 4) entire skeletons for instance for studying anatomy geographic variation or for age determination (entire skeletons are poorly represented in collections so Nagorsen and Peterson (1980) recommend preparation of at least one male and one female skeleton per species

96

Preservation of specimens in the field Formalin preservation Preservation in alcohol Preservation by cooling or freezing

97

Formalin preservation After weighing and measuring the animal and attaching an

adequate label very small specimens (up to 100 g) can be fixed whole by submerging them in 10 buffered formalin (tissue - formalin solution ratio of at least 1 12) the body cavity can be filled with formalin solution by injection until it is turgid and firm some formalin may also be injected under the skin into the body cavity larger muscles and organs If hypodermic needles are not available the body cavity can be opened ventrally by making a slit instead allowing the formalin to enter

Keeping the mouth open with a piece of wood or cotton may later allow examination of teeth Then the whole body can be immersed in formalin in the posture in which it is supposed to stay permanently because it will harden The ratio of formalin to carcass must be at least 12 to 1 to assure a good fixation Tissues can be left in buffered neutralized formalin for several months but formalin hardens specimens therefore after fixation longterm storage in alcohol may be better After preservation the carcass should therefore be washed in water and transferred into ethanol for permanent storage

Disadvantages for instance it discolours the fur after a longish immersion softens the bones and prevents further examination for microbiology

98

Preservation in alcohol

After weighing a whole animal can be preserved in a container of alcohol (70-90) Removal of the intestine prior to storage of the animal in alcohol is recommended

99

Preservation by cooling or freezing Removal of the skin with insulating fur

before cooling or freezing may help to cool the carcass down more quickly

Freezing is not recommended if histological examination is planned

100

THANK YOU

78

Trotline (longline) A series of baited drop lines

connected to a main line

Can be deployed by tying one end to the bank and tying the other end with a heavy weight

79

Shrimp (or fish) Trawl Net pulled behind

a boat along the bottom Either a beam or

otter boards keep the net open

80

Tagging Individuals Coded Wire Tags

Microwire that has a unique label

Magnetic wand detects the tag

Tag retention should be determined

T-Bar tags Can be individually

numbered External tag

PIT tags (Passive Integrated Transponders) Wand induces the tag to

transmit individual number is displayed

81

Other Tagging Methods

Toe clip Amphibian and reptile Clip of one or more toes

to identify individuals

Bird Band Place a metal band on a

bird leg Generally has

identification information

82

Preserving plant specimens Pressing and drying Long-term

preservation and storage

Alternative drying techniques

Special preservation and processing techniques

Mounting

83

Pressing and drying Techniques for pressing and drying specimens have been

established for many years There are minor variations in recommended methods but they are essentially the same worldwide

The best specimens are plants that are pressed as soon as possible after collection before wilting and shrivelling Most plants may be kept in sealed containers such as plastic bags for up to a day if it is inconvenient to press immediately However some plants show such rapid wilting particularly of the flowers that such delays are best avoided Flowers with a lot of nectar may go mouldy very quickly if excess nectar is not shaken off before pressing

Specimens are pressed flat and dried between sheets of absorbent blotters or semi-absorbent paper such as newspaper Papers with a glossy surface should be avoided because they are not absorbent enough to aid drying The plant should be carefully laid out between the drying sheets as their form at this stage largely determines their ultimate appearance The flowers should be spread out with the petals carefully arranged wilted leaves should be straightened and unnecessary shoots of excessively twiggy shrubs may be cut away

84

Microwave ovens Small numbers of specimens can be dried using a microwave

oven The technique recommended in the literature is to place the specimens between unprinted absorbent paper for example butchers paper not newspaper which is unsuitable because the chemicals present in the ink may cause a fire The specimens should be put in a special press which should be of a microwave-safe material (wood acrylic or polycarbonate sheeting eg plexiglass or perspex NO metal components) If such a press is not available sheets of cardboard can be placed above and below the specimens and then weighted down

Drying time depends on the power of your oven In most cases drying is accomplished by irradiating at maximum power for 1-2 minutes per specimen although it is often a case of trial and error It is best to process no more than 10-12 specimens of average thickness per batch Specimens are usually dried after the moisture that characteristically appears on the glass door has disappeared If the specimen is damp when taken out of the oven allow it to stand before re-radiating as moisture continues to evaporate from the specimen for some time Care must be taken not to irradiate the specimens for too long

It should be noted that microwave treatment damages seeds and the cellular structure of the plants which may reduce the long-term value of the specimens

85

Alternative drying techniquesSilica gelother desiccants amp freeze drying Alternative methods of drying plant specimens have been

used for some time but are mostly restricted to special purpose collections The main alternatives are freeze-drying and drying in a desiccant powder such as desiccant silica gel In general these techniques are used where it is essential to preserve the shape of a delicate plant of organ of the plant such as the flower Freeze-drying has also been used to preserve the chemical composition of a plant as accurately as possible for later study

Disadvantages and special conservation problems of specimens dried in these manners are that they are particularly susceptible to damage The dried parts are fragile lack support and often catch on packing materials They must therefore be packed especially carefully and stored in small boxes or tubes with some appropriate packing material that does not snag and break small projections Acid-free tissue paper is often used Drying in desiccant silica gel crystals or powder can also have the disadvantage that it is difficult to remove all traces of the silica gel after drying

86

Special preservation and processing techniquesWet or spirit collections

Very fleshy or delicate structures including small algae and orchid flowers are best preserved in an air-tight glass or plastic jar with a liquid preservative rather than by drying The type of preservative used should be clearly labelled in the jar Such material is often referred to as a spirit collection or wet collection

Most material can be satisfactorily preserved in 70 ethyl alcohol (or 70 methylated spirit or denatured alcohol) with 30 water Colours will fade quickly in spirit however so it is a good idea to keep comprehensive notes and photographs

87

Small algae Microscopic algae are often collected in a jar and in the

water in which they were found If the algae are to be stored for more than 2-3 days a preservative needs to be used Traditionally this has been the extremely toxic formalin - a small amount can be added to the water to make a 5 final solution and the container labelled This must not be sent through the post or by courier

There are some other equally toxic options for example propylene phenoxytol but none should be sent through the post A safer option is to add sufficient concentrated alcohol or methylated spirits to the water containing the algae to make a final solution of 70 alcohol This treatment dilutes the algae making them difficult to find so if they can be concentrated somehow first (eg by filtering) they can be stored in much less liquid Another option is to fix the algae in formalin (or something similar) first and then prepare a microscope glass slide with a permanent water-soluble mounting medium

88

Mounting Mounting specimens prevents most fragile material from

fragmenting and prevents specimens becoming separated from their labels If the plant collection is a long-term project specimens should be mounted on sheets of archival (permanent) cardboard or paper with archival-quality fixing media These include stitching with cotton thread dental floss nickel-plated copper wire (for heavier specimens) narrow strips of archival paper linen tape or by using an archival adhesive such as methyl cellulose adhesive

One disadvantage of mounting specimens is that it can make parts of the specimen inaccessible for examination so it is essential that this be borne in mind during specimen arrangement and mounting For example easily reversible mounting media should be used specimens should be strapped to the sheet rather than glued all over and the specimen should be carefully arranged before it is attached so that it shows all features

89

Full-size herbarium mounting sheets are usually about 43 cm long x 28 cm wide The plant name and accompanying field notes should be transcribed on a permanent label stuck to one corner of the herbarium sheet (the bottom right-hand corner being the most common) or sometimes annotations may be written directly on the sheet or card

Small pieces of material which may have become separated from the specimen (eg seeds) can be placed in small plastic bags and pinned to the sheet

90

Long-term preservation and storage The long-term preservation of dry plant

specimens is largely dependent on protection from insect attack Specimens collected by Linnaeus in the eighteenth century and by Banks and Solander on the Endeavour voyage in 1788 are still excellently preserved

91

Pests and their control A range of pests attack dried plant material The

most common pests are insects and fungi though rodents and other large animals can cause damage in poor storage conditions Insects eat the material the paper surrounding the material and the adhesives and mounting media

Such insect pests range from psocids (book lice) which attack mainly the softer parts such as flowers and soft fruits to tobacco beetles and carpet beetles which can bore holes through the toughest of specimens Many insects are particularly sensitive to relative humidity levels and do not thrive at levels below 50

92

The most common and acceptable specimen treatments for insect control are Freezing Microwave Poisoning Insect deterrents Fungal pests

93

Storage

Dried and pressed plant specimens can be stored in cardboard or plastic boxes or tied in bundles in light-weight cardboard folders placed in pigeon holes

Alternatively they can be placed in protective plastic jackets and displayed in ring folders which is recommended if they are to be frequently handled such as for a reference collection

94

Filing

Specimens should be filed in a systematic order if a relatively permanent collection is being made The major groups ie ferns and fern allies cycads conifers dicotyledons and monocotyledons are best kept separately or according to some classification scheme such as that given in a flora or handbook

Similarly the genera within each family and the species within each genus may be filed alphabetically or following some such classification

95

Preservation of entire animals

Types of collection specimens of an entire animal For reference collections mammals can be prepared as a variety of specimens The condition of the specimen may determine possible ways to preserve it if for instance decomposition of the skin has loosened the hair of a carcass so much that it can easily be pulled out or removed by rubbing (ldquoslippingrdquo fur) it will be very difficult or impossible to produce a study skin or mounted specimen The most usual types of specimens (based on Nagorsen and Peterson 1980) are 1) entire fluid-preserved animals (for studying anatomy and histology fluid preservation may change the fur colour) 2) study skins with accompanying skulls partial skeletons (some bones remain in the skin) for studying pelage colour hair quality and moulting patterns 3) mounted skins with accompanying partial or entire skeleton (some bones may remain in the skin dependant on the method of preservation) or freeze-dried specimens 4) entire skeletons for instance for studying anatomy geographic variation or for age determination (entire skeletons are poorly represented in collections so Nagorsen and Peterson (1980) recommend preparation of at least one male and one female skeleton per species

96

Preservation of specimens in the field Formalin preservation Preservation in alcohol Preservation by cooling or freezing

97

Formalin preservation After weighing and measuring the animal and attaching an

adequate label very small specimens (up to 100 g) can be fixed whole by submerging them in 10 buffered formalin (tissue - formalin solution ratio of at least 1 12) the body cavity can be filled with formalin solution by injection until it is turgid and firm some formalin may also be injected under the skin into the body cavity larger muscles and organs If hypodermic needles are not available the body cavity can be opened ventrally by making a slit instead allowing the formalin to enter

Keeping the mouth open with a piece of wood or cotton may later allow examination of teeth Then the whole body can be immersed in formalin in the posture in which it is supposed to stay permanently because it will harden The ratio of formalin to carcass must be at least 12 to 1 to assure a good fixation Tissues can be left in buffered neutralized formalin for several months but formalin hardens specimens therefore after fixation longterm storage in alcohol may be better After preservation the carcass should therefore be washed in water and transferred into ethanol for permanent storage

Disadvantages for instance it discolours the fur after a longish immersion softens the bones and prevents further examination for microbiology

98

Preservation in alcohol

After weighing a whole animal can be preserved in a container of alcohol (70-90) Removal of the intestine prior to storage of the animal in alcohol is recommended

99

Preservation by cooling or freezing Removal of the skin with insulating fur

before cooling or freezing may help to cool the carcass down more quickly

Freezing is not recommended if histological examination is planned

100

THANK YOU

79

Shrimp (or fish) Trawl Net pulled behind

a boat along the bottom Either a beam or

otter boards keep the net open

80

Tagging Individuals Coded Wire Tags

Microwire that has a unique label

Magnetic wand detects the tag

Tag retention should be determined

T-Bar tags Can be individually

numbered External tag

PIT tags (Passive Integrated Transponders) Wand induces the tag to

transmit individual number is displayed

81

Other Tagging Methods

Toe clip Amphibian and reptile Clip of one or more toes

to identify individuals

Bird Band Place a metal band on a

bird leg Generally has

identification information

82

Preserving plant specimens Pressing and drying Long-term

preservation and storage

Alternative drying techniques

Special preservation and processing techniques

Mounting

83

Pressing and drying Techniques for pressing and drying specimens have been

established for many years There are minor variations in recommended methods but they are essentially the same worldwide

The best specimens are plants that are pressed as soon as possible after collection before wilting and shrivelling Most plants may be kept in sealed containers such as plastic bags for up to a day if it is inconvenient to press immediately However some plants show such rapid wilting particularly of the flowers that such delays are best avoided Flowers with a lot of nectar may go mouldy very quickly if excess nectar is not shaken off before pressing

Specimens are pressed flat and dried between sheets of absorbent blotters or semi-absorbent paper such as newspaper Papers with a glossy surface should be avoided because they are not absorbent enough to aid drying The plant should be carefully laid out between the drying sheets as their form at this stage largely determines their ultimate appearance The flowers should be spread out with the petals carefully arranged wilted leaves should be straightened and unnecessary shoots of excessively twiggy shrubs may be cut away

84

Microwave ovens Small numbers of specimens can be dried using a microwave

oven The technique recommended in the literature is to place the specimens between unprinted absorbent paper for example butchers paper not newspaper which is unsuitable because the chemicals present in the ink may cause a fire The specimens should be put in a special press which should be of a microwave-safe material (wood acrylic or polycarbonate sheeting eg plexiglass or perspex NO metal components) If such a press is not available sheets of cardboard can be placed above and below the specimens and then weighted down

Drying time depends on the power of your oven In most cases drying is accomplished by irradiating at maximum power for 1-2 minutes per specimen although it is often a case of trial and error It is best to process no more than 10-12 specimens of average thickness per batch Specimens are usually dried after the moisture that characteristically appears on the glass door has disappeared If the specimen is damp when taken out of the oven allow it to stand before re-radiating as moisture continues to evaporate from the specimen for some time Care must be taken not to irradiate the specimens for too long

It should be noted that microwave treatment damages seeds and the cellular structure of the plants which may reduce the long-term value of the specimens

85

Alternative drying techniquesSilica gelother desiccants amp freeze drying Alternative methods of drying plant specimens have been

used for some time but are mostly restricted to special purpose collections The main alternatives are freeze-drying and drying in a desiccant powder such as desiccant silica gel In general these techniques are used where it is essential to preserve the shape of a delicate plant of organ of the plant such as the flower Freeze-drying has also been used to preserve the chemical composition of a plant as accurately as possible for later study

Disadvantages and special conservation problems of specimens dried in these manners are that they are particularly susceptible to damage The dried parts are fragile lack support and often catch on packing materials They must therefore be packed especially carefully and stored in small boxes or tubes with some appropriate packing material that does not snag and break small projections Acid-free tissue paper is often used Drying in desiccant silica gel crystals or powder can also have the disadvantage that it is difficult to remove all traces of the silica gel after drying

86

Special preservation and processing techniquesWet or spirit collections

Very fleshy or delicate structures including small algae and orchid flowers are best preserved in an air-tight glass or plastic jar with a liquid preservative rather than by drying The type of preservative used should be clearly labelled in the jar Such material is often referred to as a spirit collection or wet collection

Most material can be satisfactorily preserved in 70 ethyl alcohol (or 70 methylated spirit or denatured alcohol) with 30 water Colours will fade quickly in spirit however so it is a good idea to keep comprehensive notes and photographs

87

Small algae Microscopic algae are often collected in a jar and in the

water in which they were found If the algae are to be stored for more than 2-3 days a preservative needs to be used Traditionally this has been the extremely toxic formalin - a small amount can be added to the water to make a 5 final solution and the container labelled This must not be sent through the post or by courier

There are some other equally toxic options for example propylene phenoxytol but none should be sent through the post A safer option is to add sufficient concentrated alcohol or methylated spirits to the water containing the algae to make a final solution of 70 alcohol This treatment dilutes the algae making them difficult to find so if they can be concentrated somehow first (eg by filtering) they can be stored in much less liquid Another option is to fix the algae in formalin (or something similar) first and then prepare a microscope glass slide with a permanent water-soluble mounting medium

88

Mounting Mounting specimens prevents most fragile material from

fragmenting and prevents specimens becoming separated from their labels If the plant collection is a long-term project specimens should be mounted on sheets of archival (permanent) cardboard or paper with archival-quality fixing media These include stitching with cotton thread dental floss nickel-plated copper wire (for heavier specimens) narrow strips of archival paper linen tape or by using an archival adhesive such as methyl cellulose adhesive

One disadvantage of mounting specimens is that it can make parts of the specimen inaccessible for examination so it is essential that this be borne in mind during specimen arrangement and mounting For example easily reversible mounting media should be used specimens should be strapped to the sheet rather than glued all over and the specimen should be carefully arranged before it is attached so that it shows all features

89

Full-size herbarium mounting sheets are usually about 43 cm long x 28 cm wide The plant name and accompanying field notes should be transcribed on a permanent label stuck to one corner of the herbarium sheet (the bottom right-hand corner being the most common) or sometimes annotations may be written directly on the sheet or card

Small pieces of material which may have become separated from the specimen (eg seeds) can be placed in small plastic bags and pinned to the sheet

90

Long-term preservation and storage The long-term preservation of dry plant

specimens is largely dependent on protection from insect attack Specimens collected by Linnaeus in the eighteenth century and by Banks and Solander on the Endeavour voyage in 1788 are still excellently preserved

91

Pests and their control A range of pests attack dried plant material The

most common pests are insects and fungi though rodents and other large animals can cause damage in poor storage conditions Insects eat the material the paper surrounding the material and the adhesives and mounting media

Such insect pests range from psocids (book lice) which attack mainly the softer parts such as flowers and soft fruits to tobacco beetles and carpet beetles which can bore holes through the toughest of specimens Many insects are particularly sensitive to relative humidity levels and do not thrive at levels below 50

92

The most common and acceptable specimen treatments for insect control are Freezing Microwave Poisoning Insect deterrents Fungal pests

93

Storage

Dried and pressed plant specimens can be stored in cardboard or plastic boxes or tied in bundles in light-weight cardboard folders placed in pigeon holes

Alternatively they can be placed in protective plastic jackets and displayed in ring folders which is recommended if they are to be frequently handled such as for a reference collection

94

Filing

Specimens should be filed in a systematic order if a relatively permanent collection is being made The major groups ie ferns and fern allies cycads conifers dicotyledons and monocotyledons are best kept separately or according to some classification scheme such as that given in a flora or handbook

Similarly the genera within each family and the species within each genus may be filed alphabetically or following some such classification

95

Preservation of entire animals

Types of collection specimens of an entire animal For reference collections mammals can be prepared as a variety of specimens The condition of the specimen may determine possible ways to preserve it if for instance decomposition of the skin has loosened the hair of a carcass so much that it can easily be pulled out or removed by rubbing (ldquoslippingrdquo fur) it will be very difficult or impossible to produce a study skin or mounted specimen The most usual types of specimens (based on Nagorsen and Peterson 1980) are 1) entire fluid-preserved animals (for studying anatomy and histology fluid preservation may change the fur colour) 2) study skins with accompanying skulls partial skeletons (some bones remain in the skin) for studying pelage colour hair quality and moulting patterns 3) mounted skins with accompanying partial or entire skeleton (some bones may remain in the skin dependant on the method of preservation) or freeze-dried specimens 4) entire skeletons for instance for studying anatomy geographic variation or for age determination (entire skeletons are poorly represented in collections so Nagorsen and Peterson (1980) recommend preparation of at least one male and one female skeleton per species

96

Preservation of specimens in the field Formalin preservation Preservation in alcohol Preservation by cooling or freezing

97

Formalin preservation After weighing and measuring the animal and attaching an

adequate label very small specimens (up to 100 g) can be fixed whole by submerging them in 10 buffered formalin (tissue - formalin solution ratio of at least 1 12) the body cavity can be filled with formalin solution by injection until it is turgid and firm some formalin may also be injected under the skin into the body cavity larger muscles and organs If hypodermic needles are not available the body cavity can be opened ventrally by making a slit instead allowing the formalin to enter

Keeping the mouth open with a piece of wood or cotton may later allow examination of teeth Then the whole body can be immersed in formalin in the posture in which it is supposed to stay permanently because it will harden The ratio of formalin to carcass must be at least 12 to 1 to assure a good fixation Tissues can be left in buffered neutralized formalin for several months but formalin hardens specimens therefore after fixation longterm storage in alcohol may be better After preservation the carcass should therefore be washed in water and transferred into ethanol for permanent storage

Disadvantages for instance it discolours the fur after a longish immersion softens the bones and prevents further examination for microbiology

98

Preservation in alcohol

After weighing a whole animal can be preserved in a container of alcohol (70-90) Removal of the intestine prior to storage of the animal in alcohol is recommended

99

Preservation by cooling or freezing Removal of the skin with insulating fur

before cooling or freezing may help to cool the carcass down more quickly

Freezing is not recommended if histological examination is planned

100

THANK YOU

80

Tagging Individuals Coded Wire Tags

Microwire that has a unique label

Magnetic wand detects the tag

Tag retention should be determined

T-Bar tags Can be individually

numbered External tag

PIT tags (Passive Integrated Transponders) Wand induces the tag to

transmit individual number is displayed

81

Other Tagging Methods

Toe clip Amphibian and reptile Clip of one or more toes

to identify individuals

Bird Band Place a metal band on a

bird leg Generally has

identification information

82

Preserving plant specimens Pressing and drying Long-term

preservation and storage

Alternative drying techniques

Special preservation and processing techniques

Mounting

83

Pressing and drying Techniques for pressing and drying specimens have been

established for many years There are minor variations in recommended methods but they are essentially the same worldwide

The best specimens are plants that are pressed as soon as possible after collection before wilting and shrivelling Most plants may be kept in sealed containers such as plastic bags for up to a day if it is inconvenient to press immediately However some plants show such rapid wilting particularly of the flowers that such delays are best avoided Flowers with a lot of nectar may go mouldy very quickly if excess nectar is not shaken off before pressing

Specimens are pressed flat and dried between sheets of absorbent blotters or semi-absorbent paper such as newspaper Papers with a glossy surface should be avoided because they are not absorbent enough to aid drying The plant should be carefully laid out between the drying sheets as their form at this stage largely determines their ultimate appearance The flowers should be spread out with the petals carefully arranged wilted leaves should be straightened and unnecessary shoots of excessively twiggy shrubs may be cut away

84

Microwave ovens Small numbers of specimens can be dried using a microwave

oven The technique recommended in the literature is to place the specimens between unprinted absorbent paper for example butchers paper not newspaper which is unsuitable because the chemicals present in the ink may cause a fire The specimens should be put in a special press which should be of a microwave-safe material (wood acrylic or polycarbonate sheeting eg plexiglass or perspex NO metal components) If such a press is not available sheets of cardboard can be placed above and below the specimens and then weighted down

Drying time depends on the power of your oven In most cases drying is accomplished by irradiating at maximum power for 1-2 minutes per specimen although it is often a case of trial and error It is best to process no more than 10-12 specimens of average thickness per batch Specimens are usually dried after the moisture that characteristically appears on the glass door has disappeared If the specimen is damp when taken out of the oven allow it to stand before re-radiating as moisture continues to evaporate from the specimen for some time Care must be taken not to irradiate the specimens for too long

It should be noted that microwave treatment damages seeds and the cellular structure of the plants which may reduce the long-term value of the specimens

85

Alternative drying techniquesSilica gelother desiccants amp freeze drying Alternative methods of drying plant specimens have been

used for some time but are mostly restricted to special purpose collections The main alternatives are freeze-drying and drying in a desiccant powder such as desiccant silica gel In general these techniques are used where it is essential to preserve the shape of a delicate plant of organ of the plant such as the flower Freeze-drying has also been used to preserve the chemical composition of a plant as accurately as possible for later study

Disadvantages and special conservation problems of specimens dried in these manners are that they are particularly susceptible to damage The dried parts are fragile lack support and often catch on packing materials They must therefore be packed especially carefully and stored in small boxes or tubes with some appropriate packing material that does not snag and break small projections Acid-free tissue paper is often used Drying in desiccant silica gel crystals or powder can also have the disadvantage that it is difficult to remove all traces of the silica gel after drying

86

Special preservation and processing techniquesWet or spirit collections

Very fleshy or delicate structures including small algae and orchid flowers are best preserved in an air-tight glass or plastic jar with a liquid preservative rather than by drying The type of preservative used should be clearly labelled in the jar Such material is often referred to as a spirit collection or wet collection

Most material can be satisfactorily preserved in 70 ethyl alcohol (or 70 methylated spirit or denatured alcohol) with 30 water Colours will fade quickly in spirit however so it is a good idea to keep comprehensive notes and photographs

87

Small algae Microscopic algae are often collected in a jar and in the

water in which they were found If the algae are to be stored for more than 2-3 days a preservative needs to be used Traditionally this has been the extremely toxic formalin - a small amount can be added to the water to make a 5 final solution and the container labelled This must not be sent through the post or by courier

There are some other equally toxic options for example propylene phenoxytol but none should be sent through the post A safer option is to add sufficient concentrated alcohol or methylated spirits to the water containing the algae to make a final solution of 70 alcohol This treatment dilutes the algae making them difficult to find so if they can be concentrated somehow first (eg by filtering) they can be stored in much less liquid Another option is to fix the algae in formalin (or something similar) first and then prepare a microscope glass slide with a permanent water-soluble mounting medium

88

Mounting Mounting specimens prevents most fragile material from

fragmenting and prevents specimens becoming separated from their labels If the plant collection is a long-term project specimens should be mounted on sheets of archival (permanent) cardboard or paper with archival-quality fixing media These include stitching with cotton thread dental floss nickel-plated copper wire (for heavier specimens) narrow strips of archival paper linen tape or by using an archival adhesive such as methyl cellulose adhesive

One disadvantage of mounting specimens is that it can make parts of the specimen inaccessible for examination so it is essential that this be borne in mind during specimen arrangement and mounting For example easily reversible mounting media should be used specimens should be strapped to the sheet rather than glued all over and the specimen should be carefully arranged before it is attached so that it shows all features

89

Full-size herbarium mounting sheets are usually about 43 cm long x 28 cm wide The plant name and accompanying field notes should be transcribed on a permanent label stuck to one corner of the herbarium sheet (the bottom right-hand corner being the most common) or sometimes annotations may be written directly on the sheet or card

Small pieces of material which may have become separated from the specimen (eg seeds) can be placed in small plastic bags and pinned to the sheet

90

Long-term preservation and storage The long-term preservation of dry plant

specimens is largely dependent on protection from insect attack Specimens collected by Linnaeus in the eighteenth century and by Banks and Solander on the Endeavour voyage in 1788 are still excellently preserved

91

Pests and their control A range of pests attack dried plant material The

most common pests are insects and fungi though rodents and other large animals can cause damage in poor storage conditions Insects eat the material the paper surrounding the material and the adhesives and mounting media

Such insect pests range from psocids (book lice) which attack mainly the softer parts such as flowers and soft fruits to tobacco beetles and carpet beetles which can bore holes through the toughest of specimens Many insects are particularly sensitive to relative humidity levels and do not thrive at levels below 50

92

The most common and acceptable specimen treatments for insect control are Freezing Microwave Poisoning Insect deterrents Fungal pests

93

Storage

Dried and pressed plant specimens can be stored in cardboard or plastic boxes or tied in bundles in light-weight cardboard folders placed in pigeon holes

Alternatively they can be placed in protective plastic jackets and displayed in ring folders which is recommended if they are to be frequently handled such as for a reference collection

94

Filing

Specimens should be filed in a systematic order if a relatively permanent collection is being made The major groups ie ferns and fern allies cycads conifers dicotyledons and monocotyledons are best kept separately or according to some classification scheme such as that given in a flora or handbook

Similarly the genera within each family and the species within each genus may be filed alphabetically or following some such classification

95

Preservation of entire animals

Types of collection specimens of an entire animal For reference collections mammals can be prepared as a variety of specimens The condition of the specimen may determine possible ways to preserve it if for instance decomposition of the skin has loosened the hair of a carcass so much that it can easily be pulled out or removed by rubbing (ldquoslippingrdquo fur) it will be very difficult or impossible to produce a study skin or mounted specimen The most usual types of specimens (based on Nagorsen and Peterson 1980) are 1) entire fluid-preserved animals (for studying anatomy and histology fluid preservation may change the fur colour) 2) study skins with accompanying skulls partial skeletons (some bones remain in the skin) for studying pelage colour hair quality and moulting patterns 3) mounted skins with accompanying partial or entire skeleton (some bones may remain in the skin dependant on the method of preservation) or freeze-dried specimens 4) entire skeletons for instance for studying anatomy geographic variation or for age determination (entire skeletons are poorly represented in collections so Nagorsen and Peterson (1980) recommend preparation of at least one male and one female skeleton per species

96

Preservation of specimens in the field Formalin preservation Preservation in alcohol Preservation by cooling or freezing

97

Formalin preservation After weighing and measuring the animal and attaching an

adequate label very small specimens (up to 100 g) can be fixed whole by submerging them in 10 buffered formalin (tissue - formalin solution ratio of at least 1 12) the body cavity can be filled with formalin solution by injection until it is turgid and firm some formalin may also be injected under the skin into the body cavity larger muscles and organs If hypodermic needles are not available the body cavity can be opened ventrally by making a slit instead allowing the formalin to enter

Keeping the mouth open with a piece of wood or cotton may later allow examination of teeth Then the whole body can be immersed in formalin in the posture in which it is supposed to stay permanently because it will harden The ratio of formalin to carcass must be at least 12 to 1 to assure a good fixation Tissues can be left in buffered neutralized formalin for several months but formalin hardens specimens therefore after fixation longterm storage in alcohol may be better After preservation the carcass should therefore be washed in water and transferred into ethanol for permanent storage

Disadvantages for instance it discolours the fur after a longish immersion softens the bones and prevents further examination for microbiology

98

Preservation in alcohol

After weighing a whole animal can be preserved in a container of alcohol (70-90) Removal of the intestine prior to storage of the animal in alcohol is recommended

99

Preservation by cooling or freezing Removal of the skin with insulating fur

before cooling or freezing may help to cool the carcass down more quickly

Freezing is not recommended if histological examination is planned

100

THANK YOU

81

Other Tagging Methods

Toe clip Amphibian and reptile Clip of one or more toes

to identify individuals

Bird Band Place a metal band on a

bird leg Generally has

identification information

82

Preserving plant specimens Pressing and drying Long-term

preservation and storage

Alternative drying techniques

Special preservation and processing techniques

Mounting

83

Pressing and drying Techniques for pressing and drying specimens have been

established for many years There are minor variations in recommended methods but they are essentially the same worldwide

The best specimens are plants that are pressed as soon as possible after collection before wilting and shrivelling Most plants may be kept in sealed containers such as plastic bags for up to a day if it is inconvenient to press immediately However some plants show such rapid wilting particularly of the flowers that such delays are best avoided Flowers with a lot of nectar may go mouldy very quickly if excess nectar is not shaken off before pressing

Specimens are pressed flat and dried between sheets of absorbent blotters or semi-absorbent paper such as newspaper Papers with a glossy surface should be avoided because they are not absorbent enough to aid drying The plant should be carefully laid out between the drying sheets as their form at this stage largely determines their ultimate appearance The flowers should be spread out with the petals carefully arranged wilted leaves should be straightened and unnecessary shoots of excessively twiggy shrubs may be cut away

84

Microwave ovens Small numbers of specimens can be dried using a microwave

oven The technique recommended in the literature is to place the specimens between unprinted absorbent paper for example butchers paper not newspaper which is unsuitable because the chemicals present in the ink may cause a fire The specimens should be put in a special press which should be of a microwave-safe material (wood acrylic or polycarbonate sheeting eg plexiglass or perspex NO metal components) If such a press is not available sheets of cardboard can be placed above and below the specimens and then weighted down

Drying time depends on the power of your oven In most cases drying is accomplished by irradiating at maximum power for 1-2 minutes per specimen although it is often a case of trial and error It is best to process no more than 10-12 specimens of average thickness per batch Specimens are usually dried after the moisture that characteristically appears on the glass door has disappeared If the specimen is damp when taken out of the oven allow it to stand before re-radiating as moisture continues to evaporate from the specimen for some time Care must be taken not to irradiate the specimens for too long

It should be noted that microwave treatment damages seeds and the cellular structure of the plants which may reduce the long-term value of the specimens

85

Alternative drying techniquesSilica gelother desiccants amp freeze drying Alternative methods of drying plant specimens have been

used for some time but are mostly restricted to special purpose collections The main alternatives are freeze-drying and drying in a desiccant powder such as desiccant silica gel In general these techniques are used where it is essential to preserve the shape of a delicate plant of organ of the plant such as the flower Freeze-drying has also been used to preserve the chemical composition of a plant as accurately as possible for later study

Disadvantages and special conservation problems of specimens dried in these manners are that they are particularly susceptible to damage The dried parts are fragile lack support and often catch on packing materials They must therefore be packed especially carefully and stored in small boxes or tubes with some appropriate packing material that does not snag and break small projections Acid-free tissue paper is often used Drying in desiccant silica gel crystals or powder can also have the disadvantage that it is difficult to remove all traces of the silica gel after drying

86

Special preservation and processing techniquesWet or spirit collections

Very fleshy or delicate structures including small algae and orchid flowers are best preserved in an air-tight glass or plastic jar with a liquid preservative rather than by drying The type of preservative used should be clearly labelled in the jar Such material is often referred to as a spirit collection or wet collection

Most material can be satisfactorily preserved in 70 ethyl alcohol (or 70 methylated spirit or denatured alcohol) with 30 water Colours will fade quickly in spirit however so it is a good idea to keep comprehensive notes and photographs

87

Small algae Microscopic algae are often collected in a jar and in the

water in which they were found If the algae are to be stored for more than 2-3 days a preservative needs to be used Traditionally this has been the extremely toxic formalin - a small amount can be added to the water to make a 5 final solution and the container labelled This must not be sent through the post or by courier

There are some other equally toxic options for example propylene phenoxytol but none should be sent through the post A safer option is to add sufficient concentrated alcohol or methylated spirits to the water containing the algae to make a final solution of 70 alcohol This treatment dilutes the algae making them difficult to find so if they can be concentrated somehow first (eg by filtering) they can be stored in much less liquid Another option is to fix the algae in formalin (or something similar) first and then prepare a microscope glass slide with a permanent water-soluble mounting medium

88

Mounting Mounting specimens prevents most fragile material from

fragmenting and prevents specimens becoming separated from their labels If the plant collection is a long-term project specimens should be mounted on sheets of archival (permanent) cardboard or paper with archival-quality fixing media These include stitching with cotton thread dental floss nickel-plated copper wire (for heavier specimens) narrow strips of archival paper linen tape or by using an archival adhesive such as methyl cellulose adhesive

One disadvantage of mounting specimens is that it can make parts of the specimen inaccessible for examination so it is essential that this be borne in mind during specimen arrangement and mounting For example easily reversible mounting media should be used specimens should be strapped to the sheet rather than glued all over and the specimen should be carefully arranged before it is attached so that it shows all features

89

Full-size herbarium mounting sheets are usually about 43 cm long x 28 cm wide The plant name and accompanying field notes should be transcribed on a permanent label stuck to one corner of the herbarium sheet (the bottom right-hand corner being the most common) or sometimes annotations may be written directly on the sheet or card

Small pieces of material which may have become separated from the specimen (eg seeds) can be placed in small plastic bags and pinned to the sheet

90

Long-term preservation and storage The long-term preservation of dry plant

specimens is largely dependent on protection from insect attack Specimens collected by Linnaeus in the eighteenth century and by Banks and Solander on the Endeavour voyage in 1788 are still excellently preserved

91

Pests and their control A range of pests attack dried plant material The

most common pests are insects and fungi though rodents and other large animals can cause damage in poor storage conditions Insects eat the material the paper surrounding the material and the adhesives and mounting media

Such insect pests range from psocids (book lice) which attack mainly the softer parts such as flowers and soft fruits to tobacco beetles and carpet beetles which can bore holes through the toughest of specimens Many insects are particularly sensitive to relative humidity levels and do not thrive at levels below 50

92

The most common and acceptable specimen treatments for insect control are Freezing Microwave Poisoning Insect deterrents Fungal pests

93

Storage

Dried and pressed plant specimens can be stored in cardboard or plastic boxes or tied in bundles in light-weight cardboard folders placed in pigeon holes

Alternatively they can be placed in protective plastic jackets and displayed in ring folders which is recommended if they are to be frequently handled such as for a reference collection

94

Filing

Specimens should be filed in a systematic order if a relatively permanent collection is being made The major groups ie ferns and fern allies cycads conifers dicotyledons and monocotyledons are best kept separately or according to some classification scheme such as that given in a flora or handbook

Similarly the genera within each family and the species within each genus may be filed alphabetically or following some such classification

95

Preservation of entire animals

Types of collection specimens of an entire animal For reference collections mammals can be prepared as a variety of specimens The condition of the specimen may determine possible ways to preserve it if for instance decomposition of the skin has loosened the hair of a carcass so much that it can easily be pulled out or removed by rubbing (ldquoslippingrdquo fur) it will be very difficult or impossible to produce a study skin or mounted specimen The most usual types of specimens (based on Nagorsen and Peterson 1980) are 1) entire fluid-preserved animals (for studying anatomy and histology fluid preservation may change the fur colour) 2) study skins with accompanying skulls partial skeletons (some bones remain in the skin) for studying pelage colour hair quality and moulting patterns 3) mounted skins with accompanying partial or entire skeleton (some bones may remain in the skin dependant on the method of preservation) or freeze-dried specimens 4) entire skeletons for instance for studying anatomy geographic variation or for age determination (entire skeletons are poorly represented in collections so Nagorsen and Peterson (1980) recommend preparation of at least one male and one female skeleton per species

96

Preservation of specimens in the field Formalin preservation Preservation in alcohol Preservation by cooling or freezing

97

Formalin preservation After weighing and measuring the animal and attaching an

adequate label very small specimens (up to 100 g) can be fixed whole by submerging them in 10 buffered formalin (tissue - formalin solution ratio of at least 1 12) the body cavity can be filled with formalin solution by injection until it is turgid and firm some formalin may also be injected under the skin into the body cavity larger muscles and organs If hypodermic needles are not available the body cavity can be opened ventrally by making a slit instead allowing the formalin to enter

Keeping the mouth open with a piece of wood or cotton may later allow examination of teeth Then the whole body can be immersed in formalin in the posture in which it is supposed to stay permanently because it will harden The ratio of formalin to carcass must be at least 12 to 1 to assure a good fixation Tissues can be left in buffered neutralized formalin for several months but formalin hardens specimens therefore after fixation longterm storage in alcohol may be better After preservation the carcass should therefore be washed in water and transferred into ethanol for permanent storage

Disadvantages for instance it discolours the fur after a longish immersion softens the bones and prevents further examination for microbiology

98

Preservation in alcohol

After weighing a whole animal can be preserved in a container of alcohol (70-90) Removal of the intestine prior to storage of the animal in alcohol is recommended

99

Preservation by cooling or freezing Removal of the skin with insulating fur

before cooling or freezing may help to cool the carcass down more quickly

Freezing is not recommended if histological examination is planned

100

THANK YOU

82

Preserving plant specimens Pressing and drying Long-term

preservation and storage

Alternative drying techniques

Special preservation and processing techniques

Mounting

83

Pressing and drying Techniques for pressing and drying specimens have been

established for many years There are minor variations in recommended methods but they are essentially the same worldwide

The best specimens are plants that are pressed as soon as possible after collection before wilting and shrivelling Most plants may be kept in sealed containers such as plastic bags for up to a day if it is inconvenient to press immediately However some plants show such rapid wilting particularly of the flowers that such delays are best avoided Flowers with a lot of nectar may go mouldy very quickly if excess nectar is not shaken off before pressing

Specimens are pressed flat and dried between sheets of absorbent blotters or semi-absorbent paper such as newspaper Papers with a glossy surface should be avoided because they are not absorbent enough to aid drying The plant should be carefully laid out between the drying sheets as their form at this stage largely determines their ultimate appearance The flowers should be spread out with the petals carefully arranged wilted leaves should be straightened and unnecessary shoots of excessively twiggy shrubs may be cut away

84

Microwave ovens Small numbers of specimens can be dried using a microwave

oven The technique recommended in the literature is to place the specimens between unprinted absorbent paper for example butchers paper not newspaper which is unsuitable because the chemicals present in the ink may cause a fire The specimens should be put in a special press which should be of a microwave-safe material (wood acrylic or polycarbonate sheeting eg plexiglass or perspex NO metal components) If such a press is not available sheets of cardboard can be placed above and below the specimens and then weighted down

Drying time depends on the power of your oven In most cases drying is accomplished by irradiating at maximum power for 1-2 minutes per specimen although it is often a case of trial and error It is best to process no more than 10-12 specimens of average thickness per batch Specimens are usually dried after the moisture that characteristically appears on the glass door has disappeared If the specimen is damp when taken out of the oven allow it to stand before re-radiating as moisture continues to evaporate from the specimen for some time Care must be taken not to irradiate the specimens for too long

It should be noted that microwave treatment damages seeds and the cellular structure of the plants which may reduce the long-term value of the specimens

85

Alternative drying techniquesSilica gelother desiccants amp freeze drying Alternative methods of drying plant specimens have been

used for some time but are mostly restricted to special purpose collections The main alternatives are freeze-drying and drying in a desiccant powder such as desiccant silica gel In general these techniques are used where it is essential to preserve the shape of a delicate plant of organ of the plant such as the flower Freeze-drying has also been used to preserve the chemical composition of a plant as accurately as possible for later study

Disadvantages and special conservation problems of specimens dried in these manners are that they are particularly susceptible to damage The dried parts are fragile lack support and often catch on packing materials They must therefore be packed especially carefully and stored in small boxes or tubes with some appropriate packing material that does not snag and break small projections Acid-free tissue paper is often used Drying in desiccant silica gel crystals or powder can also have the disadvantage that it is difficult to remove all traces of the silica gel after drying

86

Special preservation and processing techniquesWet or spirit collections

Very fleshy or delicate structures including small algae and orchid flowers are best preserved in an air-tight glass or plastic jar with a liquid preservative rather than by drying The type of preservative used should be clearly labelled in the jar Such material is often referred to as a spirit collection or wet collection

Most material can be satisfactorily preserved in 70 ethyl alcohol (or 70 methylated spirit or denatured alcohol) with 30 water Colours will fade quickly in spirit however so it is a good idea to keep comprehensive notes and photographs

87

Small algae Microscopic algae are often collected in a jar and in the

water in which they were found If the algae are to be stored for more than 2-3 days a preservative needs to be used Traditionally this has been the extremely toxic formalin - a small amount can be added to the water to make a 5 final solution and the container labelled This must not be sent through the post or by courier

There are some other equally toxic options for example propylene phenoxytol but none should be sent through the post A safer option is to add sufficient concentrated alcohol or methylated spirits to the water containing the algae to make a final solution of 70 alcohol This treatment dilutes the algae making them difficult to find so if they can be concentrated somehow first (eg by filtering) they can be stored in much less liquid Another option is to fix the algae in formalin (or something similar) first and then prepare a microscope glass slide with a permanent water-soluble mounting medium

88

Mounting Mounting specimens prevents most fragile material from

fragmenting and prevents specimens becoming separated from their labels If the plant collection is a long-term project specimens should be mounted on sheets of archival (permanent) cardboard or paper with archival-quality fixing media These include stitching with cotton thread dental floss nickel-plated copper wire (for heavier specimens) narrow strips of archival paper linen tape or by using an archival adhesive such as methyl cellulose adhesive

One disadvantage of mounting specimens is that it can make parts of the specimen inaccessible for examination so it is essential that this be borne in mind during specimen arrangement and mounting For example easily reversible mounting media should be used specimens should be strapped to the sheet rather than glued all over and the specimen should be carefully arranged before it is attached so that it shows all features

89

Full-size herbarium mounting sheets are usually about 43 cm long x 28 cm wide The plant name and accompanying field notes should be transcribed on a permanent label stuck to one corner of the herbarium sheet (the bottom right-hand corner being the most common) or sometimes annotations may be written directly on the sheet or card

Small pieces of material which may have become separated from the specimen (eg seeds) can be placed in small plastic bags and pinned to the sheet

90

Long-term preservation and storage The long-term preservation of dry plant

specimens is largely dependent on protection from insect attack Specimens collected by Linnaeus in the eighteenth century and by Banks and Solander on the Endeavour voyage in 1788 are still excellently preserved

91

Pests and their control A range of pests attack dried plant material The

most common pests are insects and fungi though rodents and other large animals can cause damage in poor storage conditions Insects eat the material the paper surrounding the material and the adhesives and mounting media

Such insect pests range from psocids (book lice) which attack mainly the softer parts such as flowers and soft fruits to tobacco beetles and carpet beetles which can bore holes through the toughest of specimens Many insects are particularly sensitive to relative humidity levels and do not thrive at levels below 50

92

The most common and acceptable specimen treatments for insect control are Freezing Microwave Poisoning Insect deterrents Fungal pests

93

Storage

Dried and pressed plant specimens can be stored in cardboard or plastic boxes or tied in bundles in light-weight cardboard folders placed in pigeon holes

Alternatively they can be placed in protective plastic jackets and displayed in ring folders which is recommended if they are to be frequently handled such as for a reference collection

94

Filing

Specimens should be filed in a systematic order if a relatively permanent collection is being made The major groups ie ferns and fern allies cycads conifers dicotyledons and monocotyledons are best kept separately or according to some classification scheme such as that given in a flora or handbook

Similarly the genera within each family and the species within each genus may be filed alphabetically or following some such classification

95

Preservation of entire animals

Types of collection specimens of an entire animal For reference collections mammals can be prepared as a variety of specimens The condition of the specimen may determine possible ways to preserve it if for instance decomposition of the skin has loosened the hair of a carcass so much that it can easily be pulled out or removed by rubbing (ldquoslippingrdquo fur) it will be very difficult or impossible to produce a study skin or mounted specimen The most usual types of specimens (based on Nagorsen and Peterson 1980) are 1) entire fluid-preserved animals (for studying anatomy and histology fluid preservation may change the fur colour) 2) study skins with accompanying skulls partial skeletons (some bones remain in the skin) for studying pelage colour hair quality and moulting patterns 3) mounted skins with accompanying partial or entire skeleton (some bones may remain in the skin dependant on the method of preservation) or freeze-dried specimens 4) entire skeletons for instance for studying anatomy geographic variation or for age determination (entire skeletons are poorly represented in collections so Nagorsen and Peterson (1980) recommend preparation of at least one male and one female skeleton per species

96

Preservation of specimens in the field Formalin preservation Preservation in alcohol Preservation by cooling or freezing

97

Formalin preservation After weighing and measuring the animal and attaching an

adequate label very small specimens (up to 100 g) can be fixed whole by submerging them in 10 buffered formalin (tissue - formalin solution ratio of at least 1 12) the body cavity can be filled with formalin solution by injection until it is turgid and firm some formalin may also be injected under the skin into the body cavity larger muscles and organs If hypodermic needles are not available the body cavity can be opened ventrally by making a slit instead allowing the formalin to enter

Keeping the mouth open with a piece of wood or cotton may later allow examination of teeth Then the whole body can be immersed in formalin in the posture in which it is supposed to stay permanently because it will harden The ratio of formalin to carcass must be at least 12 to 1 to assure a good fixation Tissues can be left in buffered neutralized formalin for several months but formalin hardens specimens therefore after fixation longterm storage in alcohol may be better After preservation the carcass should therefore be washed in water and transferred into ethanol for permanent storage

Disadvantages for instance it discolours the fur after a longish immersion softens the bones and prevents further examination for microbiology

98

Preservation in alcohol

After weighing a whole animal can be preserved in a container of alcohol (70-90) Removal of the intestine prior to storage of the animal in alcohol is recommended

99

Preservation by cooling or freezing Removal of the skin with insulating fur

before cooling or freezing may help to cool the carcass down more quickly

Freezing is not recommended if histological examination is planned

100

THANK YOU

83

Pressing and drying Techniques for pressing and drying specimens have been

established for many years There are minor variations in recommended methods but they are essentially the same worldwide

The best specimens are plants that are pressed as soon as possible after collection before wilting and shrivelling Most plants may be kept in sealed containers such as plastic bags for up to a day if it is inconvenient to press immediately However some plants show such rapid wilting particularly of the flowers that such delays are best avoided Flowers with a lot of nectar may go mouldy very quickly if excess nectar is not shaken off before pressing

Specimens are pressed flat and dried between sheets of absorbent blotters or semi-absorbent paper such as newspaper Papers with a glossy surface should be avoided because they are not absorbent enough to aid drying The plant should be carefully laid out between the drying sheets as their form at this stage largely determines their ultimate appearance The flowers should be spread out with the petals carefully arranged wilted leaves should be straightened and unnecessary shoots of excessively twiggy shrubs may be cut away

84

Microwave ovens Small numbers of specimens can be dried using a microwave

oven The technique recommended in the literature is to place the specimens between unprinted absorbent paper for example butchers paper not newspaper which is unsuitable because the chemicals present in the ink may cause a fire The specimens should be put in a special press which should be of a microwave-safe material (wood acrylic or polycarbonate sheeting eg plexiglass or perspex NO metal components) If such a press is not available sheets of cardboard can be placed above and below the specimens and then weighted down

Drying time depends on the power of your oven In most cases drying is accomplished by irradiating at maximum power for 1-2 minutes per specimen although it is often a case of trial and error It is best to process no more than 10-12 specimens of average thickness per batch Specimens are usually dried after the moisture that characteristically appears on the glass door has disappeared If the specimen is damp when taken out of the oven allow it to stand before re-radiating as moisture continues to evaporate from the specimen for some time Care must be taken not to irradiate the specimens for too long

It should be noted that microwave treatment damages seeds and the cellular structure of the plants which may reduce the long-term value of the specimens

85

Alternative drying techniquesSilica gelother desiccants amp freeze drying Alternative methods of drying plant specimens have been

used for some time but are mostly restricted to special purpose collections The main alternatives are freeze-drying and drying in a desiccant powder such as desiccant silica gel In general these techniques are used where it is essential to preserve the shape of a delicate plant of organ of the plant such as the flower Freeze-drying has also been used to preserve the chemical composition of a plant as accurately as possible for later study

Disadvantages and special conservation problems of specimens dried in these manners are that they are particularly susceptible to damage The dried parts are fragile lack support and often catch on packing materials They must therefore be packed especially carefully and stored in small boxes or tubes with some appropriate packing material that does not snag and break small projections Acid-free tissue paper is often used Drying in desiccant silica gel crystals or powder can also have the disadvantage that it is difficult to remove all traces of the silica gel after drying

86

Special preservation and processing techniquesWet or spirit collections

Very fleshy or delicate structures including small algae and orchid flowers are best preserved in an air-tight glass or plastic jar with a liquid preservative rather than by drying The type of preservative used should be clearly labelled in the jar Such material is often referred to as a spirit collection or wet collection

Most material can be satisfactorily preserved in 70 ethyl alcohol (or 70 methylated spirit or denatured alcohol) with 30 water Colours will fade quickly in spirit however so it is a good idea to keep comprehensive notes and photographs

87

Small algae Microscopic algae are often collected in a jar and in the

water in which they were found If the algae are to be stored for more than 2-3 days a preservative needs to be used Traditionally this has been the extremely toxic formalin - a small amount can be added to the water to make a 5 final solution and the container labelled This must not be sent through the post or by courier

There are some other equally toxic options for example propylene phenoxytol but none should be sent through the post A safer option is to add sufficient concentrated alcohol or methylated spirits to the water containing the algae to make a final solution of 70 alcohol This treatment dilutes the algae making them difficult to find so if they can be concentrated somehow first (eg by filtering) they can be stored in much less liquid Another option is to fix the algae in formalin (or something similar) first and then prepare a microscope glass slide with a permanent water-soluble mounting medium

88

Mounting Mounting specimens prevents most fragile material from

fragmenting and prevents specimens becoming separated from their labels If the plant collection is a long-term project specimens should be mounted on sheets of archival (permanent) cardboard or paper with archival-quality fixing media These include stitching with cotton thread dental floss nickel-plated copper wire (for heavier specimens) narrow strips of archival paper linen tape or by using an archival adhesive such as methyl cellulose adhesive

One disadvantage of mounting specimens is that it can make parts of the specimen inaccessible for examination so it is essential that this be borne in mind during specimen arrangement and mounting For example easily reversible mounting media should be used specimens should be strapped to the sheet rather than glued all over and the specimen should be carefully arranged before it is attached so that it shows all features

89

Full-size herbarium mounting sheets are usually about 43 cm long x 28 cm wide The plant name and accompanying field notes should be transcribed on a permanent label stuck to one corner of the herbarium sheet (the bottom right-hand corner being the most common) or sometimes annotations may be written directly on the sheet or card

Small pieces of material which may have become separated from the specimen (eg seeds) can be placed in small plastic bags and pinned to the sheet

90

Long-term preservation and storage The long-term preservation of dry plant

specimens is largely dependent on protection from insect attack Specimens collected by Linnaeus in the eighteenth century and by Banks and Solander on the Endeavour voyage in 1788 are still excellently preserved

91

Pests and their control A range of pests attack dried plant material The

most common pests are insects and fungi though rodents and other large animals can cause damage in poor storage conditions Insects eat the material the paper surrounding the material and the adhesives and mounting media

Such insect pests range from psocids (book lice) which attack mainly the softer parts such as flowers and soft fruits to tobacco beetles and carpet beetles which can bore holes through the toughest of specimens Many insects are particularly sensitive to relative humidity levels and do not thrive at levels below 50

92

The most common and acceptable specimen treatments for insect control are Freezing Microwave Poisoning Insect deterrents Fungal pests

93

Storage

Dried and pressed plant specimens can be stored in cardboard or plastic boxes or tied in bundles in light-weight cardboard folders placed in pigeon holes

Alternatively they can be placed in protective plastic jackets and displayed in ring folders which is recommended if they are to be frequently handled such as for a reference collection

94

Filing

Specimens should be filed in a systematic order if a relatively permanent collection is being made The major groups ie ferns and fern allies cycads conifers dicotyledons and monocotyledons are best kept separately or according to some classification scheme such as that given in a flora or handbook

Similarly the genera within each family and the species within each genus may be filed alphabetically or following some such classification

95

Preservation of entire animals

Types of collection specimens of an entire animal For reference collections mammals can be prepared as a variety of specimens The condition of the specimen may determine possible ways to preserve it if for instance decomposition of the skin has loosened the hair of a carcass so much that it can easily be pulled out or removed by rubbing (ldquoslippingrdquo fur) it will be very difficult or impossible to produce a study skin or mounted specimen The most usual types of specimens (based on Nagorsen and Peterson 1980) are 1) entire fluid-preserved animals (for studying anatomy and histology fluid preservation may change the fur colour) 2) study skins with accompanying skulls partial skeletons (some bones remain in the skin) for studying pelage colour hair quality and moulting patterns 3) mounted skins with accompanying partial or entire skeleton (some bones may remain in the skin dependant on the method of preservation) or freeze-dried specimens 4) entire skeletons for instance for studying anatomy geographic variation or for age determination (entire skeletons are poorly represented in collections so Nagorsen and Peterson (1980) recommend preparation of at least one male and one female skeleton per species

96

Preservation of specimens in the field Formalin preservation Preservation in alcohol Preservation by cooling or freezing

97

Formalin preservation After weighing and measuring the animal and attaching an

adequate label very small specimens (up to 100 g) can be fixed whole by submerging them in 10 buffered formalin (tissue - formalin solution ratio of at least 1 12) the body cavity can be filled with formalin solution by injection until it is turgid and firm some formalin may also be injected under the skin into the body cavity larger muscles and organs If hypodermic needles are not available the body cavity can be opened ventrally by making a slit instead allowing the formalin to enter

Keeping the mouth open with a piece of wood or cotton may later allow examination of teeth Then the whole body can be immersed in formalin in the posture in which it is supposed to stay permanently because it will harden The ratio of formalin to carcass must be at least 12 to 1 to assure a good fixation Tissues can be left in buffered neutralized formalin for several months but formalin hardens specimens therefore after fixation longterm storage in alcohol may be better After preservation the carcass should therefore be washed in water and transferred into ethanol for permanent storage

Disadvantages for instance it discolours the fur after a longish immersion softens the bones and prevents further examination for microbiology

98

Preservation in alcohol

After weighing a whole animal can be preserved in a container of alcohol (70-90) Removal of the intestine prior to storage of the animal in alcohol is recommended

99

Preservation by cooling or freezing Removal of the skin with insulating fur

before cooling or freezing may help to cool the carcass down more quickly

Freezing is not recommended if histological examination is planned

100

THANK YOU

84

Microwave ovens Small numbers of specimens can be dried using a microwave

oven The technique recommended in the literature is to place the specimens between unprinted absorbent paper for example butchers paper not newspaper which is unsuitable because the chemicals present in the ink may cause a fire The specimens should be put in a special press which should be of a microwave-safe material (wood acrylic or polycarbonate sheeting eg plexiglass or perspex NO metal components) If such a press is not available sheets of cardboard can be placed above and below the specimens and then weighted down

Drying time depends on the power of your oven In most cases drying is accomplished by irradiating at maximum power for 1-2 minutes per specimen although it is often a case of trial and error It is best to process no more than 10-12 specimens of average thickness per batch Specimens are usually dried after the moisture that characteristically appears on the glass door has disappeared If the specimen is damp when taken out of the oven allow it to stand before re-radiating as moisture continues to evaporate from the specimen for some time Care must be taken not to irradiate the specimens for too long

It should be noted that microwave treatment damages seeds and the cellular structure of the plants which may reduce the long-term value of the specimens

85

Alternative drying techniquesSilica gelother desiccants amp freeze drying Alternative methods of drying plant specimens have been

used for some time but are mostly restricted to special purpose collections The main alternatives are freeze-drying and drying in a desiccant powder such as desiccant silica gel In general these techniques are used where it is essential to preserve the shape of a delicate plant of organ of the plant such as the flower Freeze-drying has also been used to preserve the chemical composition of a plant as accurately as possible for later study

Disadvantages and special conservation problems of specimens dried in these manners are that they are particularly susceptible to damage The dried parts are fragile lack support and often catch on packing materials They must therefore be packed especially carefully and stored in small boxes or tubes with some appropriate packing material that does not snag and break small projections Acid-free tissue paper is often used Drying in desiccant silica gel crystals or powder can also have the disadvantage that it is difficult to remove all traces of the silica gel after drying

86

Special preservation and processing techniquesWet or spirit collections

Very fleshy or delicate structures including small algae and orchid flowers are best preserved in an air-tight glass or plastic jar with a liquid preservative rather than by drying The type of preservative used should be clearly labelled in the jar Such material is often referred to as a spirit collection or wet collection

Most material can be satisfactorily preserved in 70 ethyl alcohol (or 70 methylated spirit or denatured alcohol) with 30 water Colours will fade quickly in spirit however so it is a good idea to keep comprehensive notes and photographs

87

Small algae Microscopic algae are often collected in a jar and in the

water in which they were found If the algae are to be stored for more than 2-3 days a preservative needs to be used Traditionally this has been the extremely toxic formalin - a small amount can be added to the water to make a 5 final solution and the container labelled This must not be sent through the post or by courier

There are some other equally toxic options for example propylene phenoxytol but none should be sent through the post A safer option is to add sufficient concentrated alcohol or methylated spirits to the water containing the algae to make a final solution of 70 alcohol This treatment dilutes the algae making them difficult to find so if they can be concentrated somehow first (eg by filtering) they can be stored in much less liquid Another option is to fix the algae in formalin (or something similar) first and then prepare a microscope glass slide with a permanent water-soluble mounting medium

88

Mounting Mounting specimens prevents most fragile material from

fragmenting and prevents specimens becoming separated from their labels If the plant collection is a long-term project specimens should be mounted on sheets of archival (permanent) cardboard or paper with archival-quality fixing media These include stitching with cotton thread dental floss nickel-plated copper wire (for heavier specimens) narrow strips of archival paper linen tape or by using an archival adhesive such as methyl cellulose adhesive

One disadvantage of mounting specimens is that it can make parts of the specimen inaccessible for examination so it is essential that this be borne in mind during specimen arrangement and mounting For example easily reversible mounting media should be used specimens should be strapped to the sheet rather than glued all over and the specimen should be carefully arranged before it is attached so that it shows all features

89

Full-size herbarium mounting sheets are usually about 43 cm long x 28 cm wide The plant name and accompanying field notes should be transcribed on a permanent label stuck to one corner of the herbarium sheet (the bottom right-hand corner being the most common) or sometimes annotations may be written directly on the sheet or card

Small pieces of material which may have become separated from the specimen (eg seeds) can be placed in small plastic bags and pinned to the sheet

90

Long-term preservation and storage The long-term preservation of dry plant

specimens is largely dependent on protection from insect attack Specimens collected by Linnaeus in the eighteenth century and by Banks and Solander on the Endeavour voyage in 1788 are still excellently preserved

91

Pests and their control A range of pests attack dried plant material The

most common pests are insects and fungi though rodents and other large animals can cause damage in poor storage conditions Insects eat the material the paper surrounding the material and the adhesives and mounting media

Such insect pests range from psocids (book lice) which attack mainly the softer parts such as flowers and soft fruits to tobacco beetles and carpet beetles which can bore holes through the toughest of specimens Many insects are particularly sensitive to relative humidity levels and do not thrive at levels below 50

92

The most common and acceptable specimen treatments for insect control are Freezing Microwave Poisoning Insect deterrents Fungal pests

93

Storage

Dried and pressed plant specimens can be stored in cardboard or plastic boxes or tied in bundles in light-weight cardboard folders placed in pigeon holes

Alternatively they can be placed in protective plastic jackets and displayed in ring folders which is recommended if they are to be frequently handled such as for a reference collection

94

Filing

Specimens should be filed in a systematic order if a relatively permanent collection is being made The major groups ie ferns and fern allies cycads conifers dicotyledons and monocotyledons are best kept separately or according to some classification scheme such as that given in a flora or handbook

Similarly the genera within each family and the species within each genus may be filed alphabetically or following some such classification

95

Preservation of entire animals

Types of collection specimens of an entire animal For reference collections mammals can be prepared as a variety of specimens The condition of the specimen may determine possible ways to preserve it if for instance decomposition of the skin has loosened the hair of a carcass so much that it can easily be pulled out or removed by rubbing (ldquoslippingrdquo fur) it will be very difficult or impossible to produce a study skin or mounted specimen The most usual types of specimens (based on Nagorsen and Peterson 1980) are 1) entire fluid-preserved animals (for studying anatomy and histology fluid preservation may change the fur colour) 2) study skins with accompanying skulls partial skeletons (some bones remain in the skin) for studying pelage colour hair quality and moulting patterns 3) mounted skins with accompanying partial or entire skeleton (some bones may remain in the skin dependant on the method of preservation) or freeze-dried specimens 4) entire skeletons for instance for studying anatomy geographic variation or for age determination (entire skeletons are poorly represented in collections so Nagorsen and Peterson (1980) recommend preparation of at least one male and one female skeleton per species

96

Preservation of specimens in the field Formalin preservation Preservation in alcohol Preservation by cooling or freezing

97

Formalin preservation After weighing and measuring the animal and attaching an

adequate label very small specimens (up to 100 g) can be fixed whole by submerging them in 10 buffered formalin (tissue - formalin solution ratio of at least 1 12) the body cavity can be filled with formalin solution by injection until it is turgid and firm some formalin may also be injected under the skin into the body cavity larger muscles and organs If hypodermic needles are not available the body cavity can be opened ventrally by making a slit instead allowing the formalin to enter

Keeping the mouth open with a piece of wood or cotton may later allow examination of teeth Then the whole body can be immersed in formalin in the posture in which it is supposed to stay permanently because it will harden The ratio of formalin to carcass must be at least 12 to 1 to assure a good fixation Tissues can be left in buffered neutralized formalin for several months but formalin hardens specimens therefore after fixation longterm storage in alcohol may be better After preservation the carcass should therefore be washed in water and transferred into ethanol for permanent storage

Disadvantages for instance it discolours the fur after a longish immersion softens the bones and prevents further examination for microbiology

98

Preservation in alcohol

After weighing a whole animal can be preserved in a container of alcohol (70-90) Removal of the intestine prior to storage of the animal in alcohol is recommended

99

Preservation by cooling or freezing Removal of the skin with insulating fur

before cooling or freezing may help to cool the carcass down more quickly

Freezing is not recommended if histological examination is planned

100

THANK YOU

85

Alternative drying techniquesSilica gelother desiccants amp freeze drying Alternative methods of drying plant specimens have been

used for some time but are mostly restricted to special purpose collections The main alternatives are freeze-drying and drying in a desiccant powder such as desiccant silica gel In general these techniques are used where it is essential to preserve the shape of a delicate plant of organ of the plant such as the flower Freeze-drying has also been used to preserve the chemical composition of a plant as accurately as possible for later study

Disadvantages and special conservation problems of specimens dried in these manners are that they are particularly susceptible to damage The dried parts are fragile lack support and often catch on packing materials They must therefore be packed especially carefully and stored in small boxes or tubes with some appropriate packing material that does not snag and break small projections Acid-free tissue paper is often used Drying in desiccant silica gel crystals or powder can also have the disadvantage that it is difficult to remove all traces of the silica gel after drying

86

Special preservation and processing techniquesWet or spirit collections

Very fleshy or delicate structures including small algae and orchid flowers are best preserved in an air-tight glass or plastic jar with a liquid preservative rather than by drying The type of preservative used should be clearly labelled in the jar Such material is often referred to as a spirit collection or wet collection

Most material can be satisfactorily preserved in 70 ethyl alcohol (or 70 methylated spirit or denatured alcohol) with 30 water Colours will fade quickly in spirit however so it is a good idea to keep comprehensive notes and photographs

87

Small algae Microscopic algae are often collected in a jar and in the

water in which they were found If the algae are to be stored for more than 2-3 days a preservative needs to be used Traditionally this has been the extremely toxic formalin - a small amount can be added to the water to make a 5 final solution and the container labelled This must not be sent through the post or by courier

There are some other equally toxic options for example propylene phenoxytol but none should be sent through the post A safer option is to add sufficient concentrated alcohol or methylated spirits to the water containing the algae to make a final solution of 70 alcohol This treatment dilutes the algae making them difficult to find so if they can be concentrated somehow first (eg by filtering) they can be stored in much less liquid Another option is to fix the algae in formalin (or something similar) first and then prepare a microscope glass slide with a permanent water-soluble mounting medium

88

Mounting Mounting specimens prevents most fragile material from

fragmenting and prevents specimens becoming separated from their labels If the plant collection is a long-term project specimens should be mounted on sheets of archival (permanent) cardboard or paper with archival-quality fixing media These include stitching with cotton thread dental floss nickel-plated copper wire (for heavier specimens) narrow strips of archival paper linen tape or by using an archival adhesive such as methyl cellulose adhesive

One disadvantage of mounting specimens is that it can make parts of the specimen inaccessible for examination so it is essential that this be borne in mind during specimen arrangement and mounting For example easily reversible mounting media should be used specimens should be strapped to the sheet rather than glued all over and the specimen should be carefully arranged before it is attached so that it shows all features

89

Full-size herbarium mounting sheets are usually about 43 cm long x 28 cm wide The plant name and accompanying field notes should be transcribed on a permanent label stuck to one corner of the herbarium sheet (the bottom right-hand corner being the most common) or sometimes annotations may be written directly on the sheet or card

Small pieces of material which may have become separated from the specimen (eg seeds) can be placed in small plastic bags and pinned to the sheet

90

Long-term preservation and storage The long-term preservation of dry plant

specimens is largely dependent on protection from insect attack Specimens collected by Linnaeus in the eighteenth century and by Banks and Solander on the Endeavour voyage in 1788 are still excellently preserved

91

Pests and their control A range of pests attack dried plant material The

most common pests are insects and fungi though rodents and other large animals can cause damage in poor storage conditions Insects eat the material the paper surrounding the material and the adhesives and mounting media

Such insect pests range from psocids (book lice) which attack mainly the softer parts such as flowers and soft fruits to tobacco beetles and carpet beetles which can bore holes through the toughest of specimens Many insects are particularly sensitive to relative humidity levels and do not thrive at levels below 50

92

The most common and acceptable specimen treatments for insect control are Freezing Microwave Poisoning Insect deterrents Fungal pests

93

Storage

Dried and pressed plant specimens can be stored in cardboard or plastic boxes or tied in bundles in light-weight cardboard folders placed in pigeon holes

Alternatively they can be placed in protective plastic jackets and displayed in ring folders which is recommended if they are to be frequently handled such as for a reference collection

94

Filing

Specimens should be filed in a systematic order if a relatively permanent collection is being made The major groups ie ferns and fern allies cycads conifers dicotyledons and monocotyledons are best kept separately or according to some classification scheme such as that given in a flora or handbook

Similarly the genera within each family and the species within each genus may be filed alphabetically or following some such classification

95

Preservation of entire animals

Types of collection specimens of an entire animal For reference collections mammals can be prepared as a variety of specimens The condition of the specimen may determine possible ways to preserve it if for instance decomposition of the skin has loosened the hair of a carcass so much that it can easily be pulled out or removed by rubbing (ldquoslippingrdquo fur) it will be very difficult or impossible to produce a study skin or mounted specimen The most usual types of specimens (based on Nagorsen and Peterson 1980) are 1) entire fluid-preserved animals (for studying anatomy and histology fluid preservation may change the fur colour) 2) study skins with accompanying skulls partial skeletons (some bones remain in the skin) for studying pelage colour hair quality and moulting patterns 3) mounted skins with accompanying partial or entire skeleton (some bones may remain in the skin dependant on the method of preservation) or freeze-dried specimens 4) entire skeletons for instance for studying anatomy geographic variation or for age determination (entire skeletons are poorly represented in collections so Nagorsen and Peterson (1980) recommend preparation of at least one male and one female skeleton per species

96

Preservation of specimens in the field Formalin preservation Preservation in alcohol Preservation by cooling or freezing

97

Formalin preservation After weighing and measuring the animal and attaching an

adequate label very small specimens (up to 100 g) can be fixed whole by submerging them in 10 buffered formalin (tissue - formalin solution ratio of at least 1 12) the body cavity can be filled with formalin solution by injection until it is turgid and firm some formalin may also be injected under the skin into the body cavity larger muscles and organs If hypodermic needles are not available the body cavity can be opened ventrally by making a slit instead allowing the formalin to enter

Keeping the mouth open with a piece of wood or cotton may later allow examination of teeth Then the whole body can be immersed in formalin in the posture in which it is supposed to stay permanently because it will harden The ratio of formalin to carcass must be at least 12 to 1 to assure a good fixation Tissues can be left in buffered neutralized formalin for several months but formalin hardens specimens therefore after fixation longterm storage in alcohol may be better After preservation the carcass should therefore be washed in water and transferred into ethanol for permanent storage

Disadvantages for instance it discolours the fur after a longish immersion softens the bones and prevents further examination for microbiology

98

Preservation in alcohol

After weighing a whole animal can be preserved in a container of alcohol (70-90) Removal of the intestine prior to storage of the animal in alcohol is recommended

99

Preservation by cooling or freezing Removal of the skin with insulating fur

before cooling or freezing may help to cool the carcass down more quickly

Freezing is not recommended if histological examination is planned

100

THANK YOU

86

Special preservation and processing techniquesWet or spirit collections

Very fleshy or delicate structures including small algae and orchid flowers are best preserved in an air-tight glass or plastic jar with a liquid preservative rather than by drying The type of preservative used should be clearly labelled in the jar Such material is often referred to as a spirit collection or wet collection

Most material can be satisfactorily preserved in 70 ethyl alcohol (or 70 methylated spirit or denatured alcohol) with 30 water Colours will fade quickly in spirit however so it is a good idea to keep comprehensive notes and photographs

87

Small algae Microscopic algae are often collected in a jar and in the

water in which they were found If the algae are to be stored for more than 2-3 days a preservative needs to be used Traditionally this has been the extremely toxic formalin - a small amount can be added to the water to make a 5 final solution and the container labelled This must not be sent through the post or by courier

There are some other equally toxic options for example propylene phenoxytol but none should be sent through the post A safer option is to add sufficient concentrated alcohol or methylated spirits to the water containing the algae to make a final solution of 70 alcohol This treatment dilutes the algae making them difficult to find so if they can be concentrated somehow first (eg by filtering) they can be stored in much less liquid Another option is to fix the algae in formalin (or something similar) first and then prepare a microscope glass slide with a permanent water-soluble mounting medium

88

Mounting Mounting specimens prevents most fragile material from

fragmenting and prevents specimens becoming separated from their labels If the plant collection is a long-term project specimens should be mounted on sheets of archival (permanent) cardboard or paper with archival-quality fixing media These include stitching with cotton thread dental floss nickel-plated copper wire (for heavier specimens) narrow strips of archival paper linen tape or by using an archival adhesive such as methyl cellulose adhesive

One disadvantage of mounting specimens is that it can make parts of the specimen inaccessible for examination so it is essential that this be borne in mind during specimen arrangement and mounting For example easily reversible mounting media should be used specimens should be strapped to the sheet rather than glued all over and the specimen should be carefully arranged before it is attached so that it shows all features

89

Full-size herbarium mounting sheets are usually about 43 cm long x 28 cm wide The plant name and accompanying field notes should be transcribed on a permanent label stuck to one corner of the herbarium sheet (the bottom right-hand corner being the most common) or sometimes annotations may be written directly on the sheet or card

Small pieces of material which may have become separated from the specimen (eg seeds) can be placed in small plastic bags and pinned to the sheet

90

Long-term preservation and storage The long-term preservation of dry plant

specimens is largely dependent on protection from insect attack Specimens collected by Linnaeus in the eighteenth century and by Banks and Solander on the Endeavour voyage in 1788 are still excellently preserved

91

Pests and their control A range of pests attack dried plant material The

most common pests are insects and fungi though rodents and other large animals can cause damage in poor storage conditions Insects eat the material the paper surrounding the material and the adhesives and mounting media

Such insect pests range from psocids (book lice) which attack mainly the softer parts such as flowers and soft fruits to tobacco beetles and carpet beetles which can bore holes through the toughest of specimens Many insects are particularly sensitive to relative humidity levels and do not thrive at levels below 50

92

The most common and acceptable specimen treatments for insect control are Freezing Microwave Poisoning Insect deterrents Fungal pests

93

Storage

Dried and pressed plant specimens can be stored in cardboard or plastic boxes or tied in bundles in light-weight cardboard folders placed in pigeon holes

Alternatively they can be placed in protective plastic jackets and displayed in ring folders which is recommended if they are to be frequently handled such as for a reference collection

94

Filing

Specimens should be filed in a systematic order if a relatively permanent collection is being made The major groups ie ferns and fern allies cycads conifers dicotyledons and monocotyledons are best kept separately or according to some classification scheme such as that given in a flora or handbook

Similarly the genera within each family and the species within each genus may be filed alphabetically or following some such classification

95

Preservation of entire animals

Types of collection specimens of an entire animal For reference collections mammals can be prepared as a variety of specimens The condition of the specimen may determine possible ways to preserve it if for instance decomposition of the skin has loosened the hair of a carcass so much that it can easily be pulled out or removed by rubbing (ldquoslippingrdquo fur) it will be very difficult or impossible to produce a study skin or mounted specimen The most usual types of specimens (based on Nagorsen and Peterson 1980) are 1) entire fluid-preserved animals (for studying anatomy and histology fluid preservation may change the fur colour) 2) study skins with accompanying skulls partial skeletons (some bones remain in the skin) for studying pelage colour hair quality and moulting patterns 3) mounted skins with accompanying partial or entire skeleton (some bones may remain in the skin dependant on the method of preservation) or freeze-dried specimens 4) entire skeletons for instance for studying anatomy geographic variation or for age determination (entire skeletons are poorly represented in collections so Nagorsen and Peterson (1980) recommend preparation of at least one male and one female skeleton per species

96

Preservation of specimens in the field Formalin preservation Preservation in alcohol Preservation by cooling or freezing

97

Formalin preservation After weighing and measuring the animal and attaching an

adequate label very small specimens (up to 100 g) can be fixed whole by submerging them in 10 buffered formalin (tissue - formalin solution ratio of at least 1 12) the body cavity can be filled with formalin solution by injection until it is turgid and firm some formalin may also be injected under the skin into the body cavity larger muscles and organs If hypodermic needles are not available the body cavity can be opened ventrally by making a slit instead allowing the formalin to enter

Keeping the mouth open with a piece of wood or cotton may later allow examination of teeth Then the whole body can be immersed in formalin in the posture in which it is supposed to stay permanently because it will harden The ratio of formalin to carcass must be at least 12 to 1 to assure a good fixation Tissues can be left in buffered neutralized formalin for several months but formalin hardens specimens therefore after fixation longterm storage in alcohol may be better After preservation the carcass should therefore be washed in water and transferred into ethanol for permanent storage

Disadvantages for instance it discolours the fur after a longish immersion softens the bones and prevents further examination for microbiology

98

Preservation in alcohol

After weighing a whole animal can be preserved in a container of alcohol (70-90) Removal of the intestine prior to storage of the animal in alcohol is recommended

99

Preservation by cooling or freezing Removal of the skin with insulating fur

before cooling or freezing may help to cool the carcass down more quickly

Freezing is not recommended if histological examination is planned

100

THANK YOU

87

Small algae Microscopic algae are often collected in a jar and in the

water in which they were found If the algae are to be stored for more than 2-3 days a preservative needs to be used Traditionally this has been the extremely toxic formalin - a small amount can be added to the water to make a 5 final solution and the container labelled This must not be sent through the post or by courier

There are some other equally toxic options for example propylene phenoxytol but none should be sent through the post A safer option is to add sufficient concentrated alcohol or methylated spirits to the water containing the algae to make a final solution of 70 alcohol This treatment dilutes the algae making them difficult to find so if they can be concentrated somehow first (eg by filtering) they can be stored in much less liquid Another option is to fix the algae in formalin (or something similar) first and then prepare a microscope glass slide with a permanent water-soluble mounting medium

88

Mounting Mounting specimens prevents most fragile material from

fragmenting and prevents specimens becoming separated from their labels If the plant collection is a long-term project specimens should be mounted on sheets of archival (permanent) cardboard or paper with archival-quality fixing media These include stitching with cotton thread dental floss nickel-plated copper wire (for heavier specimens) narrow strips of archival paper linen tape or by using an archival adhesive such as methyl cellulose adhesive

One disadvantage of mounting specimens is that it can make parts of the specimen inaccessible for examination so it is essential that this be borne in mind during specimen arrangement and mounting For example easily reversible mounting media should be used specimens should be strapped to the sheet rather than glued all over and the specimen should be carefully arranged before it is attached so that it shows all features

89

Full-size herbarium mounting sheets are usually about 43 cm long x 28 cm wide The plant name and accompanying field notes should be transcribed on a permanent label stuck to one corner of the herbarium sheet (the bottom right-hand corner being the most common) or sometimes annotations may be written directly on the sheet or card

Small pieces of material which may have become separated from the specimen (eg seeds) can be placed in small plastic bags and pinned to the sheet

90

Long-term preservation and storage The long-term preservation of dry plant

specimens is largely dependent on protection from insect attack Specimens collected by Linnaeus in the eighteenth century and by Banks and Solander on the Endeavour voyage in 1788 are still excellently preserved

91

Pests and their control A range of pests attack dried plant material The

most common pests are insects and fungi though rodents and other large animals can cause damage in poor storage conditions Insects eat the material the paper surrounding the material and the adhesives and mounting media

Such insect pests range from psocids (book lice) which attack mainly the softer parts such as flowers and soft fruits to tobacco beetles and carpet beetles which can bore holes through the toughest of specimens Many insects are particularly sensitive to relative humidity levels and do not thrive at levels below 50

92

The most common and acceptable specimen treatments for insect control are Freezing Microwave Poisoning Insect deterrents Fungal pests

93

Storage

Dried and pressed plant specimens can be stored in cardboard or plastic boxes or tied in bundles in light-weight cardboard folders placed in pigeon holes

Alternatively they can be placed in protective plastic jackets and displayed in ring folders which is recommended if they are to be frequently handled such as for a reference collection

94

Filing

Specimens should be filed in a systematic order if a relatively permanent collection is being made The major groups ie ferns and fern allies cycads conifers dicotyledons and monocotyledons are best kept separately or according to some classification scheme such as that given in a flora or handbook

Similarly the genera within each family and the species within each genus may be filed alphabetically or following some such classification

95

Preservation of entire animals

Types of collection specimens of an entire animal For reference collections mammals can be prepared as a variety of specimens The condition of the specimen may determine possible ways to preserve it if for instance decomposition of the skin has loosened the hair of a carcass so much that it can easily be pulled out or removed by rubbing (ldquoslippingrdquo fur) it will be very difficult or impossible to produce a study skin or mounted specimen The most usual types of specimens (based on Nagorsen and Peterson 1980) are 1) entire fluid-preserved animals (for studying anatomy and histology fluid preservation may change the fur colour) 2) study skins with accompanying skulls partial skeletons (some bones remain in the skin) for studying pelage colour hair quality and moulting patterns 3) mounted skins with accompanying partial or entire skeleton (some bones may remain in the skin dependant on the method of preservation) or freeze-dried specimens 4) entire skeletons for instance for studying anatomy geographic variation or for age determination (entire skeletons are poorly represented in collections so Nagorsen and Peterson (1980) recommend preparation of at least one male and one female skeleton per species

96

Preservation of specimens in the field Formalin preservation Preservation in alcohol Preservation by cooling or freezing

97

Formalin preservation After weighing and measuring the animal and attaching an

adequate label very small specimens (up to 100 g) can be fixed whole by submerging them in 10 buffered formalin (tissue - formalin solution ratio of at least 1 12) the body cavity can be filled with formalin solution by injection until it is turgid and firm some formalin may also be injected under the skin into the body cavity larger muscles and organs If hypodermic needles are not available the body cavity can be opened ventrally by making a slit instead allowing the formalin to enter

Keeping the mouth open with a piece of wood or cotton may later allow examination of teeth Then the whole body can be immersed in formalin in the posture in which it is supposed to stay permanently because it will harden The ratio of formalin to carcass must be at least 12 to 1 to assure a good fixation Tissues can be left in buffered neutralized formalin for several months but formalin hardens specimens therefore after fixation longterm storage in alcohol may be better After preservation the carcass should therefore be washed in water and transferred into ethanol for permanent storage

Disadvantages for instance it discolours the fur after a longish immersion softens the bones and prevents further examination for microbiology

98

Preservation in alcohol

After weighing a whole animal can be preserved in a container of alcohol (70-90) Removal of the intestine prior to storage of the animal in alcohol is recommended

99

Preservation by cooling or freezing Removal of the skin with insulating fur

before cooling or freezing may help to cool the carcass down more quickly

Freezing is not recommended if histological examination is planned

100

THANK YOU

88

Mounting Mounting specimens prevents most fragile material from

fragmenting and prevents specimens becoming separated from their labels If the plant collection is a long-term project specimens should be mounted on sheets of archival (permanent) cardboard or paper with archival-quality fixing media These include stitching with cotton thread dental floss nickel-plated copper wire (for heavier specimens) narrow strips of archival paper linen tape or by using an archival adhesive such as methyl cellulose adhesive

One disadvantage of mounting specimens is that it can make parts of the specimen inaccessible for examination so it is essential that this be borne in mind during specimen arrangement and mounting For example easily reversible mounting media should be used specimens should be strapped to the sheet rather than glued all over and the specimen should be carefully arranged before it is attached so that it shows all features

89

Full-size herbarium mounting sheets are usually about 43 cm long x 28 cm wide The plant name and accompanying field notes should be transcribed on a permanent label stuck to one corner of the herbarium sheet (the bottom right-hand corner being the most common) or sometimes annotations may be written directly on the sheet or card

Small pieces of material which may have become separated from the specimen (eg seeds) can be placed in small plastic bags and pinned to the sheet

90

Long-term preservation and storage The long-term preservation of dry plant

specimens is largely dependent on protection from insect attack Specimens collected by Linnaeus in the eighteenth century and by Banks and Solander on the Endeavour voyage in 1788 are still excellently preserved

91

Pests and their control A range of pests attack dried plant material The

most common pests are insects and fungi though rodents and other large animals can cause damage in poor storage conditions Insects eat the material the paper surrounding the material and the adhesives and mounting media

Such insect pests range from psocids (book lice) which attack mainly the softer parts such as flowers and soft fruits to tobacco beetles and carpet beetles which can bore holes through the toughest of specimens Many insects are particularly sensitive to relative humidity levels and do not thrive at levels below 50

92

The most common and acceptable specimen treatments for insect control are Freezing Microwave Poisoning Insect deterrents Fungal pests

93

Storage

Dried and pressed plant specimens can be stored in cardboard or plastic boxes or tied in bundles in light-weight cardboard folders placed in pigeon holes

Alternatively they can be placed in protective plastic jackets and displayed in ring folders which is recommended if they are to be frequently handled such as for a reference collection

94

Filing

Specimens should be filed in a systematic order if a relatively permanent collection is being made The major groups ie ferns and fern allies cycads conifers dicotyledons and monocotyledons are best kept separately or according to some classification scheme such as that given in a flora or handbook

Similarly the genera within each family and the species within each genus may be filed alphabetically or following some such classification

95

Preservation of entire animals

Types of collection specimens of an entire animal For reference collections mammals can be prepared as a variety of specimens The condition of the specimen may determine possible ways to preserve it if for instance decomposition of the skin has loosened the hair of a carcass so much that it can easily be pulled out or removed by rubbing (ldquoslippingrdquo fur) it will be very difficult or impossible to produce a study skin or mounted specimen The most usual types of specimens (based on Nagorsen and Peterson 1980) are 1) entire fluid-preserved animals (for studying anatomy and histology fluid preservation may change the fur colour) 2) study skins with accompanying skulls partial skeletons (some bones remain in the skin) for studying pelage colour hair quality and moulting patterns 3) mounted skins with accompanying partial or entire skeleton (some bones may remain in the skin dependant on the method of preservation) or freeze-dried specimens 4) entire skeletons for instance for studying anatomy geographic variation or for age determination (entire skeletons are poorly represented in collections so Nagorsen and Peterson (1980) recommend preparation of at least one male and one female skeleton per species

96

Preservation of specimens in the field Formalin preservation Preservation in alcohol Preservation by cooling or freezing

97

Formalin preservation After weighing and measuring the animal and attaching an

adequate label very small specimens (up to 100 g) can be fixed whole by submerging them in 10 buffered formalin (tissue - formalin solution ratio of at least 1 12) the body cavity can be filled with formalin solution by injection until it is turgid and firm some formalin may also be injected under the skin into the body cavity larger muscles and organs If hypodermic needles are not available the body cavity can be opened ventrally by making a slit instead allowing the formalin to enter

Keeping the mouth open with a piece of wood or cotton may later allow examination of teeth Then the whole body can be immersed in formalin in the posture in which it is supposed to stay permanently because it will harden The ratio of formalin to carcass must be at least 12 to 1 to assure a good fixation Tissues can be left in buffered neutralized formalin for several months but formalin hardens specimens therefore after fixation longterm storage in alcohol may be better After preservation the carcass should therefore be washed in water and transferred into ethanol for permanent storage

Disadvantages for instance it discolours the fur after a longish immersion softens the bones and prevents further examination for microbiology

98

Preservation in alcohol

After weighing a whole animal can be preserved in a container of alcohol (70-90) Removal of the intestine prior to storage of the animal in alcohol is recommended

99

Preservation by cooling or freezing Removal of the skin with insulating fur

before cooling or freezing may help to cool the carcass down more quickly

Freezing is not recommended if histological examination is planned

100

THANK YOU

89

Full-size herbarium mounting sheets are usually about 43 cm long x 28 cm wide The plant name and accompanying field notes should be transcribed on a permanent label stuck to one corner of the herbarium sheet (the bottom right-hand corner being the most common) or sometimes annotations may be written directly on the sheet or card

Small pieces of material which may have become separated from the specimen (eg seeds) can be placed in small plastic bags and pinned to the sheet

90

Long-term preservation and storage The long-term preservation of dry plant

specimens is largely dependent on protection from insect attack Specimens collected by Linnaeus in the eighteenth century and by Banks and Solander on the Endeavour voyage in 1788 are still excellently preserved

91

Pests and their control A range of pests attack dried plant material The

most common pests are insects and fungi though rodents and other large animals can cause damage in poor storage conditions Insects eat the material the paper surrounding the material and the adhesives and mounting media

Such insect pests range from psocids (book lice) which attack mainly the softer parts such as flowers and soft fruits to tobacco beetles and carpet beetles which can bore holes through the toughest of specimens Many insects are particularly sensitive to relative humidity levels and do not thrive at levels below 50

92

The most common and acceptable specimen treatments for insect control are Freezing Microwave Poisoning Insect deterrents Fungal pests

93

Storage

Dried and pressed plant specimens can be stored in cardboard or plastic boxes or tied in bundles in light-weight cardboard folders placed in pigeon holes

Alternatively they can be placed in protective plastic jackets and displayed in ring folders which is recommended if they are to be frequently handled such as for a reference collection

94

Filing

Specimens should be filed in a systematic order if a relatively permanent collection is being made The major groups ie ferns and fern allies cycads conifers dicotyledons and monocotyledons are best kept separately or according to some classification scheme such as that given in a flora or handbook

Similarly the genera within each family and the species within each genus may be filed alphabetically or following some such classification

95

Preservation of entire animals

Types of collection specimens of an entire animal For reference collections mammals can be prepared as a variety of specimens The condition of the specimen may determine possible ways to preserve it if for instance decomposition of the skin has loosened the hair of a carcass so much that it can easily be pulled out or removed by rubbing (ldquoslippingrdquo fur) it will be very difficult or impossible to produce a study skin or mounted specimen The most usual types of specimens (based on Nagorsen and Peterson 1980) are 1) entire fluid-preserved animals (for studying anatomy and histology fluid preservation may change the fur colour) 2) study skins with accompanying skulls partial skeletons (some bones remain in the skin) for studying pelage colour hair quality and moulting patterns 3) mounted skins with accompanying partial or entire skeleton (some bones may remain in the skin dependant on the method of preservation) or freeze-dried specimens 4) entire skeletons for instance for studying anatomy geographic variation or for age determination (entire skeletons are poorly represented in collections so Nagorsen and Peterson (1980) recommend preparation of at least one male and one female skeleton per species

96

Preservation of specimens in the field Formalin preservation Preservation in alcohol Preservation by cooling or freezing

97

Formalin preservation After weighing and measuring the animal and attaching an

adequate label very small specimens (up to 100 g) can be fixed whole by submerging them in 10 buffered formalin (tissue - formalin solution ratio of at least 1 12) the body cavity can be filled with formalin solution by injection until it is turgid and firm some formalin may also be injected under the skin into the body cavity larger muscles and organs If hypodermic needles are not available the body cavity can be opened ventrally by making a slit instead allowing the formalin to enter

Keeping the mouth open with a piece of wood or cotton may later allow examination of teeth Then the whole body can be immersed in formalin in the posture in which it is supposed to stay permanently because it will harden The ratio of formalin to carcass must be at least 12 to 1 to assure a good fixation Tissues can be left in buffered neutralized formalin for several months but formalin hardens specimens therefore after fixation longterm storage in alcohol may be better After preservation the carcass should therefore be washed in water and transferred into ethanol for permanent storage

Disadvantages for instance it discolours the fur after a longish immersion softens the bones and prevents further examination for microbiology

98

Preservation in alcohol

After weighing a whole animal can be preserved in a container of alcohol (70-90) Removal of the intestine prior to storage of the animal in alcohol is recommended

99

Preservation by cooling or freezing Removal of the skin with insulating fur

before cooling or freezing may help to cool the carcass down more quickly

Freezing is not recommended if histological examination is planned

100

THANK YOU

90

Long-term preservation and storage The long-term preservation of dry plant

specimens is largely dependent on protection from insect attack Specimens collected by Linnaeus in the eighteenth century and by Banks and Solander on the Endeavour voyage in 1788 are still excellently preserved

91

Pests and their control A range of pests attack dried plant material The

most common pests are insects and fungi though rodents and other large animals can cause damage in poor storage conditions Insects eat the material the paper surrounding the material and the adhesives and mounting media

Such insect pests range from psocids (book lice) which attack mainly the softer parts such as flowers and soft fruits to tobacco beetles and carpet beetles which can bore holes through the toughest of specimens Many insects are particularly sensitive to relative humidity levels and do not thrive at levels below 50

92

The most common and acceptable specimen treatments for insect control are Freezing Microwave Poisoning Insect deterrents Fungal pests

93

Storage

Dried and pressed plant specimens can be stored in cardboard or plastic boxes or tied in bundles in light-weight cardboard folders placed in pigeon holes

Alternatively they can be placed in protective plastic jackets and displayed in ring folders which is recommended if they are to be frequently handled such as for a reference collection

94

Filing

Specimens should be filed in a systematic order if a relatively permanent collection is being made The major groups ie ferns and fern allies cycads conifers dicotyledons and monocotyledons are best kept separately or according to some classification scheme such as that given in a flora or handbook

Similarly the genera within each family and the species within each genus may be filed alphabetically or following some such classification

95

Preservation of entire animals

Types of collection specimens of an entire animal For reference collections mammals can be prepared as a variety of specimens The condition of the specimen may determine possible ways to preserve it if for instance decomposition of the skin has loosened the hair of a carcass so much that it can easily be pulled out or removed by rubbing (ldquoslippingrdquo fur) it will be very difficult or impossible to produce a study skin or mounted specimen The most usual types of specimens (based on Nagorsen and Peterson 1980) are 1) entire fluid-preserved animals (for studying anatomy and histology fluid preservation may change the fur colour) 2) study skins with accompanying skulls partial skeletons (some bones remain in the skin) for studying pelage colour hair quality and moulting patterns 3) mounted skins with accompanying partial or entire skeleton (some bones may remain in the skin dependant on the method of preservation) or freeze-dried specimens 4) entire skeletons for instance for studying anatomy geographic variation or for age determination (entire skeletons are poorly represented in collections so Nagorsen and Peterson (1980) recommend preparation of at least one male and one female skeleton per species

96

Preservation of specimens in the field Formalin preservation Preservation in alcohol Preservation by cooling or freezing

97

Formalin preservation After weighing and measuring the animal and attaching an

adequate label very small specimens (up to 100 g) can be fixed whole by submerging them in 10 buffered formalin (tissue - formalin solution ratio of at least 1 12) the body cavity can be filled with formalin solution by injection until it is turgid and firm some formalin may also be injected under the skin into the body cavity larger muscles and organs If hypodermic needles are not available the body cavity can be opened ventrally by making a slit instead allowing the formalin to enter

Keeping the mouth open with a piece of wood or cotton may later allow examination of teeth Then the whole body can be immersed in formalin in the posture in which it is supposed to stay permanently because it will harden The ratio of formalin to carcass must be at least 12 to 1 to assure a good fixation Tissues can be left in buffered neutralized formalin for several months but formalin hardens specimens therefore after fixation longterm storage in alcohol may be better After preservation the carcass should therefore be washed in water and transferred into ethanol for permanent storage

Disadvantages for instance it discolours the fur after a longish immersion softens the bones and prevents further examination for microbiology

98

Preservation in alcohol

After weighing a whole animal can be preserved in a container of alcohol (70-90) Removal of the intestine prior to storage of the animal in alcohol is recommended

99

Preservation by cooling or freezing Removal of the skin with insulating fur

before cooling or freezing may help to cool the carcass down more quickly

Freezing is not recommended if histological examination is planned

100

THANK YOU

91

Pests and their control A range of pests attack dried plant material The

most common pests are insects and fungi though rodents and other large animals can cause damage in poor storage conditions Insects eat the material the paper surrounding the material and the adhesives and mounting media

Such insect pests range from psocids (book lice) which attack mainly the softer parts such as flowers and soft fruits to tobacco beetles and carpet beetles which can bore holes through the toughest of specimens Many insects are particularly sensitive to relative humidity levels and do not thrive at levels below 50

92

The most common and acceptable specimen treatments for insect control are Freezing Microwave Poisoning Insect deterrents Fungal pests

93

Storage

Dried and pressed plant specimens can be stored in cardboard or plastic boxes or tied in bundles in light-weight cardboard folders placed in pigeon holes

Alternatively they can be placed in protective plastic jackets and displayed in ring folders which is recommended if they are to be frequently handled such as for a reference collection

94

Filing

Specimens should be filed in a systematic order if a relatively permanent collection is being made The major groups ie ferns and fern allies cycads conifers dicotyledons and monocotyledons are best kept separately or according to some classification scheme such as that given in a flora or handbook

Similarly the genera within each family and the species within each genus may be filed alphabetically or following some such classification

95

Preservation of entire animals

Types of collection specimens of an entire animal For reference collections mammals can be prepared as a variety of specimens The condition of the specimen may determine possible ways to preserve it if for instance decomposition of the skin has loosened the hair of a carcass so much that it can easily be pulled out or removed by rubbing (ldquoslippingrdquo fur) it will be very difficult or impossible to produce a study skin or mounted specimen The most usual types of specimens (based on Nagorsen and Peterson 1980) are 1) entire fluid-preserved animals (for studying anatomy and histology fluid preservation may change the fur colour) 2) study skins with accompanying skulls partial skeletons (some bones remain in the skin) for studying pelage colour hair quality and moulting patterns 3) mounted skins with accompanying partial or entire skeleton (some bones may remain in the skin dependant on the method of preservation) or freeze-dried specimens 4) entire skeletons for instance for studying anatomy geographic variation or for age determination (entire skeletons are poorly represented in collections so Nagorsen and Peterson (1980) recommend preparation of at least one male and one female skeleton per species

96

Preservation of specimens in the field Formalin preservation Preservation in alcohol Preservation by cooling or freezing

97

Formalin preservation After weighing and measuring the animal and attaching an

adequate label very small specimens (up to 100 g) can be fixed whole by submerging them in 10 buffered formalin (tissue - formalin solution ratio of at least 1 12) the body cavity can be filled with formalin solution by injection until it is turgid and firm some formalin may also be injected under the skin into the body cavity larger muscles and organs If hypodermic needles are not available the body cavity can be opened ventrally by making a slit instead allowing the formalin to enter

Keeping the mouth open with a piece of wood or cotton may later allow examination of teeth Then the whole body can be immersed in formalin in the posture in which it is supposed to stay permanently because it will harden The ratio of formalin to carcass must be at least 12 to 1 to assure a good fixation Tissues can be left in buffered neutralized formalin for several months but formalin hardens specimens therefore after fixation longterm storage in alcohol may be better After preservation the carcass should therefore be washed in water and transferred into ethanol for permanent storage

Disadvantages for instance it discolours the fur after a longish immersion softens the bones and prevents further examination for microbiology

98

Preservation in alcohol

After weighing a whole animal can be preserved in a container of alcohol (70-90) Removal of the intestine prior to storage of the animal in alcohol is recommended

99

Preservation by cooling or freezing Removal of the skin with insulating fur

before cooling or freezing may help to cool the carcass down more quickly

Freezing is not recommended if histological examination is planned

100

THANK YOU

92

The most common and acceptable specimen treatments for insect control are Freezing Microwave Poisoning Insect deterrents Fungal pests

93

Storage

Dried and pressed plant specimens can be stored in cardboard or plastic boxes or tied in bundles in light-weight cardboard folders placed in pigeon holes

Alternatively they can be placed in protective plastic jackets and displayed in ring folders which is recommended if they are to be frequently handled such as for a reference collection

94

Filing

Specimens should be filed in a systematic order if a relatively permanent collection is being made The major groups ie ferns and fern allies cycads conifers dicotyledons and monocotyledons are best kept separately or according to some classification scheme such as that given in a flora or handbook

Similarly the genera within each family and the species within each genus may be filed alphabetically or following some such classification

95

Preservation of entire animals

Types of collection specimens of an entire animal For reference collections mammals can be prepared as a variety of specimens The condition of the specimen may determine possible ways to preserve it if for instance decomposition of the skin has loosened the hair of a carcass so much that it can easily be pulled out or removed by rubbing (ldquoslippingrdquo fur) it will be very difficult or impossible to produce a study skin or mounted specimen The most usual types of specimens (based on Nagorsen and Peterson 1980) are 1) entire fluid-preserved animals (for studying anatomy and histology fluid preservation may change the fur colour) 2) study skins with accompanying skulls partial skeletons (some bones remain in the skin) for studying pelage colour hair quality and moulting patterns 3) mounted skins with accompanying partial or entire skeleton (some bones may remain in the skin dependant on the method of preservation) or freeze-dried specimens 4) entire skeletons for instance for studying anatomy geographic variation or for age determination (entire skeletons are poorly represented in collections so Nagorsen and Peterson (1980) recommend preparation of at least one male and one female skeleton per species

96

Preservation of specimens in the field Formalin preservation Preservation in alcohol Preservation by cooling or freezing

97

Formalin preservation After weighing and measuring the animal and attaching an

adequate label very small specimens (up to 100 g) can be fixed whole by submerging them in 10 buffered formalin (tissue - formalin solution ratio of at least 1 12) the body cavity can be filled with formalin solution by injection until it is turgid and firm some formalin may also be injected under the skin into the body cavity larger muscles and organs If hypodermic needles are not available the body cavity can be opened ventrally by making a slit instead allowing the formalin to enter

Keeping the mouth open with a piece of wood or cotton may later allow examination of teeth Then the whole body can be immersed in formalin in the posture in which it is supposed to stay permanently because it will harden The ratio of formalin to carcass must be at least 12 to 1 to assure a good fixation Tissues can be left in buffered neutralized formalin for several months but formalin hardens specimens therefore after fixation longterm storage in alcohol may be better After preservation the carcass should therefore be washed in water and transferred into ethanol for permanent storage

Disadvantages for instance it discolours the fur after a longish immersion softens the bones and prevents further examination for microbiology

98

Preservation in alcohol

After weighing a whole animal can be preserved in a container of alcohol (70-90) Removal of the intestine prior to storage of the animal in alcohol is recommended

99

Preservation by cooling or freezing Removal of the skin with insulating fur

before cooling or freezing may help to cool the carcass down more quickly

Freezing is not recommended if histological examination is planned

100

THANK YOU

93

Storage

Dried and pressed plant specimens can be stored in cardboard or plastic boxes or tied in bundles in light-weight cardboard folders placed in pigeon holes

Alternatively they can be placed in protective plastic jackets and displayed in ring folders which is recommended if they are to be frequently handled such as for a reference collection

94

Filing

Specimens should be filed in a systematic order if a relatively permanent collection is being made The major groups ie ferns and fern allies cycads conifers dicotyledons and monocotyledons are best kept separately or according to some classification scheme such as that given in a flora or handbook

Similarly the genera within each family and the species within each genus may be filed alphabetically or following some such classification

95

Preservation of entire animals

Types of collection specimens of an entire animal For reference collections mammals can be prepared as a variety of specimens The condition of the specimen may determine possible ways to preserve it if for instance decomposition of the skin has loosened the hair of a carcass so much that it can easily be pulled out or removed by rubbing (ldquoslippingrdquo fur) it will be very difficult or impossible to produce a study skin or mounted specimen The most usual types of specimens (based on Nagorsen and Peterson 1980) are 1) entire fluid-preserved animals (for studying anatomy and histology fluid preservation may change the fur colour) 2) study skins with accompanying skulls partial skeletons (some bones remain in the skin) for studying pelage colour hair quality and moulting patterns 3) mounted skins with accompanying partial or entire skeleton (some bones may remain in the skin dependant on the method of preservation) or freeze-dried specimens 4) entire skeletons for instance for studying anatomy geographic variation or for age determination (entire skeletons are poorly represented in collections so Nagorsen and Peterson (1980) recommend preparation of at least one male and one female skeleton per species

96

Preservation of specimens in the field Formalin preservation Preservation in alcohol Preservation by cooling or freezing

97

Formalin preservation After weighing and measuring the animal and attaching an

adequate label very small specimens (up to 100 g) can be fixed whole by submerging them in 10 buffered formalin (tissue - formalin solution ratio of at least 1 12) the body cavity can be filled with formalin solution by injection until it is turgid and firm some formalin may also be injected under the skin into the body cavity larger muscles and organs If hypodermic needles are not available the body cavity can be opened ventrally by making a slit instead allowing the formalin to enter

Keeping the mouth open with a piece of wood or cotton may later allow examination of teeth Then the whole body can be immersed in formalin in the posture in which it is supposed to stay permanently because it will harden The ratio of formalin to carcass must be at least 12 to 1 to assure a good fixation Tissues can be left in buffered neutralized formalin for several months but formalin hardens specimens therefore after fixation longterm storage in alcohol may be better After preservation the carcass should therefore be washed in water and transferred into ethanol for permanent storage

Disadvantages for instance it discolours the fur after a longish immersion softens the bones and prevents further examination for microbiology

98

Preservation in alcohol

After weighing a whole animal can be preserved in a container of alcohol (70-90) Removal of the intestine prior to storage of the animal in alcohol is recommended

99

Preservation by cooling or freezing Removal of the skin with insulating fur

before cooling or freezing may help to cool the carcass down more quickly

Freezing is not recommended if histological examination is planned

100

THANK YOU

94

Filing

Specimens should be filed in a systematic order if a relatively permanent collection is being made The major groups ie ferns and fern allies cycads conifers dicotyledons and monocotyledons are best kept separately or according to some classification scheme such as that given in a flora or handbook

Similarly the genera within each family and the species within each genus may be filed alphabetically or following some such classification

95

Preservation of entire animals

Types of collection specimens of an entire animal For reference collections mammals can be prepared as a variety of specimens The condition of the specimen may determine possible ways to preserve it if for instance decomposition of the skin has loosened the hair of a carcass so much that it can easily be pulled out or removed by rubbing (ldquoslippingrdquo fur) it will be very difficult or impossible to produce a study skin or mounted specimen The most usual types of specimens (based on Nagorsen and Peterson 1980) are 1) entire fluid-preserved animals (for studying anatomy and histology fluid preservation may change the fur colour) 2) study skins with accompanying skulls partial skeletons (some bones remain in the skin) for studying pelage colour hair quality and moulting patterns 3) mounted skins with accompanying partial or entire skeleton (some bones may remain in the skin dependant on the method of preservation) or freeze-dried specimens 4) entire skeletons for instance for studying anatomy geographic variation or for age determination (entire skeletons are poorly represented in collections so Nagorsen and Peterson (1980) recommend preparation of at least one male and one female skeleton per species

96

Preservation of specimens in the field Formalin preservation Preservation in alcohol Preservation by cooling or freezing

97

Formalin preservation After weighing and measuring the animal and attaching an

adequate label very small specimens (up to 100 g) can be fixed whole by submerging them in 10 buffered formalin (tissue - formalin solution ratio of at least 1 12) the body cavity can be filled with formalin solution by injection until it is turgid and firm some formalin may also be injected under the skin into the body cavity larger muscles and organs If hypodermic needles are not available the body cavity can be opened ventrally by making a slit instead allowing the formalin to enter

Keeping the mouth open with a piece of wood or cotton may later allow examination of teeth Then the whole body can be immersed in formalin in the posture in which it is supposed to stay permanently because it will harden The ratio of formalin to carcass must be at least 12 to 1 to assure a good fixation Tissues can be left in buffered neutralized formalin for several months but formalin hardens specimens therefore after fixation longterm storage in alcohol may be better After preservation the carcass should therefore be washed in water and transferred into ethanol for permanent storage

Disadvantages for instance it discolours the fur after a longish immersion softens the bones and prevents further examination for microbiology

98

Preservation in alcohol

After weighing a whole animal can be preserved in a container of alcohol (70-90) Removal of the intestine prior to storage of the animal in alcohol is recommended

99

Preservation by cooling or freezing Removal of the skin with insulating fur

before cooling or freezing may help to cool the carcass down more quickly

Freezing is not recommended if histological examination is planned

100

THANK YOU

95

Preservation of entire animals

Types of collection specimens of an entire animal For reference collections mammals can be prepared as a variety of specimens The condition of the specimen may determine possible ways to preserve it if for instance decomposition of the skin has loosened the hair of a carcass so much that it can easily be pulled out or removed by rubbing (ldquoslippingrdquo fur) it will be very difficult or impossible to produce a study skin or mounted specimen The most usual types of specimens (based on Nagorsen and Peterson 1980) are 1) entire fluid-preserved animals (for studying anatomy and histology fluid preservation may change the fur colour) 2) study skins with accompanying skulls partial skeletons (some bones remain in the skin) for studying pelage colour hair quality and moulting patterns 3) mounted skins with accompanying partial or entire skeleton (some bones may remain in the skin dependant on the method of preservation) or freeze-dried specimens 4) entire skeletons for instance for studying anatomy geographic variation or for age determination (entire skeletons are poorly represented in collections so Nagorsen and Peterson (1980) recommend preparation of at least one male and one female skeleton per species

96

Preservation of specimens in the field Formalin preservation Preservation in alcohol Preservation by cooling or freezing

97

Formalin preservation After weighing and measuring the animal and attaching an

adequate label very small specimens (up to 100 g) can be fixed whole by submerging them in 10 buffered formalin (tissue - formalin solution ratio of at least 1 12) the body cavity can be filled with formalin solution by injection until it is turgid and firm some formalin may also be injected under the skin into the body cavity larger muscles and organs If hypodermic needles are not available the body cavity can be opened ventrally by making a slit instead allowing the formalin to enter

Keeping the mouth open with a piece of wood or cotton may later allow examination of teeth Then the whole body can be immersed in formalin in the posture in which it is supposed to stay permanently because it will harden The ratio of formalin to carcass must be at least 12 to 1 to assure a good fixation Tissues can be left in buffered neutralized formalin for several months but formalin hardens specimens therefore after fixation longterm storage in alcohol may be better After preservation the carcass should therefore be washed in water and transferred into ethanol for permanent storage

Disadvantages for instance it discolours the fur after a longish immersion softens the bones and prevents further examination for microbiology

98

Preservation in alcohol

After weighing a whole animal can be preserved in a container of alcohol (70-90) Removal of the intestine prior to storage of the animal in alcohol is recommended

99

Preservation by cooling or freezing Removal of the skin with insulating fur

before cooling or freezing may help to cool the carcass down more quickly

Freezing is not recommended if histological examination is planned

100

THANK YOU

96

Preservation of specimens in the field Formalin preservation Preservation in alcohol Preservation by cooling or freezing

97

Formalin preservation After weighing and measuring the animal and attaching an

adequate label very small specimens (up to 100 g) can be fixed whole by submerging them in 10 buffered formalin (tissue - formalin solution ratio of at least 1 12) the body cavity can be filled with formalin solution by injection until it is turgid and firm some formalin may also be injected under the skin into the body cavity larger muscles and organs If hypodermic needles are not available the body cavity can be opened ventrally by making a slit instead allowing the formalin to enter

Keeping the mouth open with a piece of wood or cotton may later allow examination of teeth Then the whole body can be immersed in formalin in the posture in which it is supposed to stay permanently because it will harden The ratio of formalin to carcass must be at least 12 to 1 to assure a good fixation Tissues can be left in buffered neutralized formalin for several months but formalin hardens specimens therefore after fixation longterm storage in alcohol may be better After preservation the carcass should therefore be washed in water and transferred into ethanol for permanent storage

Disadvantages for instance it discolours the fur after a longish immersion softens the bones and prevents further examination for microbiology

98

Preservation in alcohol

After weighing a whole animal can be preserved in a container of alcohol (70-90) Removal of the intestine prior to storage of the animal in alcohol is recommended

99

Preservation by cooling or freezing Removal of the skin with insulating fur

before cooling or freezing may help to cool the carcass down more quickly

Freezing is not recommended if histological examination is planned

100

THANK YOU

97

Formalin preservation After weighing and measuring the animal and attaching an

adequate label very small specimens (up to 100 g) can be fixed whole by submerging them in 10 buffered formalin (tissue - formalin solution ratio of at least 1 12) the body cavity can be filled with formalin solution by injection until it is turgid and firm some formalin may also be injected under the skin into the body cavity larger muscles and organs If hypodermic needles are not available the body cavity can be opened ventrally by making a slit instead allowing the formalin to enter

Keeping the mouth open with a piece of wood or cotton may later allow examination of teeth Then the whole body can be immersed in formalin in the posture in which it is supposed to stay permanently because it will harden The ratio of formalin to carcass must be at least 12 to 1 to assure a good fixation Tissues can be left in buffered neutralized formalin for several months but formalin hardens specimens therefore after fixation longterm storage in alcohol may be better After preservation the carcass should therefore be washed in water and transferred into ethanol for permanent storage

Disadvantages for instance it discolours the fur after a longish immersion softens the bones and prevents further examination for microbiology

98

Preservation in alcohol

After weighing a whole animal can be preserved in a container of alcohol (70-90) Removal of the intestine prior to storage of the animal in alcohol is recommended

99

Preservation by cooling or freezing Removal of the skin with insulating fur

before cooling or freezing may help to cool the carcass down more quickly

Freezing is not recommended if histological examination is planned

100

THANK YOU

98

Preservation in alcohol

After weighing a whole animal can be preserved in a container of alcohol (70-90) Removal of the intestine prior to storage of the animal in alcohol is recommended

99

Preservation by cooling or freezing Removal of the skin with insulating fur

before cooling or freezing may help to cool the carcass down more quickly

Freezing is not recommended if histological examination is planned

100

THANK YOU

99

Preservation by cooling or freezing Removal of the skin with insulating fur

before cooling or freezing may help to cool the carcass down more quickly

Freezing is not recommended if histological examination is planned

100

THANK YOU

100

THANK YOU