Rainbow Parrot Fish Thesis -- Dwk 2nd Edits

NOVA SOUTHEASTERN UNIVERSITY OCEANOGRAPHIC CENTER

A predictive habitat model for the reef fish,

rainbow parrotfish Scarus guacamaia

Ethan G.P. Machemer

Submitted to the Faculty ofNova Southeastern University Oceanographic Center

in partial fulfillment of the requirements for the degree of Master of Science with a specialty in

Marine Biology

Nova Southeastern University

Date: TBD

1. Introduction

A. Life History of the Rainbow Parrotfish

Rainbow parrotfish Scarus guacamaia is the largest herbivorous fish in the

Atlantic Ocean and Caribbean Sea and is found in both mangrove and coral reef habitats

(Mumby 2006). The rainbow parrotfish is large, heavy-bodied, and a somewhat laterally

compressed fish. It has a fusiform body shape with dull orange fins possessing streaks of

green extending into the dorsal and anal fins; median fin margins are blue in color with

the dental plates appearing a blue-green. In this species there appears to be no obvious

color differentiation based on sex (Cervigón 1994). Rainbow parrotfish are behaviorally

cautious in nature, though it sometimes may be found in schools of up to thirty

individuals (Dunlop and Pawlik 1998).

It has a limited daily home range (Smith 1997), and occupies varying depths up to

twenty-five meters. It possesses a dependence on corals for shelter and living space

(Cole et al. 2008) and seeks shelter under ledges at night or when threatened, and the

species has been shown to use the angle of the sun as an aid in returning to these shelters

(Smith 1997). Rainbow parrotfish are herbivorous fish that, like most members of the

Scaridae family, feeds mainly by scraping macro-algae from coral structure (Bellwood et

al. 2004). However, it has also been observed to feed directly on coral (Rotjan and Lewis

2006) and gut content analyses have revealed spicules from feeding on sponges (Dunlop

and Pawlik 1998).

Rainbow parrotfish life history characteristics are reasonably well known. It is a

protogynous hermaphrodite, meaning individuals in this species undergo a sex change

2

Dave Kerstetter, 11/27/09,

Compared with or to what?


Being behaviorally cautious and schooling are not mutually exclusive behaviors…


Seems odd for a Scarid…

between their initial phase, where they are generally female and terminal phase, where

they are male. Terminal phase male rainbow parrotfish defend a territory and a harem of

females, and when the male dies, the most dominant female will become the dominant

male, with her ovaries becoming functional male testes (Streelman et al. 2002). Like

other species in this family, peak spawning occurs primarily in warmer summer seasons

from May to August, but can occur year-round, and there is an active period of fish

recruitment occurring around February in this region (Haus et al. 2000). Spawning is

found to take place generally around dusk, and may correlate to either the lunar cycle or

the high tide, as this is an optimal time for egg dispersal. The initial phase is composed

of females while the terminal phase is composed of sexually mature males. Rainbow

parrotfish aggregate into territories that contain a group of females with the dominant

male pair-spawns almost exclusively (Munoz and Motta 2000).

Rainbow The rainbow parrotfish is a relatively larger reef fish, compared to most

species of reef fishes in the Caribbean, which and can achieve a maximum length of 120

cm (TL). The estimated with a K value (l/y) of 0.293 equatesing to a minimum

population doubling time of approximately four and a half to fourteen years (Robins and

Ray 1986; Randall 1962). Observations of rainbow parrotfish have been made in waters

with temperatures ranging from 12-36 °C, salinities ranging from 23.74 to 39.1 ‰ (parts

per thousand), and dissolved oxygen concentrations ranging from 2.4 to 14.07 ‰ (Serafy

et al. 2003). The species’ wide range of tolerances to these factors is most likely an

adaptation to the wide range of its known habitats. These habitats range from estuaries to

offshore areas, both of which are subject to large pulses of freshwater and storm events.

The varied thermal and oxic conditions cannot be exploited by less tolerant species and

3


Spell out… and explain a bit on how this value was estimated by these two authors.


Not a sentence – reword, please.

may be beneficial in providing refuge from predators, foraging grounds or potential

nursery areas (Rummer et al. 2009).

The diet of rainbow parrotfish has been shown to be variable across life stages

and habitats. In the Dunlop and Pawlik (1998) study, sponge spicules were found in

higher masses in the individuals collected from the mangrove sites as compared to those

from coral reefs, suggesting there are shifts in diet preference based on the food sources

available. A secondary food source is coral as rainbow parrotfish has been classified as a

facultative corallivore based on direct observations, meaning coral can be either a

majority of their diet or only a minor component. These fish impose more permanent and

chronic pressures on scleractinian corals, those that generate a hard skeleton such as

Montastrea and Porites species, meaning there is repeat scraping activity on these corals,

and the damage caused is longer lasting. However, chronic predation may play a factor

in regulating distribution, abundance and fitness of certain prey corals (Cole et al. 2008).

Though not fully known, this corallivory may be part of an ontogenetic diet shift,

meaning coral is only an important food source for part of their lives, accounting for less

than five percent of their bites. Along with this diet selectivity comes the ability to cause

significant damage to corals by biting off growing tips or large portions of skeletal

material, which means they are capable of having a disproportionately large impact on

the physical structure of Caribbean reefs (Cole et al. 2008). It has also been observed that

grazing reduced the density of zooxanthellae and increased the severity of a bleaching

event in Belize (Cole et al. 2008). Rainbow parrotfish use a feeding method of scraping

or grinding algae from the coral or other rocky substrate, and sometimes inadvertently

ingests coral animals as well. The hard coral substrate is broken down through its

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digestive system, and the excretion of this limestone material is one of the main sources

in the creation of the sand surrounding coral reefs in the Caribbean.

Parrotfishes are known to become progressively important upon reaching a certain

key size around 15-20 cm, at which point they become ‘functionally mature’ (Lokrantz et

al. 2008) and their actions provide a significant impact on the coral reef. This impact

increases exponentially as there is a non-linear relationship between body size and

scraping function, as calculations suggest that up to 75 individuals with a size of 15 cm

are required to functionally compensate for the loss of a single 35 cm individual, and a

50% decrease in body size can result in a 90% loss of function (Lokrantz et al. 2008). In

addition, grazing impact in mangrove systems is also a power function of body length. A

conservative estimate places the home range of S. guacamaia at 1600 m3, which is larger

than that of many other scarids. Rainbow parrotfish also represents approximately 14%

of the total grazing intensity measured for mangrove depauperate systems (Mumby

2008).

The main part of the rainbow parrotfish diet consists mostly of short epilithic turf

algae, cropped algae, red coralline and filamentous algae (Mumby 2008), and they feed

heavily upon Halimeda opuntia, a green calcareous alga. Juvenile scarid abundance has

also been shown to be positively related to the percent cover of Dictyota spp. algae at site

level in the Florida Keys (Kuffner et al. 2009). Similar parrotfish species have been

observed consuming whole pieces of the thallus rather than grazing on the attached

epiphytes, and taking more bites from H. opuntia and fewer bites from coral than would

be expected from the percent cover of different microhabitats (Munoz and Motta 2000).

While not quantitatively known for rainbow parrotfish, a mean home range for similar

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Run-on…

parrotfish species in the Florida Keys was observed to be 4371.5 +/- 5869.5 m2 (Munoz

and Motta 2000), with a high standard error due to a low number (n = 7) of study sites.

Due to microhabitat and foraging overlap of various parrotfish species there are

occurrences of interspecific aggression when one species attempts to use the defended

resources to the detriment of the defending species. This aggression involves vigorous

chasing over comparatively large distances, as well as biting, and the benefits gained

from this resource defense outweighed the cost. Aggression has also been observed to be

greater when encountering other parrotfish species as opposed to non-parrotfish species

and rainbow parrotfish were instigated into these aggressive encounters most often by the

focal species Scarus aurofrenatum (Munoz and Motta 2000).

Scarus guacamaia is most closely related phylogenetically to S. coelestinus and S.

iseri, with Scarus clades having root nodes at between 2 and 3 million years ago, thus

implying that most Scarus species are recent products of recent speciation. This

speciation occurred around the likely date of the complete closure of the Isthmus of

Panama at approximately 3.1-3.5 million years ago. The pantropical distribution and the

relatively recent ages of the divergence of the four main clades of Scarus imply that

fluctuations in sea level and patterns of differential cooling of the oceans during the

Pliocene and Pleistocene may be the driving forces behind the rapid radiation in this

genus, that which is today largely restricted to the complex reefs built by hard corals.

Alternatively, processes of ecological speciation and divergence due to sexual selection

remain a possible explanation for the rapid radiation of parrotfishes, which all have

pelagic larval phases and highly similar morphology. In addition tThe protogynous

mating system of parrotfishes, where species aggregate and have male-dominated

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Add citation?


Reword…


This is okay, I suppose, but it seems awkward.

haremic systems organized by color recognition, has also been proposed as a possible

driving force for speciation via sexual selection mechanisms (Smith et al. 2008). The

phylogeny of parrotfish also suggests a gradual shift from browsers living in seagrasses

to excavators inhabiting rock and/or coral reefs to scrapers found exclusively in

association with coral, with Sparisoma being the transitional genus (Streelman et al.

2002). It can be assumed that the Scarus genus has always had a habitat association with

coral reefs as the Scarus genus is the third radiation off of the Sparisoma lineage.

Of the parrotfishes, S. guacamaia is the only species that possesses an obligate

and functional dependence on the mangrove habitats (Nagelkerken 2007; Mumby 2006).

This dependency has been shown quantitatively in the Mumby et al. (2004) study in

which the species suffered local extinctions that corresponded with the removal of

mangrove stands, and the extent of mangrove coverage in a region is one of the dominant

factors in structuring reef communities. Mangrove connectivity enhances the biomass of

rainbow parrotfish on neighboring coral reefs, because grazing influences the cover of

macroalgae on reefs and high levels of parrotfish grazing has been shown to lead to a

twofold increase in recruitment of Porites and Agaricia corals in the Bahamas (Mumby

2008). Biomass of rainbow parrotfish more than doubled when the reefs were connected

to rich mangrove resources, defined as having at least 70 km of fringing Rhizophora

mangle within a region of 200 km2, equating to coverage of 35% (Mumby 2006).

Juveniles of this species, those less than 30 cm total length (TL), are observed almost

exclusively in mangrove habitats, while all individuals observed on the coral reef were

greater than 25 cm total lengthTL were observed on the coral reef (Dorenbosch 2006). ,

and aAverage sizes have been recorded of 10.1 cm and 14.6 cm total lengthTL have been

7


I inserted this abbreviation here, but you could do it earlier if you mentioned it then.


Add citation?

recorded in mangroves and seagrass beds, respectively (Nagelkerken et al. 2000). The

species of juvenile reef fishes that utilize mangroves and seagrass beds do so because of

the high food availability, the presence of shade and shelter that the mangroves provide,

and a reduced risk of predation due to the plant and root configurations and lessened

chance of interaction with predator species as well as low predator abundance and

efficiency (Verweij et al. 2006). Shallow water habitats such as mangroves and

seagrasses, are believed to contain less piscivores than the reef (Verweij et al. 2006)

possibly because the energetic costs of chasing the smaller fish in these habitats outweigh

the gains of catching one of the prey fish. The turbidity of the water can also negatively

affect predator efficiency due to scattering and reduction of light by suspended particles

(Verweij et al. 2006). There is significant interannual variability in species composition

that may be expected in mangrove fish communities, but spatial factors have been found

to contribute more to differences in fish community structure than seasonality (Robertson

and Duke 1990).

Verweij et al. (2006) tested the effects of plant structure, shade, and food upon

rainbow parrotfish foraging behavior using artificial seagrass leaves and artificial

mangrove roots. Rainbow parrotfish showed the same trends as those of pooled

herbivores, being highly significant (p<0.001) for the tested variables ofin structure, food,

structure times *food, and blocked location. In this study, 72 individuals were observed

ranging in size from 7.5-15.0 cm. The behavior observed was broken down into 2.8% of

individuals resting (spaced evenly throughout the water column), 91.7% foraging, and

5.6% swimming. Eighty-four percent of the rainbow parrotfish observed foraging in the

study were found in the artificial mangrove roots, with six percent foraging on artificial

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Explain…


With what?

seagrass leaves and it was determined that the presence of higher surface area on the root

structure provided more substrate for algae which allowed for diurnal feeding on the

fouling algae and epiphytes in mangroves and seagrass beds. Rainbow parrotfish

observed in this study were also found to be preferential to experimental units with the

highest structural complexity. Caribbean mangroves and seagrass beds function as

foraging habitats, but are not used continuously as shelter during the daytime (Verweij et

al. 2006). The value of these habitats is diminished with decreased water clarity from

turbidity originating from terrestrial run-off (Freeman et al. 2008), leading to population

declines in this and other species. Seagrass minimum light requirements differ between

species and systems. Halodule and Syringodium seagrass pecies often require more than

24-37% surface light intensity, yet they are consistently an order of magnitude higher

than terrestrial plants or other photosynthetic marine organisms. Reduced subsurface

light intensity has caused seagrass declines and the subsequent re-suspension of

unstabilized sediments has impeded recovery of these seagrass systems, increasing the

pressure placed on species such as the rainbow parrotfish that depend on them (Freeman

et al. 2008).

However, presence of preferential habitat is not the only contributing factor

determining abundance. It is possible that habitat configuration has an influence on the

connectivity between mangroves, seagrasses, and coral reefs and this configuration in

terms of providing pathways and connections to the reef affects the composition of the

fish assemblage, species richness, fish density and fish size (Dorenbosch et al. 2007).

Local recruitment can play a major role. In one study, juvenile densities on the reef were

comparable to those in seagrass beds, suggesting that this species can also use the coral

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Where? Locations are starting to be important for defining differences…


Higher what? Primary production?


Same Freeman et al. citation?

reef as a nursery (Dorenbosch et al. 2004). Dorenbosch et al. (2007) concluded that for

rainbow parrotfish, migration among these habitats most likely takes place along the

coastline. The presence of seagrass-mangrove bays along the coasts of these islands

strongly influences the distribution pattern of this species on the coral reef, and reduced

density of several of these nursery species on the coral reef is related to the absence of

seagrass beds and mangroves (Dorenbosch et al. 2004). For island sites, this migration

was observed to occur on the sheltered or leeward shores, where most adult individuals

were observed on coral reefs between 0 and 10 km from mangroves. However, no

significant linear relationship was present between mean total density of rainbow

parrotfish on these reefs and the distance to the nearest stands of mangroves (Dorenbosch

et al. 2006). There was also reduced density or complete absence of rainbow parrotfish

on the coral reefs that were farther than nine kilometers from the mangrove and seagrass

habitats used by fish of juvenile ages.

The density of these species is additionally regulated on local scales by variable

habitat structural complexity and the community of vegetation. Herbivory was highest at

the maximum habitat complexity site, which suggests that the increased shelter and food

abundance provided by denser seagrass beds may have increased fish abundance

resulting in these higher levels of herbivory (Unsworth et al. 2007). Herbivory was found

to increase away from patchy seagrass areas whilst increasing distance from a reef

reduced the rate of herbivory due to a reduction in fish migration. Observed high levels

of herbivory, however, may only be a short-term effect of irregular grazing by shoals of

juvenile and sub-adult scarids (Unsworth et al. 2007).

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This sounds like a formal term – if so, please define.


Don’t these two sentences sort of contradict themselves? Please reword and/or explain further.

Rainbow parrotfish migrate across habitats in accordance with its life history

stage, and will grow as large as possible before moving on to the next habitat. Utilization

of intermediate nursery habitats has been hypothesized to increase survivorship of small

fish (Mumby 2004). The intermediate nursery stages between mangroves, seagrass beds,

and patch reefs serve the function of alleviating predatory bottlenecks in early demersal

ontogeny (Mumby 2004). The presence of seagrass beds has also been linked to

significantly higher densities of rainbow parrotfish on coral reefs (Dorenbosch et al.

2006) while other studies (Gonzalez-Salas et al. 2008) have found differing results with

respect to these nursery habitats. Noting high abundance of juveniles and adult members

of S. guacamaia in coral reef habitats and a total absence in mangrove stands, it appears

that mangroves in certain regions do not function as obligate habitats and that seagrass

and coral rubble become the primary alternative for nursery, growth, and reproduction

(Gonzalez-Salas et al. 2008). It is possible that with removal of mangrove forests the

rainbow parrotfish are adapting to utilize other habitats that offer similar survival

benefits. The reduced benefits of these marginal habitats may not provide rainbow

parrotfish with the resources necessary to survive across their entire life history, allowing

only temporary survival through one life stage or another (Rummer et al. 2009). This

selective use, which is defined as use of a particular habitat patch disproportionately

relative to its availability, can be exhibited either seasonally or spatially, and proximity

rather than suitability has been found as the dominant pattern of habitat use (Faunce and

Serafy 2008). Mangrove shorelines across broad spatial scales are not equivalent in their

value as fish habitats due to the inherent patchiness within the ecosystem. A measure of

total habitat area will may therefore overestimate the amount of functional habitat utilized

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Citation?

by these fishes. In addition, species richness and total number of fishes collected

adjacent to mangrove shorelines has been shown to decline with increasing inland

distance from creek mouths and oceanic inlets, with water depth greatly related to fish

use (Faunce and Serafy 2008).

Rainbow parrotfish are valuable members of the communities with which they are

associated. The grazing activities of these parrotfish are beneficial in preventing algal

overgrowth and enhance coral reef resilience to algal blooms and other competitor

species (Hughes et al. 2007). The species also facilitates settlement and survival of corals

by scraping and bioeroding the hard dead coral substratum and are crucial for the

regeneration and maintenance of coral reefs (Lokrantz et al. 2008). Rainbow parrotfish

and other scarid species not only take up carbon into the food chain through direct

seagrass consumption, but also make an important indirect contribution to the detrital

food chain through the export of decaying seagrass material, which potentially results in

the widespread dispersal of seagrass material into surface waters. Detached seagrass may

also be cast onto the shore where it decays and may re-enter the system as detritus

(Unsworth et al. 2007). Rainbow parrotfish may be equally important in influencing

seagrass export from the system by the high rates of material discarded during

consumption. This material is subsequently removed from the system by weather and

currents, estimated to be as high as 11% of seagrass growth, on top of which herbivory

causes the loss of at least 16% of the seagrass growth each day (Unsworth et al. 2007).

In spite of their ecological role and importance, S. guacamaia populations are

thought to be in decline and to have been fished to ecological extinction in Brazil, as well

as similar to many other areas of the Caribbean (Floeter 2006). Rainbow parrotfish has

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been listed as vulnerable on the IUCN Red List. This designation means the species is

facing a high risk of extinction in the wild based on one or more of the following five

criteria: reduction of population size, shrinking geographic range or occupancy, a

population with fewer than 10,000 mature individuals, restricted population extent, or

quantitative analysis showing the probability of extinction in the wild is at least 10%

within 100 years; the full explanation of which are detailed in the 2004 IUCN criteria (,

version 2.3, (Roberts 1996). Given this information and the role the species occupies

within this multi-part ecosystem, developing a model that details occurrence and

abundance characteristics provides a new means in which to assess the health and

function of this parrotfish in this region. In addition, one may apply the methods not only

throughout the range of this species, but it may be possible to apply this model to other

parrotfish species and similar families.

B. Characteristics of the Biscayne Bay and Florida Reef Tract Region

Biscayne Bay is a downstream receptor of larvae and juveniles from offshore

spawning adults and as a source point for adults to migrate to the reef tract (Wang et al.

2003) and the region contains some of the most pristine habitat within the Florida Keys

(Ishman 1997). The coastal shelf of the Florida Keys is characterized by shallow and

highly variable topography, where currents are influenced by tides, wind, and the very

energetic offshore Florida current system (Haus et al. 2000). The eddies and meanders of

the Florida Current make it possible for upwelling and larval transport to occur across the

shelf, and the scale of these perturbations can vary from slow moving mesoscale gyres to

faster moving, sub-mesoscale eddies (Haus et al. 2000). Velocities of these eddies can

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Awkward… please reword.

range from 0.53 m/s to 0.80 m/s along the inshore edge of the Florida Current (Haus et al.

2000) and the variability of those velocities can have an impact on dispersal and the

resulting end locations of larvae.

Patch reefs in this region occupy a significant portion of the water column,

leading to variability in the water depth and have the potential to change the strength and

direction of the tidal flow. The northern Florida Keys contain over 4,000 patch reefs,

composed generally of cemented reef (47.3 +/- 2.2% cover) and pavement (20.1 +/-

2.1%), with varying amounts of rubble, boulders and sand (Kuffner et al. 2009). The

benthic community observed on these patch reefs is largely dominated by macrophytes,

encrusting invertebrates, and “suitable settlement substratum” found beneath a substantial

canopy of gorgonian s, or (“soft”) corals (Kuffner et al. 2009). Macroalgae occupies a

large portion of space on the reefs, especially Dictyota spp. (15.4 +/- 0.8% cover) and

Halimeda tuna (11.7 +/- 0.6% cover). Live scleractinian corals account for only 5.8+/-

0.6% of the benthos (Kuffner et al. 2009).

The tides are generally weak, with a semidiurnal height range of approximately

0.5 m, while although flows through tidal channels however, are strong enough to cause a

nodal point in the along-shelf tidal flow (Haus et al. 2000). As measured in Caesar

Creek, tidal velocity can exceed 25 cm/s, while current measurements within the inlets

have shown peak tidal velocities in excess of 0.5 m/s (Haus et al. 2000). These channels,

commonly referred to as the “ABC Channels” because of their names --– Angelfish

Creek, Broad Creek, and Caesar Creek --– form the main outlet from the southern end of

Biscayne Bay onto the Florida reef tract. The ABC Channels convey large oscillating

tidal flows and wind driven flows between the bay and the ocean, and transport through

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Isn’t this the same as 50 cm/s? Keep units similar unless there’s a reason not to…


Explain… how does this relate to your thesis?


Awkward… please reword.


Citation?

these corridors predominantly shows a semi-diurnal cycle with amplitudes of 500 m3/s,

300 m3/s, and 250 m3/s respectively (Wang et al. 2003). Based on observations, there is a

net outflow at Angelfish and Caesar Creek, but an inconsistent inflow in Broad Creek

(Wang et al. 2003). With the tidal flows and the input of freshwater, the residence times

of the water varies widely from several months in the more enclosed Barnes Sound, and

circulation restricted Card Sound (Ishman 1997) to about a month in the western parts of

South Biscayne Bay, and nearly zero in the vicinity of the ocean inlets (Wang et al.

2003).

The area encompassing Biscayne Bay south to Card Sound and Barnes Sound

forms a barrier island lagoon system that exhibits estuarine characteristics near points of

freshwater inflow during the wet and early dry season (Wang et al. 2003). This lagoon

system leads to broad salinity regimes that vary throughout the year, and greatly across a

relatively small area of only several kilometers due to high freshwater input through

canals as opposed to groundwater, and limited tidal flushing. Salinity variations in

Biscayne Bay primarily result from canal discharges through gated control structures, as

well as smaller freshwater exchanges in the Bay driven by overland runoff, rainfall, and

evaporation (Wang et al. 2003) and upwelling from groundwater (Ishman 1997). The

greatest salinity fluctuations occur near canal mouths in Barnes Sound and along the

western margin of Biscayne Bay, and smallest ranges were observed near ocean inlets

(Wang et al. 2003), where the vertical variations of salinity in the water column ranged

from less than 0.2 ‰ to a maximum salinity change of 0.8 ‰ from top to bottom in the

vicinity of the inlet mouth (Haus et al. 2000). In the Pelican Bank region of Biscayne

Bay (see Figure 20) good circulation results in regular flushing and average salinities

15

range from 33 to 35 ‰ (Ishman 1997). Also determining water flow characteristics in

this region are a network of drainage canals completed for agricultural and industrial

purposes, as well as to control flooding, which has greatly altered the distribution of

freshwater within the watershed, as well as the quantity, quality, and timing of freshwater

discharges to Biscayne Bay (Wang et al. 2003). This has lead to greater pulses with

larger peak discharges in the wet season and less freshwater reaching Biscayne Bay in the

dry season, due to reduced terrestrial storage and lowered groundwater levels (Wang et

al. 2003). Increased runoff not only affects salinity conditions in coastal waters, but also

can be a mechanism for increased nutrient loading (Rudnick et al. 2006). There also

exists a coastal ridge, bisecting the Bay, which acts as a groundwater divide, with water

west of the ridge flowing toward Florida Bay. The outputs of freshwater from the canals

have punctured massive holes through the ridge, changing the direction and

characteristics of the flow, and the qualities of the watershed (Wang et al. 2003).

This region also is characterized by large coverage of submerged aquatic

vegetation such as seagrasses, and wide availability of phytoplankton, microalgal and

macroalgal species. Florida Bay is approximately 2000 km2 in total surface area,, with

95% bottom coverage of seagrasses, characterized by sparse, patchy beds of Thalassia

testudinum interspersed with locally abundant Halodule wrightii (Fourqurean and

Robblee 1999). However, in the spring of 1991, Florida Bay exhibited a shift from a

system characterized by clear water to one of extensive and persistent turbidity and

phytoplankton blooms, which limit the ability of the seagrass to grow and function

properly, by reducing penetration of light in the water column (Fourqurean and Robblee

1999). This seagrass die-off was not accompanied or preceded by noticeable decreases in

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Even splitting this bit off from the previous paragraph, it still remains long for a paragraph…

water clarity or increases in colonization by epiphytes, however. and hHypothesized

causes for this die-off include hypoxia and sulfide toxicity, along with loss of the

estuarine nature of the system over many decades; overdevelopment of the seagrass beds;

chronic hypersalinity; in-filling of the bay due to lack of severe storms; and abnormally

warm late summer and fall temperatures (Fourqurean and Robblee 1999).

The problem this presents for rainbow parrotfish and other species of fishes is that

fish abundance and diversity is highly correlated with seagrass abundance and species

composition in Florida Bay (Fourqurean and Robblee 1999). D, and die-off events of

these seagrasses often result in causes a lack of suitable habitats, changes in trophic

position for various species, an altering of food webs, and a lessening of species biomass

due to variations in water level and salinity.

Algal blooms also present problems for S. guacamaia in the south Florida

ecosystems. Algal blooms are most commonly composed of cyanobacteria (formerly

blue-green algae) such as those of the genus Synechocystis and Synechococcus, the most

recent of which was likely initiated by an increase in total phosphorus (Rudnick et al.

2006). Southern Biscayne Bay typically has low phytoplankton biomass and low

productivity, in large part because of low phosphorus availability, these; concentrations

of total phosphorous normally ranging range from 0.006 mg/L to very rare high values of

0.02 mg/L; , yet during the 2005 bloom event, total phosphorous reached levels of 0.1

mg/L (Rudnick et al. 2006). Chlorophyll-a Cconcentrations of chlorophyll-a, which are

an indicator of phytoplankton biomass, typically have a value of 0.4 microgramsmg/ L

liter and rarely exceed 2 microgramsmg/ Lliter, but when the blooms occurred, values

reached 8 mg/ L micrograms/liter for chlorophyll-a (Rudnick et al. 2006). Factors

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Seasonal or not?


This last one seems a bit of a stretch, unless it’s a separate result. Regardless, please provide some citations in here – there should be more tan the Fourqurean and Robblee, 1999 pointing to these sorts of changes with such die-offs.


This die-off?


Work on this sentence please, trying to eliminate the semi-colons.

causing this bloom event are thought to be linked to road construction along U.S. Route 1

between the Florida mainland and Key Largo, and the hurricane impacts in the 2005

season, which were exacerbated by water management operations, diverting water

through canals as opposed to groundwater, and other anthropogenic means, such as

development that also disrupts natural groundwater flow. Similar to the seagrass die-offs,

algal blooms this affects the rainbow parrotfish, in that the by algal blooms reduceing the

available suitable habitat, alters altering the physical parameters of the ecosystem outside

of the utilizable range, and by reduces reducing the available corridors for movement

among nearshore and offshore ecosystems across the various life history stages of the

species.

C. Previous Studies and Statement of Problem

Prior work has detailed the importance of the rainbow parrotfish to the coral reef

communities of the Caribbean, Sea. hoHowever, these studies, many of which are cited

above, generally only examined rainbow parrotfish as part of a group of species with

similar functional traits, as opposed to a detailed study with a focus solely on this species.

Other studies have taken place either on sites in the Windward Islands, or in the

Bahamas, and while these reefs may be physically structured similarly, they are not

exactly the same as the coral reefs of the Florida Reef Tract. Two studies, the Mangrove

Visual Census and Reef Visual Census have taken place in this region, and this work

expands on the conclusions from their data.

D. Statement of Significance

18


Along with the deletion of this heading – which isn’t normally part of the final thesis, only the proposal – work on the transition between these paragraphs.


How/why are they different, then?


Please provide an explanation (yes, it may seem obvious, but humor me…) as well as some citations for these stated impacts from the algal blooms.


Run-on, and please provide citations.

This research has taken point count data of the rainbow parrotfish from Biscayne Bay and

Upper Florida Bay and developed a model predicting the occurrence of this species in

other similar areas and regions where such data collection has not taken place. The

Biscayne Bay and Upper Florida Bayse locations provide good examples of shoreline

mangrove forests, islands and barrier reefs, and how they are affected by anthropogenic

means in a highly developed region. As is the case with many species of reef fishes,

there is an ontogenetic shift in habitat utilization with S. guacamaia, and this ontogenetic

difference in habitat use may result from predation rate, or juveniles selecting lower

predation risk habitats such as seagrass beds (Nakamura and Tsuchiya 2008).

Thise relationship between developmental stage and habitat utilization has been

examined and quantified in greater detail. Regression and occupancy models based on

biological, physical, and anthropogenic factors were constructed to provide a numerical

representation of abundance and occurrence of the rainbow parrotfish in relation to the

life history of this species. This research gives graphical evidence to support and expand

the known habitat and life history information for this fish, information that can be

applied to similar species found in similar habitats to allow for more detailed

management and conservation decisions for this and other unstudied species of reef fish

in the future.

While there is significant information about the habitat preferences of the rainbow

parrotfish, there is not readily accessible information that substantiates the importance of

a specific location to the species, or how dependent this fish is on the oceanographic

characteristics, such as (e.g., bottom substrate), of a given site. The development of a

model for these habitat characteristics has provided numerical evidence for the

19


Abiotic?


Define/explain?


You really haven’t discussed these model types or their applications to your study species – this could/should easily be another few paragraphs of explanation here in your Intro section.


By whom? Where? Which fishes? If this (and the next) sentence refer to your work, then save these sorts of statements for the Discussion section instead of the Intro.

probability of occurrence of this fish in a particular habitat and a ranked importance of

the habitat type. Rainbow parrotfish has a functional importance and dependence within

these mangrove and reef habitats of Biscayne Bay and Upper Florida Bay, suggesting that

it makes a better study subject than a species with less of an impact. In addition to

providing a more detailed picture of habitat utilization by rainbow parrotfish across its

life stages, this model allows one to make more accurate management decisions,

particularly as they relate to human expansion and influence on this fish’s habitat.

E. Objectives

Hypothesis 1: Mangrove habitat is essential to the location of rainbow parrotfish.

It has been well established that there is a functional dependency of juvenile fish

of this speciesrainbow parrotfish on mangrove habitat (Mumby et al. 2004). However,

absence of mangroves does not automatically equate with absence of the species

(Gonzalez-Salas et al. 2008). The extent of this importance of the mangrove habitat

needs to be quantified, particularly in areas that are subject to high human development.

Characteristics such as percent vegetative cover per square kilometer, and pressures such

as population density per square kilometer were used in assessing the suitability of the

habitat to this fish. Regression and occupancy models were used to quantify habitat

locations and they were ranked for suitability. Finally, they were ranked separately for

abundance of rainbow parrotfish.

Hypothesis 2: Mangrove density is a larger factor in rainbow parrotfish survival rather

than simply mangrove presence.

20


Of humans?


How defined?


As an aside, these hypotheses aren’t really in traditional hypothesis-testing formats. While I’m of the school of thought that says we should really be moving away from such rigid, testable experiments, Dr. Spieler is not… Just a friendly heads-up.


Your model?


Defined as… ?


A better study subject for what, your analyses?

Mangroves provide this species of parrotfish with structure that in turn provides

shelter, shade, and sources of food. However, simply the presence of mangroves may not

be enough to support occupancy by rainbow parrotfish. The distance that mangrove

habitat extends from the shore was measured and correlated to parrotfish density. A

gradient corresponding to this distance was incorporated into the model to determine the

density of mangrove forests required to host a stable population of parrotfish. Based

upon this relationship, one can make suggestions about the relative importance of density

to presence and survival of this fish.

Hypothesis 3: Type of bBottom substrate plays a role in abundance and occurrence of

rainbow parrotfish.

Bottom substrate affects the plant biota present, as well as relating to the presence

of available shelter. Seagrasses grow where the bottom type tends to be sandy, whereas

encrusting algae need a hard or coralline substrate on which to attach. Rainbow

parrotfish are generally herbivorous and tend towards eating encrusting algae as noted by

scars on similar textured corals and sponges (Dunlop and Pawlik 1998). The

predominant bottom substrate type was correlated with the abundance and occupancy

results between the bottom substrate and the presence and viability of parrotfish to

determine if there is a correlation.

Hypothesis 4: Presence of preferred diet species determines location

While there is some plasticity in the diet preferences of this species of parrotfish,

there appears to be a hierarchy in the nutrient benefit provided by the different sources of

21


Citation?


It only occurred to me recently that we’ve been focusing on the movement of juveniles from mangroves to reefs. On the other hand, there should be a functional relationship of distance from pelagic larval habitats to the mangrove juvenile habitats, right? Even if it’s not something you examine, you might include it as a potential suggestion for future analyses.

prey. Comparison of the locations preferred by the diet species with the predictions

provided by the model of the highest occurrence numbers of parrotfish was measured to

show if there is a correlation between diet location and abundance of rainbow parrotfish.

Hypothesis 5: Dissolved oxygen (DO) concentration is the most important abiotic factor

determining presence or absence of parrotfish in a particular location.

Rainbow parrotfish was observed across a range of temperatures that varied 24

°C, and salinity, that varied 16 ‰, while the range for DO varied less than 12 ‰. One

could then assume that a change in DO would have a much greater consequence than

would a change in one of the other factors. This change was modeled statistically, by

altering the DO numbers in the model and determining how it affects the abundance and

occurrence numbers. A literature review was conducted to determine how algal blooms

affect these abiotic factors and how these blooms might affect this fish.

2. Materials and Methods

To evaluate these hypotheses, a predictive model was developed to explain the

occurrence of S. guacamaia in a given area. The rRainbow parrotfish was chosen as the

study species because of its role as the largest herbivorous fish in the Caribbean region

and because its population numbers are in decline and , its with an IUCN listing as

vulnerable. The rainbow parrotfish was also selected because it had broad observation

coverage across the two datasets described below, and there has been limited work done

with this species using data from the Florida Keys and Biscayne Bay region, unlike

22


You might want to restructure this section, with the general problem first, the two datasets second, and the selection of your study species third.


Seems strange to have reference to a lit review here – just fit your review findings into the Intro or Discussion sections and delete this sentence.


Wow! Just wanted to be sure that this wasn’t a typo.


Good idea, just awkwardly said…

species such as sailor’s choice Haemulon parra and gray snapper Lutjanus griseus.

These are two species appearing in the datasets that have been studied in greater detail as

more work has been done in the region on grunts and snappers.

The datasets used in developing this model are the Mangrove Visual Census and

the Reef Visual Census. Data primarily come from the Mangrove Visual Census (MVC)

conducted over the years 1998-2007, as detailed in Serafy et al. (2003). This ongoing

study examined the fish assemblages along two types of mangrove-lined shoreline using

a visual ‘belt-transect’ census method over consecutive seasons in Biscayne Bay and the

Upper Florida Bay. This method entails snorkeling 30 m long transects parallel to the

shore and recording identity, number, and size-structure (minimum, mean and maximum

total length) of fishes observed. The width of each belt-transect was 2 m, giving an area

of 60 m2 per transect. Visual surveys were conducted between 09:00 and 17:00, thereby

minimizing visual identification problems associated with low light conditions. Censuses

were conducted during consecutive wet and dry seasons (i.e., July to September and

January to March, respectively) and transect locations were chosen at random each

season. Measurements of water quality and depth were obtained for each fish census.

Water temperature, salinity and dissolved oxygen were measured using a Hydrolab®

multi-probe instrument. Depth was measured along each transect at intervals of 15 m

using a 2 m long polyvinyl chloride pole marked at 2 cm intervals (Serafy et al. 2003).

This work examined both ontogenetic shifts for various fishes from mangroves to reefs,

and studied the trophic roles of varying shoreline habitats (Serafy et al. 2003).

Secondary sets of data were used from the Reef Visual Census (RVC), which was

begun in 1979 and was conducted through 2005. This study occurred on the reef tract

23


Awkward, and needs further explanation as well.

parallel to the Florida Keys and involved sampling fish community structure in virtual

cylinders with a radius of 7.5 m around randomly selected, stationary points (Bohnsack

and Bannerot 1986). Divers in this study began each sample site by facing in one

direction and listing all fish species within the field of view. When no new species were

noted, new sectors of the cylinder were scanned by rotating in one direction for the

duration of the five-minute period slated for each site. After the initial five minutes, data

were then collected on the abundance and minimum, mean, and maximum lengths for

each species sighted. An “all-purpose tool” (APT; a ruler connected perpendicularly to

the end of a meter stick) was utilized as a reference device to reduce potential

magnification errors in fish size estimates. Species with few individuals were counted

and their size estimated immediately. Highly mobile species, such as sharks and

carangids, unlikely to remain in the area were tabulated when first observed and then

ignored (Bohnsack and Bannerot 1986).

The Mangrove Visual Census measured a wide range of physical parameters, but

is limited temporally in that it was only begun in 1999. The Reef Visual Census covered

a much longer timeframe, but also recorded fewer physical data in the observations.

These datasets are beneficial since they both employ similar methods and occurred

concurrently (for at least part of the studies). In addition, both studies were performed in

the same region using low impact assessment methods. The drawbacks in using these

censuses are that there are limited data for the sand flats, seagrass beds, and the channels

that link these two habitats. The sampling locations are both a benefit and a drawback

because it provides coverage across a large range of area, but the sites selected were

random, and a more accurate picture might have been obtained in limiting the size of the

24

sampling area. Human error is also involved, leading to measurements and observations

that will not be absolutely accurate in situ. The use of different observers over the course

of the surveys will present slight problems, too, due to the inherent differences between

each observer’s individual technique and abilities. The fact that the MVC used

snorkeling methods and RVC used SCUBA is not a limitation as the methods reflected

the differences in depth of the survey sites. In using both of these studies, it is possible to

analyze and compare traits such as ontogenetic shifts, migration and habitat utilization

that would not be possible with analyses using only one dataset.

The model was set up initially in Microsoft Excel (Microsoft Corporation,

Version 12.0.6214.1000) and included the following parameters: temperature, dissolved

oxygen, salinity range/regime, average depth, distance from corridors, and mangrove

density. Habitat type, mangrove cover, substrate type, and shoreline development were

researched and used for comparison, but not incorporated into the model. The

parameters, such as mangrove cover and substrate type, not included in the original data

sets were primarily derived from available GIS map coverage data from agencies such as

the Florida Fish and Wildlife Conservation Commission and the United States Geological

Survey. The value for mangrove cover/density is defined as the distance of continuous

mangrove cover extending from the shoreline. Using the programs R (The R Foundation

for Statistical Computing, Version 2.6.0) and SAS (SAS Institute, Version 9.2), this set-

up was evaluated by a logistic multiple regression. Occupancy probability models were

run in program Mark (Gary C. White, Colorado State, Version 5.1) that incorporates

Bayesian methods as detailed in MacKenzie et al. (2003). This gives probability of

occurrence and detection under imperfect or incomplete conditions, within a set

25


How about a table here listing which datasets were used for each data source or area coverage?

timeframe. In other words, this allows the model to estimate occupancy over a given

amount of time, while not needed to be present to observe every individual.

Logistic regression was chosen because this analysis is used to predict the

probability that an event of interest will occur as a linear function of one or more

continuous and/or dichotomous independent variables (Karp 2001). Regression modeling

used to relate the variations in large-scale distributions to key habitat variables is the

approach of habitat association modeling (Freckleton et al. 2006). It also goes that

maximum likelihood estimators in logistic regression are approximately normally

distributed, with little or no bias (Ragavan 2008), but in the same study we might often

need at least two types of models: one for description/interpretation and another for

prediction (Shtatland et al. 2001). The corresponding informational outputs and

regression values, the numerical values that resulted from the model’s initial setup

parameters, would then be ranked according to habitat, abundance, and size and plotted

spatially on a GIS map using ArcGIS (ESRI, Version 9.2).

3. Results

The data sets used for this work consisted of 1,812 sites in the Mangrove Visual

Census (MVC), of which 1,798 were used, and 13,443 sites in the Reef Visual Census

(RVC), of which 764 points were used. Sites from the MVC were omitted if there was

one or more physical parameter for which there was no data and sites from the MVC

were omitted if there was not rainbow parrotfish observed at that site. In the MVC

rainbow parrotfish was observed at 107 of the 1,798 sites, consisting of a total of 533

26


Awkward…


Avoid this “and/or” in formal writing – can you rephrase this statement?

individuals. In the RVC rainbow parrotfish was observed at 764 of the 13,443 sites,

consisting of a total of 1,499 individuals. Of these individuals, 57 were of mature size in

the MVC and 688 were of mature size in the RVC (refer to Table 1). This gives naïve

occupancy, a measure of total observed individuals divided by the total number of

locations, of 0.3052 for the MVC, and naïve occupancy of 0.1115 for the RVC.

Using the GPS-based positions points included in the respective data sets, the

locations of the rainbow parrotfish individuals were plotted on a map using ArcGIS. ,

fInitiallyirst, all observed individuals (Figure 1) were plotted, and then these individuals

were broken down into groups by size of 0-100 mm, 100-200 mm, 200-300 mm, and

greater than 300 mm (Figures 3, 4, 5, 6). Each of these maps were further separated by

number of individuals at each site, in groups corresponding to 1-5 individuals, 6-15

individuals, or 16-80 individuals. These groups were represented on the maps by with

points of increasing size, ; the breakdown of these numbers is shown in Table 2.

These numbers values are visualized shown in Figure 7, which depicts the

size distribution for the rainbow parrotfish individuals, and Figure 8, which shows the

size-frequency distribution for the rainbow parrotfish individuals. With this size

information, the sites were mapped again, broken down into the locations of observed

juvenile and mature individuals for the MVC (Figure 18) and RVC (Figure 19).

Next, a logistic regression analysis was performed using the variables in the MVC

of temperature, dissolved oxygen, salinity, average depth, and the distance from island

channels. Distance from the island channels was not included in the initial measurements

of the data set but rather was calculated by taking the GPS location in the center of each

27


Much of this is borderline Materials & Methods instead of Results. If you wanted to keep much of this text, you could list the inclusion and exclusion parameters in the M&M, then list what you used in the Results, for example.

of the eight channels (Figure 2) and measuring the distance to each site using the

equation:

Distance = R*(acos((sin(lat1/r)*sin(lat2/r))+(cos(lat1/r)*cos(lat2/r)*cos((lon2-lon1)/r)))),

where R = 6370, ( Earth’s radius (in kilometers) and r = (360/(2*πpi)).

The closest distance from each point to the channel opening was the value used.

The RVC data were omitted because the environmental (?) variables, except for other

than depth were not recorded, and depth was not taken recorded at any study sites where

a rainbow parrotfish was not observed. To set up the regression analysis, the five

aforementioned values were measured against the presence (1) or absence (0) of Scarus

guacamaia individuals at each site. Logistic regression analyses were then performed for

each of the five variables individually against presence or absence. The total regression

was found to be significant with a Pr > Chi-square values of < 0.0001 and salinity,

average depth, and channel distance were found to be significant with Pr > Chi-square

values of 0.0014, <0.0001, and 0.0001, respectively. Temperature and dissolved oxygen

were found to not be significant with Pr > Chi-square values of 0.8359 and 0.7855,

respectively.

These results coincide with the results of the ROC curve, a measure of sensitivity

versus specificity, better termed as a representation of the trade off between the false

negative and false positive rates for every possible value. An ideal test has a value of 1.0

indicating 100% sensitivity and specificity, meaning the false negative rate is high and

the false positive rate is low. When the ROC curve follows a diagonal path from the

28


Define?


Awkward…

lower left hand corner to the upper right hand corner this means that every improvement

in false positive rate is matched by a corresponding decline in the false negative rate, and

the area under the curve is closer to 0.5 indicating 50% sensitivity and 50% specificity.

For the total regression, the area under the ROC curve was a value 0.921, for temperature

it was a value of 0.544, for dissolved oxygen it was a value of 0.599, for salinity it was a

value of 0.774, for average depth it was a value of 0.821, and for distance from channel

openings, it was a value of 0.886.

The results of the logistic regression indicate that using the five variables together

is the best predictor of presence or absence; salinity, depth and distance from channel

openings are adequate predictors of presence or absence, while temperature and dissolved

oxygen are not significant in predicting presence or absence. Inflection points of the

logistic regression curves for salinity occurred at 36.4 ‰ with a predicted Y1 of 0.100

(Figure 9), 103.5 cm average depth with a predicted Y1 of 0.150 (Figure 10) and 3.5 km

distance from the closest channel opening, with a predicted Y1 of 0.11633 (Figure 11).

Out of the 1,798 sites in the MVC, 414 were above the inflection point for salinity values,

148 were above the inflection point for average depth values, and 316 were above the

inflection point for channel distance values. Table 3 shows the complete breakdown of

the predicted Y1 regression values for all of the five variables, as well as the total for the

three significant values.

The total predicted Y1 values are mapped out for the Biscayne Bay region, seen

in Figure 12, as well as for temperature (Figure 13), dissolved oxygen (Figure 14),

salinity (Figure 15), and average depth (Figure 16).

29

Table 1. Percentages of Scarus guacamaia at mature size for mangrove and reef study

sites. Number is given by individuals at mature size out of total number of individuals,

and Site is given by number of sites where mature individuals were observed out of the

total number of study sites with observations of Scarus guacamaia.

Scarus guacamaia

Mangrove (#): 10.31%

Mangrove (Site): 8.41%

Reef (#):45.90%

Reef (Site): 35.99%

(Individuals/Total)(57/553)

(Sites/Total)(9/107)

(Individuals/Total)(688/1,499)

(Sites/Total)(275/764)

30

Table 2. Number of study sites in the Mangrove Visual Census and Reef Visual Census

broken down by the size and the number of Scarus guacamaia individuals observed.

Mangrove Visual Census Reef Visual CensusNumber of Individuals: 1-5 6-15 16-80 1-5 6-15 16-800-100 mm 3 0 0 11 0 0100-200 mm 40 11 0 41 0 0200-300 mm 31 12 2 96 3 1300+ mm 4 3 1 578 27 7

31

Table 3. Number of study sites within each range of predicted Y1 regression values.

Temperature Range: 1 = 0-0.04, 2 = 0.04-0.045, 3 = 0.045-0.05, 4 = 0.05-0.055, 5 =

0.055-0.06, 6 = 0.06-0.065, 7 = 0.065-0.07, 8 = 0.07-0.075, 9 = 0.075 and greater.

Dissolved Oxygen Range: 1 = 0-0.025, 2 = 0.025-0.035, 3 = 0.035-0.045, 4 = 0.045-

0.055, 5 = 0.055-0.065, 6 = 0.065-0.075, 7 = 0.075-0.085, 8 = 0.085-0.095, 9 = 0.095-

0.105, 10 = 0.105-0.115, 11 = 0.115-0.125, 12 = 0.125-0.135 and greater.

Salinity Range: 1 = 0-0.02, 2 = 0.02-0.04, 3 = 0.04-0.075, 4 = 0.075-0.12, 5 = 0.12-0.16,

6 = 0.16-0.2, 7 = 0.2-0.233, 8 = 0.233-0.267, 9 = 0.267 and greater.

Average Depth Range: 1 = 0-0.01, 2 = 0.01-0.033, 3 = 0.033-0.067, 4 = 0.067-0.1, 5 =

0.1-0.133, 6 = 0.133-0.167, 7 = 0.167-0.2, 8 = 0.2-0.25, 9 = 0.25-0.3, 10 = 0.3-0.35, 11 =

0.35-0.45, 12 = 0.45-0.55, 13 = 0.55-0.6, 14 = 0.6-0.65, 15 = 0.65 and greater.

Channel Distance Range: 1 = 0=0.05, 2 = 0.05-0.1, 3 = 0.1-0.15, 4 = 0.15-0.2, 5 = 0.2-

0.25, 6 = 0.25-0.3, 7 = 0.3-0.333, 8 = 0.333-0.367, 9 = 0.367 and greater.

Total (Salinity + Average Depth + Channel Distance) Range: 1 = 0-0.05, 2 = 0.05-0.1, 3

= 0.1-0.15, 4 = 0.15-0.2, 5 = 0.2-0.25, 6 = 0.25-0.3, 7 = 0.3-0.35, 8 = 0.35-0.4, 9 = 0.4-

0.45, 10 = 0.45-0.5, 11 = 0.5-0.55, 12 = 0.55-0.6, 13 = 0.6-0.65, 14 = 0.65-0.7, 15 = 0.7

and greater.

Temperature Regression ValuesRange 1 2 3 4 5 6 7 8 9

32


This is confusing to the reader. I would suggest separating out each of these factors into individual tables, or at least “Table 3A”, etc.

Number 11 65 202 377 255 273 404 182 29Dissolved Oxygen Regression ValuesRange 1 2 3 4 5 6 7 8 9 10 11 12Number 17 95 267 432 393 256 139 114 60 18 4 3Salinity Regression ValuesRange 1 2 3 4 5 6 7 8 9Number 604 292 255 388 153 61 28 9 8Average Depth Regression ValuesRange 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15

Number 32 807 516 171 97 57 35 38 18 6 9 8 2 1 1Channel Distance Regression ValuesRange 1 2 3 4 5 6 7 8 9Number 1242 196 86 62 41 86 54 12 19Total Regression ValuesRange 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15

Number 389 393 244 184 129 88 74 61 76 71 39 21 13 7 9

Figure 1. Location and Size size of observed Scarus guacamaia individuals from

Mangrove Visual Census (black) and Reef Visual Census (orange) data.

33


In general, you need to make sure that all of your table and figure legends are “stand-alone”, i.e., one doesn’t have to refer to the text to understand the table or figure. Also, be sure that your font sizes are large enough to read comfortably.

Figure 2. Location and Names of Channels along Florida Keys involved in study sites.

34

Figure 3. Location of observed Scarus guacamaia individuals sized 0-100 mm from

Mangrove Visual Census and Reef Visual Census data.

35


Mangrove Visual Census and Reef Visual Census.

36


Mangrove Visual Census and Reef Visual Census.

37

Figure 6. Location of observed Scarus guacamaia individuals sized greater than 300 mm

from Mangrove Visual Census and Reef Visual Census.

38

Figure 7. Rainbow pParrotfish Ssize Ddistribution.

39


Since you have a figure legend, you don’t need the Excel-made header. Also, avoid horizontal lines in your figures – they won’t be accepted by most journal editors, so it’s just as easy to get out of the habit now!

Rainbow Parrotfish Size Distribution

0

50

100

150

200

250

300

1 3 5 7 9 11 13 15 17 19 21 23 25 27 29 31 33 35 37 39 41 43 45 47 49 51 53 55 57 59 61 63 65 67 69 71 73 75 77 79 81 83 85

Size (cm)

Num

ber

of In

divi

dual

sMangrove Data

Reef Data

mature

40

Figure 8. Rainbow Parrotfish parrotfish Sizesize-Frequency frequency

Distributiondistribution.

Rainbow Parrotfish Size-Frequency Distribution

0

0.05

0.1

0.15

0.2

0.25

1 3 5 7 9 11 13 15 17 19 21 23 25 27 29 31 33 35 37 39 41 43 45 47 49 51 53 55 57 59 61 63 65 67 69 71 73 75 77 79 81 83 85

Size (cm)

Freq

uenc

y (a

s %

of t

otal

)

Mangrove Data

Reef Data

mature

41

Figure 9. Logistic rRegression for Ssalinity, with salinity values in parts-per-thousand

(‰) on x-axis.

.

Logistic regression of Y1 by X1

0

0.1

0.2

0.3

0.4

0.5

0.6

0.7

0.8

0.9

1

0 10 20 30 40 50

X1

Y1

Active Model

Low er bound (95%) Upper bound (95%)

42


Don’t use boxes around your figures, nor around your legends within the figures.


Have one line between your figure or table legend and the figure or table itself.


You need to be clear, both here and within the text itself, what these figures indicate. Feel free to use a program like PowerPoint to add arrows, shaded boxes, etc. to highlight features of the figure, such as the inflection point/range.

43

Figure 10. Logistic Regression regression for Average average Depthdepth, with average

depth values (cm) on x-axis.


0

0.1

0.2

0.3

0.4

0.5

0.6

0.7

0.8

0.9

1

0 50 100 150 200

X1

Y1

Active Model

Low er bound (95%) Upper bound (95%)

44


I won’t go through the rest of the legends on the issue of capitalization, but correct the rest of them in the same way.


If you use page breaks, you’ll avoid shifting the figures and legends when you make edits…

Figure 11. Logistic Regression for Channel Distance, Channel Distance (km) on x-axis.


0

0.1

0.2

0.3

0.4

0.5

0.6

0.7

0.8

0.9

1

0 10 20 30 40 50

X1

Y1

Active Model

45

Figure 12. Map of study sites for Scarus guacamaia color-coded for predicted logistic

regression values combined from salinity, water depth, and distance from channels.

46


regression values for temperature measurements.

47


regression values for dissolved oxygen measurements.

48


Why is the internal legend not at the top like the rest of the figures?


regression values for salinity measurements.

49


Same as Fig. 13?


regression values for average depth measurements.

50

Figure 18. Location of observed Scarus guacamaia individuals from Mangrove Visual

Census data separated by size into juveniles and mature individuals.

51

Figure 19. Location of observed Scarus guacamaia individuals from Reef Visual Census

data separated by size into juveniles and mature individuals.

52

Figure 20. Biscayne National Park Map, detailing locations names used in study. From:

http://lib.utexas.edu/maps/national_parks/bisc_95.jpg,

53

http://lib.utexas.edu/maps/national_parks/bisc_95.jpg

http://www.nps.gov/PWR/customcf/apps/maps/showmap.cfm?

alphacode=bisc&parkname=Biscayne%20National%20Park

4. Discussion

54


What’s special about this figure that you couldn’t put into Fig. 2 (e.g., park boundaries)? This is also not the correct way to cite websites, if you need to cite them at all within figure legends.

http://www.nps.gov/PWR/customcf/apps/maps/showmap.cfm?alphacode=bisc&parkname=Biscayne%20National%20Park

http://www.nps.gov/PWR/customcf/apps/maps/showmap.cfm?alphacode=bisc&parkname=Biscayne%20National%20Park

This study has shown that in using the five aforementioned variables, it is possible

to significantly predict the occurrence of rainbow parrotfish individuals. Furthermore,

the variables of salinity, average depth, and distance from channel opening are each

significant in predicting the occurrence of rainbow parrotfish, while temperature and

dissolved oxygen are not. Dissolved oxygen was initially hypothesized to be a more

important factor than salinity, because the measurements taken of this variable were

across a smaller range than variables such as temperature and salinity, which turned out

not to be the case. Temperature and dissolved oxygen can vary greatly across very small

distances, and variations can be highly localized. The ability of this species for

movement across daily ranges of up to several thousand cubic meters means adjusting for

slight variations in temperature or dissolved oxygen to more suitable conditions would

not be a limitation. Salinity would present more of a problem of avoidance for rainbow

parrotfish should conditions become unfavorable. The problem occurs as salinity

gradients are more gradual, but fluctuations have the potential to spike drastically and

persist for greater time periods over larger areas. The inflection point for salinity

occurred at 36.4 ‰, with a predicted Y1 of 0.100, meaning that there is a lower than 10%

chance of occurrence at any site where salinity is below that value. With these values,

occurrence is much more likely to occur in waters than have salinities in the range of 35-

40 ‰, corresponding with the clear, warm, natural oligotrophic waters of the Florida reef

tract. The clear, shallow waters of coastal estuaries from Biscayne Bay to Barnes Sound

possess natural salinities near saltwater strength, providing the optimal salinity conditions

as nursery grounds and transition habitats.

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Awkward – we don’t think in this measurement unit.


List them out again here. Also, each variable should have at least its own paragraph, like you did for depth and channel distance. If you thought the variable important enough to include within the model, then you likely had support for doing so from either parrotfish-related behavior data or prior modeling work. Detail what you found on each variable and why you think you got the results you did.

Average depth is a significant variable probably due to several reasons. The

inflection point for this regression analysis was 103.5 cm, meaning a water depth of about

a meter is the critical value for predicting occurrence. The rainbow parrotfish diet

consists of benthic turf algae with incidental corallivory and it has also been shown

(Verweij et al. 2006) that plant structure is preferred by rainbow parrotfish. In depths of

water less than a meter, there is less available space for swimming, foraging and shelter,

and conditions at that depth may be suboptimal for epiphytic plant and algal growth.

Halimeda species have shown optimal photosynthesis at depths of one meter (Häder et al.

2008) and Caulerpa species have shown optimal photosynthesis at depths of five meters

(Häder et al. 1997). The Häder et al. (1997) study also showed that exposure to solar

radiation at the surface caused a drastic decline in the effective photosynthetic quantum

yield, and to a smaller extent nonreversible photodamage. Much of the coral substrate of

the Florida reef tract on which rainbow parrotfish inhabits is greater in depth than a

meter, generally depths of five to greater than ten meters (Duffy 2007), so it becomes a

question of necessity that to find suitable habitat, inhabiting depths of greater than a

meter is required. The deeper waters are also less subject to changes in sediment loads,

which can affect bay water clarity leading to changes in the benthic algae cover, as well

as seagrass and drifting macroalgal communities, which comprise most of the submerged

aquatic vegetation.

Distance from channel opening is significant due to the separate juvenile and

mature life history stages that take place in the mangrove communities, and on the coral

reef, respectively because to there needs to be a pathway for this transition to take place,

and the closer an individual is to these channels, reduces the costs due to predation,

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Citation?


Avoid “probably” in your Discussion sections…

energy expended, and search for food. Rainbow parrotfish is known to have a large

home range with an ability to swim over great distances, but the less time spent

transitioning between suitable habitat allows for allotting less energy on avoidance,

swimming, and escape, and more on foraging and reproduction.

The maps of predicted regression values for the Biscayne Bay region illustrate

these points. Mangrove-lined shorelines of the leeward keys in Biscayne Bay and Upper

Card sound have the highest predicted Y1 values. Here, the mangrove density and

coverage is the greatest and substrate coverage is hardbottom, as well as a large

proportion being part of Biscayne National Park. The next tier of Y1 values could be

found on the selected windward sites outside of Biscayne National Park, and in the areas

of Card Sound and Upper Florida Bay, where mangrove coverage is high near where the

Overseas Highway enters onto the Keys.

The lowest predicted values are found on the mainland shorelines. In this area,

there is low mangrove coverage, and low density of mangroves back from the shoreline.

The, and bottom coverage is also composed of seagrass, rather than hard substrate,

further limiting available diet resources for rainbow parrotfish. In addition, predators

such as barracuda, sharks, snappers and grunts are high in numbers in this area (MVC

data), and the anthropogenic influence is higher due to continued development in South

Florida. Sediment cores from Manatee Bay show a history of mangrove peat deposition

followed by a progressive increase in marine mud and sands. In contrast, Card Sound

and Pelican Bank show evidence of peat and high vegetation accumulation in their early

history followed by an increase in marine and or carbonate clastic deposition (Ishman

1997). The normal bottom coverage has been disrupted because of removal of natural

57


Citation?


All of your study area is within “South Florida” – while a good argument, you’ll have to be more specific here.


On juveniles?

flora in the area has impeded biophysical cycling regimes, resulting in sub-optimal

habitat. Often activities such as feeding, reproduction, and resting occur in different

habitat types, and the home range consists of two areas joined by a narrow movement

path (Kramer and Chapman 1999). This reduced viability of hardbottom banks between

mangrove and reef habitats limits the effectiveness of transitioning between life stages.

The mainland edge consists of freshwater wetlands, which contain fringing,

riverine, and basin mangrove communities, separated from marine habitats in certain

places by a mud embankment that impedes freshwater runoff. Natural freshwater input

from rainfall and runoff is now disrupted as water flows through artificial drainage canals

as opposed to natural channels and circulation. This has lead to a variable freshwater

flow in many near shore areas of Biscayne and Florida Bays, such that downstream

salinity regimes are suboptimal for freshwater, brackish, and marine organisms. Rainbow

parrotfish are pelagic spawners, leaving larvae settlement subject to flow regimes and

currents. Larval development is thus impaired in areas that are meant to function as

nursery grounds by the compounding problems of lack of suitable habitat and increased

distance from adult coral reef habitats. Greater numbers of S. guacamaia individuals are

found on the northern edge of the Florida reef tract where suitable mangrove stands are

present as opposed to farther south, where development has left much of the windward

and leeward shores absent of mangrove stands.

Rainbow parrotfish is listed as vulnerable under IUCN criteria, a designation

given due to not only a reduction in suitable habitat, but also reduced size of individuals.

Reduced individual size leaves fewer numbers of those that are functionally mature and

have a significant impact on their ecosystem. Rainbow parrotfish and other similar

58


See previous comment about larval influx and the importance of distances between cuts and mangrove habitats.


Citation?


… of what? For juvenile rainbow parrotfish?

species need to be looked at in greater focus, as to how their loss will impact the

Caribbean region. In most parts of the Caribbean, parrotfishes are a major component of

reef and subsistence fisheries, especially where their slower-growing predators have long

been depleted (Hughes et al. 2007).

Rainbow parrotfish have several crucial roles in the dynamics of tropical reefs:

they graze fleshy seaweeds that compete with juvenile and adult corals for space; , they

erode dead coral skeletons and generate reef sediments, and they are an important trophic

link between their natural predators and algal primary producers (Hughes et al. 2007).

Parrotfish density will vary spatially and temporally in response to local rates of

recruitment and mortality (Hughes et al. 2007) while habitat suitability varies spatially,

allowing populations to persist only when the habitat quality exceeds some threshold,

thus an increase in average habitat quality leads to simultaneous increases in average

densities within occupied areas, as well as the total area that is habitable (Freckleton et al.

2006).

Implementation of an adequate marine reserve in this region could help to ensure

the viability of not only this species, but also the biodiversity present across these

habitats. The Florida Keys are protected by a National Marine Sanctuary, multiple state

parks, and National Wildlife Refuges farther south than the scope of this study.

However, within these boundaries, very little area is designated as ecological reserve, and

only small, individual reefs are designated as sanctuary preservation areas. Reserves can

only protect fish species if movement of individuals remains within a localized home

range, contained fully within the reserve boundaries, during at least part of their life cycle

(Kramer and Chapman 1999). This, which is not the case for rainbow parrotfish and

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Run-on sentence.

many other reef fish species. Home range size has been shown to be a power of body

size (Kramer and Chapman 1999), so without an adequately sized preserve area, rainbow

parrotfish may face pressure or even inability to reach maximum or functional size. In

addition, on fringing coral reefs, where habitat zonation parallels depth contours, the

home ranges of larger species are considerably longer in the dimension parallel to the

depth contours than in the dimension perpendicular to it (Kramer and Chapman 1999).

This illustrates the need for not only adequately sized reserves, but also properly shaped

ones as well. Relocation of the home range is one possibility, which involves selection

for and movement to a novel habitat patch. This can occur as a response to changes in a

despotic distribution, one with a dominant male and a harem of submissive females,

either by competition with other parrotfish species or with sex change within a harem. In

this case, however, the costs of relocation will increase with the investment required to

learn the characteristics of the home range, which may be larger for species such as S.

guacamaia that use the complex substrate for feeding and refuge (Kramer and Chapman

1999).

Solutions proposed in other marine regions are “no-take” areas and networks of

Marine Protected Areas or MPAs. These MPA networks can function to sustain resident

populations both by local replenishment and through larval dispersal from other reserves

(Planes et al. 2009). Protecting spawning areas of reef fishes spills over and replenishes

neighboring areas of coral reef and related habitats, and larval subsidies from a single

reserve may contribute to the resilience of subpopulations at other reserves within a

network of MPAs (Planes et al. 2009). This has been shown to be effective for protecting

grouper spawning aggregations, but may prove difficult with rainbow parrotfish, and a

60


Don’t begin sentences with acronyms or abbreviations.


May want to define this term for clarity.


Unfamiliar term – maybe provide a definition?


You need to support this statement, with both logical argument and citations.

broader coverage net would most likely be necessary. In studies by Mumby et al. (2006),

it was found that biomass of parrotfish was reduced by 30-–60% on adjacent reefs,

compared with biomass in the no-take area., and In another study,along with the

elevated biomass of parrotfish in a no-take area resulted in an, estimated grazing intensity

that was six times higher, and the cover of seaweed within the park was five times lower

(Hughes et al. 2007).

Proper stewardship of marine parks by local communities can enhance grazing

and help to prevent regime shifts from coral- to algal-dominated systems. M, however

many marine parks have been established by central governments or foreign NGOs, but

they remain ineffective because they lack local support or adequate management (Hughes

et al. 2007). In the Florida Keys, estimates range that 33-75% of local income is due to

diving and tourism, with an additional 5-8% coming from commercial fishing (National

Marine Sanctuaries website), and to limit this use of offshore areas would put a great

strain on the residents of these communities. However, marine parks and protected areas

have shown to be effective in preserving species such as rainbow parrotfish and total

biodiversity in other regions while not impinging on the local livelihoods. In the Mumby

et al. (2006) study, populations had not leveled off even after the marine park had been in

existence for over twenty years, implying that results, no matter what is done, may not be

seen immediately. In not revising the situation, as it currently exists, and developing a

marine protected area that ensures future biodiversity and sustainable resident

populations would be to lose not only the aims of preservation, but also the livelihood

that depends on them. A concerted effort needs to be undertaken to create self-sufficient

marine preserves that incorporate mangrove and reef habitat as well as connecting

61


Awkward…


Awkward…


Need to be VERY clear here when you’re discussing uses about the differences in “no-take” regimes, which can vary between literally no taking of any resources to taking by recreational anglers. Another way of looking at this would be by delineating the differences between consumptive and non-consumptive uses.

corridors, based first on solid science, and one that incorporates the needs of all the

stakeholders.

62


Need a much stronger concluding statement.

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Rainbow Parrot Fish Thesis -- Dwk 2nd Edits

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