The discovery of the past

Georges Cuvier

Charles Lyell

To study evolution means to dig in the past.

The science of past organims is paleontology (greek: palaews:

old, logos: science)

Paleontology deal with fossils (lat. fodere = to dig)

Early paleontology mainly described ancient life within the Linnean framework

Modern paleontology tries to reconstruct ancient life.

It links therefore ecology and taxonomy.

Mary Anning (1799-1847) Richard Owen (1804-1892)

How do animals fossilize?

Taphonomy (Greek: tafos: burial; nomos: law)

Living organismDeath

Remains

Exposed remains

Buried remains

Stratinomy

Decomposition DecayBleaching

Delayed burial

Immediate burial

Ginkgo biloba Ginkgo adiantoides

Much less than 1% of all organisms fossilize

Coral fish Coral fish from Jura

FossilMineralization

Bioerosion

A fossil forest in Dorset, England formed by fossilized bacteria around old tree stumps.

Fossilized Cyanobacteria (stromatolites) from South Africa

A mammoth coprolith (fossilized excrements)A fossilized dinosaur footprint from New Mexico

Hard body materials Soft body materials

What fossilizes?

Substance Examples

Calcite (CaCO3) OctocoralliaBryozoaBrachiopodaPolychaetaAmmonitaBelemnitaEchinodermata

Aragonite (CaCO3) HydrozoaGastropoda

Calciumphosphate Vertebrata (Ca5(OH)(PO4)3) Trilobita

Crustacea

Opal (SiO2.H2O) RadiolariaDiatomeaPorifera

Chitin AlgaeFungiArthropodaCnidariaPriapulidaAnnelida

Cellulose PlantaeTunicata

Soft tissues very seldom fossilize

(of about half of all major evolutionary lines no fossils are known)

Exceptions are

Fast drying out in very arid climates

Permanent frozen

Preservation in amber or asphalt

A feathered Dinosaur:

Sinosauro-pteryx

Under what conditions do organisms fossilize?

Volcanic ashesAnaerobic conditions(moorlands)

River sediments

Moisture gradient

Nutrient rich soils

Probability of fossilization

Salinity gradient

How complete is the fossil record?

00.10.20.30.40.50.60.7

0 5 10 15 20 25 30

Me

tric

s

PZ PZ/MZ MZ/CZNZ CZOlder ------ Younger

RCI

GER

SCI

SCI: Quotient of consistent to inconsistent nodes

RCI: Relative completeness index

GAP: Gap excess index

Divergence time inferred

from cladogram

Divergence time inferred from fossils

Benton MJ, Willis MJ,  &  Hitchin R. 2000. Quality of the fossil record through time. Nature 403: 534-537.

100%

50%

0%

Com

plet

enes

s

Taxonomic levels

Species Family Class TypeOrder

Fossils of soft-bodied types are not well known

At the family level about 50% of all taxa are known from fossils.

?

Continental drift

Alfred Lothar Wegener (1880-1930)

The tectonic plates (from David Sanfwell, Scripps Inst. Oceanography)

Evidence for plate tectonics:

Fit of coastlines

Distribution of mountains

Continuity of fossils

Continuity of geological features

Isostasy: Earth acts like a fluid

From Press et al.. 2004. Understanding earth, http://www.whfreeman.com/presssiever/con_index.htm?99iex

From C. R. Scotese: http://www.scotese.com/future.htm

Continental drift

How to match phylogeny and plate tectonics

Tinamou

Moa

Rhea

Ostrich

Kiwi

Emu

Cassowary

New Guinea

Australia

South America

New Zealand

Africa

79

69

65

62

35

100

82

55

0.1

Relative dating methods

Relative dating uses geological strata to infer whether fossils are older or younger than a given stratum

Layer 1

Layer 2

Layer 2

Time

Older

Younger

Stratigraphy

Morphological primitivism

Fossil dating

Absolute dating methods

Radiometric absolute dating

Radioactive Element Stable element Half timePotassium 40 Argon 40 1.25 billion yrsRubidium 87 Strontium 87 48.8 billion yrsThorium 232 Lead 208 14 billion yearsUranium 235 Lead 207 704 million yearsUranium 238 Lead 206 4.47 billion yearsCarbon 14 Nitrogen 14 5730 years

Most minerals which contain radioactive isotopes are in igneous rocks.

The dates they give indicate the time the magma cooled.

Potassium 40 is found in: potassium feldspar (orthoclase)

muscovite amphibole glauconite

Volcanic rocks Sometimes in sediments

Uranium may be found in: zircon

urananite monazite apatite sphene

Volcanic rocks

Carbon 14 is used for bones

Daugther atoms N14

Surviving atoms C14

Modified from Andy MacRae: Radiometric Dating and the Geological Time Scale. http://www.talkorigins.org/faqs/dating.html

Raw dataRecognition of

unique events to subdivide time

Radiomtric dating of layers

Calibrating geological

time

Stratigraphy Relative time scale

Absolute time scale

Geological time scale

Radiometric dating

Volcanic ash 1

Volcanic ash 2

Last occurrence of B:

First occurrence of

First occurrence of

Last occurrence of A:

160 ± 10 mya

190 ± 8 mya

Post eruption 2

time

Post fossil B time

Fossil B time

Pre fossil B time

Pre eruption 1 time

Fossil B time

Pre fossil B time

Dep

th [m

]

165 mya

180 mya

Older than 190 mya

Fission track Dendrochronology

Fission Tracks (FT) are micrometer-sized, linear damage tracks that occur in insulating

minerals and that are caused by the spontaneous fission of heavy, unstable

nuclides (mostly 238U in natural minerals).

Dendrochronology analyses tree-ring growth patterns.

History of the earth

Nicolas Steno (1638-1686)

Steno founded stratigraphy by stating that

geological layers are horizontal and superposed.

Deeper layers are older.

The Red Rock Canyon, California

The geological time scale

Eon Era Period Age at Base (Mya) Duration (Mya)Phanerozoic Cenozoic Quarternary 2 2

Neogene 23 21    Paleogene 65 42  Mesozoic Cretaceous 140 75    Jurassic 205 65    Triassic 250 45  Paleozoic Permian 290 40    Carboniferous 355 65    Devonian 410 55    Silurian 440 30    Ordovician 490 50    Cambrian 540 50

Proterozoic Neoproterozoic Ediacaran (Vendian) 630 90    Cryogenian 850 220    Tonian 1000 150  Mesoproterozoic   1600 600  Palaeproterozoic   2500 900

Archean     3800 2950Hadean     4550 750

The reconstruction of phylogeny

The first Darwinian principle told that every phylogenetic tree has one common ancestor.

Phylogenetic analysis is the study of taxonomic relationships among lineages.

Willi Hennig (1913-1976)

Phylogenetic systematics

Cladistics (greek κλάδος: branch)Numerical taxonomy

Robert Sokal(1926-2012)

http://www.eol.org/http://tolweb.org/tree/phylogeny.htmlhttp://www.faunaeur.org/

Ancestor

a

b

c ee

d

f

The cladistic methodology

A B C D Apomorphies are common derived characters.

Autapomorphies are characters that are restricted to single lineages.

Plesiomorphies are ancestral derived characters.

adf ade abc abd

b: Synapomorphy of lineage C+D

d: Plesiomorphy of lineage A It is a symplesiomorphya: Apomorphy of the whole tree It is the ancestral state.

e: Autapomorphy of lineage D

The collective set of plesiomorphies defines the ground plan of a phylogenetic tree.

Ancestor

a

b

de

d

f

A B C

adf ade abd C is the sister taxon of A and B

Character a in lineages A, B, and C is homologous because it synapomorph

Character d in lineages A, B, and C is not homologous because it derived twice. It is homoplasious

Ancestor

b

de

d

f

A B C D E

Monophyletic taxon Paraphyletic taxon

f

bPolyphyletic taxon

The ultimate aim of taxonomy is to group

higher taxa into monophyletic subtaxa.

For this task we have to infer autapomorphies

Autapomorphy defines monophyly

Actino-pterygia Dipnoi Anura Urodela Mammalia Squamata

Therosauria

Aves

Tetrapoda

Amniota

Reptilia(paraphyletic)

Archosauria

Common ancestor Lungsplesiomorph

Tetrapod limbsapomorph

Amnionapomorph

Mammaeautapomorph

Feathersapomorph

Loss of tailapomorph

The evolutionary change within a lineage is called anagenesis

The diversification of an evolutionary tree is called cladogenesis

Linnean systematics and cladistics

Linnean approach

Hierachical encaptive system

Phenomenological method based on similarity

It uses grades (groups of similar body plan)

Different taxonomies are possible

There is no clear decision intrument for taxonomies

The number of higher taxa is rather small (Pisces, Amphibia, Reptilia, Aves, Mammalia)

It does not assume common evolutionary history

It does not reconstruct evolution

Taxonomy is independent of evolution

Hennigean approach

Hierachical encaptive system

Analytical method based on lineage branching

It uses clades (groups of identical root)

Only one taxonomic solution is allowed

Autapomorphies decide about taxonomic position

The number of higher taxa is large (Pisces, Amphibia, Reptilia are not valid taxa )

It is based on common evolutionary history

It does reconstruct evolution

Taxonomy is a part of evolutionary theory

Low resolution trees High resolution trees

The principle of maximum parsimony (Occam’s razor) holds that we should accept that phylogenetic tree that can be constructed with the least number of morphological

changes.

The construction of phylogenetic trees from numerical methods

CSpecies 1 2 3 4 5 6A 1 1 0 1 1 1B 1 1 1 1 1 1C 0 1 0 0 1 0D 0 0 1 1 0 1E 1 0 1 1 0 1

Characters

The raw data

Species A B C D EA 0 1 3 4 3B 1 0 5 3 2C 3 4 0 5 6D 4 3 5 0 1E 3 2 6 1 0

Distance matrix

We are looking for such a tree that minimizes the sum of distances.

A B ED

010010

110111

101101

001101

8 changes

111111

A B CD E

110111010111

010010

111111

101101

001101

7 changes

Outgroup

How to define the root?

Parsimony analysis

To find the most parsimonious tree we have to cross all combinations of lineages (trees) with all character combinations at the root.

SpeciesNumber of

trees2 13 34 155 1056 9457 103958 1351359 202702510 34459425

The number of possible trees

S 1

(2S 2)!N

2 (S 1)!

Assumption of the numerical methods

Characters (or transitions) have to be independent.

Impossible character states have to be excluded.

Scales

Hairs

Feathers

Loss of feathersLoss of hairsFish

MammalsBirds

Incompatible

Characters are assumed to have equal importance. In reality transitions are not comparable.

To overcome this problem you give character weights. Technically you multiply the occurrence of a character in a distance matrix

A B C1 C2 DA 1 0 1 1 6B 1 2 4 4 2C1 4 5 2 2 1C2 4 5 2 2 1D 1 0 3 3 2

Species SequenceA A A T T A A C C C A A T AB C A T T A A C C C A A T AC C G T T T G G A A T G A CD C G T G T G G A A T A A AE G G T G T G C C C A A T A

Trees from molecular data

A B C D EA 0 1 11 10 5B 1 0 10 9 5C 11 10 0 3 9D 10 9 3 0 6E 5 5 9 6 0

Distance matrix

Linus Pauling (1901-1994)

Motoo Kimura(1924-1994)

Emile Zuckerkandl(1922-2013)

Evolutionary time scalesThe molecular clock

Numbers of amino acid substitutions and therefore trespective numbers of nucleotide substitutions are for many proteins and genomes approximately

proportional to time.

Hence, numbers of substitutions are a measure of time of divergence from

the latest common ancestor.

Substitutions alone provide a relative time scale

An appropriate calibration adds the absolute time scale

0

10

20

30

40

50

60

70

80

0 200 400 600 800 1000

Paleontological divergence estimate

Nu

um

be

r o

f am

ino

c

aci

d d

iffe

ren

ces

c

Superoxide dismutase

Tomoko Ohta(1933-)

Errors

Paleontological versus molecular timescales

Morphological change

Gen

etic

al c

hang

e

Time axis

Molecular divergence of placental orders (120-140 mya)

First fossils of placental orders (65 mya)

Eomaia (125 mya)

Morphological change

Gen

etic

al c

hang

e

Time axis

Molecular divergence (4-5 mya)

First fossils of erect hominids(6-7 mya)

Gene flow up to 2 mya

Molecular estimates point frequently much more ancient divergences of lineages than estimates based on the fossil record.

The reason are different speeds of morhological and genetical changes.

Changes in genetic constitution accumulate to a point where basic regulatory elements are

involved

Changes in genetic constitution involve first basic regulatory elements.

Paleontological versus molecular timescales

Matching of molecular and paleontological timescales in Echinodermata

For the majority of Echinoderm subtaxa molecular divergence estimates are higher than

the paleontological estimates.

Taxon First recordDuration of record

Missing records

Euechinoidea Serpianotiaris coaeva 235–240 45 15Acroechinoidea Diademopsis serialis 205–210 0 0Acrosalenia chartroni Lambert 200–205 0 0Diadematoida Gymnotiara varusense 190–195 10 5Plesiechinus hawkinsi Jesionek 195–200 5 5Irregularia Plesiechinus hawkinsi 195–200 15 0Microstomata Galeropygus sublaevis 180–185 0 0Neognathostomata Galeropygus sublaevis 180–185 80 10Cassiduloida Hungaresia ovum 85–90 90 15Clypeasteroida Nucleopygus angustatus 100–105 50 0Scutellina Eoscutum doncieuxi 50–55 0 0Laganiformes Sismondia logotheti 50–55 0 0Scutelliformes Eoscutum doncieuxi 50–55 25 0Atelostomata Hyboclypus ovalis 175–180 25 0Spatangoida Disaster moeschi 160–165 65 5Paleopneustina Polydesmaster fourtaui 90–95 0 5Brissidea Micraster distinctus 95–100 45 0Meoma antiqua Arnold 40–45 0 0Eupatagus haburiensis Khanna 50–55 15 0Stirodonta Atlasaster jeanneti 195–200 30 0Camarodonta Glyptocyphus difficilis 115–120 0 0Echinoida Pseudarbacia archaici 90–95 65 65Echinoida Lytechinus axiologus 45–50 0 5Cidaroidea Eotiaris keyserlingi 250–255 255 0Echinothurioida Pelanechinus oolithicum 170–175 175 45Pedinoida Hemipedina hudsoni 205–210 210 0Aspidodiadematidae Gymnotiara varusense 190–195 195 35Diadematidae Farquharsonia crenulata 165–170 170 0Echinoneoida Pygopyrina icaunensis 160–165 165 5Cassidulidae Rhyncholampas macari 65–70 70 30Echinolampadidae Hungaresia ovum 85–90 90 35Clypeasterina Clypeaster calzadai 40–45 45 20Fibularidae Echinocyamus gurnahensis 50–55 55 0Laganidae Sismondia logotheti 50–55 55 10Mellitidae Encope ciae 20–25 25 0Astriclypeidae Amphiope duffi 25–30 30 0Holasteroida Collyrites ellipticus 165–170 170 5Schizasteridae Periaster elatus 90–95 95 0Paleopneustidae Polydesmaster fourtaui 90–95 95 0Archaeopneustids Heterobrissus salvae 40–45 45 0Brissidae Meoma antiqua 40–45 45 0Spatangidae Granopatagus lonchophorus 35–40 40 0Loveniidae Hemimaretia subrostrata 35–40 40 0Arbacioida Atopechinus cellensis 165–170 170 0Somopneustids Phymechinus mirabilis 155–160 160 0Temnopleuridae Zeuglopleurus costulatus 95–100 100 0Echinidae Psammechinus dubius 15–20 20 0Strongylocentrotidae Strongylocentrotus antiquus 20–25 25 0Echinometridae Plagiechinus priscus 25–30 30 10Toxopneustidae Lytechinus axiologus 45–50 50 5Trigonocidaridae Arbacina monilis 15–20 20 30

Sum 3210 360

Species

0

50

100

150

200

250

300

0 100 200 300

Paleontological divergence estimate

Mo

lecu

lar

div

erg

en

ce

z

est

ima

te

Data from Smith et al. (2006)

Data from Qun et al. (2007)

DivergencesEarliest fossil

recordMolecular estimates

Placental-marsupials 175–145 185–161Amniotes-amphibians 310 375–345Myriapods-chelicerates 530 705–579Mosses-vascular plants 450 899–515Crustaceans-insects 530 726-539Echinoderms-chordates <530 1001–586Spiralian-Ecdysozoans 560–540 643–544Protostomes-deuterostomes 560–540 678–556Arthropods-chordates 560–540 1200–588Cnidaria-bilaterians <600 724–615Sponges-chordates <600 1350–592

Paleontological versus molecular timescales

Have all phylogenetic trees a single root?

Darwin’s first principle: All species of a given taxon have a common ancestor.

Parsimony analysis cannot answer this question. A brush would always have a lower number of character changes

TimeSpontaneous origin of simple life forms

Sca

le o

f or

gani

zatio

n

Scala naturae

A brush means:

• No speciation.

• If we except that extinction occurs this would mean a constant decrease in the number of species.

• Character change within whole species.

• No genetic (character) variability within populations.

• Extreme longevity of lineages.

Theory of Lamarck

But horizontal gene transfer and might at least in bacteria result in networks and rings!

History of palaeontology: http://en.wikipedia.org/wiki/History_of_paleontologyHistory of earth: http://wiki.cotch.net/index.php/History_of_the_EarthRadiometric dating details: http://www.tulane.edu/~sanelson/eens211/radiometric_dating.htmGeological time scale: http://en.wikipedia.org/wiki/Geologic_time_scale

Today’s reading

Phylogenetic systematics: http://evolution.berkeley.edu/evolibrary/article/phylogenetics_01

Cladistics: http://en.wikipedia.org/wiki/Cladistics

Ernst Haeckel: Kunstformen der Natur (Internet exhibition of original drawings: http://caliban.mpiz-koeln.mpg.de/~stueber/haeckel/kunstformen/liste.html

The modern molecular clock: http://awcmee.massey.ac.nz/people/dpenny/pdf/BromhamPenny_2003.pdf