THE TIMING OF EUKARYOTIC EVOLUTION:FROM ROCKS TO RELAXED MOLECULAR CLOCKS,

AND RECIPROCALLY

Emmanuel JP DOUZERY 1

Frédéric DELSUC 1,2

& Hervé PHILIPPE 2

1 Paléontologie, Phylogénie et Paléobiologie,Institut des Sciences de l’Evolution,Université Montpellier II, France

2 CIAR, Département de Biochimie,Centre Robert-Cedergren,

Université de Montréal, Québec, Canada

1. WHEN DID ANIMALSAND OTHER EUKARYOTES APPEAR ?

2. VARIETY OF THE MOLECULAR ANSWERS

3. MOLECULAR DATING:FROM GLOBAL TO RELAXED CLOCKS

4. LARGE-SCALE PROTEIN CLOCKSFOR THE CHRONOLOGY

OF EUKARYOTES DIVERSIFICATION

[Anbar & Knoll2002]anoxic anoxic & sulfidic (S2-) oxic

EVOLUTIONOF

PROTEROZOIC OCEANS

Fe2+

deposits

Δ34S(δ34S

S2-/SO42-)

δ13C(carbonates)

Green algae

Protists

Red algaeNon identified Eukar.

Eukaryotesdiversified ~1 000 Mya

Hallucigenia

CAMBRIAN EXPLOSIONOF ANIMALS540 Ma

(Burgess, CA)

Their explosive diversificationinitiates the Primary Era.Trilobites

Sponges

Annelids

Chordates

1. WHEN DID ANIMALSAND OTHER EUKARYOTES APPEAR ?

2. VARIETY OF THE MOLECULAR ANSWERS

3. MOLECULAR DATING:FROM GLOBAL TO RELAXED CLOCKS

4. LARGE-SCALE PROTEIN CLOCKSFOR THE CHRONOLOGY

OF EUKARYOTES DIVERSIFICATION

[1965-2005]

40 yearsof

molecularclocks

"The molecular clock"

540Ma

WHEN DID BILATERIAN ANIMALS DIVERSIFY ?

Wray et al.(1996)

1 200 Ma

Aris-Brosou & Yang(2002, 2003)

582 Ma

> 586 MaBromham & Hendy

(2000)

656-573 MaPeterson et al.

(2004)

Lynch(1999)

630 Ma

Ayala et al.(1998)

736-670 Ma

850-730 MaFeng et al.

(1997)

Gu(1998)

830 Ma

Wang et al.(1999)

993 Ma

1 000 MaHedges et al.

(2004)

Variety of markers,taxa, calibrations

and methods !

[Hedges et al. 2004]

DATINGON

PROTEINS

1. Discrepancybetweenmolecules

and fossils ;

2. Noexplicit

uncertainty

1 000Mya

1 700Mya

543Mya

1. WHEN DID ANIMALSAND OTHER EUKARYOTES APPEAR ?

2. VARIETY OF THE MOLECULAR ANSWERS

3. MOLECULAR DATING:FROM GLOBAL TO RELAXED CLOCKS

4. LARGE-SCALE PROTEIN CLOCKSFOR THE CHRONOLOGY

OF EUKARYOTES DIVERSIFICATION

Gene X

MLtree

MLclock-like

tree

Fossilcalibration

Timeestimates

DATING WITH MOLECULAR CLOCKS

Gene X

MLtree

MLclock-like

tree

Slower rate,deeper timeestimates

THE PALEONTOLOGICAL ERROR

A differentfossil

calibration

Gene Y

DifferentML branchlengths

MLclock-like

tree

Different rate,different time

estimates

THE STOCHASTIC ERROR

Initialfossil

calibration

Gene Z

DifferentML branchlengths

Distorted MLclock-like

tree

Different rate,different time

estimates

THE LACK OF CLOCK

Initialfossil

calibration

Heritabilityof rates

Rates Rates gradually varyalong branches

"Closely related evolutionary lineages are likely to evolve at similar rates.

A consequence of this rate autocorrelationis that branches that are nearby in a tree

will have correlated lengths"[Thorne, Kishino & Painter 1998]

Stationary log-normaldistribution of rates

VAR ( ln rP ) = ν . tP

rrP

[Kishino, Thorne & Bruno 2001]

0

5

10

15

20

25

30

0 2000 4000 6000 8000 10000

Ages

BAYESIAN APPROACHFOR THE RELAXED MOLECULAR CLOCK

Stationary chainSampling of 9 000 values

µ = 11,0 Ma ± 2,195% credibility interval = 7,5 - 15,9 Ma

1. WHEN DID ANIMALSAND OTHER EUKARYOTES APPEAR ?

2. VARIETY OF THE MOLECULAR ANSWERS

3. MOLECULAR DATING:FROM GLOBAL TO RELAXED CLOCKS

4. LARGE-SCALE PROTEIN CLOCKSFOR THE CHRONOLOGY

OF EUKARYOTES DIVERSIFICATION

1. REDUCE THE STOCHASTIC ERRORS !

Use of a greater number of proteins

2. REDUCE THE PHYLOGENETIC ERRORS !

Use of a greater number of species

3. REDUCE THE PALEONTOLOGICAL ERRORS !

Use of multiple calibration intervals.

4. REDUCE THE DATING ERRORS ! Use of relaxed molecular clocks.

HOW TO IMPROVE THE MOLECULAR DATINGOF THE EUKARYOTIC EVOLUTION ?

129 proteins30 399 sites 0.1

Choanoflagellates

StramenopilesCiliophoraCryptosporidiumSarcocystidaePiroplasmidaPlasmodium

ALVEOLATES

Dictyostelium

ANIMALS(BILATERIANS)

[Philippe et al. 2004]

RhodophytaChlorophytaBryophytaLiliopsidaArabidopsis

PLANTS

BasidiomycetesSchizosaccharomycesSordarialesSaccharomycesCandida

FUNGI

ChelicerataDrosophilaLepidopteraHymenopteraPlatyhelminthesTrichocephalidaStrongyloididaTylenchidaSpiruridaAscarididaDiplogasteridaCaenorhabditis

PROTOSTOMES

LeishmaniaTrypanosoma bruceiTrypanosoma cruzi

KINETOPLASTIDS

UrochordataActinopterygiiMammalia

DEUTEROSTOMES

0.1

Choanoflagellates

RhodophytaChlorophytaBryophytaLiliopsidaArabidopsis

PLANTS

BasidiomycetesSchizosaccharomycesSordarialesSaccharomycesCandida

FUNGI

UrochordataActinopterygiiMammalia

DEUTEROSTOMES

ChelicerataDrosophilaLepidopteraHymenopteraPlatyhelminthesTrichocephalidaStrongyloididaTylenchidaSpiruridaAscarididaDiplogasteridaCaenorhabditis

PROTOSTOMES

StramenopilesCiliophoraCryptosporidiumSarcocystidaePiroplasmidaPlasmodium

ALVEOLATES

LeishmaniaTrypanosoma bruceiTrypanosoma cruzi

KINETOPLASTIDS

Dictyostelium

ANIMALS(BILATERIANS)

x 2

Vertebrates

[Philippe et al. 2004]

RhodophytaChlorophytaBryophytaLiliopsidaArabidopsisLeishmaniaTrypanosoma bruceiTrypanosoma cruziStramenopilesCiliophoraCryptosporidiumSarcocystidaePiroplasmidaPlasmodiumBasidiomycetesSchizosaccharomycesSordarialesSaccharomycesCandidaChoanoflagellatesUrochordataActinopterygiiMammaliaChelicerataDrosophilaLepidopteraHymenopteraPlatyhelminthesTrichocephalidaStrongyloididaTylenchidaSpiruridaAscarididaDiplogasteridaCaenorhabditis

PLANTS

FUNGI

DEUTEROSTOMES

PROTOSTOMES

ALVEOLATES

KINETOPLASTIDS

ANIMALS(BILATERIANS)

CLOCKS :lnL NO CLOCK = -779 283lnL WITH CLOCK = -783 020PLRT < 0.0001 [Douzery et al. 2004]

100Mya

RhodophytaChlorophytaBryophytaLiliopsidaArabidopsisLeishmaniaTrypanosoma bruceiTrypanosoma cruziStramenopilesCiliophoraCryptosporidiumSarcocystidaePiroplasmidaPlasmodiumBasidiomycetesSchizosaccharomycesSordarialesSaccharomycesCandidaChoanoflagellatesUrochordataActinopterygiiMammaliaChelicerataDrosophilaLepidopteraHymenopteraPlatyhelminthesTrichocephalidaStrongyloididaTylenchidaSpiruridaAscarididaDiplogasteridaCaenorhabditis

PLANTS

KINETOPLASTIDS

ALVEOLATES

FUNGI

ANIMALS

DEUTEROSTOMES

PROTOSTOMESBayesian relaxedmolecular clock

695 ± 30

984 ± 65

1085 ± 79

928 ± 60

1010 ± 69

LATEMIDDLE IIIIIIPROTEROZOIC PHANEROZOIC [Douzery et al. 2004]

CONCLUSIONS

The Bayesian relaxed molecular clock

on 129 proteins:

reduces the discrepancies between

paleontological and molecular estimates

of divergence times of major eucaryote groups ;

demonstrates the need of incorporating

variations of evolutionary rates ;

emphasizes the importance

of dense taxonomic and genetic samplings.

PERSPECTIVES

Incorporation of

phylogenetic uncertainty ;

Development and comparison

of models of evolutionary rate variation ;

Recognition of different partitions

among genes or proteins.