the timing of eukaryotic evolution · the timing of eukaryotic evolution: from rocks to relaxed...
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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
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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
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[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
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Hallucigenia
CAMBRIAN EXPLOSIONOF ANIMALS540 Ma
(Burgess, CA)
Their explosive diversificationinitiates the Primary Era.Trilobites
Sponges
Annelids
Chordates
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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
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[1965-2005]
40 yearsof
molecularclocks
"The molecular clock"
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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 !
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[Hedges et al. 2004]
DATINGON
PROTEINS
1. Discrepancybetweenmolecules
and fossils ;
2. Noexplicit
uncertainty
1 000Mya
1 700Mya
543Mya
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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
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Gene X
MLtree
MLclock-like
tree
Fossilcalibration
Timeestimates
DATING WITH MOLECULAR CLOCKS
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Gene X
MLtree
MLclock-like
tree
Slower rate,deeper timeestimates
THE PALEONTOLOGICAL ERROR
A differentfossil
calibration
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Gene Y
DifferentML branchlengths
MLclock-like
tree
Different rate,different time
estimates
THE STOCHASTIC ERROR
Initialfossil
calibration
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Gene Z
DifferentML branchlengths
Distorted MLclock-like
tree
Different rate,different time
estimates
THE LACK OF CLOCK
Initialfossil
calibration
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Heritabilityof rates
Rates Rates gradually varyalong branches
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"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]
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Stationary log-normaldistribution of rates
VAR ( ln rP ) = ν . tP
rrP
[Kishino, Thorne & Bruno 2001]
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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
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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
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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 ?
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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
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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]
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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]
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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]
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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.
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PERSPECTIVES
Incorporation of
phylogenetic uncertainty ;
Development and comparison
of models of evolutionary rate variation ;
Recognition of different partitions
among genes or proteins.