Origin of Protists & Metazoans: Fossil & Genomic Evidence€¦ · Suctorian = Acritarch 580 mya...
Transcript of Origin of Protists & Metazoans: Fossil & Genomic Evidence€¦ · Suctorian = Acritarch 580 mya...
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Origin of Protists & Metazoans:
Fossil & Genomic Evidence
Jere H. Lipps1, Yoshi Ishitani2,
Yurika Ujiie3, and Michele Weber4
1. University of California, Berkeley, CA 94720 USA; 2.Center for
Computational Sciences, University of Tsukuba, Japan, 3.Center for
Advanced Marine Core Research, Kochi University, Japan; 4.The Gordon
and Betty Moore Foundation, Palo Alto, CA 94304 USA.
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Problem: Molecular Clock
Estimates Exceed Fossil Dates
Forams: 800 vs 545 my
Hypotheses
1. Small populations.*
2. Widely spaced geographically.*
3. Absence of hard parts.*
4. Failure of hard parts to preserve.*
5. Undiscovered.*
6. Incorrect age assignments for the fossils.
7. Molecular clock estimates problematic due to
insufficient taxonomic sampling & fewer gene
datasets.
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Tintinnids?
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1600 mya
Mesoproterozoic
Huangmailing Formation
(China)
Li & Zhan, 2006 Li et al., 2009
Tintinnids= metamorphic
shards/contamination
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Tintinnids= algae?
635-715 mya
Tsagaan Oloom
Formation
(Mongolia)
Bosak et al. (2011)
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Ciliate
Suctorian
= Acritarch
580 mya
Wengan Phosphate
Member
Doushantou
Formation
(China)
Li, Chen,
Lipps, Gao,
Chi & Wu 2007
Yonyangella ovalis
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Tintinnids
= Acritarchs
580 mya
Wengan Phosphate
Member
Doushantou
Formation
(China)
Dunthorn, Lipps, & Stoeck
2010Eotintinnopsis pinniforma &
Wujiangella beidoushaneseaa
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Tintinnids:
Cretaceous
Eicher, 1965
Graneros Shale
Wyoming,
South Dakota,
Colorado
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Radiolaria:
Cambrian
Dong, Knoll & Lipps,
1997
Hunan, China
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Foraminifera= Thecamoebians
Hua , Chen, Yuan,
Xiao & Cai, 2010
~550 mya
Late Ediacaran
Dengying Formation
(China)
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Foraminifera: Platysolenites
Lower Cambrian: NewfoundlandLipps & Rozanov, 1996
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Molecular phylogeny (157 genes)
Bigelowiella natans
Paulinella chromatophora
Eucyrtidium acuminatum
Reticulomyxa filosa
Ustilago maydis
Cyanophora paradoxa
Brevimastigomonas motovehiculus
Quinqueloculina sp.
Spirillina sp.
Ammonia beccariiTextularia conica
SRT235
Alexandrium tamarense
Karenia brevis
Noctiluca scintillans
Oxyrrhis marinaPerkinsus marinus
Plasmodium falciparum
Toxoplasma gondiiTheileria parva
Tetrahymena pyriformis
Cryptosporidium parvum
Phytophthora infestans
Phaeodactylum tricomutum
Thalassiosira pseudonana
Asterionellopsis glacialis
Aureococcus anophagefferens
Ectocarpus siliculosus
62/63/1.0
100/98/-
0.1
Substitution/site
RaxML/IQTREE/PhyoByes
(LG+G+F)/(LG+G+F+C60)/(CAT+GTR)
Bold line is 100/100/1.0
100/98/97/99/
RaxML
/IQTREE(LG+F+R6)
/IQTREE(LG+G+F+C60)
/IQTREE(C60+PMSF)
/
Rh
izaria
Alv
eo
lata
Stra
me
no
pile
OUTGROUP
Fo
ram
s
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Molecular clock (Forams)
CenozoicMesozoicPaleozoicProteozoic
CretaceousJurassicTriassicPerm.Carbo.Devo.Sil.Cambr.Ordov.EdiacaranCryogenianTonian
0 (Ma)200400600
Pal. N.
E. acuminatum
R. filosa
Quinqueloculina sp.
Spirillina sp.
A. beccarii
T. conica227(CI:203-251)
417(CI:391-445)
497(CI:462-528)
588(CI:544-632)
2122(CI:1765-2621)
BEAST v. 1.8.4
Uncorrelated relaxed clock (Birth-Death
process)
(mcmc: 1e+7; Burnin: 1000)
:Lower constraint (Normal; ±10% in 95%
probability)
Foram-root as Normal (650-920 Ma)
(Groussin et al., 2011)
CenozoicMesozoicPaleozoicProteozoic
CretaceousJurassicTriassicPerm.Carbo.Devo.Sil.Cambr.Ordov.EdiacaranCryogenianTonian
0 (Ma)200400600
Pal. N.
E. acuminatum
R. filosa
Quinqueloculina sp.
Spirillina sp.
A. beccarii
T. conica274(CI:251-301)
403(CI:369-437)
512(CI:469-555)
613(CI:542-665)
1106(CI:936-1305)
BEAST v. 1.8.4
Uncorrelated relaxed clock (Birth-Death
process)
(mcmc: 1e+7; Burnin: 1000)
:Lower constraint (Log-normal; Stdev:
0.75)
Foram-root as Normal (650-920 Ma)
Fo
ram
sFo
ram
s
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Fora
ms
CenozoicMesozoicPaleozoicProteozoic
CretaceousJurassicTriassicPerm.Carbo.Devo.Sil.Cambr.Ordov.EdiacaranCryogenianTonian
0 (Ma)200400600
Pal. N.
B. natans
P. chromatophora
E. acuminatum
R. filosa
Ustilago maydis
C. paradoxa
B. motovehiculus
Quinqueloculina sp.
Spirillina sp.
A. beccarii
T. conica
SRT235
A. tamarense
K. brevis
N. scintillans
O. marina
Perkinsus marinus
P. falciparum
T. gondii
T. parva
T. pyriformis
C. parvum
P. infestans
P. tricomutum
T. pseudonana
A. glacialis
A. anophagefferens
E. siliculosus
800
Molecular clock (SAR+OUTGROUP)
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First Fossils Millions of
Years Ago
Metazoans ~600
Foraminifera 544
Radiolaria 542
Tintinnids 180
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Molecular
Clock Millions of
Years Ago
Metazoans ~680
Foraminifera 575-529
Radiolaria 566-555
Tintinnids ?
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Thanks and
be creative!
Molecular and fossil origination dates
correspond more closely now near
Precambrian/Cambrian boundary.