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A Molecular Phylogeny of Living Primates


Comparative genomic analyses of primates offer considerable potential to define and understand the processes that mold, shape, and transform the human genome. However, primate taxonomy is both complex and controversial, with marginal unifying consensus of the evolutionary hierarchy of extant primate species. Here we provide new genomic sequence (∼8 Mb) from 186 primates representing 61 (∼90%) of the described genera, and we include outgroup species from Dermoptera, Scandentia, and Lagomorpha. The resultant phylogeny is exceptionally robust and illuminates events in primate evolution from ancient to recent, clarifying numerous taxonomic controversies and providing new data on human evolution. Ongoing speciation, reticulate evolution, ancient relic lineages, unequal rates of evolution, and disparate distributions of insertions/deletions among the reconstructed primate lineages are uncovered. Our resolution of the primate phylogeny provides an essential evolutionary framework with far-reaching applications including: human selection and adaptation, global emergence of zoonotic diseases, mammalian comparative genomics, primate taxonomy, and conservation of endangered species.


Vyšlo v časopise: A Molecular Phylogeny of Living Primates. PLoS Genet 7(3): e32767. doi:10.1371/journal.pgen.1001342
Kategorie: Research Article
prolekare.web.journal.doi_sk: https://doi.org/10.1371/journal.pgen.1001342

Souhrn

Comparative genomic analyses of primates offer considerable potential to define and understand the processes that mold, shape, and transform the human genome. However, primate taxonomy is both complex and controversial, with marginal unifying consensus of the evolutionary hierarchy of extant primate species. Here we provide new genomic sequence (∼8 Mb) from 186 primates representing 61 (∼90%) of the described genera, and we include outgroup species from Dermoptera, Scandentia, and Lagomorpha. The resultant phylogeny is exceptionally robust and illuminates events in primate evolution from ancient to recent, clarifying numerous taxonomic controversies and providing new data on human evolution. Ongoing speciation, reticulate evolution, ancient relic lineages, unequal rates of evolution, and disparate distributions of insertions/deletions among the reconstructed primate lineages are uncovered. Our resolution of the primate phylogeny provides an essential evolutionary framework with far-reaching applications including: human selection and adaptation, global emergence of zoonotic diseases, mammalian comparative genomics, primate taxonomy, and conservation of endangered species.


Zdroje

1. GoodmanM

PorterCA

CzelusniakJ

PageSL

SchneiderH

1998

Toward a phylogenetic classification of Primates based on DNA evidence complemented by fossil evidence.

Molecular Phylogenetics and Evolution

9

585

598

2. GrovesCP

2001

Primate taxonomy.

Washington, DC

Smithsonian Institution Press

350

3. WilsonDE

ReederDM

2005

Mammal species of the world : a taxonomic and geographic reference.

Baltimore

Johns Hopkins University Press

2142

4. ChatterjeeHJ

HoSYW

BarnesI

GrovesC

2009

Estimating the phylogeny and divergence times of primates using a supermatrix approach.

BMC Evolutionary Biology

9

259

5. FabrePH

RodriguesA

DouzeryEJP

2009

Patterns of macroevolution among Primates inferred from a supermatrix of mitochondrial and nuclear DNA.

Molecular Phylogenetics and Evolution

53

808

825

6. Pecon-SlatteryJ

WilkersonAJP

MurphyWJ

O'BrienSJ

2004

Phylogenetic assessment of introns and SINEs within the Y chromosome using the cat family Felidae as a species tree.

Molecular Biology and Evolution

21

2299

2309

7. JohnsonWE

EizirikE

Pecon-SlatteryJ

MurphyWJ

AntunesA

2006

The Late Miocene radiation of modern Felidae: A genetic assessment.

Science

311

73

77

8. Eizirik EMW

SpringerMS

O'BrienSJ

2004

Molecular Phylogeny and Dating of Early Primate Divergences.

Ross CFKR

Anthropoid Origins: New Visions

New York

Kluwer Academic/Plenum

45

65

9. BajpaiS

KayRF

WilliamsBA

DasDP

KapurVV

2008

The oldest Asian record of Anthropoidea.

Proceedings of the National Academy of Sciences of the United States of America

105

11093

11098

10. KayRF

RossC

WilliamsBA

1997

Anthropoid origins.

Science

275

797

804

11. NowakRM

1999

Walker's mammals of the world.

Baltimore

Johns Hopkins University Press

1936

12. MurphyWJ

EizirikE

JohnsonWE

ZhangYP

RyderOA

2001

Molecular phylogenetics and the origins of placental mammals.

Nature

409

614

618

13. SchmitzJ

OhmeM

ZischlerH

2001

SINE insertions in cladistic analyses and the phylogenetic affiliations of Tarsius bancanus to other primates.

Genetics

157

777

784

14. MatsuiA

RakotondraparanyF

MunechikaI

HasegawaM

HoraiS

2009

Molecular phylogeny and evolution of prosimians based on complete sequences of mitochondrial DNAs.

Gene

441

53

66

15. ArnasonU

AdegokeJA

BodinK

BornEW

EsaYB

2002

Mammalian mitogenomic relationships and the root of the eutherian tree.

Proceedings of the National Academy of Sciences of the United States of America

99

8151

8156

16. JaneckaJE

MillerW

PringleTH

WiensF

ZitzmannA

2007

Molecular and genomic data identify the closest living relative of primates.

Science

318

792

794

17. KriegsJO

ChurakovG

JurkaJ

BrosiusJ

SchmitzJ

2007

Evolutionary history of 7SL RNA-derived SINEs in supraprimates.

Trends in Genetics

23

158

161

18. ChurakovG

KriegsJO

BaertschR

ZemannA

BrosiusJ

2009

Mosaic retroposon insertion patterns in placental mammals.

Genome Research

19

868

875

19. RoosC

SchmitzJ

ZischlerH

2004

Primate jumping genes elucidate strepsirrhine phylogeny.

Proceedings of the National Academy of Sciences of the United States of America

101

10650

10654

20. HorvathJE

WillardHF

2007

Primate comparative genomics: lemur biology and evolution.

Trends in Genetics

23

173

182

21. HorvathJE

WeisrockDW

EmbrySL

FiorentinoI

BalhoffJP

2008

Development and application of a phylogenomic toolkit: resolving the evolutionary history of Madagascar's lemurs.

Genome Research

18

489

499

22. MittermeierR

GanzhornJ

KonstantW

GlanderK

TattersallI

2008

Lemur Diversity in Madagascar.

International Journal of Primatology

29

1607

1656

23. TakaiM

AnayaF

ShigeharaN

SetoguchiT

2000

New fossil materials of the earliest new world monkey, Branisella boliviana, and the problem of platyrrhine origins.

American Journal of Physical Anthropology

111

263

281

24. TakaiM

AnayaF

1996

New specimens of the oldest fossil platyrrhine, Branisella boliviana, from Salla, Bolivia.

American Journal of Physical Anthropology

99

301

317

25. PouxC

ChevretP

HuchonD

de JongWW

DouzeryEJP

2006

Arrival and diversification of caviomorph rodents and platyrrhine primates in South America.

Systematic Biology

55

228

244

26. HodgsonJA

SternerKN

MatthewsLJ

BurrellAS

JaniRA

2009

Successive radiations, not stasis, in the South American primate fauna.

Proceedings of the National Academy of Sciences of the United States of America

106

5534

5539

27. OsterholzM

WalterL

RoosC

2008

Phylogenetic position of the langur genera Semnopithecus and Trachypithecus among Asian colobines, and genus affiliations of their species groups.

BMC Evolutionary Biology

8

58

28. OpazoJC

WildmanDE

PrychitkoT

JohnsonRM

GoodmanM

2006

Phylogenetic relationships and divergence times among New World monkeys (Platyrrhini, Primates).

Molecular Phylogenetics and Evolution

40

274

280

29. SteiperME

RuvoloM

2003

New World monkey phylogeny based on X-linked G6PD DNA sequences.

Molecular Phylogenetics and Evolution

27

121

130

30. OsterholzM

WalterL

RoosC

2009

Retropositional events consolidate the branching order among New World monkey genera.

Molecular Phylogenetics and Evolution

50

507

513

31. Ankel-SimonsF

RasmussenDT

2008

Diurnality, Nocturnality, and the Evolution of Primate Visual Systems.

American Journal of Physical Anthropology

100

117

32. FordSM

DavisLC

1992

Systematics and body size: implications for feeding adaptations in New World monkeys.

American Journal of Physical Anthropology

88

415

468

33. CroppSJ

LarsonA

CheverudJM

1999

Historical biogeography of tamarins, genus Saguinus: The molecular phylogenetic evidence.

American Journal of Physical Anthropology

108

65

89

34. CanavezFC

MoreiraMAM

SimonF

ParhamP

SeuanezHN

1999

Phylogenetic relationships of the callitrichinae (Platyrrhini, Primates) based on beta(2)-microglobulin DNA sequences.

American Journal of Primatology

48

225

236

35. FordSM

1980

Callitrichids as phyletic dwarfs, and the place of Callitrichidae in Platyrrhini.

Primates

21

31

43

36. MoynihanM

1976

The New World primates : adaptive radiation and the evolution of social behavior, languages, and intelligence.

Princeton, N.J.

Princeton University Press

262

37. FleagleJG

1988

Primate adaptation and evolution.

San Diego

Academic Press

486

38. DelsonE

1992

Evolution of Old World Monkeys.

Jones SMR

PilbeamD

The Cambridge Encyclopedia of Human Evolution

Cambridge UK

Cambridge University Press

217

222

39. XingJ

WangH

ZhangY

RayDA

TosiAJ

2007

A mobile element-based evolutionary history of guenons (tribe Cercopithecini).

BMC Biology

5

5

40. TingN

TosiAJ

LiY

ZhangYP

DisotellTR

2008

Phylogenetic incongruence between nuclear and mitochondrial markers in the Asian colobines and the evolution of the langurs and leaf monkeys.

Molecular Phylogenetics and Evolution

46

466

474

41. PageSL

GoodmanM

2001

Catarrhine phylogeny: Noncoding DNA evidence for a diphyletic origin of the mangabeys and for a human-chimpanzee clade.

Molecular Phylogenetics and Evolution

18

14

25

42. PageSL

ChiuCH

GoodmanM

1999

Molecular phylogeny of old world monkeys (Cercopithecidae) as inferred from gamma-globin DNA sequences.

Molecular Phylogenetics and Evolution

13

348

359

43. MoulinS

Gerbault-SeureauM

DutrillauxB

RichardFA

2008

Phylogenomics of African guenons.

Chromosome Research

16

783

799

44. KaranthKP

SinghL

ColluraRV

StewartCB

2008

Molecular phylogeny and biogeography of langurs and leaf monkeys of South Asia (Primates : Colobinae).

Molecular Phylogenetics and Evolution

46

683

694

45. GrovesCP

1989

Cercopithecus and company: a primate radiation.

Science

244

860

861

46. KaranthKP

2008

Primate numts and reticulate evolution of capped and golden leaf monkeys (Primates: Colobinae).

Journal of biosciences

33

761

770

47. TosiAJ

MelnickDJ

DisotellTR

2004

Sex chromosome phylogenetics indicate a single transition to terrestriality in the guenons (tribe Cercopithecini).

Journal of Human Evolution

46

223

237

48. TosiAJ

DisotellTR

MoralesJC

MelnickDJ

2003

Cercopithecine Y-chromosome data provide a test of competing morphological evolutionary hypotheses.

Molecular Phylogenetics and Evolution

27

510

521

49. ZieglerT

AbeggC

MeijaardE

Perwitasari-FarajallahD

WalterL

2007

Molecular phylogeny and evolutionary history of Southeast Asian macaques forming the M. silenus group.

Molecular Phylogenetics and Evolution

42

807

816

50. ElangoN

ThomasJW

YiSV

PrograNCS

2006

Variable molecular clocks in hominoids.

Proceedings of the National Academy of Sciences of the United States of America

103

1370

1375

51. SteiperME

2006

Population history, biogeography, and taxonomy of orangutans (Genus : Pongo) based on a population genetic meta-analysis of multiple loci.

Journal of Human Evolution

50

509

522

52. MullerS

HollatzM

WienbergJ

2003

Chromosomal phylogeny and evolution of gibbons (Hylobatidae).

Human Genetics

113

493

501

53. JauchA

WienbergJ

StanyonR

ArnoldN

TofanelliS

1992

Reconstruction of genomic rearrangements in great apes and gibbons by chromosome painting.

Proceedings of the National Academy of Sciences of the United States of America

89

8611

8615

54. MisceoD

CapozziO

RobertoR

Dell'OglioMP

RocchiM

2008

Tracking the complex flow of chromosome rearrangements from the Hominoidea Ancestor to extant Hylobates and Nomascus Gibbons by high-resolution synteny mapping.

Genome Research

18

1530

1537

55. RoosC

GeissmannT

2001

Molecular phylogeny of the major hylobatid divisions.

Molecular Phylogenetics and Evolution

19

486

494

56. ZhuLC

WangQ

TangP

ArakiH

TianDC

2009

Genomewide Association between Insertions/Deletions and the Nucleotide Diversity in Bacteria.

Molecular Biology and Evolution

26

2353

2361

57. TianDC

WangQ

ZhangPF

ArakiH

YangSH

2008

Single-nucleotide mutation rate increases close to insertions/deletions in eukaryotes.

Nature

455

105-U170

58. VolfovskyN

OleksykTK

CruzKC

TrueloveAL

StephensRM

2009

Genome and gene alterations by insertions and deletions in the evolution of human and chimpanzee chromosome 22.

BMC Genomics

10

51

59. ChenJQ

WuY

YangHW

BergelsonJ

KreitmanM

2009

Variation in the Ratio of Nucleotide Substitution and Indel Rates across Genomes in Mammals and Bacteria.

Molecular Biology and Evolution

26

1523

1531

60. Kehrer-SawatzkiH

CooperDN

2007

Understanding the recent evolution of the human genome: insights from human-chimpanzee genome comparisons.

Human Mutation

28

99

130

61. SchmitzJ

RoosC

ZischlerH

2005

Primate phylogeny: molecular evidence from retroposons.

Cytogenetic and Genome Research

108

26

37

62. TabuceR

MarivauxL

LebrunR

AdaciM

BensalahM

2009

Anthropoid versus strepsirhine status of the African Eocene primates Algeripithecus and Azibius: craniodental evidence.

Proceedings of the Royal Society B-Biological Sciences

276

4087

4094

63. YoderAD

BurnsMM

ZehrS

DelefosseT

VeronG

2003

Single origin of Malagasy Carnivora from an African ancestor.

Nature

421

734

737

64. TeelingEC

ScallyM

KaoDJ

RomagnoliML

SpringerMS

2000

Molecular evidence regarding the origin of echolocation and flight in bats.

Nature

403

188

192

65. VentaPJ

BrouilletteJA

Yuzbasiyan-GurkanV

BrewerGJ

1996

Gene-specific universal mammalian sequence-tagged sites: application to the canine genome.

Biochemical Genetics

34

321

341

66. LyonsLA

LaughlinTF

CopelandNG

JenkinsNA

WomackJE

1997

Comparative anchor tagged sequences (CATS) for integrative mapping of mammalian genomes.

Nature Genetics

15

47

56

67. MoreiraMAM

2002

SRY evolution in Cebidae (Platyrrhini: Primates).

Journal of Molecular Evolution

55

92

103

68. FlynnJJ

NedbalMA

1998

Phylogeny of the Carnivora (Mammalia): Congruence vs incompatibility among multiple data sets.

Molecular Phylogenetics and Evolution

9

414

426

69. KatohK

TohH

2008

Recent developments in the MAFFT multiple sequence alignment program.

Brief Bioinform

9

286

298

70. KatohK

AsimenosG

TohH

2009

Multiple alignment of DNA sequences with MAFFT.

Methods in Molecular Biology

537

39

64

71. RambautA

2007

Se-Al. Sequence Alignment Editor.

Oxford

University of Oxford

72. TalaveraG

CastresanaJ

2007

Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments.

Systematic Biology

56

564

577

73. PosadaD

CrandallKA

1998

MODELTEST: testing the model of DNA substitution.

Bioinformatics

14

817

818

74. SwoffordDL

2002

PAUP*. Phylogenetic Analysis Using Parsimony (*and Other Methods). Version 4. Sinauer Associates, Sunderland, Massachusetts

75. ZwicklDJ

2006

Genetic algorithm approaches for the phylogenetic analysis of large biological sequence datasets under the maximum likelihood criterion.

Austin

The University of Texas

76. DrummondAJ

RambautA

2007

BEAST: Bayesian evolutionary analysis by sampling trees.

BMC Evolutionary Biology

7

214

77. DrummondAJ

HoSYW

PhillipsMJ

RambautA

2006

Relaxed phylogenetics and dating with confidence.

PLoS Biol

4

e88

doi:10.1371/journal.pbio.0040088

78. SeiffertER

SimonsEL

AttiaY

2003

Fossil evidence for an ancient divergence of lorises and galagos.

Nature

422

421

424

79. FranzenJL

GingerichPD

HabersetzerJ

HurumJH

von KoenigswaldW

2009

Complete primate skeleton from the Middle Eocene of Messel in Germany: morphology and paleobiology.

PLoS ONE

4

e5723

doi:10.1371/journal.pone.0005723

80. PouxC

DouzeryEJ

2004

Primate phylogeny, evolutionary rate variations, and divergence times: a contribution from the nuclear gene IRBP.

American Journal of Physical Anthropology

124

1

16

81. KayRF

FleagleJG

MitchellTRT

ColbertM

BownT

2008

The anatomy of Dolichocebus gaimanensis, a stem platyrrhine monkey from Argentina.

Journal of Human Evolution

54

323

382

82. SteiperME

YoungNM

SukarnaTY

2004

Genomic data support the hominoid slowdown and an Early Oligocene estimate for the hominoid-cercopithecoid divergence.

Proceedings of the National Academy of Sciences of the United States of America

101

17021

17026

83. TosiAJ

DetwilerKM

DisotellTR

2005

X-chromosomal window into the evolutionary history of the guenons (Primates : Cercopithecini).

Molecular Phylogenetics and Evolution

36

58

66

84. VignaudP

DuringerP

MackayeHT

LikiusA

BlondelC

2002

Geology and palaeontology of the Upper Miocene Toros-Menalla hominid locality, Chad.

Nature

418

152

155

85. TavareS

MarshallCR

WillO

SoligoC

MartinRD

2002

Using the fossil record to estimate the age of the last common ancestor of extant primates.

Nature

416

726

729

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