Dataset Information

Great ape genetic diversity and population history.

ABSTRACT: Most great ape genetic variation remains uncharacterized; however, its study is critical for understanding population history, recombination, selection and susceptibility to disease. Here we sequence to high coverage a total of 79 wild- and captive-born individuals representing all six great ape species and seven subspecies and report 88.8?million single nucleotide polymorphisms. Our analysis provides support for genetically distinct populations within each species, signals of gene flow, and the split of common chimpanzees into two distinct groups: Nigeria-Cameroon/western and central/eastern populations. We find extensive inbreeding in almost all wild populations, with eastern gorillas being the most extreme. Inferred effective population sizes have varied radically over time in different lineages and this appears to have a profound effect on the genetic diversity at, or close to, genes in almost all species. We discover and assign 1,982 loss-of-function variants throughout the human and great ape lineages, determining that the rate of gene loss has not been different in the human branch compared to other internal branches in the great ape phylogeny. This comprehensive catalogue of great ape genome diversity provides a framework for understanding evolution and a resource for more effective management of wild and captive great ape populations.

SUBMITTER: Prado-Martinez J

PROVIDER: S-EPMC3822165 | biostudies-literature | 2013 Jul

REPOSITORIES: biostudies-literature

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Great ape genetic diversity and population history.

Prado-Martinez Javier J Sudmant Peter H PH Kidd Jeffrey M JM Li Heng H Kelley Joanna L JL Lorente-Galdos Belen B Veeramah Krishna R KR Woerner August E AE O'Connor Timothy D TD Santpere Gabriel G Cagan Alexander A Theunert Christoph C Casals Ferran F Laayouni Hafid H Munch Kasper K Hobolth Asger A Halager Anders E AE Malig Maika M Hernandez-Rodriguez Jessica J Hernando-Herraez Irene I Prüfer Kay K Pybus Marc M Johnstone Laurel L Lachmann Michael M Alkan Can C Twigg Dorina D Petit Natalia N Baker Carl C Hormozdiari Fereydoun F Fernandez-Callejo Marcos M Dabad Marc M Wilson Michael L ML Stevison Laurie L Camprubí Cristina C Carvalho Tiago T Ruiz-Herrera Aurora A Vives Laura L Mele Marta M Abello Teresa T Kondova Ivanela I Bontrop Ronald E RE Pusey Anne A Lankester Felix F Kiyang John A JA Bergl Richard A RA Lonsdorf Elizabeth E Myers Simon S Ventura Mario M Gagneux Pascal P Comas David D Siegismund Hans H Blanc Julie J Agueda-Calpena Lidia L Gut Marta M Fulton Lucinda L Tishkoff Sarah A SA Mullikin James C JC Wilson Richard K RK Gut Ivo G IG Gonder Mary Katherine MK Ryder Oliver A OA Hahn Beatrice H BH Navarro Arcadi A Akey Joshua M JM Bertranpetit Jaume J Reich David D Mailund Thomas T Schierup Mikkel H MH Hvilsom Christina C Andrés Aida M AM Wall Jeffrey D JD Bustamante Carlos D CD Hammer Michael F MF Eichler Evan E EE Marques-Bonet Tomas T

Nature 20130703 7459

Most great ape genetic variation remains uncharacterized; however, its study is critical for understanding population history, recombination, selection and susceptibility to disease. Here we sequence to high coverage a total of 79 wild- and captive-born individuals representing all six great ape species and seven subspecies and report 88.8 million single nucleotide polymorphisms. Our analysis provides support for genetically distinct populations within each species, signals of gene flow, and the ...[more]

PMID: 23823723

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Dataset Information

Great ape genetic diversity and population history.

Publications

Great ape genetic diversity and population history.

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