Great ape genetic diversity and population history.

Published

Journal Article

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.

Full Text

Duke Authors

Cited Authors

  • Prado-Martinez, J; Sudmant, PH; Kidd, JM; Li, H; Kelley, JL; Lorente-Galdos, B; Veeramah, KR; Woerner, AE; O'Connor, TD; Santpere, G; Cagan, A; Theunert, C; Casals, F; Laayouni, H; Munch, K; Hobolth, A; Halager, AE; Malig, M; Hernandez-Rodriguez, J; Hernando-Herraez, I; Prüfer, K; Pybus, M; Johnstone, L; Lachmann, M; Alkan, C; Twigg, D; Petit, N; Baker, C; Hormozdiari, F; Fernandez-Callejo, M; Dabad, M; Wilson, ML; Stevison, L; Camprubí, C; Carvalho, T; Ruiz-Herrera, A; Vives, L; Mele, M; Abello, T; Kondova, I; Bontrop, RE; Pusey, A; Lankester, F; Kiyang, JA; Bergl, RA; Lonsdorf, E; Myers, S; Ventura, M; Gagneux, P; Comas, D; Siegismund, H; Blanc, J; Agueda-Calpena, L; Gut, M; Fulton, L; Tishkoff, SA; Mullikin, JC; Wilson, RK; Gut, IG; Gonder, MK; Ryder, OA; Hahn, BH; Navarro, A; Akey, JM; Bertranpetit, J; Reich, D; Mailund, T; Schierup, MH; Hvilsom, C; Andrés, AM; Wall, JD; Bustamante, CD; Hammer, MF; Eichler, EE; Marques-Bonet, T

Published Date

  • July 3, 2013

Published In

Volume / Issue

  • 499 / 7459

Start / End Page

  • 471 - 475

PubMed ID

  • 23823723

Pubmed Central ID

  • 23823723

Electronic International Standard Serial Number (EISSN)

  • 1476-4687

International Standard Serial Number (ISSN)

  • 0028-0836

Digital Object Identifier (DOI)

  • 10.1038/nature12228

Language

  • eng