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      Great ape genetic diversity and population history

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      Author
      Prado-Martinez, J.
      Eichler, E. E.
      Marques-Bonet, T.
      Sudmant, P. H.
      Kidd, J. M.
      Li, H.
      Kelley, J. L.
      Lorente-Galdos, B.
      Veeramah, K. R.
      Woerner, A. E.
      O’Connor, T. D.
      Santpere, G.
      Cagan, A.
      Theunert, C.
      Casals, F.
      Laayouni, H.
      Munch, K.
      Hobolth, A.
      Halager, A. E.
      Malig, M.
      Hernandez-Rodriguez, J.
      Hernando-Herraez, I.
      Prüfer, K.
      Pybus, M.
      Johnstone, L.
      Lachmann, M.
      Alkan C.
      Twig, D.
      Petit, N.
      Baker, C.
      Hormozdiari, F.
      Fernandez-Callejo, M.
      Dabad, M.
      Wilson, M. L.
      Stevison, L.
      Camprubí, C.
      Carvalho, T.
      RuizHerrera, A.
      Vives, L.
      Mele, M.
      Abello, T.
      Kondova, I.
      Bontrop, R. E.
      Pusey, A.
      Lankester, F.
      Kiyang, J. A.
      Bergl, R. A.
      Lonsdorf, E.
      Myers, S.
      Ventura, M.
      Gagneux, P.
      Comas, D.
      Siegismund, H.
      Blanc, J.
      Agueda-Calpena, L.
      Gut, M.
      Fulton, L.
      Tishkoff, S. A.
      Mullikin, J. C.
      Wilson, R. K.
      Gut, I. G.
      Gonder, M K.
      Ryder, O. A.
      Hahn, B. H.
      Navarro, A.
      Akey, J. M.
      Bertranpetit, J.
      Reich, D.
      Mailund, T.
      Schierup, M. H.
      Hvilsom, C.
      Andrés, A. M.
      Wall, J. D.
      Bustamante, C. D.
      Hammer, M. F.
      Date
      2013
      Source Title
      Nature: international weekly journal of science
      Print ISSN
      0028-0836
      Electronic ISSN
      1476-4687
      Publisher
      Nature Publishing Group
      Volume
      499
      Issue
      7459
      Pages
      12 - 1
      Language
      English
      Type
      Article
      Item Usage Stats
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      86
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      Abstract
      Most great ape genetic variation remains uncharacterized(1,2); however, its study is critical for understanding population history(3-6), recombination(7), selection(8) and susceptibility to disease(9,10). 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.
      Keywords
      Human Genome
      Chimpanzee Genome
      Sequence
      Evolution
      Selection
      Patterns
      Decline
      Permalink
      http://hdl.handle.net/11693/12976
      Published Version (Please cite this version)
      http://dx.doi.org/10.1038/nature12228
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      • Department of Computer Engineering 1368
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