Great ape genetic diversity and population history

Research output: Contribution to journal/Conference contribution in journal/Contribution to newspaperJournal articleResearchpeer-review

  • Javier Prado-Martinez
  • ,
  • Peter H Sudmant
  • ,
  • Jeffrey M Kidd
  • ,
  • Heng Li, Denmark
  • Joanna L Kelley
  • ,
  • Belen Lorente-Galdos
  • ,
  • Krishna R Veeramah
  • ,
  • August E Woerner
  • ,
  • Timothy D O'Connor
  • ,
  • Gabriel Santpere
  • ,
  • Alexander Cagan
  • ,
  • Christoph Theunert
  • ,
  • Ferran Casals
  • ,
  • Hafid Laayouni
  • ,
  • Kasper Munch
  • Asger Hobolth
  • Anders E Halager
  • ,
  • Maika Malig
  • ,
  • Jessica Hernandez-Rodriguez
  • ,
  • Irene Hernando-Herraez
  • ,
  • Kay Prüfer
  • ,
  • Marc Pybus
  • ,
  • Laurel Johnstone
  • ,
  • Michael Lachmann
  • ,
  • Can Alkan
  • ,
  • Dorina Twigg
  • ,
  • Natalia Petit
  • ,
  • Carl Baker
  • ,
  • Fereydoun Hormozdiari
  • ,
  • Marcos Fernandez-Callejo
  • ,
  • Marc Dabad
  • ,
  • Michael L Wilson
  • ,
  • Laurie Stevison
  • ,
  • Cristina Camprubí
  • ,
  • Tiago Carvalho
  • ,
  • Aurora Ruiz-Herrera
  • ,
  • Laura Vives
  • ,
  • Marta Mele
  • ,
  • Teresa Abello
  • ,
  • Ivanela Kondova
  • ,
  • Ronald E Bontrop
  • ,
  • Anne Pusey
  • ,
  • Felix Lankester
  • ,
  • John A Kiyang
  • ,
  • Richard A Bergl
  • ,
  • Elizabeth Lonsdorf
  • ,
  • Simon Myers
  • ,
  • Mario Ventura
  • ,
  • Pascal Gagneux
  • ,
  • David Comas
  • ,
  • Hans Siegismund, Denmark
  • Julie Blanc
  • ,
  • Lidia Agueda-Calpena
  • ,
  • Marta Gut
  • ,
  • Lucinda Fulton
  • ,
  • Sarah A Tishkoff
  • ,
  • James C Mullikin
  • ,
  • Richard K Wilson
  • ,
  • Ivo G Gut
  • ,
  • Mary Katherine Gonder
  • ,
  • Oliver A Ryder
  • ,
  • Beatrice H Hahn
  • ,
  • Arcadi Navarro
  • ,
  • Joshua M Akey
  • ,
  • Jaume Bertranpetit
  • ,
  • David Reich
  • ,
  • Thomas Mailund
  • Mikkel H Schierup
  • Christina Hvilsom, Biologisk institut, Denmark
  • Aida M Andrés
  • ,
  • Jeffrey D Wall
  • ,
  • Carlos D Bustamante
  • ,
  • Michael F Hammer
  • ,
  • Evan E Eichler
  • ,
  • Tomas Marques-Bonet
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.
Original languageEnglish
JournalNature
Volume499
Pages (from-to)471–475
ISSN0028-0836
DOIs
Publication statusPublished - 2013

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