Great ape genetic diversity and population history

Details

• Alternative Title:
  Nature
• Personal Author:
  Prado-Martinez, Javier ; Sudmant, Peter H. ; Kidd, Jeffrey M. ; Li, Heng ; Kelley, Joanna L. ; Lorente-Galdos, Belen ; Veeramah, Krishna R. ; Woerner, August E. ; O’Connor, Timothy D. ; Santpere, Gabriel ; Cagan, Alexander ; Theunert, Christoph ; Casals, Ferran ; Laayouni, Hafid ; Munch, Kasper ; Hobolth, Asger ; Halager, Anders E. ; Malig, Maika ; Hernandez-Rodriguez, Jessica ; Hernando-Herraez, Irene ; Prüfer, Kay ; Pybus, Marc ; Johnstone, Laurel ; Lachmann, Michael ; Alkan, Can ; Twigg, Dorina ; Petit, Natalia ; Baker, Carl ; Hormozdiari, Fereydoun ; Fernandez-Callejo, Marcos ; Dabad, Marc ; Wilson, Michael L. ; Stevison, Laurie ; Camprubí, Cristina ; Carvalho, Tiago ; Ruiz-Herrera, Aurora ; Vives, Laura ; Mele, Marta ; Abello, Teresa ; Kondova, Ivanela ; Bontrop, Ronald E. ; Pusey, Anne ; Lankester, Felix ; Kiyang, John A. ; Bergl, Richard A. ; Lonsdorf, Elizabeth ; Myers, Simon ; Ventura, Mario ; Gagneux, Pascal ; Comas, David ; Siegismund, Hans ; Blanc, Julie ; Agueda-Calpena, Lidia ; Gut, Marta ; Fulton, Lucinda ; Tishkoff, Sarah A. ; Mullikin, James C. ; Wilson, Richard K. ; Gut, Ivo G. ; Gonder, Mary Katherine ; Ryder, Oliver A. ; Hahn, Beatrice H. ; Navarro, Arcadi ; Akey, Joshua M. ; Bertranpetit, Jaume ; Reich, David ; Mailund, Thomas ; Schierup, Mikkel H. ; Hvilsom, Christina ; Andrés, Aida M. ; Wall, Jeffrey D. ; Bustamante, Carlos D. ; Hammer, Michael F. ; Eichler, Evan E. ; Marques-Bonet, Tomas
• Description:
  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.
• Subjects:
  Africa Animals Animals, Wild Animals, Zoo Article Asia, Southeastern Evolution, Molecular Gene Flow Genetics, Population Genetic Variation Genome Gorilla Gorilla Hominidae Humans Inbreeding Pan Paniscus Pan Troglodytes Phylogeny Polymorphism, Single Nucleotide Population Density

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• Source:
  Nature. 499(7459):471-475.
• Pubmed ID:
  23823723
• Pubmed Central ID:
  PMC3822165
• Document Type:
  Journal Article
• Funding:
  090532/Wellcome Trust/United Kingdom ; DP1 ES022577/ES/NIEHS NIH HHS/United States ; DP1ES022577-04/DP/NCCDPHP CDC HHS/United States ; GM100233/GM/NIGMS NIH HHS/United States ; HG002385/HG/NHGRI NIH HHS/United States ; R01 GM095882/GM/NIGMS NIH HHS/United States ; R01 GM100233/GM/NIGMS NIH HHS/United States ; R01 HG002385/HG/NHGRI NIH HHS/United States ; R01_HG005226/HG/NHGRI NIH HHS/United States ; Howard Hughes Medical Institute/United States
• Volume:
  499
• Issue:
  7459
• Collection(s):
  CDC Public Access
• Main Document Checksum:
  urn:sha256:d7112dc0e7774a483d1ece05ef4972a89f93310f7aa8ccfbf033bf8d478b4515
• Download URL:
  https://stacks.cdc.gov/view/cdc/22484/cdc_22484_DS1.pdf
• File Type:
  [PDF - 1.05 MB ]