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CC BY-NC-SA V4.0, Open Access
Journal article
Great ape genetic diversity and population history
Nature (London), Vol.499(7459), pp.471-475
07/25/2013
Handle:
https://hdl.handle.net/2376/110816
PMCID: PMC3822165
PMID: 23823723
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.
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Details
- Title
- Great ape genetic diversity and population history
- Creators
- Javier Prado-Martinez - Institut de Biologia Evolutiva, (CSIC-Universitat Pompeu Fabra), PRBB, 08003 Barcelona, SpainPeter H Sudmant - Department of Genome Sciences, University of Washington, Seattle, Washington, USAJeffrey M Kidd - Department of Human Genetics, University of Michigan, Ann Arbor, MI, USAHeng Li - Department of Genetics, Harvard Medical School, Boston, Massachusetts, USAJoanna L Kelley - Department of Genetics, Stanford University, Stanford, CA, USABelen Lorente-Galdos - Institut de Biologia Evolutiva, (CSIC-Universitat Pompeu Fabra), PRBB, 08003 Barcelona, SpainKrishna R Veeramah - Arizona Research Laboratories, Division of Biotechnology, University of Arizona, Tucson, Arizona, USAAugust E Woerner - Arizona Research Laboratories, Division of Biotechnology, University of Arizona, Tucson, Arizona, USATimothy D O’Connor - Department of Genome Sciences, University of Washington, Seattle, Washington, USAGabriel Santpere - Institut de Biologia Evolutiva, (CSIC-Universitat Pompeu Fabra), PRBB, 08003 Barcelona, SpainAlexander Cagan - Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, GermanyChristoph Theunert - Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, GermanyFerran Casals - Institut de Biologia Evolutiva, (CSIC-Universitat Pompeu Fabra), PRBB, 08003 Barcelona, SpainHafid Laayouni - Institut de Biologia Evolutiva, (CSIC-Universitat Pompeu Fabra), PRBB, 08003 Barcelona, SpainKasper Munch - Bioinformatics Research Centre, Aarhus University, DK-8000 Aarhus C, DenmarkAsger Hobolth - Bioinformatics Research Centre, Aarhus University, DK-8000 Aarhus C, DenmarkAnders E Halager - Bioinformatics Research Centre, Aarhus University, DK-8000 Aarhus C, DenmarkMaika Malig - Department of Genome Sciences, University of Washington, Seattle, Washington, USAJessica Hernandez-Rodriguez - Institut de Biologia Evolutiva, (CSIC-Universitat Pompeu Fabra), PRBB, 08003 Barcelona, SpainIrene Hernando-Herraez - Institut de Biologia Evolutiva, (CSIC-Universitat Pompeu Fabra), PRBB, 08003 Barcelona, SpainKay Prüfer - Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, GermanyMarc Pybus - Institut de Biologia Evolutiva, (CSIC-Universitat Pompeu Fabra), PRBB, 08003 Barcelona, SpainLaurel Johnstone - Arizona Research Laboratories, Division of Biotechnology, University of Arizona, Tucson, Arizona, USAMichael Lachmann - Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, GermanyCan Alkan - Bilkent University, Ankara, TurkeyDorina Twigg - Department of Human Genetics, University of Michigan, Ann Arbor, MI, USANatalia Petit - Institut de Biologia Evolutiva, (CSIC-Universitat Pompeu Fabra), PRBB, 08003 Barcelona, SpainCarl Baker - Department of Genome Sciences, University of Washington, Seattle, Washington, USAFereydoun Hormozdiari - Department of Genome Sciences, University of Washington, Seattle, Washington, USAMarcos Fernandez-Callejo - Institut de Biologia Evolutiva, (CSIC-Universitat Pompeu Fabra), PRBB, 08003 Barcelona, SpainMarc Dabad - Institut de Biologia Evolutiva, (CSIC-Universitat Pompeu Fabra), PRBB, 08003 Barcelona, SpainMichael L Wilson - Department of Anthropology, University of Minnesota, Minneapolis, MN 55455, USALaurie Stevison - Institute for Human Genetics, University of California San Francisco, San Francisco, California, USACristina Camprubí - Departament de Biologia Cellular, Fisiologia i Immunologia, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, SpainTiago Carvalho - Institut de Biologia Evolutiva, (CSIC-Universitat Pompeu Fabra), PRBB, 08003 Barcelona, SpainAurora Ruiz-Herrera - Departament de Biologia Cellular, Fisiologia i Immunologia, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, SpainLaura Vives - Department of Genome Sciences, University of Washington, Seattle, Washington, USAMarta Mele - Institut de Biologia Evolutiva, (CSIC-Universitat Pompeu Fabra), PRBB, 08003 Barcelona, SpainTeresa Abello - Parc Zoològic de Barcelona, 08003 Barcelona, SpainIvanela Kondova - Biomedical Primate Research Centre, P.O. Box 3306, 2280 GH, Rijswijk, The NetherlandsRonald E Bontrop - Biomedical Primate Research Centre, P.O. Box 3306, 2280 GH, Rijswijk, The NetherlandsAnne Pusey - Department of Evolutionary Anthropology, Duke University, Durham, NC 27708, USAFelix Lankester - Limbe Wildlife Centre, Limbe, CameroonJohn A Kiyang - Limbe Wildlife Centre, Limbe, CameroonRichard A Bergl - North Carolina Zoological Park. Asheboro, NC 27205. USAElizabeth Lonsdorf - Department of Psychology, Franklin and Marshall College, Lancaster, PA 17604, USASimon Myers - Department of Statistics, Oxford University, 1 South Parks Road, Oxford OX1 3TG, UKMario Ventura - Department of Genetics and Microbiology, University of Bari, ItalyPascal Gagneux - Department of Cellular and Molecular Medicine, University of California San Diego, CA, USADavid Comas - Institut de Biologia Evolutiva, (CSIC-Universitat Pompeu Fabra), PRBB, 08003 Barcelona, SpainHans Siegismund - Department of Biology, Bioinformatics, University of Copenhagen, DenmarkJulie Blanc - Centro Nacional de Análisis Genómico (CNAG), 08028 Barcelona, SpainLidia Agueda-Calpena - Centro Nacional de Análisis Genómico (CNAG), 08028 Barcelona, SpainMarta Gut - Centro Nacional de Análisis Genómico (CNAG), 08028 Barcelona, SpainLucinda Fulton - Genome Sequencing Center, Washington University School of Medicine, St Louis, MO 63108, USASarah A Tishkoff - Department of Biology and Genetics. University of Pennsylvania, Philadelphia, USAJames C Mullikin - NISC, US NIH, Bethesda, Maryland, USARichard K Wilson - Genome Sequencing Center, Washington University School of Medicine, St Louis, MO 63108, USAIvo G Gut - Centro Nacional de Análisis Genómico (CNAG), 08028 Barcelona, SpainMary Katherine Gonder - Biological Sciences, University at Albany, State University of New York, Albany, NY 12222, USAOliver A Ryder - San Diego Zoo Institute for Conservation Research, San Diego Zoo Global, San Diego, CA, USABeatrice H Hahn - Departments of Medicine and Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, USAArcadi Navarro - Institut de Biologia Evolutiva, (CSIC-Universitat Pompeu Fabra), PRBB, 08003 Barcelona, SpainJoshua M Akey - Department of Genome Sciences, University of Washington, Seattle, Washington, USAJaume Bertranpetit - Institut de Biologia Evolutiva, (CSIC-Universitat Pompeu Fabra), PRBB, 08003 Barcelona, SpainDavid Reich - Department of Genetics, Harvard Medical School, Boston, Massachusetts, USAThomas Mailund - Bioinformatics Research Centre, Aarhus University, DK-8000 Aarhus C, DenmarkMikkel H Schierup - Bioinformatics Research Centre, Aarhus University, DK-8000 Aarhus C, DenmarkChristina Hvilsom - Department of Biology, Bioinformatics, University of Copenhagen, DenmarkAida M Andrés - Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, GermanyJeffrey D Wall - Institute for Human Genetics, University of California San Francisco, San Francisco, California, USACarlos D Bustamante - Department of Genetics, Stanford University, Stanford, CA, USAMichael F Hammer - Arizona Research Laboratories, Division of Biotechnology, University of Arizona, Tucson, Arizona, USAEvan E Eichler - Department of Genome Sciences, University of Washington, Seattle, Washington, USATomas Marques-Bonet - Institut de Biologia Evolutiva, (CSIC-Universitat Pompeu Fabra), PRBB, 08003 Barcelona, Spain
- Publication Details
- Nature (London), Vol.499(7459), pp.471-475
- Academic Unit
- Kelley Lab; Biological Sciences, School of; Paul G. Allen School for Global Animal Health
- Publisher
- Springer Nature
- Number of pages
- 5
- Grant note
- Max Planck Society; Foundation CELLEX HHMI; Howard Hughes Medical Institute ICREA 1032255 / NSF HOMINID HG002385; R01_HG005226; GM100233 / NIH; United States Department of Health & Human Services; National Institutes of Health (NIH) - USA G. Harold and Leila Y. Mathers Foundation R01HG002385 / NATIONAL HUMAN GENOME RESEARCH INSTITUTE; United States Department of Health & Human Services; National Institutes of Health (NIH) - USA; NIH National Human Genome Research Institute (NHGRI) 233297 / ERC Advanced Grant; European Research Council (ERC) BFU2009-13409-C02-02; BFU2012-38236 / FEDER; European Commission 2009 SGR 1101 / Direccio General de Recerca, Generalitat de Catalunya; Generalitat de Catalunya Zoo de Barcelona (Beca PRIC) EUPRIM-Net R01GM095882 / NATIONAL INSTITUTE OF GENERAL MEDICAL SCIENCES; United States Department of Health & Human Services; National Institutes of Health (NIH) - USA; NIH National Institute of General Medical Sciences (NIGMS) Danish Council for Independent Research Natural Sciences; Det Frie Forskningsrad (DFF) DP1ES022577 / NATIONAL INSTITUTE OF ENVIRONMENTAL HEALTH SCIENCES; United States Department of Health & Human Services; National Institutes of Health (NIH) - USA; NIH National Institute of Environmental Health Sciences (NIEHS) BFU2011-28549; BFU2010-19443 / MICINN(Spain); Spanish Government 0755823 / NSF; National Science Foundation (NSF) Spanish Government; European Commission 260372 / ERC; European Research Council (ERC); European Commission
- Identifiers
- 99900547358701842
- Language
- English
- Resource Type
- Journal article