Статья

The Simons Genome Diversity Project: 300 genomes from 142 diverse populations

Swapan MallickBroad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USAHeng LiBroad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USAMark LipsonDepartment of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USAIain MathiesonDepartment of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USAMelissa GymrekBroad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USAFernando RacimoDepartment of Integrative Biology, University of California, Berkeley, California 94720-3140, USAMengyao ZhaoBroad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USANiru ChennagiriBroad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USASusanne NordenfeltBroad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USAArti TandonBroad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USAPontus SkoglundBroad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USAIosif LazaridisBroad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USASriram SankararamanBroad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USAQiaomei FuBroad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USANadin RohlandBroad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USAGabriel RenaudDepartment of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, GermanyYaniv ErlichCenter for Computational Biology and Bioinformatics, Columbia University, New York, New York 10032, USAThomas WillemsComputational and Systems Biology Program, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USACarla GalloLaboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima 15102, PerúJeffrey P. SpenceComputational Biology Graduate Group, University of California, Berkeley, California 94720, USAYun S. SongComputer Science Division, University of California, Berkeley, California 94720, USAGiovanni PolettiLaboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima 15102, PerúFrançois BallouxGenetics Institute, University College London, Gower Street, London WC1E 6BT, UKGeorge van DriemInstitute of Linguistics, University of Bern, Bern CH-3012, SwitzerlandPeter de KnijffDepartment of Human and Clinical Genetics, Postzone S5-P, Leiden University Medical Center, 2333 ZA Leiden, NetherlandsIrene Gallego RomeroLee Kong Chian School of Medicine, Nanyang Technological University, 636921 SingaporeAashish R. JhaDepartment of Human Genetics, University of Chicago, Chicago, Illinois 60637, USADoron M. BeharEstonian Biocentre, Evolutionary Biology group, Tartu 51010, EstoniaCláudio M. BraviLaboratorio de Genética Molecular Poblacional, Instituto Multidisciplinario de Biología Celular (IMBICE), CCT-CONICET La Plata/CIC Buenos Aires/Universidad Nacional de La Plata, La Plata B1906APO, ArgentinaCristian CapelliDepartment of Zoology, University of Oxford, Oxford OX1 3PS, UKTor HervigDepartment of Clinical Science, University of Bergen, Bergen 5021, NorwayAndrés Moreno‐EstradaNational Laboratory of Genomics for Biodiversity (LANGEBIO), CINVESTAV, Irapuato, Guanajuato 36821, MexicoOlga L. PosukhInstitute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, RussiaElena BalanovskaResearch Centre for Medical Genetics, Moscow 115478, RussiaOleg BalanovskyMoscow Institute for Physics and Technology, Dolgoprudniy 141700, RussiaSena Karachanak-YankovaDepartment of Medical Genetics, National Human Genome Center, Medical University Sofia, Sofia 1431, BulgariaHovhannes SahakyanEstonian Biocentre, Evolutionary Biology group, Tartu 51010, EstoniaДрага ТончеваDepartment of Medical Genetics, National Human Genome Center, Medical University Sofia, Sofia 1431, BulgariaLevon YepiskoposyanLaboratory of Ethnogenomics, Institute of Molecular Biology, National Academy of Sciences of Armenia, Yerevan 0014, ArmeniaChris Tyler‐SmithThe Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UKYali XueThe Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UKMuhammad Syafiq AbdullahRIPAS Hospital, Bandar Seri Begawan, BruneiAndrés Ruiz‐LinaresDepartment of Genetics, Evolution and Environment, University College London WC1E 6BT, UKCynthia M. BeallDepartment of Anthropology, Case Western Reserve University, Cleveland, Ohio 44106-7125, USAAnna Di RienzoDepartment of Human Genetics, University of Chicago, Chicago, Illinois 60637, USAChoongwon JeongDepartment of Human Genetics, University of Chicago, Chicago, Illinois 60637, USAElena B. StarikovskayaLaboratory of Human Molecular Genetics, Institute of Molecular and Cellular Biology, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, RussiaEne MetspaluDepartment of Evolutionary Biology, University of Tartu, Tartu 51010, EstoniaJüri ParikEstonian Biocentre, Evolutionary Biology group, Tartu 51010, EstoniaRichard VillemsDepartment of Evolutionary Biology, University of Tartu, Tartu 51010, EstoniaBrenna M. HennDepartment of Ecology and Evolution, Stony Brook University, Stony Brook, New York 11794, USAUğur HodoğlugilNextBio, Illumina, Santa Clara, California 95050, USARobert W. MahleyGladstone Institutes, San Francisco, California 94158, USAAntti SajantilaDepartment of Forensic Medicine, University of Helsinki, Helsinki 00014, FinlandGeorge StamatoyannopoulosDepartment of Medicine, Division of Medical Genetics, University of Washington, Seattle, Washington 98195, USAJoseph WeeNational Cancer Centre Singapore, 169610 SingaporeР. И. ХусаиноваDepartment of Genetics and Fundamental Medicine, Bashkir State University, Ufa 450074, RussiaЭ. К. ХуснутдиноваDepartment of Genetics and Fundamental Medicine, Bashkir State University, Ufa 450074, RussiaSergey LitvinovDepartment of Genetics and Fundamental Medicine, Bashkir State University, Ufa 450074, RussiaGeorge AyodoJaramogi Oginga Odinga University of Science and Technology, Bondo 40601, KenyaDavid ComasInstitut de Biologia Evolutiva (CSIC-UPF), Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona 08003, SpainMichael F. HammerARL Division of Biotechnology, University of Arizona, Tucson, Arizona 85721, USAToomas KivisildDivision of Biological Anthropology, University of Cambridge, Fitzwilliam Street, Cambridge CB2 1QH, UKWilliam KlitzNew York Genome Center, New York, New York 10013, USACheryl A. WinklerBasic Research Laboratory, Center for Cancer Research, NCI, Leidos Biomedical Research, Inc., Frederick National Laboratory, Frederick, Maryland 21702, USADamian LabudaCHU Sainte-Justine, Pediatrics Departement, Université de Montréal, Québec H3T 1C5, CanadaMichael J. BamshadDepartment of Pediatrics, University of Washington, Seattle, Washington 98119, USALynn B. JordeDepartment of Human Genetics, University of Utah School of Medicine, Salt Lake City, Utah 84112, USASarah A. TishkoffDepartments of Genetics and Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USAW. Scott WatkinsDepartment of Human Genetics, Eccles Institute of Human Genetics, University of Utah, Salt Lake City, Utah 84112, USAMait MetspaluEstonian Biocentre, Evolutionary Biology group, Tartu 51010, EstoniaStanislav DryomovDepartment of Paleolithic Archaeology, Institute of Archaeology and Ethnography, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, RussiaR. I. SukernikAltai State University, Barnaul 656000, RussiaLalji SinghCSIR-Centre for Cellular and Molecular Biology, Hyderabad 500 007, IndiaKumarasamy ThangarajCSIR-Centre for Cellular and Molecular Biology, Hyderabad 500 007, IndiaSvante PääboDepartment of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, GermanyJanet KelsoDepartment of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, GermanyNick PattersonBroad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USADavid ReichBroad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA

2016en

ABI

Аннотация

Here we report the Simons Genome Diversity Project data set: high quality genomes from 300 individuals from 142 diverse populations. These genomes include at least 5.8 million base pairs that are not present in the human reference genome. Our analysis reveals key features of the landscape of human genome variation, including that the rate of accumulation of mutations has accelerated by about 5% in non-Africans compared to Africans since divergence. We show that the ancestors of some pairs of present-day human populations were substantially separated by 100,000 years ago, well before the archaeologically attested onset of behavioural modernity. We also demonstrate that indigenous Australians, New Guineans and Andamanese do not derive substantial ancestry from an early dispersal of modern humans; instead, their modern human ancestry is consistent with coming from the same source as that of other non-Africans. Deep whole-genome sequencing of 300 individuals from 142 diverse populations provides insights into key population genetic parameters, shows that all modern human ancestry outside of Africa including in Australasians is consistent with descending from a single founding population, and suggests a higher rate of accumulation of mutations in non-Africans compared to Africans since divergence. Three international collaborations reporting in this issue of Nature describe 787 high-quality genomes from individuals from geographically diverse populations. David Reich and colleagues analysed whole-genome sequences of 300 individuals from 142 populations. Their findings include an accelerated estimated rate of accumulation of mutations in non-Africans compared to Africans since divergence, and that indigenous Australians, New Guineans and Andamanese do not derive substantial ancestry from an early dispersal of modern humans but from the same source as that of other non-Africans. Eske Willerlsev and colleagues obtained whole-genome data for 83 Aboriginal Australians and 25 Papuans from the New Guinea Highlands. They estimate that Aboriginal Australians and Papuans diverged from Eurasian populations 51,000–72,000 years ago, following a single out-of-Africa dispersal. Luca Pagani et al. report on a dataset of 483 high-coverage human genomes from 148 populations worldwide, including 379 new genomes from 125 populations. Their analyses support the model by which all non-African populations derive most of their genetic ancestry from a single recent migration out of Africa, although a Papuan contribution suggests a trace of an earlier human expansion.

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Идентификаторы

DOI: 10.1038/nature18964

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Цитирований: 5Использованных источников: 0

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