ArticleNature2016
The Simons Genome Diversity Project: 300 genomes from 142 diverse populations.
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Article in Nature, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 827 papers, 1 of them a synthesis that pooled it.
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827citing papers in PubMed, 1 pooled it
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Who cites it
827 citing papers in PubMed, 1 synthesis or guideline pooled it, 1,740 citations in OpenAlex.
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767 more citing papers are in PubMed but not listed here.
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Authors and funding
79 authors at 20 institutions in 21 countries.
Swapan MallickDepartment of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA.
Heng LiBroad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA.
Mark LipsonDepartment of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA.
Iain MathiesonDepartment of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA.
Melissa GymrekBroad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA.
Fernando RacimoDepartment of Integrative Biology, University of California, Berkeley, California 94720-3140, USA.
Mengyao ZhaoDepartment of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA.
Niru ChennagiriDepartment of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA.
Susanne NordenfeltDepartment of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA.
Arti TandonDepartment of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA.
Pontus SkoglundDepartment of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA.
Iosif LazaridisDepartment of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA.
Sriram SankararamanDepartment of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA.
Qiaomei FuDepartment of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA.
Nadin RohlandDepartment of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA.
Gabriel RenaudDepartment of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany.
Yaniv ErlichNew York Genome Center, New York, New York 10013, USA.
Thomas WillemsNew York Genome Center, New York, New York 10013, USA.
Carla GalloLaboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima 15102, Perú.
Jeffrey P SpenceComputational Biology Graduate Group, University of California, Berkeley, California 94720, USA.
Yun S SongComputer Science Division, University of California, Berkeley, California 94720, USA.
Giovanni PolettiLaboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima 15102, Perú.
Francois BallouxGenetics Institute, University College London, Gower Street, London WC1E 6BT, UK.
George van DriemInstitute of Linguistics, University of Bern, Bern CH-3012, Switzerland.
Peter de KnijffDepartment of Human and Clinical Genetics, Postzone S5-P, Leiden University Medical Center, 2333 ZA Leiden, Netherlands.
Irene Gallego RomeroSchool of Biological Sciences, Nanyang Technological University, 637551 Singapore.
Aashish R JhaDepartment of Human Genetics, University of Chicago, Chicago, Illinois 60637, USA.
Doron M BeharEstonian Biocentre, Evolutionary Biology group, Tartu 51010, Estonia.
Claudio 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, Argentina.
Cristian CapelliDepartment of Zoology, University of Oxford, Oxford OX1 3PS, UK.
Tor HervigDepartment of Clinical Science, University of Bergen, Bergen 5021, Norway.
Andres Moreno-EstradaNational Laboratory of Genomics for Biodiversity (LANGEBIO), CINVESTAV, Irapuato, Guanajuato 36821, Mexico.
Olga L PosukhInstitute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia.
Elena BalanovskaResearch Centre for Medical Genetics, Moscow 115478, Russia.
Oleg BalanovskyResearch Centre for Medical Genetics, Moscow 115478, Russia.
Sena Karachanak-YankovaDepartment of Medical Genetics, National Human Genome Center, Medical University Sofia, Sofia 1431, Bulgaria.
Hovhannes SahakyanEstonian Biocentre, Evolutionary Biology group, Tartu 51010, Estonia.
Draga TonchevaDepartment of Medical Genetics, National Human Genome Center, Medical University Sofia, Sofia 1431, Bulgaria.
Levon YepiskoposyanLaboratory of Ethnogenomics, Institute of Molecular Biology, National Academy of Sciences of Armenia, Yerevan 0014, Armenia.
Chris Tyler-SmithThe Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK.
Yali XueThe Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK.
M Syafiq AbdullahRIPAS Hospital, Bandar Seri Begawan, Brunei.
Andres Ruiz-LinaresDepartment of Genetics, Evolution and Environment, University College London WC1E 6BT, UK.
Cynthia M BeallDepartment of Anthropology, Case Western Reserve University, Cleveland, Ohio 44106-7125, USA.
Anna Di RienzoDepartment of Human Genetics, University of Chicago, Chicago, Illinois 60637, USA.
Choongwon JeongDepartment of Human Genetics, University of Chicago, Chicago, Illinois 60637, USA.
Elena B StarikovskayaLaboratory of Human Molecular Genetics, Institute of Molecular and Cellular Biology, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia.
Ene MetspaluEstonian Biocentre, Evolutionary Biology group, Tartu 51010, Estonia.
Jüri ParikEstonian Biocentre, Evolutionary Biology group, Tartu 51010, Estonia.
Richard VillemsEstonian Biocentre, Evolutionary Biology group, Tartu 51010, Estonia.
Brenna M HennDepartment of Ecology and Evolution, Stony Brook University, Stony Brook, New York 11794, USA.
Ugur HodoglugilNextBio, Illumina, Santa Clara, California 95050, USA.
Robert MahleyGladstone Institutes, San Francisco, California 94158, USA.
Antti SajantilaDepartment of Forensic Medicine, University of Helsinki, Helsinki 00014, Finland.
George StamatoyannopoulosDepartment of Medicine, Division of Medical Genetics, University of Washington, Seattle, Washington 98195, USA.
Joseph T S WeeNational Cancer Centre Singapore, 169610 Singapore.
Rita KhusainovaInstitute of Biochemistry and Genetics, Ufa Research Centre, Russian Academy of Sciences, Ufa 450054, Russia.
Elza KhusnutdinovaInstitute of Biochemistry and Genetics, Ufa Research Centre, Russian Academy of Sciences, Ufa 450054, Russia.
Sergey LitvinovEstonian Biocentre, Evolutionary Biology group, Tartu 51010, Estonia.
George AyodoJaramogi Oginga Odinga University of Science and Technology, Bondo 40601, Kenya.
David ComasInstitut de Biologia Evolutiva (CSIC-UPF), Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona 08003, Spain.
Michael F HammerARL Division of Biotechnology, University of Arizona, Tucson, Arizona 85721, USA.
Toomas KivisildEstonian Biocentre, Evolutionary Biology group, Tartu 51010, Estonia.
William KlitzNew York Genome Center, New York, New York 10013, USA.
Cheryl A WinklerBasic Research Laboratory, Center for Cancer Research, NCI, Leidos Biomedical Research, Inc., Frederick National Laboratory, Frederick, Maryland 21702, USA.
Damian LabudaCHU Sainte-Justine, Pediatrics Departement, Université de Montréal, Québec H3T 1C5, Canada.
Michael BamshadDepartment of Pediatrics, University of Washington, Seattle, Washington 98119, USA.
Lynn B JordeDepartment of Human Genetics, University of Utah School of Medicine, Salt Lake City, Utah 84112, USA.
Sarah A TishkoffDepartments of Genetics and Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA.
W Scott WatkinsDepartment of Human Genetics, Eccles Institute of Human Genetics, University of Utah, Salt Lake City, Utah 84112, USA.
Mait MetspaluEstonian Biocentre, Evolutionary Biology group, Tartu 51010, Estonia.
Stanislav DryomovLaboratory of Human Molecular Genetics, Institute of Molecular and Cellular Biology, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia.
Rem SukernikLaboratory of Human Molecular Genetics, Institute of Molecular and Cellular Biology, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia.
Lalji SinghCSIR-Centre for Cellular and Molecular Biology, Hyderabad 500 007, India.
Kumarasamy ThangarajCSIR-Centre for Cellular and Molecular Biology, Hyderabad 500 007, India.
Svante PääboDepartment of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany.
Janet KelsoDepartment of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany.
Nick PattersonBroad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA.
David ReichDepartment of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA.
Estonian Biocentre · EEBroad Institute · USHarvard University · USHoward Hughes Medical Institute · USMax Planck Institute for Evolutionary Anthropology · DERussian Academy of Sciences · RUUniversity of Chicago · USBashkir State University · RUCentre for Cellular and Molecular Biology · INMedical University of Sofia · BGNew York Genome Center · USUniversidad Peruana Cayetano Heredia · PEUniversity College London · GBUniversity of California, Berkeley · USUniversity of Utah · USWellcome Sanger Institute · GBCase Western Reserve University · USCenter for Cancer Research · USCentre Hospitalier Universitaire Sainte-Justine · CACentro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional · MX
Funding
University of Utah Center for Clinical and Translational ScienceUL1TR001067 · NCATS · UNIVERSITY OF UTAH · PI DERE, WILLARD H., HESS, RACHEL · 2013 to 2017
$19.8MPOPULATION GENETICS OF MOBILE ELEMENTSR01GM059290 · NIGMS · UNIVERSITY OF UTAH · PI BATZER, MARK A, FESCHOTTE, CEDRIC · 1999 to 2018
$8.5MMethods for Genome-wide Association Studies in Admixed PopulationsR01HG006399 · NHGRI · HARVARD UNIVERSITY D/B/A HARVARD SCHOOL OF PUBLIC HEALTH · PI PRICE, ALKES L · 2011 to 2024
$6.3MIntegrative Genomics of Body Size and Metabolism in Ethnically Diverse AfricansR01GM113657 · NIGMS · UNIVERSITY OF PENNSYLVANIA · PI TISHKOFF, SARAH ANNE · 2015 to 2019
$2.8MPopulation mixture in evolutionary and medical geneticsR01GM100233 · NIGMS · HARVARD MEDICAL SCHOOL · PI PATTERSON, NICK J, REICH, DAVID E · 2012 to 2019
$2.7MMathematical Models and Statistical Methods for Large-Scale Population GenomicsR01GM094402 · NIGMS · UNIVERSITY OF CALIFORNIA BERKELEY · PI SONG, YUN S · 2010 to 2018
$2.2MAfrican Odyssey: An Integrative Genomics Analysis of Complex Physiologic TraitsDP1ES022577 · NIEHS · UNIVERSITY OF PENNSYLVANIA · PI TISHKOFF, SARAH ANNE · 2012 to 2013
$1.6MIntegrative nutrigenomic and metabolomic analyses of Africans with variable dietsR01DK104339 · NIDDK · UNIVERSITY OF PENNSYLVANIA · PI TISHKOFF, SARAH ANNE · 2015 to 2018
$1.4MStatistical methods to infer structure and impact of ancient admixtureR00GM111744 · NIGMS · UNIVERSITY OF CALIFORNIA LOS ANGELES · PI SANKARARAMAN, SRIRAM · 2016 to 2017
$498kNCATS NIH HHS UL1 TR001067NHGRI NIH HHS R01 HG006399NIDDK NIH HHS R01 DK104339NIEHS NIH HHS DP1 ES022577NIGMS NIH HHS R00 GM111744NIGMS NIH HHS R01 GM059290NIGMS NIH HHS R01 GM094402NIGMS NIH HHS R01 GM100233NIGMS NIH HHS R01 GM113657Wellcome Trust
Abstract
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.
Indexed as
GenomicsMutation RatePhylogenyAnimalsAustraliaBlack PeopleDatasets as TopicGenetics, PopulationGenetic VariationGenome, HumanHistory, AncientHuman MigrationHumansNeanderthalsNew GuineaRacial Groups
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