The Simons Genome Diversity Project: 300 genomes from 142 diverse populations.
Mallick SDepartment of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA.
Li HBroad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA.
Lipson MDepartment of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA.
Mathieson IDepartment of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA.
Gymrek MBroad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA.
Racimo FDepartment of Integrative Biology, University of California, Berkeley, California 94720-3140, USA.
Zhao MDepartment of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA.
Chennagiri NDepartment of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA.
Nordenfelt SDepartment of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA.
Tandon ADepartment of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA.
Skoglund PDepartment of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA.
Lazaridis IDepartment of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA.
Sankararaman SDepartment of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA.
Fu QDepartment of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA.
Rohland NDepartment of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA.
Renaud GDepartment of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany.
Erlich YNew York Genome Center, New York, New York 10013, USA.
Willems TNew York Genome Center, New York, New York 10013, USA.
Gallo CLaboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima 15102, Perú.
Spence JPComputational Biology Graduate Group, University of California, Berkeley, California 94720, USA.
Song YSComputer Science Division, University of California, Berkeley, California 94720, USA.
Poletti GLaboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima 15102, Perú.
Balloux FGenetics Institute, University College London, Gower Street, London WC1E 6BT, UK.
van Driem GInstitute of Linguistics, University of Bern, Bern CH-3012, Switzerland.
de Knijff PDepartment of Human and Clinical Genetics, Postzone S5-P, Leiden University Medical Center, 2333 ZA Leiden, Netherlands.
Romero IGSchool of Biological Sciences, Nanyang Technological University, 637551 Singapore.
Jha ARDepartment of Human Genetics, University of Chicago, Chicago, Illinois 60637, USA.
Behar DMEstonian Biocentre, Evolutionary Biology group, Tartu 51010, Estonia.
Bravi CMLaboratorio 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.
Capelli CDepartment of Zoology, University of Oxford, Oxford OX1 3PS, UK.
Hervig TDepartment of Clinical Science, University of Bergen, Bergen 5021, Norway.
Moreno-Estrada ANational Laboratory of Genomics for Biodiversity (LANGEBIO), CINVESTAV, Irapuato, Guanajuato 36821, Mexico.
Posukh OLInstitute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia.
Balanovska EResearch Centre for Medical Genetics, Moscow 115478, Russia.
Balanovsky OResearch Centre for Medical Genetics, Moscow 115478, Russia.
Karachanak-Yankova SDepartment of Medical Genetics, National Human Genome Center, Medical University Sofia, Sofia 1431, Bulgaria.
Sahakyan HEstonian Biocentre, Evolutionary Biology group, Tartu 51010, Estonia.
Toncheva DDepartment of Medical Genetics, National Human Genome Center, Medical University Sofia, Sofia 1431, Bulgaria.
Yepiskoposyan LLaboratory of Ethnogenomics, Institute of Molecular Biology, National Academy of Sciences of Armenia, Yerevan 0014, Armenia.
Abdullah MSRIPAS Hospital, Bandar Seri Begawan, Brunei.
Ruiz-Linares ADepartment of Genetics, Evolution and Environment, University College London WC1E 6BT, UK.
Beall CMDepartment of Anthropology, Case Western Reserve University, Cleveland, Ohio 44106-7125, USA.
Di Rienzo ADepartment of Human Genetics, University of Chicago, Chicago, Illinois 60637, USA.
Jeong CDepartment of Human Genetics, University of Chicago, Chicago, Illinois 60637, USA.
Starikovskaya EBLaboratory of Human Molecular Genetics, Institute of Molecular and Cellular Biology, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia.
Metspalu EEstonian Biocentre, Evolutionary Biology group, Tartu 51010, Estonia.
Parik JEstonian Biocentre, Evolutionary Biology group, Tartu 51010, Estonia.
Villems REstonian Biocentre, Evolutionary Biology group, Tartu 51010, Estonia.
Henn BMDepartment of Ecology and Evolution, Stony Brook University, Stony Brook, New York 11794, USA.
Hodoglugil UNextBio, Illumina, Santa Clara, California 95050, USA.
Mahley RGladstone Institutes, San Francisco, California 94158, USA.
Sajantila ADepartment of Forensic Medicine, University of Helsinki, Helsinki 00014, Finland.
Stamatoyannopoulos GDepartment of Medicine, Division of Medical Genetics, University of Washington, Seattle, Washington 98195, USA.
Wee JTNational Cancer Centre Singapore, 169610 Singapore.
Khusainova RInstitute of Biochemistry and Genetics, Ufa Research Centre, Russian Academy of Sciences, Ufa 450054, Russia.
Khusnutdinova EInstitute of Biochemistry and Genetics, Ufa Research Centre, Russian Academy of Sciences, Ufa 450054, Russia.
Litvinov SEstonian Biocentre, Evolutionary Biology group, Tartu 51010, Estonia.
Ayodo GJaramogi Oginga Odinga University of Science and Technology, Bondo 40601, Kenya.
Comas DInstitut de Biologia Evolutiva (CSIC-UPF), Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona 08003, Spain.
Hammer MFARL Division of Biotechnology, University of Arizona, Tucson, Arizona 85721, USA.
Kivisild TEstonian Biocentre, Evolutionary Biology group, Tartu 51010, Estonia.
Klitz WNew York Genome Center, New York, New York 10013, USA.
Winkler CABasic Research Laboratory, Center for Cancer Research, NCI, Leidos Biomedical Research, Inc., Frederick National Laboratory, Frederick, Maryland 21702, USA.
Bamshad MDepartment of Pediatrics, University of Washington, Seattle, Washington 98119, USA.
Jorde LBDepartment of Human Genetics, University of Utah School of Medicine, Salt Lake City, Utah 84112, USA.
Tishkoff SADepartments of Genetics and Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA.
Watkins WSDepartment of Human Genetics, Eccles Institute of Human Genetics, University of Utah, Salt Lake City, Utah 84112, USA.
Metspalu MEstonian Biocentre, Evolutionary Biology group, Tartu 51010, Estonia.
Dryomov SLaboratory of Human Molecular Genetics, Institute of Molecular and Cellular Biology, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia.
Sukernik RLaboratory of Human Molecular Genetics, Institute of Molecular and Cellular Biology, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia.
Singh LCSIR-Centre for Cellular and Molecular Biology, Hyderabad 500 007, India.
Thangaraj KCSIR-Centre for Cellular and Molecular Biology, Hyderabad 500 007, India.
Pääbo SDepartment of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany.
Kelso JDepartment of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany.
Patterson NBroad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA.
Reich DDepartment of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA.
English
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.