title: The Simons Genome Diversity Project: 300 genomes from 142 diverse populations.
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.
authors.affiliation: Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA.|Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA.|Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts 02115, USA.
authors.forename: Swapan
authors.initials: S
authors.lastname: Mallick
authors.affiliation: Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA.
authors.forename: Heng
authors.initials: H
authors.lastname: Li
authors.affiliation: Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA.
authors.forename: Mark
authors.initials: M
authors.lastname: Lipson
authors.affiliation: Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA.
authors.forename: Iain
authors.initials: I
authors.lastname: Mathieson
authors.affiliation: Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA.|Whitehead Institute for Biomedical Research, Cambridge, Massachusetts 02142, USA.|Harvard-MIT Division of Health Sciences and Technology, MIT, Cambridge, Massachusetts 02139, USA.|New York Genome Center, New York, New York 10013, USA.
authors.forename: Melissa
authors.initials: M
authors.lastname: Gymrek
authors.affiliation: Department of Integrative Biology, University of California, Berkeley, California 94720-3140, USA.
authors.forename: Fernando
authors.initials: F
authors.lastname: Racimo
authors.affiliation: Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA.|Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA.|Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts 02115, USA.
authors.forename: Mengyao
authors.initials: M
authors.lastname: Zhao
authors.affiliation: Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA.|Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA.|Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts 02115, USA.
authors.forename: Niru
authors.initials: N
authors.lastname: Chennagiri
authors.affiliation: Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA.|Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA.|Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts 02115, USA.
authors.forename: Susanne
authors.initials: S
authors.lastname: Nordenfelt
authors.affiliation: Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA.|Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA.
authors.forename: Arti
authors.initials: A
authors.lastname: Tandon
authors.affiliation: Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA.|Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA.
authors.forename: Pontus
authors.initials: P
authors.lastname: Skoglund
authors.affiliation: Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA.|Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA.
authors.forename: Iosif
authors.initials: I
authors.lastname: Lazaridis
authors.affiliation: Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA.|Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA.
authors.forename: Sriram
authors.initials: S
authors.lastname: Sankararaman
authors.affiliation: Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA.|Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA.|Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, IVPP, CAS, Beijing 100044, China.
authors.forename: Qiaomei
authors.initials: Q
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authors.affiliation: Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA.|Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA.
authors.forename: Nadin
authors.initials: N
authors.lastname: Rohland
authors.affiliation: Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany.
authors.forename: Gabriel
authors.initials: G
authors.lastname: Renaud
authors.affiliation: New York Genome Center, New York, New York 10013, USA.|Department of Computer Science, Columbia University, New York, New York 10027, USA.|Center for Computational Biology and Bioinformatics, Columbia University, New York, New York 10032, USA.
authors.forename: Yaniv
authors.initials: Y
authors.lastname: Erlich
authors.affiliation: New York Genome Center, New York, New York 10013, USA.|Computational and Systems Biology Program, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.
authors.forename: Thomas
authors.initials: T
authors.lastname: Willems
authors.affiliation: Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima 15102, Perú.
authors.forename: Carla
authors.initials: C
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authors.affiliation: Computational Biology Graduate Group, University of California, Berkeley, California 94720, USA.
authors.forename: Jeffrey P
authors.initials: JP
authors.lastname: Spence
authors.affiliation: Computer Science Division, University of California, Berkeley, California 94720, USA.|Department of Statistics, University of California, Berkeley, California 94720, USA.|Department of Mathematics and Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA.
authors.forename: Yun S
authors.initials: YS
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authors.affiliation: Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima 15102, Perú.
authors.forename: Giovanni
authors.initials: G
authors.lastname: Poletti
authors.affiliation: Genetics Institute, University College London, Gower Street, London WC1E 6BT, UK.
authors.forename: Francois
authors.initials: F
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authors.affiliation: Institute of Linguistics, University of Bern, Bern CH-3012, Switzerland.
authors.forename: George
authors.initials: G
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authors.affiliation: Department of Human and Clinical Genetics, Postzone S5-P, Leiden University Medical Center, 2333 ZA Leiden, Netherlands.
authors.forename: Peter
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authors.lastname: de Knijff
authors.affiliation: School of Biological Sciences, Nanyang Technological University, 637551 Singapore.|Lee Kong Chian School of Medicine, Nanyang Technological University, 636921 Singapore.
authors.forename: Irene Gallego
authors.initials: IG
authors.lastname: Romero
authors.affiliation: Department of Human Genetics, University of Chicago, Chicago, Illinois 60637, USA.
authors.forename: Aashish R
authors.initials: AR
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authors.affiliation: Estonian Biocentre, Evolutionary Biology group, Tartu 51010, Estonia.
authors.forename: Doron M
authors.initials: DM
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authors.affiliation: Laboratorio 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.
authors.forename: Claudio M
authors.initials: CM
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authors.affiliation: Department of Zoology, University of Oxford, Oxford OX1 3PS, UK.
authors.forename: Cristian
authors.initials: C
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authors.affiliation: Department of Clinical Science, University of Bergen, Bergen 5021, Norway.
authors.forename: Tor
authors.initials: T
authors.lastname: Hervig
authors.affiliation: National Laboratory of Genomics for Biodiversity (LANGEBIO), CINVESTAV, Irapuato, Guanajuato 36821, Mexico.
authors.forename: Andres
authors.initials: A
authors.lastname: Moreno-Estrada
authors.affiliation: Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia.|Novosibirsk State University, Novosibirsk 630090, Russia.
authors.forename: Olga L
authors.initials: OL
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authors.affiliation: Research Centre for Medical Genetics, Moscow 115478, Russia.
authors.forename: Elena
authors.initials: E
authors.lastname: Balanovska
authors.affiliation: Research Centre for Medical Genetics, Moscow 115478, Russia.|Vavilov Institute for General Genetics, Moscow 119991, Russia.|Moscow Institute for Physics and Technology, Dolgoprudniy 141700, Russia.
authors.forename: Oleg
authors.initials: O
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authors.affiliation: Department of Medical Genetics, National Human Genome Center, Medical University Sofia, Sofia 1431, Bulgaria.
authors.forename: Sena
authors.initials: S
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authors.affiliation: Estonian Biocentre, Evolutionary Biology group, Tartu 51010, Estonia.|Laboratory of Ethnogenomics, Institute of Molecular Biology, National Academy of Sciences of Armenia, Yerevan 0014, Armenia.
authors.forename: Hovhannes
authors.initials: H
authors.lastname: Sahakyan
authors.affiliation: Department of Medical Genetics, National Human Genome Center, Medical University Sofia, Sofia 1431, Bulgaria.
authors.forename: Draga
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authors.affiliation: Laboratory of Ethnogenomics, Institute of Molecular Biology, National Academy of Sciences of Armenia, Yerevan 0014, Armenia.
authors.forename: Levon
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authors.lastname: Yepiskoposyan
authors.affiliation: The Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK.
authors.forename: Chris
authors.initials: C
authors.lastname: Tyler-Smith
authors.affiliation: The Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK.
authors.forename: Yali
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authors.affiliation: RIPAS Hospital, Bandar Seri Begawan, Brunei.
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authors.affiliation: Department of Genetics, Evolution and Environment, University College London WC1E 6BT, UK.
authors.forename: Andres
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authors.affiliation: Department of Anthropology, Case Western Reserve University, Cleveland, Ohio 44106-7125, USA.
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authors.initials: CM
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authors.affiliation: Department of Human Genetics, University of Chicago, Chicago, Illinois 60637, USA.
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authors.affiliation: Department of Human Genetics, University of Chicago, Chicago, Illinois 60637, USA.
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authors.affiliation: Laboratory of Human Molecular Genetics, Institute of Molecular and Cellular Biology, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia.
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authors.initials: EB
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authors.affiliation: Estonian Biocentre, Evolutionary Biology group, Tartu 51010, Estonia.|Department of Evolutionary Biology, University of Tartu, Tartu 51010, Estonia.
authors.forename: Ene
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authors.affiliation: Estonian Biocentre, Evolutionary Biology group, Tartu 51010, Estonia.
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authors.affiliation: Estonian Biocentre, Evolutionary Biology group, Tartu 51010, Estonia.|Department of Evolutionary Biology, University of Tartu, Tartu 51010, Estonia.|Estonian Academy of Sciences, Tallinn 10130, Estonia.
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authors.affiliation: Department of Ecology and Evolution, Stony Brook University, Stony Brook, New York 11794, USA.
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authors.affiliation: NextBio, Illumina, Santa Clara, California 95050, USA.
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authors.affiliation: Gladstone Institutes, San Francisco, California 94158, USA.
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authors.affiliation: Department of Forensic Medicine, University of Helsinki, Helsinki 00014, Finland.
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authors.initials: JT
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authors.affiliation: Institute of Biochemistry and Genetics, Ufa Research Centre, Russian Academy of Sciences, Ufa 450054, Russia.|Department of Genetics and Fundamental Medicine, Bashkir State University, Ufa 450074, Russia.
authors.forename: Rita
authors.initials: R
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authors.affiliation: Institute of Biochemistry and Genetics, Ufa Research Centre, Russian Academy of Sciences, Ufa 450054, Russia.|Department of Genetics and Fundamental Medicine, Bashkir State University, Ufa 450074, Russia.
authors.forename: Elza
authors.initials: E
authors.lastname: Khusnutdinova
authors.affiliation: Estonian Biocentre, Evolutionary Biology group, Tartu 51010, Estonia.|Institute of Biochemistry and Genetics, Ufa Research Centre, Russian Academy of Sciences, Ufa 450054, Russia.|Department of Genetics and Fundamental Medicine, Bashkir State University, Ufa 450074, Russia.
authors.forename: Sergey
authors.initials: S
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authors.affiliation: Jaramogi Oginga Odinga University of Science and Technology, Bondo 40601, Kenya.
authors.forename: George
authors.initials: G
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authors.affiliation: Institut de Biologia Evolutiva (CSIC-UPF), Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona 08003, Spain.
authors.forename: David
authors.initials: D
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authors.affiliation: ARL Division of Biotechnology, University of Arizona, Tucson, Arizona 85721, USA.
authors.forename: Michael F
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authors.affiliation: Estonian Biocentre, Evolutionary Biology group, Tartu 51010, Estonia.|Division of Biological Anthropology, University of Cambridge, Fitzwilliam Street, Cambridge CB2 1QH, UK.
authors.forename: Toomas
authors.initials: T
authors.lastname: Kivisild
authors.affiliation: New York Genome Center, New York, New York 10013, USA.
authors.forename: William
authors.initials: W
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authors.affiliation: Basic Research Laboratory, Center for Cancer Research, NCI, Leidos Biomedical Research, Inc., Frederick National Laboratory, Frederick, Maryland 21702, USA.
authors.forename: Cheryl A
authors.initials: CA
authors.lastname: Winkler
authors.affiliation: CHU Sainte-Justine, Pediatrics Departement, Université de Montréal, Québec H3T 1C5, Canada.
authors.forename: Damian
authors.initials: D
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authors.affiliation: Department of Pediatrics, University of Washington, Seattle, Washington 98119, USA.
authors.forename: Michael
authors.initials: M
authors.lastname: Bamshad
authors.affiliation: Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, Utah 84112, USA.
authors.forename: Lynn B
authors.initials: LB
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authors.affiliation: Departments of Genetics and Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA.
authors.forename: Sarah A
authors.initials: SA
authors.lastname: Tishkoff
authors.affiliation: Department of Human Genetics, Eccles Institute of Human Genetics, University of Utah, Salt Lake City, Utah 84112, USA.
authors.forename: W Scott
authors.initials: WS
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authors.affiliation: Estonian Biocentre, Evolutionary Biology group, Tartu 51010, Estonia.
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authors.initials: M
authors.lastname: Metspalu
authors.affiliation: Laboratory of Human Molecular Genetics, Institute of Molecular and Cellular Biology, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia.|Department of Paleolithic Archaeology, Institute of Archaeology and Ethnography, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia.
authors.forename: Stanislav
authors.initials: S
authors.lastname: Dryomov
authors.affiliation: Laboratory of Human Molecular Genetics, Institute of Molecular and Cellular Biology, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia.|Altai State University, Barnaul 656000, Russia.
authors.forename: Rem
authors.initials: R
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authors.affiliation: CSIR-Centre for Cellular and Molecular Biology, Hyderabad 500 007, India.
authors.forename: Lalji
authors.initials: L
authors.lastname: Singh
authors.affiliation: CSIR-Centre for Cellular and Molecular Biology, Hyderabad 500 007, India.
authors.forename: Kumarasamy
authors.initials: K
authors.lastname: Thangaraj
authors.affiliation: Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany.
authors.forename: Svante
authors.initials: S
authors.lastname: Pääbo
authors.affiliation: Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany.
authors.forename: Janet
authors.initials: J
authors.lastname: Kelso
authors.affiliation: Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA.
authors.forename: Nick
authors.initials: N
authors.lastname: Patterson
authors.affiliation: Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA.|Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA.|Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts 02115, USA.
authors.forename: David
authors.initials: D
authors.lastname: Reich
mesh_terms: D000818:Animals; D001315:Australia; D044383:Black People / Q000235:genetics; D066264:Datasets as Topic; D014644:Genetic Variation / Q000235:genetics*; D005828:Genetics, Population; D015894:Genome, Human / Q000235:genetics*; D023281:Genomics; D049690:History, Ancient; D063426:Human Migration / Q000266:history; D006801:Humans; D059645:Mutation Rate; D059125:Neanderthals / Q000235:genetics; D009512:New Guinea; D010802:Phylogeny; D044469:Racial Groups / Q000235:genetics*; D017422:Sequence Analysis, DNA; D013045:Species Specificity; D013997:Time Factors