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The Simons Genome Diversity Project: 300 genomes from 142 diverse populations
Open accessAbstract
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.
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“It has been shown that Papuans and Indigenous Australians carry the largest amount of Denisovan introgression (∼1% to 5%), followed by East and South Asians (∼0.06% to 0.5%), and Indigenous Americans (∼0.05% to 0.4%) (Reich et al. 2010; Racimo et al. 2015; Mallick et al. 2016; Sankararaman et al. 2016; Browning et al. 2018).”
From The Human Accelerated Region HAR202 Controls NPAS3 Expression in the Developing Forebrain Displaying Differential Enhancer Activity Between Modern and Archaic Human Sequences (2024) · cites this paper as Mallick et al. 2016
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“We caution, however, that our approach can artificially shorten haplotype block lengths (see Supplementary Methods and figs. S21 and S22), especially for populations such as Papuans and Australians that were absent from the 1000 Genomes Project panel (24) that was used for phasing (14).”
From An ancestral recombination graph of human, Neanderthal, and Denisovan genomes (2021) · cites this paper as [14]
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“Applying our approach to Neanderthal aSNPs segregating within present-day West Eurasians [31] replicates most of our findings, as well as previously reported signals including a depletion of Neanderthal variants within enhancer-like elements [12].”
From Denisovan introgression has shaped the immune system of present-day Papuans (2022) · cites this paper as [31]
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Self-citation
Metadata
- Authors
- Mallick, S., Li, H., Lipson, M., Mathieson, I., Gymrek, M., Racimo, F., Zhao, M., Chennagiri, N., Nordenfelt, S., Tandon, A., Skoglund, P., Lazaridis, I., Sankararaman, S., Fu, Q., Rohland, N., Renaud, G., Erlich, Y., Willems, T., Gallo, C., Spence, J. P., Song, Y. S., Poletti, G., Balloux, F., van Driem, G., de Knijff, P., Romero, I. G., Jha, A. R., Behar, D. M., Bravi, C. M., Capelli, C., Hervig, T., Moreno-Estrada, A., Posukh, O. L., Balanovska, E., Balanovsky, O., Karachanak-Yankova, S., Sahakyan, H., Toncheva, D., Yepiskoposyan, L., Tyler-Smith, C., Xue, Y., Abdullah, M. S., Ruiz-Linares, A., Beall, C. M., Di Rienzo, A., Jeong, C., Starikovskaya, E. B., Metspalu, E., Parik, J., Villems, R., Henn, B. M., Hodoglugil, U., Mahley, R., Sajantila, A., Stamatoyannopoulos, G., Wee, J. T. S., Khusainova, R., Khusnutdinova, E., Litvinov, S., Ayodo, G., Comas, D., Hammer, M. F., Kivisild, T., Klitz, W., Winkler, C. A., Labuda, D., Bamshad, M., Jorde, L. B., Tishkoff, S. A., Watkins, W. S., Metspalu, M., Dryomov, S., Sukernik, R., Singh, L., Thangaraj, K., Pääbo, S., Kelso, J., Patterson, N., & Reich, D.
- Affiliations
- Broad Institute (US)
- Harvard University (US)
- University of California, Berkeley (US)
- Max Planck Institute for Evolutionary Anthropology (DE)
- New York Genome Center (US)
- Universidad Peruana Cayetano Heredia (PE)
- University of Pennsylvania (US)
- Nanyang Technological University (SG)
- University of Chicago (US)
- Estonian Biocentre (EE)
- University of Oxford (GB)
- University of Bergen (NO)
- Russian Academy of Sciences (RU)
- Research Centre for Medical Genetics (RU)
- Moscow Institute of Physics and Technology (RU)
- Medical University of Sofia (BG)
- Institute of Molecular Biology (AM)
- Wellcome Sanger Institute (GB)
- Raja Isteri Pengiran Anak Saleha Hospital (BN)
- Case Western Reserve University (US)
- Estonian Academy of Sciences (EE)
- Stony Brook University (US)
- Gladstone Institutes (US)
- University of Helsinki (FI)
- University of Washington (US)
- National Cancer Centre Singapore (SG)
- Jaramogi Oginga Odinga University of Science and Technology (KE)
- Universitat Pompeu Fabra (ES)
- University of Arizona (US)
- University of Cambridge (GB)
- Frederick National Laboratory for Cancer Research (US)
- Centre Hospitalier Universitaire Sainte-Justine (CA)
- University of Utah (US)
- Centre for Cellular and Molecular Biology (IN)
- Corresponding author
- Mallick, Swapan
- Reich, David
- ORCID
- Mallick, Swapan
- Li, Heng
- Lipson, Mark
- Mathieson, Iain
- Gymrek, Melissa
- Racimo, Fernando
- Zhao, Mengyao
- Skoglund, Pontus
- Lazaridis, Iosif
- Sankararaman, Sriram
- Fu, Qiaomei
- Rohland, Nadin
- Renaud, Gabriel
- Erlich, Yaniv
- Willems, Thomas
- Gallo, Carla
- Spence, Jeffrey P.
- Song, Yun S.
- Poletti, Giovanni
- Romero, Irene Gallego
- Jha, Aashish R.
- Behar, Doron M.
- Capelli, Cristian
- Hervig, Tor
- Posukh, Olga L.
- Balanovska, Elena
- Karachanak-Yankova, Sena
- Sahakyan, Hovhannes
- Toncheva, Draga
- Yepiskoposyan, Levon
- Abdullah, M. Syafiq
- Beall, Cynthia M.
- Jeong, Choongwon
- Starikovskaya, Elena B.
- Metspalu, Ene
- Villems, Richard
- Henn, Brenna M.
- Mahley, Robert
- Sajantila, Antti
- Wee, Joseph T. S.
- Khusainova, Rita
- Litvinov, Sergey
- Ayodo, George
- Comas, David
- Hammer, Michael F.
- Kivisild, Toomas
- Winkler, Cheryl A.
- Labuda, Damian
- Bamshad, Michael
- Jorde, Lynn B.
- Tishkoff, Sarah A.
- Watkins, W. Scott
- Metspalu, Mait
- Sukernik, Rem
- Singh, Lalji
- Pääbo, Svante
- Kelso, Janet
- Patterson, Nick
- Reich, David
- Venue
- Nature
- Published
- 2016-09-21
- Volume
- 538
- Issue
- 7624
- Pages
- 201-206
- ISSN
- 0028-0836 (ISSN-L)
- 1476-4687
- PMC
- PMC5161557
- OpenAlex
- W2522993044
- Cited by
- 1,584
- References
- 47
- Citations by year
- 2026: 100 · 2025: 187 · 2024: 188 · 2023: 155 · 2022: 189 · 2021: 179 · 2020: 173 · 2019: 152 · 2018: 142 · 2017: 104 · 2016: 10
- FWCI
- 109.87
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- Nature (publishedVersion)
- PubMed (publishedVersion)
- Universidad Peruana Cayetano Heredia Institutional Repository (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- Digital Access to Scholarship at Harvard (DASH) (Harvard University) (acceptedVersion)
- RECERCAT (Consorci de Serveis Universitaris de Catalunya) (acceptedVersion, other-oa)
- LA Referencia (Red Federada de Repositorios Institucionales de Publicaciones Científicas) (submittedVersion, cc-by-nc-sa)
- eScholarship (California Digital Library) (submittedVersion)
- Data Archiving and Networked Services (DANS) (submittedVersion)
- RePEc: Research Papers in Economics (submittedVersion)
- Leiden Repository (Leiden University) (submittedVersion)
- BORIS (University Library Bern) (submittedVersion)
- UCL Discovery (University College London) (submittedVersion)
- Max Planck Digital Library (submittedVersion)
- Minerva Access (University of Melbourne) (submittedVersion)
- MPG.PuRe (Max Planck Society) (submittedVersion)
- Repositori digital de la UPF (Universitat Pompeu Fabra) (submittedVersion)
- CONICET Digital (CONICET) (submittedVersion, cc-by-nc-sa)
- RUNE (Research UNE) (submittedVersion)
- Seoul National University Open Repository (Seoul National University) (submittedVersion)
- Funders
- National Science Foundation (1153911, 0924726, 02543, 1032255)
- Wellcome Trust (098051)
- Simons Foundation Autism Research Initiative
- European Commission (15,16, 28,29)
- Russian Foundation for Basic Research (16-06-00364, 16-06-00303)
- Eesti Teadusagentuur (IUT24-1, IUT2-4)
- Max-Planck-Gesellschaft
- Vetenskapsrådet (16,17, 02543, 2014-453)
- Tartu Ülikool
- National Institutes of Health (5ul1tr001067-05, 16,17, 10,11, GM100233)
- Biotechnology and Biological Sciences Research Council (BB/H008802/1, BB/H008802/2)
- European Regional Development Fund (IUT24-1)
- National Human Genome Research Institute (R01HG006399)
- National Institute of General Medical Sciences (R01GM113657, R01GM059290, R01GM100233, R00GM111744, R01GM094402)
- National Institute of Diabetes and Digestive and Kidney Diseases (R01DK104339)
- National Institute of Environmental Health Sciences (DP1ES022577)
- National Center for Advancing Translational Sciences (UL1-TR001067)
- FP7 Ideas: European Research Council (261213)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Forensic and Genetic Research
- Social Sciences › Anthropology › Pleistocene-Era Hominins and Archaeology
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic diversity and population structure
- Keywords
- human genetic variation, dispersal out of Africa, human ancestry, mutation rate, African populations, Aboriginal Australians, Papuans, Andamanese, Indigenous Australians, non-African populations
- MeSH terms
- Animals, Australia, Genetics, Population, Humans, New Guinea, Phylogeny, Species Specificity, Time Factors, Genetic Variation, Genome, Human, Sequence Analysis, DNA, Genomics, Black People, Native Hawaiian or Other Pacific Islander, Racial Groups, History, Ancient, Neanderthals, Mutation Rate, Human Migration, Datasets as Topic
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Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
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