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

Mallick, Swapan; Li, Heng; Lipson, Mark; Mathieson, Ian; Gymrek, Melissa; Racimo, Fernando; Zhao, Mengyao; Chennagiri, Niru; Nordenfelt, Susanne; Tandom, Arti; 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; Balloux, François; van Driem, George; de Knijff, Peter; Gallego Romero, Irene; Jha, Aashish R.; Behar, Doron M.; Bravi, Claudio M.; Capelli, Cristian; Hervig, Tor; Moreno Estrada, Andrés; Posukh, Olga L.; Balanovska, Elena; Balanovsky, Oleg; Karachanak-Yankova, Sena; Sahakyan, Hovhannes; Toncheva, Draga; Yepiskoposyan, Levon; Tyler-Smith, Chris; Xue, Yali; Abdullah, M. Syafiq; Ruiz-Linares,  Andres; Beall, Cynthia M.; Di Rienzo, Anna; Jeong, Choongwon; Starikovskaya, Elena B.; Metspalu, Ene; Parik, Jüri; Villems, Richard; Henn, Brenna M.; Hodoglugil, Ugur; Mahley, Robert; Sajantila, Antii; Stamatoyannopoulos, George; Wee, Joseph T.S.; Khusainova, Rita; Khusnutdinova, Elza; Litvinov, Sergey; Ayodo, George; Comas, David, 1969-; Hammer, Michael; Kivisild, Toomas; Klitz, William; Winkler, Cheryl; Labuda, Damian; Bamshad, Michael; Jorde, Lynn B.; Tishkoff, Sarah A.; Watkins, W. Scott; Metspalu, Mait; Dryomov, Stanislav; Sukernik, Rem; Singh, Lalji; Thangaraj, Kumarasamy; Pääbo, Svante; Kelso, Janet; Patterson, Nick; Reich, David

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

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dc.contributor.author Mallick, Swapan
dc.contributor.author Li, Heng
dc.contributor.author Lipson, Mark
dc.contributor.author Mathieson, Ian
dc.contributor.author Gymrek, Melissa
dc.contributor.author Racimo, Fernando
dc.contributor.author Zhao, Mengyao
dc.contributor.author Chennagiri, Niru
dc.contributor.author Nordenfelt, Susanne
dc.contributor.author Tandom, Arti
dc.contributor.author Skoglund, Pontus
dc.contributor.author Lazaridis, Iosif
dc.contributor.author Sankararaman, Sriram
dc.contributor.author Fu, Qiaomei
dc.contributor.author Rohland, Nadin
dc.contributor.author Renaud, Gabriel
dc.contributor.author Erlich, Yaniv
dc.contributor.author Willems, Thomas
dc.contributor.author Gallo, Carla
dc.contributor.author Spence, Jeffrey P.
dc.contributor.author Song, Yun S.
dc.contributor.author Poletti, Giovanni
dc.contributor.author Balloux, François
dc.contributor.author van Driem, George
dc.contributor.author de Knijff, Peter
dc.contributor.author Gallego Romero, Irene
dc.contributor.author Jha, Aashish R.
dc.contributor.author Behar, Doron M.
dc.contributor.author Bravi, Claudio M.
dc.contributor.author Capelli, Cristian
dc.contributor.author Hervig, Tor
dc.contributor.author Moreno Estrada, Andrés
dc.contributor.author Posukh, Olga L.
dc.contributor.author Balanovska, Elena
dc.contributor.author Balanovsky, Oleg
dc.contributor.author Karachanak-Yankova, Sena
dc.contributor.author Sahakyan, Hovhannes
dc.contributor.author Toncheva, Draga
dc.contributor.author Yepiskoposyan, Levon
dc.contributor.author Tyler-Smith, Chris
dc.contributor.author Xue, Yali
dc.contributor.author Abdullah, M. Syafiq
dc.contributor.author Ruiz-Linares, Andres
dc.contributor.author Beall, Cynthia M.
dc.contributor.author Di Rienzo, Anna
dc.contributor.author Jeong, Choongwon
dc.contributor.author Starikovskaya, Elena B.
dc.contributor.author Metspalu, Ene
dc.contributor.author Parik, Jüri
dc.contributor.author Villems, Richard
dc.contributor.author Henn, Brenna M.
dc.contributor.author Hodoglugil, Ugur
dc.contributor.author Mahley, Robert
dc.contributor.author Sajantila, Antii
dc.contributor.author Stamatoyannopoulos, George
dc.contributor.author Wee, Joseph T.S.
dc.contributor.author Khusainova, Rita
dc.contributor.author Khusnutdinova, Elza
dc.contributor.author Litvinov, Sergey
dc.contributor.author Ayodo, George
dc.contributor.author Comas, David, 1969-
dc.contributor.author Hammer, Michael
dc.contributor.author Kivisild, Toomas
dc.contributor.author Klitz, William
dc.contributor.author Winkler, Cheryl
dc.contributor.author Labuda, Damian
dc.contributor.author Bamshad, Michael
dc.contributor.author Jorde, Lynn B.
dc.contributor.author Tishkoff, Sarah A.
dc.contributor.author Watkins, W. Scott
dc.contributor.author Metspalu, Mait
dc.contributor.author Dryomov, Stanislav
dc.contributor.author Sukernik, Rem
dc.contributor.author Singh, Lalji
dc.contributor.author Thangaraj, Kumarasamy
dc.contributor.author Pääbo, Svante
dc.contributor.author Kelso, Janet
dc.contributor.author Patterson, Nick
dc.contributor.author Reich, David
dc.date.accessioned 2018-11-30T09:43:26Z
dc.date.available 2018-11-30T09:43:26Z
dc.date.issued 2016
dc.description.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.
dc.description.sponsorship The sequencing was funded by the Simons Foundation (SFARI 280376) and the US National Science Foundation (BCS-1032255). I.M. was supported by a Long Term Fellowship grant LT001095/2014 from the Human Frontier Science program. P.S. was supported by the Wenner-Gren foundation and the Swedish Research Council (VR grant 2014-453). T.W. and M.G. were supported by an NIJ grant 2014-DN-BX-K089. Y.E. was supported by a Career Award at the Scientific Interface from the Burroughs Wellcome Fund and by NIJ grant 2014-DN-BX-K089. D.L. was supported by the Natural Sciences and Engineering Research Council of Canada. T.K. was supported by ERC Starting Investigator grant FP7 - 261213. R.S. received support from Russian Foundation for Basic Research (#15-04-02543). S.D. received support from the Russian Foundation for Basic Research (#16-34-00599). R.K., E.K. and S.L. were supported by the Russian Foundation for Basic Research (11-04-00725-a). E.B. was supported by the Russian Foundation for Basic Research (16-06-00303). O.B. was supported by the Russian Scientific Fund (14-04-00827) and by the Russian Foundation for Basic Research (16-04-00890). D.M.B., H.S., E.M., R.V. and M.M. were supported by Institutional Research Funding from the Estonian Research Council IUT24-1 and by the European Regional Development Fund (European Union) through the Centre of Excellence in Genomics to Estonian Biocentre and University of Tartu. D.C. was supported by the Spanish MINECO grant CGL-44351-P. L.B.J. and W.S.W. were supported by NIH grant GM59290. S.A.T. was supported by NIH grants 5DP1ES022577 05, 1R01DK104339-01, and 1R01GM113657-01. C.T.-S. and Y.X. were supported by The Wellcome Trust grant 098051. C.M.B. was supported by NSF grants 0924726 and 1153911. K.T. was supported by CSIR Network Project grant (GENESIS: BSC0121). J.P.S. and Y.S.S. were supported in part by an NIH grant R01-GM094402, and a Packard Fellowship for Science and Engineering. G.R., J.K and S.P. were funded by the Max Planck Society. N.P. and D.R. were supported by NIH grant GM100233 and D.R. is a Howard Hughes Medical Institute investigator
dc.format.mimetype application/pdf
dc.identifier.citation Mallick S, Li H, Lipson M, Mathieson I, Gymrek M, Racimo F et al. The Simons Genome Diversity Project: 300 genomes from 142 diverse populations. Nature. 2016 Oct 13;538(7624):201-6. DOI: 10.1038/nature18964
dc.identifier.doi http://dx.doi.org/10.1038/nature18964
dc.identifier.issn 0028-0836
dc.identifier.uri http://hdl.handle.net/10230/35915
dc.language.iso eng
dc.publisher Nature Publishing Group
dc.relation.ispartof Nature. 2016 Oct 13;538(7624):201-6
dc.relation.projectID info:eu-repo/grantAgreement/EC/FP7/261213
dc.rights © Nature Publishing Group. Mallick S, Li H, Lipson M, Mathieson I, Gymrek M, Racimo F et al. The Simons Genome Diversity Project: 300 genomes from 142 diverse populations. Nature. 2016 Oct 13; 538(7624): 201-206. http://dx.doi.org/10.1038/nature18964
dc.rights.accessRights info:eu-repo/semantics/openAccess
dc.subject.other Genètica
dc.subject.other Genoma humà
dc.subject.other Genòmica
dc.subject.other Filogènia
dc.title The Simons Genome Diversity Project: 300 genomes from 142 diverse populations
dc.type info:eu-repo/semantics/article
dc.type.version info:eu-repo/semantics/acceptedVersion

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