The peopling of the Americas has been the subject of extensive genetic, archaeological and linguistic research; however, central questions remain unresolved1,2,3,4,5. One contentious issue is whether the settlement occurred by means of a single6,7,8 migration or multiple streams of migration from Siberia9,10,11,12,13,14,15. The pattern of dispersals within the Americas is also poorly understood. To address these questions at a higher resolution than was previously possible, we assembled data from 52 Native American and 17 Siberian groups genotyped at 364,470 single nucleotide polymorphisms. Here we show that Native Americans descend from at least three streams of Asian gene flow. Most descend entirely from a single ancestral population that we call ‘First American’. However, speakers of Eskimo–Aleut languages from the Arctic inherit almost half their ancestry from a second stream of Asian gene flow, and the Na-Dene-speaking Chipewyan from Canada inherit roughly one-tenth of their ancestry from a third stream. We show that the initial peopling followed a southward expansion facilitated by the coast, with sequential population splits and little gene flow after divergence, especially in South America. A major exception is in Chibchan speakers on both sides of the Panama isthmus, who have ancestry from both North and South America.
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We thank the volunteers who provided the samples that made this study possible. We thank E. D. Ruiz for assistance in the collection involving the Mixtec, Zapotec and Mixe; and P. Herrera for assistance in the collection involving the Quechua; A. Carnevale, M. Crawford, M. Metspalu, F. C. Nielsen, X. Soberon, R. Villems and E. Willerslev for facilitating sharing of data from Mexican, Siberian and Arctic populations; C. Stevens and A. Crenshaw for assistance with genotyping; and P. Bellwood, D. Bolnick, K. Bryc, J. Diamond, T. Dillehay, R. Gonzalez-José, M. Hammer, J. Hill, B. Kemp, S. LeBlanc, D. Meltzer, P. Moorjani, A. Moreno-Estrada, B. Pakendorf, J. Pickrell, M. Ruhlen, D. G. Smith, M. Stoneking, N. Tuross and A. Williams for critiques and discussions. Support was provided by National Institutes of Health grants NS043538 (A.R.-L.), NS037484 and MH075007 (N.B.F.), GM079558 (A.D.), GM079558-S1 (A.D.), GM057672 (K.K.K. and J.R.K.), and HG006399 (D.R., N.P. & A.L.P); by a Biotechnology and Biological Sciences Research Council grant BB/1021213/1; by a National Science Foundation HOMINID grant BCS-1032255 (D.R. and N.P.); by a Canadian Institutes of Health Research grant (D.L.); by a Universidad de Antioquia CODI grant (G.B.); by a Fondo de Investigación Sanitaria grant PS 09/2368 (A.C.); by a Ministerio de Ciencia e Innovacion grant SAF2011-26983 (A.S.); by a Wenner-Gren Foundation grant ICRG-65 (A.D. and R.S.); by Russian Foundation for Basic Research grants 06-04-048182 (R.S.) and 02-06-80524a (L.O.); by a Siberian Branch Russian Academy of Sciences field grant (L.O.); by a Centre National de la Recherche Scientifique Programme Interdisciplinaire de Recherche Amazonie grant (J.-M.D.); and by startup funds from Harvard Medical School (D.R.) and the Harvard School of Public Health (A.L.P.).
This file contains Supplementary Text 1-7, Supplementary Figures 1-5 and Supplementary Tables 1-3.