• A Corrigendum to this article was published on 07 November 2012

Abstract

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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Acknowledgements

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.).

Author information

Author notes

    • Irma Silva-Zolezzi
    •  & Gerardo Jimenez-Sanchez

    Present addresses: BioAnalytical Science Department Nestec Ltd, Nestlé Research Center, 1000 Lausanne, Switzerland (I.S.-Z.); Global Biotech Consulting Group, México City 09010, México (G.J.-S.).

Affiliations

  1. Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA

    • David Reich
    •  & Arti Tandon
  2. Broad Institute of Harvard and the Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, USA

    • David Reich
    • , Nick Patterson
    • , Arti Tandon
    •  & Alkes L. Price
  3. Department of Genetics, Evolution and Environment, University College London WC1E 6BT, UK

    • Desmond Campbell
    • , Stéphane Mazieres
    • , Maria V. Parra
    • , Winston Rojas
    • , Constanza Duque
    • , Natalia Mesa
    • , Claudio M. Bravi
    • , Tábita Hünemeier
    •  & Andrés Ruiz-Linares
  4. Department of Psychiatry and Centre for Genomic Sciences, The University of Hong Kong, Pokfulam, Hong Kong SAR

    • Desmond Campbell
  5. Anthropologie Bio-culturelle, Droit, Ethique et Santé (ADES), UMR 7268, Aix-Marseille Université/CNRS/EFS, Marseille 13344, France

    • Stéphane Mazieres
  6. Institute for Environmental Sciences, and Forel Institute, University of Geneva, Geneva 1227, Switzerland

    • Nicolas Ray
  7. Universidad de Antioquia, Medellín, Colombia

    • Maria V. Parra
    • , Winston Rojas
    • , Constanza Duque
    • , Natalia Mesa
    • , Luis F. García
    • , Omar Triana
    • , Silvia Blair
    • , Amanda Maestre
    •  & Gabriel Bedoya
  8. Fundación Salud para el Trópico, Santa Marta, Colombia

    • Juan C. Dib
  9. Instituto Multidisciplinario de Biología Celular (CCT La Plata-CONICET, CICPCA), 1900 La Plata, Argentina

    • Claudio M. Bravi
    •  & Graciela Bailliet
  10. Servicio de Huellas Digitales Genéticas and CONICET, Universidad de Buenos Aires, Argentina

    • Daniel Corach
  11. Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre 91501-970, Brazil

    • Tábita Hünemeier
    • , Maria Cátira Bortolini
    •  & Francisco M. Salzano
  12. Departamento de Genética, Universidade Federal do Paraná, Curitiba 81531-980, Brazil

    • María Luiza Petzl-Erler
  13. National Institute of Anthropology and History, México City 06100, México

    • Victor Acuña-Alonzo
  14. Departamento de Endocrinología y Metabolismo, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, México City 14100, México

    • Carlos Aguilar-Salinas
  15. Unidad de Biología Molecular y Medicina Genómica, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán/Universidad Nacional Autónoma de México, México City 14000, México

    • Samuel Canizales-Quinteros
    • , Teresa Tusié-Luna
    •  & Laura Riba
  16. Departamento de Biología, Facultad de Química, Universidad Nacional Autónoma de México, México City 04510, México

    • Samuel Canizales-Quinteros
  17. Unidad de Investigación Médica en Nutrición, Hospital de Pediatría, CMNSXXI, Instituto Mexicano del Seguro Social, México City 06720, México

    • Maricela Rodríguez-Cruz
    •  & Mardia Lopez-Alarcón
  18. Sección de Posgrado, Escuela Superior de Medicina del Instituto Politécnico Nacional, México City 11340, México

    • Ramón Coral-Vazquez
  19. Laboratorio de Biología de la Reproducción, Departamento de Salud Reproductiva y Genética, Centro de Investigaciones Regionales, Mérida Yucatán 97000, México

    • Thelma Canto-Cetina
  20. Instituto Nacional de Medicina Genómica, México City 14610, México

    • Irma Silva-Zolezzi
    • , Juan Carlos Fernandez-Lopez
    • , Alejandra V. Contreras
    •  & Gerardo Jimenez-Sanchez
  21. Universidad Autónoma de Nuevo León, San Nicolás de los Garza, Nuevo León 66451, México

    • Maria José Gómez-Vázquez
  22. Centro de Investigaciones Biomédicas de Guatemala, Ciudad de Guatemala, Guatemala

    • Julio Molina
  23. Instituto de Ciencias Forenses, Universidade de Santiago de Compostela, Fundación de Medicina Xenómica (SERGAS), CIBERER, Santiago de Compostela, Galicia 15782, Spain

    • Ángel Carracedo
    •  & Antonio Salas
  24. Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima 15102, Peru

    • Carla Gallo
    •  & Giovanni Poletti
  25. Department of Human Genetics, University of Chicago, Chicago 60637, USA

    • David B. Witonsky
    • , Gorka Alkorta-Aranburu
    •  & Anna Di Rienzo
  26. Laboratory of Human Molecular Genetics, Institute of Molecular and Cellular Biology, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia

    • Rem I. Sukernik
  27. Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia

    • Ludmila Osipova
  28. Department of Molecular Genetics, Yakut Research Center of Complex Medical Problems and North-East Federal University, Yakutsk, Sakha (Yakutia) 677010, Russia

    • Sardana A. Fedorova
  29. Instituto Boliviano de Biología de la Altura, Universidad Autonoma Tomás Frías, Potosí, Bolivia

    • René Vasquez
    •  & Mercedes Villena
  30. Département de Pédiatrie, Centre de Recherche du CHU Sainte-Justine, Université de Montréal, Montréal, Quebec H3T 1C5, Canada

    • Claudia Moreau
    •  & Damian Labuda
  31. Escuela de Biología, Universidad de Costa Rica, San José, Costa Rica

    • Ramiro Barrantes
  32. Center for Human Genetic Research, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114, USA

    • David Pauls
  33. Computational and Molecular Population Genetics Laboratory, Institute of Ecology and Evolution, University of Bern, 3012 Bern, Switzerland

    • Laurent Excoffier
  34. Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland

    • Laurent Excoffier
  35. Instituto de Alta Investigación, Universidad de Tarapacá, Programa de Genética Humana ICBM Facultad de Medicina Universidad de Chile and Centro de Investigaciones del Hombre en el Desierto, Arica 1001236, Chile

    • Francisco Rothhammer
  36. Anthropologie Moléculaire et Imagerie de Synthèse, CNRS UMR 5288, Université Paul Sabatier Toulouse III, Toulouse 31000, France

    • Jean-Michel Dugoujon
    •  & Georges Larrouy
  37. School of Public Health, University of California, Berkeley, California 94720, USA

    • William Klitz
  38. Department of Genetics, Yale University School of Medicine, New Haven, Connecticut 06520, USA

    • Judith Kidd
    •  & Kenneth Kidd
  39. Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, University of California Los Angeles, Los Angeles, California 90095, USA

    • Nelson B. Freimer
  40. Departments of Epidemiology and Biostatistics, Harvard School of Public Health, Boston, Massachusetts 02115, USA

    • Alkes L. Price

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Contributions

D.R., N.B.F., A.L.P. and A.R-L. conceived the project. D.R., N.P., D.C., A.T., S.M., N.R. and A.R-L. performed analyses. D.R. and A. R.-L. wrote the paper with input from all the co-authors. A.R.-L. assembled the sample collection, directed experimental work and coordinated the study. All other authors contributed to the collection of samples and data.

Competing interests

The authors declare no competing financial interests.

Corresponding authors

Correspondence to David Reich or Andrés Ruiz-Linares.

The data analysed here are available for non-profit research on population history under an inter-institutional data access agreement with the Universidad de Antioquia, Colombia; queries regarding data access should be sent to A.R.-L. (a.ruizlin@ucl.ac.uk).

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    Supplementary Information

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https://doi.org/10.1038/nature11258

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