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Reconstructing Native American population history

A Corrigendum to this article was published on 07 November 2012


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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Figure 1: Geographic, linguistic and genetic overview of 52 Native American populations.
Figure 2: Distinct streams of gene flow from Asia into America.
Figure 3: A model fitting populations of entirely First American ancestry.


  1. 1

    Cavalli-Sforza, L. L., Menozzi, P. & Piazza, A. The History and Geography of Human Genes (Princeton Univ. Press, 1994)

    MATH  Google Scholar 

  2. 2

    Meltzer, D. J. First Peoples in a New World: Colonizing Ice Age America (Univ. of California Press, 2009)

    Google Scholar 

  3. 3

    Goebel, T., Waters, M. R. & O’Rourke, D. H. The late Pleistocene dispersal of modern humans in the Americas. Science 319, 1497–1502 (2008)

    ADS  CAS  Article  Google Scholar 

  4. 4

    Dillehay, T. D. Probing deeper into first American studies. Proc. Natl Acad. Sci. USA 106, 971–978 (2009)

    ADS  CAS  Article  Google Scholar 

  5. 5

    O’Rourke, D. H. & Raff, J. A. The human genetic history of the Americas: the final frontier. Curr. Biol. 20, R202–R207 (2010)

    Article  Google Scholar 

  6. 6

    Tamm, E. et al. Beringian standstill and spread of Native American founders. PLoS ONE 2, e829 (2007)

    ADS  Article  Google Scholar 

  7. 7

    Kitchen, A., Miyamoto, M. M. & Mulligan, C. J. A three-stage colonization model for the peopling of the Americas. PLoS ONE 3, e1596 (2008)

    ADS  Article  Google Scholar 

  8. 8

    Fagundes, N. J. et al. Mitochondrial population genomics supports a single pre-Clovis origin with a coastal route for the peopling of the Americas. Am. J. Hum. Genet. 82, 583–592 (2008)

    CAS  Article  Google Scholar 

  9. 9

    Greenberg, J. H., Turner, C. G. & Zegura, S. L. The settlement of the Americas: a comparison of the linguistic, dental, and genetic evidence. Curr. Anthropol. 27, 477–497 (1986)

    Article  Google Scholar 

  10. 10

    Lell, J. T. et al. The dual origin and Siberian affinities of Native American Y chromosomes. Am. J. Hum. Genet. 70, 192–206 (2002)

    CAS  Article  Google Scholar 

  11. 11

    Bortolini, M. C. et al. Y-chromosome evidence for differing ancient demographic histories in the Americas. Am. J. Hum. Genet. 73, 524–539 (2003)

    CAS  Article  Google Scholar 

  12. 12

    Volodko, N. V. et al. Mitochondrial genome diversity in arctic Siberians, with particular reference to the evolutionary history of Beringia and Pleistocenic peopling of the Americas. Am. J. Hum. Genet. 82, 1084–1100 (2008)

    CAS  Article  Google Scholar 

  13. 13

    Ray, N. et al. A statistical evaluation of models for the initial settlement of the American continent emphasizes the importance of gene flow with Asia. Mol. Biol. Evol. 27, 337–345 (2010)

    CAS  Article  Google Scholar 

  14. 14

    de Azevedo, S. et al. Evaluating microevolutionary models for the early settlement of the New World: the importance of recurrent gene flow with Asia. Am. J. Phys. Anthropol. 146, 539–552 (2011)

    Article  Google Scholar 

  15. 15

    Perego, U. A. et al. Distinctive Paleo-Indian migration routes from Beringia marked by two rare mtDNA haplogroups. Curr. Biol. 19, 1–8 (2009)

    CAS  Article  Google Scholar 

  16. 16

    Alexander, D. H., Novembre, J. & Lange, K. Fast model-based estimation of ancestry in unrelated individuals. Genome Res. 19, 1655–1664 (2009)

    CAS  Article  Google Scholar 

  17. 17

    Ruhlen, M. A Guide to the World’s Languages (Stanford Univ. Press, 1991)

    Google Scholar 

  18. 18

    Schroeder, K. B. et al. A private allele ubiquitous in the Americas. Biol. Lett. 3, 218–223 (2007)

    CAS  Article  Google Scholar 

  19. 19

    Ray, N. PATHMATRIX: a geographical information system tool to compute effective distances among samples. Mol. Ecol. Notes 5, 177–180 (2005)

    Article  Google Scholar 

  20. 20

    Wang, S. et al. Genetic variation and population structure in native Americans. PLoS Genet. 3, e185 (2007)

    Article  Google Scholar 

  21. 21

    Yang, N. N. et al. Contrasting patterns of nuclear and mtDNA diversity in Native American populations. Ann. Hum. Genet. 74, 525–538 (2010)

    CAS  Article  Google Scholar 

  22. 22

    Brown, M. D. et al. mtDNA haplogroup X: an ancient link between Europe/Western Asia and North America? Am. J. Hum. Genet. 63, 1852–1861 (1998)

    CAS  Article  Google Scholar 

  23. 23

    Karafet, T. M. et al. Ancestral Asian source(s) of new world Y-chromosome founder haplotypes. Am. J. Hum. Genet. 64, 817–831 (1999)

    CAS  Article  Google Scholar 

  24. 24

    Reich, D., Thangaraj, K., Patterson, N., Price, A. L. & Singh, L. Reconstructing Indian population history. Nature 461, 489–494 (2009)

    ADS  CAS  Article  Google Scholar 

  25. 25

    Rasmussen, M. et al. Ancient human genome sequence of an extinct Palaeo-Eskimo. Nature 463, 757–762 (2010)

    ADS  CAS  Article  Google Scholar 

  26. 26

    Balter, M. Archaeology. The peopling of the Aleutians. Science 335, 158–161 (2012)

    ADS  CAS  Article  Google Scholar 

  27. 27

    Cooke, R. Prehistory of native Americans on the Central American land bridge: Colonization, dispersal, and divergence. J. Archaeol. Res. 13, 129–187 (2005)

    Article  Google Scholar 

  28. 28

    Wang, S. et al. Geographic patterns of genome admixture in Latin American Mestizos. PLoS Genet. 4, e1000037 (2008)

    Article  Google Scholar 

  29. 29

    Bryc, K. et al. Colloquium paper: genome-wide patterns of population structure and admixture among Hispanic/Latino populations. Proc. Natl Acad. Sci. USA 107 (Suppl 2). 8954–8961 (2010)

    ADS  CAS  Article  Google Scholar 

  30. 30

    Wall, J. D. et al. Genetic variation in Native Americans, inferred from Latino SNP and resequencing data. Mol. Biol. Evol. 28, 2231–2237 (2011)

    CAS  Article  Google Scholar 

  31. 31

    Price, A. L. et al. Sensitive detection of chromosomal segments of distinct ancestry in admixed populations. PLoS Genet. 5, e1000519 (2009)

    Article  Google Scholar 

  32. 32

    Browning, S. R. & Browning, B. L. Rapid and accurate haplotype phasing and missing-data inference for whole-genome association studies by use of localized haplotype clustering. Am. J. Hum. Genet. 81, 1084–1097 (2007)

    CAS  Article  Google Scholar 

  33. 33

    Patterson, N., Price, A. L. & Reich, D. Population structure and eigenanalysis. PLoS Genet. 2, e190 (2006)

    Article  Google Scholar 

  34. 34

    Saitou, N. & Nei, M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4, 406–425 (1987)

    CAS  Google Scholar 

  35. 35

    Liu, K. & Muse, S. V. PowerMarker: an integrated analysis environment for genetic marker analysis. Bioinformatics 21, 2128–2129 (2005)

    CAS  Article  Google Scholar 

  36. 36

    Greenberg, J. H. Language in the Americas (Stanford Univ. Press, 1987)

    Google Scholar 

  37. 37

    Campbell, L. American Indian languages: the historical linguistics of Native America (Oxford Univ. Press, 1997)

    Google Scholar 

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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.).

Author information




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.

Corresponding authors

Correspondence to David Reich or Andrés Ruiz-Linares.

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The authors declare no competing financial interests.

Additional information

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. (

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Reich, D., Patterson, N., Campbell, D. et al. Reconstructing Native American population history. Nature 488, 370–374 (2012).

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