Genetic evidence for two founding populations of the Americas

Published online:


Genetic studies have consistently indicated a single common origin of Native American groups from Central and South America1,2,3,4. However, some morphological studies have suggested a more complex picture, whereby the northeast Asian affinities of present-day Native Americans contrast with a distinctive morphology seen in some of the earliest American skeletons, which share traits with present-day Australasians (indigenous groups in Australia, Melanesia, and island Southeast Asia)5,6,7,8. Here we analyse genome-wide data to show that some Amazonian Native Americans descend partly from a Native American founding population that carried ancestry more closely related to indigenous Australians, New Guineans and Andaman Islanders than to any present-day Eurasians or Native Americans. This signature is not present to the same extent, or at all, in present-day Northern and Central Americans or in a 12,600-year-old Clovis-associated genome, suggesting a more diverse set of founding populations of the Americas than previously accepted.

  • Subscribe to Nature for full access:



Additional access options:

Already a subscriber?  Log in  now or  Register  for online access.


  1. 1.

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

  2. 2.

    et al. Reconstructing Native American population history. Nature 488, 370–374 (2012)

  3. 3.

    et al. The genome of a Late Pleistocene human from a Clovis burial site in western Montana. Nature 506, 225–229 (2014)

  4. 4.

    et al. Upper Palaeolithic Siberian genome reveals dual ancestry of Native Americans. Nature 505, 87–91 (2014)

  5. 5.

    & The origins of the first Americans—an analysis based on the cranial morphology of early South American remains. Am. J. Phys. Anthropol. 81, 274 (1990)

  6. 6.

    et al. Early Holocene human skeletal remains from Cerca Grande, Lagoa Santa, Central Brazil, and the origins of the first Americans. World Archaeol. 36, 479–501 (2004)

  7. 7.

    , , , & Early Holocene human skeletal remains from Santana do Riacho, Brazil: implications for the settlement of the New World. J. Hum. Evol. 45, 19–42 (2003)

  8. 8.

    et al. Late Pleistocene/Holocene craniofacial morphology in Mesoamerican Paleoindians: implications for the peopling of the New World. Am. J. Phys. Anthropol. 128, 772–780 (2005)

  9. 9.

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

  10. 10.

    et al. The genetic prehistory of the New World Arctic. Science 345, (2014)

  11. 11.

    et al. DNA from pre-Clovis human coprolites in Oregon, North America. Science 320, 786–789 (2008)

  12. 12.

    et al. Late Pleistocene human skeleton and mtDNA link Paleoamericans and modern Native Americans. Science 344, 750–754 (2014)

  13. 13.

    & Variation among early North American crania. Am. J. Phys. Anthropol. 114, 146–155 (2001)

  14. 14.

    , & Human skeletal remains from Sabana de Bogota, Colombia: a case of Paleoamerican morphology late survival in South America? Am. J. Phys. Anthropol. 133, 1080–1098 (2007)

  15. 15.

    et al. Craniometric evidence for Palaeoamerican survival in Baja California. Nature 425, 62–65 (2003)

  16. 16.

    & A reassessment of human cranial plasticity: Boas revisited. Proc. Natl Acad. Sci. USA 99, 14636–14639 (2002)

  17. 17.

    Apportionment of global human genetic diversity based on craniometrics and skin color. Am. J. Phys. Anthropol. 118, 393–398 (2002)

  18. 18.

    et al. Ancient admixture in human history. Genetics 192, 1065–1093 (2012)

  19. 19.

    et al. Ancient human genomes suggest three ancestral populations for present-day Europeans. Nature 513, 409–413 (2014)

  20. 20.

    & Denisovan ancestry in East Eurasian and Native American populations. Mol. Biol. Evol. (2015)

  21. 21.

    et al. A draft sequence of the Neandertal genome. Science 328, 710–722 (2010)

  22. 22.

    et al. A high-coverage genome sequence from an Archaic Denisovan individual. Science 338, 222–226 (2012)

  23. 23.

    et al. The complete genome sequence of a Neanderthal from the Altai Mountains. Nature 505, 43–49 (2014)

  24. 24.

    , , & Widespread genomic signatures of natural selection in hominid evolution. PLoS Genet. 5, e1000471 (2009)

  25. 25.

    Genetic drift in an infinite population: the pseudohitchhiking model. Genetics 155, 909–919 (2000)

  26. 26.

    et al. The role of geography in human adaptation. PLoS Genet. 5, e1000500 (2009)

  27. 27.

    et al. The history of African gene flow into Southern Europeans, Levantines, and Jews. PLoS Genet. 7, e1001373 (2011)

  28. 28.

    et al. A genetic atlas of human admixture history. Science 343, 747–751 (2014)

  29. 29.

    , , , & The date of interbreeding between Neandertals and modern humans. PLoS Genet. 8, e1002947 (2012)

  30. 30.

    , , & Inference of population structure using dense haplotype data. PLoS Genet. 8, e1002453 (2012)

  31. 31.

    , & A linear complexity phasing method for thousands of genomes. Nature Methods 9, 179–181 (2011)

  32. 32.

    & Fast and accurate short read alignment with Burrows–Wheeler transform. Bioinformatics 25, 1754–1760 (2009)

  33. 33.

    et al. The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 20, 1297–1303 (2010)

  34. 34.

    , & Delete-m jackknife for unequal m. Stat. Comput. 9, 3–8 (1999)

  35. 35.

    , , , & Reconstructing Indian population history. Nature 461, 489–494 (2009)

  36. 36.

    Some applications of mathematics to breeding problems III. Genetics 3, 375–389 (1918)

  37. 37.

    & Maps in S. AT&T Bell Laboratories Statistics Research Report [93.2] (1993)

  38. 38.

    , & Fast model-based estimation of ancestry in unrelated individuals. Genome Res. 19, 1655–1664 (2009)

Download references


We are grateful to the Native American volunteers who contributed the DNA samples used to generate the new data reported in this study and to the Fundação Nacional do Índio (FUNAI, Brazil) for logistical support in sample collection. We thank W. Klitz and C. Winkler for sharing samples for whole-genome sequencing. We thank L. Fehren-Schmitz, Q. Fu, G. Hellenthal, A. Kim, I. Lazaridis, M. Lipson, I. Mathieson, D. Meltzer, P. Moorjani and J. Pickrell for comments and A. Tandon for technical assistance. We thank T. Ferraz and R. Bisso-Machado for assistance with DNA extraction for the genotyping of Brazilian samples. We performed whole-genome sequencing as part of the Simons Genome Diversity Project. Genotyping of the Brazilian samples was performed at the Children’s Hospital of Philadelphia and we particularly thank C. Hou for her support in this. M.C.B., T.H., M.L.P.-E. and F.M.S. were supported by Conselho Nacional do Desenvolvimento Científico e Tecnológico and Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (Brazil). P.S. was supported by the Wenner-Gren foundation and the Swedish Research Council (VR grant 2014-453). D.R. was supported by US National Science Foundation HOMINID grant BCS-1032255, US National Institutes of Health grant GM100233, Simons Foundation Grant 280376 and the Howard Hughes Medical Institute.

Author information


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

    • Pontus Skoglund
    • , Swapan Mallick
    • , Niru Chennagiri
    •  & David Reich
  2. Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA

    • Pontus Skoglund
    • , Swapan Mallick
    • , Niru Chennagiri
    • , Nick Patterson
    •  & David Reich
  3. Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts 02115, USA

    • Swapan Mallick
    •  & David Reich
  4. Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, 91501-970 Porto Alegre, RS, Brazil

    • Maria Cátira Bortolini
    •  & Francisco Mauro Salzano
  5. Departamento de Genética e Biologia Evolutiva, Universidade de São Paulo, 05508-090, SP, Brazil

    • Tábita Hünemeier
  6. Departamento de Genética, Universidade Federal do Paraná, 81531-980 Curitiba, PR, Brazil

    • Maria Luiza Petzl-Erler


  1. Search for Pontus Skoglund in:

  2. Search for Swapan Mallick in:

  3. Search for Maria Cátira Bortolini in:

  4. Search for Niru Chennagiri in:

  5. Search for Tábita Hünemeier in:

  6. Search for Maria Luiza Petzl-Erler in:

  7. Search for Francisco Mauro Salzano in:

  8. Search for Nick Patterson in:

  9. Search for David Reich in:


P.S. performed analyses. P.S., S.M., M.C.B., N.C., T.H., M.L.P.-E., F.M.S., N.P. and D.R. prepared datasets. P.S. and D.R. wrote the paper.

Competing interests

The authors declare no competing financial interests.

Corresponding authors

Correspondence to Pontus Skoglund or David Reich.

Genome sequence data is available from (https://www.simonsfoundation.org/life-sciences/simons-genome-diversity-project-dataset/). New Affymetrix Human Origins array genotype data are available to researchers who send D.R. a signed letter agreeing to respect specific conditions (Supplementary Information section 1).

Extended data

Supplementary information

PDF files

  1. 1.

    Supplementary Information

    This file contains Supplementary Text and Data 1-6, Supplementary Tables and additional references.


By submitting a comment you agree to abide by our Terms and Community Guidelines. If you find something abusive or that does not comply with our terms or guidelines please flag it as inappropriate.