Reconstructing Native American population history (original) (raw)

References

1. Cavalli-Sforza, L. L., Menozzi, P. & Piazza, A. The History and Geography of Human Genes (Princeton Univ. Press, 1994)
   MATH Google Scholar
2. Meltzer, D. J. First Peoples in a New World: Colonizing Ice Age America (Univ. of California Press, 2009)
   Google Scholar
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)
   Article ADS CAS Google Scholar
4. Dillehay, T. D. Probing deeper into first American studies. Proc. Natl Acad. Sci. USA 106, 971–978 (2009)
   Article ADS CAS Google Scholar
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. Tamm, E. et al. Beringian standstill and spread of Native American founders. PLoS ONE 2, e829 (2007)
   Article ADS Google Scholar
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)
   Article ADS Google Scholar
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)
   Article CAS Google Scholar
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. Lell, J. T. et al. The dual origin and Siberian affinities of Native American Y chromosomes. Am. J. Hum. Genet. 70, 192–206 (2002)
    Article CAS Google Scholar
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)
    Article CAS Google Scholar
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)
    Article CAS Google Scholar
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)
    Article CAS Google Scholar
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. Perego, U. A. et al. Distinctive Paleo-Indian migration routes from Beringia marked by two rare mtDNA haplogroups. Curr. Biol. 19, 1–8 (2009)
    Article CAS Google Scholar
16. Alexander, D. H., Novembre, J. & Lange, K. Fast model-based estimation of ancestry in unrelated individuals. Genome Res. 19, 1655–1664 (2009)
    Article CAS Google Scholar
17. Ruhlen, M. A Guide to the World’s Languages (Stanford Univ. Press, 1991)
    Google Scholar
18. Schroeder, K. B. et al. A private allele ubiquitous in the Americas. Biol. Lett. 3, 218–223 (2007)
    Article CAS Google Scholar
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. Wang, S. et al. Genetic variation and population structure in native Americans. PLoS Genet. 3, e185 (2007)
    Article Google Scholar
21. Yang, N. N. et al. Contrasting patterns of nuclear and mtDNA diversity in Native American populations. Ann. Hum. Genet. 74, 525–538 (2010)
    Article CAS Google Scholar
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)
    Article CAS Google Scholar
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)
    Article CAS Google Scholar
24. Reich, D., Thangaraj, K., Patterson, N., Price, A. L. & Singh, L. Reconstructing Indian population history. Nature 461, 489–494 (2009)
    Article ADS CAS Google Scholar
25. Rasmussen, M. et al. Ancient human genome sequence of an extinct Palaeo-Eskimo. Nature 463, 757–762 (2010)
    Article ADS CAS Google Scholar
26. Balter, M. Archaeology. The peopling of the Aleutians. Science 335, 158–161 (2012)
    Article ADS CAS Google Scholar
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. Wang, S. et al. Geographic patterns of genome admixture in Latin American Mestizos. PLoS Genet. 4, e1000037 (2008)
    Article Google Scholar
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)
    Article ADS CAS Google Scholar
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)
    Article CAS Google Scholar
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. 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)
    Article CAS Google Scholar
33. Patterson, N., Price, A. L. & Reich, D. Population structure and eigenanalysis. PLoS Genet. 2, e190 (2006)
    Article Google Scholar
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. Liu, K. & Muse, S. V. PowerMarker: an integrated analysis environment for genetic marker analysis. Bioinformatics 21, 2128–2129 (2005)
    Article CAS Google Scholar
36. Greenberg, J. H. Language in the Americas (Stanford Univ. Press, 1987)
    Google Scholar
37. Campbell, L. American Indian languages: the historical linguistics of Native America (Oxford Univ. Press, 1997)
    Google Scholar

Download references

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

1. Irma Silva-Zolezzi & Gerardo Jimenez-Sanchez
   Present address: 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.).,

Authors and Affiliations

1. Department of Genetics, Harvard Medical School, Boston, 02115, Massachusetts, USA
   David Reich & Arti Tandon
2. Broad Institute of Harvard and the Massachusetts Institute of Technology, Cambridge, 02142, Massachusetts, 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. Departamento de Salud Reproductiva y Genética, Laboratorio de Biología de la Reproducción, 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, 02114, Massachusetts, 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, 94720, California, USA
    William Klitz
38. Department of Genetics, Yale University School of Medicine, New Haven, 06520, Connecticut, USA
    Judith Kidd & Kenneth Kidd
39. Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, University of California Los Angeles, Los Angeles, 90095, California, USA
    Nelson B. Freimer
40. Departments of Epidemiology and Biostatistics, Harvard School of Public Health, Boston, 02115, Massachusetts, USA
    Alkes L. Price

Authors

1. David Reich
   You can also search for this author inPubMed Google Scholar
2. Nick Patterson
   You can also search for this author inPubMed Google Scholar
3. Desmond Campbell
   You can also search for this author inPubMed Google Scholar
4. Arti Tandon
   You can also search for this author inPubMed Google Scholar
5. Stéphane Mazieres
   You can also search for this author inPubMed Google Scholar
6. Nicolas Ray
   You can also search for this author inPubMed Google Scholar
7. Maria V. Parra
   You can also search for this author inPubMed Google Scholar
8. Winston Rojas
   You can also search for this author inPubMed Google Scholar
9. Constanza Duque
   You can also search for this author inPubMed Google Scholar
10. Natalia Mesa
    You can also search for this author inPubMed Google Scholar
11. Luis F. García
    You can also search for this author inPubMed Google Scholar
12. Omar Triana
    You can also search for this author inPubMed Google Scholar
13. Silvia Blair
    You can also search for this author inPubMed Google Scholar
14. Amanda Maestre
    You can also search for this author inPubMed Google Scholar
15. Juan C. Dib
    You can also search for this author inPubMed Google Scholar
16. Claudio M. Bravi
    You can also search for this author inPubMed Google Scholar
17. Graciela Bailliet
    You can also search for this author inPubMed Google Scholar
18. Daniel Corach
    You can also search for this author inPubMed Google Scholar
19. Tábita Hünemeier
    You can also search for this author inPubMed Google Scholar
20. Maria Cátira Bortolini
    You can also search for this author inPubMed Google Scholar
21. Francisco M. Salzano
    You can also search for this author inPubMed Google Scholar
22. María Luiza Petzl-Erler
    You can also search for this author inPubMed Google Scholar
23. Victor Acuña-Alonzo
    You can also search for this author inPubMed Google Scholar
24. Carlos Aguilar-Salinas
    You can also search for this author inPubMed Google Scholar
25. Samuel Canizales-Quinteros
    You can also search for this author inPubMed Google Scholar
26. Teresa Tusié-Luna
    You can also search for this author inPubMed Google Scholar
27. Laura Riba
    You can also search for this author inPubMed Google Scholar
28. Maricela Rodríguez-Cruz
    You can also search for this author inPubMed Google Scholar
29. Mardia Lopez-Alarcón
    You can also search for this author inPubMed Google Scholar
30. Ramón Coral-Vazquez
    You can also search for this author inPubMed Google Scholar
31. Thelma Canto-Cetina
    You can also search for this author inPubMed Google Scholar
32. Irma Silva-Zolezzi
    You can also search for this author inPubMed Google Scholar
33. Juan Carlos Fernandez-Lopez
    You can also search for this author inPubMed Google Scholar
34. Alejandra V. Contreras
    You can also search for this author inPubMed Google Scholar
35. Gerardo Jimenez-Sanchez
    You can also search for this author inPubMed Google Scholar
36. Maria José Gómez-Vázquez
    You can also search for this author inPubMed Google Scholar
37. Julio Molina
    You can also search for this author inPubMed Google Scholar
38. Ángel Carracedo
    You can also search for this author inPubMed Google Scholar
39. Antonio Salas
    You can also search for this author inPubMed Google Scholar
40. Carla Gallo
    You can also search for this author inPubMed Google Scholar
41. Giovanni Poletti
    You can also search for this author inPubMed Google Scholar
42. David B. Witonsky
    You can also search for this author inPubMed Google Scholar
43. Gorka Alkorta-Aranburu
    You can also search for this author inPubMed Google Scholar
44. Rem I. Sukernik
    You can also search for this author inPubMed Google Scholar
45. Ludmila Osipova
    You can also search for this author inPubMed Google Scholar
46. Sardana A. Fedorova
    You can also search for this author inPubMed Google Scholar
47. René Vasquez
    You can also search for this author inPubMed Google Scholar
48. Mercedes Villena
    You can also search for this author inPubMed Google Scholar
49. Claudia Moreau
    You can also search for this author inPubMed Google Scholar
50. Ramiro Barrantes
    You can also search for this author inPubMed Google Scholar
51. David Pauls
    You can also search for this author inPubMed Google Scholar
52. Laurent Excoffier
    You can also search for this author inPubMed Google Scholar
53. Gabriel Bedoya
    You can also search for this author inPubMed Google Scholar
54. Francisco Rothhammer
    You can also search for this author inPubMed Google Scholar
55. Jean-Michel Dugoujon
    You can also search for this author inPubMed Google Scholar
56. Georges Larrouy
    You can also search for this author inPubMed Google Scholar
57. William Klitz
    You can also search for this author inPubMed Google Scholar
58. Damian Labuda
    You can also search for this author inPubMed Google Scholar
59. Judith Kidd
    You can also search for this author inPubMed Google Scholar
60. Kenneth Kidd
    You can also search for this author inPubMed Google Scholar
61. Anna Di Rienzo
    You can also search for this author inPubMed Google Scholar
62. Nelson B. Freimer
    You can also search for this author inPubMed Google Scholar
63. Alkes L. Price
    You can also search for this author inPubMed Google Scholar
64. Andrés Ruiz-Linares
    You can also search for this author inPubMed Google Scholar

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.

Corresponding authors

Correspondence toDavid Reich or Andrés Ruiz-Linares.

Ethics declarations

Competing interests

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. (a.ruizlin@ucl.ac.uk).

Supplementary information

Supplementary Information

This file contains Supplementary Text 1-7, Supplementary Figures 1-5 and Supplementary Tables 1-3. (PDF 2279 kb)

PowerPoint slides

Rights and permissions

About this article

Cite this article

Reich, D., Patterson, N., Campbell, D. et al. Reconstructing Native American population history.Nature 488, 370–374 (2012). https://doi.org/10.1038/nature11258

Download citation

• Received: 01 September 2011
• Accepted: 25 May 2012
• Published: 11 July 2012
• Issue Date: 16 August 2012
• DOI: https://doi.org/10.1038/nature11258