Research Article

Genomic evidence for the Pleistocene and recent population history of Native Americans

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Science  21 Aug 2015:
Vol. 349, Issue 6250, aab3884
DOI: 10.1126/science.aab3884

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vol. 349 no. 6250

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History: 
  • Received for publication May 4, 2015
  • Accepted for publication July 15, 2015
  • .

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  1. Maanasa Raghavan1,*,
  2. Matthias Steinrücken2,3,4,*,
  3. Kelley Harris5,*,
  4. Stephan Schiffels6,*,
  5. Simon Rasmussen7,*,
  6. Michael DeGiorgio8,*,
  7. Anders Albrechtsen9,*,
  8. Cristina Valdiosera1,10,*,
  9. María C. Ávila-Arcos1,11,*,
  10. Anna-Sapfo Malaspinas1,*,
  11. Anders Eriksson12,13,
  12. Ida Moltke9,
  13. Mait Metspalu14,15,
  14. Julian R. Homburger11,
  15. Jeff Wall16,
  16. Omar E. Cornejo17,
  17. J. Víctor Moreno-Mayar1,
  18. Thorfinn S. Korneliussen1,
  19. Tracey Pierre1,
  20. Morten Rasmussen1,11,
  21. Paula F. Campos1,18,
  22. Peter de Barros Damgaard1,
  23. Morten E. Allentoft1,
  24. John Lindo19,
  25. Ene Metspalu14,15,
  26. Ricardo Rodríguez-Varela20,
  27. Josefina Mansilla21,
  28. Celeste Henrickson22,
  29. Andaine Seguin-Orlando1,
  30. Helena Malmström23,
  31. Thomas Stafford Jr.1,24,
  32. Suyash S. Shringarpure11,
  33. Andrés Moreno-Estrada11,25,
  34. Monika Karmin14,15,
  35. Kristiina Tambets14,
  36. Anders Bergström6,
  37. Yali Xue6,
  38. Vera Warmuth26,27,
  39. Andrew D. Friend28,
  40. Joy Singarayer29,
  41. Paul Valdes30,
  42. Francois Balloux26,
  43. Ilán Leboreiro21,
  44. Jose Luis Vera31,
  45. Hector Rangel-Villalobos32,
  46. Davide Pettener33,
  47. Donata Luiselli33,
  48. Loren G. Davis34,
  49. Evelyne Heyer35,
  50. Christoph P. E. Zollikofer36,
  51. Marcia S. Ponce de León36,
  52. Colin I. Smith10,
  53. Vaughan Grimes37,38,
  54. Kelly-Anne Pike37,
  55. Michael Deal37,
  56. Benjamin T. Fuller39,
  57. Bernardo Arriaza40,
  58. Vivien Standen41,
  59. Maria F. Luz42,
  60. Francois Ricaut43,
  61. Niede Guidon42,
  62. Ludmila Osipova44,45,
  63. Mikhail I. Voevoda44,46,47,
  64. Olga L. Posukh44,45,
  65. Oleg Balanovsky48,49,
  66. Maria Lavryashina50,
  67. Yuri Bogunov48,
  68. Elza Khusnutdinova51,52,
  69. Marina Gubina44,
  70. Elena Balanovska49,
  71. Sardana Fedorova53,54,
  72. Sergey Litvinov14,51,
  73. Boris Malyarchuk55,
  74. Miroslava Derenko55,
  75. M. J. Mosher56,
  76. David Archer57,
  77. Jerome Cybulski58,59,60,
  78. Barbara Petzelt61,
  79. Joycelynn Mitchell61,
  80. Rosita Worl62,
  81. Paul J. Norman63,
  82. Peter Parham63,
  83. Brian M. Kemp17,64,
  84. Toomas Kivisild14,65,
  85. Chris Tyler-Smith6,
  86. Manjinder S. Sandhu6, 66,
  87. Michael Crawford67,
  88. Richard Villems14,15,
  89. David Glenn Smith68,
  90. Michael R. Waters69,70,71,
  91. Ted Goebel69,
  92. John R. Johnson72,
  93. Ripan S. Malhi19,73,
  94. Mattias Jakobsson23,
  95. David J. Meltzer1,74,
  96. Andrea Manica12,
  97. Richard Durbin6,
  98. Carlos D. Bustamante11,
  99. Yun S. Song2,3,75,,
  100. Rasmus Nielsen75,,
  101. Eske Willerslev1,
  1. 1Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5–7, 1350 Copenhagen, Denmark.
  2. 2Computer Science Division, University of California, Berkeley, Berkeley, CA 94720, USA.
  3. 3Department of Statistics, University of California, Berkeley, Berkeley, CA 94720, USA.
  4. 4Department of Biostatistics and Epidemiology, University of Massachusetts, Amherst, MA 01003, USA.
  5. 5Department of Mathematics, University of California, Berkeley, Berkeley, CA 94720, USA.
  6. 6Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK.
  7. 7Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Kemitorvet, Building 208, 2800 Kongens Lyngby, Denmark.
  8. 8Departments of Biology and Statistics, Pennsylvania State University, 502 Wartik Laboratory, University Park, PA 16802, USA.
  9. 9The Bioinformatics Centre, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen, Denmark.
  10. 10Department of Archaeology and History, La Trobe University, Melbourne, Victoria 3086, Australia.
  11. 11Department of Genetics, School of Medicine, Stanford University, 300 Pasteur Drive, Lane Building, Room L331, Stanford, CA 94305, USA.
  12. 12Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK.
  13. 13Integrative Systems Biology Laboratory, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia.
  14. 14Estonian Biocentre, Evolutionary Biology Group, Tartu 51010, Estonia.
  15. 15Department of Evolutionary Biology, University of Tartu, Tartu 51010, Estonia.
  16. 16Institute for Human Genetics, University of California San Francisco, 513 Parnassus Avenue, San Francisco, CA 94143, USA.
  17. 17School of Biological Sciences, Washington State University, Post Office Box 644236, Heald 429, Pullman, WA 99164, USA.
  18. 18Centro de Investigación en Ciencias del Mar y Limnología/Centro Interdisciplinar de Investigação Marinha e Ambiental, Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Rua dos Bragas 289, 4050-123 Porto, Portugal.
  19. 19Department of Anthropology, University of Illinois at Urbana-Champaign, 607 S. Mathews Avenue, Urbana, IL 61801, USA.
  20. 20Centro Mixto, Universidad Complutense de Madrid–Instituto de Salud Carlos III de Evolución y Comportamiento Humano, Madrid, Spain.
  21. 21Instituto Nacional de Antropología e Historia, Moneda 13, Centro, Cuauhtémoc, 06060 Mexico City, Mexico.
  22. 22University of Utah, Department of Anthropology, 270 S 1400 E, Salt Lake City, UT 84112, USA.
  23. 23Department of Evolutionary Biology and Science for Life Laboratory, Uppsala University, Norbyvägen 18D, SE-752 36 Uppsala, Sweden.
  24. 24Acceleration Mass Spectrometry 14C Dating Centre, Department of Physics and Astronomy, Aarhus University, Ny Munkegade 120, 8000 Aarhus, Denmark.
  25. 25Laboratorio Nacional de Genómica para la Biodiversidad (LANGEBIO), Centro de Investigación y de Estudios Avanzados, Irapuato, Guanajuato 36821, Mexico.
  26. 26Genetics Institute, University College London, Gower Street, London WC1E 6BT, UK.
  27. 27Evolutionsbiologiskt Centrum, Norbyvägen 18D, 75236 Uppsala, Sweden.
  28. 28Department of Geography, University of Cambridge, Downing Place, Cambridge CB2 3EN, UK.
  29. 29Centre for Past Climate Change and Department of Meteorology, University of Reading, Earley Gate, Post Office Box 243, Reading, UK.
  30. 30School of Geographical Sciences, University Road, Clifton, Bristol BS8 1SS, UK.
  31. 31Escuela Nacional de AntropologÍa e Historia, Periférico Sur y Zapote s/n Colonia Isidro Fabela, Tlalpan, Isidro Fabela, 14030 Mexico City, Mexico.
  32. 32Instituto de Investigación en Genética Molecular, Universidad de Guadalajara, Ocotlán, Mexico.
  33. 33Dipartimento di Scienze Biologiche, Geologiche e Ambientali (BiGeA), Università di Bologna, Via Selmi 3, 40126 Bologna, Italy.
  34. 34Department of Anthropology, Oregon State University, 238 Waldo Hall, Corvallis, OR 97331 USA.
  35. 35Museum National d'Histoire Naturelle, CNRS, Université Paris 7 Diderot, Sorbonne Paris Cité, Sorbonne Universités, Unité Eco-Anthropologie et Ethnobiologie (UMR7206), Paris, France.
  36. 36Anthropological Institute and Museum, University of Zürich, Winterthurerstrasse 190, 8057 Zürich, Switzerland.
  37. 37Department of Archaeology, Memorial University, Queen’s College, 210 Prince Philip Drive, St. John’s, Newfoundland A1C 5S7, Canada.
  38. 38Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, Leipzig 04103, Germany.
  39. 39Department of Earth System Science, University of California, Irvine, Keck Carbon Cycle Accelerator Mass Spectrometry Group, B321 Croul Hall, Irvine, CA 92697, USA.
  40. 40Instituto de Alta Investigación, Universidad de Tarapacá, 18 de Septiembre 2222, Carsilla 6-D Arica, Chile.
  41. 41Departamento de Antropologia, Universidad de Tarapacá, 18 de Septiembre 2222, Carsilla 6-D Arica, Chile.
  42. 42Fundação Museu do Homem Americano, Centro Cultural Sérgio Motta, Campestre, 64770-000 Sao Raimundo Nonato, Brazil.
  43. 43Laboratoire d’Anthropologie Moléculaire et Imagérie de Synthèse UMR-5288, CNRS, Université de Toulouse, 31073 Toulouse, France.
  44. 44Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Prospekt Lavrentyeva 10, 630090 Novosibirsk, Russia.
  45. 45Novosibirsk State University, 2 Pirogova Street, 630090 Novosibirsk, Russia.
  46. 46Institute of Internal Medicine, Siberian Branch of RAS, 175/1 ul. B. Bogatkova, Novosibirsk 630089, Russia.
  47. 47Novosibirsk State University, Laboratory of Molecular Epidemiology and Bioinformatics, 630090 Novosibirsk, Russia.
  48. 48Vavilov Institute of General Genetics, Gubkina 3, 119333 Moscow, Russia.
  49. 49Research Centre for Medical Genetics, Moskvorechie 1, 115478 Moscow, Russia.
  50. 50Kemerovo State University, Krasnaya 3, 650000 Kemerovo, Russia.
  51. 51Institute of Biochemistry and Genetics, Ufa Scientific Center of Russian Academy of Sciences, Prospekt Oktyabrya 71, 450054 Ufa, Russia.
  52. 52Department of Genetics and Fundamental Medicine, Bashkir State University, Zaki Validi 32, 450076 Ufa, Russia.
  53. 53Department of Molecular Genetics, Yakut Scientific Centre of Complex Medical Problems, Sergelyahskoe Shosse 4, 677010 Yakutsk, Russia.
  54. 54Laboratory of Molecular Biology, Institute of Natural Sciences, M. K. Ammosov North-Eastern Federal University, 677000 Yakutsk, Russia.
  55. 55Institute of Biological Problems of the North, Russian Academy of Sciences, Portovaya Street 18, Magadan 685000, Russia.
  56. 56Department of Anthropology, Western Washington University, Bellingham, WA 98225, USA.
  57. 57Department of Anthropology, Northwest Community College, 353 Fifth Street, Prince Rupert, British Columbia V8J 3L6, Canada.
  58. 58Canadian Museum of History, 100 Rue Laurier, Gatineau, Quebec K1A 0M8, Canada.
  59. 59University of Western Ontario, London, Ontario N6A 3K7, Canada.
  60. 60Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada.
  61. 61Metlakatla Treaty Office, Post Office Box 224, Prince Rupert, BC V8J 3P6, Canada.
  62. 62Sealaska Heritage Institute, 105 S. Seward Street, Juneau, AK 99801, USA.
  63. 63Department of Structural Biology, Stanford University School of Medicine, D100 Fairchild Science Building, Stanford, CA 94305-5126, USA.
  64. 64Department of Anthropology, Washington State University, Pullman, WA 99163, USA.
  65. 65Division of Biological Anthropology, University of Cambridge, Henry Wellcome Building, Fitzwilliam Street, Cambridge CB2 1QH, UK.
  66. 66Department of Medicine, University of Cambridge, Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK.
  67. 67Laboratory of Biological Anthropology, University of Kansas, 1415 Jayhawk Boulevard, 622 Fraser Hall, Lawrence, KS 66045, USA.
  68. 68Molecular Anthropology Laboratory, 209 Young Hall, Department of Anthropology, University of California, One Shields Avenue, Davis, CA 95616, USA.
  69. 69Center for the Study of the First Americans, Texas A&M University, College Station, TX 77843-4352, USA.
  70. 70Department of Anthropology, Texas A&M University, College Station, TX 77843-4352, USA.
  71. 71Department of Geography, Texas A&M University, College Station, TX 77843-4352, USA.
  72. 72Santa Barbara Museum of Natural History, 2559 Puesta del Sol, Santa Barbara, CA 93105, USA.
  73. 73Carle R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
  74. 74Department of Anthropology, Southern Methodist University, Dallas, TX 75275, USA.
  75. 75Department of Integrative Biology, University of California, 3060 Valley Life Sciences Building 3140, Berkeley, CA 94720, USA.
  1. Corresponding authors. E-mail: ewillierslev{at}snm.ku.dk (E.W.); rasmus_nielsen{at}berkeley.edu (R.N.); yss{at}berkeley.edu (Y.S.S.)
  1. * These authors contributed equally to this work.

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