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

doi:10.1126/science.aab3884

. 2015 Aug 21;349(6250):aab3884.

doi: 10.1126/science.aab3884. Epub 2015 Jul 21.

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

Maanasa Raghavan^#¹, Matthias Steinrücken^#^{2

3

4}, Kelley Harris^#⁵, Stephan Schiffels^#⁶, Simon Rasmussen^#⁷, Michael DeGiorgio^#⁸, Anders Albrechtsen^#⁹, Cristina Valdiosera^#^{1

10}, María C Ávila-Arcos^#^{1

11}, Anna-Sapfo Malaspinas^#¹, Anders Eriksson^{12

13}, Ida Moltke⁹, Mait Metspalu^{14

15}, Julian R Homburger¹¹, Jeff Wall¹⁶, Omar E Cornejo¹⁷, J Víctor Moreno-Mayar¹, Thorfinn S Korneliussen¹, Tracey Pierre¹, Morten Rasmussen^{1

11}, Paula F Campos^{1

18}, Peter de Barros Damgaard¹, Morten E Allentoft¹, John Lindo¹⁹, Ene Metspalu^{14

15}, Ricardo Rodríguez-Varela²⁰, Josefina Mansilla²¹, Celeste Henrickson²², Andaine Seguin-Orlando¹, Helena Malmström²³, Thomas Stafford Jr^{1

24}, Suyash S Shringarpure¹¹, Andrés Moreno-Estrada^{11

25}, Monika Karmin^{14

15}, Kristiina Tambets¹⁴, Anders Bergström⁶, Yali Xue⁶, Vera Warmuth^{26

27}, Andrew D Friend²⁸, Joy Singarayer²⁹, Paul Valdes³⁰, Francois Balloux²⁶, Ilán Leboreiro²¹, Jose Luis Vera³¹, Hector Rangel-Villalobos³², Davide Pettener³³, Donata Luiselli³³, Loren G Davis³⁴, Evelyne Heyer³⁵, Christoph P E Zollikofer³⁶, Marcia S Ponce de León³⁶, Colin I Smith¹⁰, Vaughan Grimes^{37

38}, Kelly-Anne Pike³⁷, Michael Deal³⁷, Benjamin T Fuller³⁹, Bernardo Arriaza⁴⁰, Vivien Standen⁴¹, Maria F Luz⁴², Francois Ricaut⁴³, Niede Guidon⁴², Ludmila Osipova^{44

45}, Mikhail I Voevoda^{44

46

47}, Olga L Posukh^{44

45}, Oleg Balanovsky^{48

49}, Maria Lavryashina⁵⁰, Yuri Bogunov⁴⁸, Elza Khusnutdinova^{51

52}, Marina Gubina⁴², Elena Balanovska⁴⁹, Sardana Fedorova^{53

54}, Sergey Litvinov^{14

51}, Boris Malyarchuk⁵⁵, Miroslava Derenko⁵⁵, M J Mosher⁵⁶, David Archer⁵⁷, Jerome Cybulski^{58

59

60}, Barbara Petzelt⁶¹, Joycelynn Mitchell⁶¹, Rosita Worl⁶², Paul J Norman⁶³, Peter Parham⁶³, Brian M Kemp^{17

64}, Toomas Kivisild^{14

65}, Chris Tyler-Smith⁶, Manjinder S Sandhu^{6

66}, Michael Crawford⁶⁷, Richard Villems^{14

15}, David Glenn Smith⁶⁸, Michael R Waters^{69

70

71}, Ted Goebel⁶⁹, John R Johnson⁷², Ripan S Malhi^{19

73}, Mattias Jakobsson²³, David J Meltzer^{1

74}, Andrea Manica¹², Richard Durbin⁶, Carlos D Bustamante¹¹, Yun S Song^{2

3

75}, Rasmus Nielsen⁷⁵, Eske Willerslev¹

Affiliations

¹ Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark.
² Computer Science Division, University of California, Berkeley, CA 94720, USA.
³ Department of Statistics, University of California, Berkeley, CA 94720, USA.
⁴ Department of Biostatistics and Epidemiology, University of Massachusetts, Amherst, MA 01003, USA.
⁵ Department of Mathematics, University of California, Berkeley, CA 94720, USA.
⁶ Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK.
⁷ Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Kemitorvet, Building 208, 2800 Kongens Lyngby, Denmark.
⁸ Departments of Biology and Statistics, Pennsylvania State University, 502 Wartik Laboratory, University Park, PA 16802, USA.
⁹ The Bioinformatics Centre, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen, Denmark.
¹⁰ Department of Archaeology and History, La Trobe University, Melbourne, Victoria 3086, Australia.
¹¹ Department of Genetics, School of Medicine, Stanford University, 300 Pasteur Dr. Lane Bldg Room L331, Stanford, California 94305, USA.
¹² Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK.
¹³ Integrative Systems Biology Laboratory, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia.
¹⁴ Estonian Biocentre, Evolutionary Biology Group, Tartu 51010, Estonia.
¹⁵ Department of Evolutionary Biology, University of Tartu, Tartu 51010, Estonia.
¹⁶ Institute for Human Genetics, University of California San Francisco, 513 Parnassus Avenue, San Francisco, CA 94143, USA.
¹⁷ School of Biological Sciences, Washington State University, PO Box 644236, Heald 429, Pullman, Washington 99164, USA.
¹⁸ CIMAR/CIIMAR, Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Rua dos Bragas 289, 4050-123 Porto, Portugal.
¹⁹ Department of Anthropology, University of Illinois at Urbana-Champaign, 607 S. Mathews Ave, Urbana, IL 61801, USA.
²⁰ Centro Mixto, Universidad Complutense de Madrid-Instituto de Salud Carlos III de Evolución y Comportamiento Humano, Madrid, Spain.
²¹ Instituto Nacional de Antropología e Historia, Moneda 13, Centro, Cuauhtémoc, 06060 Mexico Mexico City, Mexico.
²² University of Utah, Department of Anthropology, 270 S 1400 E, Salt Lake City, Utah 84112, USA.
²³ Department of Evolutionary Biology and Science for Life Laboratory, Uppsala University, Norbyvägen 18D, SE-752 36 Uppsala, Sweden.
²⁴ AMS 14C Dating Centre, Department of Physics and Astronomy, Aarhus University, Ny Munkegade 120, 8000 Aarhus, Denmark.
²⁵ Laboratorio Nacional de Genómica para la Biodiversidad (LANGEBIO), CINVESTAV, Irapuato, Guanajuato 36821, Mexico.
²⁶ UCL Genetics Institute, Gower Street, London WC1E 6BT, UK.
²⁷ Evolutionsbiologiskt Centrum, Norbyvägen 18D, 75236 Uppsala, Sweden.
²⁸ Department of Geography, University of Cambridge, Downing Place, Cambridge CB2 3EN, UK.
²⁹ Centre for Past Climate Change and Department of Meteorology, University of Reading, Earley Gate, PO Box 243, Reading, UK.
³⁰ School of Geographical Sciences, University Road, Clifton, Bristol BS8 1SS, UK.
³¹ Escuela Nacional de AntropologÍa e Historia, Periférico Sur y Zapote s/n. Colonia Isidro Fabela, Tlalpan, Isidro Fabela, 14030 Mexico City, Mexico.
³² Instituto de Investigación en Genética Molecular, Universidad de Guadalajara, Ocotlán, Mexico.
³³ Dipartimento di Scienze Biologiche, Geologiche e Ambientali (BiGeA), Università di Bologna, Via Selmi 3, 40126 Bologna, Italy.
³⁴ Department of Anthropology, Oregon State University, 238 Waldo Hall, Corvallis, OR, 97331 USA.
³⁵ Museum National d'Histoire Naturelle, CNRS, Université Paris 7 Diderot, Sorbonne Paris Cité, Sorbonne Universités, Unité Eco-Anthropologie et Ethnobiologie (UMR7206), Paris, France.
³⁶ Anthropological Institute and Museum, University of Zürich, Winterthurerstrasse 190, 8057 Zürich, Switzerland.
³⁷ Department of Archaeology, Memorial University, Queen's College, 210 Prince Philip Drive, St. John's, Newfoundland, A1C 5S7, Canada.
³⁸ Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, Leipzig 04103, Germany.
³⁹ Department of Earth System Science, University of California, Irvine, Keck CCAMS Group, B321 Croul Hall, Irvine, California, 92697, USA.
⁴⁰ Instituto de Alta Investigación, Universidad de Tarapacá, 18 de Septiembre 2222, Carsilla 6-D Arica, Chile.
⁴¹ Departamento de Antropologia, Universidad de Tarapacá, 18 de Septiembre 2222. Casilla 6-D Arica, Chile.
⁴² Fundação Museu do Homem Americano, Centro Cultural Sérgio Motta, Campestre, 64770-000 Sao Raimundo Nonato, Brazil.
⁴³ Laboratoire d'Anthropologie Moléculaire et Imagérie de Synthèse UMR-5288, CNRS, Université de Toulouse, 31073 Toulouse, France.
⁴⁴ Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Prospekt Lavrentyeva 10, 630090 Novosibirsk, Russia.
⁴⁵ Novosibirsk State University, 2 Pirogova Str., 630090 Novosibirsk, Russia.
⁴⁶ Institute of Internal Medicine, Siberian Branch of RAS, 175/1 ul. B. Bogatkova, Novosibirsk 630089, Russia.
⁴⁷ Novosibirsk State University, Laboratory of Molecular Epidemiology and Bioinformatics, 630090 Novosibirsk, Russia.
⁴⁸ Vavilov Institute of General Genetics, Gubkina 3, 119333 Moscow, Russia.
⁴⁹ Research Centre for Medical Genetics, Moskvorechie 1, 115478 Moscow, Russia.
⁵⁰ Kemerovo State University, Krasnaya 3, 650000 Kemerovo, Russia.
⁵¹ Institute of Biochemistry and Genetics, Ufa Scientific Center of RAS, Prospekt Oktyabrya 71, 450054 Ufa, Russia.
⁵² Department of Genetics and Fundamental Medicine, Bashkir State University, Zaki Validi 32, 450076 Ufa, Russia.
⁵³ Department of Molecular Genetics, Yakut Scientific Centre of Complex Medical Problems, Sergelyahskoe Shosse 4, 677010 Yakutsk, Russia.
⁵⁴ Laboratory of Molecular Biology, Institute of Natural Sciences, M.K. Ammosov North-Eastern Federal University, 677000 Yakutsk, Russia.
⁵⁵ Institute of Biological Problems of the North, Russian Academy of Sciences, Portovaya Street 18, Magadan 685000, Russia.
⁵⁶ Department of Anthropology, Western Washington University, Bellingham Washington 98225, USA.
⁵⁷ Department of Anthropology, Northwest Community College, 353 Fifth Street, Prince Rupert, British Columbia V8J 3L6, Canada.
⁵⁸ Canadian Museum of History, 100 Rue Laurier, Gatineau, Quebec K1A 0M8, Canada.
⁵⁹ University of Western Ontario, London, Ontario N6A 3K7, Canada.
⁶⁰ Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada.
⁶¹ Metlakatla Treaty Office, PO Box 224, Prince Rupert, BC, Canada V8J 3P6.
⁶² Sealaska Heritage Institute, 105 S. Seward Street, Juneau, Alaska 99801, USA.
⁶³ Department of Structural Biology, Stanford University School of Medicine, D100 Fairchild Science Building, Stanford, California 94305-5126, USA.
⁶⁴ Department of Anthropology, Washington State University, Pullman Washington 99163, USA.
⁶⁵ Division of Biological Anthropology, University of Cambridge, Henry Wellcome Building, Fitzwilliam Street, CB2 1QH, Cambridge, UK.
⁶⁶ Dept of Medicine, University of Cambridge, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK.
⁶⁷ Laboratory of Biological Anthropology, University of Kansas, 1415 Jayhawk Blvd., 622 Fraser Hall, Lawrence, Kansas 66045, USA.
⁶⁸ Molecular Anthropology Laboratory, 209 Young Hall, Department of Anthropology, University of California, One Shields Avenue, Davis, California 95616, USA.
⁶⁹ Center for the Study of the First Americans, Texas A&M University, College Station, Texas 77843-4352, USA.
⁷⁰ Department of Anthropology, Texas A&M University, College Station, Texas 77843-4352, USA.
⁷¹ Department of Geography, Texas A&M University, College Station, Texas 77843-4352, USA.
⁷² Santa Barbara Museum of Natural History, 2559 Puesta del Sol, Santa Barbara, CA 93105, USA.
⁷³ Carle R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, 61801, USA.
⁷⁴ Department of Anthropology, Southern Methodist University, Dallas, Texas 75275, USA.
⁷⁵ Department of Integrative Biology, University of California, 3060 Valley Life Sciences Bldg #3140, Berkeley, CA 94720, USA.

^# Contributed equally.

PMID: 26198033
PMCID: PMC4733658
DOI: 10.1126/science.aab3884

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

Maanasa Raghavan et al. Science. 2015.

. 2015 Aug 21;349(6250):aab3884.

doi: 10.1126/science.aab3884. Epub 2015 Jul 21.

Authors

Affiliations

¹ Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark.
² Computer Science Division, University of California, Berkeley, CA 94720, USA.
³ Department of Statistics, University of California, Berkeley, CA 94720, USA.
⁴ Department of Biostatistics and Epidemiology, University of Massachusetts, Amherst, MA 01003, USA.
⁵ Department of Mathematics, University of California, Berkeley, CA 94720, USA.
⁶ Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK.
⁷ Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Kemitorvet, Building 208, 2800 Kongens Lyngby, Denmark.
⁸ Departments of Biology and Statistics, Pennsylvania State University, 502 Wartik Laboratory, University Park, PA 16802, USA.
⁹ The Bioinformatics Centre, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen, Denmark.
¹⁰ Department of Archaeology and History, La Trobe University, Melbourne, Victoria 3086, Australia.
¹¹ Department of Genetics, School of Medicine, Stanford University, 300 Pasteur Dr. Lane Bldg Room L331, Stanford, California 94305, USA.
¹² Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK.
¹³ Integrative Systems Biology Laboratory, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia.
¹⁴ Estonian Biocentre, Evolutionary Biology Group, Tartu 51010, Estonia.
¹⁵ Department of Evolutionary Biology, University of Tartu, Tartu 51010, Estonia.
¹⁶ Institute for Human Genetics, University of California San Francisco, 513 Parnassus Avenue, San Francisco, CA 94143, USA.
¹⁷ School of Biological Sciences, Washington State University, PO Box 644236, Heald 429, Pullman, Washington 99164, USA.
¹⁸ CIMAR/CIIMAR, Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Rua dos Bragas 289, 4050-123 Porto, Portugal.
¹⁹ Department of Anthropology, University of Illinois at Urbana-Champaign, 607 S. Mathews Ave, Urbana, IL 61801, USA.
²⁰ Centro Mixto, Universidad Complutense de Madrid-Instituto de Salud Carlos III de Evolución y Comportamiento Humano, Madrid, Spain.
²¹ Instituto Nacional de Antropología e Historia, Moneda 13, Centro, Cuauhtémoc, 06060 Mexico Mexico City, Mexico.
²² University of Utah, Department of Anthropology, 270 S 1400 E, Salt Lake City, Utah 84112, USA.
²³ Department of Evolutionary Biology and Science for Life Laboratory, Uppsala University, Norbyvägen 18D, SE-752 36 Uppsala, Sweden.
²⁴ AMS 14C Dating Centre, Department of Physics and Astronomy, Aarhus University, Ny Munkegade 120, 8000 Aarhus, Denmark.
²⁵ Laboratorio Nacional de Genómica para la Biodiversidad (LANGEBIO), CINVESTAV, Irapuato, Guanajuato 36821, Mexico.
²⁶ UCL Genetics Institute, Gower Street, London WC1E 6BT, UK.
²⁷ Evolutionsbiologiskt Centrum, Norbyvägen 18D, 75236 Uppsala, Sweden.
²⁸ Department of Geography, University of Cambridge, Downing Place, Cambridge CB2 3EN, UK.
²⁹ Centre for Past Climate Change and Department of Meteorology, University of Reading, Earley Gate, PO Box 243, Reading, UK.
³⁰ School of Geographical Sciences, University Road, Clifton, Bristol BS8 1SS, UK.
³¹ Escuela Nacional de AntropologÍa e Historia, Periférico Sur y Zapote s/n. Colonia Isidro Fabela, Tlalpan, Isidro Fabela, 14030 Mexico City, Mexico.
³² Instituto de Investigación en Genética Molecular, Universidad de Guadalajara, Ocotlán, Mexico.
³³ Dipartimento di Scienze Biologiche, Geologiche e Ambientali (BiGeA), Università di Bologna, Via Selmi 3, 40126 Bologna, Italy.
³⁴ Department of Anthropology, Oregon State University, 238 Waldo Hall, Corvallis, OR, 97331 USA.
³⁵ Museum National d'Histoire Naturelle, CNRS, Université Paris 7 Diderot, Sorbonne Paris Cité, Sorbonne Universités, Unité Eco-Anthropologie et Ethnobiologie (UMR7206), Paris, France.
³⁶ Anthropological Institute and Museum, University of Zürich, Winterthurerstrasse 190, 8057 Zürich, Switzerland.
³⁷ Department of Archaeology, Memorial University, Queen's College, 210 Prince Philip Drive, St. John's, Newfoundland, A1C 5S7, Canada.
³⁸ Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, Leipzig 04103, Germany.
³⁹ Department of Earth System Science, University of California, Irvine, Keck CCAMS Group, B321 Croul Hall, Irvine, California, 92697, USA.
⁴⁰ Instituto de Alta Investigación, Universidad de Tarapacá, 18 de Septiembre 2222, Carsilla 6-D Arica, Chile.
⁴¹ Departamento de Antropologia, Universidad de Tarapacá, 18 de Septiembre 2222. Casilla 6-D Arica, Chile.
⁴² Fundação Museu do Homem Americano, Centro Cultural Sérgio Motta, Campestre, 64770-000 Sao Raimundo Nonato, Brazil.
⁴³ Laboratoire d'Anthropologie Moléculaire et Imagérie de Synthèse UMR-5288, CNRS, Université de Toulouse, 31073 Toulouse, France.
⁴⁴ Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Prospekt Lavrentyeva 10, 630090 Novosibirsk, Russia.
⁴⁵ Novosibirsk State University, 2 Pirogova Str., 630090 Novosibirsk, Russia.
⁴⁶ Institute of Internal Medicine, Siberian Branch of RAS, 175/1 ul. B. Bogatkova, Novosibirsk 630089, Russia.
⁴⁷ Novosibirsk State University, Laboratory of Molecular Epidemiology and Bioinformatics, 630090 Novosibirsk, Russia.
⁴⁸ Vavilov Institute of General Genetics, Gubkina 3, 119333 Moscow, Russia.
⁴⁹ Research Centre for Medical Genetics, Moskvorechie 1, 115478 Moscow, Russia.
⁵⁰ Kemerovo State University, Krasnaya 3, 650000 Kemerovo, Russia.
⁵¹ Institute of Biochemistry and Genetics, Ufa Scientific Center of RAS, Prospekt Oktyabrya 71, 450054 Ufa, Russia.
⁵² Department of Genetics and Fundamental Medicine, Bashkir State University, Zaki Validi 32, 450076 Ufa, Russia.
⁵³ Department of Molecular Genetics, Yakut Scientific Centre of Complex Medical Problems, Sergelyahskoe Shosse 4, 677010 Yakutsk, Russia.
⁵⁴ Laboratory of Molecular Biology, Institute of Natural Sciences, M.K. Ammosov North-Eastern Federal University, 677000 Yakutsk, Russia.
⁵⁵ Institute of Biological Problems of the North, Russian Academy of Sciences, Portovaya Street 18, Magadan 685000, Russia.
⁵⁶ Department of Anthropology, Western Washington University, Bellingham Washington 98225, USA.
⁵⁷ Department of Anthropology, Northwest Community College, 353 Fifth Street, Prince Rupert, British Columbia V8J 3L6, Canada.
⁵⁸ Canadian Museum of History, 100 Rue Laurier, Gatineau, Quebec K1A 0M8, Canada.
⁵⁹ University of Western Ontario, London, Ontario N6A 3K7, Canada.
⁶⁰ Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada.
⁶¹ Metlakatla Treaty Office, PO Box 224, Prince Rupert, BC, Canada V8J 3P6.
⁶² Sealaska Heritage Institute, 105 S. Seward Street, Juneau, Alaska 99801, USA.
⁶³ Department of Structural Biology, Stanford University School of Medicine, D100 Fairchild Science Building, Stanford, California 94305-5126, USA.
⁶⁴ Department of Anthropology, Washington State University, Pullman Washington 99163, USA.
⁶⁵ Division of Biological Anthropology, University of Cambridge, Henry Wellcome Building, Fitzwilliam Street, CB2 1QH, Cambridge, UK.
⁶⁶ Dept of Medicine, University of Cambridge, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK.
⁶⁷ Laboratory of Biological Anthropology, University of Kansas, 1415 Jayhawk Blvd., 622 Fraser Hall, Lawrence, Kansas 66045, USA.
⁶⁸ Molecular Anthropology Laboratory, 209 Young Hall, Department of Anthropology, University of California, One Shields Avenue, Davis, California 95616, USA.
⁶⁹ Center for the Study of the First Americans, Texas A&M University, College Station, Texas 77843-4352, USA.
⁷⁰ Department of Anthropology, Texas A&M University, College Station, Texas 77843-4352, USA.
⁷¹ Department of Geography, Texas A&M University, College Station, Texas 77843-4352, USA.
⁷² Santa Barbara Museum of Natural History, 2559 Puesta del Sol, Santa Barbara, CA 93105, USA.
⁷³ Carle R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, 61801, USA.
⁷⁴ Department of Anthropology, Southern Methodist University, Dallas, Texas 75275, USA.
⁷⁵ Department of Integrative Biology, University of California, 3060 Valley Life Sciences Bldg #3140, Berkeley, CA 94720, USA.

^# Contributed equally.

PMID: 26198033
PMCID: PMC4733658
DOI: 10.1126/science.aab3884

Abstract

How and when the Americas were populated remains contentious. Using ancient and modern genome-wide data, we found that the ancestors of all present-day Native Americans, including Athabascans and Amerindians, entered the Americas as a single migration wave from Siberia no earlier than 23 thousand years ago (ka) and after no more than an 8000-year isolation period in Beringia. After their arrival to the Americas, ancestral Native Americans diversified into two basal genetic branches around 13 ka, one that is now dispersed across North and South America and the other restricted to North America. Subsequent gene flow resulted in some Native Americans sharing ancestry with present-day East Asians (including Siberians) and, more distantly, Australo-Melanesians. Putative "Paleoamerican" relict populations, including the historical Mexican Pericúes and South American Fuego-Patagonians, are not directly related to modern Australo-Melanesians as suggested by the Paleoamerican Model.

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Figures

**Fig. 1. Origins and population history of Native Americans**
(A) Our results show that the ancestors of all present-day Native Americans, including Amerindians and Athabascans, derived from a single migration wave into the Americas (purple), separate from the Inuit (green). This migration from East Asia occurred no later than 23 KYA and is in agreement with archaeological evidence from sites such as Monte Verde (50). A split between the northern and southern branches of Native Americans occurred ca. 13 KYA, with the former comprising Athabascans and northern Amerindians and the latter consisting of Amerindians in northern North America and Central and South America including the Anzick-1 individual (5). There is an admixture signal between Inuit and Athabascans and some northern Amerindians (yellow line); however, the gene flow direction is unresolved due to the complexity of the admixture events (28). Additionally, we see a weak signal related to Australo-Melanesians in some Native Americans, which may have been mediated through East Asians and Aleutian Islanders (yellow arrows). Also shown is the Mal’ta gene flow into Native American ancestors some 23 KYA (yellow arrow) (4). It is currently not possible for us to ascertain the exact geographical locations of the depicted events; hence, the positioning of the arrows should not be considered a reflection of these. B. Admixture plot created on the basis of *TreeMix* results (fig. S5) shows that all Native Americans form a clade, separate from the Inuit, with gene flow between some Native Americans and the North American Arctic. The number of genome-sequenced individuals included in the analysis is shown in brackets.

**Fig. 2. Divergence estimates between Native Americans and Siberian Koryak**
(A) The demographic model used allows for continuous gene flow between populations 1 and 2, starting from the time *T_DIV* of divergence and ending at *T_M*. The backward probability of migration per individual per generation is denoted by m. The bottleneck at *T_B* captures the out-of-Africa event. (B) The red and black solid curves depict empirical distributions of IBS tracts shared between Karitiana-Koryak and Athabascan-Koryak, respectively. The orange, pink, dashed blue and dashed green curves depict IBS tracts shared between the two population pairs, simulated under two demographic models based on results from *diCal2.0*. Overall, for Karitiana-Koryak and Athabascan-Koryak, the migration scenarios (orange and pink, respectively) match the empirical curves (red and black, respectively) better than the clean split scenarios (dashed blue and dashed green, respectively), with more long IBS tracts showing evidence of recent common ancestry between Koryaks and Native Americans. (C and D) Relative cross coalescence rates (CCR) for the Karitiana-Koryak and Athabascan-Koryak divergence (red), respectively, including data simulated under the two demographic models in panel B. In both cases, the model with gene flow (orange) fits the data (red) better than the clean split model (blue). The migration model explains a broader CCR tail in the case of Karitiana-Koryak and the relatively late onset of the CCR decay for Athabascan-Koryak.

**Fig. 3. Testing migrations into the Americas using a climate-informed model**
Estimates of difference in genetic divergence between Amerindians (from southern North America and Central and South America) or Koryak versus Athabascan and Greenlandic Inuit and the ancient Saqqaq and Anzick-1 genomes (black vertical lines), compared to posterior probability distribution predicted from a climate-informed spatial genetic model reconstructing a single wave into the Americas (curves, the colored part represents the 95% credibility interval). ΔT for population X is defined as T(X,Koryak)-T(X,Central and South Amerindians) (28). Both Anzick-1 and the Athabascans were part of the same wave into the Americas to which other Amerindian populations from southern North America and Central and South America belonged, while the Inuit and Saqqaq are the descendants of different waves (observed values outside the 95% credibility interval).

**Fig. 4. Diversification within the Americas**
SNP chip genotype data-based outgroup f₃ statistics (47) of the form f₃(X, Ancient; Yoruba) were used to estimate the shared ancestry between ancient samples from the Americas and a large panel of worldwide present-day populations (X), including Athabascan and Amerindian groups from North America (table S3), some of which were masked for non-Native ancestry prior to the analysis (28). The outgroup f₃ statistics are depicted as heat maps with the sampling location of the ancient sample marked by the dotted lines, and corresponding ranked plots with error bars are shown in fig. S14. BP refers to time before present. We find the Anzick-1 sample to share most ancestry with the ‘southern’ branch of Native Americans when using multiple northern Native Americans sequenced in this study, consistent with (5). The seven Holocene aged samples share most ancestry with Native Americans, with a general tendency to be genetically closer to present-day Native American populations from the same geographical region.

**Fig. 5. The Paleoamerican model**
(A) Principal Component Analysis plot of 19 ancient samples combined with a worldwide reference panel, including 1,823 individuals from (6). Our samples plot exclusively with American samples. For plots with other reference panels consisting of Native American populations, see fig. S32. (B) Population structure in the ancient Pericú, Mexican mummy and Fuego-Patagonian individuals from this study. Ancestry proportions are shown when assuming six ancestral populations (K = 6). The top bar shows the ancestry proportions of the 19 ancient individuals, Anzick-1 (5), and two present-day Native American genomes from this study (Huichol and Aymara). The plot at the bottom illustrates the ancestry proportions for 1,823 individuals from (6). Our samples show primarily Native American (ivory, >92%) and Siberian (red, ca. 5%) ancestry. For the plot with K =13, see fig. S33.

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References

1. Dillehay TD. The late Pleistocene cultures of South America. Evol. Anthropol. 1999;7:206–216. doi:10.1002/(SICI)1520-6505(1999)7:6<206::AID-EVAN5>3.0.CO;2-G. - DOI
1. Jenkins DL, Davis LG, Stafford TW, Jr., Campos PF, Hockett B, Jones GT, Cummings LS, Yost C, Connolly TJ, Yohe RM, 2nd, Gibbons SC, Raghavan M, Rasmussen M, Paijmans JL, Hofreiter M, Kemp BM, Barta JL, Monroe C, Gilbert MT, Willerslev E. Clovis age Western Stemmed projectile points and human coprolites at the Paisley Caves. Science. 2012;337:223–228. - PubMed
1. Meltzer DJ. First Peoples in a New World: Colonizing Ice Age America. University of California Press; Berkeley: 2009.
1. Raghavan M, Skoglund P, Graf KE, Metspalu M, Albrechtsen A, Moltke I, Rasmussen S, Stafford TW, Jr., Orlando L, Metspalu E, Karmin M, Tambets K, Rootsi S, Mägi R, Campos PF, Balanovska E, Balanovsky O, Khusnutdinova E, Litvinov S, Osipova LP, Fedorova SA, Voevoda MI, DeGiorgio M, Sicheritz-Ponten T, Brunak S, Demeshchenko S, Kivisild T, Villems R, Nielsen R, Jakobsson M, Willerslev E. Upper Palaeolithic Siberian genome reveals dual ancestry of Native Americans. Nature. 2014;505:87–91. doi: 10.1038/nature12736. - DOI - PMC - PubMed
1. Rasmussen M, Anzick SL, Waters MR, Skoglund P, DeGiorgio M, Stafford TW, Jr., Rasmussen S, Moltke I, Albrechtsen A, Doyle SM, Poznik GD, Gudmundsdottir V, Yadav R, Malaspinas A-S, White SS, 5th, Allentoft ME, Cornejo OE, Tambets K, Eriksson A, Heintzman PD, Karmin M, Korneliussen TS, Meltzer DJ, Pierre TL, Stenderup J, Saag L, Warmuth VM, Lopes MC, Malhi RS, Brunak S, Sicheritz-Ponten T, Barnes I, Collins M, Orlando L, Balloux F, Manica A, Gupta R, Metspalu M, Bustamante CD, Jakobsson M, Nielsen R, Willerslev E. The genome of a Late Pleistocene human from a Clovis burial site in western Montana. Nature. 2014;506:225–229. doi: 10.1038/nature13025. - DOI - PMC - PubMed

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[1] Dillehay TD. The late Pleistocene cultures of South America. Evol. Anthropol. 1999;7:206–216. doi:10.1002/(SICI)1520-6505(1999)7:6<206::AID-EVAN5>3.0.CO;2-G. - DOI

[2] Dillehay TD. The late Pleistocene cultures of South America. Evol. Anthropol. 1999;7:206–216. doi:10.1002/(SICI)1520-6505(1999)7:6<206::AID-EVAN5>3.0.CO;2-G. - DOI

[3] Jenkins DL, Davis LG, Stafford TW, Jr., Campos PF, Hockett B, Jones GT, Cummings LS, Yost C, Connolly TJ, Yohe RM, 2nd, Gibbons SC, Raghavan M, Rasmussen M, Paijmans JL, Hofreiter M, Kemp BM, Barta JL, Monroe C, Gilbert MT, Willerslev E. Clovis age Western Stemmed projectile points and human coprolites at the Paisley Caves. Science. 2012;337:223–228. - PubMed

[4] Jenkins DL, Davis LG, Stafford TW, Jr., Campos PF, Hockett B, Jones GT, Cummings LS, Yost C, Connolly TJ, Yohe RM, 2nd, Gibbons SC, Raghavan M, Rasmussen M, Paijmans JL, Hofreiter M, Kemp BM, Barta JL, Monroe C, Gilbert MT, Willerslev E. Clovis age Western Stemmed projectile points and human coprolites at the Paisley Caves. Science. 2012;337:223–228. - PubMed

[5] Meltzer DJ. First Peoples in a New World: Colonizing Ice Age America. University of California Press; Berkeley: 2009.

[6] Meltzer DJ. First Peoples in a New World: Colonizing Ice Age America. University of California Press; Berkeley: 2009.

[7] Raghavan M, Skoglund P, Graf KE, Metspalu M, Albrechtsen A, Moltke I, Rasmussen S, Stafford TW, Jr., Orlando L, Metspalu E, Karmin M, Tambets K, Rootsi S, Mägi R, Campos PF, Balanovska E, Balanovsky O, Khusnutdinova E, Litvinov S, Osipova LP, Fedorova SA, Voevoda MI, DeGiorgio M, Sicheritz-Ponten T, Brunak S, Demeshchenko S, Kivisild T, Villems R, Nielsen R, Jakobsson M, Willerslev E. Upper Palaeolithic Siberian genome reveals dual ancestry of Native Americans. Nature. 2014;505:87–91. doi: 10.1038/nature12736. - DOI - PMC - PubMed

[8] Raghavan M, Skoglund P, Graf KE, Metspalu M, Albrechtsen A, Moltke I, Rasmussen S, Stafford TW, Jr., Orlando L, Metspalu E, Karmin M, Tambets K, Rootsi S, Mägi R, Campos PF, Balanovska E, Balanovsky O, Khusnutdinova E, Litvinov S, Osipova LP, Fedorova SA, Voevoda MI, DeGiorgio M, Sicheritz-Ponten T, Brunak S, Demeshchenko S, Kivisild T, Villems R, Nielsen R, Jakobsson M, Willerslev E. Upper Palaeolithic Siberian genome reveals dual ancestry of Native Americans. Nature. 2014;505:87–91. doi: 10.1038/nature12736. - DOI - PMC - PubMed

[9] Rasmussen M, Anzick SL, Waters MR, Skoglund P, DeGiorgio M, Stafford TW, Jr., Rasmussen S, Moltke I, Albrechtsen A, Doyle SM, Poznik GD, Gudmundsdottir V, Yadav R, Malaspinas A-S, White SS, 5th, Allentoft ME, Cornejo OE, Tambets K, Eriksson A, Heintzman PD, Karmin M, Korneliussen TS, Meltzer DJ, Pierre TL, Stenderup J, Saag L, Warmuth VM, Lopes MC, Malhi RS, Brunak S, Sicheritz-Ponten T, Barnes I, Collins M, Orlando L, Balloux F, Manica A, Gupta R, Metspalu M, Bustamante CD, Jakobsson M, Nielsen R, Willerslev E. The genome of a Late Pleistocene human from a Clovis burial site in western Montana. Nature. 2014;506:225–229. doi: 10.1038/nature13025. - DOI - PMC - PubMed

[10] Rasmussen M, Anzick SL, Waters MR, Skoglund P, DeGiorgio M, Stafford TW, Jr., Rasmussen S, Moltke I, Albrechtsen A, Doyle SM, Poznik GD, Gudmundsdottir V, Yadav R, Malaspinas A-S, White SS, 5th, Allentoft ME, Cornejo OE, Tambets K, Eriksson A, Heintzman PD, Karmin M, Korneliussen TS, Meltzer DJ, Pierre TL, Stenderup J, Saag L, Warmuth VM, Lopes MC, Malhi RS, Brunak S, Sicheritz-Ponten T, Barnes I, Collins M, Orlando L, Balloux F, Manica A, Gupta R, Metspalu M, Bustamante CD, Jakobsson M, Nielsen R, Willerslev E. The genome of a Late Pleistocene human from a Clovis burial site in western Montana. Nature. 2014;506:225–229. doi: 10.1038/nature13025. - DOI - PMC - PubMed

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

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

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