The genome of a Late Pleistocene human from a Clovis burial site in western Montana

Handle URI:
http://hdl.handle.net/10754/563390
Title:
The genome of a Late Pleistocene human from a Clovis burial site in western Montana
Authors:
Rasmussen, Morten Arendt Rendt; Anzick, Sarah L.; Waters, Michael R.; Skoglund, Pontus; Degiorgio, Michael; Stafford, Thomas W Jr; Rasmussen, Simon B.; Moltke, Ida; Albrechtsen, Anders; Doyle, Shane M.; Poznik, G. David; Gudmundsdottir, Valborg; Yadav, Rachita; Malaspinas, Anna Sapfo; Samuel Stockton White, V.; Allentoft, Morten Erik; Cornejo, Omar Eduardo; Tambets, Kristiina; Eriksson, Anders ( 0000-0003-3436-3726 ) ; Heintzman, Peter D.; Karmin, Monika; Korneliussen, Thorfinn Sand; Meltzer, David J.; Pierre, Tracey L.; Stenderup, Jesper T.; Saag, Lauri; Warmuth, Vera M.; Lopes, Margarida C.; Malhi, Ripan Singh; Brunak, Sören; Sicheritz-Pontén, Thomas; Barnes, Ian; Collins, Matthew J.; Orlando, Ludovic A A; Balloux, François; Manica, Andrea; Gupta, Ramneek; Metspalu, Mait; Bustamante, Carlos D.; Jakobsson, Mattias; Nielsen, Rasmus Wedel; Willerslev, Eske
Abstract:
Clovis, with its distinctive biface, blade and osseous technologies, is the oldest widespread archaeological complex defined in North America, dating from 11,100 to 10,700 14 C years before present (bp) (13,000 to 12,600 calendar years bp). Nearly 50 years of archaeological research point to the Clovis complex as having developed south of the North American ice sheets from an ancestral technology. However, both the origins and the genetic legacy of the people who manufactured Clovis tools remain under debate. It is generally believed that these people ultimately derived from Asia and were directly related to contemporary Native Americans. An alternative, Solutrean, hypothesis posits that the Clovis predecessors emigrated from southwestern Europe during the Last Glacial Maximum. Here we report the genome sequence of a male infant (Anzick-1) recovered from the Anzick burial site in western Montana. The human bones date to 10,705 ± 35 14 C years bp (approximately 12,707-12,556 calendar years bp) and were directly associated with Clovis tools. We sequenced the genome to an average depth of 14.4× and show that the gene flow from the Siberian Upper Palaeolithic Mal'ta population into Native American ancestors is also shared by the Anzick-1 individual and thus happened before 12,600 years bp. We also show that the Anzick-1 individual is more closely related to all indigenous American populations than to any other group. Our data are compatible with the hypothesis that Anzick-1 belonged to a population directly ancestral to many contemporary Native Americans. Finally, we find evidence of a deep divergence in Native American populations that predates the Anzick-1 individual. © 2014 Macmillan Publishers Limited. All rights reserved.
KAUST Department:
Integrative Systems Biology Lab; Bioscience Program
Publisher:
Springer Nature
Journal:
Nature
Issue Date:
12-Feb-2014
DOI:
10.1038/nature13025
Type:
Article
ISSN:
00280836
Sponsors:
We thank the Danish National High-throughput DNA Sequencing Centre for help with sequencing, B. Henn and J. Kidd for assistance with Human Genome Diversity Project data, J. Keene for help with illustrations, M. Li, P. L. F. Johnson and M. Stoneking for help with the mtDNA analysis, L. A. Lahren for input to the site description and for establishing contact with the Native American groups, and J. E. Morrow, S. Fiedel and E. Lorenzen for comments on the manuscript. GeoGenetics were supported by the Lundbeck Foundation and the Danish National Research Foundation (DNRF94). M. D. was supported by the US National Science Foundation (grant DBI-1103639). A.-S.M. was supported by the Swiss National Science foundation. G. D. P. was supported by National Science Foundation (NSF) graduate research fellowship DGE-1147470. M. M., M. K., K. T. and L. S. were supported by the European Regional Development Fund through the Centre of Excellence in Genomics to Estonian Biocentre and University of Tartu, Estonian Basic Research (grant SF0270177As08) and Estonian Science Foundation (grant 8973). Computations in Uppsala were performed on resources provided by SNIC-UPPMAX (project b2012063) and in Tartu using the High Performance Computing Centre of the University of Tartu. A. E., V. M. W., M. C. L., F. B. and A. M. were supported by the Biotechnology and Biological Sciences Research Council (grant P25032 and BB/H005854/1). We thank the North Star Archaeological Research Program, Center for the Study of the First Americans, Texas A&M University, E. Hill, and Stafford Research, Inc. for funding some of the project.
Appears in Collections:
Articles; Bioscience Program

Full metadata record

DC FieldValue Language
dc.contributor.authorRasmussen, Morten Arendt Rendten
dc.contributor.authorAnzick, Sarah L.en
dc.contributor.authorWaters, Michael R.en
dc.contributor.authorSkoglund, Pontusen
dc.contributor.authorDegiorgio, Michaelen
dc.contributor.authorStafford, Thomas W Jren
dc.contributor.authorRasmussen, Simon B.en
dc.contributor.authorMoltke, Idaen
dc.contributor.authorAlbrechtsen, Andersen
dc.contributor.authorDoyle, Shane M.en
dc.contributor.authorPoznik, G. Daviden
dc.contributor.authorGudmundsdottir, Valborgen
dc.contributor.authorYadav, Rachitaen
dc.contributor.authorMalaspinas, Anna Sapfoen
dc.contributor.authorSamuel Stockton White, V.en
dc.contributor.authorAllentoft, Morten Eriken
dc.contributor.authorCornejo, Omar Eduardoen
dc.contributor.authorTambets, Kristiinaen
dc.contributor.authorEriksson, Andersen
dc.contributor.authorHeintzman, Peter D.en
dc.contributor.authorKarmin, Monikaen
dc.contributor.authorKorneliussen, Thorfinn Sanden
dc.contributor.authorMeltzer, David J.en
dc.contributor.authorPierre, Tracey L.en
dc.contributor.authorStenderup, Jesper T.en
dc.contributor.authorSaag, Laurien
dc.contributor.authorWarmuth, Vera M.en
dc.contributor.authorLopes, Margarida C.en
dc.contributor.authorMalhi, Ripan Singhen
dc.contributor.authorBrunak, Sörenen
dc.contributor.authorSicheritz-Pontén, Thomasen
dc.contributor.authorBarnes, Ianen
dc.contributor.authorCollins, Matthew J.en
dc.contributor.authorOrlando, Ludovic A Aen
dc.contributor.authorBalloux, Françoisen
dc.contributor.authorManica, Andreaen
dc.contributor.authorGupta, Ramneeken
dc.contributor.authorMetspalu, Maiten
dc.contributor.authorBustamante, Carlos D.en
dc.contributor.authorJakobsson, Mattiasen
dc.contributor.authorNielsen, Rasmus Wedelen
dc.contributor.authorWillerslev, Eskeen
dc.date.accessioned2015-08-03T11:47:23Zen
dc.date.available2015-08-03T11:47:23Zen
dc.date.issued2014-02-12en
dc.identifier.issn00280836en
dc.identifier.doi10.1038/nature13025en
dc.identifier.urihttp://hdl.handle.net/10754/563390en
dc.description.abstractClovis, with its distinctive biface, blade and osseous technologies, is the oldest widespread archaeological complex defined in North America, dating from 11,100 to 10,700 14 C years before present (bp) (13,000 to 12,600 calendar years bp). Nearly 50 years of archaeological research point to the Clovis complex as having developed south of the North American ice sheets from an ancestral technology. However, both the origins and the genetic legacy of the people who manufactured Clovis tools remain under debate. It is generally believed that these people ultimately derived from Asia and were directly related to contemporary Native Americans. An alternative, Solutrean, hypothesis posits that the Clovis predecessors emigrated from southwestern Europe during the Last Glacial Maximum. Here we report the genome sequence of a male infant (Anzick-1) recovered from the Anzick burial site in western Montana. The human bones date to 10,705 ± 35 14 C years bp (approximately 12,707-12,556 calendar years bp) and were directly associated with Clovis tools. We sequenced the genome to an average depth of 14.4× and show that the gene flow from the Siberian Upper Palaeolithic Mal'ta population into Native American ancestors is also shared by the Anzick-1 individual and thus happened before 12,600 years bp. We also show that the Anzick-1 individual is more closely related to all indigenous American populations than to any other group. Our data are compatible with the hypothesis that Anzick-1 belonged to a population directly ancestral to many contemporary Native Americans. Finally, we find evidence of a deep divergence in Native American populations that predates the Anzick-1 individual. © 2014 Macmillan Publishers Limited. All rights reserved.en
dc.description.sponsorshipWe thank the Danish National High-throughput DNA Sequencing Centre for help with sequencing, B. Henn and J. Kidd for assistance with Human Genome Diversity Project data, J. Keene for help with illustrations, M. Li, P. L. F. Johnson and M. Stoneking for help with the mtDNA analysis, L. A. Lahren for input to the site description and for establishing contact with the Native American groups, and J. E. Morrow, S. Fiedel and E. Lorenzen for comments on the manuscript. GeoGenetics were supported by the Lundbeck Foundation and the Danish National Research Foundation (DNRF94). M. D. was supported by the US National Science Foundation (grant DBI-1103639). A.-S.M. was supported by the Swiss National Science foundation. G. D. P. was supported by National Science Foundation (NSF) graduate research fellowship DGE-1147470. M. M., M. K., K. T. and L. S. were supported by the European Regional Development Fund through the Centre of Excellence in Genomics to Estonian Biocentre and University of Tartu, Estonian Basic Research (grant SF0270177As08) and Estonian Science Foundation (grant 8973). Computations in Uppsala were performed on resources provided by SNIC-UPPMAX (project b2012063) and in Tartu using the High Performance Computing Centre of the University of Tartu. A. E., V. M. W., M. C. L., F. B. and A. M. were supported by the Biotechnology and Biological Sciences Research Council (grant P25032 and BB/H005854/1). We thank the North Star Archaeological Research Program, Center for the Study of the First Americans, Texas A&M University, E. Hill, and Stafford Research, Inc. for funding some of the project.en
dc.publisherSpringer Natureen
dc.titleThe genome of a Late Pleistocene human from a Clovis burial site in western Montanaen
dc.typeArticleen
dc.contributor.departmentIntegrative Systems Biology Laben
dc.contributor.departmentBioscience Programen
dc.identifier.journalNatureen
dc.contributor.institutionCentre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, DK-1350 Copenhagen K, Denmarken
dc.contributor.institutionAnzick Family, 31 Old Clyde Park Road, Livingston, MT 59047, United Statesen
dc.contributor.institutionCenter for the Study of the First Americans, Departments of Anthropology and Geography, Texas A and M University, College Station, TX 77843-4352, United Statesen
dc.contributor.institutionDepartment of Evolutionary Biology, Uppsala University, Norbyvägen 18D, 752 36 Uppsala, Swedenen
dc.contributor.institutionDepartment of Integrative Biology, University of California, Berkeley, 4134 Valley Life Sciences Building, Berkeley, CA 94720, United Statesen
dc.contributor.institutionAMS 14C Dating Centre, Department of Physics and Astronomy, University of Aarhus, Ny Munkegade 120, DK-8000 Aarhus C, Denmarken
dc.contributor.institutionCenter for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Kemitorvet 208, Kgs. Lyngby DK-2800, Denmarken
dc.contributor.institutionBioinformatics Centre, Department of Biology, University of Copenhagen, Ole Maaloes Vej 5, DK-2200 Copenhagen N, Denmarken
dc.contributor.institutionDepartment of Human Genetics, University of Chicago, 920 E. 58th Street, Chicago, IL 60637, United Statesen
dc.contributor.institutionEducation Department, Montana State University, Box 5103, Bozeman, MT 59717, United Statesen
dc.contributor.institutionProgram in Biomedical Informatics, Department of Statistics, Stanford University, Stanford, CA 94305, United Statesen
dc.contributor.institutionAnthropology Department, PhD Program, University of Montana, 4100 Mullan Road, no. 217, Missoula, MT 59808, United Statesen
dc.contributor.institutionSchool of Biological Sciences, Washington State University, Eastlick Hall 395, PO Box 644236, Pullman, WA 99164, United Statesen
dc.contributor.institutionDepartment of Evolutionary Biology, Estonian Biocentre, University of Tartu, Riia 23b, 51010 Tartu, Estoniaen
dc.contributor.institutionDepartment of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, United Kingdomen
dc.contributor.institutionSchool of Biological Sciences, Royal Holloway, University of London, Egham, Surrey TW20 0EX, United Kingdomen
dc.contributor.institutionDepartment of Anthropology, Southern Methodist University, Dallas, TX 75275, United Statesen
dc.contributor.institutionDepartment of Genetics, Evolution and Environment, University College London, Gower Street, London WC1E 6BT, United Kingdomen
dc.contributor.institutionDepartment of Anthropology, Institute for Genomic Biology, University of Illinois Urbana-Champaign, 607 Matthews Avenue, Urbana, IL 61801, United Statesen
dc.contributor.institutionBioArCh, Departments of Biology, Archaeology and Chemistry, University of York, Wentworth Way, York YO10 5DD, United Kingdomen
dc.contributor.institutionMRC Centre for Outbreak, Analysis and Modelling, Department of Infectious Disease Epidemiology, Imperial College London, London W2 1PG, United Kingdomen
dc.contributor.institutionDepartment of Genetics, School of Medicine, Stanford University, Stanford, CA 94305, United Statesen
dc.contributor.institutionCenter for Evolutionary and Human Genomics, Stanford University, Littlefield Center, Stanford, CA 94305, United Statesen
dc.contributor.institutionScience for Life Laboratory, Uppsala University, Norbyvägen 18D, 752 36 Uppsala, Swedenen
dc.contributor.institutionEarth Sciences Department, Natural History Museum, Cromwell Road, London SW7 5BD, United Kingdomen
dc.contributor.institutionDepartment of Biology, Pennsylvania State University, 502 Wartik Laboratory, University Park, PA 16802, United Statesen
kaust.authorEriksson, Andersen
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