title: The genome of a Late Pleistocene human from a Clovis burial site in western Montana.
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.
authors: 1] Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, DK-1350 Copenhagen K, Denmark [2].
authors: Morten
authors: M
authors: Rasmussen
authors: 1] Anzick Family, 31 Old Clyde Park Road, Livingston, Montana 59047, USA [2].
authors: Sarah L
authors: SL
authors: Anzick
authors: Center for the Study of the First Americans, Departments of Anthropology and Geography, Texas A&M University, 4352 TAMU, College Station, Texas 77843-4352, USA.
authors: Michael R
authors: MR
authors: Waters
authors: Department of Evolutionary Biology, Uppsala University, Norbyvägen 18D, 752 36 Uppsala, Sweden.
authors: Pontus
authors: P
authors: Skoglund
authors: 1] Department of Integrative Biology, University of California, Berkeley, 4134 Valley Life Sciences Building, Berkeley, California 94720, USA [2] Earth Sciences Department, Natural History Museum, Cromwell Road, London SW7 5BD, UK (I.B.); Department of Biology, Pennsylvania State University, 502 Wartik Laboratory, University Park, Pennsylvania 16802, USA (M.D.).
authors: Michael
authors: M
authors: DeGiorgio
authors: 1] Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, DK-1350 Copenhagen K, Denmark [2] AMS 14C Dating Centre, Department of Physics & Astronomy, University of Aarhus, Ny Munkegade 120, DK-8000 Aarhus C, Denmark.
authors: Thomas W
authors: TW
authors: Stafford
authors: Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Kemitorvet 208, Kgs. Lyngby DK-2800, Denmark.
authors: Simon
authors: S
authors: Rasmussen
authors: 1] The Bioinformatics Centre, Department of Biology, University of Copenhagen, Ole Maaloes Vej 5, DK-2200 Copenhagen N, Denmark [2] Department of Human Genetics, University of Chicago, 920 E. 58th Street, CLSC 4th floor, Chicago, Illinois 60637, USA.
authors: Ida
authors: I
authors: Moltke
authors: The Bioinformatics Centre, Department of Biology, University of Copenhagen, Ole Maaloes Vej 5, DK-2200 Copenhagen N, Denmark.
authors: Anders
authors: A
authors: Albrechtsen
authors: Education Department, Montana State University, Box 5103, Bozeman, Montana 59717, USA.
authors: Shane M
authors: SM
authors: Doyle
authors: Program in Biomedical Informatics and Department of Statistics, Stanford University, Stanford, California 94305, USA.
authors: G David
authors: GD
authors: Poznik
authors: Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Kemitorvet 208, Kgs. Lyngby DK-2800, Denmark.
authors: Valborg
authors: V
authors: Gudmundsdottir
authors: Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Kemitorvet 208, Kgs. Lyngby DK-2800, Denmark.
authors: Rachita
authors: R
authors: Yadav
authors: Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, DK-1350 Copenhagen K, Denmark.
authors: Anna-Sapfo
authors: AS
authors: Malaspinas
authors: Anthropology Department, PhD Program, University of Montana, 4100 Mullan Road, no. 217, Missoula, Montana 59808, USA.
authors: Samuel Stockton
authors: SS
authors: White
authors: Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, DK-1350 Copenhagen K, Denmark.
authors: Morten E
authors: ME
authors: Allentoft
authors: School of Biological Sciences, Washington State University, PO Box 644236, Eastlick Hall 395, Pullman, Washington 99164, USA.
authors: Omar E
authors: OE
authors: Cornejo
authors: Department of Evolutionary Biology, Estonian Biocentre and University of Tartu, Riia 23b, 51010 Tartu, Estonia.
authors: Kristiina
authors: K
authors: Tambets
authors: 1] Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK [2] Integrative Systems Biology Laboratory, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Kingdom of Saudi Arabia.
authors: Anders
authors: A
authors: Eriksson
authors: School of Biological Sciences, Royal Holloway, University of London, Egham, Surrey TW20 0EX, UK.
authors: Peter D
authors: PD
authors: Heintzman
authors: Department of Evolutionary Biology, Estonian Biocentre and University of Tartu, Riia 23b, 51010 Tartu, Estonia.
authors: Monika
authors: M
authors: Karmin
authors: Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, DK-1350 Copenhagen K, Denmark.
authors: Thorfinn Sand
authors: TS
authors: Korneliussen
authors: Department of Anthropology, Southern Methodist University, Dallas, Texas 75275, USA.
authors: David J
authors: DJ
authors: Meltzer
authors: Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, DK-1350 Copenhagen K, Denmark.
authors: Tracey L
authors: TL
authors: Pierre
authors: Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, DK-1350 Copenhagen K, Denmark.
authors: Jesper
authors: J
authors: Stenderup
authors: Department of Evolutionary Biology, Estonian Biocentre and University of Tartu, Riia 23b, 51010 Tartu, Estonia.
authors: Lauri
authors: L
authors: Saag
authors: 1] Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK [2] Department of Genetics, Evolution and Environment, University College London, Gower Street, London WC1E 6BT, UK.
authors: Vera M
authors: VM
authors: Warmuth
authors: Department of Genetics, Evolution and Environment, University College London, Gower Street, London WC1E 6BT, UK.
authors: Margarida C
authors: MC
authors: Lopes
authors: Department of Anthropology and Institute for Genomic Biology, University of Illinois Urbana-Champaign, 209F Davenport Hall, 607 Matthews Avenue, Urbana, Illinois 61801, USA.
authors: Ripan S
authors: RS
authors: Malhi
authors: Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Kemitorvet 208, Kgs. Lyngby DK-2800, Denmark.
authors: Søren
authors: S
authors: Brunak
authors: Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Kemitorvet 208, Kgs. Lyngby DK-2800, Denmark.
authors: Thomas
authors: T
authors: Sicheritz-Ponten
authors: 1] School of Biological Sciences, Royal Holloway, University of London, Egham, Surrey TW20 0EX, UK [2] Earth Sciences Department, Natural History Museum, Cromwell Road, London SW7 5BD, UK (I.B.); Department of Biology, Pennsylvania State University, 502 Wartik Laboratory, University Park, Pennsylvania 16802, USA (M.D.).
authors: Ian
authors: I
authors: Barnes
authors: BioArCh, Departments of Biology, Archaeology and Chemistry, University of York, Wentworth Way, York YO10 5DD, UK.
authors: Matthew
authors: M
authors: Collins
authors: Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, DK-1350 Copenhagen K, Denmark.
authors: Ludovic
authors: L
authors: Orlando
authors: MRC Centre for Outbreak, Analysis and Modelling, Department of Infectious Disease Epidemiology, Imperial College London, Imperial College Faculty of Medicine, London W2 1PG, UK.
authors: Francois
authors: F
authors: Balloux
authors: Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK.
authors: Andrea
authors: A
authors: Manica
authors: Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Kemitorvet 208, Kgs. Lyngby DK-2800, Denmark.
authors: Ramneek
authors: R
authors: Gupta
authors: Department of Evolutionary Biology, Estonian Biocentre and University of Tartu, Riia 23b, 51010 Tartu, Estonia.
authors: Mait
authors: M
authors: Metspalu
authors: 1] Department of Genetics, School of Medicine, Stanford University, Littlefield Center, Stanford, California 94305, USA [2] Center for Evolutionary and Human Genomics, Stanford University, Littlefield Center, Stanford, California 94305, USA.
authors: Carlos D
authors: CD
authors: Bustamante
authors: 1] Department of Evolutionary Biology, Uppsala University, Norbyvägen 18D, 752 36 Uppsala, Sweden [2] Science for Life Laboratory, Uppsala University, Norbyvägen 18D, 752 36 Uppsala, Sweden.
authors: Mattias
authors: M
authors: Jakobsson
authors: Department of Integrative Biology, University of California, Berkeley, 4134 Valley Life Sciences Building, Berkeley, California 94720, USA.
authors: Rasmus
authors: R
authors: Nielsen
authors: Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, DK-1350 Copenhagen K, Denmark.
authors: Eske
authors: E
authors: Willerslev
mesh_terms: D001106:Archaeology; D001208:Asia / Q000208:ethnology; D001842:Bone and Bones; D002048:Burial; D041322:Chromosomes, Human, Y / Q000235:genetics; D004272:DNA, Mitochondrial / Q000235:genetics; D004641:Emigration and Immigration / Q000266:history; D005060:Europe / Q000208:ethnology; D051456:Gene Flow / Q000235:genetics; D015894:Genome, Human / Q000235:genetics*; D006239:Haplotypes / Q000235:genetics; D049690:History, Ancient; D006801:Humans; D007198:Indians, North American / Q000235:genetics*; D007223:Infant; D008297:Male; D008957:Models, Genetic; D008969:Molecular Sequence Data; D009009:Montana; D010802:Phylogeny; D011157:Population Dynamics; D055110:Radiometric Dating
chemical_list: D004272:DNA, Mitochondrial