title: Upper Palaeolithic Siberian genome reveals dual ancestry of Native Americans.
abstract: The origins of the First Americans remain contentious. Although Native Americans seem to be genetically most closely related to east Asians, there is no consensus with regard to which specific Old World populations they are closest to. Here we sequence the draft genome of an approximately 24,000-year-old individual (MA-1), from Mal'ta in south-central Siberia, to an average depth of 1×. To our knowledge this is the oldest anatomically modern human genome reported to date. The MA-1 mitochondrial genome belongs to haplogroup U, which has also been found at high frequency among Upper Palaeolithic and Mesolithic European hunter-gatherers, and the Y chromosome of MA-1 is basal to modern-day western Eurasians and near the root of most Native American lineages. Similarly, we find autosomal evidence that MA-1 is basal to modern-day western Eurasians and genetically closely related to modern-day Native Americans, with no close affinity to east Asians. This suggests that populations related to contemporary western Eurasians had a more north-easterly distribution 24,000 years ago than commonly thought. Furthermore, we estimate that 14 to 38% of Native American ancestry may originate through gene flow from this ancient population. This is likely to have occurred after the divergence of Native American ancestors from east Asian ancestors, but before the diversification of Native American populations in the New World. Gene flow from the MA-1 lineage into Native American ancestors could explain why several crania from the First Americans have been reported as bearing morphological characteristics that do not resemble those of east Asians. Sequencing of another south-central Siberian, Afontova Gora-2 dating to approximately 17,000 years ago, revealed similar autosomal genetic signatures as MA-1, suggesting that the region was continuously occupied by humans throughout the Last Glacial Maximum. Our findings reveal that western Eurasian genetic signatures in modern-day Native Americans derive not only from post-Columbian admixture, as commonly thought, but also from a mixed ancestry of the First Americans.
authors.affiliation: 1] Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark [2].
authors.forename: Maanasa
authors.initials: M
authors.lastname: Raghavan
authors.affiliation: 1] Department of Evolutionary Biology, Uppsala University, Norbyvägen 18D, Uppsala 752 36, Sweden [2].
authors.forename: Pontus
authors.initials: P
authors.lastname: Skoglund
authors.affiliation: Center for the Study of the First Americans, Texas A&M University, TAMU-4352, College Station, Texas 77845-4352, USA.
authors.forename: Kelly E
authors.initials: KE
authors.lastname: Graf
authors.affiliation: 1] Estonian Biocentre, Evolutionary Biology group, Tartu 51010, Estonia [2] Department of Integrative Biology, University of California, Berkeley, California 94720, USA [3] Department of Evolutionary Biology, University of Tartu, Tartu 51010, Estonia.
authors.forename: Mait
authors.initials: M
authors.lastname: Metspalu
authors.affiliation: The Bioinformatics Centre, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, Copenhagen 2200, Denmark.
authors.forename: Anders
authors.initials: A
authors.lastname: Albrechtsen
authors.affiliation: 1] The Bioinformatics Centre, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, Copenhagen 2200, Denmark [2] Department of Human Genetics, The University of Chicago, Chicago, Illinois 60637, USA.
authors.forename: Ida
authors.initials: I
authors.lastname: Moltke
authors.affiliation: Center for Biological Sequence Analysis, Technical University of Denmark, Kongens Lyngby 2800, Denmark.
authors.forename: Simon
authors.initials: S
authors.lastname: Rasmussen
authors.affiliation: 1] Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark [2] AMS 14C Dating Centre, Department of Physics and Astronomy, University of Aarhus, Ny Munkegade 120, Aarhus DK-8000, Denmark.
authors.forename: Thomas W
authors.initials: TW
authors.lastname: Stafford
authors.affiliation: Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark.
authors.forename: Ludovic
authors.initials: L
authors.lastname: Orlando
authors.affiliation: Department of Evolutionary Biology, University of Tartu, Tartu 51010, Estonia.
authors.forename: Ene
authors.initials: E
authors.lastname: Metspalu
authors.affiliation: 1] Estonian Biocentre, Evolutionary Biology group, Tartu 51010, Estonia [2] Department of Evolutionary Biology, University of Tartu, Tartu 51010, Estonia.
authors.forename: Monika
authors.initials: M
authors.lastname: Karmin
authors.affiliation: Estonian Biocentre, Evolutionary Biology group, Tartu 51010, Estonia.
authors.forename: Kristiina
authors.initials: K
authors.lastname: Tambets
authors.affiliation: Estonian Biocentre, Evolutionary Biology group, Tartu 51010, Estonia.
authors.forename: Siiri
authors.initials: S
authors.lastname: Rootsi
authors.affiliation: Estonian Genome Center, University of Tartu, Tartu 51010, Estonia.
authors.forename: Reedik
authors.initials: R
authors.lastname: Mägi
authors.affiliation: Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark.
authors.forename: Paula F
authors.initials: PF
authors.lastname: Campos
authors.affiliation: Research Centre for Medical Genetics, Russian Academy of Medical Sciences, Moskvorechie Street 1, Moscow 115479, Russia.
authors.forename: Elena
authors.initials: E
authors.lastname: Balanovska
authors.affiliation: 1] Research Centre for Medical Genetics, Russian Academy of Medical Sciences, Moskvorechie Street 1, Moscow 115479, Russia [2] Vavilov Institute of General Genetics, Russian Academy of Sciences, Gubkina Street 3, Moscow 119991, Russia.
authors.forename: Oleg
authors.initials: O
authors.lastname: Balanovsky
authors.affiliation: 1] Institute of Biochemistry and Genetics, Ufa Scientific Centre, Russian Academy of Sciences, Ufa, Bashkorostan 450054, Russia [2] Biology Department, Bashkir State University, Ufa, Bashkorostan 450074, Russia.
authors.forename: Elza
authors.initials: E
authors.lastname: Khusnutdinova
authors.affiliation: 1] Estonian Biocentre, Evolutionary Biology group, Tartu 51010, Estonia [2] Institute of Biochemistry and Genetics, Ufa Scientific Centre, Russian Academy of Sciences, Ufa, Bashkorostan 450054, Russia.
authors.forename: Sergey
authors.initials: S
authors.lastname: Litvinov
authors.affiliation: The Institute of Cytology and Genetics, Center for Brain Neurobiology and Neurogenetics, Siberian Branch of the Russian Academy of Sciences, Lavrentyeva Avenue, Novosibirsk 630090, Russia.
authors.forename: Ludmila P
authors.initials: LP
authors.lastname: Osipova
authors.affiliation: Department of Molecular Genetics, Yakut Research Center of Complex Medical Problems, Russian Academy of Medical Sciences and North-Eastern Federal University, Yakutsk, Sakha (Yakutia) 677010, Russia.
authors.forename: Sardana A
authors.initials: SA
authors.lastname: Fedorova
authors.affiliation: 1] The Institute of Cytology and Genetics, Center for Brain Neurobiology and Neurogenetics, Siberian Branch of the Russian Academy of Sciences, Lavrentyeva Avenue, Novosibirsk 630090, Russia [2] Institute of Internal Medicine, Siberian Branch of the Russian Academy of Medical Sciences, Borisa Bogatkova 175/1, Novosibirsk 630089, Russia.
authors.forename: Mikhail I
authors.initials: MI
authors.lastname: Voevoda
authors.affiliation: Department of Integrative Biology, University of California, Berkeley, California 94720, USA.
authors.forename: Michael
authors.initials: M
authors.lastname: DeGiorgio
authors.affiliation: 1] Center for Biological Sequence Analysis, Technical University of Denmark, Kongens Lyngby 2800, Denmark [2] Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby 2800, Denmark.
authors.forename: Thomas
authors.initials: T
authors.lastname: Sicheritz-Ponten
authors.affiliation: 1] Center for Biological Sequence Analysis, Technical University of Denmark, Kongens Lyngby 2800, Denmark [2] Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby 2800, Denmark.
authors.forename: Søren
authors.initials: S
authors.lastname: Brunak
authors.affiliation: The State Hermitage Museum, 2, Dvortsovaya Ploshchad, St. Petersberg 190000, Russia.
authors.forename: Svetlana
authors.initials: S
authors.lastname: Demeshchenko
authors.affiliation: 1] Estonian Biocentre, Evolutionary Biology group, Tartu 51010, Estonia [2] Department of Biological Anthropology, University of Cambridge, Cambridge CB2 1QH, UK.
authors.forename: Toomas
authors.initials: T
authors.lastname: Kivisild
authors.affiliation: 1] Estonian Biocentre, Evolutionary Biology group, Tartu 51010, Estonia [2] Department of Evolutionary Biology, University of Tartu, Tartu 51010, Estonia [3] Estonian Academy of Sciences, Tallinn 10130, Estonia.
authors.forename: Richard
authors.initials: R
authors.lastname: Villems
authors.affiliation: Department of Integrative Biology, University of California, Berkeley, California 94720, USA.
authors.forename: Rasmus
authors.initials: R
authors.lastname: Nielsen
authors.affiliation: 1] Department of Evolutionary Biology, Uppsala University, Norbyvägen 18D, Uppsala 752 36, Sweden [2] Science for Life Laboratory, Uppsala University, Norbyvägen 18D, 752 36 Uppsala, Sweden.
authors.forename: Mattias
authors.initials: M
authors.lastname: Jakobsson
authors.affiliation: Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark.
authors.forename: Eske
authors.initials: E
authors.lastname: Willerslev
mesh_terms: D000818:Animals; D001208:Asia / Q000208:ethnology; D044466:Asian People / Q000235:genetics*; D041322:Chromosomes, Human, Y / Q000235:genetics; D004272:DNA, Mitochondrial / Q000235:genetics; D004641:Emigration and Immigration; D051456:Gene Flow / Q000235:genetics; D015894:Genome, Human / Q000235:genetics*; D054629:Genome, Mitochondrial / Q000235:genetics; D006239:Haplotypes / Q000235:genetics; D006801:Humans; D007198:Indians, North American / Q000145:classification / Q000208:ethnology* / Q000235:genetics*; D008297:Male; D010802:Phylogeny; D058974:Phylogeography; D012800:Siberia / Q000208:ethnology; D012863:Skeleton; D044465:White People / Q000235:genetics*
chemical_list: D004272:DNA, Mitochondrial