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Ancient human genome sequence of an extinct Palaeo-Eskimo

Author

Listed:
  • Morten Rasmussen

    (Centre for GeoGenetics, University of Copenhagen, Universitetsparken 15, DK-2100 Copenhagen, Denmark
    Sino-Danish Genomics Center, BGI-Shenzhen, Shenzhen 518083, China, and University of Copenhagen)

  • Yingrui Li

    (Sino-Danish Genomics Center, BGI-Shenzhen, Shenzhen 518083, China, and University of Copenhagen
    BGI-Shenzhen)

  • Stinus Lindgreen

    (Centre for GeoGenetics, University of Copenhagen, Universitetsparken 15, DK-2100 Copenhagen, Denmark
    University of Copenhagen, Ole Maaloes Vej 5, DK-2200 Copenhagen, Denmark)

  • Jakob Skou Pedersen

    (University of Copenhagen, Ole Maaloes Vej 5, DK-2200 Copenhagen, Denmark)

  • Anders Albrechtsen

    (University of Copenhagen, Ole Maaloes Vej 5, DK-2200 Copenhagen, Denmark)

  • Ida Moltke

    (University of Copenhagen, Ole Maaloes Vej 5, DK-2200 Copenhagen, Denmark)

  • Mait Metspalu

    (Tartu University and Estonian Biocentre, 23 Riia Street, 510101 Tartu, Estonia)

  • Ene Metspalu

    (Tartu University and Estonian Biocentre, 23 Riia Street, 510101 Tartu, Estonia)

  • Toomas Kivisild

    (Tartu University and Estonian Biocentre, 23 Riia Street, 510101 Tartu, Estonia
    Leverhulme Centre for Human Evolutionary Studies, Henry Wellcome Building, Fitzwilliam Street, University of Cambridge)

  • Ramneek Gupta

    (Center for Biological Sequence Analysis, Technical University of Denmark)

  • Marcelo Bertalan

    (Center for Biological Sequence Analysis, Technical University of Denmark)

  • Kasper Nielsen

    (Center for Biological Sequence Analysis, Technical University of Denmark)

  • M. Thomas P. Gilbert

    (Centre for GeoGenetics, University of Copenhagen, Universitetsparken 15, DK-2100 Copenhagen, Denmark
    Sino-Danish Genomics Center, BGI-Shenzhen, Shenzhen 518083, China, and University of Copenhagen)

  • Yong Wang

    (UC-Berkeley, 4098 VLSB, Berkeley, California 94720, USA)

  • Maanasa Raghavan

    (Centre for GeoGenetics, University of Copenhagen, Universitetsparken 15, DK-2100 Copenhagen, Denmark
    Research Laboratory for Archaeology and the History of Art, Dyson Perrins Building, South Parks Road, Oxford OX1 3QY, UK)

  • Paula F. Campos

    (Centre for GeoGenetics, University of Copenhagen, Universitetsparken 15, DK-2100 Copenhagen, Denmark)

  • Hanne Munkholm Kamp

    (Centre for GeoGenetics, University of Copenhagen, Universitetsparken 15, DK-2100 Copenhagen, Denmark
    University of Copenhagen, Ole Maaloes Vej 5, DK-2200 Copenhagen, Denmark)

  • Andrew S. Wilson

    (School of Life Sciences, University of Bradford, West Yorkshire, Bradford BD7 1DP, UK)

  • Andrew Gledhill

    (School of Life Sciences, University of Bradford, West Yorkshire, Bradford BD7 1DP, UK)

  • Silvana Tridico

    (Biological Criminalistics, Australian Federal Police, 1 Unwin Place, Weston, ACT 2611, Australia
    Ancient DNA Laboratory, School of Biological Sciences and Biotechnology, Murdoch University)

  • Michael Bunce

    (Ancient DNA Laboratory, School of Biological Sciences and Biotechnology, Murdoch University)

  • Eline D. Lorenzen

    (Centre for GeoGenetics, University of Copenhagen, Universitetsparken 15, DK-2100 Copenhagen, Denmark)

  • Jonas Binladen

    (Centre for GeoGenetics, University of Copenhagen, Universitetsparken 15, DK-2100 Copenhagen, Denmark)

  • Xiaosen Guo

    (Sino-Danish Genomics Center, BGI-Shenzhen, Shenzhen 518083, China, and University of Copenhagen
    BGI-Shenzhen)

  • Jing Zhao

    (Sino-Danish Genomics Center, BGI-Shenzhen, Shenzhen 518083, China, and University of Copenhagen
    BGI-Shenzhen)

  • Xiuqing Zhang

    (Sino-Danish Genomics Center, BGI-Shenzhen, Shenzhen 518083, China, and University of Copenhagen
    BGI-Shenzhen)

  • Hao Zhang

    (Sino-Danish Genomics Center, BGI-Shenzhen, Shenzhen 518083, China, and University of Copenhagen
    BGI-Shenzhen)

  • Zhuo Li

    (Sino-Danish Genomics Center, BGI-Shenzhen, Shenzhen 518083, China, and University of Copenhagen
    BGI-Shenzhen)

  • Minfeng Chen

    (Sino-Danish Genomics Center, BGI-Shenzhen, Shenzhen 518083, China, and University of Copenhagen
    BGI-Shenzhen)

  • Ludovic Orlando

    (Paleogenetics and Molecular Evolution, Institut de Génomique Fonctionnelle de Lyon, Université de Lyon, Université Lyon 1, CNRS, INRA, Ecole Normale Supérieure de Lyon, 46 allée d’Italie, 69364 Lyon Cedex 07, France)

  • Karsten Kristiansen

    (Sino-Danish Genomics Center, BGI-Shenzhen, Shenzhen 518083, China, and University of Copenhagen
    BGI-Shenzhen
    University of Copenhagen, Ole Maaloes Vej 5, DK-2200 Copenhagen, Denmark)

  • Mads Bak

    (Wilhelm Johannsen Centre For Functional Genome Research, University of Copenhagen, The Panum Institute, Blegdamsvej 3A, DK-2200 Copenhagen, Denmark)

  • Niels Tommerup

    (Wilhelm Johannsen Centre For Functional Genome Research, University of Copenhagen, The Panum Institute, Blegdamsvej 3A, DK-2200 Copenhagen, Denmark)

  • Christian Bendixen

    (Aarhus University, Blichers Allé 20PO BOX 50, DK-8830 Tjele, Denmark)

  • Tracey L. Pierre

    (University of Cambridge)

  • Bjarne Grønnow

    (Ethnographic Collections, National Museum of Denmark, Frederiksholms Kanal 12, DK-1220 Copenhagen, Denmark)

  • Morten Meldgaard

    (Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, DK-1350 Copenhagen, Denmark)

  • Claus Andreasen

    (Greenland National Museum and Archives, PO Box 145, DK-3900 Nuuk, Greenland)

  • Sardana A. Fedorova

    (Tartu University and Estonian Biocentre, 23 Riia Street, 510101 Tartu, Estonia
    Yakut Research Centre, Russian Academy of Medical Sciences, 4 Sergelyahonskoe Shosse, Yakutsk 677019, Sakha, Russia)

  • Ludmila P. Osipova

    (The Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Lavrentyeva Ave. Novosibirsk 630090, Russia)

  • Thomas F. G. Higham

    (Research Laboratory for Archaeology and the History of Art, Dyson Perrins Building, South Parks Road, Oxford OX1 3QY, UK)

  • Christopher Bronk Ramsey

    (School of Life Sciences, University of Bradford, West Yorkshire, Bradford BD7 1DP, UK)

  • Thomas v. O. Hansen

    (Rigshospitalet, University of Copenhagen)

  • Finn C. Nielsen

    (Rigshospitalet, University of Copenhagen)

  • Michael H. Crawford

    (University of Kansas, Lawrence, Kansas 66045, USA)

  • Søren Brunak

    (Center for Biological Sequence Analysis, Technical University of Denmark
    Novo Nordisk Foundation Center for Protein Research, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3A, DK-2200 Copenhagen, Denmark)

  • Thomas Sicheritz-Pontén

    (Center for Biological Sequence Analysis, Technical University of Denmark)

  • Richard Villems

    (Tartu University and Estonian Biocentre, 23 Riia Street, 510101 Tartu, Estonia)

  • Rasmus Nielsen

    (University of Copenhagen, Ole Maaloes Vej 5, DK-2200 Copenhagen, Denmark
    UC-Berkeley, 4098 VLSB, Berkeley, California 94720, USA)

  • Anders Krogh

    (Sino-Danish Genomics Center, BGI-Shenzhen, Shenzhen 518083, China, and University of Copenhagen
    University of Copenhagen, Ole Maaloes Vej 5, DK-2200 Copenhagen, Denmark)

  • Jun Wang

    (Sino-Danish Genomics Center, BGI-Shenzhen, Shenzhen 518083, China, and University of Copenhagen
    BGI-Shenzhen
    University of Copenhagen, Ole Maaloes Vej 5, DK-2200 Copenhagen, Denmark)

  • Eske Willerslev

    (Centre for GeoGenetics, University of Copenhagen, Universitetsparken 15, DK-2100 Copenhagen, Denmark
    Sino-Danish Genomics Center, BGI-Shenzhen, Shenzhen 518083, China, and University of Copenhagen)

Abstract

We report here the genome sequence of an ancient human. Obtained from ∼4,000-year-old permafrost-preserved hair, the genome represents a male individual from the first known culture to settle in Greenland. Sequenced to an average depth of 20×, we recover 79% of the diploid genome, an amount close to the practical limit of current sequencing technologies. We identify 353,151 high-confidence single-nucleotide polymorphisms (SNPs), of which 6.8% have not been reported previously. We estimate raw read contamination to be no higher than 0.8%. We use functional SNP assessment to assign possible phenotypic characteristics of the individual that belonged to a culture whose location has yielded only trace human remains. We compare the high-confidence SNPs to those of contemporary populations to find the populations most closely related to the individual. This provides evidence for a migration from Siberia into the New World some 5,500 years ago, independent of that giving rise to the modern Native Americans and Inuit.

Suggested Citation

  • Morten Rasmussen & Yingrui Li & Stinus Lindgreen & Jakob Skou Pedersen & Anders Albrechtsen & Ida Moltke & Mait Metspalu & Ene Metspalu & Toomas Kivisild & Ramneek Gupta & Marcelo Bertalan & Kasper Ni, 2010. "Ancient human genome sequence of an extinct Palaeo-Eskimo," Nature, Nature, vol. 463(7282), pages 757-762, February.
    • Handle: RePEc:nat:nature:v:463:y:2010:i:7282:d:10.1038_nature08835
    DOI: 10.1038/nature08835
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    Cited by:

    1. Bárbara Sousa da Mota & Simone Rubinacci & Diana Ivette Cruz Dávalos & Carlos Eduardo G. Amorim & Martin Sikora & Niels N. Johannsen & Marzena H. Szmyt & Piotr Włodarczak & Anita Szczepanek & Marcin M, 2023. "Imputation of ancient human genomes," Nature Communications, Nature, vol. 14(1), pages 1-17, December.

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