Ancient human genome sequence of an extinct Palaeo-Eskimo

Morten Rasmussen, Yingrui Li, Stinus Lindgreen, Jakob Skou Pedersen, Anders Albrechtsen, Ida Moltke, Mait Metspalu, Ene Metspalu, Toomas Kivisild, Ramneek Gupta, Marcelo Bertalan, Kasper Nielsen, M. Thomas P. Gilbert, Yong Wang, Maanasa Raghavan, Paula F. Campos, Hanne Munkholm Kamp, Andrew S. Wilson, Andrew Gledhill, Silvana Tridico, Michael Bunce, Eline D. Lorenzen, Jonas Binladen, Xiaosen Guo, Jing Zhao, Xiuqing Zhang, Hao Zhang, Zhuo Li, Minfeng Chen, Ludovic Orlando, Karsten Kristiansen, Mads Bak, Niels Tommerup, Christian Bendixen, Tracey L. Pierre, Bjarne Grønnow, Morten Meldgaard, Claus Andreasen, Sardana A. Fedorova, Ludmila P. Osipova, Thomas F. G. Higham, Christopher Bronk Ramsey, Thomas v. O. Hansen, Finn C. Nielsen, Michael H. Crawford, Søren Brunak, Thomas Sicheritz-Pontén, Richard Villems, Rasmus Nielsen, Anders Krogh, Jun Wang () and Eske Willerslev ()
Additional contact information
Morten Rasmussen: Centre for GeoGenetics, University of Copenhagen, Universitetsparken 15, DK-2100 Copenhagen, Denmark
Yingrui Li: Sino-Danish Genomics Center, BGI-Shenzhen, Shenzhen 518083, China, and University of Copenhagen
Stinus Lindgreen: Centre for GeoGenetics, University of Copenhagen, Universitetsparken 15, DK-2100 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
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
Yong Wang: UC-Berkeley, 4098 VLSB, Berkeley, California 94720, USA
Maanasa Raghavan: Centre for GeoGenetics, University of Copenhagen, Universitetsparken 15, DK-2100 Copenhagen, Denmark
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
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
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
Jing Zhao: Sino-Danish Genomics Center, BGI-Shenzhen, Shenzhen 518083, China, and University of Copenhagen
Xiuqing Zhang: Sino-Danish Genomics Center, BGI-Shenzhen, Shenzhen 518083, China, and University of Copenhagen
Hao Zhang: Sino-Danish Genomics Center, BGI-Shenzhen, Shenzhen 518083, China, and University of Copenhagen
Zhuo Li: Sino-Danish Genomics Center, BGI-Shenzhen, Shenzhen 518083, China, and University of Copenhagen
Minfeng Chen: Sino-Danish Genomics Center, BGI-Shenzhen, Shenzhen 518083, China, and University of Copenhagen
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
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
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
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
Anders Krogh: Sino-Danish Genomics Center, BGI-Shenzhen, Shenzhen 518083, China, and University of Copenhagen
Jun Wang: Sino-Danish Genomics Center, BGI-Shenzhen, Shenzhen 518083, China, and University of Copenhagen
Eske Willerslev: Centre for GeoGenetics, University of Copenhagen, Universitetsparken 15, DK-2100 Copenhagen, Denmark

Nature, 2010, vol. 463, issue 7282, 757-762

Abstract: 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.

Date: 2010
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DOI: 10.1038/nature08835

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