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A genomic history of Aboriginal Australia

Malaspinas AS 1 , Westaway MC 2 , Muller C 1 , Sousa VC 3 , Lao O 4 , Alves I 3 Show all authors , Bergström A 5 , Athanasiadis G 6 , Cheng JY 6 , Crawford JE 7 , Heupink TH 2 , Macholdt E 8 , Peischl S 9 , Rasmussen S 10 , Schiffels S 11 , Subramanian S 2 , Wright JL 2 , Albrechtsen A 12 , Barbieri C 8 , Dupanloup I 3 , Eriksson A 13 , Margaryan A 1 , Moltke I 12 , Pugach I 8 , Korneliussen TS 1 , Levkivskyi IP 14 , Moreno-Mayar JV 1 , Ni S 8 , Racimo F 7 , Sikora M 1 , Xue Y 5 , Aghakhanian FA 15 , Brucato N 16 , Brunak S 17 , Campos PF 1 , Clark W 18 , Ellingvåg S 19 , Fourmile G 20 , Gerbault P 21 , Injie D 22 , Koki G 23 , Leavesley M 24 , Logan B 25 , Lynch A 26 , Matisoo-Smith EA 27 , McAllister PJ 28 , Mentzer AJ 29 , Metspalu M 30 , Migliano AB 31 , Murgha L 32 , Phipps ME 15 , Pomat W 23 , Reynolds D 33 , Ricaut FX 16 , Siba P 23 , Thomas MG 21 , Wales T 34 , Wall CM 35 , Oppenheimer SJ 36 , Tyler-Smith C 5 , Durbin R 5 , Dortch J 37 , Manica A 13 , Schierup MH 6 , Foley RA 1 , Lahr MM 1 , Bowern C 38 , Wall JD 39 , Mailund T 6 , Stoneking M 8 , Nielsen R 1 , Sandhu MS 5 , Excoffier L 3 , Lambert DM 2 , Willerslev E 1

Affiliations 

  • 1 Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
  • 2 Research Centre for Human Evolution, Environmental Futures Research Institute, Griffith University, Nathan, Queensland 4111, Australia
  • 3 Institute of Ecology and Evolution, University of Bern, Baltzerstrasse 6, 3012 Bern, Switzerland
  • 4 CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028 Barcelona, Spain
  • 5 Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
  • 6 Bioinformatics Research Centre, Aarhus University, 8000 Aarhus, Denmark
  • 7 Department of Integrative Biology, University of California, Berkeley, California 94720, USA
  • 8 Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany
  • 9 Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
  • 10 Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Kemitorvet, Building 208, 2800 Kongens Lyngby, Denmark
  • 11 Department for Archaeogenetics, Max Planck Institute for the Science of Human History, Kahlaische Straße 10, D-07745 Jena, Germany
  • 12 The Bioinformatics Centre, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen, Denmark
  • 13 Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK
  • 14 Institute for Theoretical Physics, ETH Zürich, Wolfgang-Pauli-Str. 27, 8093 Zürich, Switzerland
  • 15 Jeffrey Cheah School of Medicine &Health Sciences, Monash University Malaysia, Jalan Lagoon Selatan, Sunway City, 46150 Selangor, Malaysia
  • 16 Evolutionary Medicine Group, Laboratoire d'Anthropologie Moléculaire et Imagerie de Synthèse, UMR 5288, Centre National de la Recherche Scientifique, Université de Toulouse 3, 31073 Toulouse, France
  • 17 Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen N, Denmark
  • 18 National Parks and Wildlife, Sturt Highway, Buronga, New South Wales 2739, Australia
  • 19 Explico Foundation, Vågavegen 16, 6900 Florø, Norway
  • 20 Giriwandi, Gimuy Yidinji Country, Queensland 4868, Australia
  • 21 Research Department of Genetics, Evolution and Environment, University College London, Gower Street, London WC1E 6BT, UK
  • 22 Yinhawangka elder, Perth, Western Australia 6062, Australia
  • 23 Papua New Guinea Institute of Medical Research, PO Box 60, Goroka, Papua New Guinea
  • 24 Archaeology, School of Humanities &Social Sciences, University PO Box 320, University of Papua New Guinea &College of Arts, Society &Education, James Cook University, Cairns, Queensland 4811, Australia
  • 25 Ngadju elder, Coolgardie, Western Australia 6429, Australia
  • 26 Wongatha elder, Kurrawang, Western Australia 6430, Australia
  • 27 Department of Anatomy, University of Otago, Dunedin 9054, New Zealand
  • 28 2209 Springbrook Road, Springbrook, Queensland 4213, Australia
  • 29 Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
  • 30 Estonian Biocentre, Riia 23b, Tartu 51010, Estonia
  • 31 UCL Department of Anthropology, 14 Taviton Street, London WC1H 0BW, UK
  • 32 86 Workshop Road, Yarrabah, Queensland 4871, Australia
  • 33 Esperance Nyungar elder, Esperance, Western Australia 6450, Australia
  • 34 Atakani Street, Napranum, Queensland 4874, Australia
  • 35 2 Wynnum North Road, Wynnum, Queensland 4178, Australia
  • 36 School of Anthropology and Museum Ethnography, Oxford University, Oxford OX2 6PE, UK
  • 37 Centre for Rock Art Research and Management, M257, University of Western Australia, Perth, Western Australia 6009, Australia
  • 38 Department of Linguistics, Yale University, 370 Temple Street, New Haven, Connecticut 06520, USA
  • 39 Institute for Human Genetics, University of California, San Francisco, California 94143, USA
Nature, 2016 Oct 13;538(7624):207-214.
PMID: 27654914 DOI: 10.1038/nature18299

Abstract

The population history of Aboriginal Australians remains largely uncharacterized. Here we generate high-coverage genomes for 83 Aboriginal Australians (speakers of Pama-Nyungan languages) and 25 Papuans from the New Guinea Highlands. We find that Papuan and Aboriginal Australian ancestors diversified 25-40 thousand years ago (kya), suggesting pre-Holocene population structure in the ancient continent of Sahul (Australia, New Guinea and Tasmania). However, all of the studied Aboriginal Australians descend from a single founding population that differentiated ~10-32 kya. We infer a population expansion in northeast Australia during the Holocene epoch (past 10,000 years) associated with limited gene flow from this region to the rest of Australia, consistent with the spread of the Pama-Nyungan languages. We estimate that Aboriginal Australians and Papuans diverged from Eurasians 51-72 kya, following a single out-of-Africa dispersal, and subsequently admixed with archaic populations. Finally, we report evidence of selection in Aboriginal Australians potentially associated with living in the desert.

* Title and MeSH Headings from MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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