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Nature. 2016 Oct 13;538(7624):207-214. doi: 10.1038/nature18299. Epub 2016 Sep 21.

A genomic history of Aboriginal Australia.

Author information

1
Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark.
2
Institute of Ecology and Evolution, University of Bern, Baltzerstrasse 6, 3012 Bern, Switzerland.
3
Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland.
4
Research Centre for Human Evolution, Environmental Futures Research Institute, Griffith University, Nathan, Queensland 4111, Australia.
5
CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028 Barcelona, Spain.
6
Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain.
7
Population and Conservation Genetics Group, Instituto Gulbenkian de Ciência, 2780-156 Oeiras, Portugal.
8
Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK.
9
Bioinformatics Research Centre, Aarhus University, 8000 Aarhus, Denmark.
10
Department of Integrative Biology, University of California, Berkeley, California 94720, USA.
11
Verily Life Sciences, 2425 Garcia Ave, Mountain View, California 94043, USA.
12
Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany.
13
Interfaculty Bioinformatics Unit University of Bern, Baltzerstrasse 6, CH-3012 Bern, Switzerland.
14
Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Kemitorvet, Building 208, 2800 Kongens Lyngby, Denmark.
15
Department for Archaeogenetics, Max Planck Institute for the Science of Human History, Kahlaische Straße 10, D-07745 Jena, Germany.
16
The Bioinformatics Centre, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen, Denmark.
17
Department of Linguistic and Cultural Evolution, Max Planck Institute for the Science of Human History, Kahlaische Straße 10, D-07745 Jena, Germany.
18
Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK.
19
Integrative Systems Biology Laboratory, Division of Biological and Environmental Sciences &Engineering, King Abdullah University of Science and Technology, 23955-6900 Thuwal, Saudi Arabia.
20
Institute for Theoretical Physics, ETH Zürich, Wolfgang-Pauli-Str. 27, 8093 Zürich, Switzerland.
21
Jeffrey Cheah School of Medicine &Health Sciences, Monash University Malaysia, Jalan Lagoon Selatan, Sunway City, 46150 Selangor, Malaysia.
22
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.
23
Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen N, Denmark.
24
CIMAR/CIIMAR, Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Rua dos Bragas 289, 4050-123 Porto, Portugal.
25
National Parks and Wildlife, Sturt Highway, Buronga, New South Wales 2739, Australia.
26
Explico Foundation, Vågavegen 16, 6900 Florø, Norway.
27
Giriwandi, Gimuy Yidinji Country, Queensland 4868, Australia.
28
Research Department of Genetics, Evolution and Environment, University College London, Gower Street, London WC1E 6BT, UK.
29
UCL Department of Anthropology, 14 Taviton Street, London WC1H 0BW, UK.
30
Yinhawangka elder, Perth, Western Australia 6062, Australia.
31
Papua New Guinea Institute of Medical Research, PO Box 60, Goroka, Papua New Guinea.
32
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.
33
Ngadju elder, Coolgardie, Western Australia 6429, Australia.
34
Wongatha elder, Kurrawang, Western Australia 6430, Australia.
35
Department of Anatomy, University of Otago, Dunedin 9054, New Zealand.
36
2209 Springbrook Road, Springbrook, Queensland 4213, Australia.
37
Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK.
38
Estonian Biocentre, Riia 23b, Tartu 51010, Estonia.
39
86 Workshop Road, Yarrabah, Queensland 4871, Australia.
40
Esperance Nyungar elder, Esperance, Western Australia 6450, Australia.
41
Atakani Street, Napranum, Queensland 4874, Australia.
42
2 Wynnum North Road, Wynnum, Queensland 4178, Australia.
43
School of Anthropology and Museum Ethnography, Oxford University, Oxford OX2 6PE, UK.
44
Centre for Rock Art Research and Management, M257, University of Western Australia, Perth, Western Australia 6009, Australia.
45
Leverhulme Centre for Human Evolutionary Studies, Department of Archaeology and Anthropology, University of Cambridge, Fitzwilliam Street, Cambridge CB2 1QH, UK.
46
Department of Linguistics, Yale University, 370 Temple Street, New Haven, Connecticut 06520, USA.
47
Institute for Human Genetics, University of California, San Francisco, California 94143, USA.
48
Departments of Integrative Biology and Statistics, University of California, Berkeley, California 94720, USA.

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.

PMID:
27654914
DOI:
10.1038/nature18299
[Indexed for MEDLINE]

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