title: A genomic history of Aboriginal Australia.
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.
authors.affiliation: Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark.|Institute of Ecology and Evolution, University of Bern, Baltzerstrasse 6, 3012 Bern, Switzerland.|Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland.
authors.forename: Anna-Sapfo
authors.initials: AS
authors.lastname: Malaspinas
authors.affiliation: Research Centre for Human Evolution, Environmental Futures Research Institute, Griffith University, Nathan, Queensland 4111, Australia.
authors.forename: Michael C
authors.initials: MC
authors.lastname: Westaway
authors.affiliation: Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark.
authors.forename: Craig
authors.initials: C
authors.lastname: Muller
authors.affiliation: Institute of Ecology and Evolution, University of Bern, Baltzerstrasse 6, 3012 Bern, Switzerland.|Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland.
authors.forename: Vitor C
authors.initials: VC
authors.lastname: Sousa
authors.affiliation: CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028 Barcelona, Spain.|Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain.
authors.forename: Oscar
authors.initials: O
authors.lastname: Lao
authors.affiliation: Institute of Ecology and Evolution, University of Bern, Baltzerstrasse 6, 3012 Bern, Switzerland.|Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland.|Population and Conservation Genetics Group, Instituto Gulbenkian de Ciência, 2780-156 Oeiras, Portugal.
authors.forename: Isabel
authors.initials: I
authors.lastname: Alves
authors.affiliation: Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK.
authors.forename: Anders
authors.initials: A
authors.lastname: Bergström
authors.affiliation: Bioinformatics Research Centre, Aarhus University, 8000 Aarhus, Denmark.
authors.forename: Georgios
authors.initials: G
authors.lastname: Athanasiadis
authors.affiliation: Bioinformatics Research Centre, Aarhus University, 8000 Aarhus, Denmark.|Department of Integrative Biology, University of California, Berkeley, California 94720, USA.
authors.forename: Jade Y
authors.initials: JY
authors.lastname: Cheng
authors.affiliation: Department of Integrative Biology, University of California, Berkeley, California 94720, USA.|Verily Life Sciences, 2425 Garcia Ave, Mountain View, California 94043, USA.
authors.forename: Jacob E
authors.initials: JE
authors.lastname: Crawford
authors.affiliation: Research Centre for Human Evolution, Environmental Futures Research Institute, Griffith University, Nathan, Queensland 4111, Australia.
authors.forename: Tim H
authors.initials: TH
authors.lastname: Heupink
authors.affiliation: Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany.
authors.forename: Enrico
authors.initials: E
authors.lastname: Macholdt
authors.affiliation: Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland.|Interfaculty Bioinformatics Unit University of Bern, Baltzerstrasse 6, CH-3012 Bern, Switzerland.
authors.forename: Stephan
authors.initials: S
authors.lastname: Peischl
authors.affiliation: Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Kemitorvet, Building 208, 2800 Kongens Lyngby, Denmark.
authors.forename: Simon
authors.initials: S
authors.lastname: Rasmussen
authors.affiliation: Department for Archaeogenetics, Max Planck Institute for the Science of Human History, Kahlaische Straße 10, D-07745 Jena, Germany.
authors.forename: Stephan
authors.initials: S
authors.lastname: Schiffels
authors.affiliation: Research Centre for Human Evolution, Environmental Futures Research Institute, Griffith University, Nathan, Queensland 4111, Australia.
authors.forename: Sankar
authors.initials: S
authors.lastname: Subramanian
authors.affiliation: Research Centre for Human Evolution, Environmental Futures Research Institute, Griffith University, Nathan, Queensland 4111, Australia.
authors.forename: Joanne L
authors.initials: JL
authors.lastname: Wright
authors.affiliation: The Bioinformatics Centre, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen, Denmark.
authors.forename: Anders
authors.initials: A
authors.lastname: Albrechtsen
authors.affiliation: Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany.|Department of Linguistic and Cultural Evolution, Max Planck Institute for the Science of Human History, Kahlaische Straße 10, D-07745 Jena, Germany.
authors.forename: Chiara
authors.initials: C
authors.lastname: Barbieri
authors.affiliation: Institute of Ecology and Evolution, University of Bern, Baltzerstrasse 6, 3012 Bern, Switzerland.|Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland.
authors.forename: Isabelle
authors.initials: I
authors.lastname: Dupanloup
authors.affiliation: Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK.|Integrative Systems Biology Laboratory, Division of Biological and Environmental Sciences &Engineering, King Abdullah University of Science and Technology, 23955-6900 Thuwal, Saudi Arabia.
authors.forename: Anders
authors.initials: A
authors.lastname: Eriksson
authors.affiliation: Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark.
authors.forename: Ashot
authors.initials: A
authors.lastname: Margaryan
authors.affiliation: The Bioinformatics Centre, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen, Denmark.
authors.forename: Ida
authors.initials: I
authors.lastname: Moltke
authors.affiliation: Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany.
authors.forename: Irina
authors.initials: I
authors.lastname: Pugach
authors.affiliation: Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark.
authors.forename: Thorfinn S
authors.initials: TS
authors.lastname: Korneliussen
authors.affiliation: Institute for Theoretical Physics, ETH Zürich, Wolfgang-Pauli-Str. 27, 8093 Zürich, Switzerland.
authors.forename: Ivan P
authors.initials: IP
authors.lastname: Levkivskyi
authors.affiliation: Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark.
authors.forename: J Víctor
authors.initials: JV
authors.lastname: Moreno-Mayar
authors.affiliation: Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany.
authors.forename: Shengyu
authors.initials: S
authors.lastname: Ni
authors.affiliation: Department of Integrative Biology, University of California, Berkeley, California 94720, USA.
authors.forename: Fernando
authors.initials: F
authors.lastname: Racimo
authors.affiliation: Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark.
authors.forename: Martin
authors.initials: M
authors.lastname: Sikora
authors.affiliation: Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK.
authors.forename: Yali
authors.initials: Y
authors.lastname: Xue
authors.affiliation: Jeffrey Cheah School of Medicine &Health Sciences, Monash University Malaysia, Jalan Lagoon Selatan, Sunway City, 46150 Selangor, Malaysia.
authors.forename: Farhang A
authors.initials: FA
authors.lastname: Aghakhanian
authors.affiliation: 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.
authors.forename: Nicolas
authors.initials: N
authors.lastname: Brucato
authors.affiliation: Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen N, Denmark.
authors.forename: Søren
authors.initials: S
authors.lastname: Brunak
authors.affiliation: Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark.|CIMAR/CIIMAR, Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Rua dos Bragas 289, 4050-123 Porto, Portugal.
authors.forename: Paula F
authors.initials: PF
authors.lastname: Campos
authors.affiliation: National Parks and Wildlife, Sturt Highway, Buronga, New South Wales 2739, Australia.
authors.forename: Warren
authors.initials: W
authors.lastname: Clark
authors.affiliation: Explico Foundation, Vågavegen 16, 6900 Florø, Norway.
authors.forename: Sturla
authors.initials: S
authors.lastname: Ellingvåg
authors.affiliation: Giriwandi, Gimuy Yidinji Country, Queensland 4868, Australia.
authors.forename: Gudjugudju
authors.initials: G
authors.lastname: Fourmile
authors.affiliation: Research Department of Genetics, Evolution and Environment, University College London, Gower Street, London WC1E 6BT, UK.|UCL Department of Anthropology, 14 Taviton Street, London WC1H 0BW, UK.
authors.forename: Pascale
authors.initials: P
authors.lastname: Gerbault
authors.affiliation: Yinhawangka elder, Perth, Western Australia 6062, Australia.
authors.forename: Darren
authors.initials: D
authors.lastname: Injie
authors.affiliation: Papua New Guinea Institute of Medical Research, PO Box 60, Goroka, Papua New Guinea.
authors.forename: George
authors.initials: G
authors.lastname: Koki
authors.affiliation: 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.
authors.forename: Matthew
authors.initials: M
authors.lastname: Leavesley
authors.affiliation: Ngadju elder, Coolgardie, Western Australia 6429, Australia.
authors.forename: Betty
authors.initials: B
authors.lastname: Logan
authors.affiliation: Wongatha elder, Kurrawang, Western Australia 6430, Australia.
authors.forename: Aubrey
authors.initials: A
authors.lastname: Lynch
authors.affiliation: Department of Anatomy, University of Otago, Dunedin 9054, New Zealand.
authors.forename: Elizabeth A
authors.initials: EA
authors.lastname: Matisoo-Smith
authors.affiliation: 2209 Springbrook Road, Springbrook, Queensland 4213, Australia.
authors.forename: Peter J
authors.initials: PJ
authors.lastname: McAllister
authors.affiliation: Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK.
authors.forename: Alexander J
authors.initials: AJ
authors.lastname: Mentzer
authors.affiliation: Estonian Biocentre, Riia 23b, Tartu 51010, Estonia.
authors.forename: Mait
authors.initials: M
authors.lastname: Metspalu
authors.affiliation: UCL Department of Anthropology, 14 Taviton Street, London WC1H 0BW, UK.
authors.forename: Andrea B
authors.initials: AB
authors.lastname: Migliano
authors.affiliation: 86 Workshop Road, Yarrabah, Queensland 4871, Australia.
authors.forename: Les
authors.initials: L
authors.lastname: Murgha
authors.affiliation: Jeffrey Cheah School of Medicine &Health Sciences, Monash University Malaysia, Jalan Lagoon Selatan, Sunway City, 46150 Selangor, Malaysia.
authors.forename: Maude E
authors.initials: ME
authors.lastname: Phipps
authors.affiliation: Papua New Guinea Institute of Medical Research, PO Box 60, Goroka, Papua New Guinea.
authors.forename: William
authors.initials: W
authors.lastname: Pomat
authors.affiliation: Esperance Nyungar elder, Esperance, Western Australia 6450, Australia.
authors.forename: Doc
authors.initials: D
authors.lastname: Reynolds
authors.affiliation: 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.
authors.forename: Francois-Xavier
authors.initials: FX
authors.lastname: Ricaut
authors.affiliation: Papua New Guinea Institute of Medical Research, PO Box 60, Goroka, Papua New Guinea.
authors.forename: Peter
authors.initials: P
authors.lastname: Siba
authors.affiliation: Research Department of Genetics, Evolution and Environment, University College London, Gower Street, London WC1E 6BT, UK.
authors.forename: Mark G
authors.initials: MG
authors.lastname: Thomas
authors.affiliation: Atakani Street, Napranum, Queensland 4874, Australia.
authors.forename: Thomas
authors.initials: T
authors.lastname: Wales
authors.affiliation: 2 Wynnum North Road, Wynnum, Queensland 4178, Australia.
authors.forename: Colleen Ma'run
authors.initials: CM
authors.lastname: Wall
authors.affiliation: School of Anthropology and Museum Ethnography, Oxford University, Oxford OX2 6PE, UK.
authors.forename: Stephen J
authors.initials: SJ
authors.lastname: Oppenheimer
authors.affiliation: Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK.
authors.forename: Chris
authors.initials: C
authors.lastname: Tyler-Smith
authors.affiliation: Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK.
authors.forename: Richard
authors.initials: R
authors.lastname: Durbin
authors.affiliation: Centre for Rock Art Research and Management, M257, University of Western Australia, Perth, Western Australia 6009, Australia.
authors.forename: Joe
authors.initials: J
authors.lastname: Dortch
authors.affiliation: Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK.
authors.forename: Andrea
authors.initials: A
authors.lastname: Manica
authors.affiliation: Bioinformatics Research Centre, Aarhus University, 8000 Aarhus, Denmark.
authors.forename: Mikkel H
authors.initials: MH
authors.lastname: Schierup
authors.affiliation: Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark.|Leverhulme Centre for Human Evolutionary Studies, Department of Archaeology and Anthropology, University of Cambridge, Fitzwilliam Street, Cambridge CB2 1QH, UK.
authors.forename: Robert A
authors.initials: RA
authors.lastname: Foley
authors.affiliation: Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark.|Leverhulme Centre for Human Evolutionary Studies, Department of Archaeology and Anthropology, University of Cambridge, Fitzwilliam Street, Cambridge CB2 1QH, UK.
authors.forename: Marta Mirazón
authors.initials: MM
authors.lastname: Lahr
authors.affiliation: Department of Linguistics, Yale University, 370 Temple Street, New Haven, Connecticut 06520, USA.
authors.forename: Claire
authors.initials: C
authors.lastname: Bowern
authors.affiliation: Institute for Human Genetics, University of California, San Francisco, California 94143, USA.
authors.forename: Jeffrey D
authors.initials: JD
authors.lastname: Wall
authors.affiliation: Bioinformatics Research Centre, Aarhus University, 8000 Aarhus, Denmark.
authors.forename: Thomas
authors.initials: T
authors.lastname: Mailund
authors.affiliation: Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany.
authors.forename: Mark
authors.initials: M
authors.lastname: Stoneking
authors.affiliation: Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark.|Departments of Integrative Biology and Statistics, University of California, Berkeley, California 94720, USA.
authors.forename: Rasmus
authors.initials: R
authors.lastname: Nielsen
authors.affiliation: Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK.
authors.forename: Manjinder S
authors.initials: MS
authors.lastname: Sandhu
authors.affiliation: Institute of Ecology and Evolution, University of Bern, Baltzerstrasse 6, 3012 Bern, Switzerland.|Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland.
authors.forename: Laurent
authors.initials: L
authors.lastname: Excoffier
authors.affiliation: Research Centre for Human Evolution, Environmental Futures Research Institute, Griffith University, Nathan, Queensland 4111, Australia.
authors.forename: David M
authors.initials: DM
authors.lastname: Lambert
authors.affiliation: Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark.|Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK.|Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK.
authors.forename: Eske
authors.initials: E
authors.lastname: Willerslev
mesh_terms: D000349:Africa / Q000208:ethnology; D001315:Australia; D066264:Datasets as Topic; D003889:Desert Climate; D051456:Gene Flow; D005828:Genetics, Population; D015894:Genome, Human / Q000235:genetics*; D023281:Genomics; D049690:History, Ancient; D063426:Human Migration / Q000266:history; D006801:Humans; D007802:Language; D009512:New Guinea; D010802:Phylogeny; D011157:Population Dynamics; D044469:Racial Groups / Q000235:genetics*; D013648:Tasmania