A genomic history of Aboriginal Australia

Anna-Sapfo Malaspinas, Michael C. Westaway, Craig Muller, Vitor C. Sousa, Oscar Lao, Isabel Alves, Anders Bergström, Georgios Athanasiadis, Jade Y. Cheng, Jacob E. Crawford, Tim H. Heupink, Enrico Macholdt, Stephan Peischl, Simon Rasmussen, Stephan Schiffels, Sankar Subramanian, Joanne L. Wright, Anders Albrechtsen, Chiara Barbieri, Isabelle Dupanloup, Anders Eriksson, Ashot Margaryan, Ida Moltke, Irina Pugach, Thorfinn S. Korneliussen, Ivan P. Levkivskyi, J. Víctor Moreno-Mayar, Shengyu Ni, Fernando Racimo, Martin Sikora, Yali Xue, Farhang A. Aghakhanian, Nicolas Brucato, Søren Brunak, Paula F. Campos, Warren Clark, Sturla Ellingvåg, Gudjugudju Fourmile, Pascale Gerbault, Darren Injie, George Koki, Matthew Leavesley, Betty Logan, Aubrey Lynch, Elizabeth A. Matisoo-Smith, Peter J. McAllister, Alexander J. Mentzer, Mait Metspalu, Andrea B. Migliano, Les Murgha, Maude E. Phipps, William Pomat, Doc Reynolds, Francois-Xavier Ricaut, Peter Siba, Mark G. Thomas, Thomas Wales, Colleen Ma’run Wall, Stephen J. Oppenheimer, Chris Tyler-Smith, Richard Durbin, Joe Dortch, Andrea Manica, Mikkel H. Schierup, Robert A. Foley, Marta Mirazón Lahr, Claire Bowern, Jeffrey D. Wall, Thomas Mailund, Mark Stoneking, Rasmus Nielsen, Manjinder S. Sandhu (), Laurent Excoffier (), David M. Lambert () and Eske Willerslev ()
Additional contact information
Anna-Sapfo Malaspinas: Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen
Michael C. Westaway: Research Centre for Human Evolution, Environmental Futures Research Institute, Griffith University
Craig Muller: Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen
Vitor C. Sousa: Institute of Ecology and Evolution, University of Bern
Oscar Lao: CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST)
Isabel Alves: Institute of Ecology and Evolution, University of Bern
Anders Bergström: Wellcome Trust Sanger Institute, Wellcome Genome Campus
Georgios Athanasiadis: Bioinformatics Research Centre, Aarhus University
Jade Y. Cheng: Bioinformatics Research Centre, Aarhus University
Jacob E. Crawford: University of California
Tim H. Heupink: Research Centre for Human Evolution, Environmental Futures Research Institute, Griffith University
Enrico Macholdt: Max Planck Institute for Evolutionary Anthropology
Stephan Peischl: Swiss Institute of Bioinformatics
Simon Rasmussen: Center for Biological Sequence Analysis, Technical University of Denmark
Stephan Schiffels: Max Planck Institute for the Science of Human History
Sankar Subramanian: Research Centre for Human Evolution, Environmental Futures Research Institute, Griffith University
Joanne L. Wright: Research Centre for Human Evolution, Environmental Futures Research Institute, Griffith University
Anders Albrechtsen: The Bioinformatics Centre, University of Copenhagen
Chiara Barbieri: Max Planck Institute for Evolutionary Anthropology
Isabelle Dupanloup: Institute of Ecology and Evolution, University of Bern
Anders Eriksson: University of Cambridge
Ashot Margaryan: Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen
Ida Moltke: The Bioinformatics Centre, University of Copenhagen
Irina Pugach: Max Planck Institute for Evolutionary Anthropology
Thorfinn S. Korneliussen: Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen
Ivan P. Levkivskyi: Institute for Theoretical Physics, ETH Zürich
J. Víctor Moreno-Mayar: Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen
Shengyu Ni: Max Planck Institute for Evolutionary Anthropology
Fernando Racimo: University of California
Martin Sikora: Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen
Yali Xue: Wellcome Trust Sanger Institute, Wellcome Genome Campus
Farhang A. Aghakhanian: Jeffrey Cheah School of Medicine & Health Sciences, Monash University Malaysia
Nicolas Brucato: Evolutionary Medicine Group, Laboratoire d’Anthropologie Moléculaire et Imagerie de Synthèse, UMR 5288, Centre National de la Recherche Scientifique, Université de Toulouse 3
Søren Brunak: Novo Nordisk Foundation Center for Protein Research, University of Copenhagen
Paula F. Campos: Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen
Warren Clark: National Parks and Wildlife
Sturla Ellingvåg: Explico Foundation
Gudjugudju Fourmile: Giriwandi, Gimuy Yidinji Country
Pascale Gerbault: Evolution and Environment, University College London
Darren Injie: Yinhawangka elder
George Koki: Papua New Guinea Institute of Medical Research
Matthew Leavesley: Archaeology, School of Humanities & Social Sciences, University PO Box 320, University of Papua New Guinea & College of Arts, Society & Education, James Cook University
Betty Logan: Ngadju elder
Aubrey Lynch: Wongatha elder
Elizabeth A. Matisoo-Smith: University of Otago
Peter J. McAllister: 2209 Springbrook Road
Alexander J. Mentzer: Wellcome Trust Centre for Human Genetics, University of Oxford
Mait Metspalu: Estonian Biocentre
Andrea B. Migliano: UCL Department of Anthropology
Les Murgha: 86 Workshop Road
Maude E. Phipps: Jeffrey Cheah School of Medicine & Health Sciences, Monash University Malaysia
William Pomat: Papua New Guinea Institute of Medical Research
Doc Reynolds: Esperance Nyungar elder
Francois-Xavier Ricaut: Evolutionary Medicine Group, Laboratoire d’Anthropologie Moléculaire et Imagerie de Synthèse, UMR 5288, Centre National de la Recherche Scientifique, Université de Toulouse 3
Peter Siba: Papua New Guinea Institute of Medical Research
Mark G. Thomas: Evolution and Environment, University College London
Thomas Wales: Atakani Street
Colleen Ma’run Wall: 2 Wynnum North Road
Stephen J. Oppenheimer: School of Anthropology and Museum Ethnography, Oxford University
Chris Tyler-Smith: Wellcome Trust Sanger Institute, Wellcome Genome Campus
Richard Durbin: Wellcome Trust Sanger Institute, Wellcome Genome Campus
Joe Dortch: Centre for Rock Art Research and Management, M257, University of Western Australia
Andrea Manica: University of Cambridge
Mikkel H. Schierup: Bioinformatics Research Centre, Aarhus University
Robert A. Foley: Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen
Marta Mirazón Lahr: Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen
Claire Bowern: Yale University
Jeffrey D. Wall: Institute for Human Genetics, University of California
Thomas Mailund: Bioinformatics Research Centre, Aarhus University
Mark Stoneking: Max Planck Institute for Evolutionary Anthropology
Rasmus Nielsen: Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen
Manjinder S. Sandhu: Wellcome Trust Sanger Institute, Wellcome Genome Campus
Laurent Excoffier: Institute of Ecology and Evolution, University of Bern
David M. Lambert: Research Centre for Human Evolution, Environmental Futures Research Institute, Griffith University
Eske Willerslev: Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen

Nature, 2016, vol. 538, issue 7624, 207-214

Abstract: 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.

Date: 2016
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DOI: 10.1038/nature18299

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