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A genomic history of Aboriginal Australia

Author

Listed:
  • Anna-Sapfo Malaspinas

    (Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen
    Institute of Ecology and Evolution, University of Bern
    Swiss Institute of Bioinformatics)

  • 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
    Swiss Institute of Bioinformatics)

  • Oscar Lao

    (CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST)
    Universitat Pompeu Fabra (UPF))

  • Isabel Alves

    (Institute of Ecology and Evolution, University of Bern
    Swiss Institute of Bioinformatics
    Population and Conservation Genetics Group, Instituto Gulbenkian de Ciência)

  • Anders Bergström

    (Wellcome Trust Sanger Institute, Wellcome Genome Campus)

  • Georgios Athanasiadis

    (Bioinformatics Research Centre, Aarhus University)

  • Jade Y. Cheng

    (Bioinformatics Research Centre, Aarhus University
    University of California)

  • Jacob E. Crawford

    (University of California
    Verily Life Sciences)

  • 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
    Interfaculty Bioinformatics Unit University of Bern)

  • 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
    Max Planck Institute for the Science of Human History)

  • Isabelle Dupanloup

    (Institute of Ecology and Evolution, University of Bern
    Swiss Institute of Bioinformatics)

  • Anders Eriksson

    (University of Cambridge
    Integrative Systems Biology Laboratory, King Abdullah University of Science and Technology)

  • 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
    CIMAR/CIIMAR, Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto)

  • Warren Clark

    (National Parks and Wildlife)

  • Sturla Ellingvåg

    (Explico Foundation)

  • Gudjugudju Fourmile

    (Giriwandi, Gimuy Yidinji Country)

  • Pascale Gerbault

    (Evolution and Environment, University College London
    UCL Department of Anthropology)

  • 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
    Leverhulme Centre for Human Evolutionary Studies, University of Cambridge)

  • Marta Mirazón Lahr

    (Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen
    Leverhulme Centre for Human Evolutionary Studies, University of Cambridge)

  • 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
    University of California)

  • Manjinder S. Sandhu

    (Wellcome Trust Sanger Institute, Wellcome Genome Campus)

  • Laurent Excoffier

    (Institute of Ecology and Evolution, University of Bern
    Swiss Institute of Bioinformatics)

  • 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
    Wellcome Trust Sanger Institute, Wellcome Genome Campus
    University of Cambridge)

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.

Suggested Citation

  • 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 &, 2016. "A genomic history of Aboriginal Australia," Nature, Nature, vol. 538(7624), pages 207-214, October.
    • Handle: RePEc:nat:nature:v:538:y:2016:i:7624:d:10.1038_nature18299
    DOI: 10.1038/nature18299
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    Cited by:

    1. Sarah E. Freidline & Kira E. Westaway & Renaud Joannes-Boyau & Philippe Duringer & Jean-Luc Ponche & Mike W. Morley & Vito C. Hernandez & Meghan S. McAllister-Hayward & Hugh McColl & Clément Zanolli &, 2023. "Early presence of Homo sapiens in Southeast Asia by 86–68 kyr at Tam Pà Ling, Northern Laos," Nature Communications, Nature, vol. 14(1), pages 1-21, December.
    2. Alexandros G. Sotiropoulos & Epifanía Arango-Isaza & Tomohiro Ban & Chiara Barbieri & Salim Bourras & Christina Cowger & Paweł C. Czembor & Roi Ben-David & Amos Dinoor & Simon R. Ellwood & Johannes Gr, 2022. "Global genomic analyses of wheat powdery mildew reveal association of pathogen spread with historical human migration and trade," Nature Communications, Nature, vol. 13(1), pages 1-14, December.
    3. Tristan Salles & Renaud Joannes-Boyau & Ian Moffat & Laurent Husson & Manon Lorcery, 2024. "Physiography, foraging mobility, and the first peopling of Sahul," Nature Communications, Nature, vol. 15(1), pages 1-14, December.
    4. Ceri Shipton & Mike W. Morley & Shimona Kealy & Kasih Norman & Clara Boulanger & Stuart Hawkins & Mirani Litster & Caitlin Withnell & Sue O’Connor, 2024. "Abrupt onset of intensive human occupation 44,000 years ago on the threshold of Sahul," Nature Communications, Nature, vol. 15(1), pages 1-15, December.
    5. Mathilde André & Nicolas Brucato & Georgi Hudjasov & Vasili Pankratov & Danat Yermakovich & Francesco Montinaro & Rita Kreevan & Jason Kariwiga & John Muke & Anne Boland & Jean-François Deleuze & Vinc, 2024. "Positive selection in the genomes of two Papua New Guinean populations at distinct altitude levels," Nature Communications, Nature, vol. 15(1), pages 1-15, December.
    6. Leonardo Vallini & Carlo Zampieri & Mohamed Javad Shoaee & Eugenio Bortolini & Giulia Marciani & Serena Aneli & Telmo Pievani & Stefano Benazzi & Alberto Barausse & Massimo Mezzavilla & Michael D. Pet, 2024. "The Persian plateau served as hub for Homo sapiens after the main out of Africa dispersal," Nature Communications, Nature, vol. 15(1), pages 1-13, December.
    7. Katie McGill & Amir Salem & Tanya L. Hanstock & Todd R. Heard & Leonie Garvey & Bernard Leckning & Ian Whyte & Andrew Page & Greg Carter, 2022. "Indigeneity and Likelihood of Discharge to Psychiatric Hospital in an Australian Deliberate Self-Poisoning Hospital-Treated Cohort," IJERPH, MDPI, vol. 19(19), pages 1-16, September.
    8. Emma Haynes & Alice Mitchell & Stephanie Enkel & Rosemary Wyber & Dawn Bessarab, 2020. "Voices behind the Statistics: A Systematic Literature Review of the Lived Experience of Rheumatic Heart Disease," IJERPH, MDPI, vol. 17(4), pages 1-25, February.
    9. Kai Yuan & Xumin Ni & Chang Liu & Yuwen Pan & Lian Deng & Rui Zhang & Yang Gao & Xueling Ge & Jiaojiao Liu & Xixian Ma & Haiyi Lou & Taoyang Wu & Shuhua Xu, 2021. "Refining models of archaic admixture in Eurasia with ArchaicSeeker 2.0," Nature Communications, Nature, vol. 12(1), pages 1-15, December.

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