Article | Published:

A genomic history of Aboriginal Australia

Nature volume 538, pages 207214 (13 October 2016) | Download Citation

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.

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Data deposits

The Aboriginal Australian and Papuan whole genome sequence data generated in this study have been deposited at the European Genome-phenome Archive (EGA, http://www.ebi.ac.uk/ega/), which is hosted by the EBI, under the accession numbers EGAS00001001766 and EGAS00001001247, respectively. The Papuan SNP array data generated in this study can be found under http://geogenetics.ku.dk/latest-news/alle_nyheder/2016/data.

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Acknowledgements

We thank all sample donors for contributing to this study. We thank Macrogen (http://www.macrogen.com/) for sequencing of the Aboriginal Australian genomes, M. Rasmussen, C. Der Sarkissian, M. Allentoft, D. Cooper, R. Gray, S. Greenhill, A. Seguin-Orlando, T. Carstensen, M. Przeworski, J. D. Jensen and L. Orlando for helpful discussions. We thank E. Thorsby for sample collection and contributing the DNA extract for the P2077 genome, I. Lissimore for support with data storage and distribution. We thank T. Parks, K. Auckland, K. Robson, A. V. Hill, J. B. Clegg, D. Higgs, D. J. Weatherall and M. Alpers for assistance in sample collection and discussion. L.E., V.C.S., I.A., I.D. and S.P. are grateful to the High Performance Computation platform of the University of Bern for providing access to the UBELIX cluster. This work was supported by the Danish National Research Foundation, the Lundbeck Foundation, the KU2016 grant and the Australian Research Council. A.-S.M. was supported by an ambizione grant with reference PZ00P3_154717 from the Swiss National Science Foundation (SNSF). M.C.W. was supported by the Australian Research Council (ARC) Discovery grants DP110102635 and DP140101405 and by a Linkage grant LP140100387. V.C.S., I.D. and S.P. were supported by SNSF grants to L.E. with references 31003A-143393 and CRSII3_141940. O.L. was supported by a Ramón y Cajal grant from the Spanish Ministerio de Economia y Competitividad (MINECO) with reference RYC-2013-14797 and by a BFU2015-68759-P (MINECO/FEDER) grant. I.A. was supported by a grant with reference SFRH/BD/73150/2010 from the Portuguese Foundation for Science and Technology (FCT). A.B., S.Sc., Y.X., C.T.-S. and R.D. were supported by a Wellcome Trust grant with reference WT098051. E.M., C.Ba., I.P., S.N. and M.St. acknowledge the Max Planck Society. S.Su. was supported by an ARC Discovery grant with reference DP140101405. J.L.W. was supported by a PhD scholarship from Griffith University. A.A. acknowledges the Villum foundation. I.M. was supported by a grant from the Danish Council for Independent Research with reference DFF–4090-00244. J.V.M.-M. acknowledges the Consejo Nacional de Ciencia y Tecnología (Mexico) for funding. N.B. and F.-X.R. were supported by the French Ministry of Foreign and European Affairs and French ANR with the grant ANR14-CE31-0013-01. S.B. was supported by a Novo Nordisk Foundation grant with reference NNF14CC0001. P.G. and A.B.M. were supported by a Leverhulme Programme grant number RP2011-R-045 to A.B.M. at UCL Department of Anthropology and M.G.T. at UCL Department of Genetics, Evolution and Environment. A.J.M. was supported by a Wellcome Trust grant with reference 106289/Z/14/Z. M.M. acknowledges the EU European Regional Development Fund through the Centre of Excellence in Genomics to Estonian Biocentre; Estonian Institutional Research grant IUT24-1. M.G.T. was supported by a Wellcome Trust Senior Investigator Award with grant number 100719/Z/12/Z. S.J.O. was supported by a Wellcome Trust Core Award Grant Number 090532/Z/09/Z. A.Man. was supported by an ERC Consolidator Grant 647787 ‘LocalAdaptation’. M.E.P. would like to acknowledge the cardio-metabolic research cluster at Jeffrey Cheah School of Medicine & Health Sciences, Monash University Malaysia and Ministry of Science, Technology & Innovation, Malaysia for research grant 100-RM1/BIOTEK 16/6/2B. M.H.S. was supported by a grant from the Danish Independence Research Council with reference FNU 12-125062. R.A.F. was supported by the Leverhulme Trust. M.M.L. is supported by an ERC Advanced Grant 295907 ‘In-Africa’. C.Bo. was supported by USA National Science Foundation (NSF) grants BCS-0844550 and BCS-1423711, awarded to C.Bo. and Yale University. T.M. was supported by a grant from the Danish Independence Research Council with reference FNU 1323-00749. M.S.S. was supported by a Wellcome Trust grant with reference WT098051. L.E. was supported by Swiss NSF grant number 31003A-143393, D.M.L. was supported by ARC Discovery Grants DP110102635 and DP140101405 and Linkage grants LP140100387, LP120200144 and LP150100583. E.W. is grateful to St John’s College in Cambridge for help and support.

Author information

Author notes

    • Anna-Sapfo Malaspinas
    • , Michael C. Westaway
    • , Craig Muller
    • , Vitor C. Sousa
    • , Oscar Lao
    • , Isabel Alves
    •  & Anders Bergström

    These authors contributed equally to this work.

Affiliations

  1. Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5–7, 1350 Copenhagen, Denmark

    • Anna-Sapfo Malaspinas
    • , Craig Muller
    • , Ashot Margaryan
    • , Thorfinn S. Korneliussen
    • , J. Víctor Moreno-Mayar
    • , Martin Sikora
    • , Paula F. Campos
    • , Robert A. Foley
    • , Marta Mirazón Lahr
    • , Rasmus Nielsen
    •  & Eske Willerslev
  2. Institute of Ecology and Evolution, University of Bern, Baltzerstrasse 6, 3012 Bern, Switzerland

    • Anna-Sapfo Malaspinas
    • , Vitor C. Sousa
    • , Isabel Alves
    • , Isabelle Dupanloup
    •  & Laurent Excoffier
  3. Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland

    • Anna-Sapfo Malaspinas
    • , Vitor C. Sousa
    • , Isabel Alves
    • , Stephan Peischl
    • , Isabelle Dupanloup
    •  & Laurent Excoffier
  4. Research Centre for Human Evolution, Environmental Futures Research Institute, Griffith University, Nathan, Queensland 4111, Australia

    • Michael C. Westaway
    • , Tim H. Heupink
    • , Sankar Subramanian
    • , Joanne L. Wright
    •  & David M. Lambert
  5. CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028 Barcelona, Spain

    • Oscar Lao
  6. Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain

    • Oscar Lao
  7. Population and Conservation Genetics Group, Instituto Gulbenkian de Ciência, 2780-156 Oeiras, Portugal

    • Isabel Alves
  8. Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK

    • Anders Bergström
    • , Yali Xue
    • , Chris Tyler-Smith
    • , Richard Durbin
    • , Manjinder S. Sandhu
    •  & Eske Willerslev
  9. Bioinformatics Research Centre, Aarhus University, 8000 Aarhus, Denmark

    • Georgios Athanasiadis
    • , Jade Y. Cheng
    • , Mikkel H. Schierup
    •  & Thomas Mailund
  10. Department of Integrative Biology, University of California, Berkeley, California 94720, USA

    • Jade Y. Cheng
    • , Jacob E. Crawford
    •  & Fernando Racimo
  11. Verily Life Sciences, 2425 Garcia Ave, Mountain View, California 94043, USA

    • Jacob E. Crawford
  12. Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany

    • Enrico Macholdt
    • , Chiara Barbieri
    • , Irina Pugach
    • , Shengyu Ni
    •  & Mark Stoneking
  13. Interfaculty Bioinformatics Unit University of Bern, Baltzerstrasse 6, CH-3012 Bern, Switzerland

    • Stephan Peischl
  14. Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Kemitorvet, Building 208, 2800 Kongens Lyngby, Denmark

    • Simon Rasmussen
  15. Department for Archaeogenetics, Max Planck Institute for the Science of Human History, Kahlaische Straße 10, D-07745 Jena, Germany

    • Stephan Schiffels
  16. The Bioinformatics Centre, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen, Denmark

    • Anders Albrechtsen
    •  & Ida Moltke
  17. Department of Linguistic and Cultural Evolution, Max Planck Institute for the Science of Human History, Kahlaische Straße 10, D-07745 Jena, Germany

    • Chiara Barbieri
  18. Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK

    • Anders Eriksson
    • , Andrea Manica
    •  & Eske Willerslev
  19. Integrative Systems Biology Laboratory, Division of Biological and Environmental Sciences & Engineering, King Abdullah University of Science and Technology, 23955-6900 Thuwal, Saudi Arabia

    • Anders Eriksson
  20. Institute for Theoretical Physics, ETH Zürich, Wolfgang-Pauli-Str. 27, 8093 Zürich, Switzerland

    • Ivan P. Levkivskyi
  21. Jeffrey Cheah School of Medicine & Health Sciences, Monash University Malaysia, Jalan Lagoon Selatan, Sunway City, 46150 Selangor, Malaysia

    • Farhang A. Aghakhanian
    •  & Maude E. Phipps
  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

    • Nicolas Brucato
    •  & Francois-Xavier Ricaut
  23. Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen N, Denmark

    • Søren Brunak
  24. CIMAR/CIIMAR, Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Rua dos Bragas 289, 4050-123 Porto, Portugal

    • Paula F. Campos
  25. National Parks and Wildlife, Sturt Highway, Buronga, New South Wales 2739, Australia

    • Warren Clark
  26. Explico Foundation, Vågavegen 16, 6900 Florø, Norway

    • Sturla Ellingvåg
  27. Giriwandi, Gimuy Yidinji Country, Queensland 4868, Australia

    • Gudjugudju Fourmile
  28. Research Department of Genetics, Evolution and Environment, University College London, Gower Street, London WC1E 6BT, UK

    • Pascale Gerbault
    •  & Mark G. Thomas
  29. UCL Department of Anthropology, 14 Taviton Street, London WC1H 0BW, UK

    • Pascale Gerbault
    •  & Andrea B. Migliano
  30. Yinhawangka elder, Perth, Western Australia 6062, Australia

    • Darren Injie
  31. Papua New Guinea Institute of Medical Research, PO Box 60, Goroka, Papua New Guinea

    • George Koki
    • , William Pomat
    •  & Peter Siba
  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

    • Matthew Leavesley
  33. Ngadju elder, Coolgardie, Western Australia 6429, Australia

    • Betty Logan
  34. Wongatha elder, Kurrawang, Western Australia 6430, Australia

    • Aubrey Lynch
  35. Department of Anatomy, University of Otago, Dunedin 9054, New Zealand

    • Elizabeth A. Matisoo-Smith
  36. 2209 Springbrook Road, Springbrook, Queensland 4213, Australia

    • Peter J. McAllister
  37. Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK

    • Alexander J. Mentzer
  38. Estonian Biocentre, Riia 23b, Tartu 51010, Estonia

    • Mait Metspalu
  39. 86 Workshop Road, Yarrabah, Queensland 4871, Australia

    • Les Murgha
  40. Esperance Nyungar elder, Esperance, Western Australia 6450, Australia

    • Doc Reynolds
  41. Atakani Street, Napranum, Queensland 4874, Australia

    • Thomas Wales
  42. 2 Wynnum North Road, Wynnum, Queensland 4178, Australia

    • Colleen Ma’run Wall
  43. School of Anthropology and Museum Ethnography, Oxford University, Oxford OX2 6PE, UK

    • Stephen J. Oppenheimer
  44. Centre for Rock Art Research and Management, M257, University of Western Australia, Perth, Western Australia 6009, Australia

    • Joe Dortch
  45. Leverhulme Centre for Human Evolutionary Studies, Department of Archaeology and Anthropology, University of Cambridge, Fitzwilliam Street, Cambridge CB2 1QH, UK

    • Robert A. Foley
    •  & Marta Mirazón Lahr
  46. Department of Linguistics, Yale University, 370 Temple Street, New Haven, Connecticut 06520, USA

    • Claire Bowern
  47. Institute for Human Genetics, University of California, San Francisco, California 94143, USA

    • Jeffrey D. Wall
  48. Departments of Integrative Biology and Statistics, University of California, Berkeley, California 94720, USA

    • Rasmus Nielsen

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Contributions

G.A., J.Y.C., J.E.C., T.H.H., E.M., S.P., S.R., S.Sc., S.Su. and J.L.W. contributed equally and are listed alphabetically in the author list; A.A., C.Ba., I.D., A.E., A.Mar., I.M. and I.P. contributed equally and are listed alphabetically in the author list; T.S.K., I.P.L., J.V.M.-M., S.N., F.R., M.Si. and Y.X. contributed equally and are listed alphabetically in the author list. E.W. and D.M.L. initially conceived and headed the project. L.E. led the genetic load and the SFS-based demographic analyses. M.S.S. headed the research at the Wellcome Trust Sanger Institute. A.-S.M. planned and coordinated the genetic analyses and the sequencing of the Aboriginal Australian genomes. C.M., J.L.W., T.H.H., P.F.C., W.C., G.F., D.I., B.L., A.L., P.J.M., L.M., D.R., T.W., C.W., J.D., M.C.W. and E.W. collaborated with local groups to collect Aboriginal Australian samples. N.B., P.G., G.K., M.L., A.J.M., A.B.M., W.P., F.-X.R., P.S., M.G.T. and S.J.O. collaborated with local groups to collect Papuan samples. S.E. collaborated with local groups to collect the Rapanui sample. A.Mar. extracted DNA for the Aboriginal Australian genomes. M.S.S., A.B. and C.T.-S. coordinated the design and sequencing of the Papuan genomes. O.L., V.C.S., I.A., A.-S.M., A.B., G.A., J.Y.C., J.E.C., T.H.H., E.M., S.P., S.R., S.Sc., S.Su., J.L.W., A.A., C.Ba., I.D., A.E., A.Man., I.M., I.P., T.S.K., I.P.L., J.V.M.-M., S.N., F.R., M.Si., F.A., S.B., L.E., J.D.W. and T.M. analysed genetic data. C.Bo. collected and analysed linguistic data. L.E., E.W., D.M.L., Y.X., M.E.P., C.T.-S., R.D., M.S.S., A.Man., M.H.S., T.M., M.St. and R.N. supervised genetic analyses. M.C.W., C.M., W.C., G.F., D.I., B.L., A.L., P.J.M., L.M., D.R., T.W., C.W., E.A.M.-S., M.M., M.E.P., S.J.O., J.D., A.B.M., R.A.F. and M.M.L. provided archaeological, anthropological and historical context. A.-S.M., V.C.S., O.L., I.A., A.B., M.M.L., R.N., L.E., D.M.L. and E.W. wrote the manuscript with critical input from G.A., T.H.H., E.M., S.Sc., S.Su., J.L.W., C.Ba., A.E., I.P., E.A.M.-S., M.S.S., S.J.O., C.T.-S., R.D., M.G.T., J.D., A.Man., M.H.S., R.A.F., C.Bo., J.D.W., T.M., M.St. and all other coauthors. A.-S.M., V.C.S., O.L., I.A. and A.B. revised and compiled the Supplementary Information.

Competing interests

The authors declare no competing financial interests.

Corresponding authors

Correspondence to Manjinder S. Sandhu or Laurent Excoffier or David M. Lambert or Eske Willerslev.

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    Supplementary Information

    This file contains Supplementary Text and Data, Supplementary Figures, Supplementary Tables and additional references (see Contents for more details).

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https://doi.org/10.1038/nature18299

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