A genomic history of Aboriginal Australia

Handle URI:
http://hdl.handle.net/10754/622366
Title:
A genomic history of Aboriginal Australia
Authors:
Malaspinas, Anna-Sapfo; Westaway, Michael C.; Muller, Craig; Sousa, Vitor C.; Lao, Oscar; Alves, Isabel; Bergström, Anders; Athanasiadis, Georgios; Cheng, Jade Y.; Crawford, Jacob E.; Heupink, Tim H.; Macholdt, Enrico; Peischl, Stephan; Rasmussen, Simon; Schiffels, Stephan; Subramanian, Sankar; Wright, Joanne L.; Albrechtsen, Anders; Barbieri, Chiara; Dupanloup, Isabelle; Eriksson, Anders ( 0000-0003-3436-3726 ) ; Margaryan, Ashot; Moltke, Ida; Pugach, Irina; Korneliussen, Thorfinn S.; Levkivskyi, Ivan P.; Moreno-Mayar, J. Víctor; Ni, Shengyu; Racimo, Fernando; Sikora, Martin; Xue, Yali; Aghakhanian, Farhang A.; Brucato, Nicolas; Brunak, Søren; Campos, Paula F.; Clark, Warren; Ellingvåg, Sturla; Fourmile, Gudjugudju; Gerbault, Pascale; Injie, Darren; Koki, George; Leavesley, Matthew; Logan, Betty; Lynch, Aubrey; Matisoo-Smith, Elizabeth A.; McAllister, Peter J.; Mentzer, Alexander J.; Metspalu, Mait; Migliano, Andrea B.; Murgha, Les; Phipps, Maude E.; Pomat, William; Reynolds, Doc; Ricaut, Francois-Xavier; Siba, Peter; Thomas, Mark G.; Wales, Thomas; Wall, Colleen Ma’run; Oppenheimer, Stephen J.; Tyler-Smith, Chris; Durbin, Richard; Dortch, Joe; Manica, Andrea; Schierup, Mikkel H.; Foley, Robert A.; Lahr, Marta Mirazón; Bowern, Claire; Wall, Jeffrey D.; Mailund, Thomas; Stoneking, Mark; Nielsen, Rasmus; Sandhu, Manjinder S.; Excoffier, Laurent; Lambert, David M.; Willerslev, Eske
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. © 2016 Macmillan Publishers Limited, part of Springer Nature. All rights reserved
KAUST Department:
Biological and Environmental Sciences and Engineering (BESE) Division; Integrative Systems Biology Lab
Citation:
Malaspinas A-S, Westaway MC, Muller C, Sousa VC, Lao O, et al. (2016) A genomic history of Aboriginal Australia. Nature 538: 207–214. Available: http://dx.doi.org/10.1038/nature18299.
Publisher:
Springer Nature
Journal:
Nature
Issue Date:
20-Sep-2016
DOI:
10.1038/nature18299
Type:
Article
ISSN:
0028-0836; 1476-4687
Sponsors:
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.
Additional Links:
http://www.nature.com/nature/journal/v538/n7624/full/nature18299.html
Appears in Collections:
Articles; Biological and Environmental Sciences and Engineering (BESE) Division

Full metadata record

DC FieldValue Language
dc.contributor.authorMalaspinas, Anna-Sapfoen
dc.contributor.authorWestaway, Michael C.en
dc.contributor.authorMuller, Craigen
dc.contributor.authorSousa, Vitor C.en
dc.contributor.authorLao, Oscaren
dc.contributor.authorAlves, Isabelen
dc.contributor.authorBergström, Andersen
dc.contributor.authorAthanasiadis, Georgiosen
dc.contributor.authorCheng, Jade Y.en
dc.contributor.authorCrawford, Jacob E.en
dc.contributor.authorHeupink, Tim H.en
dc.contributor.authorMacholdt, Enricoen
dc.contributor.authorPeischl, Stephanen
dc.contributor.authorRasmussen, Simonen
dc.contributor.authorSchiffels, Stephanen
dc.contributor.authorSubramanian, Sankaren
dc.contributor.authorWright, Joanne L.en
dc.contributor.authorAlbrechtsen, Andersen
dc.contributor.authorBarbieri, Chiaraen
dc.contributor.authorDupanloup, Isabelleen
dc.contributor.authorEriksson, Andersen
dc.contributor.authorMargaryan, Ashoten
dc.contributor.authorMoltke, Idaen
dc.contributor.authorPugach, Irinaen
dc.contributor.authorKorneliussen, Thorfinn S.en
dc.contributor.authorLevkivskyi, Ivan P.en
dc.contributor.authorMoreno-Mayar, J. Víctoren
dc.contributor.authorNi, Shengyuen
dc.contributor.authorRacimo, Fernandoen
dc.contributor.authorSikora, Martinen
dc.contributor.authorXue, Yalien
dc.contributor.authorAghakhanian, Farhang A.en
dc.contributor.authorBrucato, Nicolasen
dc.contributor.authorBrunak, Sørenen
dc.contributor.authorCampos, Paula F.en
dc.contributor.authorClark, Warrenen
dc.contributor.authorEllingvåg, Sturlaen
dc.contributor.authorFourmile, Gudjugudjuen
dc.contributor.authorGerbault, Pascaleen
dc.contributor.authorInjie, Darrenen
dc.contributor.authorKoki, Georgeen
dc.contributor.authorLeavesley, Matthewen
dc.contributor.authorLogan, Bettyen
dc.contributor.authorLynch, Aubreyen
dc.contributor.authorMatisoo-Smith, Elizabeth A.en
dc.contributor.authorMcAllister, Peter J.en
dc.contributor.authorMentzer, Alexander J.en
dc.contributor.authorMetspalu, Maiten
dc.contributor.authorMigliano, Andrea B.en
dc.contributor.authorMurgha, Lesen
dc.contributor.authorPhipps, Maude E.en
dc.contributor.authorPomat, Williamen
dc.contributor.authorReynolds, Docen
dc.contributor.authorRicaut, Francois-Xavieren
dc.contributor.authorSiba, Peteren
dc.contributor.authorThomas, Mark G.en
dc.contributor.authorWales, Thomasen
dc.contributor.authorWall, Colleen Ma’runen
dc.contributor.authorOppenheimer, Stephen J.en
dc.contributor.authorTyler-Smith, Chrisen
dc.contributor.authorDurbin, Richarden
dc.contributor.authorDortch, Joeen
dc.contributor.authorManica, Andreaen
dc.contributor.authorSchierup, Mikkel H.en
dc.contributor.authorFoley, Robert A.en
dc.contributor.authorLahr, Marta Mirazónen
dc.contributor.authorBowern, Claireen
dc.contributor.authorWall, Jeffrey D.en
dc.contributor.authorMailund, Thomasen
dc.contributor.authorStoneking, Marken
dc.contributor.authorNielsen, Rasmusen
dc.contributor.authorSandhu, Manjinder S.en
dc.contributor.authorExcoffier, Laurenten
dc.contributor.authorLambert, David M.en
dc.contributor.authorWillerslev, Eskeen
dc.date.accessioned2017-01-02T09:28:26Z-
dc.date.available2017-01-02T09:28:26Z-
dc.date.issued2016-09-20en
dc.identifier.citationMalaspinas A-S, Westaway MC, Muller C, Sousa VC, Lao O, et al. (2016) A genomic history of Aboriginal Australia. Nature 538: 207–214. Available: http://dx.doi.org/10.1038/nature18299.en
dc.identifier.issn0028-0836en
dc.identifier.issn1476-4687en
dc.identifier.doi10.1038/nature18299en
dc.identifier.urihttp://hdl.handle.net/10754/622366-
dc.description.abstractThe 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. © 2016 Macmillan Publishers Limited, part of Springer Nature. All rights reserveden
dc.description.sponsorshipWe 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.en
dc.publisherSpringer Natureen
dc.relation.urlhttp://www.nature.com/nature/journal/v538/n7624/full/nature18299.htmlen
dc.titleA genomic history of Aboriginal Australiaen
dc.typeArticleen
dc.contributor.departmentBiological and Environmental Sciences and Engineering (BESE) Divisionen
dc.contributor.departmentIntegrative Systems Biology Laben
dc.identifier.journalNatureen
dc.contributor.institutionCentre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Oster Voldgade 5-7, Copenhagen, Denmarken
dc.contributor.institutionInstitute of Ecology and Evolution, University of Bern, Baltzerstrasse 6, Bern, Switzerlanden
dc.contributor.institutionSwiss Institute of Bioinformatics, Lausanne, Switzerlanden
dc.contributor.institutionResearch Centre for Human Evolution, Environmental Futures Research Institute, Griffith University, Nathan, Ql, Australiaen
dc.contributor.institutionCNAG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, Barcelona, Spainen
dc.contributor.institutionUniversitat Pompeu Fabra (UPF), Barcelona, Spainen
dc.contributor.institutionPopulation and Conservation Genetics Group, Instituto Gulbenkian de Ciência, Oeiras, Portugalen
dc.contributor.institutionWellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdomen
dc.contributor.institutionBioinformatics Research Centre, Aarhus University, Aarhus, Denmarken
dc.contributor.institutionDepartment of Integrative Biology, University of California, Berkeley, CA, United Statesen
dc.contributor.institutionVerily Life Sciences, 2425 Garcia Ave, Mountain View, CA, United Statesen
dc.contributor.institutionDepartment of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, Leipzig, Germanyen
dc.contributor.institutionInterfaculty Bioinformatics Unit, University of Bern, Baltzerstrasse 6, Bern, Switzerlanden
dc.contributor.institutionCenter for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Kemitorvet Building 208, Kongens, Lyngby, Denmarken
dc.contributor.institutionDepartment for Archaeogenetics, Max Planck Institute for the Science of Human History, Kahlaische Straße 10, Jena, Germanyen
dc.contributor.institutionBioinformatics Centre, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, Copenhagen, Denmarken
dc.contributor.institutionDepartment of Linguistic and Cultural Evolution, Max Planck Institute for the Science of Human History, Kahlaische Straße 10, Jena, Germanyen
dc.contributor.institutionDepartment of Zoology, University of Cambridge, Downing Street, Cambridge, United Kingdomen
dc.contributor.institutionInstitute for Theoretical Physics, ETH Zürich, Wolfgang-Pauli-Str. 27, Zürich, Switzerlanden
dc.contributor.institutionJeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia, Sunway City, Selangor, Malaysiaen
dc.contributor.institutionEvolutionary Medicine Group, Laboratoire d'Anthropologie Moléculaire et Imagerie de Synthèse, Centre National de la Recherche Scientifique, Université de Toulouse 3, Toulouse, Franceen
dc.contributor.institutionNovo Nordisk Foundation, Center for Protein Research, University of Copenhagen, Blegdamsvej 3B, Copenhagen, Denmarken
dc.contributor.institutionCIMAR, Centro Interdisciplinar de Investigacaõ Marinha e Ambiental, Universidade Do Porto, Rua dos Bragas 289, Porto, Portugalen
dc.contributor.institutionNational Parks and Wildlife, Sturt Highway, Buronga, NSW, Australiaen
dc.contributor.institutionExplico Foundation, Vågavegen 16, Florø, Norwayen
dc.contributor.institutionGiriwandi, Gimuy Yidinji Country, QL, Australiaen
dc.contributor.institutionResearch Department of Genetics, Evolution and Environment, University College London, Gower Street, London, United Kingdomen
dc.contributor.institutionUCL Department of Anthropology, 14 Taviton Street, London, United Kingdomen
dc.contributor.institutionYinhawangka elder, Perth, WA, Australiaen
dc.contributor.institutionPapua New Guinea Institute of Medical Research, PO Box 60, Goroka, Papua New Guineaen
dc.contributor.institutionDept of Archaeology, School of Humanities and Social Sciences, University PO Box 320, Cairns, QL, Australiaen
dc.contributor.institutionNgadju elder, Coolgardie, WA, Australiaen
dc.contributor.institutionWongatha elder, Kurrawang, WA, Australiaen
dc.contributor.institutionDepartment of Anatomy, University of Otago, Dunedin, New Zealanden
dc.contributor.institution2209 Springbrook Road, Springbrook, QL, Australiaen
dc.contributor.institutionWellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdomen
dc.contributor.institutionEstonian Biocentre, Riia 23b, Tartu, Estoniaen
dc.contributor.institution86 Workshop Road, Yarrabah, QL, Australiaen
dc.contributor.institutionEsperance Nyungar Elder, Esperance, WA, Australiaen
dc.contributor.institutionAtakani Street, Napranum, QL, Australiaen
dc.contributor.institution2 Wynnum North Road, Wynnum, QL, Australiaen
dc.contributor.institutionSchool of Anthropology and Museum Ethnography, Oxford University, Oxford, United Kingdomen
dc.contributor.institutionCentre for Rock Art Research and Management, University of Western Australia, Perth, WA, Australiaen
dc.contributor.institutionLeverhulme Centre for Human Evolutionary Studies, Department of Archaeology and Anthropology, University of Cambridge, Fitzwilliam Street, Cambridge, United Kingdomen
dc.contributor.institutionDepartment of Linguistics, Yale University, 370 Temple Street, New Haven, CT, United Statesen
dc.contributor.institutionInstitute for Human Genetics, University of California, San Francisco, CA, United Statesen
dc.contributor.institutionDepartments of Integrative Biology and Statistics, University of California, Berkeley, CA, United Statesen
kaust.authorEriksson, Andersen
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