A genomic history of aboriginal Australia

Anna Sapfo Malaspinas; Michael C. Westaway; Craig Edwin Muller; Vitor C. Sousa; Oscar Lao; Isabel Alves; Anders Bergström; Georgios Athanasiadis; Jade Yu 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 Sand Korneliussen; Ivan P. Levkivskyi; José Victor Moreno Mayar; Shengyu Ni; Fernando Racimo; Martin Sikora; Yali Xue; Farhang A. Aghakhanian; Nicolas Brucato; Søren Brunak; Paula 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; Eske Willerslev

doi:10.1038/nature18299

A genomic history of aboriginal Australia

Anna Sapfo Malaspinas, Michael C. Westaway, Craig Edwin Muller, Vitor C. Sousa, Oscar Lao, Isabel Alves, Anders Bergström, Georgios Athanasiadis, Jade Yu 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 DupanloupAnders Eriksson, Ashot Margaryan, Ida Moltke, Irina Pugach, Thorfinn Sand Korneliussen, Ivan P. Levkivskyi, José Victor Moreno Mayar, Shengyu Ni, Fernando Racimo, Martin Sikora, Yali Xue, Farhang A. Aghakhanian, Nicolas Brucato, Søren Brunak, Paula 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, Eske Willerslev

186 Citations (Scopus)

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.

Original language	English
Journal	Nature
Volume	538
Issue number	7624
Pages (from-to)	207-214
Number of pages	8
ISSN	0028-0836
DOIs	https://doi.org/10.1038/nature18299
Publication status	Published - 2016

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Malaspinas, A. S., Westaway, M. C., Muller, C. E., Sousa, V. C., Lao, O., Alves, I., Bergström, A., Athanasiadis, G., Cheng, J. Y., Crawford, J. E., Heupink, T. H., Macholdt, E., Peischl, S., Rasmussen, S., Schiffels, S., Subramanian, S., Wright, J. L., Albrechtsen, A., Barbieri, C., ... Willerslev, E. (2016). A genomic history of aboriginal Australia. Nature, 538(7624), 207-214. https://doi.org/10.1038/nature18299

Malaspinas, AS, Westaway, MC, Muller, CE, Sousa, VC, Lao, O, Alves, I, Bergström, A, Athanasiadis, G, Cheng, JY, Crawford, JE, Heupink, TH, Macholdt, E, Peischl, S, Rasmussen, S, Schiffels, S, Subramanian, S, Wright, JL, Albrechtsen, A, Barbieri, C, Dupanloup, I, Eriksson, A, Margaryan, A , Moltke, I, Pugach, I, Korneliussen, TS, Levkivskyi, IP, Moreno Mayar, JV, Ni, S, Racimo, F, Sikora, M, Xue, Y, Aghakhanian, FA, Brucato, N, Brunak, S, Campos, P, Clark, W, Ellingvåg, S, Fourmile, G, Gerbault, P, Injie, D, Koki, G, Leavesley, M, Logan, B, Lynch, A, Matisoo-Smith, EA, McAllister, PJ, Mentzer, AJ, Metspalu, M, Migliano, AB, Murgha, L, Phipps, ME, Pomat, W, Reynolds, D, Ricaut, F-X, Siba, P, Thomas, MG, Wales, T, Wall, CM, Oppenheimer, SJ, Tyler-Smith, C, Durbin, R, Dortch, J, Manica, A, Schierup, MH, Foley, RA, Lahr, MM, Bowern, C, Wall, JD, Mailund, T, Stoneking, M, Nielsen, R, Sandhu, MS, Excoffier, L, Lambert, DM & Willerslev, E 2016, 'A genomic history of aboriginal Australia', Nature, vol. 538, no. 7624, pp. 207-214. https://doi.org/10.1038/nature18299

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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.",

author = "Malaspinas, {Anna Sapfo} and Westaway, {Michael C.} and Muller, {Craig Edwin} and Sousa, {Vitor C.} and Oscar Lao and Isabel Alves and Anders Bergstr{\"o}m and Georgios Athanasiadis and Cheng, {Jade Yu} and Crawford, {Jacob E.} and Heupink, {Tim H.} and Enrico Macholdt and Stephan Peischl and Simon Rasmussen and Stephan Schiffels and Sankar Subramanian and Wright, {Joanne L} and Anders Albrechtsen and Chiara Barbieri and Isabelle Dupanloup and Anders Eriksson and Ashot Margaryan and Ida Moltke and Irina Pugach and Korneliussen, {Thorfinn Sand} and Levkivskyi, {Ivan P.} and {Moreno Mayar}, {Jos{\'e} Victor} and Shengyu Ni and Fernando Racimo and Martin Sikora and Yali Xue and Aghakhanian, {Farhang A.} and Nicolas Brucato and S{\o}ren Brunak and Paula Campos and Warren Clark and Sturla Ellingv{\aa}g and Gudjugudju Fourmile and Pascale Gerbault and Darren Injie and George Koki and Matthew Leavesley and Betty Logan and Aubrey Lynch and Matisoo-Smith, {Elizabeth A.} and McAllister, {Peter J.} and Mentzer, {Alexander J.} and Mait Metspalu and Migliano, {Andrea B} and Les Murgha and Phipps, {Maude E} and William Pomat and Doc Reynolds and Francois-Xavier Ricaut and Peter Siba and Thomas, {Mark G.} and Thomas Wales and Wall, {Colleen Ma'run} and Oppenheimer, {Stephen J} and Chris Tyler-Smith and Richard Durbin and Joe Dortch and Andrea Manica and Schierup, {Mikkel H.} and Foley, {Robert A.} and Lahr, {Marta Miraz{\'o}n} and Claire Bowern and Wall, {Jeffrey D.} and Thomas Mailund and Mark Stoneking and Rasmus Nielsen and Sandhu, {Manjinder S.} and Laurent Excoffier and Lambert, {David M.} and Eske Willerslev",

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AU - Malaspinas, Anna Sapfo

AU - Westaway, Michael C.

AU - Muller, Craig Edwin

AU - Sousa, Vitor C.

AU - Lao, Oscar

AU - Alves, Isabel

AU - Bergström, Anders

AU - Athanasiadis, Georgios

AU - Cheng, Jade Yu

AU - Crawford, Jacob E.

AU - Heupink, Tim H.

AU - Macholdt, Enrico

AU - Peischl, Stephan

AU - Rasmussen, Simon

AU - Schiffels, Stephan

AU - Subramanian, Sankar

AU - Wright, Joanne L

AU - Albrechtsen, Anders

AU - Barbieri, Chiara

AU - Dupanloup, Isabelle

AU - Eriksson, Anders

AU - Margaryan, Ashot

AU - Moltke, Ida

AU - Pugach, Irina

AU - Korneliussen, Thorfinn Sand

AU - Levkivskyi, Ivan P.

AU - Moreno Mayar, José Victor

AU - Ni, Shengyu

AU - Racimo, Fernando

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AU - Ellingvåg, Sturla

AU - Fourmile, Gudjugudju

AU - Gerbault, Pascale

AU - Injie, Darren

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AU - Logan, Betty

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AU - Migliano, Andrea B

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AU - Siba, Peter

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AU - Foley, Robert A.

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AU - Mailund, Thomas

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N2 - 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.

AB - 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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DO - 10.1038/nature18299

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VL - 538

SP - 207

EP - 214

JO - Nature

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ER -

A genomic history of aboriginal Australia

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