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A Genomic History of Aboriginal Australia

ABSTRACT: The population history of Aboriginal Australians remains largely uncharacterised. We generated 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 early population structure in the ancient continent of Sahul (Australia, New Guinea and Tasmania). However, all 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 (past c.10 kya) 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 different archaic populations. Finally, we report evidence of selection in Aboriginal Australians potentially associated with living in the desert.

PROVIDER: EGAS00001001766 | EGA |

REPOSITORIES: EGA

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A genomic history of Aboriginal Australia.

Malaspinas Anna-Sapfo AS Westaway Michael C MC Muller Craig C Sousa Vitor C VC Lao Oscar O Alves Isabel I Bergström Anders A Athanasiadis Georgios G Cheng Jade Y JY Crawford Jacob E JE Heupink Tim H TH Macholdt Enrico E Peischl Stephan S Rasmussen Simon S Schiffels Stephan S Subramanian Sankar S Wright Joanne L JL Albrechtsen Anders A Barbieri Chiara C Dupanloup Isabelle I Eriksson Anders A Margaryan Ashot A Moltke Ida I Pugach Irina I Korneliussen Thorfinn S TS Levkivskyi Ivan P IP Moreno-Mayar J Víctor JV Ni Shengyu S Racimo Fernando F Sikora Martin M Xue Yali Y Aghakhanian Farhang A FA Brucato Nicolas N Brunak Søren S Campos Paula F PF Clark Warren W Ellingvåg Sturla S Fourmile Gudjugudju G Gerbault Pascale P Injie Darren D Koki George G Leavesley Matthew M Logan Betty B Lynch Aubrey A Matisoo-Smith Elizabeth A EA McAllister Peter J PJ Mentzer Alexander J AJ Metspalu Mait M Migliano Andrea B AB Murgha Les L Phipps Maude E ME Pomat William W Reynolds Doc D Ricaut Francois-Xavier FX Siba Peter P Thomas Mark G MG Wales Thomas T Wall Colleen Ma'run CM Oppenheimer Stephen J SJ Tyler-Smith Chris C Durbin Richard R Dortch Joe J Manica Andrea A Schierup Mikkel H MH Foley Robert A RA Lahr Marta Mirazón MM Bowern Claire C Wall Jeffrey D JD Mailund Thomas T Stoneking Mark M Nielsen Rasmus R Sandhu Manjinder S MS Excoffier Laurent L Lambert David M DM Willerslev Eske E

Nature 20160921 7624

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 Australian ...[more]

PMID: 27654914

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Project description:Introduction: Early life is characterized by heightened susceptibility to infections and is recognized as a major determinant of the immune system development and the overall health for the entire human lifespan. However, our knowledge of the development of the neonatal immune system is incomplete, limiting the development of novel preventative and therapeutic strategies, especially in newborns. To gain insight into the early immune system development and plasma proteome ontogeny, the Expanded Program on Immunization Consortium (EPIC) led by Professor Ofer Levy MD at Boston Children’s Hospital, Harvard Medical School and Tobias R. Kollmann Telethon Kids Institute, Australia as part of the Human Immunological Project Consortium (HIPC), established two independent cohorts of plasma from healthy newborns born by vaginal delivery during the first week of life. Methods: Blood samples were collected from 30 newborns in The Gambia (Medical Research Council Unit, The Gambia) at the day of birth (day of life, DOL 0) and at one of the follow-up visits on DOL1, DOL3, or DOL7. A similar validation cohort was collected in Papua New Guinea (PNG) (Institute for Medical Research, Papua New Guinea, Australasian) from 19 newborns. The plasma proteome was characterized by LC-MS on a Q Exactive using the proven and published plasma proteomics platform developed in the Steen Laboratory, led by Dr Hanno Steen, Director of Proteomics at Boston Children’s Hospital, Harvard Medical School, employing only microliter of plasma prepared in a 96-well plate format. The data was analyzed with MaxQuant. Results: We characterized 385 blood-plasma proteins. Utilizing the paired study design, we identified consistent changes related to ontogeny and cellular growth pathways in the blood-plasma proteome. Conclusion: This dataset allows for studying the early ontogeny of the plasma proteome, and in extension the early immune system development, in two independent healthy cohorts. Characterization of the plasma proteome may provide novel insight into new approaches to prevent, detect, and treat infectious diseases. Acknowledgements: We would like to thank all the participating families and all past and current members of the EPIC-HIPC, and the Steen Laboratory, without whom this study would not be possible. A special recognition goes to the teams who established the unique cohorts in The Gambia, by Professor Beate Kampmann and Dr Olubukola T. Idoko at The Gambia at the London School of Hygiene and Tropical Medicine, The Gambia, and in PNG, by Anita H.J. van der Biggelaar and William S. Pomat at Wesfarmers Centre of Vaccines and Infectious Diseases, Telethon Kids Institute, University of Western Australia Perth, Australia.

Dataset Information

A Genomic History of Aboriginal Australia

Publications

A genomic history of Aboriginal Australia.

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