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Mitochondrial DNA diversity of present-day Aboriginal Australians and implications for human evolution in Oceania

Abstract

Aboriginal Australians are one of the more poorly studied populations from the standpoint of human evolution and genetic diversity. Thus, to investigate their genetic diversity, the possible date of their ancestors’ arrival and their relationships with neighboring populations, we analyzed mitochondrial DNA (mtDNA) diversity in a large sample of Aboriginal Australians. Selected mtDNA single-nucleotide polymorphisms and the hypervariable segment haplotypes were analyzed in 594 Aboriginal Australians drawn from locations across the continent, chiefly from regions not previously sampled. Most (~78%) samples could be assigned to mtDNA haplogroups indigenous to Australia. The indigenous haplogroups were all ancient (with estimated ages >40 000 years) and geographically widespread across the continent. The most common haplogroup was P (44%) followed by S (23%) and M42a (9%). There was some geographic structure at the haplotype level. The estimated ages of the indigenous haplogroups range from 39 000 to 55 000 years, dates that fit well with the estimated date of colonization of Australia based on archeological evidence (~47 000 years ago). The distribution of mtDNA haplogroups in Australia and New Guinea supports the hypothesis that the ancestors of Aboriginal Australians entered Sahul through at least two entry points. The mtDNA data give no support to the hypothesis of secondary gene flow into Australia during the Holocene, but instead suggest long-term isolation of the continent.

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Acknowledgements

This work was supported by National Geographic Society, IBM, Waitt Family Foundation. We gratefully acknowledge the participation of Aboriginal Australians from Victoria, Queensland, the Northern Territory, South Australia, Western Australia and Tasmania whose collaboration made this study possible. We owe Tammy Williams and Jason Tatipata many thanks for their support throughout this study. We also thank the jurisdictional forensic departments for access to their samples. YLX and CTS were supported by The Wellcome Trust (098051), and MK, MvO and KNB were supported by Erasmus MC.

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Correspondence to R John Mitchell.

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The authors declare no conflict of interest.

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Syama Adhikarla11, Christina J Adler12, Elena Balanovska13, Oleg Balanovsky13, Jaume Bertranpetit14, Andrew C Clarke15, David Comas14, Alan Cooper12, Clio SI Der Sarkissian12, Matthew C Dulik, Jill B Gaieski, ArunKumar GaneshPrasad11, Wolfgang Haak12, Marc Haber14,16, Angela Hobbs17, Asif Javed18, Li Jin19, Matthew E Kaplan20, Shilin Li19, Begoña Martínez-Cruz14, Elizabeth A Matisoo-Smith15, Marta Melé14, Nirav C Merchant20, Amanda C Owings, Laxmi Parida18, Ramasamy Pitchappan11, Daniel E Platt18, Lluis Quintana-Murci21, Colin Renfrew22, Ajay K Royyuru18, Arun Varatharajan Santhakumari11, Fabrício R Santos23, Himla Soodyall17, David F Soria Hernanz24, Pandikumar Swamikrishnan25, Miguel G Vilar24, R Spencer Wells16, Pierre A Zalloua26 and Janet S Ziegle26, 11Madurai Kamaraj University, Madurai, Tamil Nadu, India;12University of Adelaide, South Australia, Australia; 13Research Centre for Medical Genetics, Russian Academy of Medical Sciences, Moscow, Russia; 14Universitat Pompeu Fabra, Barcelona, Spain; 15University of Otago, Dunedin, New Zealand; 16Lebanese American University, Chouran, Beirut, Lebanon; 17National Health Laboratory Service, Johannesburg, South Africa; 18IBM, Yorktown Heights, NY, USA; 19Fudan University, Shanghai, China; 20University of Arizona, Tucson, AZ, USA; 21Institut Pasteur, Paris, France; 22University of Cambridge, Cambridge, United Kingdom; 23Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil; 24National Geographic Society, Washington, DC, USA; 25IBM, Somers, NY, USA and 26Applied Biosystems, Foster City, CA, USA.

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Nagle, N., Ballantyne, K., van Oven, M. et al. Mitochondrial DNA diversity of present-day Aboriginal Australians and implications for human evolution in Oceania. J Hum Genet 62, 343–353 (2017). https://doi.org/10.1038/jhg.2016.147

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