Indigenous Australian genomes show deep structure and rich novel variation

Matthew Silcocks, Ashley Farlow, Azure Hermes, Georgia Tsambos, Hardip R. Patel, Sharon Huebner, Gareth Baynam, Misty R. Jenkins, Damjan Vukcevic, Simon Easteal and Stephen Leslie ()
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Matthew Silcocks: Australian National University
Ashley Farlow: Australian National University
Azure Hermes: Australian National University
Georgia Tsambos: University of Melbourne, School of Mathematics and Statistics
Hardip R. Patel: Australian National University
Sharon Huebner: Australian National University
Gareth Baynam: Australian National University
Misty R. Jenkins: Australian National University
Damjan Vukcevic: University of Melbourne, School of Mathematics and Statistics
Simon Easteal: Australian National University
Stephen Leslie: Australian National University

Nature, 2023, vol. 624, issue 7992, 593-601

Abstract: Abstract The Indigenous peoples of Australia have a rich linguistic and cultural history. How this relates to genetic diversity remains largely unknown because of their limited engagement with genomic studies. Here we analyse the genomes of 159 individuals from four remote Indigenous communities, including people who speak a language (Tiwi) not from the most widespread family (Pama–Nyungan). This large collection of Indigenous Australian genomes was made possible by careful community engagement and consultation. We observe exceptionally strong population structure across Australia, driven by divergence times between communities of 26,000–35,000 years ago and long-term low but stable effective population sizes. This demographic history, including early divergence from Papua New Guinean (47,000 years ago) and Eurasian groups1, has generated the highest proportion of previously undescribed genetic variation seen outside Africa and the most extended homozygosity compared with global samples. A substantial proportion of this variation is not observed in global reference panels or clinical datasets, and variation with predicted functional consequence is more likely to be homozygous than in other populations, with consequent implications for medical genomics2. Our results show that Indigenous Australians are not a single homogeneous genetic group and their genetic relationship with the peoples of New Guinea is not uniform. These patterns imply that the full breadth of Indigenous Australian genetic diversity remains uncharacterized, potentially limiting genomic medicine and equitable healthcare for Indigenous Australians.

Date: 2023
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DOI: 10.1038/s41586-023-06831-w

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