Aboriginal Australian mitochondrial genome variation – an increased understanding of population antiquity and diversity

Abstract

Aboriginal Australians represent one of the oldest continuous cultures outside Africa, with evidence indicating that their ancestors arrived in the ancient landmass of Sahul (present-day New Guinea and Australia) ~55 thousand years ago. Genetic studies, though limited, have demonstrated both the uniqueness and antiquity of Aboriginal Australian genomes. We have further resolved known Aboriginal Australian mitochondrial haplogroups and discovered novel indigenous lineages by sequencing the mitogenomes of 127 contemporary Aboriginal Australians. In particular, the more common haplogroups observed in our dataset included M42a, M42c, S, P5 and P12, followed by rarer haplogroups M15, M16, N13, O, P3, P6 and P8. We propose some major phylogenetic rearrangements, such as in haplogroup P where we delinked P4a and P4b and redefined them as P4 (New Guinean) and P11 (Australian), respectively. Haplogroup P2b was identified as a novel clade potentially restricted to Torres Strait Islanders. Nearly all Aboriginal Australian mitochondrial haplogroups detected appear to be ancient, with no evidence of later introgression during the Holocene. Our findings greatly increase knowledge about the geographic distribution and phylogenetic structure of mitochondrial lineages that have survived in contemporary descendants of Australia’s first settlers.

A different paradigm for the initial colonisation of Sahul

“…In two recent studies of whole genome and control region mitochondrial diversity in samples obtained from hundreds of living Aborigines in many parts of Australia, Nagle et al . (, ) identified at least three common haplogroups – M42, S N and P R – together with M15, M16, O N and N13. All are highly diversified, implying long‐term presence on the continent.…”

“…Nagle et al . (, ) offer a more comprehensive set of TMRCA estimates based on both the Fu et al . and Soares et al .…”

“…Others prefer an intra‐Sahul emergence based on similar estimated time depths for P9‐10 versus Australian P subtypes (Nagle et al . , ; John Mitchell pers. comm.…”

“…) that may be a product of recent history (Nagle et al . , ). The Y‐chromosome data indicate similar deep time splits.…”

What we were told: Responses to 65,000 years of Aboriginal history

“…27 Redd and Stoneking 1999: 808-28. 28 Bergström et al 2016Nagle et al 2017: 43041. 29 Paterson 2011.…”