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. Europe PMC Funders Author Manuscripts During most of the last 100 ky, Australia, Tasmania and New Guinea formed a single continent, Sahul, which was separated from Sunda (the continental landmass including mainland and western island Southeast Asia) by a series of deep oceanic troughs never exposed by changes in sea level. Colonisation of Sahul is thought to have required at least 8-10 sea crossings between islands, potentially constraining the occupation of Australia and New Guinea by earlier hominins1. Recent assessments suggest that Sahul was settled by 47.5-55 kya2,3 (Figure 1). These dates overlap with those for the earliest evidence for modern humans in Sunda4. The distinctiveness of the Australian archaeological and fossil record has led to the suggestion that the ancestors of Aboriginal Australians and Papuans (“Australo-Papuans” hereafter) left the African continent earlier than the ancestors of present-day Eurasians5. Although some genetic studies support such multiple dispersals from Africa6, others favour only one out of Africa (OoA) event, with one or two independent founding waves into Asia, of which the earlier contributed to Australo-Papuan ancestry7,8. In addition, recent genomic studies have shown that both Aboriginal Australian8 and Papuan9 ancestors admixed with Neanderthal and Denisovan archaic hominins after leaving Africa. …