biostudies-literatureMalaspinas ASSwiss National Science FoundationEuropean Research CouncilNovo Nordisk Foundation Center for Protein ResearchWellcome TrustLundbeck FoundationBiotechnology and Biological Sciences Research Council207-214https://www.ebi.ac.uk/biostudies/studies/S-EPMC7617037biostudies-literatureUnknown538(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 Australians descend from a single founding population that differentiated ~10-32 kya. We infer a population expansion in northeast Australia during the Holocene epoch (past 10,000 years) 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 archaic populations. Finally, we report evidence of selection in Aboriginal Australians potentially associated with living in the desert.NatureA genomic history of Aboriginal Australia.PMC7617037647787R155-2013-16338106289100719/Z/12/Z154717090532143393R215-2015-4174R109-2012-9995PI Søren Brunak100719R70-2010-6286098051R38-2008-3048BB/H005854/1R24-2008-2527Bergstrom ACampos PFRasmussen SEllingvag SWall CMExcoffier LMcAllister PJAlves IWestaway MCWillerslev EBrunak SAlbrechtsen AReynolds DLevkivskyi IPSchierup MHSousa VCCheng JYSubramanian SDurbin RFoley RASikora MMigliano ABMoltke IMargaryan ABrucato NMalaspinas ASMailund TEriksson AXue YLogan BClark WSiba PLynch AMuller CWright JLMurgha LPhipps MEKoki GAghakhanian FAWales TDortch JMatisoo-Smith EAAthanasiadis GMacholdt EStoneking MManica ALahr MMDupanloup ISchiffels SHeupink THTyler-Smith CPugach IPomat WMoreno-Mayar JVNielsen RWall JDCrawford JEThomas MGLeavesley MMentzer AJLambert DMRicaut FXInjie DFourmile GGerbault PMetspalu MOppenheimer SJNi SBowern CBarbieri CPeischl SLao OSandhu MSRacimo FKorneliussen TSfalseA genomic history of Aboriginal Australia.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 Australians descend from a single founding population that differentiated ~10-32 kya. We infer a population expansion in northeast Australia during the Holocene epoch (past 10,000 years) 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 archaic populations. Finally, we report evidence of selection in Aboriginal Australians potentially associated with living in the desert.2016-01-01T00:00:00Z2016 Oct2026-06-03T00:54:19.14Z2025-04-06T15:08:27.649ZS-EPMC76170372765491410.1038/nature18299