title: Genomics, Languages and the Prehistory of Aboriginal Australia
Creators: name: Kumar, Manoharan
Publisher: name: Griffith University
Year: 2021
Subjects: subject: Aboriginal Australians
subject: Indigenous Australian languages
subject: Pama-Nyungan
subject: Non-Pama- Nyungan

description: When European settlers first arrived in Australia in 1788, Aboriginal Australians, or Traditional Owners, spoke more than 250 languages. Indigenous Australian languages are now broadly categorised into two groups: Pama-Nyungan (PN) and Non-Pama-Nyungan (NPN) languages. PN speakers traditionally inhabited more than 90% of the land mass of mainland Australia, whereas NPN speakers traditionally occupied only 10% of the land area, and this was in the far northwest of the continent. The NPN language group in particular shows very high linguistic diversity. Studies of nuclear DNA variation can provide valuable information on population polymorphism, structure, and demographics such as expansion, settlement and to date, there have been no such studies on NPN populations. Hence, population genetic studies are important to understand the genetic structure and history of NPN speaking populations. To understand the settlement of NPN language speakers in Australia and their genetic relationship with PN speakers, I undertook a comprehensive population genetic analysis of Aboriginal Australians across the continent. I obtained 56 samples with approval of Aboriginal Australian Elders from six different regions of the country, including Groote Eylandt Island (Anindilyakwa language speaker; NPN), Mornington Island (where Lardil, Kaidal and Yangkaal language speaker; NPN), northeast Arnhem Land (Yolngu language speakers; PN) and Normanton (Gkuthaarn/Kukatj language), Cairns (Gunggandjii) and Stradbroke Island (Jandai language speakers; PN). I performed whole genome sequencing with coverage (30-60X) and population genetic analysis of individuals representing three PN-speakers from three locations and four NPN-speaking populations from two locations. The 56 new genomes reported here were combined with previously published whole genome sequences of contemporary (100) and high coverage (5X) ancient (4) individuals to understand maternal and paternal ancestry, as well as nuclear genetic diversity. Mitochondrial DNA analyses revealed that Aboriginal Australians comprise four major haplogroups. These comprised N and S haplogroups that are unique to Aboriginal Australians while P, M haplogroups are shared with their neighbours from Papua and South East Asia. Phylogenetic analysis of whole mitochondrial genomic sequences showed NPN and PN speakers have shared ancestry within Australia and outside Australia, prior to European settlement. Analysis of Y-Chromosome haplogroups showed that NPN language speakers from Gulf of Carpentaria Island regions and PN speakers (Yolngu) from northeast Arnhem land have experienced very little admixture with Europeans since they arrived. However, Y-Chromosome marker from individuals belong to Stradbroke Island and Normanton showed that 90-100% of samples have European and East Asian ancestry. In addition, Y-Chromosome sequences from the Arnhem Land region showed that members of the Yolngu speaking population have a higher level of shared male ancestry with NPN speakers from Groote Eylandt and Mornington Islands than with other PN populations. Analyses of nuclear whole genome data, including PCA, ADMIXTURE &amp; Out-group F3-statistics, revealed that NPN have distinct ancestry shared among NPNs. In addition, genetic analysis shows that PNs are the closest population to NPNs. This suggests that Australia were likely colonised by a single founder population. Furthermore, Nuclear analysis of PN speaking Arnhem Land population show that they are more closely related to NPN speakers than any other PN speakers in Australia. This is owing to the geographical proximity between these populations than their linguistic relatedness. Finally, the above 56 Aboriginal Australians samples were used to address the intriguing hypothesis, first proposed by Thomas Henry Huxley in 1870, that a close genetic relationship exists between the Indigenous peoples of Australia and India. To investigate this hypothesis, I sampled 14 genomes from South Asia and sequenced these to 30X coverage. These were compared to 160 Aboriginal Australian genomes which comprised newly sequenced (56) and previously published modern (100) together with ancient (4) samples. Population genetic analysis revealed that Aboriginal Australians do have Indian ancestry, ranging from 1-7%. However, due to the low proportion of Indian ancestry in a very few individuals I could not further confirm the potential Holocene migration from India to Australia. Future studies based on more modern and ancient Aboriginal Australian genomes could help to confirm or reject the hypothesis. The datasets presented in this thesis provide new knowledge about Aboriginal Australians including insights into their uniparental sequence ancestry, as well as genetic structure and settlement of NPN language speakers. These results will be invaluable for future research on contemporary Aboriginal Australians and will provide important implications for the identification of unprovenanced remains from regions across Australia.