A high-resolution genomic study of the Pama-Nyungan speaking Yolngu people of northeast Arnhem Land, Australia.

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Abstract: Objectives: About 300 Aboriginal languages were spoken in Australia. These were classified into two groups: Pama-Nyungan (PN), comprised of one language Family, and Non-Pama-Nyungan (NPN) with more than 20 language Families. The Yolngu people belong to the larger PN Family and live in Arnhem Land in northern Australia. They are surrounded by groups who speak NPN languages. This study, using nuclear genomic and mitochondrial DNA data, was undertaken to shed light on the origins of the Yolngu people and their language. The nuclear genomic sequences of Yolngu people were compared to those of other Indigenous Australians, as well as Papuan, African, East Asian and European people. Materials and methods: With the agreement of Indigenous participants, samples were collected from 13 Yolngu individuals and 4 people from neighbouring NPN speakers and their nuclear genomes sequenced to a 30? coverage. Using the short-read DNA BGISEQ-500 technology, these sequences were mapped to a reference genome and identified ~24.86 million Single Nucleotide Variants (SNVs). The Yolngu SNVs were then compared to those of 36 individuals from 10 other Indigenous populations/locations across Australia and four worldwide populations using multidimensional scaling, population structure, F3 statistics and phylogenetic analyses. Results: Using the above methods, we infer that Yolngu speakers are closely related to neighbouring NPN speakers, followed by the Weipa population. No European or East Asian admixture was detected in the genomes of the Yolngu speakers studied here, which contrasts with the genomes of many other PN speakers that have been studied. Our results show that Yolngu speakers are more closely related to other PN speakers in the northeast of Australia than to those in central and western Australia studied here. Yolngu and the other Australian populations from this study share Papuans as an out-group. Discussion: The study presented here provides an account of the nuclear and mitochondrial genomic diversity within the PN Yolngu Aboriginal population. The results show the Yolngu sample and their NPN neighbours have a strong genetic relationship. They also offer evidence of ancestral links between the Yolngu and PN-speaking populations in Cape York. From earlier fingerprint studies, consistent with the genomic results shown here, we suggest that there was a movement of people from the east into northeast Arnhem Land, associated with the flooding of the Sahul Shelf, and that this occurred between about 11 Kya and 8 Kya ago. Several Yolngu myths point to such a movement. It is suggested that the spread of the PN language or its speakers may have influenced the population structure of the Yolngu. Further genomic studies, with larger samples, of populations to the east of the Yolngu around the Gulf of Carpentaria into Cape York are required to test this hypothesis. Our results imply that PN did not spread with the movement of people across the continent, rather, the PN languages diffused among the different populations. It seems clear that the languages dispersed and not the people. The low level of relatedness detected between the Yolngu people and the people of the central arid desert of Australia suggests a long period of separation with different patterns of migration. Beyond Australia, Yolngu are most closely related to the Papuan people of New Guinea.