Papua New Guinean Genomes Reveal the Complex Settlement of North Sahul

Abstract

The settlement of Sahul, the lost continent of Oceania, remains one of the most ancient and debated human migrations. Modern New Guineans inherited a unique genetic diversity tracing back 50,000 years, and yet there is currently no model reconstructing their past population dynamics. We generated 58 new whole genome sequences from Papua New Guinea, filling geographical gaps in previous sampling, specifically to address alternative scenarios of the initial migration to Sahul and the settlement of New Guinea. Here, we present the first genomic models for the settlement of northeast Sahul considering one or two migrations from Wallacea. Both models fit our dataset, reinforcing the idea that ancestral groups to New Guinean and Indigenous Australians split early, potentially during their migration in Wallacea where the northern route could have been favored. The earliest period of human presence in Sahul was an era of interactions and gene flow between related but already differentiated groups, from whom all modern New Guineans, Bismarck islanders and Indigenous Australians descend. The settlement of New Guinea was probably initiated from its southeast region, where the oldest archaeological sites have been found. This was followed by two migrations into the south and north lowlands that ultimately reached the west and east highlands. We also identify ancient gene flows between populations in New Guinea, Australia, East Indonesia and the Bismarck Archipelago, emphasizing the fact that the anthropological landscape during the early period of Sahul settlement was highly dynamic rather than the traditional view of extensive isolation.

Assessing human genome-wide variation in the Massim region of Papua New Guinea and implications for the Kula trading tradition

“…8A), and Austronesian segments are widely shared among the PNG lowland and island groups but not with the highlands (Fig. 8B), in keeping with previous observations of a lack of Austronesianassociated ancestry in the PNG highlands (27,28,32,34). However, sharing of Papuan segments is strictly either among mainland PNG and Massim groups, or among groups from the Bismarcks and Solomons; there is no sharing of Papuan-related IBD segments between any mainland PNG or Massim group and any group from the Bismarcks or Solomons (Fig.…”

“…Previous studies of genome-wide data have shown a major distinction between Papuan ancestries in the PNG Highlands vs. Bougainville (32), and in the western vs. eastern regions of the PNG Highlands (27,28). We find support for both of these distinctions, as well as for a novel Papuan-related ancestry on Rossel (Figs.…”

“…Second, the Papuan-related ancestry of Papuan-speaking Rossel Islanders is distinct from Papuan-related ancestries identified previously and elsewhere in Near Oceania. Previous studies of genome-wide data have shown a major distinction between Papuan ancestries in the PNG Highlands vs. Bougainville ( 32 ), and in the western vs. eastern regions of the PNG Highlands ( 27, 28 ). We find support for both of these distinctions, as well as for a novel Papuan-related ancestry on Rossel (Figs.…”

“…However, IBD sharing of segments of 1 to 5 cM reflects a time span of a few thousand years, and so the results in Fig. 8C could also reflect movement of people prior to the arrival of the Austronesians, or movement unrelated to the arrival of the Austronesians ( 28 ). For example, the flooding of the shallow continental shelf east of New Guinea, following the Last Glacial Maximum, appears to have led to depopulation of the current islands of the Massim region, with subsequent recolonization after ~5 kya ( 19 ); perhaps the IBD-sharing results reflect these movements.…”

“…This was interpreted as a potential signature of the Kula, as the travel between islands to perform the trading of the goods is mostly mediated by males, which could reduce inter-island genetic differences for the Y chromosome but not for mtDNA. However, studies of genome-wide data provide much richer information concerning admixture and population history, as shown by two recent genome-wide studies of PNG ( 27, 28 ), but genome-wide studies of the Massim are lacking as of yet. Here, we report the results of comprehensive genome-wide analyses of the Massim region with resulting insights into the genetic history of Oceania in general and implications for the Kula tradition in particular.…”