Papuan mitochondrial genomes and the settlement of Sahul

Abstract

New Guineans represent one of the oldest locally continuous populations outside Africa, harboring among the greatest linguistic and genetic diversity on the planet. Archeological and genetic evidence suggest that their ancestors reached Sahul (present day New Guinea and Australia) by at least 55,000 years ago (kya). However, little is known about this early settlement phase or subsequent dispersal and population structuring over the subsequent period of time. Here we report 379 complete Papuan mitochondrial genomes from across Papua New Guinea, which allow us to reconstruct the phylogenetic and phylogeographic history of northern Sahul. Our results support the arrival of two groups of settlers in Sahul within the same broad time window (50-65 kya), each carrying a different set of maternal lineages and settling Northern and Southern Sahul separately. Strong geographic structure in northern Sahul remains visible today, indicating limited dispersal over time despite major climatic, cultural, and historical changes. However, following a period of isolation lasting nearly 20 ky after initial settlement, environmental changes postdating the Last Glacial Maximum stimulated diversification of mtDNA lineages and greater interactions within and beyond Northern Sahul, to Southern Sahul, Wallacea and beyond. Later, in the Holocene, populations from New Guinea, in contrast to those of Australia, participated in early interactions with incoming Asian populations from Island Southeast Asia and continuing into Oceania.

A different paradigm for the colonisation of Sahul

“…If that were so, then the mutations that define all “daughter” lineages found in modern indigenous Sahul populations must have occurred after those macro‐haplogroups arrived in the continent. Veth, Clarkson and Norman endorse low haplogroup diversity among founders, citing Pedro and colleagues’ (2020) recent TMRCA estimates >>50 ka for some of those lineages. They confuse these TMRCA estimates with dates for their presence in Sahul.…”

“…Any fall back on genetic estimates of c.50 ka for the occupation of Sahul is overturned by the most recent genetic estimates indicating settlement by at least ∼55 ka (95% CI: 42–67 ka) (Pedro et al . 2020), with peopling taking place via both the northern and southern routes. Evidence also exists for an earlier Out of Africa remnant contribution (albeit small) to Sahul genomes (Pagani et al .…”

“…While some of this diversity may reflect later movements, multiple maternal (Pedro et al . 2020) and paternal (Bergström et al . 2016) lineages date back before 50 ka.…”

“…Recent mtDNA analyses show that two groups of settlers arrived between 50 and 65 ka settling Northern (Papuan) and Southern Sahul (Pedro et al . 2020). Lineages became geographically structured between 10 and 32 ka (Tobler et al .…”

“…Pedro et al . (2020) agree:

The scenario we might postulate from these results suggests (1) the diversification of ancestral Sahul lineages in a population located in Sunda, (2) two (or more) dispersal events to Sahul within the same narrow time frame around 45–55 ka, (3) a dispersal to Sahul of a group of settlers carrying lineages observed today in Northern Sahul (M27, M28, M29’Q, P1, P2, P4a, P10, P13b), (4) another dispersal to Sahul of a group of settlers carrying the lineages observed today in Southern Sahul (O, S, N13, M42a'c, P5, P6, P7, P8, and other P) …

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