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.

Fig. 1

Genetic relationships and increasing population sizes across Sunda and Sahul. a Seven geographical regions: coastal PNG (light blue), highland PNG (dark blue), Near Oceania (pink), Remote Oceania (red), Australia (Orange), Wallacea (light green), and Sunda (dark green). b Tree of haplogroup P. Subclades are represented by triangles, while single lineages are represented by lines. The tree is scaled to kya (thousands of years ago) using the maximum likelihood molecular clock for the whole mtDNA genome with the mutation rate of Fu et al. (details of age estimates are reported in Table S1). c Tree of haplogroups M and Q. d Bayesian skyline plot representing median estimates of effective population size for each the seven geographic regions based on P, M, and Q mtDNA lineages

Fig. 2

Spatial distribution of main Sahul mtDNA haplogroups. Inverse distance weighted interpolation shows areas with higher frequencies in darker shading, taking into account only the effects of distance (color scale in regions with few or no samples should not be considered as having high statistical confidence). Data details are provided in Table S5 and the triangles represent the central point for each region used in the interpolation. a Distribution of haplogroup M27. b Haplogroup M28. c Haplogroup M29. d Haplogroup P. e Haplogroup Q

Fig. 3

Proposed movements of maternal lineages P, M, and Q. Dark shading represents modern coastlines; light shading illustrates the extent of the Sunda continent at the Last Glacial Maximum. Red octagrams represent the probable approximate origins of haplogroups. Arrows represent probable migration paths during: a the initial settlement of Sahul (~50 kya; green); b the Last Glacial Maximum (~28 kya; blue); c the postglacial warming period through to the Holocene (~18 kya; pink); and d the Late Holocene (~3.5 kya; orange)