The Genetic Structure of Pacific Islanders

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Abstract
Human genetic diversity in the Pacific has not been adequately sampled, particularly in Melanesia. As a result, population relationships there have been open to debate. A genome scan of autosomal markers (687 microsatellites and 203 insertions/deletions) on 952 individuals from 41 Pacific populations now provides the basis for understanding the remarkable nature of Melanesian variation, and for a more accurate comparison of these Pacific populations with previously studied groups from other regions. It also shows how textured human population variation can be in particular circumstances. Genetic diversity within individual Pacific populations is shown to be very low, while differentiation among Melanesian groups is high. Melanesian differentiation varies not only between islands, but also by island size and topographical complexity. The greatest distinctions are among the isolated groups in large island interiors, which are also the most internally homogeneous. The pattern loosely tracks language distinctions. Papuan-speaking groups are the most differentiated, and Austronesian or Oceanic-speaking groups, which tend to live along the coastlines, are more intermixed. A small “Austronesian” genetic signature (always <20%) was detected in less than half the Melanesian groups that speak Austronesian languages, and is entirely lacking in Papuan-speaking groups. Although the Polynesians are also distinctive, they tend to cluster with Micronesians, Taiwan Aborigines, and East Asians, and not Melanesians. These findings contribute to a resolution to the debates over Polynesian origins and their past interactions with Melanesians. With regard to genetics, the earlier studies had heavily relied on the evidence from single locus mitochondrial DNA or Y chromosome variation. Neither of these provided an unequivocal signal of phylogenetic relations or population intermixture proportions in the Pacific. Our analysis indicates the ancestors of Polynesians moved through Melanesia relatively rapidly and only intermixed to a very modest degree with the indigenous populations there. The origins and current genetic relationships of Pacific Islanders have been the subjects of interest and controversy for many decades. By analyzing the variation of a large number (687) of genetic markers in almost 1,000 individuals from 41 Pacific populations, and comparing these with East Asians and others, we contribute to the clarification and resolution of many of these issues. To judge by the populations in our survey, we find that Polynesians and Micronesians have almost no genetic relation to Melanesians, but instead are strongly related to East Asians, and particularly Taiwan Aborigines. A minority of Island Melanesian populations have indications of a small shared genetic ancestry with Polynesians and Micronesians (the ones that have this tie all speak related Austronesian languages). Inland groups who speak Papuan languages are particularly divergent and internally homogeneous. The genetic divergence among Island Melanesian populations, which is neatly organized by island, island size/topography, as well as their coastal or inland locations, is remarkable for such a small region, and enlarges our understanding of the texture of contemporary human variation.