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Reconstructing Austronesian Population History in Island Southeast Asia

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Reconstructing Austronesian Population History in Island Southeast Asia

Mark Lipson et al. Nat Commun.

Abstract

Austronesian languages are spread across half the globe, from Easter Island to Madagascar. Evidence from linguistics and archaeology indicates that the 'Austronesian expansion,' which began 4,000-5,000 years ago, likely had roots in Taiwan, but the ancestry of present-day Austronesian-speaking populations remains controversial. Here, we analyse genome-wide data from 56 populations using new methods for tracing ancestral gene flow, focusing primarily on Island Southeast Asia. We show that all sampled Austronesian groups harbour ancestry that is more closely related to aboriginal Taiwanese than to any present-day mainland population. Surprisingly, western Island Southeast Asian populations have also inherited ancestry from a source nested within the variation of present-day populations speaking Austro-Asiatic languages, which have historically been nearly exclusive to the mainland. Thus, either there was once a substantial Austro-Asiatic presence in Island Southeast Asia, or Austronesian speakers migrated to and through the mainland, admixing there before continuing to western Indonesia.

Figures

Figure 1
Figure 1. Inferred sources of ancestry for selected admixed Austronesian-speaking populations.
Shaded ranges represent 95% bootstrap confidence intervals for branching positions; see Supplementary Tables 10 and 11 for complete mixing branch distributions. The topology of the scaffold tree is shown using the full data set (slight variations are possible across bootstrap replicates). (a) Overview of the three best-fitting admixture models. (bd) Detailed results for highest-confidence models of populations from (b) the Philippines, (c) eastern Indonesia and (d) western ISEA. In d, the Austronesian and Negrito branch positions are fixed in MixMapper to equal those for Manobo. Batak Toba are omitted for display purposes, as 8% of replicates place their third ancestry component on a non-adjacent branch in the scaffold (Supplementary Table 11). Three other populations (Manggarai Ngada, Manggarai Rampasasa and Toraja) fall into an additional category of three-way admixed eastern Indonesians, while Oceanians (Fiji and Polynesia) are inferred to have similar ancestry to the populations in c, but their confidence intervals are not directly comparable because they have fewer SNPs available (see Fig. 2 and Supplementary Tables 10 and 11).
Figure 2
Figure 2. Locations and best-fit mixture proportions for Austronesian-speaking and other populations, with possible directions of human migrations supported by our analyses.
For Toraja, we could not distinguish between Negrito and Melanesian ancestry and show this component as red/orange.

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