Resolving the ancestry of Austronesian-speaking populations

TLDR

Island Southeast Asia’s prehistory is contested, with one view favoring a major Late Holocene expansion of Austronesian speakers from Taiwan and another attributing genetic patterns to autochthonous dispersals triggered by sea‑level rises, though the latter cannot explain the language spread. The study aimed to reconcile competing models of ISEA prehistory by integrating mitochondrial, Y‑chromosome, and genome‑wide data. Using a comprehensive analysis of mitochondrial, Y‑chromosome, and genome‑wide markers, the authors achieved highly consistent results across all three systems. The data reveal a shared pre‑Neolithic ancestry for Taiwan and ISEA, plus two minor Late Holocene migrations from Mainland Southeast Asia and South China via Taiwan that likely mediated Austronesian language dispersal through small‑scale migration and language shift.

Abstract

There are two very different interpretations of the prehistory of Island Southeast Asia (ISEA), with genetic evidence invoked in support of both. The "out-of-Taiwan" model proposes a major Late Holocene expansion of Neolithic Austronesian speakers from Taiwan. An alternative, proposing that Late Glacial/postglacial sea-level rises triggered largely autochthonous dispersals, accounts for some otherwise enigmatic genetic patterns, but fails to explain the Austronesian language dispersal. Combining mitochondrial DNA (mtDNA), Y-chromosome and genome-wide data, we performed the most comprehensive analysis of the region to date, obtaining highly consistent results across all three systems and allowing us to reconcile the models. We infer a primarily common ancestry for Taiwan/ISEA populations established before the Neolithic, but also detected clear signals of two minor Late Holocene migrations, probably representing Neolithic input from both Mainland Southeast Asia and South China, via Taiwan. This latter may therefore have mediated the Austronesian language dispersal, implying small-scale migration and language shift rather than large-scale expansion.