Resolving the ancestry of Austronesian‑speaking populations

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.This work was supported by FCT, the Portuguese Foundation for Science and Technology, through the project PTDC/IVC-ANT/4917/2012. PS is supported by FCT, European Social Fund, Programa Operacional Potencial Humano and the FCT Investigator Programme and acknowledges FCT/MEC for support to CBMA through Portuguese funds (PIDDAC)—PEst-OE/BIA/ UI4050/2014. PS was also supported through the course of this work by a Marie Curie Early Stage Training Grant and FCT grant SFRH/ BPD/64233/2009. MBR thanks the British Academy for financial support through project LRG-42440 and PS and MBR also thank the de Laszlo Foundation and the British Academy (project BARDA- 48208). IPATIMUP is an Associate Laboratory of the Portuguese Ministry of Science, Technology and Higher Education and is partially supported by FCT, the Portuguese Foundation for Science and Technology