Quantifying the legacy of the Chinese Neolithic on the maternal genetic heritage of Taiwan and Island Southeast Asia

There has been a long-standing debate concerning the extent to which the spread of Neolithic ceramics and Malay-Polynesian languages in Island Southeast Asia (ISEA) were coupled to an agriculturally driven demic dispersal out of Taiwan 4000 years ago (4 ka). We previously addressed this question using founder analysis of mitochondrial DNA (mtDNA) control-region sequences to identify major lineage clusters most likely to have dispersed from Taiwan into ISEA, proposing that the dispersal had a relatively minor impact on the extant genetic structure of ISEA, and that the role of agriculture in the expansion of the Austronesian languages was therefore likely to have been correspondingly minor. Here we test these conclusions by sequencing whole mtDNAs from across Taiwan and ISEA, using their higher chronological precision to resolve the overall proportion that participated in the "out-of-Taiwan" mid-Holocene dispersal as opposed to earlier, postglacial expansions in the Early Holocene. We show that, in total, about 20 % of mtDNA lineages in the modern ISEA pool result from the "out-of-Taiwan" dispersal, with most of the remainder signifying earlier processes, mainly due to sea-level rises after the Last Glacial Maximum. Notably, we show that every one of these founder clusters previously entered Taiwan from China, 6-7 ka, where rice-farming originated, and remained distinct from the indigenous Taiwanese population until after the subsequent dispersal into ISEA.We thank Freda Oppenheimer, Onchansamone Ninethaphone, Nouphanh Keosouda and Bounheuang Bouasisengpaseuth for the Laos samples, A. S. M. Sofro and John Clegg for Indonesian samples, and Sean O’Riordan for Vietnamese samples. This work was supported by FEDER funds through “Programa Operacional Factores de Competitividade—COMPETE (FCOMP-01-0124FEDER-029291)” and by national funds through FCT, the Portuguese Foundation for Science and Technology (FCT) through the research project (PTDC/IVC-ANT/4917/2012). AB has a PhD grant from FCT (SFRH/BD/78990/2011). PS is supported by FCT, European Social Fund, Programa Operacional Potencial Humano and the FCT Investigator Programme (IF/01641/2013). IPATIMUP integrates the i3S Research Unit, which is partially supported by FCT. This work is supported by FEDER funds through the Operational Programme for Competitiveness Factors-COMPETE and National Funds through FCT, under the project “PEst-C/SAU/LA0003/2013” (IPATIMUP), byinfrastructure support through NORTE-07-0162-FEDER-00018 and NORTE-07-0162-FEDER-000067, by Programa Operacional Regional do Norte (ON.2—O Novo Norte) through FEDER funds under the Quadro de Referência Estratégico Nacional (QREN) and by FCT I.P. and ERDF (COMPETE 2020- POCI) through the strategic funding programme UID/BIA/04050/2013 (POCI-01-0145-FEDER-007569) (CBMA). 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)