Ancient genomes document multiple waves of migration in Southeast Asian prehistory

Abstract

Southeast Asia is home to rich human genetic and linguistic diversity, but the details of past population movements in the region are not well known. Here, we report genome-wide ancient DNA data from thirteen Southeast Asian individuals spanning from the Neolithic period through the Iron Age (4100–1700 years ago). Early agriculturalists from Man Bac in Vietnam possessed a mixture of East Asian (southern Chinese farmer) and deeply diverged eastern Eurasian (hunter-gatherer) ancestry characteristic of Austroasiatic speakers, with similar ancestry as far south as Indonesia providing evidence for an expansive initial spread of Austroasiatic languages. In a striking parallel with Europe, later sites from across the region show closer connections to present-day majority groups, reflecting a second major influx of migrants by the time of the Bronze Age. The archaeological record of Southeast Asia documents a complex history of human occupation, with the first archaic hominins arriving at least 1.6 million years ago (yBP) and anatomically modern humans becoming widely established by 50,000 yBP [1–3]. Particularly profound changes in human culture were propelled by the spread of agriculture. Rice farming began in the region approximately 4500–4000 yBP and was accompanied by a relatively uniform and widespread suite of tools and pottery styles showing connections to southern China [4–6]. It has been hypothesized that this cultural transition was effected by a migration of people who were not closely related to the indigenous hunter-gatherers of Southeast Asia [5, 7–10] and who may have spoken Austroasiatic languages, which today have a wide but fragmented distribution in the region [4, 5, 11–14]. In this scenario, the languages spoken by the majority of present-day people in Southeast Asia (e.g., Lao, Thai, Burmese, Malay) reflect later population movements. However, no genetic study has resolved the extent to which the spread of agriculture into the region and subsequent 3 bioRxiv preprint doi: https://doi.org/10.1101/279646; this version posted March 10, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license. cultural and technological shifts were achieved by movement of people or ideas. …