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 18 Southeast Asian individuals spanning from the Neolithic period through the Iron Age (4100 to 1700 years ago). Early farmers from Man Bac in Vietnam exhibit a mixture of East Asian (southern Chinese agriculturalist) 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. By the Bronze Age, in a parallel pattern to Europe, sites in Vietnam and Myanmar show close connections to present-day majority groups, reflecting substantial additional influxes of migrants.

Fig. 1.

Overview of samples. (A) Locations and dates of ancient individuals. Overlapping positions are shifted slightly for visibility. (B) PCA with East and Southeast Asians. We projected the ancient samples onto axes computed using the present-day populations (with the exception of Mlabri, who were projected instead due to their large population-specific drift). Present-day colors indicate language family affiliation: green, Austroasiatic; blue, Austronesian; orange, Hmong-Mien; black, Sino-Tibetan; magenta, Tai-Kadai. Map data from http://www.freeworldmaps.net/asia/southeastasia/physical.html.

Fig. 2.

Relative amounts of deeply diverged ancestry. The Y-axis shows f₄(X, Kinh; Australasian, Han) (multiplied by 10⁴) for populations X listed on the x-axis (present-day as aggregate; ancient samples individually, except for points labeled “all”). Symbols are as in Fig. 1. Bars give two standard errors in each direction; dotted lines indicate the levels in Man Bac (top, blue) and Kinh (zero, black). B. C., Ban Chiang.

Fig. 3.

Schematics of admixture graph results. (A) Wider phylogenetic context. (B) Details of the Austroasiatic clade. Branch lengths are not to scale, and the order of the two events on the Nicobarese lineage in (B) is not well determined [19].