Exploring the genomic population structure and history of Austroasiatic speakers in Mainland Southeast Asia

Multidisciplinary evidence indicates that the Austroasiatic (AA) language family is the earliest known language in Mainland Southeast Asia (MSEA), dating back to the Neolithic. Yet, the genomic formation and structure of MSEA AA groups remain understudied. Here, we generate genome-wide data for seven AA-speaking and two Sino-Tibetan-speaking populations from Thailand/Laos/Myanmar, which together with published data comprises the largest AA genome-wide dataset to date. We find substantial genetic heterogeneity across both geographic regions and linguistic branches, with the greatest observed in Northern Mon-Khmer highland groups. Analyses with ancient DNA data indicate that northern AA groups exhibit higher East Asian ancestry linking to Iron Age northern Thailand/Cambodia, whereas southern AA groups display additional South Asian ancestry and affinities with Neolithic Laos/Vietnam. Notably, the South Asian-related ancestry is detectable in Neolithic MSEA. Overall, both isolation and contact have together shaped the pronounced genetic heterogeneity observed across linguistic branches of MSEA AA groups.