Reconstructing the human genetic history of mainland Southeast Asia: insights from genome-wide data from Thailand and Laos

Abstract

2 Thailand and Laos, located in the center of Mainland Southeast Asia (MSEA), harbor diverse 3 ethnolinguistic groups encompassing all five language families of MSEA: Tai-Kadai (TK), 4 Austroasiatic (AA), Sino-Tibetan (ST), Hmong-Mien (HM) and Austronesian (AN). Previous genetic 5 studies of Thai/Lao populations have focused almost exclusively on uniparental markers and there is a 6 paucity of genome-wide studies. We therefore generated genome-wide SNP data for 33 ethnolinguistic 7 groups, belonging to the five MSEA language families from Thailand and Laos, and analysed these 8 together with data from modern Asian populations and SEA ancient samples. Overall, we find genetic 9 structure according to language family, albeit with heterogeneity in the AA-, HM- and ST-speaking 10 groups, and in the hill tribes, that reflects both population interactions and genetic drift. For the TK 11 speaking groups, we find localized genetic structure that is driven by different levels of interaction with 12 other groups in the same geographic region. Several Thai groups exhibit admixture from South Asia, 13 which we date to ~600-1000 years ago, corresponding to a time of intensive international trade networks 14 that had a major cultural impact on Thailand. An AN group from Southern Thailand shows both South 15 Asian admixture as well as overall affinities with AA-speaking groups in the region, suggesting an 16 impact of cultural diffusion. Overall, we provide the first detailed insights into the genetic profiles of 17 Thai/Lao ethnolinguistic groups, which should be helpful for reconstructing human genetic history in 18 MSEA and selecting populations for participation in ongoing whole genome sequence and biomedical 19 studies. 20 21 Keywords: genome-wide, Mainland Southeast Asia, population interaction, South Asian admixture, 22 cultural diffusion 23 24