Indian genetic heritage in Southeast Asian populations

Abstract

24 The great ethnolinguistic diversity found today in mainland Southeast Asia (MSEA) reflects 25 multiple migration waves of people in the past. Deeply divergent East Eurasian hunter-gatherers were 26 the first anatomically modern human population known to migrate to the region. Agriculturalists from 27 South China migrated to the region and admixed with the local hunter-gatherers during the Neolithic 28 period. During the Bronze and Iron Ages, the genetic makeup of people in MSEA changed again, 29 indicating an additional influx of populations from South China. Maritime trading between MSEA and 30 India was established at the latest 300 BCE, and the formation of early states in Southeast Asia during 31 the first millennium CE was strongly influenced by Indian culture, and this cultural influence is still 32 prominent today. Several ancient Indian-influenced states were located in present-day Thailand, and 33 various populations in the country are likely to be descendants of people from those states. To 34 systematically explore Indian genetic heritage in MSEA, we generated genome-wide SNP data (the 35 HumanOrigins array) for 119 present-day individuals belonging to 10 ethnic groups from Thailand and 36 co-analyzed them with published data from MSEA using the PCA, ADMIXTURE, f3-statistics, qpAdm, 37 and qpGraph methods. We found South Asian low-level admixture in various MSEA populations which 38 are probably descendants of people from the ancient Indian-influenced states, but failed to find a South 39 Asian genetic component in present-day hunter-gatherer groups and relatively isolated groups from 40 highlands in Northern Thailand. Our results also support close genetic affinity between Kra-Dai- 41 speaking (also known as Tai-Kadai) and Austronesian-speaking populations, which fits a linguistic 42 hypothesis suggesting cladality of the two language families. 43 44 45 2 bioRxiv preprint doi: https://doi.org/10.1101/2021.01.21.427591; this version posted January 22, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.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. 46 Author Summary 47 Mainland Southeast Asia is a region with great ethnolinguistic diversity and complex population 48 history. We studied genetic population history of present-day mainland Southeast Asian populations 49 using genome-wide SNP data (the HumanOrigins array). We generated new data for 10 present-day 50 ethnic groups from Thailand, which we further combined with published data from mainland and island 51 Southeast Asians and worldwide populations. We revealed South Asian genetic admixture in various 52 mainland Southeast Asian ethnic groups which are highly influenced by Indian culture, but failed to 53 find it in groups who remained culturally isolated until recently. Our finding suggests that a massive 54 migration of Indian people in the past was responsible for the spread of Indian culture in mainland 55 Southeast Asia. We also found support for a close genetic affinity between Kra-Dai- and Austronesian- 56 speaking populations, which fits a linguistic hypothesis suggesting cladality of the two language 57 families. 58 59