Maternal genetic origin of Chao Lay coastal maritime populations from Thailand

Abstract

Background The Chao Lay, also known as sea nomads, include the Austronesian-speaking Moken, Moklen, and Urak Lawoi, who traditionally inhabit the coastal regions and islands of the Andaman Sea in southern Thailand. Their maritime lifestyle has attracted significant interest in their genetic origins and relationships with other sea nomad groups in Island Southeast Asia (ISEA); however, comprehensive genetic data on these communities remain scarce. Here, we generated complete mitochondrial genome sequences from Moken and Moklen groups, along with the Tai-Kadai-speaking southern Thai population and additional Austroasiatic-speaking Maniq samples (hunter-gatherer) from southern Thailand. Results Our findings indicate that the Chao Lay display lower genetic diversity compared to the majority of southern Thai populations. Furthermore, the results suggest the absence of recent maternal expansions among the Chao Lay. Notably, haplogroups D4e1a, E1a1a1a, M21b2, M46a, M50a1, and M71c are predominant among the Chao Lay, underscoring their genetic distinctiveness. Bayesian coalescent age estimates of clades characteristic to Chao Lay for these haplogroups point to the time associated with the Austronesian expansion period. Conclusions The Chao Lay populations were closer to each other than to other groups and exhibited more genetic connections to Mainland Southeast Asian (MSEA) populations than ISEA populations. However, we do not exclude potential origins of the Chao Lay in ISEA or Taiwan, as it is possible that ancestral Chao Lay males incorporated MSEA females into their communities upon arriving in Thailand. Further studies on genome-wide and Y chromosome data would provide more insights into their genetic history. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-025-02252-5.