Male-specific Y-chromosome data for a Tai-Kadai speaking Southern Thai group. undefined

Previous genome-wide studies have reported South Asian ancestry in several Mainland Southeast Asian (MSEA) populations; however, additional details concerning population history, in particular the role of sex-biased admixture, are more easily addressed with uniparental markers than with autosomal markers. To provide new insights into sex-specific aspects of the South Asian admixture in MSEA, we generated ∼2.3 mB sequences of the male-specific portions of the Y chromosome (MSY) of a Tai-Kadai (TK)-speaking Southern Thai group (SouthernThai_TK), and complete mitochondrial (mtDNA) genomes of the SouthernThai_TK and an Austronesian (AN)-speaking Southern Thai (SouthernThai_AN) group. South Asian prevalent mtDNA and MSY haplogroups were observed at frequencies of ~30-50% in the Southern Thai groups; both of them showed more genetic relatedness to Austroasiatic (AA)-speaking Mon than to any other group. We observed variable amounts of sex-biased admixture involving South Asian mtDNA and MSY haplogroups in several MSEA populations; in general, most AA- and AN speaking groups in MSEA were closer to South Asian than to TK groups based on mtDNA, but the opposite pattern was observed for the MSY. Overall, our results indicate that sex-biased migration and admixture, as well as residence pattern, has influenced the genetic structure of MSEA, attesting to the additional value that uniparental markers can add to studies of genome-wide variation.