Map showing the locations of 88 populations from Southeast and South Asia that were analyzed for mtDNA (74 populations) and MSY (55 populations) variation.

The map was generated using the Quantum GIS, QGIS Development Team (2023), QGIS Geographic Information System. Open Source Geospatial Foundation (https://www.qgis.org) and boundaries were adapted and modified from https://public.opendatasoft.com/explore/dataset/worldadministrative-boundaries/export/.</p

General information on additional mtDNA sequences of haplogroup Q3, used in the network analysis.

General information on additional mtDNA sequences of haplogroup Q3, used in the network analysis.</p

Parameters in the admixture analysis.

Previous genome-wide studies have reported South Asian (SA) ancestry in several Mainland Southeast Asian (MSEA) populations; however, additional details concerning population history, in particular the role of sex-specific aspects of the SA admixture in MSEA populations can be addressed with uniparental markers. Here, 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. We identified new mtDNA haplogroups, e.g. Q3, E1a1a1, B4a1a and M7c1c3 that have not previously reported in Thai populations, but are frequent in Island Southeast Asia and Oceania, suggesting interactions between MSEA and these regions. SA prevalent mtDNA haplogroups were observed at frequencies of ~35–45% in the Southern Thai groups; both of them showed more genetic relatedness to Austroasiatic (AA) speaking Mon than to any other group. For MSY, SouthernThai_TK had ~35% SA prevalent haplogroups and exhibited closer genetic affinity to Central Thais. We also analyzed published data from other MSEA populations and observed SA ancestry in some additional MSEA populations that also reflects sex-biased admixture; in general, most AA- and AN-speaking groups in MSEA were closer to SA than to TK groups based on mtDNA, but the opposite pattern was observed for the MSY. Overall, our results of new genetic lineages and sex-biased admixture from SA to MSEA groups attest to the additional value that uniparental markers can add to studies of genome-wide variation.</div

Bar plot of percentages of each major mtDNA haplogroup in four groups of populations: SouthernThai_TK, SouthernThai_AN, Southeast Asian/East Asian (SEA/EA) and South Asian (SA).

Data from 56 SEA/EA populations, and 16 SA populations. (TIF)</p

Estimated admixture proportions in admixed populations based on mtDNA sequences.

Estimated admixture proportions in admixed populations based on mtDNA sequences.</p

Bar plot of percentages of three categories of MSY haplogroups: Southeast Asian/East Asian (SEA/EA) prevalent, South Asian (SA) prevalent, and other haplogroups, in 55 populations.

Bar plot of percentages of three categories of MSY haplogroups: Southeast Asian/East Asian (SEA/EA) prevalent, South Asian (SA) prevalent, and other haplogroups, in 55 populations.</p

Median-joining network based on 72 mtDNA genomes of haplogroup E1a1a1 from Southern Thailand, Taiwan, the Philippines, Indonesia and Saudi Arabia.

Number of substitutions are shown on the lines connecting the nodes. (TIF)</p

Estimated admixture proportions in admixed populations based on MSY sequences.

Estimated admixture proportions in admixed populations based on MSY sequences.</p

Frequency of shared mtDNA (a) and MSY (b) haplotypes within and between populations.

The font color of the population name indicates language family and the colored bar at the top indicates geographic region; the heat plot shows the frequency of shared types according to the key on the right. The new populations analyzed in this study are indicated by stars.</p

Sequencing coverage and MSY haplogroup of each SouthernThai_TK individual.

Sequencing coverage and MSY haplogroup of each SouthernThai_TK individual.</p