Genetic diversity and ancestry of the Khmuic-speaking ethnic groups in Thailand: a genome-wide perspective

Abstract

The Khmuic-speaking populations are believed to be the descendants of one of the earliest groups to settle in Mainland Southeast Asia. In Thailand, there are two agricultural Khmuic-speaking ethnic groups, the Khamu and Lua (Htin). These peoples primarily reside in scattered locations along the mountainous Thailand-Laos border in Nan province. In this study, we conducted genome-wide SNP analysis on 81 individuals from three Khamu and two Lua villages in northern Thailand. Our findings revealed that both the Khamu and Lua groups possess genetic structures that are distinct from other ethnicities in Southeast Asia, indicating a unique history of migration and settlement. Within the Khmuic group, the Khamu populations living in different locations exhibited similar genetic structures and displayed genetic affinities only with some hill-tribes and Tai-Kadai (Kra-Dai)-speaking groups in Thailand, suggesting potential intermixing or cultural exchange. Furthermore, the Lua people displayed a distinctive population structure, which could be attributed to the founder effect and endogamous marriage practices. Additionally, we discovered a relationship between the Khmuic-speaking populations in Thailand and a Neolithic ancient sample obtained from the Tham Pha Ling archaeological site in Laos. This study provides new insight into genetic substructure within the Khmuic-speaking people and their potential relationship to the indigenous inhabitants of Mainland Southeast Asia.

Figure 1

Map showing the location of the 5 Khmuic-speaking villages analyzed in this study. Drawing was adapted and used under license from Shutterstock.com. Original drawings can be found at https://www.shutterstock.com/image-vector/bluegray-detailed-map-thailand-administrative-divisions-1722049933, https://www.shutterstock.com/image-illustration/nan-province-thailand-colored-elevation-map-2281467625.

Figure 2

Plot of PC1 versus PC2 for the genome-wide SNP data of individuals from South Asia, Northeast Asia, and Southeast Asia is shown on the right. A high-resolution version of this plot can be found in Supplementary Fig. 1. Each individual is colored by linguistic family according to the key at the right panel. Plot focusing on the Khamu and Lua populations is zoomed-in to the left. Ancient samples are labeled for their archeological site.

Figure 3

ADMIXTURE results of modern Asian populations and the outgroup, African Mbuti and European French, for K values ranging from 2 to 10. Each individual is represented by a bar divided into K colored segments, indicating their estimated membership fractions in each of the K ancestry component. Populations are separated by black lines. The names of the populations whose genome-wide data are generated in this study are indicated in red on the lower-left side. The bar at the bottom represents the linguistic families of each ethnic group.

Figure 4

Heatmap showing population allele sharing profiles based on f3 statistics. The colored bar on the right map indicates the statistical values, while that on the left side indicates the linguistic family of each ethnic group. The Khmuic-speaking populations are emphasized with a black box in the upper-left corner.

Figure 5

f4 statistics comparing Khmuic-speaking populations from two different subgroups of the Austroasiatic language family. Z-scores are for f4 (W, X; Y, Mbuti), where W is a selected Austroasiatic-speaking Soa ethnic group, X is another population in Khmuic branch in Austroasiatic family, and Y is a population not in Austroasiatic family whose ethnic name was labeled on the left side. Different symbols denote different populations for X: black corresponds to Khamu, blue to Lua/Htin, and orange to Mlabri. The bar on the left represents the linguistic family of each ethnic group. The vertical black dashed lines denote + 3/− 3.

Figure 6

f4 statistics comparing ethnic populations in Thailand labeled on the left to Neolithic ancient samples from Laos and Vietnam on the top grey bar. Z-scores are for f4 (ancient sample, Han Chinese; ethnic population, French). The vertical grey lines denote 0. The dots and error bars are colored according to language family, as indicated by the key at the bottom. Empty circles denote nonsignificant Z-scores (|Z|= < 3) and solid circles denote significant Z-scores (|Z|> 3).

Figure 7

Admixture graphs for the backbone population (left) and the Austroasiatic-speaking group (right). Backbone population labels are colored for different language family. Dashed arrows represent admixture edges, while solid arrows are drift edges reported in units of Fst × 1000.