Background Fine-scale genetic structure of ethnolinguistically diverse Chinese populations can fill the gap in the missing diversity and evolutionary landscape of East Asians, particularly for anthropologically informed Chinese minorities. Hmong–Mien (HM) people were one of the most significant indigenous populations in South China and Southeast Asia, which were suggested to be the descendants of the ancient Yangtze rice farmers based on linguistic and archeological evidence. However, their deep population history and biological adaptative features remained to be fully characterized. Objectives To explore the evolutionary and adaptive characteristics of the Miao people, we genotyped genome-wide SNP data in Guizhou HM-speaking populations and merged it with modern and ancient reference populations via a comprehensive population genetic analysis and evolutionary admixture modeling. Results The overall genetic admixture landscape of Guizhou Miao showed genetic differentiation between them and other linguistically diverse Guizhou populations. Admixture models further confirmed that Miao people derived their primary ancestry from geographically close Guangxi Gaohuahua people. The estimated identity by descent and effective population size confirmed a plausible population bottleneck, contributing to their unique genetic diversity and population structure patterns. We finally identified several natural selection candidate genes associated with several biological pathways. Conclusions Guizhou Miao possessed a specific genetic structure and harbored a close genetic relationship with geographically close southern Chinese indigenous populations and Guangxi historical people. Miao people derived their major ancestry from geographically close Guangxi Gaohuahua people and experienced a plausible population bottleneck which contributed to the unique pattern of their genetic diversity and structure. Future ancient DNA from Shijiahe and Qujialing will provide new insights into the origin of the Miao people.

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Background Fine-scale genetic structure of ethnolinguistically diverse Chinese populations can fill the gap in the missing diversity and evolutionary landscape of East Asians, especially anthropologically informed Chinese minorities. Hmong-Mien (HM) people were one of the most important indigenous populations from South China and Southeast Asia, which were suggested to be the descendants of the Yangtze rice farmers based on linguistic and archeological evidence. Guizhou Miao, possessing a specific genetic structure, harbored a close genetic relationship with geographically close Guizhou populations and Guangxi historical people. We genotyped genome-wide SNP data in Guizhou HM-speaking populations and merged it with modern and ancient reference populations to explore the evolutionary and adaptive characteristics of Miao people via a comprehensive population genetic analysis. Results The overall genetic admixture landscape of Guizhou Miao showed genetic differentiation between them and other linguistically diverse Guizhou populations. Admixture models further confirmed that Miao people derived their primary ancestry from geographically close Guangxi Gaohuahua people. The estimated identity by descent (IBD) and effective population size further confirmed a plausible population bottleneck, contributing to their unique genetic diversity and structure pattern. We finally identified several natural selection candidate genes associated with several biological pathways. Conclusions We found Guizhou Miao with a specific genetic structure harbored a close genetic relationship with geographically close Guizhou populations and Guangxi historic people. Miao people derived their major ancestry from geographically close Guangxi Gaohuahua people and a plausible population bottleneck which contributed to the unique pattern of their genetic diversity and structure. Future ancient DNA from Shijiahe and Qujialing would further promote new insights into the origin of the Miao people.