Inferring the population structure and admixture history of three Hmong-Mien-speaking Miao tribes from southwest China based on genome-wide SNP genotyping

Abstract

Background

Hmong-Mien speaking Miao, also called Hmong, is the sixth largest ethnic group in mainland China. However, the fine-scale genetic profiles and population history of Miao populations in southwest China, especially in Guizhou province, remain uncharacterised due to a scarcity of samples of genome-wide data from different tribes.

Aim

To further investigate the population substructure and admixture history of the Guizhou Miao minority.

Subjects and methods

We collected 29 samples from three Miao tribes of Guizhou province in southwest China and genotyped about 700,000 genome-wide SNPs of each sample. We analysed newly generated data in together with published modern/ancient East Asian populations datasets via a series of population genetic methods, including principal component analysis (PCA), ADMIXTURE, Fst, TreeMix, f-statistics, qpWave, and qpAdm.

Results

PCA and ADMIXTURE results showed that the three studied Guizhou Miao groups consistently fell on the Hmong-Mien-related genetic cline and were relatively genetically homogeneous, displaying a genetic affinity with neighbouring Tai-Kadai speaking populations such as Dong. These results were further confirmed by the observed genetic clade in Fst, TreeMix, outgroup-f₃-statistics, and f₄-statistics. Furthermore, f₄-based allele sharing patterns illustrated that compared with Hunan Miao in central China, Guizhou Miao shared more alleles with Hmong-Mien-speaking Vietnam Hmong and Tai-Kadai-speaking CoLao, Dong, while exhibiting less northeast Asian-related ancestry. Admixture-f₃ and f₄-statistics revealed the North-South admixture pattern for the studied Guizhou Miao. A qpAdm-based two-way admixture model further revealed that the studied Guizhou Miao harboured 44%–55.4% indigenous Austronesian-speaking Atayal-related ancestry and 44.6%–56% Late Neolithic Yellow River farmer-related ancestry.

Conclusions

The population structure within Hmong-Mien-related populations showed a geographic correlation. Hmong-Mien speaking Hunan Miao, Guizhou Miao, and Vietnam Hmong presented close genetic relationships although they dwelt in different regions, suggesting the preservation of the original Hmong-related genetic diversity. The results based on genome-wide SNPs data generally matched the migration history for the Miao population. Our study contributes to a better knowledge of Miao populations and the population structure in southwest China.

Keywords:

• Guizhou Miao population
• population structure
• genetic admixture
• East Asian

Ethical approval

The studies involving human participants were reviewed and approved by the Medical Ethics Committee of Xiamen University (Approval Number: XDYX2019009). The participants provided their written informed consent to participate in this study.

Acknowledgements

S. Fang and Z. Xu from Information and Network Center of Xiamen University are acknowledged for the help with the high-performance computing.

Disclosure statement

No potential conflict of interest was reported by the author(s).

Data availability statement

The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found below: https://zenodo.org/record/5151495, doi: 10.5281/zenodo.5151495.

Additional information

Funding

This work was supported by the National Natural Science Foundation of China [NSFC 31801040], the “Double First Class University Plan” key construction project of Xiamen University (the origin and evolution of East Asian populations and the spread of Chinese civilization), the Nanqiang Outstanding Young Talents Program of Xiamen University [X2123302], the Fundamental Research Funds for the Central Universities [ZK1144], the Major Project of the National Social Science Foundation of China [20&ZD248], European Research Council (ERC) grant [ERC-2019-ADG-883700-TRAM].