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The genomic history of southwestern Chinese populations demonstrated massive population migration and admixture among proto-Hmong–Mien speakers and incoming migrants

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Abstract

Southwest China was the crossroad for the initial settler people of East Asia, which shows the highest diversity in languages and genetics. This region played a significant role in the formation of the genetic makeup of the proto-Hmong–Mien-speaking people and in the north-to-south human expansion during the Neolithic-to-historic transformation. Their genetic history covering migration events and the admixture processes still needs to be further explored. Therefore, in the current study, we have generated genome-wide data from three genomic aspects covering autosomal, mitochondrial and Y-chromosomal regions in 260 Hmong–Mien, Tibeto-Burman, and Sinitic people from 29 different southwestern Chinese groups, and further analyzed them with 2676 published modern and ancient Eurasian genomes. Here, we have noticed a new southwestern East Asian genetic cline composed of the Hmong–Mien-specific ancestry enriched in modern Hmong and Pathen. This newly identified southern inland East Asian lineage contributed to a great extent of the gene pool in the modern southern East Asians. We also have observed genetic substructure among Hmong–Mien-speaking populations. The southern Hmong–Mien-speaking people showed more genetic affinity with modern Tai–Kadai/Austroasiatic people, while the northern Hmong–Mien speakers expressed a closer genetic connection with the Neolithic-to-modern northern East Asians. Moreover, southwestern Sinitic populations had a strong genomic affinity with the adjacent Hmong–Mien-speaking populations and the lowlander Tibeto-Burman-speaking populations, which suggested the large-scale genetic admixture occurred between them. Allele-sharing-based qpAdm/qpGraph results further confirmed that all included southwestern Chinese populations could be modeled as a mixed result of the major ancestry component from the northern millet farmers in the Yellow River basin and the minor ancestry component from the southern rice farmers in the Yangtze River basin. Usually, this newly identified Hmong–Mien-associated southern East Asian ancestry could improve our understanding of the full-scale genetic landscape of the evolutionary and admixture history of southwestern East Asians. Further ancient genomic studies from southeastern China are required to shed deeper light on our established phylogeny context.

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Fig. 1
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source via f3(Source1, Taiwan_Hanben; Miao_Pengshui). B Top mixed signals for Qianjiang Miao with Yellow River basin ancients as the plausible northern source via f3(Source1, X; Miao_Qianjang). X was, respectively, represented Boshan_EN, Lajia_LN, Wadian_LN, and Wanggou_MN. C Multidimensional scaling plots (MDS) based on the inverse f3-based genetic matrixes showed the patterns of genetic relationship between modern and ancient East Asians. D Phylogenetic relationships without gene flow events were reconstructed via the inverted f3-based genetic matrix

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Data availability

We Followed the informed consent of this project and the regulations of the Human Genetic Resources Administration of China (HGRAC), the generated raw data can be shared via personal communication with the corresponding authors with the following conditions, (i) the data can be only used for studying population history, (ii) the data will not be used for commercial purposes, (iii) the data will not be used to identify the sample donors, (iv) the data will not be used for studying natural/cultural selections, medical or other related studies.

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Acknowledgements

GHL was supported by the China Postdoctoral Science Foundation (2021M691879). RKT was supported by the Science and Technology Project of Yubei District (X4487).

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Author notes

  1. Yicheng Wang, Xing Zou, Mengge Wang and Guanglin He contributed equally to this work and should be considered co-first authors.

Authors and Affiliations

  1. Department of Forensic Medicine, College of Basic Medicine, Chongqing Medical University, Chongqing, 400331, China

    Yicheng Wang, Didi Yuan, Li Yang, Yujie Zeng, Fang Cheng & Renkuan Tang

  2. Institute of Forensic Medicine, West China School of Basic Science and Forensic Medicine, Sichuan University, Chengdu, 610065, China

    Xing Zou & Mengge Wang

  3. School of Medicine, Chongqing University, Chongqing, 400044, China

    Xing Zou

  4. Guangzhou Forensic Science Institute, Guangzhou, 510055, China

    Mengge Wang

  5. Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, 510275, China

    Mengge Wang

  6. State Key Laboratory of Cellular Stress Biology, National Institute for Data Science in Health and Medicine, School of Life Sciences, Xiamen University, Xiamen, 361005, China

    Guanglin He

  7. Department of Anthropology and Ethnology, Institute of Anthropology, School of Sociology and Anthropology, Xiamen University, Xiamen, 361005, China

    Guanglin He

  8. State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, 361005, China

    Guanglin He

  9. School of Humanities, Nanyang Technological University, Singapore, 224050, Singapore

    Guanglin He

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  1. Yicheng Wang
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Contributions

GH, RT and XZ designed this study. GH, YW, XZ and MW wrote the manuscript. YW and XZ conducted the experiment. YW, XZ, MW, DY, LY, YZ, FC and GH analyzed the results. RT, XZ, MW and GH revised the manuscript. All authors reviewed the manuscript.

Corresponding authors

Correspondence to Xing Zou, Renkuan Tang or Guanglin He.

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The author declares no conflict of interest.

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We followed the recommendations of the Helsinki Declaration of 2000, the regulations of the Human Genetic Resources Administration of China (HGRAC) and requirements of the genetic survey of Human populations published by the Medical Ethics Committee in Chongqing Medical University along with the Medical Ethics Committee of Xiamen University (XDYX201909).

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Communicated by Shuhua Xu.

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Wang, Y., Zou, X., Wang, M. et al. The genomic history of southwestern Chinese populations demonstrated massive population migration and admixture among proto-Hmong–Mien speakers and incoming migrants. Mol Genet Genomics 297, 241–262 (2022). https://doi.org/10.1007/s00438-021-01837-3

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