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Inferring the population history of Tai-Kadai-speaking people and southernmost Han Chinese on Hainan Island by genome-wide array genotyping

European Journal of Human Genetics volume 28, pages 1111–1123 (2020)Cite this article

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Abstract

Hainan Island, located between East Asia and Southeast Asia, represents an ideal region for the study of the genetic architecture of geographically isolated populations. However, the genetic structure and demographic history of the indigenous Tai-Kadai-speaking Hlai people and recent expanded southernmost Han Chinese on this island are poorly characterized due to a lack of genetic data. Thus, we collected and genotyped 36 Qiongzhong Hlai and 48 Haikou Han individuals at 497,637 single nucleotide polymorphisms (SNPs). We applied principal component analysis, ADMIXTURE, symmetrical D-statistics, admixture-f3 statistics, qpWave, and qpAdm analysis to infer the population history. Our results revealed the East Asian populations are characterized by a north-south genetic cline with Hlai at the southernmost end. We have not detected recent gene flow from neighboring populations into Hlai, therefore, we used Hlai as an unadmixed proxy to model the admixture history of mainland Tai-Kadai-speaking populations and southern Han Chinese. The mainland Tai-Kadai-speaking populations are suggested deriving a larger number of their ancestry from Hlai-related lineage, but also having admixture from South Asian-related or other neighboring populations. The Hlai group is also suggested to contribute about half of the ancestry to Han Chinese in Hainan. The complex patterns of genetic structure in East Asia were shaped via language categories, geographical boundaries, and large southward population movements with language dispersal and agriculture propagation.

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Fig. 1: Genetic affinity and population structure between Qiongzhong Hlai, Haikou Han and other reference populations included in the HapMap 3 and HGDP-CEPH projects.
Fig. 2: Shared alleles between Hlai, and Han and other references inferred from three or four-population tests.
Fig. 3: Genetic affinity between modern East Asians and ancient people.
Fig. 4: The model for origin, evolutionary and demographic history of Tai-Kadai-speaking populations and southernmost Han Chinese.

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Acknowledgements

CCW was supported by the National Natural Science Foundation of China (31801040), Nanqiang Outstanding Young Talents Program of Xiamen University (X2123302), and Fundamental Research Funds for the Central Universities (ZK1144). YH was supported by grants from the Opening Project of Shanghai Key Laboratory of Crime Scene Evidence (2016XCWZK12), the National Natural Science Foundation of China (81571854) and the Fundamental Research Funds for the Central Universities (20826041A4408, YJ201651, and 2012017yjsy187).

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Authors and Affiliations

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

    Guanglin He, Zheng Wang, Mengge Wang, Xing Zou, Jing Liu & Yiping Hou

  2. Department of Anthropology and Ethnology, Institute of Anthropology, National Institute for Data Science in Health and Medicine, and School of Life Sciences, Xiamen University, Xiamen, China

    Guanglin He, Jianxin Guo, Yingxiang Li, Rong Hu, Lan-Hai Wei & Chuan-Chao Wang

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

    Renkuan Tang

  4. Department of Forensic Medicine, Guizhou Medical University, Guiyang, China

    Han Zhang

  5. WeGene, Shenzhen, 518040, China

    Gang Chen

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  1. Guanglin He
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He, G., Wang, Z., Guo, J. et al. Inferring the population history of Tai-Kadai-speaking people and southernmost Han Chinese on Hainan Island by genome-wide array genotyping. Eur J Hum Genet 28, 1111–1123 (2020). https://doi.org/10.1038/s41431-020-0599-7

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