J Syst Evol ›› 2022, Vol. 60 ›› Issue (4): 955-972.DOI: 10.1111/jse.12715

• Research Articles • Previous Articles    

Fine-scale north-to-south genetic admixture profile in Shaanxi Han Chinese revealed by genome-wide demographic history reconstruction

Guang-Lin He1,2† , Meng-Ge Wang2† , Ying-Xiang Li1† , Xing Zou2 , Hui-Yuan Yeh3 , Ren-Kuan Tang4 , Xiao-Min Yang1 , Zheng Wang2 , Jian-Xin Guo1 , Ting Luo1 , Jing Zhao1 , Jin Sun1 , Rong Hu1 , Lan-Hai Wei1 , Gang Chen5*, Yi-Ping Hou2*, and Chuan-Chao Wang1*   

  1. 1 Department of Anthropology and Ethnology, Institute of Anthropology, National Institute for Data Science in Health and Medicine, State Key Laboratory of Marine Environmental Science, State Key Laboratory of Cellular Stress Biology, and School of Life Sciences, Xiamen University, Xiamen 361005, China
    2 Institute of Forensic Medicine, West China School of Basic Science and Forensic Medicine, Sichuan University, Chengdu 610065, China
    3 School of Humanities, Nanyang Technological University, Nanyang 639798, Singapore
    4 Department of Forensic Medicine, College of Basic Medicine, Chongqing Medical University, Chongqing 400331, China
    5 Hunan Key Laboratory of Bioinformatics, School of Computer Science and Engineering, Central South University, Changsha 410075, China

    These authors contributed equally to this work.
    Authors for correspondence. Gang Chen. E‐mail: chengangcs@gmail.com; Yi‐Ping Hou. E‐mail: forensic@scu.edu.cn; Chuan‐Chao Wang. E‐mail: wang@xmu.edu.cn
  • Received:2020-05-12 Accepted:2020-11-24 Online:2020-12-11 Published:2022-07-01


The Han Chinese are the world's largest ethnic group residing across China. Shaanxi province in northern China was a pastoral–agricultural interlacing region sensitive to climate change since Neolithic times, which makes it a vital place for studying population dynamics. However, genetic studies of Shaanxi Han are underrepresented due to the lack of high-density sampling and genome-wide data. Here, we genotyped 700 000 single nucleotide polymorphisms (SNPs) in 200 Han individuals from nine populations in Shaanxi and compared with available modern and ancient Eurasian individuals. We revealed a north–south genetic cline in Han Chinese with Shaanxi Han locating at the northern side of the cline. We detected the western Eurasian-related admixture in Shaanxi populations, especially in Guanzhong and Shanbei Han Chinese in proportions of 2%–4.6%. Shaanxi Han were suggested to derive a large part of ancestry (39%–69%) from a lineage that also contributed largely to ancient and present-day Tibetans (85%) as well as southern Han, supporting the common northern China origin of modern Sino-Tibetan-speaking populations and southwestward expansion of millet farmers from the middle-upper Yellow River Basin to the Tibetan Plateau and to southern China. The rest of the ancestry of Shaanxi Han was from a lineage closely related to ancient and present-day Austronesian and Tai-Kadai speaking populations in southern China and Southeast Asia. We also observed a genetic substructure in Shaanxi Han in terms of north–south-related ancestry corresponding well to the latitudes. Maternal mitochondrial DNA and paternal Y-chromosome lineages further demonstrated the aforementioned admixture pattern of Han Chinese in Shaanxi province.

Key words: ancestral makeup, genetic relationship, haplogroup, Northern Han, population substructure, western Eurasian admixture