Paleolithic divergence and multiple Neolithic expansions of ancestral nomadic emperor-related paternal lineages

Mengge Wang; Qiuxia Sun; Yuhang Feng; Lan-Hai Wei; Kaijun Liu; Lintao Luo; Yuguo Huang; Kun Zhou; Haibing Yuan; Hongliang Lv; Yu Lu; Jing Cheng; Shaoqing Wen; Chuan-Chao Wang; Renkuan Tang; Fengxiao Bu; Chao Liu; Huijun Yuan; Zhiyong Wang; Guanglin He

doi:10.1016/j.jgg.2024.11.012

Volume 52 Issue 4

Apr. 2025

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Paleolithic divergence and multiple Neolithic expansions of ancestral nomadic emperor-related paternal lineages

doi: 10.1016/j.jgg.2024.11.012

a. Institute of Rare Diseases, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, Sichuan 610000, China;
b. Center for Archaeological Science, Sichuan University, Chengdu, Sichuan 610000, China;
c. Anti-Drug Technology Center of Guangdong Province, Guangzhou, Guangdong 510230, China;
d. Department of Forensic Medicine, College of Basic Medicine, Chongqing Medical University, Chongqing 400331, China;
e. Human Genetics and Forensic Genomics Research Institute, College of Basic Medicine, Chongqing Medical University, Chongqing 400331, China;
f. Institute of Humanities and Human Sciences, Inner Mongolia Normal University, Hohhot, Inner Mongolia 010022, China;
g. Institute of 23Mofang, Tianfu Software Park, Chengdu, Sichuan 610042, China;
h. MOE Laboratory for National Development and Intelligent Governance, Fudan University, Shanghai 200433, China;
i. State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, Fujian 361102, China

Funds:

We acknowledge the financial support received from the National Natural Science Foundation of China (82202078) for M.W. and from the National Social Science Foundation of China (23&ZD203) for G.H. Additional support for G.H. includes National Natural Science Foundation of China (82402203), the Open Project of the Key Laboratory of Forensic Genetics of the Ministry of Public Security (2022FGKFKT05), the Center for Archaeological Science of Sichuan University (23SASA01), the 1·3·5 Project for Disciplines of Excellence at West China Hospital, Sichuan University (ZYJC20002), and the Sichuan Science and Technology Program (2024NSFSC1518).

Received Date: 2024-06-11
Accepted Date: 2024-11-20
Rev Recd Date: 2024-11-17

Available Online: 2025-07-11

Publish Date: 2024-11-27

Abstract

Abstract

The reconstruction of demographic history using ancient and modern genomic resources reveals extensive interactions and admixture between ancient nomadic pastoralists and the social organizations of the Chinese Central Plain. However, the extent to which Y-chromosome genetic legacies from nomadic emperor-related ancestral lineages influence the Chinese paternal gene pool remains unclear. Here, we genotype 2717 ethnolinguistically diverse samples belonging to C2a lineages, perform whole-genome sequencing on 997 representative samples, and integrate these data with ancient genomic sequences. We reconstruct the evolutionary histories of Northern Zhou-, Qing emperor-, and pastoralist-related lineages to assess their genetic impact on modern Chinese populations. This reassembled fine-scale Y-chromosome phylogeny identifies deep divergence and five Neolithic expansion events contributing differently to the formation of northern Chinese populations. Phylogeographic modeling indicates that the nomadic empires of the Northern Zhou and Qing dynasties genetically originated from the Mongolian Plateau. Phylogenetic topology and shared haplotype patterns show that three upstream ancestors of Northern Zhou (C2a1a1b1a2a1b-FGC28857), Donghu tribe (C2a1a1b1-F1756), and Qing (C2a1a3a2-F10283) emperor-related lineages expanded during the middle Neolithic, contributing significantly to genetic flow between ancient northeastern Asians and modern East Asians. Notably, this study reveals limited direct contributions of Emperor Wu of Northern Zhou's lineages to modern East Asians.
- Paternal lineage,
- Founding lineage,
- Genetic origin,
- Emperor lineage,
- Y-chromosome

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