Population genetic admixture and evolutionary history in the Shandong Peninsula inferred from integrative modern and ancient genomic resources

作者全名：Su, Haoran; Wang, Mengge; Li, Xiangping; Duan, Shuhan; Sun, Qiuxia; Sun, Yuntao; Wang, Zhiyong; Yang, Qingxin; Huang, Yuguo; Zhong, Jie; Chen, Jing; Jiang, Xiucheng; Ma, Jinyue; Yang, Ting; Liu, Yunhui; Luo, Lintao; Liu, Yan; Yang, Junbao; Chen, Gang; Liu, Chao; Cai, Yan; He, Guanglin

作者地址：[Su, Haoran; Cai, Yan] North Sichuan Med Coll, Ctr Genet & Prenatal Diag, Affiliated Hosp, Nanchong 637007, Sichuan, Peoples R China; [Su, Haoran; Wang, Mengge; Li, Xiangping; Duan, Shuhan; Sun, Qiuxia; Sun, Yuntao; Wang, Zhiyong; Yang, Qingxin; Huang, Yuguo; Zhong, Jie; Chen, Jing; Jiang, Xiucheng; Ma, Jinyue; Yang, Ting; Liu, Yunhui; Luo, Lintao; Liu, Yan; He, Guanglin] Sichuan Univ, West China Hosp, Inst Rare Dis, Chengdu 610000, Peoples R China; [Su, Haoran] North Sichuan Med Coll, Sch Lab Med, Nanchong 637007, Sichuan, Peoples R China; [Wang, Mengge; He, Guanglin] Sichuan Univ, Ctr Archaeol Sci, Chengdu 610000, Peoples R China; [Wang, Mengge; Duan, Shuhan; Jiang, Xiucheng; Ma, Jinyue; Liu, Yan; Yang, Junbao; He, Guanglin] North Sichuan Med Coll, Res Ctr Genom Med, Nanchong 637100, Peoples R China; [Li, Xiangping; Wang, Zhiyong; Yang, Qingxin; Yang, Ting] Kunming Med Univ, Sch Forens Med, Kunming 650500, Peoples R China; [Duan, Shuhan; Jiang, Xiucheng; Ma, Jinyue; Liu, Yan; Yang, Junbao] North Sichuan Med Coll, Inst Basic Med & Forens Med, North Sichuan Med Coll & Genet, Affiliated Hosp, Nanchong 637007, Sichuan, Peoples R China; [Duan, Shuhan; Jiang, Xiucheng; Ma, Jinyue; Liu, Yan; Yang, Junbao] North Sichuan Med Coll, Prenatal Diag Ctr, Affiliated Hosp, Nanchong 637007, Sichuan, Peoples R China; [Sun, Qiuxia; Liu, Yunhui; Luo, Lintao] Chongqing Med Univ, Coll Basic Med, Dept Forens Med, Chongqing 400331, Peoples R China; [Sun, Yuntao] Sichuan Univ, West China Sch Basic Med Sci & Forens Med, Chengdu 610041, Peoples R China; [Chen, Jing] Shanxi Med Univ, Sch Forens Med, Jinzhong 030001, Peoples R China; [Liu, Chao] Antidrug Technol Ctr Guangdong Prov, Guangzhou 510230, Peoples R China; [Chen, Gang] Cent South Univ, Sch Comp Sci & Engn, Hunan Key Lab Bioinformat, Changsha 410075, Peoples R China

通信作者：Cai, Y (通讯作者)，North Sichuan Med Coll, Ctr Genet & Prenatal Diag, Affiliated Hosp, Nanchong 637007, Sichuan, Peoples R China.; Wang, MG; He, GL (通讯作者)，Sichuan Univ, West China Hosp, Inst Rare Dis, Chengdu 610000, Peoples R China.; Wang, MG; He, GL (通讯作者)，Sichuan Univ, Ctr Archaeol Sci, Chengdu 610000, Peoples R China.; Wang, MG; He, GL (通讯作者)，North Sichuan Med Coll, Res Ctr Genom Med, Nanchong 637100, Peoples R China.; Liu, C (通讯作者)，Antidrug Technol Ctr Guangdong Prov, Guangzhou 510230, Peoples R China.

来源：BMC GENOMICS

ESI学科分类：MOLECULAR BIOLOGY & GENETICS

WOS号：WOS:001252061800002

JCR分区：Q2

影响因子：3.5

年份：2024

卷号：25

期号：1

开始页：　

结束页：　

文献类型：Article

关键词：Population genetics; Northern Han; Evolution; Genomics; Adaptation

摘要：Background Ancient northern East Asians (ANEA) from the Yellow River region, who pioneered millet cultivation, play a crucial role in understanding the origins of ethnolinguistically diverse populations in modern China and the entire landscape of deep genetic structure and variation discovery in modern East Asians. However, the direct links between ANEA and geographically proximate modern populations, as well as the biological adaptive processes involved, remain poorly understood.Results Here, we generated genome-wide SNP data for 264 individuals from geographically different Han populations in Shandong. An integrated genomic resource encompassing both modern and ancient East Asians was compiled to examine fine-scale population admixture scenarios and adaptive traits. The reconstruction of demographic history and hierarchical clustering patterns revealed that individuals from the Shandong Peninsula share a close genetic affinity with ANEA, indicating long-term genetic continuity and mobility in the lower Yellow River basin since the early Neolithic period. Biological adaptive signatures, including those related to immune and metabolic pathways, were identified through analyses of haplotype homozygosity and allele frequency spectra. These signatures are linked to complex traits such as height and body mass index, which may be associated with adaptations to cold environments, dietary practices, and pathogen exposure. Additionally, allele frequency trajectories over time and a haplotype network of two highly differentiated genes, ABCC11 and SLC10A1, were delineated. These genes, which are associated with axillary odor and bilirubin metabolism, respectively, illustrate how local adaptations can influence the diversification of traits in East Asians.Conclusions Our findings provide a comprehensive genomic dataset that elucidates the fine-scale genetic history and evolutionary trajectory of natural selection signals and disease susceptibility in Han Chinese populations. This study serves as a paradigm for integrating spatiotemporally diverse ancient genomes in the era of population genomic medicine.

基金机构：National Natural Science Foundation of China [82202078]; Major Project of the National Social Science Foundation of China [23ZD203]; Open Project of the Key Laboratory of Forensic Genetics of the Ministry of Public Security [2022FGKFKT05]; Center for Archaeological Science of Sichuan University [23SASA01]; The 1.3.5 Project for Disciplines of Excellence, West China Hospital, Sichuan University [ZYJC20002]; Sichuan Science and Technology Program [2024NSFSC1518]

基金资助正文：This study was supported by the National Natural Science Foundation of China (82202078), the Major Project of the National Social Science Foundation of China (23&ZD203), 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, West China Hospital, Sichuan University (ZYJC20002), and the Sichuan Science and Technology Program (2024NSFSC1518).