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Su H, Wang M, Li X, Duan S, Sun Q, Sun Y, Wang Z, Yang Q, Huang Y, Zhong J, Chen J, Jiang X, Ma J, Yang T, Liu Y, Luo L, Liu Y, Yang J, Chen G, Liu C, Cai Y, He G. Population genetic admixture and evolutionary history in the Shandong Peninsula inferred from integrative modern and ancient genomic resources. BMC Genomics 2024; 25:611. [PMID: 38890579 PMCID: PMC11184692 DOI: 10.1186/s12864-024-10514-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Accepted: 06/11/2024] [Indexed: 06/20/2024] Open
Abstract
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.
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Affiliation(s)
- Haoran Su
- Genetic and Prenatal Diagnosis Center, Affiliated Hospital of North Sichuan Medical College, Nanchong, 637007, Sichuan, China
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, 610000, China
- School of Laboratory Medicine, North Sichuan Medical College, Nanchong, 637007, Sichuan, China
| | - Mengge Wang
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, 610000, China.
- Center for Archaeological Science, Sichuan University, Chengdu, 610000, China.
- Research Center for Genomic Medicine, North Sichuan Medical College, Nanchong, 637100, China.
| | - Xiangping Li
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, 610000, China
- School of Forensic Medicine, Kunming Medical University, Kunming, 650500, China
| | - Shuhan Duan
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, 610000, China
- Research Center for Genomic Medicine, North Sichuan Medical College, Nanchong, 637100, China
- Institute of Basic Medicine and Forensic Medicine, North Sichuan Medical College and Genetic and Prenatal Diagnosis Center, Affiliated Hospital of North Sichuan Medical College, Nanchong, 637007, Sichuan, China
| | - Qiuxia Sun
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, 610000, China
- Department of Forensic Medicine, College of Basic Medicine, Chongqing Medical University, Chongqing, 400331, China
| | - Yuntao Sun
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, 610000, China
- West China School of Basic Science & Forensic Medicine, Sichuan University, Chengdu, 610041, China
| | - Zhiyong Wang
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, 610000, China
- School of Forensic Medicine, Kunming Medical University, Kunming, 650500, China
| | - Qingxin Yang
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, 610000, China
- School of Forensic Medicine, Kunming Medical University, Kunming, 650500, China
| | - Yuguo Huang
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, 610000, China
| | - Jie Zhong
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, 610000, China
| | - Jing Chen
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, 610000, China
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, 030001, China
| | - Xiucheng Jiang
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, 610000, China
- Research Center for Genomic Medicine, North Sichuan Medical College, Nanchong, 637100, China
- Institute of Basic Medicine and Forensic Medicine, North Sichuan Medical College and Genetic and Prenatal Diagnosis Center, Affiliated Hospital of North Sichuan Medical College, Nanchong, 637007, Sichuan, China
| | - Jinyue Ma
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, 610000, China
- Research Center for Genomic Medicine, North Sichuan Medical College, Nanchong, 637100, China
- Institute of Basic Medicine and Forensic Medicine, North Sichuan Medical College and Genetic and Prenatal Diagnosis Center, Affiliated Hospital of North Sichuan Medical College, Nanchong, 637007, Sichuan, China
| | - Ting Yang
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, 610000, China
- School of Forensic Medicine, Kunming Medical University, Kunming, 650500, China
| | - Yunhui Liu
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, 610000, China
- Department of Forensic Medicine, College of Basic Medicine, Chongqing Medical University, Chongqing, 400331, China
| | - Lintao Luo
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, 610000, China
- Department of Forensic Medicine, College of Basic Medicine, Chongqing Medical University, Chongqing, 400331, China
| | - Yan Liu
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, 610000, China
- Research Center for Genomic Medicine, North Sichuan Medical College, Nanchong, 637100, China
- Institute of Basic Medicine and Forensic Medicine, North Sichuan Medical College and Genetic and Prenatal Diagnosis Center, Affiliated Hospital of North Sichuan Medical College, Nanchong, 637007, Sichuan, China
| | - Junbao Yang
- Research Center for Genomic Medicine, North Sichuan Medical College, Nanchong, 637100, China
- Institute of Basic Medicine and Forensic Medicine, North Sichuan Medical College and Genetic and Prenatal Diagnosis Center, Affiliated Hospital of North Sichuan Medical College, Nanchong, 637007, Sichuan, China
| | - Gang Chen
- Hunan Key Laboratory of Bioinformatics, School of Computer Science and Engineering, Central South University, Changsha, 410075, China
| | - Chao Liu
- Anti-Drug Technology Center of Guangdong Province, Guangzhou, 510230, China.
| | - Yan Cai
- Genetic and Prenatal Diagnosis Center, Affiliated Hospital of North Sichuan Medical College, Nanchong, 637007, Sichuan, China.
| | - Guanglin He
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, 610000, China.
- Center for Archaeological Science, Sichuan University, Chengdu, 610000, China.
- Research Center for Genomic Medicine, North Sichuan Medical College, Nanchong, 637100, China.
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2
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Zhang H, Yang M, Zhang H, Ren Z, Wang Q, Liu Y, Jin X, Ji J, Feng Y, Cai C, Ran Q, Li C, Huang J. Forensic features and phylogenetic structure survey of four populations from southwest China via the autosomal insertion/deletion markers. Forensic Sci Res 2024; 9:owad052. [PMID: 38765700 PMCID: PMC11102079 DOI: 10.1093/fsr/owad052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 05/09/2023] [Indexed: 05/22/2024] Open
Abstract
Insertion/Deletion (InDel) polymorphisms, characterized by their smaller amplicons, reduced mutation rates, and compatibility with the prevalent capillary electrophoresis (CE) platforms in forensic laboratories, significantly contribute to the advancement and application of genetic analysis. Guizhou province in China serves as an important region for investigating the genetic structure, ethnic group origins, and human evolution. However, DNA data and the sampling of present-day populations are lacking, especially about the InDel markers. Here, we reported data on 47 autosomal InDels from 592 individuals from four populations in Guizhou (Han, Dong, Yi, and Chuanqing). Genotyping was performed with the AGCU InDel 50 kit to evaluate their utility for forensic purposes and to explore the population genetic structure. Our findings showed no significant deviations from Hardy-Weinberg and linkage equilibriums. The combined power of discrimination (CPD) and the combined power of exclusion (CPE) for each population demonstrated that the kit could be applied to forensic individual identification and was an effective supplement for parentage testing. Genetic structure analyses, including principal component analysis, multidimensional scaling, genetic distance calculation, STRUCTURE, and phylogenetic analysis, highlighted that the genetic proximity of the studied populations correlates with linguistic, geographical, and cultural factors. The observed genetic variances within four research populations were less pronounced than those discerned between populations across different regions. Notably, the Guizhou Han, Dong, and Chuanqing populations showed closer genetic affiliations with linguistically similar groups than the Guizhou Yi. These results underscore the potential of InDel markers in forensic science and provide insights into the genetic landscape and human evolution in multi-ethnic regions like Guizhou. Key points InDel markers show promise for forensic individual identification and parentage testing via the AGCU InDel 50 kit.Genetic analysis of Guizhou populations reveals correlations with linguistic, geographical, and cultural factors.Guizhou Han, Dong, and Chuanqing populations showed closer genetic affiliations with linguistically similar groups than the Guizhou Yi.
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Affiliation(s)
- Han Zhang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, Guizhou, China
- Institute of Forensic Science, Fudan University, Shanghai, China
| | - Meiqing Yang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, Guizhou, China
| | - Hongling Zhang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, Guizhou, China
| | - Zheng Ren
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, Guizhou, China
| | - Qiyan Wang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, Guizhou, China
| | - Yubo Liu
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, Guizhou, China
| | - Xiaoye Jin
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, Guizhou, China
| | - Jingyan Ji
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, Guizhou, China
| | - Yuhang Feng
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, Guizhou, China
| | - Changsheng Cai
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, Guizhou, China
| | - Qianchong Ran
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, Guizhou, China
| | - Chengtao Li
- Institute of Forensic Science, Fudan University, Shanghai, China
| | - Jiang Huang
- The Key Laboratory of Environmental Pollution Monitoring and Disease Control, Ministry of Education, Guizhou Medical University, Guiyang, China
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3
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Jia L, Wang M, Duan S, Chen J, Zhao M, Ji S, Lv B, Jiang X, He G, Yang J. Genetic history of esophageal cancer group in southwestern China revealed by Y-chromosome STRs and genomic evolutionary connection analysis. Heliyon 2024; 10:e29867. [PMID: 38720733 PMCID: PMC11076658 DOI: 10.1016/j.heliyon.2024.e29867] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Revised: 04/09/2024] [Accepted: 04/16/2024] [Indexed: 05/12/2024] Open
Abstract
Genetic and environmental factors play crucial roles in the development of esophageal cancer (EC) and contribute uniquely or cooperatively to human cancer susceptibility. Sichuan is located in the interior of southwestern China, and the northern part of Sichuan is one of the regions with a high occurrence of EC. However, the factors influencing the high incidence rate of EC in the Sichuan Han Chinese population and its corresponding genetic background and origins are still poorly understood. Here, we utilized genome-wide single nucleotide polymorphisms (SNPs) and Y-chromosome short tandem repeats (Y-STRs) to characterize the genetic structure, connection, and origin of cancer groups and general populations. We generated Y-STR-based haplotype data from 214 Sichuan individuals, including the Han Chinese EC population and a control group of Han Chinese individuals. Our results, obtained from Y-STR-based population statistical methods (analysis of molecular variance (AMOVA), principal component analysis (PCA), and phylogenetic analysis), demonstrated that there was a genetic substructure difference between the EC population in the high-incidence area of northern Sichuan Province and the control population. Additionally, there was a strong genetic relationship between the EC population in the northern Sichuan high-incidence area and those at high risk in both the Fujian and Chaoshan areas. In addition, we obtained high-density SNP data from saliva samples of 60 healthy Han Chinese individuals from three high-prevalence areas of EC in China: Sichuan Nanchong, Fujian Quanzhou, and Henan Xinxiang. As inferred from the allele frequency of SNPs and sharing patterns of haplotype segments, the evolutionary history and admixture events suggested that the Han population from Nanchong in northern Sichuan Province shared a close genetic relationship with the Han populations from Xinxiang in Henan Province and Quanzhou in Fujian Province, both of which are regions with a high prevalence of EC. Our study illuminated the genetic profile and connection of the Northern Sichuan Han population and enriched the genomic resources and features of the Han Chinese populations in China, especially for the Y-STR genetic data of the Han Chinese EC population. Populations living in different regions with high incidences of EC may share similar genetic backgrounds, which offers new insights for further exploring the genetic mechanisms underlying EC.
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Affiliation(s)
- Lihua Jia
- Institute of Basic Medicine and Forensic Medicine, North Sichuan Medical College and Center for Genetics and Prenatal diagnosis, Affiliated Hospital of Northern Sichuan Medical College, Nanchong, Sichuan, 637007, China
| | - Mengge Wang
- Center for Archaeological Science, Sichuan University, Chengdu, 610000, China
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, 610000, China
| | - Shuhan Duan
- Institute of Basic Medicine and Forensic Medicine, North Sichuan Medical College and Center for Genetics and Prenatal diagnosis, Affiliated Hospital of Northern Sichuan Medical College, Nanchong, Sichuan, 637007, China
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, 610000, China
| | - Jianghua Chen
- Institute of Basic Medicine and Forensic Medicine, North Sichuan Medical College and Center for Genetics and Prenatal diagnosis, Affiliated Hospital of Northern Sichuan Medical College, Nanchong, Sichuan, 637007, China
| | - Mei Zhao
- Institute of Basic Medicine and Forensic Medicine, North Sichuan Medical College and Center for Genetics and Prenatal diagnosis, Affiliated Hospital of Northern Sichuan Medical College, Nanchong, Sichuan, 637007, China
| | - Simeng Ji
- School of Laboratory Medicine, North Sichuan Medical College, Nanchong, Sichuan, 637000, China
| | - Bingbing Lv
- School of Laboratory Medicine, North Sichuan Medical College, Nanchong, Sichuan, 637000, China
| | - Xiucheng Jiang
- Institute of Basic Medicine and Forensic Medicine, North Sichuan Medical College and Center for Genetics and Prenatal diagnosis, Affiliated Hospital of Northern Sichuan Medical College, Nanchong, Sichuan, 637007, China
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, 610000, China
| | - Guanglin He
- Center for Archaeological Science, Sichuan University, Chengdu, 610000, China
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, 610000, China
| | - Junbao Yang
- Institute of Basic Medicine and Forensic Medicine, North Sichuan Medical College and Center for Genetics and Prenatal diagnosis, Affiliated Hospital of Northern Sichuan Medical College, Nanchong, Sichuan, 637007, China
- School of Laboratory Medicine, North Sichuan Medical College, Nanchong, Sichuan, 637000, China
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4
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Duan S, Wang M, Wang Z, Liu Y, Jiang X, Su H, Cai Y, Sun Q, Sun Y, Li X, Chen J, Zhang Y, Yan J, Nie S, Hu L, Tang R, Yun L, Wang CC, Liu C, Yang J, He G. Malaria resistance-related biological adaptation and complex evolutionary footprints inferred from one integrative Tai-Kadai-related genomic resource. Heliyon 2024; 10:e29235. [PMID: 38665582 PMCID: PMC11043949 DOI: 10.1016/j.heliyon.2024.e29235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 04/01/2024] [Accepted: 04/03/2024] [Indexed: 04/28/2024] Open
Abstract
Pathogen‒host adaptative interactions and complex population demographical processes, including admixture, drift, and Darwen selection, have considerably shaped the Neolithic-to-Modern Western Eurasian population structure and genetic susceptibility to modern human diseases. However, the genetic footprints of evolutionary events in East Asia remain unknown due to the underrepresentation of genomic diversity and the design of large-scale population studies. We reported one aggregated database of genome-wide SNP variations from 796 Tai-Kadai (TK) genomes, including that of Bouyei first reported here, to explore the genetic history, population structure, and biological adaptative features of TK people from southern China and Southeast Asia. We found geography-related population substructure among TK people using the state-of-the-art population genetic structure reconstruction techniques based on the allele frequency spectrum and haplotype-resolved phased fragments. We found that the northern TK people from Guizhou harbored one TK-dominant ancestry maximized in the Bouyei people, and the southern TK people from Thailand were more influenced by Southeast Asians and indigenous people. We reconstructed fitted admixture models and demographic graphs, which showed that TK people received gene flow from ancient southern rice farmer-related lineages related to the Hmong-Mien and Austroasiatic people and from northern millet farmers associated with the Sino-Tibetan people. Biological adaptation focused on our identified unique TK lineages related to Bouyei, which showed many adaptive signatures conferring Malaria resistance and low-rate lipid metabolism. Further gene enrichment, the allele frequency distribution of derived alleles, and their correlation with the incidence of Malaria further confirmed that CR1 played an essential role in the resistance of Malaria in the ancient "Baiyue" tribes.
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Affiliation(s)
- Shuhan Duan
- Institute of Basic Medicine and Forensic Medicine, North Sichuan Medical College and Center for Genetics and Prenatal Diagnosis, Affiliated Hospital of North Sichuan Medical College, Nanchong, Sichuan, 637007, China
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, 610000, China
| | - Mengge Wang
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, 610000, China
- Center for Archaeological Science, Sichuan University, Chengdu, 610000, China
| | - Zhiyong Wang
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, 610000, China
- School of Forensic Medicine, Kunming Medical University, Kunming, 650500, China
| | - Yan Liu
- Institute of Basic Medicine and Forensic Medicine, North Sichuan Medical College and Center for Genetics and Prenatal Diagnosis, Affiliated Hospital of North Sichuan Medical College, Nanchong, Sichuan, 637007, China
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, 610000, China
| | - Xiucheng Jiang
- Institute of Basic Medicine and Forensic Medicine, North Sichuan Medical College and Center for Genetics and Prenatal Diagnosis, Affiliated Hospital of North Sichuan Medical College, Nanchong, Sichuan, 637007, China
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, 610000, China
| | - Haoran Su
- Institute of Basic Medicine and Forensic Medicine, North Sichuan Medical College and Center for Genetics and Prenatal Diagnosis, Affiliated Hospital of North Sichuan Medical College, Nanchong, Sichuan, 637007, China
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, 610000, China
| | - Yan Cai
- Institute of Basic Medicine and Forensic Medicine, North Sichuan Medical College and Center for Genetics and Prenatal Diagnosis, Affiliated Hospital of North Sichuan Medical College, Nanchong, Sichuan, 637007, China
- Research Center for Genomic Medicine, North Sichuan Medical College, Nanchong, 637100, China
| | - Qiuxia Sun
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, 610000, China
- Department of Forensic Medicine, College of Basic Medicine, Chongqing Medical University, Chongqing, 400331, China
| | - Yuntao Sun
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, 610000, China
- West China School of Basic Science & Forensic Medicine, Sichuan University, Chengdu, 610041, China
| | - Xiangping Li
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, 610000, China
- School of Forensic Medicine, Kunming Medical University, Kunming, 650500, China
| | - Jing Chen
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, 610000, China
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, 030001, China
| | - Yijiu Zhang
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, 610000, China
- Department of Forensic Medicine, College of Basic Medicine, Chongqing Medical University, Chongqing, 400331, China
| | - Jiangwei Yan
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, 030001, China
| | - Shengjie Nie
- School of Forensic Medicine, Kunming Medical University, Kunming, 650500, China
| | - Liping Hu
- School of Forensic Medicine, Kunming Medical University, Kunming, 650500, China
| | - Renkuan Tang
- Department of Forensic Medicine, College of Basic Medicine, Chongqing Medical University, Chongqing, 400331, China
| | - Libing Yun
- West China School of Basic Science & Forensic Medicine, Sichuan University, Chengdu, 610041, China
| | - Chuan-Chao Wang
- State Key Laboratory of Cellular Stress Biology, National Institute for Data Science in Health and Medicine, School of Life Sciences, Xiamen University, Xiamen, 361005, Fujian, China
| | - Chao Liu
- Anti-Drug Technology Center of Guangdong Province, Guangzhou, 510230, China
| | - Junbao Yang
- Institute of Basic Medicine and Forensic Medicine, North Sichuan Medical College and Center for Genetics and Prenatal Diagnosis, Affiliated Hospital of North Sichuan Medical College, Nanchong, Sichuan, 637007, China
- Research Center for Genomic Medicine, North Sichuan Medical College, Nanchong, 637100, China
| | - Guanglin He
- Institute of Basic Medicine and Forensic Medicine, North Sichuan Medical College and Center for Genetics and Prenatal Diagnosis, Affiliated Hospital of North Sichuan Medical College, Nanchong, Sichuan, 637007, China
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, 610000, China
- Research Center for Genomic Medicine, North Sichuan Medical College, Nanchong, 637100, China
- Center for Archaeological Science, Sichuan University, Chengdu, 610000, China
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5
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Sun Q, Wang M, Lu T, Duan S, Liu Y, Chen J, Wang Z, Sun Y, Li X, Wang S, Lu L, Hu L, Yun L, Yang J, Yan J, Nie S, Zhu Y, Chen G, Wang CC, Liu C, He G, Tang R. Differentiated adaptative genetic architecture and language-related demographical history in South China inferred from 619 genomes from 56 populations. BMC Biol 2024; 22:55. [PMID: 38448908 PMCID: PMC10918984 DOI: 10.1186/s12915-024-01854-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 02/26/2024] [Indexed: 03/08/2024] Open
Abstract
BACKGROUND The underrepresentation of human genomic resources from Southern Chinese populations limited their health equality in the precision medicine era and complete understanding of their genetic formation, admixture, and adaptive features. Besides, linguistical and genetic evidence supported the controversial hypothesis of their origin processes. One hotspot case was from the Chinese Guangxi Pinghua Han people (GPH), whose language was significantly similar to Southern Chinese dialects but whose uniparental gene pool was phylogenetically associated with the indigenous Tai-Kadai (TK) people. Here, we analyzed genome-wide SNP data in 619 people from four language families and 56 geographically different populations, in which 261 people from 21 geographically distinct populations were first reported here. RESULTS We identified significant population stratification among ethnolinguistically diverse Guangxi populations, suggesting their differentiated genetic origin and admixture processes. GPH shared more alleles related to Zhuang than Southern Han Chinese but received more northern ancestry relative to Zhuang. Admixture models and estimates of genetic distances showed that GPH had a close genetic relationship with geographically close TK compared to Northern Han Chinese, supporting their admixture origin hypothesis. Further admixture time and demographic history reconstruction supported GPH was formed via admixture between Northern Han Chinese and Southern TK people. We identified robust signatures associated with lipid metabolisms, such as fatty acid desaturases (FADS) and medically relevant loci associated with Mendelian disorder (GJB2) and complex diseases. We also explored the shared and unique selection signatures of ethnically different but linguistically related Guangxi lineages and found some shared signals related to immune and malaria resistance. CONCLUSIONS Our genetic analysis illuminated the language-related fine-scale genetic structure and provided robust genetic evidence to support the admixture hypothesis that can explain the pattern of observed genetic diversity and formation of GPH. This work presented one comprehensive analysis focused on the population history and demographical adaptative process, which provided genetic evidence for personal health management and disease risk prediction models from Guangxi people. Further large-scale whole-genome sequencing projects would provide the entire landscape of southern Chinese genomic diversity and their contributions to human health and disease traits.
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Affiliation(s)
- Qiuxia Sun
- Department of Forensic Medicine, College of Basic Medicine, Chongqing Medical University, Chongqing, 400331, China
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, 610000, China
| | - Mengge Wang
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, 610000, China.
- Center for Archaeological Science, Sichuan University, Chengdu, 610000, China.
| | - Tao Lu
- Department of Forensic Medicine, College of Basic Medicine, Chongqing Medical University, Chongqing, 400331, China
| | - Shuhan Duan
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, 610000, China
- School of Basic Medical Sciences, North Sichuan Medical College, Nanchong, 637100, China
| | - Yan Liu
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, 610000, China
- School of Basic Medical Sciences, North Sichuan Medical College, Nanchong, 637100, China
| | - Jing Chen
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, 610000, China
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, 030001, China
| | - Zhiyong Wang
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, 610000, China
- School of Forensic Medicine, Kunming Medical University, Kunming, 650500, China
| | - Yuntao Sun
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, 610000, China
- West China School of Basic Science & Forensic Medicine, Sichuan University, Chengdu, 610041, China
| | - Xiangping Li
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, 610000, China
- School of Forensic Medicine, Kunming Medical University, Kunming, 650500, China
| | - Shaomei Wang
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, 610000, China
- Department of Public Health, Chengdu Medical College, Chengdu, 610500, China
| | - Liuyi Lu
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, 610000, China
- School of Clinical Medical Sciences, North Sichuan Medical College, Nanchong, 637100, China
| | - Liping Hu
- School of Forensic Medicine, Kunming Medical University, Kunming, 650500, China
| | - Libing Yun
- West China School of Basic Science & Forensic Medicine, Sichuan University, Chengdu, 610041, China
| | - Junbao Yang
- School of Clinical Medical Sciences, North Sichuan Medical College, Nanchong, 637100, China
| | - Jiangwei Yan
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, 030001, China
| | - Shengjie Nie
- School of Forensic Medicine, Kunming Medical University, Kunming, 650500, China
| | - Yanfeng Zhu
- Department of Public Health, Chengdu Medical College, Chengdu, 610500, China
| | - Gang Chen
- Hunan Key Lab of Bioinformatics, School of Computer Science and Engineering, Central South University, Changsha, 410075, China
| | - Chuan-Chao Wang
- State Key Laboratory of Cellular Stress Biology, National Institute for Data Science in Health and Medicine, School of Life Sciences, Xiamen University, Xiamen, 361005, Fujian, China
| | - Chao Liu
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, 510275, China
- Guangzhou Forensic Science Institute, Guangzhou, 510055, China
- Anti-Drug Technology Center of Guangdong Province, Guangzhou, 510230, China
| | - Guanglin He
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, 610000, China.
- Center for Archaeological Science, Sichuan University, Chengdu, 610000, China.
| | - Renkuan Tang
- Department of Forensic Medicine, College of Basic Medicine, Chongqing Medical University, Chongqing, 400331, China.
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6
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Tao Y, Wei Y, Ge J, Pan Y, Wang W, Bi Q, Sheng P, Fu C, Pan W, Jin L, Zheng HX, Zhang M. Phylogenetic evidence reveals early Kra-Dai divergence and dispersal in the late Holocene. Nat Commun 2023; 14:6924. [PMID: 37903755 PMCID: PMC10616200 DOI: 10.1038/s41467-023-42761-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Accepted: 10/18/2023] [Indexed: 11/01/2023] Open
Abstract
Studying language evolution brings a crucial perspective to bear on questions of human prehistory. As the most linguistically diverse region on earth, East and Southeast Asia have witnessed extensive sociocultural and ethnic contacts among different language communities. Especially, the Kra-Dai language family exhibits tremendous socio-cultural importance in these regions. Due to limited historical accounts, however, there are several controversies on their linguistic relatedness, ambiguities regarding the divergence time, and uncertainties on the dispersal patterns. To address these issues, here we apply Bayesian phylogenetic methods to analyze the largest lexical dataset containing 646 cognate sets compiled for 100 Kra-Dai languages. Our dated phylogenetic tree showed their initial divergence occurring approximately 4000 years BP. Phylogeographic results supported the early Kra-Dai language dispersal from the Guangxi-Guangdong area of South China towards Mainland Southeast Asia. Coupled with genetic, archaeological, paleoecologic, and paleoclimatic data, we demonstrated that the Kra-Dai language diversification could have coincided with their demic diffusion and agricultural spread shaped by the global climate change in the late Holocene. The interdisciplinary alignments shed light on reconstructing the prehistory of Kra-Dai languages and provide an indispensable piece of the puzzle for further studying prehistoric human activities in East and Southeast Asia.
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Affiliation(s)
- Yuxin Tao
- State Key Laboratory of Genetic Engineering, Center for Evolutionary Biology, Human Phenome Institute, Zhangjiang Fudan International Innovation Center, School of Life Science, Fudan University, Shanghai, 200438, China
| | - Yuancheng Wei
- School of Chinese Language and Literature, Guangxi Minzu University, Guangxi Zhuang Autonomous Region, Nanning, China
| | - Jiaqi Ge
- Department of Chinese Language and Literature, Fudan University, Shanghai, China
| | - Yan Pan
- Department of Cultural Heritage and Museology, Fudan University, Shanghai, China
| | - Wenmin Wang
- College of Nationalities, Guangdong Polytechnic Normal University, Guangzhou, China
| | - Qianqi Bi
- College of Communication, East China University of Political Science and Law, Shanghai, China
| | - Pengfei Sheng
- Institute of Archaeological Science, Fudan University, Shanghai, China
| | - Changzhong Fu
- College of Nationalities, Guangdong Polytechnic Normal University, Guangzhou, China
| | - Wuyun Pan
- Institute of Modern Languages and Linguistics, Fudan University, Shanghai, China
- Institute for Humanities and Social Science Data, School of Data Science, Fudan University, Shanghai, China
| | - Li Jin
- State Key Laboratory of Genetic Engineering, Center for Evolutionary Biology, Human Phenome Institute, Zhangjiang Fudan International Innovation Center, School of Life Science, Fudan University, Shanghai, 200438, China
| | - Hong-Xiang Zheng
- Ministry of Education Key Laboratory of Contemporary Anthropology, Department of Anthropology and Human Genetics, School of Life Sciences, Fudan University, Shanghai, China.
| | - Menghan Zhang
- Institute of Modern Languages and Linguistics, Fudan University, Shanghai, China.
- Ministry of Education Key Laboratory of Contemporary Anthropology, Department of Anthropology and Human Genetics, School of Life Sciences, Fudan University, Shanghai, China.
- Research Institute of Intelligent Complex Systems, Fudan University, Shanghai, China.
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7
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Wang J, Wu J, Sun Q, Wu Q, Li Y, Duan S, Yang L, Wu W, Wang Z, Liu Y, Tang R, Yang J, Wang C, Liu C, Xu J, Wang M, He G. Extensive genetic admixture between Tai-Kadai-speaking people and their neighbours in the northeastern region of the Yungui Plateau inferred from genome-wide variations. BMC Genomics 2023; 24:317. [PMID: 37308851 DOI: 10.1186/s12864-023-09412-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 05/27/2023] [Indexed: 06/14/2023] Open
Abstract
BACKGROUND Yungui Plateau in Southwest China is characterized by multi-language and multi-ethnic communities and is one of the regions with the wealthiest ethnolinguistic, cultural and genetic diversity in East Asia. There are numerous Tai-Kadai (TK)-speaking populations, but their detailed evolutionary history and biological adaptations are still unclear. RESULTS Here, we genotyped genome-wide SNP data of 77 unrelated TK-speaking Zhuang and Dong individuals from the Yungui Plateau and explored their detailed admixture history and adaptive features using clustering patterns, allele frequency differentiation and sharing haplotype patterns. TK-speaking Zhuang and Dong people in Guizhou are closely related to geographically close TK and Hmong-Mien (HM)-speaking populations. Besides, we identified that Guizhou TK-speaking people have a close genetic relationship with Austronesian (AN)-speaking Atayal and Paiwan people, which is supported by the common origin of the ancient Baiyue tribe. We additionally found subtle genetic differences among the newly studied TK people and previously reported Dais via the fine-scale genetic substructure analysis based on the shared haplotype chunks. Finally, we identified specific selection candidate signatures associated with several essential human immune systems and neurological disorders, which could provide evolutionary evidence for the allele frequency distribution pattern of genetic risk loci. CONCLUSIONS Our comprehensive genetic characterization of TK people suggested the strong genetic affinity within TK groups and extensive gene flow with geographically close HM and Han people. We also provided genetic evidence that supported the common origin hypothesis of TK and AN people. The best-fitted admixture models further suggested that ancestral sources from northern millet farmers and southern inland and coastal people contributed to the formation of the gene pool of the Zhuang and Dong people.
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Affiliation(s)
- Jiawen Wang
- School of Forensic Medicine, Guizhou Medical University, Guiyang, 550004, China.
| | - Jun Wu
- School of Forensic Medicine, Guizhou Medical University, Guiyang, 550004, China
| | - Qiuxia Sun
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, 610000, China
- Department of Forensic Medicine, College of Basic Medicine, Chongqing Medical University, Chongqing, 400331, China
| | - Qian Wu
- Qiannan Prefecture People's Hospital, Buyi and Miao Autonomous Prefecture of QianNan, Buyi and Miao Autonomous Prefecture of QianNan, 558000, China
| | - Youjing Li
- Congjiang People's Hospital, Congjiang, 557499, China
| | - Shuhan Duan
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, 610000, China
- School of Basic Medical Sciences, North Sichuan Medical College, Nanchong, 637000, China
| | - Lin Yang
- School of Forensic Medicine, Guizhou Medical University, Guiyang, 550004, China
| | - Wenxin Wu
- School of Forensic Medicine, Guizhou Medical University, Guiyang, 550004, China
| | - Zheng Wang
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, 610041, China
| | - Yan Liu
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, 610000, China
- School of Basic Medical Sciences, North Sichuan Medical College, Nanchong, 637000, China
| | - Renkuan Tang
- Department of Forensic Medicine, College of Basic Medicine, Chongqing Medical University, Chongqing, 400331, China
| | - Junbao Yang
- School of Basic Medical Sciences, North Sichuan Medical College, Nanchong, 637000, China
| | - Chuanchao Wang
- Department of Anthropology and Ethnology, School of Sociology and Anthropology, Institute of Anthropology, Xiamen University, Xiamen, 361000, China
| | - Chao Liu
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Jianwei Xu
- Department of Pharmacology, School of Basic Medicine, Guizhou Medical University, Guiyang, 550004, China.
| | - Mengge Wang
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, 510275, China.
| | - Guanglin He
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, 610000, China.
- Center for Archaeological Science, Sichuan University, Chengdu, 610000, China.
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8
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Liu D, Ko AMS, Stoneking M. The genomic diversity of Taiwanese Austronesian groups: Implications for the "Into- and Out-of-Taiwan" models. PNAS NEXUS 2023; 2:pgad122. [PMID: 37200801 PMCID: PMC10187666 DOI: 10.1093/pnasnexus/pgad122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 03/29/2023] [Accepted: 03/30/2023] [Indexed: 05/20/2023]
Abstract
The origin and dispersal of the Austronesian language family, one of the largest and most widespread in the world, have long attracted the attention of linguists, archaeologists, and geneticists. Even though there is a growing consensus that Taiwan is the source of the spread of Austronesian languages, little is known about the migration patterns of the early Austronesians who settled in and left Taiwan, i.e. the "Into-Taiwan" and "out-of-Taiwan" events. In particular, the genetic diversity and structure within Taiwan and how this relates to the into-/out-of-Taiwan events are largely unexplored, primarily because most genomic studies have largely utilized data from just two of the 16 recognized Highland Austronesian groups in Taiwan. In this study, we generated the largest genome-wide data set of Taiwanese Austronesians to date, including six Highland groups and one Lowland group from across the island and two Taiwanese Han groups. We identified fine-scale genomic structure in Taiwan, inferred the ancestry profile of the ancestors of Austronesians, and found that the southern Taiwanese Austronesians show excess genetic affinities with the Austronesians outside of Taiwan. Our findings thus shed new light on the Into- and Out-of-Taiwan dispersals.
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Affiliation(s)
- Dang Liu
- To whom correspondence should be addressed: ;
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He G, Wang M, Miao L, Chen J, Zhao J, Sun Q, Duan S, Wang Z, Xu X, Sun Y, Liu Y, Liu J, Wang Z, Wei L, Liu C, Ye J, Wang L. Multiple founding paternal lineages inferred from the newly-developed 639-plex Y-SNP panel suggested the complex admixture and migration history of Chinese people. Hum Genomics 2023; 17:29. [PMID: 36973821 PMCID: PMC10045532 DOI: 10.1186/s40246-023-00476-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 03/15/2023] [Indexed: 03/29/2023] Open
Abstract
BACKGROUND Non-recombining regions of the Y-chromosome recorded the evolutionary traces of male human populations and are inherited haplotype-dependently and male-specifically. Recent whole Y-chromosome sequencing studies have identified previously unrecognized population divergence, expansion and admixture processes, which promotes a better understanding and application of the observed patterns of Y-chromosome genetic diversity. RESULTS Here, we developed one highest-resolution Y-chromosome single nucleotide polymorphism (Y-SNP) panel targeted for uniparental genealogy reconstruction and paternal biogeographical ancestry inference, which included 639 phylogenetically informative SNPs. We genotyped these loci in 1033 Chinese male individuals from 33 ethnolinguistically diverse populations and identified 256 terminal Y-chromosomal lineages with frequency ranging from 0.0010 (singleton) to 0.0687. We identified six dominant common founding lineages associated with different ethnolinguistic backgrounds, which included O2a2b1a1a1a1a1a1a1-M6539, O2a1b1a1a1a1a1a1-F17, O2a2b1a1a1a1a1b1a1b-MF15397, O2a2b2a1b1-A16609, O1b1a1a1a1b2a1a1-F2517, and O2a2b1a1a1a1a1a1-F155. The AMOVA and nucleotide diversity estimates revealed considerable differences and high genetic diversity among ethnolinguistically different populations. We constructed one representative phylogenetic tree among 33 studied populations based on the haplogroup frequency spectrum and sequence variations. Clustering patterns in principal component analysis and multidimensional scaling results showed a genetic differentiation between Tai-Kadai-speaking Li, Mongolic-speaking Mongolian, and other Sinitic-speaking Han Chinese populations. Phylogenetic topology inferred from the BEAST and Network relationships reconstructed from the popART further showed the founding lineages from culturally/linguistically diverse populations, such as C2a/C2b was dominant in Mongolian people and O1a/O1b was dominant in island Li people. We also identified many lineages shared by more than two ethnolinguistically different populations with a high proportion, suggesting their extensive admixture and migration history. CONCLUSIONS Our findings indicated that our developed high-resolution Y-SNP panel included major dominant Y-lineages of Chinese populations from different ethnic groups and geographical regions, which can be used as the primary and powerful tool for forensic practice. We should emphasize the necessity and importance of whole sequencing of more ethnolinguistically different populations, which can help identify more unrecognized population-specific variations for the promotion of Y-chromosome-based forensic applications.
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Affiliation(s)
- Guanglin He
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, 610041, China.
| | - Mengge Wang
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Lei Miao
- National Engineering Laboratory for Forensic Science, Key Laboratory of Forensic Genetics of Ministry of Public Security, Institute of Forensic Science, Ministry of Public Security, Beijing, 100038, China
| | - Jing Chen
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, 030001, China
| | - Jie Zhao
- National Engineering Laboratory for Forensic Science, Key Laboratory of Forensic Genetics of Ministry of Public Security, Institute of Forensic Science, Ministry of Public Security, Beijing, 100038, China
| | - Qiuxia Sun
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, 610041, China
- Department of Forensic Medicine, College of Basic Medicine, Chongqing Medical University, Chongqing, 400331, China
| | - Shuhan Duan
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, 610041, China
- School of Basic Medical Sciences, North Sichuan Medical College, Nanchong, 637000, China
| | - Zhiyong Wang
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, 610041, China
- School of Forensic Medicine, Kunming Medical University, Kunming, 650500, China
| | - Xiaofei Xu
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, 610041, China
| | - Yuntao Sun
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, 610041, China
- Institute of Forensic Medicine, West China School of Basic Science and Forensic Medicine, Sichuan University, Chengdu, 610041, China
| | - Yan Liu
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, 610041, China
- School of Basic Medical Sciences, North Sichuan Medical College, Nanchong, 637000, China
| | - Jing Liu
- Institute of Forensic Medicine, West China School of Basic Science and Forensic Medicine, Sichuan University, Chengdu, 610041, China
| | - Zheng Wang
- Institute of Forensic Medicine, West China School of Basic Science and Forensic Medicine, Sichuan University, Chengdu, 610041, China
| | - Lanhai Wei
- School of Ethnology and Anthropology, Inner Mongolia Normal University, Hohhot, 010028, Inner Mongolia, China
| | - Chao Liu
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, 510275, China
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, 510515, China
| | - Jian Ye
- National Engineering Laboratory for Forensic Science, Key Laboratory of Forensic Genetics of Ministry of Public Security, Institute of Forensic Science, Ministry of Public Security, Beijing, 100038, China.
| | - Le Wang
- National Engineering Laboratory for Forensic Science, Key Laboratory of Forensic Genetics of Ministry of Public Security, Institute of Forensic Science, Ministry of Public Security, Beijing, 100038, China.
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10
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Zhou J, Zhang X, Li X, Sui J, Zhang S, Zhong H, Zhang Q, Zhang X, Huang H, Wen Y. Genetic structure and demographic history of Northern Han people in Liaoning Province inferred from genome-wide array data. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.1014024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
In this study, we used typical and advanced population genetic analysis methods [principal component analysis (PCA), ADMIXTURE, FST, f3-statistics, f4-statistics, qpAdm/qpWave, qpGraph, ALDER (Admixture-induced Linkage Disequilibrium for Evolutionary Relationships) and TreeMix] to explore the genetic structure of 80 Han individuals from four different cities in Liaoning Province and reconstruct their demographic history based on the newly generated genome-wide data. We found that Liaoning Han people have genetic similarities with other northern Han people (Shandong, Henan, and Shanxi) and Liaoning Manchu people. Millet farmers in the Yellow River Basin (YRB) and the West Liao River Basin (WLRB) (57–98%) and hunter-gatherers in the Mongolian Plateau (MP) and the Amur River Basin (ARB) (40–43%) are the main ancestral sources of the Liaoning Han people. Our study further supports the “northern origin hypothesis”; YRB-related ancestry accounts for 83–98% of the genetic makeup of the Liaoning Han population. There are clear genetic influences of northern East Asian populations in the Liaoning Han people, ancient Northeast Asian-related ancestry is another dominant ancestral component, and large-scale population admixture has happened between Tungusic Manchu people and Han people. There are genetic differences among the Liaoning Han people, and we found that these differences are associated with different migration routes of Hans during the “Chuang Guandong” period in historical records.
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11
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Chen H, Lin R, Lu Y, Zhang R, Gao Y, He Y, Xu S. Tracing Bai-Yue Ancestry in Aboriginal Li People on Hainan Island. Mol Biol Evol 2022; 39:6731089. [PMID: 36173765 PMCID: PMC9585476 DOI: 10.1093/molbev/msac210] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
As the most prevalent aboriginal group on Hainan Island located between South China and the mainland of Southeast Asia, the Li people are believed to preserve some unique genetic information due to their isolated circumstances, although this has been largely uninvestigated. We performed the first whole-genome sequencing of 55 Hainan Li (HNL) individuals with high coverage (∼30-50×) to gain insight into their genetic history and potential adaptations. We identified the ancestry enriched in HNL (∼85%) is well preserved in present-day Tai-Kadai speakers residing in South China and North Vietnam, that is, Bai-Yue populations. A lack of admixture signature due to the geographical restriction exacerbated the bottleneck in the present-day HNL. The genetic divergence among Bai-Yue populations began ∼4,000-3,000 years ago when the proto-HNL underwent migration and the settling of Hainan Island. Finally, we identified signatures of positive selection in the HNL, some outstanding examples included FADS1 and FADS2 related to a diet rich in polyunsaturated fatty acids. In addition, we observed that malaria-driven selection had occurred in the HNL, with population-specific variants of malaria-related genes (e.g., CR1) present. Interestingly, HNL harbors a high prevalence of malaria leveraged gene variants related to hematopoietic function (e.g., CD3G) that may explain the high incidence of blood disorders such as B-cell lymphomas in the present-day HNL. The results have advanced our understanding of the genetic history of the Bai-Yue populations and have provided new insights into the adaptive scenarios of the Li people.
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Affiliation(s)
| | | | - Yan Lu
- State Key Laboratory of Genetic Engineering, Center for Evolutionary Biology, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai 200438, China,Human Phenome Institute, Zhangjiang Fudan International Innovation Center, and Ministry of Education Key Laboratory of Contemporary Anthropology, Fudan University, Shanghai 201203, China
| | - Rui Zhang
- Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Yang Gao
- Human Phenome Institute, Zhangjiang Fudan International Innovation Center, and Ministry of Education Key Laboratory of Contemporary Anthropology, Fudan University, Shanghai 201203, China
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12
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Ren Z, Yang M, Jin X, Wang Q, Liu Y, Zhang H, Ji J, Wang CC, Huang J. Genetic substructure of Guizhou Tai-Kadai-speaking people inferred from genome-wide single nucleotide polymorphisms data. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.995783] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The genome-wide characteristics and admixture history of the Tai-Kadai-speaking populations are essential for understanding the population genetic diversity in southern China. We genotyped about 700,000 single nucleotide polymorphisms (SNPs) of 239 individuals from six Tai-Kadai-speaking populations residing in the mountainous Guizhou Province of southwestern China. We merged the genome-wide data with available populations and ancients in East and Southeast Asia to infer Tai-Kadai-speaking populations’ admixture history and genetic structure. We observed a genetic substructure within the studied six populations in the PCA, ADMIXTURE, ChromoPainter, GLOBETROTTER, f-statistics, and qpWave analysis. The Dong, Zhuang, and Bouyei people had a strong genetic affinity with other Tai-Kadai-speaking and Austronesian groups in the surrounding area. However, Gelao showed an affinity to Sino-Tibetan groups, and Mulao people were genetically close to Hmong-Mien populations. qpAdm further illuminated that Gelao and Dong_Tongren composited more Han-related ancestry than Dong, Zhuang, Bouyei, and Mulao people. Meanwhile, we observed high frequencies of Y-chromosome haplogroup O in studied Tai-Kadai-speaking groups except for Gelao people with a high haplogroup N frequency. From the maternal side, haplogroup M7 was frequent in studied populations except for Tongren Dong, who had a high frequency of haplogroup B5. Our newly reported data are helpful for further exploring population dynamics in southern China.
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Huang X, Xia ZY, Bin X, He G, Guo J, Adnan A, Yin L, Huang Y, Zhao J, Yang Y, Ma F, Li Y, Hu R, Yang T, Wei LH, Wang CC. Genomic Insights Into the Demographic History of the Southern Chinese. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.853391] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Southern China is the birthplace of rice-cultivating agriculture and different language families and has also witnessed various human migrations that facilitated cultural diffusions. The fine-scale demographic history in situ that forms present-day local populations, however, remains unclear. To comprehensively cover the genetic diversity in East and Southeast Asia, we generated genome-wide SNP data from 211 present-day Southern Chinese and co-analyzed them with ∼1,200 ancient and modern genomes. In Southern China, language classification is significantly associated with genetic variation but with a different extent of predictability, and there is strong evidence for recent shared genetic history particularly in Hmong–Mien and Austronesian speakers. A geography-related genetic sub-structure that represents the major genetic variation in Southern East Asians is established pre-Holocene and its extremes are represented by Neolithic Fujianese and First Farmers in Mainland Southeast Asia. This sub-structure is largely reduced by admixture in ancient Southern Chinese since > ∼2,000 BP, which forms a “Southern Chinese Cluster” with a high level of genetic homogeneity. Further admixture characterizes the demographic history of the majority of Hmong–Mien speakers and some Kra-Dai speakers in Southwest China happened ∼1,500–1,000 BP, coeval to the reigns of local chiefdoms. In Yellow River Basin, we identify a connection of local populations to genetic sub-structure in Southern China with geographical correspondence appearing > ∼9,000 BP, while the gene flow likely closely related to “Southern Chinese Cluster” since the Longshan period (∼5,000–4,000 BP) forms ancestry profile of Han Chinese Cline.
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14
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Yang M, He G, Ren Z, Wang Q, Liu Y, Zhang H, Zhang H, Chen J, Ji J, Zhao J, Guo J, Zhu K, Yang X, Wang R, Ma H, Wang CC, Huang J. Genomic Insights Into the Unique Demographic History and Genetic Structure of Five Hmong-Mien-Speaking Miao and Yao Populations in Southwest China. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.849195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Southern China was the original center of multiple ancestral populations related to modern Hmong-Mien, Tai-Kadai, Austroasiatic, and Austronesian people. More recent genetic surveys have focused on the fine-scale genetic structure and admixture history of southern Chinese populations, but the genetic formation and diversification of Hmong-Mien speakers are far from clear due to the sparse genetic sampling. Here, we reported nearly 700,000 single-nucleotide polymorphisms (SNPs) data from 130 Guizhou Miao and Yao individuals. We used principal component analysis, ADMIXTURE, f-statistics, qpAdm, phylogenetic tree, fineSTRUCTURE, and ALDER to explore the fine-scale population genetic structure and admixture pattern of Hmong-Mien people. The sharing allele patterns showed that our studied populations had a strong genetic affinity with ancient and modern groups from southern and southeastern East Asia. We identified one unique ancestry component maximized in Yao people, which widely existed in other Hmong-Mien-speaking populations in southern China and Southeast Asia and ancient samples of Guangxi. Guizhou Hmong-Mien speakers harbored the dominant proportions of ancestry related to southern indigenous East Asians and minor proportions of northern ancestry related to Yellow River farmers, suggesting the possibility of genetic admixture between Hmong-Mien people and recent southward Sino-Tibetan-related populations. Furthermore, we found a genetic substructure among geographically different Miao and Yao people in Leishan and Songtao. The Yao and Miao people in Leishan harbored more southern East Asian ancestry, but Miao in Songtao received more northern East Asian genetic influence. We observed high mtDNA but low Y-chromosome diversity in studied Hmong-Mien groups, supporting the role of sex-specific residence in influencing human genetic variation. Our data provide valuable clues for further exploring population dynamics in southern China.
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15
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Yang M, Yang X, Ren Z, He G, Zhang H, Wang Q, Liu Y, Zhang H, Ji J, Chen J, Guo J, Huang J, Wang CC. Genetic Admixture History and Forensic Characteristics of Guizhou Sui People Inferred From Autosomal Insertion/Deletion and Genome-Wide Single-Nucleotide Polymorphisms. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.844761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Insertion-deletion (Indel) serves as one of the important markers in forensic personal identification and parentage testing, especially for cases with degraded samples. However, the genetic diversity and forensic features in ethnolinguistically diverse southwestern Chinese populations remain to be explored. Sui, one Tai-Kadai-speaking population residing in Guizhou, has a complex genetic history based on linguistic, historic, and anthropological evidence. In this study, we genotyped 30 Indels from 511 Guizhou Sui individuals and obtained approximately 700,000 genome-wide single-nucleotide polymorphisms (SNPs) in 15 representative Sui individuals to comprehensively characterize the genetic diversity, forensic characteristics, and genomic landscape of Guizhou Sui people. The estimated forensic statistically allele frequency spectrum and parameters demonstrated that this Indels panel was polymorphic and informative in Tai-Kadai populations in southern China. Results of principal component analysis (PCA), STRUCTURE, and phylogenetic trees showed that Guizhou Sui had a close genetic relationship with geographically close Tai-Kadai and Hmong-Mien people. Furthermore, genomic analysis based on the Fst and f4-statistics further suggested the genetic affinity within southern Chinese Tai-Kadai-speaking populations and a close relationship with geographically adjoining Guizhou populations. Admixture models based on the ADMIXTURE, f4, three-way qpAdm, and ALDER results demonstrated the interaction between the common ancestor for Tai-Kadai/Austronesian, Hmong-Mien, and Austroasiatic speaking populations played a significant role in the formation of modern Tai-Kadai people. We observed a sex-biased influence in Sui people by finding that the dominant Y chromosomal type was a Hmong-Mien specific lineage O2a2a1a2a1a2-N5 but the mtDNA lineages were commonly found in Tai-Kadai populations. The additional southward expansion of millet farmers in the Yellow River Basin has impacted the gene pool of southern populations including Tai-Kadai. The whole-genome sequencing in the future will shed more light on the finer genetic profile of Guizhou populations.
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16
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He G, Zhang Y, Wei L, Wang M, Yang X, Guo J, Hu R, Wang C, Zhang X. The genomic formation of Tanka people, an isolated “gypsies in water” in the coastal region of Southeast China. AMERICAN JOURNAL OF BIOLOGICAL ANTHROPOLOGY 2022. [DOI: 10.1002/ajpa.24495] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Guanglin He
- Institute of Rare Diseases West China Hospital of Sichuan University, Sichuan University Chengdu China
- Department of Anthropology and Ethnology, Institute of Anthropology, National Institute for Data Science in Health and Medicine, State Key Laboratory of Cellular Stress Biology, School of Life Sciences, State Key Laboratory of Marine Environmental Science Xiamen University Xiamen China
- School of Humanities Nanyang Technological University Singapore
| | - Yunhe Zhang
- School of Public Administration Zhejiang Gongshang University Hangzhou China
| | - Lan‐Hai Wei
- Department of Anthropology and Ethnology, Institute of Anthropology, National Institute for Data Science in Health and Medicine, State Key Laboratory of Cellular Stress Biology, School of Life Sciences, State Key Laboratory of Marine Environmental Science Xiamen University Xiamen China
- B&R International Joint Laboratory for Eurasian Anthropology Fudan University Shanghai China
| | - Mengge Wang
- Guangzhou Forensic Science Institute Guangzhou China
- Faculty of Forensic Medicine Zhongshan School of Medicine, Sun Yat‐sen University Guangzhou China
| | - Xiaomin Yang
- Department of Anthropology and Ethnology, Institute of Anthropology, National Institute for Data Science in Health and Medicine, State Key Laboratory of Cellular Stress Biology, School of Life Sciences, State Key Laboratory of Marine Environmental Science Xiamen University Xiamen China
| | - Jianxin Guo
- Department of Anthropology and Ethnology, Institute of Anthropology, National Institute for Data Science in Health and Medicine, State Key Laboratory of Cellular Stress Biology, School of Life Sciences, State Key Laboratory of Marine Environmental Science Xiamen University Xiamen China
| | - Rong Hu
- Department of Anthropology and Ethnology, Institute of Anthropology, National Institute for Data Science in Health and Medicine, State Key Laboratory of Cellular Stress Biology, School of Life Sciences, State Key Laboratory of Marine Environmental Science Xiamen University Xiamen China
| | - Chuan‐Chao Wang
- Department of Anthropology and Ethnology, Institute of Anthropology, National Institute for Data Science in Health and Medicine, State Key Laboratory of Cellular Stress Biology, School of Life Sciences, State Key Laboratory of Marine Environmental Science Xiamen University Xiamen China
- School of Basic Medical Sciences Zhejiang University School of Medicine Hangzhou China
- Institute of Asian Civilizations, Zhejiang University Hangzhou China
| | - Xianqing Zhang
- Department of Anthropology and Ethnology, Institute of Anthropology, National Institute for Data Science in Health and Medicine, State Key Laboratory of Cellular Stress Biology, School of Life Sciences, State Key Laboratory of Marine Environmental Science Xiamen University Xiamen China
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Zou X, He G, Liu J, Jiang L, Wang M, Chen P, Hou Y, Wang Z. Screening and selection of 21 novel microhaplotype markers for ancestry inference in ten Chinese subpopulations. Forensic Sci Int Genet 2022; 58:102687. [DOI: 10.1016/j.fsigen.2022.102687] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 02/20/2022] [Accepted: 03/11/2022] [Indexed: 11/04/2022]
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18
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Wang M, He G, Zou X, Chen P, Wang Z, Tang R, Yang X, Chen J, Yang M, Li Y, Liu J, Wang F, Zhao J, Guo J, Hu R, Wei L, Chen G, Yeh H, Wang C. Reconstructing the genetic admixture history of Tai‐Kadai and Sinitic people: Insights from genome‐wide SNP data from South China. JOURNAL OF SYSTEMATICS AND EVOLUTION 2022. [DOI: 10.1111/jse.12825] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Meng‐Ge Wang
- State Key Laboratory of Cellular Stress Biology, National Institute for Data Science in Health and Medicine, School of Life Sciences Xiamen University Xiamen 361005 Fujian China
- Department of Anthropology and Ethnology, Institute of Anthropology, School of Sociology and Anthropology Xiamen University Xiamen 361005 Fujian China
- Institute of Forensic Medicine, West China School of Basic Science and Forensic Medicine Sichuan University Chengdu 610000 China
- Guangzhou Forensic Science Institute Guangzhou 510080 China
- Faculty of Forensic Medicine, Zhongshan School of Medicine Sun Yat‐sen University Guangzhou 510080 China
| | - Guang‐Lin He
- State Key Laboratory of Cellular Stress Biology, National Institute for Data Science in Health and Medicine, School of Life Sciences Xiamen University Xiamen 361005 Fujian China
- Department of Anthropology and Ethnology, Institute of Anthropology, School of Sociology and Anthropology Xiamen University Xiamen 361005 Fujian China
- Institute of Forensic Medicine, West China School of Basic Science and Forensic Medicine Sichuan University Chengdu 610000 China
- Institute Of Rare Diseases West China Hospital of Sichuan University Chengdu 610000 China
- School of Humanities Nanyang Technological University Singapore 224050 Singapore
| | - Xing Zou
- Institute of Forensic Medicine, West China School of Basic Science and Forensic Medicine Sichuan University Chengdu 610000 China
- College of Medicine Chongqing University Chongqing 400016 China
| | - Peng‐Yu Chen
- School of Forensic Medicine Zunyi Medical University Zunyi 563000 Guizhou China
| | - Zheng Wang
- Institute of Forensic Medicine, West China School of Basic Science and Forensic Medicine Sichuan University Chengdu 610000 China
| | - Ren‐Kuan Tang
- Department of Forensic Medicine, College of Basic Medicine Chongqing Medical University Chongqing 400016 China
| | - Xiao‐Min Yang
- State Key Laboratory of Cellular Stress Biology, National Institute for Data Science in Health and Medicine, School of Life Sciences Xiamen University Xiamen 361005 Fujian China
- Institute Of Rare Diseases West China Hospital of Sichuan University Chengdu 610000 China
- State Key Laboratory of Marine Environmental Science Xiamen University Xiamen 361005 Fujian China
| | - Jing Chen
- Department of Forensic Medicine Guizhou Medical University Guiyang 550000 China
| | - Mei‐Qing Yang
- Department of Forensic Medicine Guizhou Medical University Guiyang 550000 China
| | - Ying‐Xiang Li
- State Key Laboratory of Cellular Stress Biology, National Institute for Data Science in Health and Medicine, School of Life Sciences Xiamen University Xiamen 361005 Fujian China
- Institute Of Rare Diseases West China Hospital of Sichuan University Chengdu 610000 China
- State Key Laboratory of Marine Environmental Science Xiamen University Xiamen 361005 Fujian China
| | - Jing Liu
- Institute of Forensic Medicine, West China School of Basic Science and Forensic Medicine Sichuan University Chengdu 610000 China
| | - Fei Wang
- Institute of Forensic Medicine, West China School of Basic Science and Forensic Medicine Sichuan University Chengdu 610000 China
| | - Jing Zhao
- State Key Laboratory of Cellular Stress Biology, National Institute for Data Science in Health and Medicine, School of Life Sciences Xiamen University Xiamen 361005 Fujian China
- Institute Of Rare Diseases West China Hospital of Sichuan University Chengdu 610000 China
- State Key Laboratory of Marine Environmental Science Xiamen University Xiamen 361005 Fujian China
| | - Jian‐Xin Guo
- State Key Laboratory of Cellular Stress Biology, National Institute for Data Science in Health and Medicine, School of Life Sciences Xiamen University Xiamen 361005 Fujian China
- Institute Of Rare Diseases West China Hospital of Sichuan University Chengdu 610000 China
- State Key Laboratory of Marine Environmental Science Xiamen University Xiamen 361005 Fujian China
| | - Rong Hu
- State Key Laboratory of Cellular Stress Biology, National Institute for Data Science in Health and Medicine, School of Life Sciences Xiamen University Xiamen 361005 Fujian China
- Institute Of Rare Diseases West China Hospital of Sichuan University Chengdu 610000 China
- State Key Laboratory of Marine Environmental Science Xiamen University Xiamen 361005 Fujian China
| | - Lan‐Hai Wei
- State Key Laboratory of Cellular Stress Biology, National Institute for Data Science in Health and Medicine, School of Life Sciences Xiamen University Xiamen 361005 Fujian China
- Institute Of Rare Diseases West China Hospital of Sichuan University Chengdu 610000 China
- State Key Laboratory of Marine Environmental Science Xiamen University Xiamen 361005 Fujian China
| | - Gang Chen
- Hunan Key Lab of Bioinformatics, School of Computer Science and Engineering Central South University Changsha 410075 China
| | - Hui‐Yuan Yeh
- School of Humanities Nanyang Technological University Singapore 224050 Singapore
| | - Chuan‐Chao Wang
- State Key Laboratory of Cellular Stress Biology, National Institute for Data Science in Health and Medicine, School of Life Sciences Xiamen University Xiamen 361005 Fujian China
- Institute Of Rare Diseases West China Hospital of Sichuan University Chengdu 610000 China
- State Key Laboratory of Marine Environmental Science Xiamen University Xiamen 361005 Fujian China
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19
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Chen J, He G, Ren Z, Wang Q, Liu Y, Zhang H, Yang M, Zhang H, Ji J, Zhao J, Guo J, Chen J, Zhu K, Yang X, Wang R, Ma H, Tao L, Liu Y, Shen Q, Yang W, Wang CC, Huang J. Fine-Scale Population Admixture Landscape of Tai–Kadai-Speaking Maonan in Southwest China Inferred From Genome-Wide SNP Data. Front Genet 2022; 13:815285. [PMID: 35251126 PMCID: PMC8891617 DOI: 10.3389/fgene.2022.815285] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 01/27/2022] [Indexed: 12/27/2022] Open
Abstract
Guizhou Province harbors extensive ethnolinguistic and cultural diversity with Sino-Tibetan-, Hmong–Mien-, and Tai–Kadai-speaking populations. However, previous genetic analyses mainly focused on the genetic admixture history of the former two linguistic groups. The admixture history of Tai–Kadai-speaking populations in Guizhou needed to be characterized further. Thus, we genotyped genome-wide SNP data from 41 Tai–Kadai-speaking Maonan people and made a comprehensive population genetic analysis to explore their genetic origin and admixture history based on the pattern of the sharing alleles and haplotypes. We found a genetic affinity among geographically different Tai–Kadai-speaking populations, especially for Guizhou Maonan people and reference Maonan from Guangxi. Furthermore, formal tests based on the f3/f4-statistics further identified an adjacent connection between Maonan and geographically adjacent Hmong–Mien and Sino-Tibetan people, which was consistent with their historically documented shared material culture (Zhang et al., iScience, 2020, 23, 101032). Fitted qpAdm-based two-way admixture models with ancestral sources from northern and southern East Asians demonstrated that Maonan people were an admixed population with primary ancestry related to Guangxi historical people and a minor proportion of ancestry from Northeast Asians, consistent with their linguistically supported southern China origin. Here, we presented the landscape of genetic structure and diversity of Maonan people and a simple demographic model for their evolutionary process. Further whole-genome-sequence–based projects can be presented with more detailed information about the population history and adaptative history of the Guizhou Maonan people.
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Affiliation(s)
- Jing Chen
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, China
| | - Guanglin He
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China
- Department of Anthropology and Ethnology, School of Sociology and Anthropology, Institute of Anthropology, National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, China
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, China
- Institute Of Rare Diseases, West China Hospital of Sichuan University, Chengdu, China
| | - Zheng Ren
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, China
| | - Qiyan Wang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, China
| | - Yubo Liu
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, China
| | - Hongling Zhang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, China
| | - Meiqing Yang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, China
| | - Han Zhang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, China
| | - Jingyan Ji
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, China
| | - Jing Zhao
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China
- Department of Anthropology and Ethnology, School of Sociology and Anthropology, Institute of Anthropology, National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, China
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, China
| | - Jianxin Guo
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China
- Department of Anthropology and Ethnology, School of Sociology and Anthropology, Institute of Anthropology, National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, China
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, China
| | - Jinwen Chen
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China
- Department of Anthropology and Ethnology, School of Sociology and Anthropology, Institute of Anthropology, National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, China
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, China
| | - Kongyang Zhu
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China
- Department of Anthropology and Ethnology, School of Sociology and Anthropology, Institute of Anthropology, National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, China
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, China
| | - Xiaomin Yang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China
- Department of Anthropology and Ethnology, School of Sociology and Anthropology, Institute of Anthropology, National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, China
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, China
| | - Rui Wang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China
- Department of Anthropology and Ethnology, School of Sociology and Anthropology, Institute of Anthropology, National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, China
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, China
| | - Hao Ma
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China
- Department of Anthropology and Ethnology, School of Sociology and Anthropology, Institute of Anthropology, National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, China
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, China
| | - Le Tao
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China
- Department of Anthropology and Ethnology, School of Sociology and Anthropology, Institute of Anthropology, National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, China
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, China
| | - Yilan Liu
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China
- Department of Anthropology and Ethnology, School of Sociology and Anthropology, Institute of Anthropology, National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, China
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, China
| | - Qu Shen
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China
- Department of Anthropology and Ethnology, School of Sociology and Anthropology, Institute of Anthropology, National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, China
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, China
| | - Wenjiao Yang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China
- Department of Anthropology and Ethnology, School of Sociology and Anthropology, Institute of Anthropology, National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, China
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, China
| | - Chuan-Chao Wang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China
- Department of Anthropology and Ethnology, School of Sociology and Anthropology, Institute of Anthropology, National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, China
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, China
- *Correspondence: Chuan-Chao Wang, ; Jiang Huang,
| | - Jiang Huang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, China
- *Correspondence: Chuan-Chao Wang, ; Jiang Huang,
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Changmai P, Jaisamut K, Kampuansai J, Kutanan W, Altınışık NE, Flegontova O, Inta A, Yüncü E, Boonthai W, Pamjav H, Reich D, Flegontov P. Indian genetic heritage in Southeast Asian populations. PLoS Genet 2022; 18:e1010036. [PMID: 35176016 PMCID: PMC8853555 DOI: 10.1371/journal.pgen.1010036] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Accepted: 01/12/2022] [Indexed: 11/20/2022] Open
Abstract
The great ethnolinguistic diversity found today in mainland Southeast Asia (MSEA) reflects multiple migration waves of people in the past. Maritime trading between MSEA and India was established at the latest 300 BCE, and the formation of early states in Southeast Asia during the first millennium CE was strongly influenced by Indian culture, a cultural influence that is still prominent today. Several ancient Indian-influenced states were located in present-day Thailand, and various populations in the country are likely to be descendants of people from those states. To systematically explore Indian genetic heritage in MSEA populations, we generated genome-wide SNP data (using the Affymetrix Human Origins array) for 119 present-day individuals belonging to 10 ethnic groups from Thailand and co-analyzed them with published data using PCA, ADMIXTURE, and methods relying on f-statistics and on autosomal haplotypes. We found low levels of South Asian admixture in various MSEA populations for whom there is evidence of historical connections with the ancient Indian-influenced states but failed to find this genetic component in present-day hunter-gatherer groups and relatively isolated groups from the highlands of Northern Thailand. The results suggest that migration of Indian populations to MSEA may have been responsible for the spread of Indian culture in the region. Our results also support close genetic affinity between Kra-Dai-speaking (also known as Tai-Kadai) and Austronesian-speaking populations, which fits a linguistic hypothesis suggesting cladality of the two language families.
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Affiliation(s)
- Piya Changmai
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Kitipong Jaisamut
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Jatupol Kampuansai
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand
- Research Center in Bioresources for Agriculture, Industry and Medicine, Chiang Mai University, Chiang Mai, Thailand
| | - Wibhu Kutanan
- Department of Biology, Faculty of Science, Khon Kaen University, Khon Kaen, Thailand
| | - N Ezgi Altınışık
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Olga Flegontova
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Angkhana Inta
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand
- Research Center in Bioresources for Agriculture, Industry and Medicine, Chiang Mai University, Chiang Mai, Thailand
| | - Eren Yüncü
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Worrawit Boonthai
- Research Unit in Physical Anthropology and Health Science, Thammasat University, Pathum thani, Thailand
| | - Horolma Pamjav
- Hungarian Institute for Forensic Sciences, Institute of Forensic Genetics, Budapest, Hungary
| | - David Reich
- Department of Human Evolutionary Biology, Harvard University, Cambridge, Massachusetts, United States of America
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
- Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Pavel Flegontov
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
- Department of Human Evolutionary Biology, Harvard University, Cambridge, Massachusetts, United States of America
- Kalmyk Research Center of the Russian Academy of Sciences, Elista, Kalmykia, Russia
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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. Mol Genet Genomics 2022; 297:241-262. [PMID: 35031862 DOI: 10.1007/s00438-021-01837-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 11/10/2021] [Indexed: 10/19/2022]
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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Wei Q. ACE and ACTN3 Gene Polymorphisms and Genetic Traits of Rowing Athletes in the Northern Han Chinese Population. Front Genet 2021; 12:736876. [PMID: 34721527 PMCID: PMC8551674 DOI: 10.3389/fgene.2021.736876] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 09/20/2021] [Indexed: 01/12/2023] Open
Abstract
This investigation aimed to explore the effects of ACE I/D and ACTN3 R577X gene polymorphisms on specific quantitative variables, including height, weight, arm span, biacromial breadth, forced vital capacity (FVC), FVC/weight, maximal oxygen uptake (VO2max), prone bench pull (PBP), loaded barbell squat (LBS), and 3,000-m run, in 243 Chinese rowing athletes. The ACE and ACTN3 genotypes were obtained for each athlete via polymerase chain reaction on saliva samples, and the genotype frequency was analyzed. The ACE genotype frequency of rowing athletes were 45.8% II, 42.2% ID, and 12% DD for males and 33.6% II, 48% ID, and 18.4% DD for females. There were significant differences in weight in male athletes, PBP in female athletes, and ACE genotypes. A linear regression analysis using PBP and LBS as different dependent variables and ACE genotypes as independent variables based on the ACE I allele additive genetic effect showed a statistical significance in female athletes (p < 0.05). There was a significant difference in the distribution of the three genotypes among male athletes (36.7% XX, 38.5% RX, and 24.8% RR, χ2 = 5.191, df = 2, p = 0.022 < 0.05). There were no significant differences in the distribution of the three genotypes among female athletes (23.8% XX, 47.8% RX, 28.4% RR, χ 2 = 0.24, df = 2, p = 0.619 > 0.05). The ACTN3 gene polymorphism of male rowing athletes was dominated by the ACTN3 577X allele. There were significant differences in the χ 2 test between groups of male athletes. The ACTN3 R577 allele was dominant in female athletes. There were significant differences between PBP and FVC/body weight and ACTN3 genotypes in male athletes by ANOVA, respectively (p < 0.05). A linear regression analysis using FVC and FVC/body weight as dependent variables and ACTN3 genotypes as independent variables based on the ACTN3 577X allele recessive genetic effect showed statistical significance in male athletes (p < 0.05). These results suggested that ACE and ACTN3 gene polymorphisms may be used as biomarkers of genetic traits in Chinese rowing athletes.
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Affiliation(s)
- Qi Wei
- Key Laboratory of General Administration of Sport of China, Wuhan, China
- Hubei Institute of Sports Science, Wuhan, China
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23
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Bin X, Wang R, Huang Y, Wei R, Zhu K, Yang X, Ma H, He G, Guo J, Zhao J, Yang M, Chen J, Zhang X, Tao L, Liu Y, Huang X, Wang CC. Genomic Insight Into the Population Structure and Admixture History of Tai-Kadai-Speaking Sui People in Southwest China. Front Genet 2021; 12:735084. [PMID: 34616433 PMCID: PMC8489805 DOI: 10.3389/fgene.2021.735084] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 08/23/2021] [Indexed: 12/14/2022] Open
Abstract
Sui people, which belong to the Tai-Kadai-speaking family, remain poorly characterized due to a lack of genome-wide data. To infer the fine-scale population genetic structure and putative genetic sources of the Sui people, we genotyped 498,655 genome-wide single-nucleotide polymorphisms (SNPs) using SNP arrays in 68 Sui individuals from seven indigenous populations in Guizhou province and Guangxi Zhuang Autonomous Region in Southwest China and co-analyzed with available East Asians via a series of population genetic methods including principal component analysis (PCA), ADMIXTURE, pairwise Fst genetic distance, f-statistics, qpWave, and qpAdm. Our results revealed that Guangxi and Guizhou Sui people showed a strong genetic affinity with populations from southern China and Southeast Asia, especially Tai-Kadai- and Hmong-Mien-speaking populations as well as ancient Iron Age Taiwan Hanben, Gongguan individuals supporting the hypothesis that Sui people came from southern China originally. The indigenous Tai-Kadai-related ancestry (represented by Li), Northern East Asian-related ancestry, and Hmong-Mien-related lineage contributed to the formation processes of the Sui people. We identified the genetic substructure within Sui groups: Guizhou Sui people were relatively homogeneous and possessed similar genetic profiles with neighboring Tai-Kadai-related populations, such as Maonan. While Sui people in Yizhou and Huanjiang of Guangxi might receive unique, additional gene flow from Hmong-Mien-speaking populations and Northern East Asians, respectively, after the divergence within other Sui populations. Sui people could be modeled as the admixture of ancient Yellow River Basin farmer-related ancestry (36.2-54.7%) and ancient coastal Southeast Asian-related ancestry (45.3-63.8%). We also identified the potential positive selection signals related to the disease susceptibility in Sui people via integrated haplotype score (iHS) and number of segregating sites by length (nSL) scores. These genomic findings provided new insights into the demographic history of Tai-Kadai-speaking Sui people and their interaction with neighboring populations in Southern China.
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Affiliation(s)
- Xiaoyun Bin
- College of Basic Medical Sciences, Youjiang Medical University for Nationalities, Baise, China
| | - Rui Wang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China.,Department of Anthropology and Ethnology, Institute of Anthropology, School of Sociology and Anthropology, National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, China.,State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, China
| | - Youyi Huang
- College of Basic Medical Sciences, Youjiang Medical University for Nationalities, Baise, China
| | - Rongyao Wei
- College of Basic Medical Sciences, Youjiang Medical University for Nationalities, Baise, China
| | - Kongyang Zhu
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China.,Department of Anthropology and Ethnology, Institute of Anthropology, School of Sociology and Anthropology, National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, China.,State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, China
| | - Xiaomin Yang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China.,Department of Anthropology and Ethnology, Institute of Anthropology, School of Sociology and Anthropology, National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, China.,State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, China
| | - Hao Ma
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China.,Department of Anthropology and Ethnology, Institute of Anthropology, School of Sociology and Anthropology, National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, China.,State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, China
| | - Guanglin He
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China.,Department of Anthropology and Ethnology, Institute of Anthropology, School of Sociology and Anthropology, National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, China.,State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, China
| | - Jianxin Guo
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China.,Department of Anthropology and Ethnology, Institute of Anthropology, School of Sociology and Anthropology, National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, China.,State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, China
| | - Jing Zhao
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China.,Department of Anthropology and Ethnology, Institute of Anthropology, School of Sociology and Anthropology, National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, China.,State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, China
| | - Meiqing Yang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, China
| | - Jing Chen
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, China
| | | | - Le Tao
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China.,Department of Anthropology and Ethnology, Institute of Anthropology, School of Sociology and Anthropology, National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, China.,State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, China
| | - Yilan Liu
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China.,Department of Anthropology and Ethnology, Institute of Anthropology, School of Sociology and Anthropology, National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, China.,State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, China
| | - Xiufeng Huang
- College of Basic Medical Sciences, Youjiang Medical University for Nationalities, Baise, China
| | - Chuan-Chao Wang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China.,Department of Anthropology and Ethnology, Institute of Anthropology, School of Sociology and Anthropology, National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, China.,State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, China
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24
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Zhang X, He G, Li W, Wang Y, Li X, Chen Y, Qu Q, Wang Y, Xi H, Wang CC, Wen Y. Genomic Insight Into the Population Admixture History of Tungusic-Speaking Manchu People in Northeast China. Front Genet 2021; 12:754492. [PMID: 34659368 PMCID: PMC8515022 DOI: 10.3389/fgene.2021.754492] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 08/30/2021] [Indexed: 11/13/2022] Open
Abstract
Manchu is the third-largest ethnic minority in China and has the largest population size among the Tungusic-speaking groups. However, the genetic origin and admixture history of the Manchu people are far from clear due to the sparse sampling and a limited number of markers genotyped. Here, we provided the first batch of genome-wide data of genotyping approximate 700,000 single-nucleotide polymorphisms (SNPs) in 93 Manchu individuals collected from northeast China. We merged the newly generated data with data of publicly available modern and ancient East Asians to comprehensively characterize the genetic diversity and fine-scale population structure, as well as explore the genetic origin and admixture history of northern Chinese Manchus. We applied both descriptive methods of ADMIXTURE, fineSTRUCTURE, F ST , TreeMix, identity by decedent (IBD), principal component analysis (PCA), and qualitative f-statistics (f 3, f 4, qpAdm, and qpWave). We found that Liaoning Manchus have a close genetic relationship and significant admixture signal with northern Han Chinese, which is in line with the cluster patterns in the haplotype-based results. Additionally, the qpAdm-based admixture models showed that modern Manchu people were formed as major ancestry related to Yellow River farmers and minor ancestry linked to ancient populations from Amur River Bain, or others. In summary, the northeastern Chinese Manchu people in Liaoning were an exception to the coherent genetic structure of Tungusic-speaking populations, probably due to the large-scale population migrations and genetic admixtures in the past few hundred years.
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Affiliation(s)
- Xianpeng Zhang
- Institute of Biological Anthropology, Jinzhou Medical University, Jinzhou, China
| | - Guanglin He
- State Key Laboratory of Cellular Stress Biology, National Institute for Data Science in Health and Medicine, School of Life Sciences, Xiamen University, Xiamen, China
- Department of Anthropology and Ethnology, Institute of Anthropology, School of Sociology and Anthropology, Xiamen University, Xiamen, China
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, China
- School of Humanities, Nanyang Technological University, Singapore, Singapore
| | - Wenhui Li
- Institute of Biological Anthropology, Jinzhou Medical University, Jinzhou, China
| | - Yunfeng Wang
- Xinbin Manchu Autonomous County People’s Hospital, Fushun, China
| | - Xin Li
- Institute of Biological Anthropology, Jinzhou Medical University, Jinzhou, China
| | - Ying Chen
- Institute of Biological Anthropology, Jinzhou Medical University, Jinzhou, China
| | - Quanying Qu
- Institute of Biological Anthropology, Jinzhou Medical University, Jinzhou, China
| | - Ying Wang
- Institute of Biological Anthropology, Jinzhou Medical University, Jinzhou, China
| | - Huanjiu Xi
- Institute of Biological Anthropology, Jinzhou Medical University, Jinzhou, China
| | - Chuan-Chao Wang
- State Key Laboratory of Cellular Stress Biology, National Institute for Data Science in Health and Medicine, School of Life Sciences, Xiamen University, Xiamen, China
- Department of Anthropology and Ethnology, Institute of Anthropology, School of Sociology and Anthropology, Xiamen University, Xiamen, China
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, China
| | - Youfeng Wen
- Institute of Biological Anthropology, Jinzhou Medical University, Jinzhou, China
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25
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Wang M, Yuan D, Zou X, Wang Z, Yeh HY, Liu J, Wei LH, Wang CC, Zhu B, Liu C, He G. Fine-Scale Genetic Structure and Natural Selection Signatures of Southwestern Hans Inferred From Patterns of Genome-Wide Allele, Haplotype, and Haplogroup Lineages. Front Genet 2021; 12:727821. [PMID: 34504517 PMCID: PMC8421688 DOI: 10.3389/fgene.2021.727821] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2021] [Accepted: 07/29/2021] [Indexed: 12/15/2022] Open
Abstract
The evolutionary and admixture history of Han Chinese have been widely discussed via traditional autosomal and uniparental genetic markers [e.g., short tandem repeats, low-density single nucleotide polymorphisms). However, their fine-scale genetic landscapes (admixture scenarios and natural selection signatures) based on the high-density allele/haplotype sharing patterns have not been deeply characterized. Here, we collected and generated genome-wide data of 50 Han Chinese individuals from four populations in Guizhou Province, one of the most ethnolinguistically diverse regions, and merged it with over 3,000 publicly available modern and ancient Eurasians to describe the genetic origin and population admixture history of Guizhou Hans and their neighbors. PCA and ADMIXTURE results showed that the studied four populations were homogeneous and grouped closely to central East Asians. Genetic homogeneity within Guizhou populations was further confirmed via the observed strong genetic affinity with inland Hmong-Mien people through the observed genetic clade in Fst and outgroup f3/f4-statistics. qpGraph-based phylogenies and f4-based demographic models illuminated that Guizhou Hans were well fitted via the admixture of ancient Yellow River Millet farmers related to Lajia people and southern Yangtze River farmers related to Hanben people. Further ChromoPainter-based chromosome painting profiles and GLOBETROTTER-based admixture signatures confirmed the two best source matches for southwestern Hans, respectively, from northern Shaanxi Hans and southern indigenes with variable mixture proportions in the historical period. Further three-way admixture models revealed larger genetic contributions from coastal southern East Asians into Guizhou Hans compared with the proposed inland ancient source from mainland Southeast Asia. We also identified candidate loci (e.g., MTUS2, NOTCH4, EDAR, ADH1B, and ABCG2) with strong natural selection signatures in Guizhou Hans via iHS, nSL, and ihh, which were associated with the susceptibility of the multiple complex diseases, morphology formation, alcohol and lipid metabolism. Generally, we provided a case and ideal strategy to reconstruct the detailed demographic evolutionary history of Guizhou Hans, which provided new insights into the fine-scale genomic formation of one ethnolinguistically specific targeted population from the comprehensive perspectives of the shared unlinked alleles, linked haplotypes, and paternal and maternal lineages.
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Affiliation(s)
- Mengge Wang
- Guangzhou Forensic Science Institute, Guangzhou, China.,Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Didi Yuan
- Department of Forensic Medicine, College of Basic Medicine, Chongqing Medical University, Chongqing, China
| | - Xing Zou
- College of Basic Medicine, Chongqing University, Chongqing, China
| | - Zheng Wang
- Institute of Forensic Medicine, West China School of Basic Science and Forensic Medicine, Sichuan University, Chengdu, China
| | - Hui-Yuan Yeh
- School of Humanities, Nanyang Technological University, Singapore, Singapore
| | - Jing Liu
- Institute of Forensic Medicine, West China School of Basic Science and Forensic Medicine, Sichuan University, Chengdu, China
| | - Lan-Hai Wei
- State Key Laboratory of Marine Environmental Science, State Key Laboratory of Cellular Stress Biology, Department of Anthropology and Ethnology, Institute of Anthropology, National Institute for Data Science in Health and Medicine, School of Life Sciences, Xiamen University, Xiamen, China
| | - Chuan-Chao Wang
- State Key Laboratory of Marine Environmental Science, State Key Laboratory of Cellular Stress Biology, Department of Anthropology and Ethnology, Institute of Anthropology, National Institute for Data Science in Health and Medicine, School of Life Sciences, Xiamen University, Xiamen, China
| | - Bofeng Zhu
- Department of Forensic Genetics, School of Forensic Medicine, Southern Medical University, Guangzhou, China.,Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, China.,Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology, Xi'an Jiaotong University, Xi'an, China
| | - Chao Liu
- Guangzhou Forensic Science Institute, Guangzhou, China.,Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China.,Department of Forensic Genetics, School of Forensic Medicine, Southern Medical University, Guangzhou, China
| | - Guanglin He
- School of Humanities, Nanyang Technological University, Singapore, Singapore.,State Key Laboratory of Marine Environmental Science, State Key Laboratory of Cellular Stress Biology, Department of Anthropology and Ethnology, Institute of Anthropology, National Institute for Data Science in Health and Medicine, School of Life Sciences, Xiamen University, Xiamen, China
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26
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Chen J, He G, Ren Z, Wang Q, Liu Y, Zhang H, Yang M, Zhang H, Ji J, Zhao J, Guo J, Zhu K, Yang X, Wang R, Ma H, Wang CC, Huang J. Genomic Insights Into the Admixture History of Mongolic- and Tungusic-Speaking Populations From Southwestern East Asia. Front Genet 2021; 12:685285. [PMID: 34239544 PMCID: PMC8258170 DOI: 10.3389/fgene.2021.685285] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Accepted: 05/05/2021] [Indexed: 12/17/2022] Open
Abstract
As a major part of the modern Trans-Eurasian or Altaic language family, most of the Mongolic and Tungusic languages were mainly spoken in northern China, Mongolia, and southern Siberia, but some were also found in southern China. Previous genetic surveys only focused on the dissection of genetic structure of northern Altaic-speaking populations; however, the ancestral origin and genomic diversification of Mongolic and Tungusic-speaking populations from southwestern East Asia remain poorly understood because of the paucity of high-density sampling and genome-wide data. Here, we generated genome-wide data at nearly 700,000 single-nucleotide polymorphisms (SNPs) in 26 Mongolians and 55 Manchus collected from Guizhou province in southwestern China. We applied principal component analysis (PCA), ADMIXTURE, f statistics, qpWave/qpAdm analysis, qpGraph, TreeMix, Fst, and ALDER to infer the fine-scale population genetic structure and admixture history. We found significant genetic differentiation between northern and southern Mongolic and Tungusic speakers, as one specific genetic cline of Manchu and Mongolian was identified in Guizhou province. Further results from ADMIXTURE and f statistics showed that the studied Guizhou Mongolians and Manchus had a strong genetic affinity with southern East Asians, especially for inland southern East Asians. The qpAdm-based estimates of ancestry admixture proportion demonstrated that Guizhou Mongolians and Manchus people could be modeled as the admixtures of one northern ancestry related to northern Tungusic/Mongolic speakers or Yellow River farmers and one southern ancestry associated with Austronesian, Tai-Kadai, and Austroasiatic speakers. The qpGraph-based phylogeny and neighbor-joining tree further confirmed that Guizhou Manchus and Mongolians derived approximately half of the ancestry from their northern ancestors and the other half from southern Indigenous East Asians. The estimated admixture time ranged from 600 to 1,000 years ago, which further confirmed the admixture events were mediated via the Mongolians Empire expansion during the formation of the Yuan dynasty.
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Affiliation(s)
- Jing Chen
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, China
| | - Guanglin He
- State Key Laboratory of Cellular Stress Biology, State Key Laboratory of Marine Environmental Science, Department of Anthropology and Ethnology, Institute of Anthropology, National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, China
| | - Zheng Ren
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, China
| | - Qiyan Wang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, China
| | - Yubo Liu
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, China
| | - Hongling Zhang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, China
| | - Meiqing Yang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, China
| | - Han Zhang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, China
| | - Jingyan Ji
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, China
| | - Jing Zhao
- State Key Laboratory of Cellular Stress Biology, State Key Laboratory of Marine Environmental Science, Department of Anthropology and Ethnology, Institute of Anthropology, National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, China
| | - Jianxin Guo
- State Key Laboratory of Cellular Stress Biology, State Key Laboratory of Marine Environmental Science, Department of Anthropology and Ethnology, Institute of Anthropology, National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, China
| | - Kongyang Zhu
- State Key Laboratory of Cellular Stress Biology, State Key Laboratory of Marine Environmental Science, Department of Anthropology and Ethnology, Institute of Anthropology, National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, China
| | - Xiaomin Yang
- State Key Laboratory of Cellular Stress Biology, State Key Laboratory of Marine Environmental Science, Department of Anthropology and Ethnology, Institute of Anthropology, National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, China
| | - Rui Wang
- State Key Laboratory of Cellular Stress Biology, State Key Laboratory of Marine Environmental Science, Department of Anthropology and Ethnology, Institute of Anthropology, National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, China
| | - Hao Ma
- State Key Laboratory of Cellular Stress Biology, State Key Laboratory of Marine Environmental Science, Department of Anthropology and Ethnology, Institute of Anthropology, National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, China
| | - Chuan-Chao Wang
- State Key Laboratory of Cellular Stress Biology, State Key Laboratory of Marine Environmental Science, Department of Anthropology and Ethnology, Institute of Anthropology, National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, China
- School of Basic Medical Sciences, Zhejiang University School of Medicine, Hangzhou, China
| | - Jiang Huang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, China
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27
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Wang M, He G, Gao S, Jia F, Zou X, Liu J, Wang S, Ye Z, Hou Y, Wang Z. Molecular genetic survey and forensic characterization of Chinese Mongolians via the 47 autosomal insertion/deletion marker. Genomics 2021; 113:2199-2210. [PMID: 34022340 DOI: 10.1016/j.ygeno.2021.05.010] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 03/06/2021] [Accepted: 05/17/2021] [Indexed: 12/16/2022]
Abstract
The Mongolians are mainly distributed in the modern state of Mongolia, China, Russia, and other countries. While the historic and archaeological records of the rise and fall of the Mongol Empire are well documented, little has been known about the genetic legacy of modern Mongolian populations. Here, 611 Mongolian individuals from Hohhot, Hulunbuir, and Ordos of China were genotyped via the 47 Insertion/Deletion markers. Forensically statistical parameters indicated that this InDel system could be applied to forensic investigation in Mongolian populations. The comprehensive population comparisons indicated that targeted Mongolian populations are a homogeneous population, which kept close genetic proximity with geographically northern East Asians. The findings of the model-based clustering analysis revealed a southern East Asian-specific ancestral component, which was maximized in Hainan Li, and Mongolian populations harbored relatively less Hainan Li-related ancestry and more northern East Asian-related ancestry compared with reference Tai-Kadai, Austroasiatic and Sinitic people.
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Affiliation(s)
- Mengge Wang
- Shanghai Key Laboratory of Forensic Medicine, Academy of Forensic Sciences, Ministry of Justice, Shanghai 200063, China; Institute of Forensic Medicine, West China School of Basic Science and Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Guanglin He
- Institute of Forensic Medicine, West China School of Basic Science and Forensic Medicine, Sichuan University, Chengdu 610041, China; 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 361005, China
| | - Shuang Gao
- Public Security Bureau of Ordos City, Inner Mongolia Autonomous Region 017010, China
| | - Fuquan Jia
- Department of Forensic Medicine, Inner Mongolia Medical University, Hohhot 010110, China
| | - Xing Zou
- Institute of Forensic Medicine, West China School of Basic Science and Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Jing Liu
- Institute of Forensic Medicine, West China School of Basic Science and Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Shouyu Wang
- Institute of Forensic Medicine, West China School of Basic Science and Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Ziwei Ye
- Institute of Forensic Medicine, West China School of Basic Science and Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Yiping Hou
- Institute of Forensic Medicine, West China School of Basic Science and Forensic Medicine, Sichuan University, Chengdu 610041, China.
| | - Zheng Wang
- Shanghai Key Laboratory of Forensic Medicine, Academy of Forensic Sciences, Ministry of Justice, Shanghai 200063, China; Institute of Forensic Medicine, West China School of Basic Science and Forensic Medicine, Sichuan University, Chengdu 610041, China.
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28
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The forensic landscape and the population genetic analyses of Hainan Li based on massively parallel sequencing DNA profiling. Int J Legal Med 2021; 135:1295-1317. [PMID: 33847803 DOI: 10.1007/s00414-021-02590-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Accepted: 03/26/2021] [Indexed: 12/30/2022]
Abstract
Due to the formation of the Qiongzhou Strait by climate change and marine transition, Hainan island was isolated from the mainland southern China during the Last Glacial Maximum. Hainan island, located at the southernmost part of China and separated from the Leizhou Peninsula by the Qiongzhou Strait, laid on one of the modern human northward migration routes from Southeast Asia to East Asia. The Hlai language-speaking Li minority, the second largest population after Han Chinese in Hainan island, is the direct descendants of the initial migrants in Hainan island and has unique ethnic properties and derived characteristics; however, the forensic-associated studies on Hainan Li population are still insufficient. Hence, 136 Hainan Li individuals were genotyped in this study using the MPS-based ForenSeq™ DNA Signature Prep Kit (DNA Primer Set A, DPMA) to characterize the forensic genetic polymorphism landscape, and DNA profiles were obtained from 152 different molecular genetic markers (27 autosomal STRs, 24 Y-STRs, 7 X-STRs, and 94 iiSNPs). A total of 419 distinct length variants and 586 repeat sequence sub-variants, with 31 novel alleles (at 17 loci), were identified across the 58 STR loci from the DNA profiles of Hainan Li population. We evaluated the forensic characteristics and efficiencies of DPMA, demonstrating that the STRs and iiSNPs in DPMA were highly polymorphic in Hainan Li population and could be employed in forensic applications. In addition, we set up three datasets, which included the genetic data of (i) iiSNPs (27 populations, 2640 individuals), (ii) Y-STRs (42 populations, 8281 individuals), and (iii) Y haplogroups (123 populations, 4837 individuals) along with the population ancestries and language families, to perform population genetic analyses separately from different perspectives. In conclusion, the phylogenetic analyses indicated that Hainan Li, with a southern East Asia origin and Tai-Kadai language-speaking language, is an isolated population relatively. But the genetic pool of Hainan Li influenced by the limited gene flows from other Tai-Kadai populations and Hainan populations. Furthermore, the establishment of isolated population models will be beneficial to clarify the exquisite population structures and develop specific genetic markers for subpopulations in forensic genetic fields.
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29
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Yao H, Wang M, Zou X, Li Y, Yang X, Li A, Yeh HY, Wang P, Wang Z, Bai J, Guo J, Chen J, Ding X, Zhang Y, Lin B, Wang CC, He G. New insights into the fine-scale history of western-eastern admixture of the northwestern Chinese population in the Hexi Corridor via genome-wide genetic legacy. Mol Genet Genomics 2021; 296:631-651. [PMID: 33650010 DOI: 10.1007/s00438-021-01767-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2020] [Accepted: 02/08/2021] [Indexed: 02/06/2023]
Abstract
Trans-Eurasian cultural and genetic exchanges have significantly influenced the demographic dynamics of Eurasian populations. The Hexi Corridor, located along the southeastern edge of the Eurasian steppe, served as an important passage of the ancient Silk Road in Northwest China and intensified the transcontinental exchange and interaction between populations on the Central Plain and in Western Eurasia. Historical and archeological records indicate that the Western Eurasian cultural elements were largely brought into North China via this geographical corridor, but there is debate on the extent to which the spread of barley/wheat agriculture into North China and subsequent Bronze Age cultural and technological mixture/shifts were achieved by the movement of people or dissemination of ideas. Here, we presented higher-resolution genome-wide autosomal and uniparental Y/mtDNA SNP or STR data for 599 northwestern Han Chinese individuals and conducted 2 different comprehensive genetic studies among Neolithic-to-present-day Eurasians. Genetic studies based on lower-resolution STR markers via PCA, STRUCTURE, and phylogenetic trees showed that northwestern Han Chinese individuals had increased genetic homogeneity relative to northern Mongolic/Turkic/Tungusic speakers and Tibeto-Burman groups. The genomic signature constructed based on modern/ancient DNA further illustrated that the primary ancestry of the northwestern Han was derived from northern millet farmer ancestors, which was consistent with the hypothesis of Han origin in North China and more recent northwestward population expansion. This was subsequently confirmed via excess shared derived alleles in f3/f4 statistical analyses and by more northern East Asian-related ancestry in the qpAdm/qpGraph models. Interestingly, we identified one western Eurasian admixture signature that was present in northwestern Han but absent from southern Han, with an admixture time dated to approximately 1000 CE (Tang and Song dynasties). Generally, we provided supporting evidence that historic Trans-Eurasian communication was primarily maintained through population movement, not simply cultural diffusion. The observed population dynamics in northwestern Han Chinese not only support the North China origin hypothesis but also reflect the multiple sources of the genetic diversity observed in this population.
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Affiliation(s)
- Hongbin Yao
- Belt and Road Research Center for Forensic Molecular Anthropology Gansu University of Political Science and Law, Lanzhou, 730000, China.
| | - Mengge Wang
- Institute of Forensic Medicine, West China School of Basic Science and Forensic Medicine, Sichuan University, Chengdu, 610065, China
| | - Xing Zou
- Institute of Forensic Medicine, West China School of Basic Science and Forensic Medicine, Sichuan University, Chengdu, 610065, China
| | - Yingxiang Li
- Department of Anthropology and Ethnology, Institute of Anthropology, National Institute for Data Science in Health and Medicine, School of Life Sciences, Xiamen University, Xiamen, 361005, China.,AnLan AI, Shenzhen, China
| | - Xiaomin Yang
- Department of Anthropology and Ethnology, Institute of Anthropology, National Institute for Data Science in Health and Medicine, School of Life Sciences, Xiamen University, Xiamen, 361005, China
| | - Ailin Li
- Belt and Road Research Center for Forensic Molecular Anthropology Gansu University of Political Science and Law, Lanzhou, 730000, China
| | - Hui-Yuan Yeh
- School of Humanities, Nanyang Technological University, Nanyang, Singapore, 639798, Singapore
| | - Peixin Wang
- College of Medical Information, Chongqing Medical University, Chongqing, 400331, China
| | - Zheng Wang
- Institute of Forensic Medicine, West China School of Basic Science and Forensic Medicine, Sichuan University, Chengdu, 610065, China
| | - Jingya Bai
- Department of Medicine, Northwest Minzu University, Lanzhou, 730000, Gansu, China.,Key Laboratory for Physique and Health of the Minorities, Northwest Minzu University, Lanzhou, 730000, Gansu, China
| | - Jianxin Guo
- Department of Anthropology and Ethnology, Institute of Anthropology, National Institute for Data Science in Health and Medicine, School of Life Sciences, Xiamen University, Xiamen, 361005, China
| | - Jinwen Chen
- Department of Anthropology and Ethnology, Institute of Anthropology, National Institute for Data Science in Health and Medicine, School of Life Sciences, Xiamen University, Xiamen, 361005, China
| | - Xiao Ding
- Belt and Road Research Center for Forensic Molecular Anthropology Gansu University of Political Science and Law, Lanzhou, 730000, China
| | - Yan Zhang
- Belt and Road Research Center for Forensic Molecular Anthropology Gansu University of Political Science and Law, Lanzhou, 730000, China
| | - Baoquan Lin
- Belt and Road Research Center for Forensic Molecular Anthropology Gansu University of Political Science and Law, Lanzhou, 730000, China
| | - Chuan-Chao Wang
- Department of Anthropology and Ethnology, Institute of Anthropology, National Institute for Data Science in Health and Medicine, School of Life Sciences, Xiamen University, Xiamen, 361005, China.
| | - Guanglin He
- Belt and Road Research Center for Forensic Molecular Anthropology Gansu University of Political Science and Law, Lanzhou, 730000, China. .,Department of Anthropology and Ethnology, Institute of Anthropology, National Institute for Data Science in Health and Medicine, School of Life Sciences, Xiamen University, Xiamen, 361005, China.
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30
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Liu Y, Wang M, Chen P, Wang Z, Liu J, Yao L, Wang F, Tang R, Zou X, He G. Combined Low-/High-Density Modern and Ancient Genome-Wide Data Document Genomic Admixture History of High-Altitude East Asians. Front Genet 2021; 12:582357. [PMID: 33643377 PMCID: PMC7905318 DOI: 10.3389/fgene.2021.582357] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2020] [Accepted: 01/05/2021] [Indexed: 01/26/2023] Open
Abstract
The Tibetan Plateau (TP) is considered to be one of the last terrestrial environments conquered by the anatomically modern human. Understanding of the genetic background of highland Tibetans plays a pivotal role in archeology, anthropology, genetics, and forensic investigations. Here, we genotyped 22 forensic genetic markers in 1,089 Tibetans residing in Nagqu Prefecture and collected 1,233,013 single nucleotide polymorphisms (SNPs) in the highland East Asians (Sherpa and Tibetan) from the Simons Genome Diversity Project and ancient Tibetans from Nepal and Neolithic farmers from northeastern Qinghai-Tibetan Plateau from public databases. We subsequently merged our two datasets with other worldwide reference populations or eastern ancient Eurasians to gain new insights into the genetic diversity, population movements, and admixtures of high-altitude East Asians via comprehensive population genetic statistical tools [principal component analysis (PCA), multidimensional scaling plot (MDS), STRUCTURE/ADMIXTURE, f3 , f4 , qpWave/qpAdm, and qpGraph]. Besides, we also explored their forensic characteristics and extended the Chinese National Database based on STR data. We identified 231 alleles with the corresponding allele frequencies spanning from 0.0005 to 0.5624 in the forensic low-density dataset, in which the combined powers of discrimination and the probability of exclusion were 1-1.22E-24 and 0.999999998, respectively. Additionally, comprehensive population comparisons in our low-density data among 57 worldwide populations via the Nei's genetic distance, PCA, MDS, NJ tree, and STRUCTURE analysis indicated that the highland Tibeto-Burman speakers kept the close genetic relationship with ethnically close populations. Findings from the 1240K high-density dataset not only confirmed the close genetic connection between modern Highlanders, Nepal ancients (Samdzong, Mebrak, and Chokhopani), and the upper Yellow River Qijia people, suggesting the northeastern edge of the TP served as a geographical corridor for ancient population migrations and interactions between highland and lowland regions, but also evidenced that late Neolithic farmers permanently colonized into the TP by adopting cold-tolerant barley agriculture that was mediated via the acculturation of idea via the millet farmer and not via the movement of barley agriculturalist as no obvious western Eurasian admixture signals were identified in our analyzed modern and ancient populations. Besides, results from the qpAdm-based admixture proportion estimation and qpGraph-based phylogenetic relationship reconstruction consistently demonstrated that all ancient and modern highland East Asians harbored and shared the deeply diverged Onge/Hoabinhian-related eastern Eurasian lineage, suggesting a common Paleolithic genetic legacy existed in high-altitude East Asians as the first layer of their gene pool.
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Affiliation(s)
- Yan Liu
- School of Basic Medical Sciences, North Sichuan Medical College, Nanchong, China
| | - Mengge Wang
- Institute of Forensic Medicine, West China School of Basic Science and Forensic Medicine, Sichuan University, Chengdu, China
| | - Pengyu Chen
- Key Laboratory of Cell Engineering in Guizhou Province, Affiliated Hospital of Zunyi Medical University, Zunyi, China
- Center of Forensic Expertise, Affiliated Hospital of Zunyi Medical University, Zunyi, China
| | - Zheng Wang
- Institute of Forensic Medicine, West China School of Basic Science and Forensic Medicine, Sichuan University, Chengdu, China
| | - Jing Liu
- Institute of Forensic Medicine, West China School of Basic Science and Forensic Medicine, Sichuan University, Chengdu, China
| | - Lilan Yao
- Key Laboratory of Cell Engineering in Guizhou Province, Affiliated Hospital of Zunyi Medical University, Zunyi, China
- Center of Forensic Expertise, Affiliated Hospital of Zunyi Medical University, Zunyi, China
| | - Fei Wang
- Institute of Forensic Medicine, West China School of Basic Science and Forensic Medicine, Sichuan University, Chengdu, China
| | - Renkuan Tang
- Department of Forensic Medicine, College of Basic Medicine, Chongqing Medical University, Chongqing, China
| | - Xing Zou
- Institute of Forensic Medicine, West China School of Basic Science and Forensic Medicine, Sichuan University, Chengdu, China
| | - Guanglin He
- Institute of Forensic Medicine, West China School of Basic Science and Forensic Medicine, Sichuan University, Chengdu, China
- 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
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31
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Massively parallel sequencing of 165 ancestry-informative SNPs and forensic biogeographical ancestry inference in three southern Chinese Sinitic/Tai-Kadai populations. Forensic Sci Int Genet 2021; 52:102475. [PMID: 33561661 DOI: 10.1016/j.fsigen.2021.102475] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2020] [Revised: 12/06/2020] [Accepted: 01/20/2021] [Indexed: 01/01/2023]
Abstract
Ancestry informative markers (AIMs), which are distributed throughout the human genome, harbor significant allele frequency differences among diverse ethnic groups. The use of sets of AIMs to reconstruct population history and genetic relationships is attracting interest in the forensic community, because biogeographic ancestry information for a casework sample can potentially be predicted and used to guide the investigative process. However, subpopulation ancestry inference within East Asia remains in its infancy due to a lack of population reference data collection and incomplete validation work on newly developed or commercial AIM sets. In the present study, 316 Chinese persons, including 85 Sinitic-speaking Haikou Han, 120 Qiongzhong Hlai and 111 Daozhen Gelao individuals belonging to Tai-Kadai-speaking populations, were analyzed using the Precision ID Ancestry Panel (165 AISNPs). Combined with our previous 165-AISNP data (375 individuals from 6 populations), the 1000 Genomes Project and forensic literature, comprehensive population genetic comparisons and ancestry inference were further performed via ADMIXTURE, TreeMix, PCA, f-statistics and N-J tree. Although several nonpolymorphic loci were identified in the three southern Chinese populations, the forensic parameters of this ancestry inference panel were better than those for the 23 STR-based Huaxia Platinum System, which is suitable for use as a robust tool in forensic individual identification and parentage testing. The results based on the ancestry assignment and admixture proportion evaluation revealed that this panel could be used successfully to assign individuals at a continental scale but also possessed obvious limitations in discriminatory power in intercontinental individuals, especially for European-Asian admixed Uyghurs or in populations lacking reference databases. Population genetic analyses further revealed five continental population clusters and three East Asian-focused population subgroups, which is consistent with linguistic affiliations. Ancestry composition and multiple phylogenetic analysis further demonstrated that the geographically isolated Qiongzhong Hlai harbored a close phylogenetic relationship with Austronesian speakers and possessed a homogenous Tai-Kadai-dominant ancestry, which could be used as the ancestral source proxy in population history reconstruction of Tai-Kadai-speaking populations and as one of the representatives for forensic database establishment. In summary, more population-specific AIM sets focused on East Asian subpopulations, comprehensive algorithms and high-coverage population reference data should be developed and validated in the next step.
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32
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Li C, Tian D, Tang B, Liu X, Teng X, Zhao W, Zhang Z, Song S. Genome Variation Map: a worldwide collection of genome variations across multiple species. Nucleic Acids Res 2021; 49:D1186-D1191. [PMID: 33170268 PMCID: PMC7778933 DOI: 10.1093/nar/gkaa1005] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 10/10/2020] [Accepted: 10/14/2020] [Indexed: 12/13/2022] Open
Abstract
The Genome Variation Map (GVM; http://bigd.big.ac.cn/gvm/) is a public data repository of genome variations. It aims to collect and integrate genome variations for a wide range of species, accepts submissions of different variation types from all over the world and provides free open access to all publicly available data in support of worldwide research activities. Compared with the previous version, particularly, a total of 22 species, 115 projects, 55 935 samples, 463 429 609 variants, 66 220 associations and 56 submissions (as of 7 September 2020) were newly added in the current version of GVM. In the current release, GVM houses a total of ∼960 million variants from 41 species, including 13 animals, 25 plants and 3 viruses. Moreover, it incorporates 64 819 individual genotypes and 260 393 manually curated high-quality genotype-to-phenotype associations. Since its inception, GVM has archived genomic variation data of 43 754 samples submitted by worldwide users and served >1 million data download requests. Collectively, as a core resource in the National Genomics Data Center, GVM provides valuable genome variations for a diversity of species and thus plays an important role in both functional genomics studies and molecular breeding.
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Affiliation(s)
- Cuiping Li
- China National Center for Bioinformation, Beijing 100101, China.,National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Dongmei Tian
- China National Center for Bioinformation, Beijing 100101, China.,National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Bixia Tang
- China National Center for Bioinformation, Beijing 100101, China.,National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Xiaonan Liu
- China National Center for Bioinformation, Beijing 100101, China.,National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.,CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xufei Teng
- China National Center for Bioinformation, Beijing 100101, China.,National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.,CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wenming Zhao
- China National Center for Bioinformation, Beijing 100101, China.,National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.,CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhang Zhang
- China National Center for Bioinformation, Beijing 100101, China.,National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.,CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shuhui Song
- China National Center for Bioinformation, Beijing 100101, China.,National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.,CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
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33
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Mengge W, Guanglin H, Yongdong S, Shouyu W, Xing Z, Jing L, Zheng W, Hou Y. Massively parallel sequencing of mitogenome sequences reveals the forensic features and maternal diversity of tai-kadai-speaking hlai islanders. Forensic Sci Int Genet 2020; 47:102303. [PMID: 32361554 DOI: 10.1016/j.fsigen.2020.102303] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2019] [Revised: 03/30/2020] [Accepted: 04/16/2020] [Indexed: 12/11/2022]
Abstract
As a single maternally inherited locus, human mitochondrial DNA (mtDNA) is geographically arranged and plays a key role in forensic applications. Hlai population has been evidenced as the most typical and unmixed representative of the Tai-Kadai-speaking populations via genome-wide analyses. However, forensic features and maternal diversity of the complete mitogenomes in this Tai-Kadai ancestrally related population are scarce. Thus, we sequenced the complete mitogenomes in 127 Hainan Hlais and found 109 distinct haplotypes belonging to 43 terminal haplogroups resulting in the haplotype diversity of 0.9970. Our results of comprehensive population comparisons showed that Hlai islanders had a close genetic affinity with Tai-Kadai-speaking populations from Southeast Asia, which is consistent with the back-migration of Chinese Neolithic farmers into this region via the inland route. Besides, maternally genetic evidence further revealed a close genetic relationship between Tai-Kadai-speaking and Austronesian-speaking populations when only East Asian dataset was considered, which is consistent with the common origin from Yangtze rice farmers and then spread southward along the inland and coastal routes, respectively. In the reconstructed phylogenetic tree and median-joining networks, the vast majority of Hlais were clustered in exclusive clades, which demonstrated that Hlai people probably had undergone founder effect or genetic bottleneck in their history, and remained genetically isolated for a long time. Collectively, Hainan Hlai did not exhibit detectable maternal gene flow from surrounding or incoming populations. Mitogenome information generated in this study is a contribution in mitigating the underrepresentation of Chinese data in forensic mitogenetics and will assist geography-, metapopulation-, as well as phylogeny-based queries.
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Affiliation(s)
- Wang Mengge
- Institute of Forensic Medicine, West China School of Basic Science & Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - He Guanglin
- Institute of Forensic Medicine, West China School of Basic Science & Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Su Yongdong
- Forensic Identification Center, Public Security Bureau of Tibet Tibetan Autonomous Region, Lhasa, Tibet Tibetan Autonomous Region, 850000, China
| | - Wang Shouyu
- Institute of Forensic Medicine, West China School of Basic Science & Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Zou Xing
- Institute of Forensic Medicine, West China School of Basic Science & Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Liu Jing
- Institute of Forensic Medicine, West China School of Basic Science & Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Wang Zheng
- Institute of Forensic Medicine, West China School of Basic Science & Forensic Medicine, Sichuan University, Chengdu 610041, China.
| | - Yiping Hou
- Institute of Forensic Medicine, West China School of Basic Science & Forensic Medicine, Sichuan University, Chengdu 610041, China.
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