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Wang M, Huang Y, Liu K, Wang Z, Zhang M, Yuan H, Duan S, Wei L, Yao H, Sun Q, Zhong J, Tang R, Chen J, Sun Y, Li X, Su H, Yang Q, Hu L, Yun L, Yang J, Nie S, Cai Y, Yan J, Zhou K, Wang C, Zhu B, Liu C, He G. Multiple Human Population Movements and Cultural Dispersal Events Shaped the Landscape of Chinese Paternal Heritage. Mol Biol Evol 2024; 41:msae122. [PMID: 38885310 PMCID: PMC11232699 DOI: 10.1093/molbev/msae122] [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: 08/29/2023] [Revised: 05/30/2024] [Accepted: 06/13/2024] [Indexed: 06/20/2024] Open
Abstract
Large-scale genomic projects and ancient DNA innovations have ushered in a new paradigm for exploring human evolutionary history. However, the genetic legacy of spatiotemporally diverse ancient Eurasians within Chinese paternal lineages remains unresolved. Here, we report an integrated Y-chromosome genomic database encompassing 15,563 individuals from both modern and ancient Eurasians, including 919 newly reported individuals, to investigate the Chinese paternal genomic diversity. The high-resolution, time-stamped phylogeny reveals multiple diversification events and extensive expansions in the early and middle Neolithic. We identify four major ancient population movements, each associated with technological innovations that have shaped the Chinese paternal landscape. First, the expansion of early East Asians and millet farmers from the Yellow River Basin predominantly carrying O2/D subclades significantly influenced the formation of the Sino-Tibetan people and facilitated the permanent settlement of the Tibetan Plateau. Second, the dispersal of rice farmers from the Yangtze River Valley carrying O1 and certain O2 sublineages reshapes the genetic makeup of southern Han Chinese, as well as the Tai-Kadai, Austronesian, Hmong-Mien, and Austroasiatic people. Third, the Neolithic Siberian Q/C paternal lineages originated and proliferated among hunter-gatherers on the Mongolian Plateau and the Amur River Basin, leaving a significant imprint on the gene pools of northern China. Fourth, the J/G/R paternal lineages derived from western Eurasia, which were initially spread by Yamnaya-related steppe pastoralists, maintain their presence primarily in northwestern China. Overall, our research provides comprehensive genetic evidence elucidating the significant impact of interactions with culturally distinct ancient Eurasians on the patterns of paternal diversity in modern Chinese populations.
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Affiliation(s)
- 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
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510275, China
| | - Yuguo Huang
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu 610000, China
| | - Kaijun Liu
- School of International Tourism and Culture, Guizhou Normal University, Guiyang 550025, China
- MoFang Human Genome Research Institute, Tianfu Software Park, Chengdu, Sichuan 610042, 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
| | - Menghan Zhang
- Institute of Modern Languages and Linguistics, Fudan University, Shanghai 200433, China
- Research Institute of Intelligent Complex Systems, Fudan University, Shanghai 200433, China
| | - Haibing Yuan
- Center for Archaeological Science, Sichuan University, Chengdu 610000, 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
| | - Lanhai Wei
- School of Ethnology and Anthropology, Institute of Humanities and Human Sciences, Inner Mongolia Normal University, Hohhot 010022, China
| | - Hongbing Yao
- Belt and Road Research Center for Forensic Molecular Anthropology Gansu University of Political Science and Law, Lanzhou 730000, 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
| | - Jie Zhong
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu 610000, China
| | - Renkuan Tang
- Department of Forensic Medicine, College of Basic Medicine, Chongqing Medical University, Chongqing 400331, 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
| | - Yuntao Sun
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu 610000, China
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & 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
| | - Haoran Su
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu 610000, China
- School of Laboratory Medicine and Center for Genetics and Prenatal Diagnosis, Affiliated Hospital of North Sichuan Medical College, Nanchong, Sichuan 637007, 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
| | - Liping Hu
- School of Forensic Medicine, Kunming Medical University, Kunming 650500, China
| | - Libing Yun
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, 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
| | - Shengjie Nie
- School of Forensic Medicine, Kunming Medical University, Kunming 650500, China
| | - Yan Cai
- School of Laboratory Medicine and Center for Genetics and Prenatal Diagnosis, Affiliated Hospital of North Sichuan Medical College, Nanchong, Sichuan 637007, China
| | - Jiangwei Yan
- School of Forensic Medicine, Shanxi Medical University, Jinzhong 030001, China
| | - Kun Zhou
- MoFang Human Genome Research Institute, Tianfu Software Park, Chengdu, Sichuan 610042, China
| | - Chuanchao Wang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen 361005, China
| | - Bofeng Zhu
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou 510515, China
- Microbiome Medicine Center, Department of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong 510515, China
| | - Chao Liu
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou 510515, 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
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2
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Thao DH, Dinh TH, Mitsunaga S, Duy LD, Phuong NT, Anh NP, Anh NT, Duc BM, Hue HTT, Ha NH, Ton ND, Hübner A, Pakendorf B, Stoneking M, Inoue I, Duong NT, Hai NV. Investigating demic versus cultural diffusion and sex bias in the spread of Austronesian languages in Vietnam. PLoS One 2024; 19:e0304964. [PMID: 38885215 PMCID: PMC11182502 DOI: 10.1371/journal.pone.0304964] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2024] [Accepted: 05/21/2024] [Indexed: 06/20/2024] Open
Abstract
Austronesian (AN) is the second-largest language family in the world, particularly widespread in Island Southeast Asia (ISEA) and Oceania. In Mainland Southeast Asia (MSEA), groups speaking these languages are concentrated in the highlands of Vietnam. However, our knowledge of the spread of AN-speaking populations in MSEA remains limited; in particular, it is not clear if AN languages were spread by demic or cultural diffusion. In this study, we present and analyze new data consisting of complete mitogenomes from 369 individuals and 847 Y-chromosomal single nucleotide polymorphisms (SNPs) from 170 individuals from all five Vietnamese Austronesian groups (VN-AN) and five neighboring Vietnamese Austroasiatic groups (VN-AA). We found genetic signals consistent with matrilocality in some, but not all, of the VN-AN groups. Population affinity analyses indicated connections between the AN-speaking Giarai and certain Taiwanese AN groups (Rukai, Paiwan, and Bunun). However, overall, there were closer genetic affinities between VN-AN groups and neighboring VN-AA groups, suggesting language shifts. Our study provides insights into the genetic structure of AN-speaking communities in MSEA, characterized by some contact with Taiwan and language shift in neighboring groups, indicating that the expansion of AN speakers in MSEA was a combination of cultural and demic diffusion.
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Affiliation(s)
- Dinh Huong Thao
- Institute of Genome Research, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Hanoi, Vietnam
| | - Tran Huu Dinh
- Institute of Genome Research, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Hanoi, Vietnam
| | - Shigeki Mitsunaga
- Division of Human Genetics, National Institute of Genetics, Shizuoka, Japan
| | - La Duc Duy
- Institute of Genome Research, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Hanoi, Vietnam
| | - Nguyen Thanh Phuong
- Institute of Genome Research, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Hanoi, Vietnam
- Division of Human Genetics, National Institute of Genetics, Shizuoka, Japan
| | - Nguyen Phuong Anh
- Institute of Genome Research, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Hanoi, Vietnam
| | - Nguyen Tho Anh
- Institute of Genome Research, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Hanoi, Vietnam
| | - Bui Minh Duc
- Institute of Genome Research, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Hanoi, Vietnam
| | - Huynh Thi Thu Hue
- Institute of Genome Research, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Hanoi, Vietnam
| | - Nguyen Hai Ha
- Institute of Genome Research, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Hanoi, Vietnam
| | - Nguyen Dang Ton
- Institute of Genome Research, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Hanoi, Vietnam
| | - Alexander Hübner
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, Leipzig, Germany
| | | | - Mark Stoneking
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, Leipzig, Germany
- Laboratoire de Biométrie et Biologie Evolutive, Université Lyon 1, CNRS, UMR 5558, Villeurbanne, France
| | - Ituro Inoue
- Division of Human Genetics, National Institute of Genetics, Shizuoka, Japan
| | - Nguyen Thuy Duong
- Institute of Genome Research, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Hanoi, Vietnam
| | - Nong Van Hai
- Institute of Genome Research, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Hanoi, Vietnam
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3
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Chen C, Guo Y, Fang Y, Shi J, Meng H, Qu L, Zhang X, Zhu B. The maternal phylogenetic insights of Yunnan Miao group revealed by complete mitogenomes. Gene 2024; 901:148046. [PMID: 38081335 DOI: 10.1016/j.gene.2023.148046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Accepted: 11/28/2023] [Indexed: 01/21/2024]
Abstract
The Miao group is one of the representative Hmong-Mien-speaking populations and primarily scattered in southern China and Southeast Asia, which has experienced massive migrations in history and thus forms distinctive evolutionary genetics. Yet, the genetic explorations of Miao group are relatively limited based on complete mitochondrial genome (mitogenome), especially for the Miao group from Yunnan Province (YNM). Here, we sequenced complete mitogenomes of 132 Miao individuals from Yunnan Province using massively parallel sequencing method. Total 132 Miao individuals could be allocated to 119 various haplotypes, which were mainly dominated by haplogroups prevalent in southern East Asia (B, F, M7 and R9), and rarely occupied by northern lineages (A, D, G and M8). In order to dissect the genetic background of YNM more comprehensively, we introduced 99 published population data with 7135 complete mitochondrial sequences for population genetic comparisons. YNM exhibited closer genetic relationships with Hmong-Mien, Tai-Kadai, Sino-Tibetan and Austroasiatic populations, especially for Hmong-Mien populations; we further speculated that Miao group might have certain direct or indirect gene exchanges with ancient Baiyue groups. Several maternal lineages, such as B5a1c1a, F1g1, B4a5 and D4e1a3, were found to be specifically shared by YNM and other Hmong-Mien populations, and these matrilineal expansions occurred roughly during the Neolithic period. Eventually, according to the population dynamic analyses of YNM, the population size began to emerge recovery ∼1-0.5 kya after a long-term population reduction ∼1-5 kya, during which the B5a1c1a haplogroup manifested relatively apparent lineage expansion.
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Affiliation(s)
- Chong Chen
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an 710004, China; Department of Forensic Medicine, Faculty of Basic Medical Science, Chongqing Medical University, Chongqing 400016, China
| | - Yuxin Guo
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an 710004, China
| | - Yating Fang
- School of Basic Medical Sciences, Anhui Medical University, Anhui 230031, China
| | - Jianfeng Shi
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an 710004, China
| | - Haotian Meng
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an 710004, China
| | - Li Qu
- Department of Rheumatology and Immunology, Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi 710004, China
| | - Xingru Zhang
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an 710004, China; College of Forensic Medicine, Xi'an Jiaotong University Health Science Center, Xi'an 710061, China
| | - Bofeng Zhu
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an 710004, China; College of Forensic Medicine, Xi'an Jiaotong University Health Science Center, Xi'an 710061, China; Multi-Omics Innovative Research Center of Forensic Identification, Department of Forensic Genetics, School of Forensic Medicine, Southern Medical University, Guangzhou 510515, China.
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Jaisamut K, Pitiwararom R, Sukawutthiya P, Sathirapatya T, Noh H, Worrapitirungsi W, Vongpaisarnsin K. Unraveling the mitochondrial phylogenetic landscape of Thailand reveals complex admixture and demographic dynamics. Sci Rep 2023; 13:20396. [PMID: 37990137 PMCID: PMC10663463 DOI: 10.1038/s41598-023-47762-w] [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: 08/31/2023] [Accepted: 11/17/2023] [Indexed: 11/23/2023] Open
Abstract
The evolutionary dynamics of mitochondrial DNA within the Thai population were comprehensively explored with a specific focus on the influence of South Asian admixture. A total of 166 samples were collected through randomized sampling, ensuring a diverse representation. Our findings unveil substantial genetic and haplogroup diversity within the Thai population. We have identified 164 haplotypes categorized into 97 haplogroups, with a notable inclusion of 20 novel haplogroups. The distribution of haplogroups exhibited variations across different populations and countries. The central Thai population displayed a high diversity of haplogroups from both the M and N clades. Maternal lineage affinities were discerned between several Mainland Southeast Asia (MSEA) and South Asian populations, implying ancestral genetic connections and a substantial influence of South Asian women in establishing these relationships. f4-statistics indicates the presence of a Tibeto-Burman genetic component within the Mon population from Thailand. New findings demonstrate two phases of population expansion occurring 22,000-26,000 and 2500-3800 years ago, coinciding with the Last Glacial Maximum, and Neolithic demographic transition, respectively. This research significantly enhances our understanding of the maternal genetic history of Thailand and MSEA, emphasizing the influence of South Asian admixture. Moreover, it underscores the critical role of prior information, such as mutation rates, within the Bayesian framework for accurate estimation of coalescence times and inferring demographic history.
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Affiliation(s)
- Kitipong Jaisamut
- Forensic Genetics Research Unit, Department of Forensic Medicine, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
- Department of Forensic Medicine, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Rachtipan Pitiwararom
- Forensic Genetics Research Unit, Department of Forensic Medicine, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
- Department of Forensic Medicine, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Poonyapat Sukawutthiya
- Forensic Genetics Research Unit, Department of Forensic Medicine, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
- Department of Forensic Medicine, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Tikumphorn Sathirapatya
- Forensic Genetics Research Unit, Department of Forensic Medicine, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
- Department of Forensic Medicine, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Hasnee Noh
- Forensic Genetics Research Unit, Department of Forensic Medicine, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
- Department of Forensic Medicine, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Wikanda Worrapitirungsi
- Forensic Genetics Research Unit, Department of Forensic Medicine, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
- Department of Forensic Medicine, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Kornkiat Vongpaisarnsin
- Forensic Genetics Research Unit, Department of Forensic Medicine, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand.
- Department of Forensic Medicine, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand.
- Forensic Serology and DNA, King Chulalongkorn Memorial Hospital and Thai Red Cross Society, Bangkok, Thailand.
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Chen J, Zhang H, Yang M, Wang R, Zhang H, Ren Z, Wang Q, Liu Y, Chen J, Ji J, Zhao J, He G, Guo J, Zhu K, Yang X, Ma H, Wang CC, Huang J. Genomic formation of Tibeto-Burman speaking populations in Guizhou, Southwest China. BMC Genomics 2023; 24:672. [PMID: 37936086 PMCID: PMC10630991 DOI: 10.1186/s12864-023-09767-7] [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: 05/27/2023] [Accepted: 10/25/2023] [Indexed: 11/09/2023] Open
Abstract
Sino-Tibetan is the most prominent language family in East Asia. Previous genetic studies mainly focused on the Tibetan and Han Chinese populations. However, due to the sparse sampling, the genetic structure and admixture history of Tibeto-Burman-speaking populations in the low-altitude region of Southwest China still need to be clarified. We collected DNA from 157 individuals from four Tibeto-Burman-speaking groups from the Guizhou province in Southwest China. We genotyped the samples at about 700,000 genome-wide single nucleotide polymorphisms. Our results indicate that the genetic variation of the four Tibeto-Burman-speaking groups in Guizhou is at the intermediate position in the modern Tibetan-Tai-Kadai/Austronesian genetic cline. This suggests that the formation of Tibetan-Burman groups involved a large-scale gene flow from lowland southern Chinese. The southern ancestry could be further modelled as deriving from Vietnam's Late Neolithic-related inland Southeast Asia agricultural populations and Taiwan's Iron Age-related coastal rice-farming populations. Compared to the Tibeto-Burman speakers in the Tibetan-Yi Corridor reported previously, the Tibeto-Burman groups in the Guizhou region received additional gene flow from the southeast coastal area of China. We show a difference between the genetic profiles of the Tibeto-Burman speakers of the Tibetan-Yi Corridor and the Guizhou province. Vast mountain ranges and rivers in Southwest China may have decelerated the westward expansion of the southeast coastal East Asians. Our results demonstrate the complex genetic profile in the Guizhou region in Southwest China and support the multiple waves of human migration in the southern area of East Asia.
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Affiliation(s)
- Jinwen Chen
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, 361102, China
| | - Han Zhang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, China
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Science, Ministry of Justice, Shanghai, 200063, China
| | - Meiqing Yang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, China
| | - Rui Wang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, 361102, China
- Department of Anthropology and Ethnology, Institute of Anthropology, School of Sociology and Anthropology, Xiamen University, Xiamen, 361005, China
| | - Hongling Zhang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, 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
| | - Jing Chen
- 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, 361102, China
- Department of Anthropology and Ethnology, Institute of Anthropology, School of Sociology and Anthropology, Xiamen University, Xiamen, 361005, China
| | - Guanglin He
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, 361102, China
- Department of Anthropology and Ethnology, Institute of Anthropology, School of Sociology and Anthropology, Xiamen University, Xiamen, 361005, China
| | - Jianxin Guo
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, 361102, China
- Department of Anthropology and Ethnology, Institute of Anthropology, School of Sociology and Anthropology, Xiamen University, Xiamen, 361005, China
| | - Kongyang Zhu
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, 361102, China
- Department of Anthropology and Ethnology, Institute of Anthropology, School of Sociology and Anthropology, Xiamen University, Xiamen, 361005, China
| | - Xiaomin Yang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, 361102, China
- Department of Anthropology and Ethnology, Institute of Anthropology, School of Sociology and Anthropology, Xiamen University, Xiamen, 361005, China
| | - Hao Ma
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, 361102, China
- Department of Anthropology and Ethnology, Institute of Anthropology, School of Sociology and Anthropology, Xiamen University, Xiamen, 361005, China
| | - Chuan-Chao Wang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, 361102, China.
- Department of Anthropology and Ethnology, Institute of Anthropology, School of Sociology and Anthropology, Xiamen University, Xiamen, 361005, China.
- Department of Anthropology and Human Genetics, Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, China.
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, 361102, China.
- Institute of Artificial Intelligence, Xiamen University, Xiamen, 361005, Fujian, China.
| | - Jiang Huang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, China.
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6
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Woravatin W, Stoneking M, Srikummool M, Kampuansai J, Arias L, Kutanan W. South Asian maternal and paternal lineages in southern Thailand and the role of sex-biased admixture. PLoS One 2023; 18:e0291547. [PMID: 37708147 PMCID: PMC10501589 DOI: 10.1371/journal.pone.0291547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 08/31/2023] [Indexed: 09/16/2023] Open
Abstract
Previous genome-wide studies have reported South Asian (SA) ancestry in several Mainland Southeast Asian (MSEA) populations; however, additional details concerning population history, in particular the role of sex-specific aspects of the SA admixture in MSEA populations can be addressed with uniparental markers. Here, we generated ∼2.3 mB sequences of the male-specific portions of the Y chromosome (MSY) of a Tai-Kadai (TK)-speaking Southern Thai group (SouthernThai_TK), and complete mitochondrial (mtDNA) genomes of the SouthernThai_TK and an Austronesian (AN)-speaking Southern Thai (SouthernThai_AN) group. We identified new mtDNA haplogroups, e.g. Q3, E1a1a1, B4a1a and M7c1c3 that have not previously reported in Thai populations, but are frequent in Island Southeast Asia and Oceania, suggesting interactions between MSEA and these regions. SA prevalent mtDNA haplogroups were observed at frequencies of ~35-45% in the Southern Thai groups; both of them showed more genetic relatedness to Austroasiatic (AA) speaking Mon than to any other group. For MSY, SouthernThai_TK had ~35% SA prevalent haplogroups and exhibited closer genetic affinity to Central Thais. We also analyzed published data from other MSEA populations and observed SA ancestry in some additional MSEA populations that also reflects sex-biased admixture; in general, most AA- and AN-speaking groups in MSEA were closer to SA than to TK groups based on mtDNA, but the opposite pattern was observed for the MSY. Overall, our results of new genetic lineages and sex-biased admixture from SA to MSEA groups attest to the additional value that uniparental markers can add to studies of genome-wide variation.
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Affiliation(s)
- Wipada Woravatin
- Department of Biology, Faculty of Science, Khon Kaen University, Khon Kaen, Thailand
| | - Mark Stoneking
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Biométrie et Biologie Évolutive, UMR 5558, CNRS & Université de Lyon, Lyon, France
| | - Metawee Srikummool
- Department of Biochemistry, Faculty of Medical Science, Naresuan University, Phitsanulok, Thailand
| | - 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
| | - Leonardo Arias
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Centre for Linguistics, Faculty of Humanities, Leiden University, Leiden, The Netherlands
| | - Wibhu Kutanan
- Department of Biology, Faculty of Science, Khon Kaen University, Khon Kaen, Thailand
- Department of Biology, Faculty of Science, Naresuan University, Phitsanulok, Thailand
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7
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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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8
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Molecular Characterization and Genotype-Phenotype Correlation of G6PD Mutations in Five Ethnicities of Northern Vietnam. Anemia 2022; 2022:2653089. [PMID: 35845714 PMCID: PMC9277213 DOI: 10.1155/2022/2653089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Accepted: 06/10/2022] [Indexed: 11/17/2022] Open
Abstract
Glucose-6-phosphate dehydrogenase (G6PD) deficiency is the most common enzyme disorder and is caused by G6PD gene mutations. To date, more than 400 variants in the G6PD gene have been discovered, and about 160 identified variants are associated with a significant decrease in the G6PD enzyme activity. However, the molecular characterization and epidemiological study of G6PD deficiency are still limited in Vietnam. Therefore, we conducted this study to determine the G6PD variants among the Vietnamese populations and evaluate their correlation to G6PD enzyme activity. A total of 339 patients (302 males and 37 females) were enrolled in this study. The G6PD variants were identified by Sanger sequencing. Our results indicate that males are more severely deficient in G6PD than females. This enzyme activity in males (1.27 ± 1.06 IU/g·Hb) is significantly lower than in females (2.98 ± 1.57 IU/g·Hb) (p < 0.0001). The enzyme activity of the heterozygous-homozygous females and heterozygous females-hemizygous males was found to be significantly different (p < 0.05), which is interpreted due to random X-inactivation. For G6PD molecular characteristics, Viangchan (c.871G>A), Canton (c.1376G>T) and Kaiping (c.1388G>A) variants were the most dominant, accounting for 24.48%, 17.70%, and 22.42%, respectively, whereas the highest frequency of complex variants was observed in Viangchan/Silent with 20.35%. In terms of G6PD activity, the Union variant presented the lowest mean value (1.03 IU/g·Hb) compared to the other variants (p < 0.05). Computational analysis using Polyphen-2 tool investigated that all variants were relative to G6PD deficiency and separated the levels as benign and damaged. The result will establish effective methods to screen G6PD variants in Vietnam.
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9
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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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10
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Nguyen VT, Braun A, Kraft J, Ta TMT, Panagiotaropoulou GM, Nguyen VP, Nguyen TH, Trubetskoy V, Le CT, Le TTH, Pham XT, Heuser-Collier I, Lam NH, Böge K, Hahne IM, Bajbouj M, Zierhut MM, Hahn E, Ripke S. Increasing sample diversity in psychiatric genetics - Introducing a new cohort of patients with schizophrenia and controls from Vietnam - Results from a pilot study. World J Biol Psychiatry 2022; 23:219-227. [PMID: 34449294 DOI: 10.1080/15622975.2021.1951474] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
OBJECTIVES Genome-Wide Association Studies (GWAS) of Schizophrenia (SCZ) have provided new biological insights; however, most cohorts are of European ancestry. As a result, derived polygenic risk scores (PRS) show decreased predictive power when applied to populations of different ancestries. We aimed to assess the feasibility of a large-scale data collection in Hanoi, Vietnam, contribute to international efforts to diversify ancestry in SCZ genetic research and examine the transferability of SCZ-PRS to individuals of Vietnamese Kinh ancestry. METHODS In a pilot study, 368 individuals (including 190 SCZ cases) were recruited at the Hanoi Medical University's associated psychiatric hospitals and outpatient facilities. Data collection included sociodemographic data, baseline clinical data, clinical interviews assessing symptom severity and genome-wide SNP genotyping. SCZ-PRS were generated using different training data sets: (i) European, (ii) East-Asian and (iii) trans-ancestry GWAS summary statistics from the latest SCZ GWAS meta-analysis. RESULTS SCZ-PRS significantly predicted case status in Vietnamese individuals using mixed-ancestry (R2 liability = 4.9%, p = 6.83 × 10-8), East-Asian (R2 liability = 4.5%, p = 2.73 × 10-7) and European (R2 liability = 3.8%, p = 1.79 × 10-6) discovery samples. DISCUSSION Our results corroborate previous findings of reduced PRS predictive power across populations, highlighting the importance of ancestral diversity in GWA studies.
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Affiliation(s)
- V T Nguyen
- Department of Psychiatry, Hanoi Medical University, Hà Nội, Việt Nam.,National Institute of Mental Health, Bach Mai Hospital, Hà Nội, Việt Nam
| | - A Braun
- Charité - Universitätsmedizin Berlin, Department of Psychiatry and Psychotherapy, Campus Charité Mitte, Berlin, Germany
| | - J Kraft
- Charité - Universitätsmedizin Berlin, Department of Psychiatry and Psychotherapy, Campus Charité Mitte, Berlin, Germany
| | - T M T Ta
- Berlin Institute of Health, Charité - Universitätsmedizin Berlin, BIH Academy, Clinician Scientist Program, Berlin, Germany.,Charité - Universitätsmedizin Berlin, Department of Psychiatry and Psychotherapy, Campus Benjamin Franklin, Berlin, Germany
| | - G M Panagiotaropoulou
- Charité - Universitätsmedizin Berlin, Department of Psychiatry and Psychotherapy, Campus Charité Mitte, Berlin, Germany
| | - V P Nguyen
- Department of Psychiatry, Hanoi Medical University, Hà Nội, Việt Nam
| | - T H Nguyen
- Department of Psychiatry, Hanoi Medical University, Hà Nội, Việt Nam.,Charité - Universitätsmedizin Berlin, Department of Psychiatry and Psychotherapy, Campus Benjamin Franklin, Berlin, Germany
| | - V Trubetskoy
- Charité - Universitätsmedizin Berlin, Department of Psychiatry and Psychotherapy, Campus Charité Mitte, Berlin, Germany
| | - C T Le
- Department of Psychiatry, Hanoi Medical University, Hà Nội, Việt Nam.,National Institute of Mental Health, Bach Mai Hospital, Hà Nội, Việt Nam
| | - T T H Le
- Department of Psychiatry, Hanoi Medical University, Hà Nội, Việt Nam.,National Institute of Mental Health, Bach Mai Hospital, Hà Nội, Việt Nam
| | - X T Pham
- Department of Psychiatry, Hanoi Medical University, Hà Nội, Việt Nam
| | - I Heuser-Collier
- Charité - Universitätsmedizin Berlin, Department of Psychiatry and Psychotherapy, Campus Benjamin Franklin, Berlin, Germany
| | - N H Lam
- Hanoi Mental Hospital, Hà Nội, Việt Nam
| | - K Böge
- Charité - Universitätsmedizin Berlin, Department of Psychiatry and Psychotherapy, Campus Benjamin Franklin, Berlin, Germany
| | - I M Hahne
- Charité - Universitätsmedizin Berlin, Department of Psychiatry and Psychotherapy, Campus Benjamin Franklin, Berlin, Germany
| | - M Bajbouj
- Charité - Universitätsmedizin Berlin, Department of Psychiatry and Psychotherapy, Campus Benjamin Franklin, Berlin, Germany
| | - M M Zierhut
- Berlin Institute of Health, Charité - Universitätsmedizin Berlin, BIH Academy, Clinician Scientist Program, Berlin, Germany.,Charité - Universitätsmedizin Berlin, Department of Psychiatry and Psychotherapy, Campus Benjamin Franklin, Berlin, Germany
| | - E Hahn
- Charité - Universitätsmedizin Berlin, Department of Psychiatry and Psychotherapy, Campus Benjamin Franklin, Berlin, Germany
| | - S Ripke
- Charité - Universitätsmedizin Berlin, Department of Psychiatry and Psychotherapy, Campus Charité Mitte, Berlin, Germany.,Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
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11
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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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12
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Tran LH, Chu PTM, Nguyen TH, La HV, Nguyen HTH, Tran HT, Nguyen HM, Hoang H, Chu HH. Genetic structure and population connection of two Bouyei populations in northern Vietnam based on short tandem repeat analysis. Am J Hum Biol 2021; 34:e23702. [PMID: 34784439 DOI: 10.1002/ajhb.23702] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 10/05/2021] [Accepted: 11/01/2021] [Indexed: 11/07/2022] Open
Abstract
OBJECTIVES Genetic characteristics were investigated based on short tandem repeat (STR) data to assess the relationship between two Vietnamese Bouyei populations in Vietnam. METHODS We collected hair and buccal swab samples from two separate Bouyei populations in the mountainous region of Northern Vietnam, which are the Bo Y in Ha Giang Province and the Tu Di in Lao Cai Province. The study included data of 23 autosomal and 27 Y-chromosome STRs loci of 96 unrelated participants from a total Vietnamese Bouyei population of under 3300 individuals. RESULTS The results showed that these STR markers are valuable for differentiation of individuals and human genetic studies in Vietnamese Bouyei populations. Genetic analysis indicated that Tu Di and Bo Y people were from the same Bouyei population in China. CONCLUSIONS The results supported the official historical records of the region and the classification of the Vietnamese government. Furthermore, the genetic data provided in this study will be helpful in investigating the genetic genealogy evolution and settlement or migration patterns of the Bouyei populations in Vietnam.
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Affiliation(s)
- Linh Huyen Tran
- National Key Laboratory of Gene Technology, Institute of Biotechnology (IBT), Vietnam Academy of Science and Technology (VAST), Hanoi, Vietnam
| | | | - Trang Hong Nguyen
- National Key Laboratory of Gene Technology, Institute of Biotechnology (IBT), Vietnam Academy of Science and Technology (VAST), Hanoi, Vietnam
| | - Hong Viet La
- Hanoi Pedagogical University 2, Vinh Phuc, Vietnam
| | - Hanh Thi Hong Nguyen
- National Key Laboratory of Gene Technology, Institute of Biotechnology (IBT), Vietnam Academy of Science and Technology (VAST), Hanoi, Vietnam
| | - Hoai Thu Tran
- National Key Laboratory of Gene Technology, Institute of Biotechnology (IBT), Vietnam Academy of Science and Technology (VAST), Hanoi, Vietnam
| | | | - Ha Hoang
- National Key Laboratory of Gene Technology, Institute of Biotechnology (IBT), Vietnam Academy of Science and Technology (VAST), Hanoi, Vietnam.,Centre of DNA Identification, IBT, VAST, Hanoi, Vietnam
| | - Hoang Ha Chu
- National Key Laboratory of Gene Technology, Institute of Biotechnology (IBT), Vietnam Academy of Science and Technology (VAST), Hanoi, Vietnam.,Graduate University of Science and Technology, VAST, Hanoi, Vietnam
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13
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Guo J, Wang W, Zhao K, Li G, He G, Zhao J, Yang X, Chen J, Zhu K, Wang R, Ma H, Xu B, Wang C. Genomic insights into
Neolithic
farming‐related migrations in the junction of east and southeast
Asia. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2021. [DOI: 10.1002/ajpa.24434] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Jianxin Guo
- Department of Anthropology and Ethnology, Institute of Anthropology, School of Sociology and Anthropology, State Key Laboratory of Cellular Stress Biology, School of Life Sciences, State Key Laboratory of Marine Environmental Science Xiamen University Xiamen China
| | - Weitao Wang
- Yunnan Modern Forensic Institute Kunming China
| | - Kai Zhao
- Yunnan Modern Forensic Institute Kunming China
| | | | - Guanglin He
- Department of Anthropology and Ethnology, Institute of Anthropology, School of Sociology and Anthropology, State Key Laboratory of Cellular Stress Biology, School of Life Sciences, State Key Laboratory of Marine Environmental Science Xiamen University Xiamen China
| | - Jing Zhao
- Department of Anthropology and Ethnology, Institute of Anthropology, School of Sociology and Anthropology, State Key Laboratory of Cellular Stress Biology, School of Life Sciences, State Key Laboratory of Marine Environmental Science Xiamen University Xiamen China
| | - Xiaomin Yang
- Department of Anthropology and Ethnology, Institute of Anthropology, School of Sociology and Anthropology, State Key Laboratory of Cellular Stress Biology, School of Life Sciences, State Key Laboratory of Marine Environmental Science Xiamen University Xiamen China
| | - Jinwen Chen
- Department of Anthropology and Ethnology, Institute of Anthropology, School of Sociology and Anthropology, State Key Laboratory of Cellular Stress Biology, School of Life Sciences, State Key Laboratory of Marine Environmental Science Xiamen University Xiamen China
| | - Kongyang Zhu
- Department of Anthropology and Ethnology, Institute of Anthropology, School of Sociology and Anthropology, State Key Laboratory of Cellular Stress Biology, School of Life Sciences, State Key Laboratory of Marine Environmental Science Xiamen University Xiamen China
| | - Rui Wang
- Department of Anthropology and Ethnology, Institute of Anthropology, School of Sociology and Anthropology, State Key Laboratory of Cellular Stress Biology, School of Life Sciences, State Key Laboratory of Marine Environmental Science Xiamen University Xiamen China
| | - Hao Ma
- Department of Anthropology and Ethnology, Institute of Anthropology, School of Sociology and Anthropology, State Key Laboratory of Cellular Stress Biology, School of Life Sciences, State Key Laboratory of Marine Environmental Science Xiamen University Xiamen China
| | - Bingying Xu
- Research Center of Biomedical Engineering Kunming Medical University Kunming China
| | - Chuan‐Chao Wang
- Department of Anthropology and Ethnology, Institute of Anthropology, School of Sociology and Anthropology, 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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14
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Luo T, Wang R, Wang CC. Inferring the population structure and admixture history of three Hmong-Mien-speaking Miao tribes from southwest China based on Genome-wide SNP genotyping. Ann Hum Biol 2021; 48:418-429. [PMID: 34763584 DOI: 10.1080/03014460.2021.2005825] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
BACKGROUND Hmong-Mien speaking Miao, also called Hmong, is the sixthlargest ethnic group in mainland China. However, the fine-scale genetic profiles and population history of Miao populations in southwest China, especially in Guizhou province, remain uncharacterised due to a scarcity of samples of genome-wide data from different tribes. AIM To further investigate the population substructure and admixture history of the Guizhou Miao minority. SUBJECTS AND METHODS We collected 29 samples from three Miao tribes of Guizhou province in southwest China and genotyped about 700,000 genome-wide SNPs of each sample. We analysed newly generated data in together with published modern/ancient East Asian populations datasets via a series of population genetic methods, including principal component analysis (PCA), ADMIXTURE, Fst, TreeMix, f-statistics, qpWave, and qpAdm. RESULTS PCA and ADMIXTURE results showed that the three studied Guizhou Miao groups consistently fell on the Hmong-Mien-related genetic cline and were relatively genetically homogeneous, displayingd a genetic affinity with neighbouring Tai-Kadai speaking populations such as Dong. These results were further confirmed by the observed genetic clade in Fst, TreeMix, outgroup-f3 -statistics, and f4 -statistics. Furthermore, f4 -based allele sharing patterns illustrated that compared with Hunan Miao in central China, Guizhou Miao shared more alleles with Hmong-Mien-speaking Vietnam Hmong and Tai-Kadai-speaking CoLao, Dong, while exhibiting less northeast Asian-related ancestry. Admixture-f3 and f4 statistics revealed the North-South admixture pattern for the studied Guizhou Miao. A qpAdm-based two-way admixture model further revealed that the studied Guizhou Miao harboured 44%∼55.4% indigenous Austronesian-speaking Atayal-related ancestry and 44.6%∼56% Late Neolithic Yellow River farmer-related ancestry. CONCLUSIONS The population structure within Hmong-Mien-related populations showed a geographic correlation. Hmong-Mien speaking Hunan Miao, Guizhou Miao, and Vietnam Hmong presented closer genetic relationships although they dwelt in different regions, suggesting the preservation of the original Hmong-related genetic diversity. The results based on genome-wide SNPs data generally matched the migration history for the Miao population. Our study contributes to a better knowledge of Miao populations and the population structure in southwest China.
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Affiliation(s)
- Ting Luo
- Department of Anthropology and Ethnology, Institute of Anthropology, School of Sociology and Anthropology, Xiamen University, Xiamen, China
| | - Rui Wang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China
| | - Chuan-Chao Wang
- Department of Anthropology and Ethnology, Institute of Anthropology, School of Sociology and Anthropology, Xiamen University, Xiamen, China.,State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China.,State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, China
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15
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An in-depth analysis of the mitochondrial phylogenetic landscape of Cambodia. Sci Rep 2021; 11:10816. [PMID: 34031453 PMCID: PMC8144189 DOI: 10.1038/s41598-021-90145-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 05/07/2021] [Indexed: 11/08/2022] Open
Abstract
Cambodia harbours a variety of human aboriginal populations that have scarcely been studied in terms of genetic diversity of entire mitochondrial genomes. Here we present the matrilineal gene pool of 299 Cambodian refugees from three different ethnic groups (Cham, Khmer, and Khmer Loeu) deriving from 16 Cambodian districts. After establishing a DNA-saving high-throughput strategy for mitochondrial whole-genome Sanger sequencing, a HaploGrep based workflow was used for quality control, haplogroup classification and phylogenetic reconstruction. The application of diverse phylogenetic algorithms revealed an exciting picture of the genetic diversity of Cambodia, especially in relation to populations from Southeast Asia and from the whole world. A total of 224 unique haplotypes were identified, which were mostly classified under haplogroups B5a1, F1a1, or categorized as newly defined basal haplogroups or basal sub-branches of R, N and M clades. The presence of autochthonous maternal lineages could be confirmed as reported in previous studies. The exceptional homogeneity observed between and within the three investigated Cambodian ethnic groups indicates genetic isolation of the whole population. Between ethnicities, genetic barriers were not detected. The mtDNA data presented here increases the phylogenetic resolution in Cambodia significantly, thereby highlighting the need for an update of the current human mtDNA phylogeny.
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Liu D, Duong NT, Ton ND, Van Phong N, Pakendorf B, Van Hai N, Stoneking M. Extensive Ethnolinguistic Diversity in Vietnam Reflects Multiple Sources of Genetic Diversity. Mol Biol Evol 2021; 37:2503-2519. [PMID: 32344428 PMCID: PMC7475039 DOI: 10.1093/molbev/msaa099] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Vietnam features extensive ethnolinguistic diversity and occupies a key position in Mainland Southeast Asia. Yet, the genetic diversity of Vietnam remains relatively unexplored, especially with genome-wide data, because previous studies have focused mainly on the majority Kinh group. Here, we analyze newly generated genome-wide single-nucleotide polymorphism data for the Kinh and 21 additional ethnic groups in Vietnam, encompassing all five major language families in Mainland Southeast Asia. In addition to analyzing the allele and haplotype sharing within the Vietnamese groups, we incorporate published data from both nearby modern populations and ancient samples for comparison. In contrast to previous studies that suggested a largely indigenous origin for Vietnamese genetic diversity, we find that Vietnamese ethnolinguistic groups harbor multiple sources of genetic diversity that likely reflect different sources for the ancestry associated with each language family. However, linguistic diversity does not completely match genetic diversity: There have been extensive interactions between the Hmong-Mien and Tai-Kadai groups; different Austro-Asiatic groups show different affinities with other ethnolinguistic groups; and we identified a likely case of cultural diffusion in which some Austro-Asiatic groups shifted to Austronesian languages during the past 2,500 years. Overall, our results highlight the importance of genome-wide data from dense sampling of ethnolinguistic groups in providing new insights into the genetic diversity and history of an ethnolinguistically diverse region, such as Vietnam.
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Affiliation(s)
- Dang Liu
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Nguyen Thuy Duong
- Institute of Genome Research, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Nguyen Dang Ton
- Institute of Genome Research, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Nguyen Van Phong
- Institute of Genome Research, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Brigitte Pakendorf
- Laboratoire Dynamique du Langage, UMR5596, CNRS & Université de Lyon, Lyon, France
| | - Nong Van Hai
- Institute of Genome Research, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Mark Stoneking
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
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Sun J, Li YX, Ma PC, Yan S, Cheng HZ, Fan ZQ, Deng XH, Ru K, Wang CC, Chen G, Wei LH. Shared paternal ancestry of Han, Tai-Kadai-speaking, and Austronesian-speaking populations as revealed by the high resolution phylogeny of O1a-M119 and distribution of its sub-lineages within China. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2021; 174:686-700. [PMID: 33555039 DOI: 10.1002/ajpa.24240] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Revised: 01/06/2021] [Accepted: 01/12/2021] [Indexed: 12/27/2022]
Abstract
OBJECTIVES The aim of this research was to explore the origin, diversification, and demographic history of O1a-M119 over the past 10,000 years, as well as its role during the formation of East Asian and Southeast Asian populations, particularly the Han, Tai-Kadai-speaking, and Austronesian-speaking populations. MATERIALS AND METHODS Y-chromosome sequences (n = 141) of the O1a-M119 lineage, including 17 newly generated in this study, were used to reconstruct a revised phylogenetic tree with age estimates, and identify sub-lineages. The geographic distribution of 12 O1a-M119 sub-lineages was summarized, based on 7325 O1a-M119 individuals identified among 60,009 Chinese males. RESULTS A revised phylogenetic tree, age estimation, and distribution maps indicated continuous expansion of haplogroup O1a-M119 over the past 10,000 years, and differences in demographic history across geographic regions. We propose several sub-lineages of O1a-M119 as founding paternal lineages of Han, Tai-Kadai-speaking, and Austronesian-speaking populations. The sharing of several young O1a-M119 sub-lineages with expansion times less than 6000 years between these three population groups supports a partial common ancestry for them in the Neolithic Age; however, the paternal genetic divergence pattern is much more complex than previous hypotheses based on ethnology, archeology, and linguistics. DISCUSSION Our analyses contribute to a better understanding of the demographic history of O1a-M119 sub-lineages over the past 10,000 years during the emergence of Han, Austronesians, Tai-Kadai-speaking populations. The data described in this study will assist in understanding of the history of Han, Tai-Kadai-speaking, and Austronesian-speaking populations from ethnology, archeology, and linguistic perspectives in the future.
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Affiliation(s)
- Jin Sun
- Xingyi Normal University for Nationalities, Xingyi, China
- Department of Anthropology and Ethnology, Institute of Anthropology, School of Sociology and Anthropology, Xiamen University, Xiamen, China
| | - Ying-Xiang Li
- Department of Anthropology and Ethnology, Institute of Anthropology, School of Sociology and Anthropology, Xiamen University, Xiamen, China
| | - Peng-Cheng Ma
- School of Life Sciences, Jilin University, Changchun, China
| | - Shi Yan
- School of Ethnology and Sociology, Minzu University of China, Beijing, China
| | - Hui-Zhen Cheng
- Department of Anthropology and Ethnology, Institute of Anthropology, School of Sociology and Anthropology, Xiamen University, Xiamen, China
| | - Zhi-Quan Fan
- Department of Anthropology and Ethnology, Institute of Anthropology, School of Sociology and Anthropology, Xiamen University, Xiamen, China
| | - Xiao-Hua Deng
- Department of Anthropology and Ethnology, Institute of Anthropology, School of Sociology and Anthropology, Xiamen University, Xiamen, China
- Center for collation and studies of Fujian local literature, Fujian University of Technology, Fuzhou, China
| | - Kai Ru
- Enlighten Co., Ltd., Shanghai, China
| | - Chuan-Chao Wang
- Department of Anthropology and Ethnology, Institute of Anthropology, School of Sociology and Anthropology, Xiamen University, Xiamen, China
| | - Gang Chen
- Hunan Key Lab of Bioinformatics, School of Computer Science and Engineering, Central South University, Changsha, China
| | - Lan-Hai Wei
- Department of Anthropology and Ethnology, Institute of Anthropology, School of Sociology and Anthropology, Xiamen University, Xiamen, China
- B&R International Joint Laboratory for Eurasian Anthropology, Fudan University, Shanghai, China
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Kutanan W, Shoocongdej R, Srikummool M, Hübner A, Suttipai T, Srithawong S, Kampuansai J, Stoneking M. Cultural variation impacts paternal and maternal genetic lineages of the Hmong-Mien and Sino-Tibetan groups from Thailand. Eur J Hum Genet 2020; 28:1563-1579. [PMID: 32690935 PMCID: PMC7576213 DOI: 10.1038/s41431-020-0693-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2020] [Revised: 06/17/2020] [Accepted: 06/26/2020] [Indexed: 11/09/2022] Open
Abstract
The Hmong-Mien (HM) and Sino-Tibetan (ST) speaking groups are known as hill tribes in Thailand; they were the subject of the first studies to show an impact of patrilocality vs. matrilocality on patterns of mitochondrial (mt) DNA vs. male-specific portion of the Y chromosome (MSY) variation. However, HM and ST groups have not been studied in as much detail as other Thai groups; here we report and analyze 234 partial MSY sequences (∼2.3 mB) and 416 complete mtDNA sequences from 14 populations that, when combined with our previous published data, provides the largest dataset yet for the hill tribes. We find a striking difference between Hmong and IuMien (Mien-speaking) groups: the Hmong are genetically different from both the IuMien and all other Thai groups, whereas the IuMien are genetically more similar to other linguistic groups than to the Hmong. In general, we find less of an impact of patrilocality vs. matrilocality on patterns of mtDNA vs. MSY variation than previous studies. However, there is a dramatic difference in the frequency of MSY and mtDNA lineages of Northeast Asian (NEA) origin vs. Southeast Asian (SEA) origin in HM vs. ST groups: HM groups have high frequencies of NEA MSY lineages but lower frequencies of NEA mtDNA lineages, while ST groups show the opposite. A potential explanation is that the ancestors of Thai HM groups were patrilocal, while the ancestors of Thai ST groups were matrilocal. Overall, these results attest to the impact of cultural practices on patterns of mtDNA vs. MSY variation.
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Affiliation(s)
- Wibhu Kutanan
- Department of Biology, Faculty of Science, Khon Kaen University, Khon Kaen, 40002, Thailand. .,Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103, Leipzig, Germany.
| | - Rasmi Shoocongdej
- Department of Archaeology, Faculty of Archaeology, Silpakorn University, Bangkok, 10200, Thailand
| | - Metawee Srikummool
- Department of Biochemistry, Faculty of Medical Science, Naresuan University, Phitsanulok, 65000, Thailand
| | - Alexander Hübner
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103, Leipzig, Germany
| | - Thanatip Suttipai
- Department of Biology, Faculty of Science, Khon Kaen University, Khon Kaen, 40002, Thailand
| | - Suparat Srithawong
- Department of Biology, Faculty of Science, Khon Kaen University, Khon Kaen, 40002, Thailand
| | - Jatupol Kampuansai
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, 50202, Thailand.,Research Center in Bioresources for Agriculture, Industry and Medicine, Chiang Mai University, Chiang Mai, 50202, Thailand
| | - Mark Stoneking
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103, Leipzig, Germany.
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