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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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2
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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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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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4
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Lin M, Trejaut JA. Diversity and distribution of mitochondrial DNA in non-Austronesian-speaking Taiwanese individuals. Hum Genome Var 2023; 10:2. [PMID: 36653363 PMCID: PMC9849472 DOI: 10.1038/s41439-022-00228-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 11/12/2022] [Accepted: 11/22/2022] [Indexed: 01/19/2023] Open
Abstract
Many studies have described the diversity of Austronesian-speaking Taiwanese people to shed more light on their origin and their connection with the "Out of Taiwan" migrations. However, the genetic relationship between the non-Austronesian-speaking groups of Taiwan and the populations of continental Asia is still unclear. Here, we studied the diversity of mtDNA in 767 non-Austronesian speakers from 16 locations in Taiwan using partial sequencing obtained from the hypervariable segment I (HVS-I) and coding regions 8,001-9,000 and 9.801-10,900 and 85 complete mtDNA genome sequences. Bayesian analysis of population structure was used to examine their relationship with over 3662 individuals representing indigenous groups of Taiwan, continental East Asia, Japan, and Island Southeast Asia. The whole analysis identified 278 haplotypes. Complete genomes revealed 62 novel subhaplogroups, of which 31 were exclusive to Taiwan. Estimates of coalescence times of all subhaplogroups showed peaks of diversification greater than 5.0 kya, likely characterizing gene flow from continental East Asian groups but not excluding in situ Taiwanese ancestry. Furthermore, a significant number of clades exclusive to non-Austronesian speakers of Taiwan (NAN_Tw) showed coalescence peaks between 1.0 and 2.6 kya, suggesting possible late Neolithic to early metal age settlements of NAN_Tw and local expansion in Taiwan.
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Affiliation(s)
- Marie Lin
- Molecular Anthropology and Transfusion Medicine Research Laboratory, Mackay Memorial Hospital, Taipei, Taiwan.
| | - Jean A Trejaut
- Molecular Anthropology and Transfusion Medicine Research Laboratory, Mackay Memorial Hospital, Taipei, Taiwan.
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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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6
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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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7
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Xu R, Aranday-Cortes E, Leitch ECM, Hughes J, Singer JB, Sreenu V, Tong L, da Silva Filipe A, Bamford CGG, Rong X, Huang J, Wang M, Fu Y, McLauchlan J. The evolutionary dynamics and epidemiological history of hepatitis C virus genotype 6, including unique strains from the Li community of Hainan Island, China. Virus Evol 2022; 8:veac012. [PMID: 35600095 PMCID: PMC9115904 DOI: 10.1093/ve/veac012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 01/17/2022] [Accepted: 02/15/2022] [Indexed: 12/09/2022] Open
Abstract
Hepatitis C virus (HCV) is a highly diverse pathogen that frequently establishes a chronic long-term infection, but the origins and drivers of HCV diversity in the human population remain unclear. Previously unidentified strains of HCV genotype 6 (gt6) were recently discovered in chronically infected individuals of the Li ethnic group living in Baisha County, Hainan Island, China. The Li community, who were early settlers on Hainan Island, has a distinct host genetic background and cultural identity compared to other ethnic groups on the island and mainland China. In this report, we generated 33 whole virus genome sequences to conduct a comprehensive molecular epidemiological analysis of these novel gt6 strains in the context of gt6 isolates present in Southeast Asia. With the exception of one gt6a isolate, the Li gt6 sequences formed three novel clades from two lineages which constituted 3 newly assigned gt6 subtypes and 30 unassigned strains. Using Bayesian inference methods, we dated the most recent common ancestor for all available gt6 whole virus genome sequences to approximately 2767 bce (95 per cent highest posterior density (HPD) intervals, 3670-1397 bce), which is far earlier than previous estimates. The substitution rate was 1.20 × 10-4 substitutions/site/year (s/s/y), and this rate varied across the genome regions, from 1.02 × 10-5 s/s/y in the 5'untranslated region (UTR) region to 3.07 × 10-4 s/s/y in E2. Thus, our study on an isolated ethnic minority group within a small geographical area of Hainan Island has substantially increased the known diversity of HCV gt6, already acknowledged as the most diverse HCV genotype. The extant HCV gt6 sequences from this study were probably transmitted to the Li through at least three independent events dating perhaps from around 4,000 years ago. This analysis describes deeper insight into basic aspects of HCV gt6 molecular evolution including the extensive diversity of gt6 sequences in the isolated Li ethnic group.
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Affiliation(s)
| | - Elihu Aranday-Cortes
- MRC-University of Glasgow Centre for Virus Research, Sir Michael Stoker Building, Garscube Campus, 464 Bearsden Road, Glasgow G61 1QH, UK
| | - E Carol McWilliam Leitch
- MRC-University of Glasgow Centre for Virus Research, Sir Michael Stoker Building, Garscube Campus, 464 Bearsden Road, Glasgow G61 1QH, UK
| | - Joseph Hughes
- MRC-University of Glasgow Centre for Virus Research, Sir Michael Stoker Building, Garscube Campus, 464 Bearsden Road, Glasgow G61 1QH, UK
| | - Joshua B Singer
- MRC-University of Glasgow Centre for Virus Research, Sir Michael Stoker Building, Garscube Campus, 464 Bearsden Road, Glasgow G61 1QH, UK
| | - Vattipally Sreenu
- MRC-University of Glasgow Centre for Virus Research, Sir Michael Stoker Building, Garscube Campus, 464 Bearsden Road, Glasgow G61 1QH, UK
| | - Lily Tong
- MRC-University of Glasgow Centre for Virus Research, Sir Michael Stoker Building, Garscube Campus, 464 Bearsden Road, Glasgow G61 1QH, UK
| | - Ana da Silva Filipe
- MRC-University of Glasgow Centre for Virus Research, Sir Michael Stoker Building, Garscube Campus, 464 Bearsden Road, Glasgow G61 1QH, UK
| | - Connor G G Bamford
- MRC-University of Glasgow Centre for Virus Research, Sir Michael Stoker Building, Garscube Campus, 464 Bearsden Road, Glasgow G61 1QH, UK
| | - Xia Rong
- Guangzhou Blood Center, Institute of Clinical Blood Transfusion, Guangzhou Blood Center, 31 LuYuan Road, Guangzhou, Guangdong 510095, P.R. China
| | - Jieting Huang
- Guangzhou Blood Center, Institute of Clinical Blood Transfusion, Guangzhou Blood Center, 31 LuYuan Road, Guangzhou, Guangdong 510095, P.R. China
| | - Min Wang
- Guangzhou Blood Center, Institute of Clinical Blood Transfusion, Guangzhou Blood Center, 31 LuYuan Road, Guangzhou, Guangdong 510095, P.R. China
| | - Yongshui Fu
- Guangzhou Blood Center, Institute of Clinical Blood Transfusion, Guangzhou Blood Center, 31 LuYuan Road, Guangzhou, Guangdong 510095, P.R. China
| | - John McLauchlan
- MRC-University of Glasgow Centre for Virus Research, Sir Michael Stoker Building, Garscube Campus, 464 Bearsden Road, Glasgow G61 1QH, UK
- Guangzhou Blood Center, Institute of Clinical Blood Transfusion, Guangzhou Blood Center, 31 LuYuan Road, Guangzhou, Guangdong 510095, P.R. China
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8
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Tao Y, Chen B, Kang M, Liu Y, Wang J. Genome-Wide Evidence for Complex Hybridization and Demographic History in a Group of Cycas From China. Front Genet 2021; 12:717200. [PMID: 34527022 PMCID: PMC8435751 DOI: 10.3389/fgene.2021.717200] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2021] [Accepted: 08/10/2021] [Indexed: 11/24/2022] Open
Abstract
Cycads represent one of the most ancestral living seed plants as well as one of the most threatened plant groups in the world. South China is a major center and potential origin of Cycas, the most rapidly diversified lineage of cycads. However, genomic-wide diversity of Cycas remains poorly understood due to the challenge of generating genomic markers associated with their inherent large genomes. Here, we perform a comprehensive conservation genomic study based on restriction-site associated DNA sequencing (RADseq) data in six representative species of Cycas in South China. Consistently low genetic diversity and strong genetic differentiation were detected across species. Both phylogenetic inference and genetic structure analysis via several methods revealed generally congruent groups among the six Cycas species. The analysis with ADMIXTURE showed low mixing of genetic composition among species, while individuals of C. dolichophylla exhibited substantial genetic admixture with C. bifida, C. changjiangensis, and C. balansae. Furthermore, the results from Treemix, f4-statistic, and ABBA-BABA test were generally consistent and revealed the complex patterns of interspecific gene flow. Relatively strong signals of hybridization were detected between C. dolichophylla and C. szechuanensis, and the ancestor of C. taiwaniana and C. changjiangensis. Distinct patterns of demographic history were inferred for these species by Stairway Plot, and our results suggested that both climate fluctuation and frequent geological activities during the late Pleistocene exerted deep impacts on the population dynamics of these species in South China. Finally, we explore the practical implications of our findings for the development of conservation strategies in Cycas. The present study demonstrates the efficiency of RADseq for conservation genomic studies on non-model species with large and complex genomes. Given the great significance of cycads as a radical transition in the evolution of plant biodiversity, our study provides important insights into the mechanisms of diversification in such recently radiated living fossil taxa.
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Affiliation(s)
- Yueqi Tao
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Bin Chen
- Shanghai Chenshan Botanical Garden, Shanghai, China.,Eastern China Conservation Center for Wild Endangered Plant Resources, Shanghai, China
| | - Ming Kang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China.,Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou, China
| | - Yongbo Liu
- State Environment Protection Key Laboratory of Regional Ecological Process and Functional Assessment, Chinese Research Academy of Environmental Sciences, Beijing, China
| | - Jing Wang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China.,Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou, China
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9
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Nizamani MM, Harris AJ, Cheng X, Zhu Z, Jim CY, Wang H. Positive relationships among aboveground biomass, tree species diversity, and urban greening management in tropical coastal city of Haikou. Ecol Evol 2021; 11:12204-12219. [PMID: 34522371 PMCID: PMC8427621 DOI: 10.1002/ece3.7985] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 07/15/2021] [Accepted: 07/21/2021] [Indexed: 01/19/2023] Open
Abstract
Within urban green spaces, tree species diversity is believed to correlate with aboveground biomass, though there is some disagreement within the literature on the strength and directionality of the relationship. Therefore, we assessed the relationship between the biodiversity of woody species and the aboveground biomass of woody plant species in the tropical, coastal city of Haikou in southern China. To accomplish this, we obtained comprehensive tree and site data through field sampling of 190 urban functional units (UFUs, or work units) corresponding to six types of land uses governmental-institutional, industrial-commercial, park-recreational, residential, transport infrastructure, and undeveloped area. Based on our field data, we investigated the relationship between tree species diversity and aboveground biomass using multiple regression, which revealed significant relationships across all five types of land uses. Aboveground biomass in green spaces was also correlated with anthropogenic factors, especially time since urban development, or site age, annual maintenance frequency by human caretakers, and human population density. Among these factors, maintenance is the strongest predictor of aboveground biomass in urban green space. Therefore, this study highlights the critical role of maintenance of urban green space in promoting both aboveground biomass and woody biodiversity in urban ecosystems and, consequently, on urban ecosystem services. Our findings contribute to a deeper understanding of the ecosystem services provided by communities of woody plant species in urban areas.
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Affiliation(s)
- Mir Muhammad Nizamani
- Key Laboratory of Tropical Biological Resources of Ministry of EducationCollege of Tropical CropsHainan UniversityHaikouChina
| | - AJ Harris
- Key Laboratory of Plant Resources Conservation and Sustainable UtilizationSouth China Botanical GardenChinese Academy of ScienceGuangzhouChina
| | - Xia‐Lan Cheng
- Key Laboratory of Tropical Biological Resources of Ministry of EducationCollege of Tropical CropsHainan UniversityHaikouChina
| | - Zhi‐Xin Zhu
- Key Laboratory of Tropical Biological Resources of Ministry of EducationCollege of Tropical CropsHainan UniversityHaikouChina
| | - Chi Yung Jim
- Department of Social SciencesEducation University of Hong KongHong KongChina
| | - Hua‐Feng Wang
- Key Laboratory of Tropical Biological Resources of Ministry of EducationCollege of Tropical CropsHainan UniversityHaikouChina
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10
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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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11
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Chen C, Li Y, Tao R, Jin X, Guo Y, Cui W, Chen A, Yang Y, Zhang X, Zhang J, Li C, Zhu B. The Genetic Structure of Chinese Hui Ethnic Group Revealed by Complete Mitochondrial Genome Analyses Using Massively Parallel Sequencing. Genes (Basel) 2020; 11:E1352. [PMID: 33202591 PMCID: PMC7698084 DOI: 10.3390/genes11111352] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2020] [Revised: 11/03/2020] [Accepted: 11/09/2020] [Indexed: 01/10/2023] Open
Abstract
Mitochondrial DNA (mtDNA), coupled with maternal inheritance and relatively high mutation rates, provides a pivotal way for us to investigate the formation histories of populations. The Hui minority with Islamic faith is one of the most widely distributed ethnic groups in China. However, the exploration of Hui's genetic architecture from the complete mitochondrial genome perspective has not been detected yet. Therefore, in this study, we employed the complete mitochondrial genomes of 98 healthy and unrelated individuals from Northwest China, as well as 99 previously published populations containing 7274 individuals from all over the world as reference data, to comprehensively dissect the matrilineal landscape of Hui group. Our results demonstrated that Hui group exhibited closer genetic relationships with Chinese Han populations from different regions, which was largely attributable to the widespread of haplogroups D4, D5, M7, B4, and F1 in these populations. The demographic expansion of Hui group might occur during the Late Pleistocene. Finally, we also found that Hui group might have gene exchanges with Uygur, Tibetan, and Tajik groups in different degrees and retained minor genetic imprint of European-specific lineages, therefore, hinting the existence of multi-ethnic integration events in shaping the genetic landscape of Chinese Hui group.
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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; (C.C.); (X.J.); (Y.G.); (X.Z.)
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Science, Ministry of Justice, Shanghai 200063, China; (R.T.); (A.C.); (Y.Y.); (J.Z.)
- Multi-Omics Innovative Research Center of Forensic Identification, Department of Forensic Genetics, School of Forensic Medicine, Southern Medical University, Guangzhou 510515, China;
| | - Yuchun Li
- State Key Laboratory of Genetic Resources and Evolution/Key Laboratory of Healthy Aging Research of Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China;
| | - Ruiyang Tao
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Science, Ministry of Justice, Shanghai 200063, China; (R.T.); (A.C.); (Y.Y.); (J.Z.)
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610017, China
| | - Xiaoye Jin
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi’an Jiaotong University, Xi’an 710004, China; (C.C.); (X.J.); (Y.G.); (X.Z.)
| | - Yuxin Guo
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi’an Jiaotong University, Xi’an 710004, China; (C.C.); (X.J.); (Y.G.); (X.Z.)
| | - Wei Cui
- Multi-Omics Innovative Research Center of Forensic Identification, Department of Forensic Genetics, School of Forensic Medicine, Southern Medical University, Guangzhou 510515, China;
| | - Anqi Chen
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Science, Ministry of Justice, Shanghai 200063, China; (R.T.); (A.C.); (Y.Y.); (J.Z.)
- Department of Forensic Medicine, Shanghai Medical College of Fudan University, Shanghai 200032, China
| | - Yue Yang
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Science, Ministry of Justice, Shanghai 200063, China; (R.T.); (A.C.); (Y.Y.); (J.Z.)
- School of Basic Medicine, Inner Mongolia Medical University, Hohhot 010030, China
| | - Xingru Zhang
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi’an Jiaotong University, Xi’an 710004, China; (C.C.); (X.J.); (Y.G.); (X.Z.)
| | - Jingyi Zhang
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Science, Ministry of Justice, Shanghai 200063, China; (R.T.); (A.C.); (Y.Y.); (J.Z.)
| | - Chengtao Li
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Science, Ministry of Justice, Shanghai 200063, China; (R.T.); (A.C.); (Y.Y.); (J.Z.)
- Multi-Omics Innovative Research Center of Forensic Identification, Department of Forensic Genetics, School of Forensic Medicine, Southern Medical University, Guangzhou 510515, China;
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610017, China
- Department of Forensic Medicine, Shanghai Medical College of Fudan University, Shanghai 200032, China
- School of Basic Medicine, Inner Mongolia Medical University, Hohhot 010030, China
| | - Bofeng Zhu
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi’an Jiaotong University, Xi’an 710004, China; (C.C.); (X.J.); (Y.G.); (X.Z.)
- Multi-Omics Innovative Research Center of Forensic Identification, Department of Forensic Genetics, School of Forensic Medicine, Southern Medical University, Guangzhou 510515, China;
- College of Forensic Medicine, Xi’an Jiaotong University Health Science Center, Xi’an 710061, China
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12
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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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13
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Inferring the population history of Tai-Kadai-speaking people and southernmost Han Chinese on Hainan Island by genome-wide array genotyping. Eur J Hum Genet 2020; 28:1111-1123. [PMID: 32123326 DOI: 10.1038/s41431-020-0599-7] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 12/19/2019] [Accepted: 02/04/2020] [Indexed: 11/08/2022] Open
Abstract
Hainan Island, located between East Asia and Southeast Asia, represents an ideal region for the study of the genetic architecture of geographically isolated populations. However, the genetic structure and demographic history of the indigenous Tai-Kadai-speaking Hlai people and recent expanded southernmost Han Chinese on this island are poorly characterized due to a lack of genetic data. Thus, we collected and genotyped 36 Qiongzhong Hlai and 48 Haikou Han individuals at 497,637 single nucleotide polymorphisms (SNPs). We applied principal component analysis, ADMIXTURE, symmetrical D-statistics, admixture-f3 statistics, qpWave, and qpAdm analysis to infer the population history. Our results revealed the East Asian populations are characterized by a north-south genetic cline with Hlai at the southernmost end. We have not detected recent gene flow from neighboring populations into Hlai, therefore, we used Hlai as an unadmixed proxy to model the admixture history of mainland Tai-Kadai-speaking populations and southern Han Chinese. The mainland Tai-Kadai-speaking populations are suggested deriving a larger number of their ancestry from Hlai-related lineage, but also having admixture from South Asian-related or other neighboring populations. The Hlai group is also suggested to contribute about half of the ancestry to Han Chinese in Hainan. The complex patterns of genetic structure in East Asia were shaped via language categories, geographical boundaries, and large southward population movements with language dispersal and agriculture propagation.
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14
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Liu J, Du W, Wang M, Liu C, Wang S, He G, Wang Z. Forensic features, genetic diversity and structure analysis of three Chinese populations using 47 autosomal InDels. Forensic Sci Int Genet 2019; 45:102227. [PMID: 31865224 DOI: 10.1016/j.fsigen.2019.102227] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Revised: 12/08/2019] [Accepted: 12/16/2019] [Indexed: 12/31/2022]
Abstract
Insertion/deletion polymorphisms (InDels), which combine the desirable features of both short tandem repeats (STRs) and single-nucleotide polymorphisms (SNPs), have become widely used genetic markers for forensic investigations, anthropology and population genetics. The AGCU InDel 50 kit is a newly developed panel that contains 47 autosomal InDels (A-InDels), 2 Y-chromosomal InDels (Y-InDels) and Amelogenin and is designed to provide a higher discriminatory power in Chinese populations compared with the Qiagen DIPplex kit. In this study, 542 unrelated individuals were first genotyped to evaluate the forensic efficiency of this novel panel in three Chinese ethnicities (Hainan Han, Hainan Li and Zunyi Gelao groups). Additionally, genetic relationships among the three investigated populations (geographically close but linguistically different populations: Han and Li; geographically diverse but from the same language family: Li and Gelao) and 31 worldwide populations were analyzed using pairwise genetic distances, multidimensional scaling (MDS), phylogenetic tree, principal component analysis (PCA) and STRUCTURE. The combined powers of discrimination (CPD) for the Han, Li and Gelao groups were 0.999999999999999999635, 0.999999999999999997668 and 0.999999999999999999840, respectively, and the combined powers of exclusion (CPE) were 0.999715, 0.999283 and 0.999575, respectively. The genetic relationship between the Hainan Han and Zunyi Gelao groups was relatively closer than that between the Hainan Li and Zunyi Gelao groups, demonstrating that there was little gene communication between Li and Han living on Hainan Island as well as between Li and Gelao in the Tai-Kadai language family. The aforementioned results suggest that the AGCU InDel 50 kit is an effective tool that is appropriate for personal identification and population genetics.
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Affiliation(s)
- Jing Liu
- Institute of Forensic Medicine, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Weian Du
- School of Forensic Medicine, Southern Medical University, Guangzhou 510515, China; AGCU ScienTech Incorporation, Wuxi 214174, China
| | - Mengge Wang
- Institute of Forensic Medicine, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Changhui Liu
- Guangzhou Forensic Science Institute, Guangzhou 510000, China
| | - Shouyu Wang
- Institute of Forensic Medicine, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Guanglin He
- Institute of Forensic Medicine, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Zheng Wang
- Institute of Forensic Medicine, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu 610041, China.
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15
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Liu J, Ye Z, Wang Z, Zou X, He G, Wang M, Wang S, Hou Y. Genetic diversity and phylogenetic analysis of Chinese Han and Li ethnic populations from Hainan Island by 30 autosomal insertion/deletion polymorphisms. Forensic Sci Res 2019; 7:189-195. [PMID: 35784419 PMCID: PMC9245983 DOI: 10.1080/20961790.2019.1672933] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
With the characteristics of low mutation rate, length variation and short amplicon size, insertion/deletion polymorphisms (InDels) have the advantages of both short tandem repeats (STRs) and single nucleotide polymorphisms (SNPs). Herein, people of two ethnicities from Hainan Island were genotyped for the first time using the Investigator DIPplex kit. We investigated the forensic parameters of the 30 InDels and the phylogenetic relationships among different populations. The accumulated powers of discrimination and powers of exclusion were 0.999 999 999 9646 and 0.9897 in the Hainan Han population and 0.999 999 999 9292 and 0.9861 in the Hainan Li population, respectively. Additionally, population comparisons among geographically, ethnically and linguistically diverse populations via cluster heatmap, multidimensional scaling, principal component analysis, phylogenetic tree and STRUCTURE analyses demonstrated that the Hainan Han population had genetic similarities to the other Han, She and Tujia populations, while the Hainan Li population had close genetic relationships to the Zhuang and Miao groups; both populations had a high degree of genetic differentiation from most Turkic-speaking populations. Aforementioned results suggested that the 30 autosomal InDels are highly polymorphic and informative, which are suitable for human identification and population genetics. Four hundred and forty-five Chinese individuals from two ethnicities (Hainan Han and Hainan Li) were firstly analyzed by 30 autosomal InDels included in the Investigator DIPplex panel. Forensic parameters of the 30 InDels in the two populations showed high polymorphism and universality for human identification purposes. The Investigator DIPplex panel had a certain capacity of differentiating intercontinental populations and different language populations.
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Affiliation(s)
- Jing Liu
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, China
| | - Ziwei Ye
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, China
| | - Zheng Wang
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, China
| | - Xing Zou
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, China
| | - Guanglin He
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, China
| | - Mengge Wang
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, China
| | - Shouyu Wang
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, China
| | - Yiping Hou
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, China
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16
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Genetic polymorphism of 30 autosomal InDel loci in Chinese Hainan Li population. FORENSIC SCIENCE INTERNATIONAL GENETICS SUPPLEMENT SERIES 2019. [DOI: 10.1016/j.fsigss.2019.09.042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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17
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Wang M, Wang Z, He G, Wang S, Zou X, Liu J, Wang F, Ye Z, Hou Y. Whole mitochondrial genome analysis of highland Tibetan ethnicity using massively parallel sequencing. Forensic Sci Int Genet 2019; 44:102197. [PMID: 31756629 DOI: 10.1016/j.fsigen.2019.102197] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Revised: 10/29/2019] [Accepted: 10/30/2019] [Indexed: 01/12/2023]
Abstract
Mitochondrial DNA (mtDNA) is a key player in numerous multifaceted and intricate biological processes and plays a pivotal role in dissecting the peopling of different populations, due to its maternally inherited property and comparatively high mutation rate. In this study, 119 Tibetan individuals from the Muli Tibetan Autonomous County of China (average altitude above 3,000 m) were employed in mitochondrial genome (mitogenome) sequencing by massively parallel sequencing (MPS) techniques using the Precision ID mtDNA Whole Genome Panel on an Ion S5XL system. The dataset presented 88 distinct haplotypes, resulting in the haplotype diversity of 0.9909. The majority of haplotypes were assigned to East Asian lineages and the distribution of haplogroups of Muli Tibetan significantly differed from reference Tibetan populations. The maximum parsimony phylogeny reconstructed by 119 newly generated mitogenomes revealed 12 major Muli Tibetan lineages. Intriguingly, a Sherpa-specific sub-haplogroup A15c1 with the lack of mutations at 4216 and 15,924 was discerned in our dataset, which suggested that the maternal gene pool of Sherpas may derive from Tibetan populations. The shared haplogroups between Muli Tibetan and lowland Han Chinese hinted that these lineages may derive from non-Tibetans and have already differentiated before their arrival on the Tibetan Plateau. Furthermore, extensive pairwise population comparisons displayed that Muli Tibetan had a closer genetic relationship with ethnically or linguistically close Nyingtri Tibetan, Nyingtri Lhoba and Chamdo Tibetan populations. Genetic affinity was also observed between the Muli Tibetan and North Han Chinese. Collectively, the results generated in this study enriched the existing forensic mtDNA database and raised additional interest in the application of whole mitogenome sequencing in forensic investigations.
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Affiliation(s)
- Mengge Wang
- Institute of Forensic Medicine, West China School of Basic Science & Forensic Medicine, Sichuan University, Chengdu, 610041, China
| | - Zheng Wang
- Institute of Forensic Medicine, West China School of Basic Science & Forensic Medicine, Sichuan University, Chengdu, 610041, China
| | - Guanglin He
- Institute of Forensic Medicine, West China School of Basic Science & Forensic Medicine, Sichuan University, Chengdu, 610041, China
| | - Shouyu Wang
- Institute of Forensic Medicine, West China School of Basic Science & Forensic Medicine, Sichuan University, Chengdu, 610041, China
| | - Xing Zou
- Institute of Forensic Medicine, West China School of Basic Science & Forensic Medicine, Sichuan University, Chengdu, 610041, China
| | - Jing Liu
- Institute of Forensic Medicine, West China School of Basic Science & Forensic Medicine, Sichuan University, Chengdu, 610041, China
| | - Fei Wang
- Institute of Forensic Medicine, West China School of Basic Science & Forensic Medicine, Sichuan University, Chengdu, 610041, China
| | - Ziwei Ye
- 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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Zhang L, Zhu S, Yang F, Bai X, Yao Y, Li J. Genetic diversity of 23 STR loci in Guangxi Zhuang population and its phylogenetic relationship with 25 other populations. Ann Hum Biol 2019; 46:502-508. [PMID: 31559867 DOI: 10.1080/03014460.2019.1673481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Aim: To estimate genetic diversity of 23 STR loci included in the DNA TyperTM 25 Kit, and evaluate its effectiveness in forensic application.Subjects and methods: A total of 450 (251 males and 179 females) unrelated healthy individuals from Guangxi Zhuang population were amplified with DNA TyperTM 25 Kit, isolated by the 3730 Series Genetic AnalyzerTM, and genotyped using the GeneMapper ID-X. Genetic parameters and population relationships were analysed.Results: Allele frequencies ranged from 0.001 to 0.5889. The combined power of discrimination (CPD) and the combined power of exclusion (CPE) of the 23 STR loci were 0.999999999999999999 and 0.999996765, respectively. No deviations from Hardy-Weinberg equilibrium and linkage disequilibrium were observed. Inter-population comparison based on Fst, PCA, genetic distance, phylogenetic trees, and MDS showed that Zhuang population clustered with the populations holding a close geographic distance with Zhuang (Guangdong Han and Hainan Li populations).Conclusions: Our study indicated that the 23 autosomal STR loci included in DNA TyperTM 25 Kit can be used as forensic tools for individual identification and parentage testing. Moreover, the result of our mass investigation will enrich the forensic database of Chinese populations and serve for further study of the origin of anthropology.
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Affiliation(s)
- Li Zhang
- Department of Forensic Medicine, Faculty of Basic Medical Sciences, Chongqing Medical University, Chongqing, China
| | - Shisheng Zhu
- Faculty of Medical Technology, Chongqing Medical and Pharmaceutical College, Chongqing, China
| | - Fan Yang
- Institute of Forensic Science, Ministry of Public Security of China, Beijing, China
| | - Xue Bai
- Institute of Forensic Science, Ministry of Public Security of China, Beijing, China
| | - Yiren Yao
- Institute of Forensic Science, Ministry of Public Security of China, Beijing, China
| | - Jianbo Li
- Department of Forensic Medicine, Faculty of Basic Medical Sciences, Chongqing Medical University, Chongqing, China
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19
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Wang Y, Dang Z, Zhang G, Li S, Liu Q, Li C, Hou X, Li H, Chen S, Cui W, Wang D, Kong X, Man D. Genetic diversity and haplotype structure of 27 Y-STR loci in a Han population from Jining, Shandong province, eastern China. Forensic Sci Int Genet 2019; 42:e25-e26. [PMID: 31230972 DOI: 10.1016/j.fsigen.2019.06.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Revised: 05/13/2019] [Accepted: 06/13/2019] [Indexed: 12/09/2022]
Affiliation(s)
- Yequan Wang
- Institute of Forensic Medicine and Laboratory Medicine, Jining Medical University, Forensic Science Center of Jining Medical University, Jining, Shandong, PR China.
| | - Zhen Dang
- Institute of Forensic Medicine and Laboratory Medicine, Jining Medical University, Forensic Science Center of Jining Medical University, Jining, Shandong, PR China
| | - Guoan Zhang
- Institute of Forensic Medicine and Laboratory Medicine, Jining Medical University, Forensic Science Center of Jining Medical University, Jining, Shandong, PR China
| | - Shuyue Li
- Institute of Forensic Medicine and Laboratory Medicine, Jining Medical University, Forensic Science Center of Jining Medical University, Jining, Shandong, PR China
| | - Qi Liu
- Institute of Forensic Medicine and Laboratory Medicine, Jining Medical University, Forensic Science Center of Jining Medical University, Jining, Shandong, PR China
| | - Changzheng Li
- Institute of Forensic Medicine and Laboratory Medicine, Jining Medical University, Forensic Science Center of Jining Medical University, Jining, Shandong, PR China
| | - Xiudi Hou
- Institute of Forensic Medicine and Laboratory Medicine, Jining Medical University, Forensic Science Center of Jining Medical University, Jining, Shandong, PR China
| | - Haibin Li
- Institute of Forensic Medicine and Laboratory Medicine, Jining Medical University, Forensic Science Center of Jining Medical University, Jining, Shandong, PR China
| | - Su Chen
- Institute of Forensic Medicine and Laboratory Medicine, Jining Medical University, Forensic Science Center of Jining Medical University, Jining, Shandong, PR China.
| | - Wen Cui
- Institute of Forensic Medicine and Laboratory Medicine, Jining Medical University, Forensic Science Center of Jining Medical University, Jining, Shandong, PR China.
| | - Dan Wang
- Institute of Forensic Medicine and Laboratory Medicine, Jining Medical University, Jining, Shandong, PR China; College of Pharmaceutical Science, Zhejiang University, Hangzhou, Zhejiang, PR China
| | - Xia Kong
- The First People's Hospital Affiliated to Jining Medical University, Jining, Shandong, PR China
| | - Dongmei Man
- Affiliated Hospital of Jining Medical University, Jining, Shandong, PR China
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20
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Forensic characteristics and phylogenetic analysis of both Y-STR and Y-SNP in the Li and Han ethnic groups from Hainan Island of China. Forensic Sci Int Genet 2019; 39:e14-e20. [DOI: 10.1016/j.fsigen.2018.11.016] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Revised: 10/24/2018] [Accepted: 11/26/2018] [Indexed: 11/21/2022]
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21
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Chen J, Xie B, Yang Y, Yang M, Liu C, Lv Y, Chen C, Liu X, Fang X, Wu H, Yan J. Genetic variability and forensic efficiency of 39 microsatellite loci in the Li ethnic group from Hainan Island in the South China Sea. Ann Hum Biol 2016; 44:467-474. [PMID: 27670224 DOI: 10.1080/03014460.2016.1241300] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
BACKGROUND Investigation of allele and genotype frequencies of microsatellite loci in various populations is an essential pre-requisite in forensic application. AIM The present study obtained population genetic data and forensic parameters of 39 autosomal Short Tandem Repeats (STRs) loci from a Chinese Li ethnic group and estimated the genetic relationships between Li and other reference populations. SUBJECTS AND METHODS Thirty-nine STR loci, which include D19S433, D5S818, D21S11, D18S51, D6S1043, D3S1358, D13S317, D7S820, D16S539, CSF1PO, Penta D, D2S441, vWA, D8S1179, TPOX, Penta E, TH01, D12S391, D2S1338, FGA, D6S477, D18S535, D19S253, D15S659, D11S2368, D20S470, D1S1656, D22-GATA198B05, D8S1132, D4S2366, D21S1270, D13S325, D9S925, D3S3045, D14S608, D10S1435, D7S3048, D17S1290 and D5S2500, were amplified in two multiplex DNA-STR fluorescence detection systems for 189 unrelated healthy individuals of the Chinese Li ethnic group. The allele frequency distribution and several parameters commonly used in forensic science were statistically analysed. RESULTS A total of 378 alleles were observed with corresponding allelic frequencies ranging from 0.0026-0.5899. The power of discrimination and power of exclusion ranged from 0.7569-0.9672 and 0.2513-0.7355, respectively. The power of exclusion (PE) ranged from 0.2580-0.7943 for trio paternity cases and 0.1693-0.5940 for duo paternity cases. The polymorphism information content (PIC) ranged from 0.5001-0.8611. The cumulative match probability across these 39 loci was 2.4242 × 10-38. CONCLUSION The results indicate that 39 STR loci are polymorphic among the Li ethnic group in Hainan Island in the South China Sea. This set of polymorphic STR loci provide highly polymorphic information and forensic efficiency for forensic individual identification and paternity testing, as well as basic population data for population genetics and anthropological research.
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Affiliation(s)
- Jing Chen
- a CAS Key Laboratory of Genome Sciences and Information , Beijing Institute of Genomics, Chinese Academy of Sciences , Beijing , PR China
| | - Bingbing Xie
- a CAS Key Laboratory of Genome Sciences and Information , Beijing Institute of Genomics, Chinese Academy of Sciences , Beijing , PR China
| | - Yaran Yang
- a CAS Key Laboratory of Genome Sciences and Information , Beijing Institute of Genomics, Chinese Academy of Sciences , Beijing , PR China
| | - Meng Yang
- a CAS Key Laboratory of Genome Sciences and Information , Beijing Institute of Genomics, Chinese Academy of Sciences , Beijing , PR China
| | - Chao Liu
- b Guangzhou Forensic Science Institute , Guangdong , PR China
| | - Yuexin Lv
- c Beijing Microread Genetics Co., Ltd , Beijing , PR China
| | - Chuguang Chen
- c Beijing Microread Genetics Co., Ltd , Beijing , PR China
| | - Xu Liu
- d Beijing Center for Physical and Chemical Analysis , Beijing , PR China.,e Beijing Engineering Technology Research Center of Gene Sequencing and Gene Function Analysis , Beijing , PR China
| | - Xiangdong Fang
- a CAS Key Laboratory of Genome Sciences and Information , Beijing Institute of Genomics, Chinese Academy of Sciences , Beijing , PR China
| | - Huijuan Wu
- d Beijing Center for Physical and Chemical Analysis , Beijing , PR China.,e Beijing Engineering Technology Research Center of Gene Sequencing and Gene Function Analysis , Beijing , PR China
| | - Jiangwei Yan
- a CAS Key Laboratory of Genome Sciences and Information , Beijing Institute of Genomics, Chinese Academy of Sciences , Beijing , PR China
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22
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Marrero P, Abu-Amero KK, Larruga JM, Cabrera VM. Carriers of human mitochondrial DNA macrohaplogroup M colonized India from southeastern Asia. BMC Evol Biol 2016; 16:246. [PMID: 27832758 PMCID: PMC5105315 DOI: 10.1186/s12862-016-0816-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2016] [Accepted: 10/28/2016] [Indexed: 11/23/2022] Open
Abstract
Background From a mtDNA dominant perspective, the exit from Africa of modern humans to colonize Eurasia occurred once, around 60 kya, following a southern coastal route across Arabia and India to reach Australia short after. These pioneers carried with them the currently dominant Eurasian lineages M and N. Based also on mtDNA phylogenetic and phylogeographic grounds, some authors have proposed the coeval existence of a northern route across the Levant that brought mtDNA macrohaplogroup N to Australia. To contrast both hypothesis, here we reanalyzed the phylogeography and respective ages of mtDNA haplogroups belonging to macrohaplogroup M in different regions of Eurasia and Australasia. Results The macrohaplogroup M has a historical implantation in West Eurasia, including the Arabian Peninsula. Founder ages of M lineages in India are significantly younger than those in East Asia, Southeast Asia and Near Oceania. Moreover, there is a significant positive correlation between the age of the M haplogroups and its longitudinal geographical distribution. These results point to a colonization of the Indian subcontinent by modern humans carrying M lineages from the east instead the west side. Conclusions The existence of a northern route, previously proposed for the mtDNA macrohaplogroup N, is confirmed here for the macrohaplogroup M. Both mtDNA macrolineages seem to have differentiated in South East Asia from ancestral L3 lineages. Taking this genetic evidence and those reported by other disciplines we have constructed a new and more conciliatory model to explain the history of modern humans out of Africa. Electronic supplementary material The online version of this article (doi:10.1186/s12862-016-0816-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Patricia Marrero
- School of Biological Sciences, University of East Anglia, Norwich, NR4 7TJ, Norfolk, UK
| | - Khaled K Abu-Amero
- Glaucoma Research Chair, Department of ophthalmology, College of Medicine, King Saud University, Riyadh, Saudi Arabia
| | - Jose M Larruga
- Departamento de Genética, Facultad de Biología, Universidad de La Laguna, La Laguna, Tenerife, Spain
| | - Vicente M Cabrera
- Departamento de Genética, Facultad de Biología, Universidad de La Laguna, La Laguna, Tenerife, Spain.
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23
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Fregel R, Cabrera V, Larruga JM, Abu-Amero KK, González AM. Carriers of Mitochondrial DNA Macrohaplogroup N Lineages Reached Australia around 50,000 Years Ago following a Northern Asian Route. PLoS One 2015; 10:e0129839. [PMID: 26053380 PMCID: PMC4460043 DOI: 10.1371/journal.pone.0129839] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2014] [Accepted: 05/13/2015] [Indexed: 01/17/2023] Open
Abstract
Background The modern human colonization of Eurasia and Australia is mostly explained by a single-out-of-Africa exit following a southern coastal route throughout Arabia and India. However, dispersal across the Levant would better explain the introgression with Neanderthals, and more than one exit would fit better with the different ancient genomic components discovered in indigenous Australians and in ancient Europeans. The existence of an additional Northern route used by modern humans to reach Australia was previously deduced from the phylogeography of mtDNA macrohaplogroup N. Here, we present new mtDNA data and new multidisciplinary information that add more support to this northern route. Methods MtDNA hypervariable segments and haplogroup diagnostic coding positions were analyzed in 2,278 Saudi Arabs, from which 1,725 are new samples. Besides, we used 623 published mtDNA genomes belonging to macrohaplogroup N, but not R, to build updated phylogenetic trees to calculate their coalescence ages, and more than 70,000 partial mtDNA sequences were screened to establish their respective geographic ranges. Results The Saudi mtDNA profile confirms the absence of autochthonous mtDNA lineages in Arabia with coalescence ages deep enough to support population continuity in the region since the out-of-Africa episode. In contrast to Australia, where N(xR) haplogroups are found in high frequency and with deep coalescence ages, there are not autochthonous N(xR) lineages in India nor N(xR) branches with coalescence ages as deep as those found in Australia. These patterns are at odds with the supposition that Australian colonizers harboring N(xR) lineages used a route involving India as a stage. The most ancient N(xR) lineages in Eurasia are found in China, and inconsistently with the coastal route, N(xR) haplogroups with the southernmost geographical range have all more recent radiations than the Australians. Conclusions Apart from a single migration event via a southern route, phylogeny and phylogeography of N(xR) lineages support that people carrying mtDNA N lineages could have reach Australia following a northern route through Asia. Data from other disciplines also support this scenario.
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Affiliation(s)
- Rosa Fregel
- Departamento de Genética, Facultad de Biología, Universidad de La Laguna, La Laguna, Tenerife, Spain
- * E-mail:
| | - Vicente Cabrera
- Departamento de Genética, Facultad de Biología, Universidad de La Laguna, La Laguna, Tenerife, Spain
| | - Jose M. Larruga
- Departamento de Genética, Facultad de Biología, Universidad de La Laguna, La Laguna, Tenerife, Spain
| | - Khaled K. Abu-Amero
- Department of Ophthalmology, College of Medicine, King Saud University, Riyadh, Saudi Arabia
| | - Ana M. González
- Departamento de Genética, Facultad de Biología, Universidad de La Laguna, La Laguna, Tenerife, Spain
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24
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Gomes SM, Bodner M, Souto L, Zimmermann B, Huber G, Strobl C, Röck AW, Achilli A, Olivieri A, Torroni A, Côrte-Real F, Parson W. Human settlement history between Sunda and Sahul: a focus on East Timor (Timor-Leste) and the Pleistocenic mtDNA diversity. BMC Genomics 2015; 16:70. [PMID: 25757516 PMCID: PMC4342813 DOI: 10.1186/s12864-014-1201-x] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2014] [Accepted: 12/22/2014] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Distinct, partly competing, "waves" have been proposed to explain human migration in(to) today's Island Southeast Asia and Australia based on genetic (and other) evidence. The paucity of high quality and high resolution data has impeded insights so far. In this study, one of the first in a forensic environment, we used the Ion Torrent Personal Genome Machine (PGM) for generating complete mitogenome sequences via stand-alone massively parallel sequencing and describe a standard data validation practice. RESULTS In this first representative investigation on the mitochondrial DNA (mtDNA) variation of East Timor (Timor-Leste) population including >300 individuals, we put special emphasis on the reconstruction of the initial settlement, in particular on the previously poorly resolved haplogroup P1, an indigenous lineage of the Southwest Pacific region. Our results suggest a colonization of southern Sahul (Australia) >37 kya, limited subsequent exchange, and a parallel incubation of initial settlers in northern Sahul (New Guinea) followed by westward migrations <28 kya. CONCLUSIONS The temporal proximity and possible coincidence of these latter dispersals, which encompassed autochthonous haplogroups, with the postulated "later" events of (South) East Asian origin pinpoints a highly dynamic migratory phase.
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Affiliation(s)
- Sibylle M Gomes
- Department of Biology, University of Aveiro, Campus de Santiago, Aveiro, Portugal.
| | - Martin Bodner
- Institute of Legal Medicine, Medical University of Innsbruck, Müllerstr. 44, 6020, Innsbruck, Austria.
| | - Luis Souto
- Department of Biology, University of Aveiro, Campus de Santiago, Aveiro, Portugal.
- Cencifor Centro de Ciências Forenses, Coimbra, Portugal.
| | - Bettina Zimmermann
- Institute of Legal Medicine, Medical University of Innsbruck, Müllerstr. 44, 6020, Innsbruck, Austria.
| | - Gabriela Huber
- Institute of Legal Medicine, Medical University of Innsbruck, Müllerstr. 44, 6020, Innsbruck, Austria.
| | - Christina Strobl
- Institute of Legal Medicine, Medical University of Innsbruck, Müllerstr. 44, 6020, Innsbruck, Austria.
| | - Alexander W Röck
- Institute of Legal Medicine, Medical University of Innsbruck, Müllerstr. 44, 6020, Innsbruck, Austria.
| | - Alessandro Achilli
- Dipartimento di Biologia e Biotecnologie "L. Spallanzani", University of Pavia, Pavia, Italy.
- Dipartimento di Chimica, Biologia e Biotecnologie, University of Perugia, Perugia, Italy.
| | - Anna Olivieri
- Dipartimento di Biologia e Biotecnologie "L. Spallanzani", University of Pavia, Pavia, Italy.
| | - Antonio Torroni
- Dipartimento di Biologia e Biotecnologie "L. Spallanzani", University of Pavia, Pavia, Italy.
| | | | - Walther Parson
- Institute of Legal Medicine, Medical University of Innsbruck, Müllerstr. 44, 6020, Innsbruck, Austria.
- Penn State Eberly College of Science, University Park, PA, USA.
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25
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Li C, Barnes E, Newton PN, Fu Y, Vongsouvath M, Klenerman P, Okamoto H, Abe K, Pybus OG, Lu L. An expanded taxonomy of hepatitis C virus genotype 6: Characterization of 22 new full-length viral genomes. Virology 2015; 476:355-363. [PMID: 25589238 PMCID: PMC4376965 DOI: 10.1016/j.virol.2014.12.025] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2014] [Revised: 12/06/2014] [Accepted: 12/16/2014] [Indexed: 12/25/2022]
Abstract
We characterized the full-length genomes of 22 hepatitis C virus genotype 6 (HCV-6) isolates: 10 from Vietnam (classified into subtypes 6e, 6h, 6p, 6r, 6s, and 6u), one from China (confirmed as a new subtype 6xd), and 11 from the Lao PDR (representing a new subtype 6xe plus eight novel variants). With these 22 new genomes, HCV-6 now has a diverse and extended taxonomic structure, comprised of 28 assigned subtypes (denoted 6a-6xe) and 27 unassigned lineages, all of which have been represented by full-length genomes. Our phylogenetic analyses also included many partially-sequenced novel variants of HCV-6 from Lao PDR. This revealed that Lao HCV isolates are genetically very diverse and are phylogenetically distributed in multiple lineages within genotype 6. Our results suggest that HCV-6 has been maintained in Laos, a landlocked country, since the common ancestor of genotype 6 and indicates historical dispersal of HCV-6 across Southeast Asia. We characterized 22 full-length genomes of HCV-6. They confirmed two new subtypes 6xd and 6xe plus eight novel variants. We also reanalyzed many partially-sequenced novel HCV-6 variants from Lao PDR. They are phylogenetically distributed across the whole of genotype 6. They indicate historical dispersal of HCV-6 across Southeast Asia.
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Affiliation(s)
- Chunhua Li
- The Viral Oncology Center, Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS, USA
| | - Eleanor Barnes
- The Peter Medawar Building for Pathogen Research, University of Oxford, South Parks Road and Oxford NIHR Biomedical Research Centre, OX1 3SY, UK
| | - Paul N Newton
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao Democratic People's Republic; Centre for Tropical Medicine and Global Health, Churchill Hospital, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK
| | - Yongshui Fu
- Guangzhou Blood Center, Guangzhou 510095, China
| | - Manivanh Vongsouvath
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao Democratic People's Republic
| | - Paul Klenerman
- The Peter Medawar Building for Pathogen Research, University of Oxford, South Parks Road and Oxford NIHR Biomedical Research Centre, OX1 3SY, UK
| | - Hiroaki Okamoto
- Division of Virology, Department of Infection and Immunity, Jichi Medical University School of Medicine, 3311-1 Yakushiji, Shimotsuke-shi Tochigi 329-0498, Japan
| | - Kenji Abe
- Department of Pathology, National Institute of Infectious Diseases, Shinjuku-ku, Tokyo 162-8640, Japan
| | - Oliver G Pybus
- Department of Zoology, University of Oxford, South Parks Road, OX1 3PS, UK
| | - Ling Lu
- The Viral Oncology Center, Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS, USA.
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An Y, Wu T, Wang M, Lu L, Li C, Zhou Y, Fu Y, Chen G. Conservation in China of a novel group of HCV variants dating to six centuries ago. Virology 2014; 464-465:21-25. [PMID: 25043585 DOI: 10.1016/j.virol.2014.06.011] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2014] [Revised: 05/15/2014] [Accepted: 06/10/2014] [Indexed: 12/18/2022]
Abstract
UNLABELLED We characterized a novel group of HCV variants that are genetically related but distinct from each other belonging to genotype 6 (HCV-6). From 26 infected Austronesian-descended aborigines on Hainan Island, China, HCV sequences were determined followed by genetic analyses. Six nearly full-length genomes and 20 E1 sequences of HCV were obtained, which differ from each other and from all known HCV lineages by nucleotides above the intra-subtype level of 13%. Together with subtypes 6g and 6w, they constitute a phylogenetic group sharing a common ancestor dating from the end of the 12th century. CONCLUSION Our data indicate the maintenance of an isolated HCV-6 indigenous circulation on Hainan Island at least for six centuries.
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Affiliation(s)
- Yuling An
- Department of Liver Transplantation, Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong 510630, China
| | - Tao Wu
- Department of Infectious Disease, Southern Medical University, Guangzhou, Guangdong 510515, China; Department of Infectious Disease, Hainan General Hospital, Haikou, Hainan 570311, China
| | - Min Wang
- Guangzhou Blood Center, Guangzhou, Guangdong 510095, China
| | - Ling Lu
- Department of Liver Transplantation, Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong 510630, China; Center for Viral Oncology, Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS 66160, USA.
| | - Chunhua Li
- Center for Viral Oncology, Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Yuanpin Zhou
- Department of Infectious Disease, Southern Medical University, Guangzhou, Guangdong 510515, China
| | - Yongshui Fu
- Guangzhou Blood Center, Guangzhou, Guangdong 510095, China
| | - Guihua Chen
- Department of Liver Transplantation, Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong 510630, China
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27
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Chen K, Ablimit A, Ling F, Wu W, Shan W, Qin W, Keweier T, Zuo H, Zhang F, Ma Z, Zheng X. Paternal and maternal genetic analysis of a desert Keriyan population: Keriyans are not the descendants of Guge Tibetans. PLoS One 2014; 9:e100479. [PMID: 24968299 PMCID: PMC4072674 DOI: 10.1371/journal.pone.0100479] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2014] [Accepted: 05/23/2014] [Indexed: 12/02/2022] Open
Abstract
The Keriyan people live in an isolated village in the Taklimakan Desert in Xinjiang, Western China. The origin and migration of the Keriyans remains unclear. We studied paternal and maternal genetic variance through typing Y-STR loci and sequencing the complete control region of the mtDNA and compared them with other adjacent populations. Data show that the Keriyan have relatively low genetic diversity on both the paternal and maternal lineages and possess both European and Asian specific haplogroups, indicating Keriyan is an admixture population of West and East. There is a gender-bias in the extent of contribution from Europe vs. Asia to the Keriyan gene pool. Keriyans have more genetic affinity to Uyghurs than to Tibetans. The Keriyan are not the descendants of the Guge Tibetans.
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Affiliation(s)
- Kaixu Chen
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi, Xinjiang, China
| | - Abdurahman Ablimit
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi, Xinjiang, China
| | - Fengjun Ling
- Beijing Entry-Exit Inspection and Quarantine Bureau, Beijing, China
| | - Weiwei Wu
- Institute of Forensic Science of Zhejiang, Hongzhou, China
| | - Wenjuan Shan
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi, Xinjiang, China
| | - Wenbei Qin
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi, Xinjiang, China
| | | | | | - Fuchun Zhang
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi, Xinjiang, China
| | - Zhenghai Ma
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi, Xinjiang, China
- * E-mail: (XZ); (ZM)
| | - Xiufen Zheng
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi, Xinjiang, China
- Department of Pathology, The University of Western Ontario, London, Canada
- Lawson Health Research Institute, London, Canada
- * E-mail: (XZ); (ZM)
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Yao H, Chen X, Lin L, Wu C, Fu X, Wang H, Yao Z, Chen W, Huang L, Tang R, Rao R, Wang S, Ding Y. The spectrum of α- and β-thalassemia mutations of the Li people in Hainan Province of China. Blood Cells Mol Dis 2014; 53:16-20. [DOI: 10.1016/j.bcmd.2014.01.003] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2013] [Revised: 12/07/2013] [Accepted: 12/16/2013] [Indexed: 10/25/2022]
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Analysis of mitochondrial genome diversity identifies new and ancient maternal lineages in Cambodian aborigines. Nat Commun 2013; 4:2599. [DOI: 10.1038/ncomms3599] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2013] [Accepted: 09/11/2013] [Indexed: 01/05/2023] Open
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Patterns of human oral yeast species distribution on Hainan Island in China. Mycopathologia 2013; 176:359-68. [PMID: 24085613 DOI: 10.1007/s11046-013-9703-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2013] [Accepted: 09/09/2013] [Indexed: 10/26/2022]
Abstract
Infections by yeast strains of the genus Candida are among the most prevalent fungal infections of humans. These yeasts are common residents of the oral mucosa and other body surfaces. Since most yeast infections are due to endogenous strains and that species of Candida differ in virulence properties and in intrinsic susceptibilities to antifungal drugs, understanding the human commensal yeast flora can help designing effective treatment and prevention strategies against yeast infections. Here, we report the patterns of yeast species distributions in the oral cavities of 1,799 people from Hainan Island in southern China. Based on sequence information at the fungal barcode locus ITS regions, 368 of the 415 obtained oral yeast strains were identified as belonging to 26 yeast species, while the remaining 47 strains all showed significant sequence divergence to the currently described species. The four most common yeast species were C. albicans (42 %), C. tropicalis (20 %), C. glabrata (5.5 %), and C. parapsilosis (4.1 %) and 10 of the 26 yeast species were represented by only one strain each. Our analyses identified that the gender of hosts and ethnical background showed no contribution to oral yeast species distributions. However, the health status, place of birth, current residency, and the age of hosts all showed significant contributions to the distributions of the four dominant yeast species. We compared our results with those reported previously and discussed the potential mechanisms for the observed differences in oral yeast species distributions.
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Abstract
Human genetic diversity refers to genomic variation among races, ethnic groups, isolated populations and individuals worldwide, and is one major resource and tool on discovering human evolution and migration, interaction between genetic background and environment, and factors associated with human diseases and health. China has abundant and valuable resource of human genetic diversity due to 56 ethnic groups and a large population accounting for one fifth of the total population in the world. After decades of efforts, a large number of research data on human genetic diversity have been accumulated in China, and some of outcomes reach advanced international level. This review mainly focuses on the recent progress and outcomes achieved in applying genetic markers including morphological markers, biochemical and immunological markers and DNA markers in research of genetic diversity, and the application of mitochondrial DNA, Y chromosomal DNA, HLA and others in research of the origin and relationship of Chinese ethic groups, and the origin and mi-of modern East Asian populations. This review also summarizes the advances in the research fields of preservation and utilization of Chinese genetic resource, identification of genes associated with disease selective and adaptive for natural pressure, application of whole genome association study and next generation sequencing, and Chinese human genome as well.
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Khusnutdinova EK, Litvinov SS, Kutuev IA, Yunusbayev BB, Khusainova RI, Ahmetova VL, Ahatova FS, Metspalu E, Rootsi S, Villems R. Gene pool of ethnic groups of the Caucasus: Results of integrated study of the Y chromosome and mitochondrial DNA and genome-wide data. RUSS J GENET+ 2012. [DOI: 10.1134/s1022795412060063] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Zheng HX, Yan S, Qin ZD, Wang Y, Tan JZ, Li H, Jin L. Major population expansion of East Asians began before neolithic time: evidence of mtDNA genomes. PLoS One 2011; 6:e25835. [PMID: 21998705 PMCID: PMC3188578 DOI: 10.1371/journal.pone.0025835] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2011] [Accepted: 09/12/2011] [Indexed: 11/19/2022] Open
Abstract
It is a major question in archaeology and anthropology whether human populations started to grow primarily after the advent of agriculture, i.e., the Neolithic time, especially in East Asia, which was one of the centers of ancient agricultural civilization. To answer this question requires an accurate estimation of the time of lineage expansion as well as that of population expansion in a population sample without ascertainment bias. In this study, we analyzed all available mtDNA genomes of East Asians ascertained by random sampling, a total of 367 complete mtDNA sequences generated by the 1000 Genome Project, including 249 Chinese (CHB, CHD, and CHS) and 118 Japanese (JPT). We found that major mtDNA lineages underwent expansions, all of which, except for two JPT-specific lineages, including D4, D4b2b, D4a, D4j, D5a2a, A, N9a, F1a1'4, F2, B4, B4a, G2a1 and M7b1'2'4, occurred before 10 kya, i.e., before the Neolithic time (symbolized by Dadiwan Culture at 7.9 kya) in East Asia. Consistent to this observation, the further analysis showed that the population expansion in East Asia started at 13 kya and lasted until 4 kya. The results suggest that the population growth in East Asia constituted a need for the introduction of agriculture and might be one of the driving forces that led to the further development of agriculture.
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Affiliation(s)
- Hong-Xiang Zheng
- State Key Laboratory of Genetic Engineering and MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences and Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Shi Yan
- State Key Laboratory of Genetic Engineering and MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences and Institutes of Biomedical Sciences, Fudan University, Shanghai, China
- Chinese Academy of Sciences and Max-Planck Society (CAS-MPG) Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
- Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Chinese Academy of Sciences, Shanghai, China
| | - Zhen-Dong Qin
- State Key Laboratory of Genetic Engineering and MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences and Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Yi Wang
- State Key Laboratory of Genetic Engineering and MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences and Institutes of Biomedical Sciences, Fudan University, Shanghai, China
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
| | - Jing-Ze Tan
- State Key Laboratory of Genetic Engineering and MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences and Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Hui Li
- State Key Laboratory of Genetic Engineering and MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences and Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Li Jin
- State Key Laboratory of Genetic Engineering and MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences and Institutes of Biomedical Sciences, Fudan University, Shanghai, China
- Chinese Academy of Sciences and Max-Planck Society (CAS-MPG) Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
- Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Chinese Academy of Sciences, Shanghai, China
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