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Chen L, Feng Y, Pan S, Wang L, Zhang H, Jin X, Wang Q, Liu Y, Yang M, Huang X, Tian S, Gu C, Huang J, Ren Z. Maternal genetic architecture of Guizhou's Hmong-Mien populations via whole mitogenome. Genomics 2025; 117:111041. [PMID: 40139472 DOI: 10.1016/j.ygeno.2025.111041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2024] [Revised: 02/07/2025] [Accepted: 03/23/2025] [Indexed: 03/29/2025]
Abstract
The Hmong-Mien (HM) language family, majorly distributed across southern China and Southeast Asia, has remained underexplored in population genetics, particularly concerning whole mitogenome studies. In this study, we sequenced the whole mitogenomes of 261 individuals from Guizhou Hmong-Mien-speaking populations (HM-G), comprising Miao, Yao, and She individuals. The haplogroup distribution was dominated by southern East Asian haplogroups (B, M7, and F). The neutrality test revealed significantly negative values, and mismatch distribution analyses showed a pronounced unimodal distribution, indicating high genetic diversity and recent population expansion in populations. For a comprehensive understanding of the matrilineal genetic background of the HM-speaking population, we merged whole mitogenome data from 83 populations worldwide. Our findings showed that the HM-G exhibited relatively close genetic distances to HM- and Tai-Kadai-speaking populations from East and Southeast Asia. These results provide crucial insights into the genetic structure and evolutionary history of HM-G.
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Affiliation(s)
- Li Chen
- School of Forensic Medicine, Guizhou Medical University, Guiyang 550004, Guizhou, China
| | - Yuhang Feng
- Institute of Rare Diseases, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu 610000, China; Center for Archaeological Science, Sichuan University, Chengdu 610000, China
| | - Shuaiji Pan
- School of Forensic Medicine, Guizhou Medical University, Guiyang 550004, Guizhou, China
| | - Lin Wang
- School of Forensic Medicine, Guizhou Medical University, Guiyang 550004, Guizhou, China
| | - Hongling Zhang
- School of Forensic Medicine, Guizhou Medical University, Guiyang 550004, Guizhou, China
| | - Xiaoye Jin
- School of Forensic Medicine, Guizhou Medical University, Guiyang 550004, Guizhou, China
| | - Qiyan Wang
- School of Forensic Medicine, Guizhou Medical University, Guiyang 550004, Guizhou, China
| | - Yubo Liu
- School of Forensic Medicine, Guizhou Medical University, Guiyang 550004, Guizhou, China
| | - Meiqing Yang
- School of Forensic Medicine, Guizhou Medical University, Guiyang 550004, Guizhou, China
| | - Xiaolan Huang
- School of Forensic Medicine, Guizhou Medical University, Guiyang 550004, Guizhou, China
| | - Shunyi Tian
- School of Forensic Medicine, Guizhou Medical University, Guiyang 550004, Guizhou, China
| | - Changyun Gu
- School of Forensic Medicine, Guizhou Medical University, Guiyang 550004, Guizhou, China
| | - Jiang Huang
- School of Public Health, the Key Laboratory of Environmental Pollution Monitoring and Disease Control, Ministry of Education, Guizhou Medical University, Guiyang 550004, Guizhou, China.
| | - Zheng Ren
- School of Forensic Medicine, Guizhou Medical University, Guiyang 550004, Guizhou, China.
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2
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Zhang X, Zhang F. Island ancient genomes reveal dynamic populations interactions in the northern China. Front Microbiol 2025; 16:1584315. [PMID: 40309111 PMCID: PMC12040904 DOI: 10.3389/fmicb.2025.1584315] [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: 02/27/2025] [Accepted: 03/24/2025] [Indexed: 05/02/2025] Open
Abstract
The Longshan period (2500-1900 BC) was a transformative era in central China, marked by the emergence of complex social structures and early state formation. While human mobility likely played a role in these developments, the scale and nature of migration during this period remain poorly understood. Previous ancient DNA studies on Longshan culture populations have focused on individuals from inland Shandong, with no ancient DNA data available from island populations. In this study, we present the first ancient DNA analysis from individuals associated with the Longshan and subsequent Yueshi cultures on the Tuoji Island. Our findings indicate that, despite the widespread cultural influence of the inland Longshan culture in Shandong, the genetic ancestry of the Tuoji Island individuals primarily reflects connections to the preceding Dawenkou culture, with additional ancestry linked to the coastal regions of southern China. This suggests an earlier population movement into Tuoji Island before the Longshan period. However, during the Longshan period, the spread of Longshan cultural materials on Tuoji Island appears to represent the diffusion of ideas rather than significant population admixture from the inland. Additionally, our study shows genetic continuity of Longshan and Yueshi cultures in Tuoji Island highlighting the dynamic nature of coastal migration, as the Tuoji Island populations exhibit more genetic influence from coastal regions than from the inland. In contrast, inland populations during the Longshan period show no significant genetic influx from neighboring regions. This study not only advances our understanding of the prehistoric populations in Neolithic China but also provides new insights into patterns of migration and cultural exchange during this critical period.
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Affiliation(s)
- Xu Zhang
- Key Laboratory of Archaeological Sciences and Cultural Heritage, Chinese Academy of Social Sciences, Beijing, China
| | - Fan Zhang
- School of Archaeology and Museology, Sichuan University, Chengdu, China
- Center for Archaeological Science, Sichuan University, Chengdu, China
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3
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Chen H, Xu S. Population genomics advances in frontier ethnic minorities in China. SCIENCE CHINA. LIFE SCIENCES 2025; 68:961-973. [PMID: 39643831 DOI: 10.1007/s11427-024-2659-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2024] [Accepted: 06/18/2024] [Indexed: 12/09/2024]
Abstract
China, with its large geographic span, possesses rich genetic diversity across vast frontier regions in addition to the Han Chinese majority. Importantly, demographic events and various natural and cultural environments in Chinese frontier regions have shaped the genomic diversity of ethnic minorities via local adaptations. Thus, insights into the genetic diversity and adaptive evolution of these under-represented ethnic groups are crucial for understanding evolutionary scenarios and biomedical implications in East Asian populations. Here, we focus on ethnic minorities in Chinese frontier regions and review research advances regarding genomic diversity, genetic structure, population history, genetic admixture, and local adaptation. We first provide an overview of the extensive genetic diversity across populations in different Chinese frontier regions. Next, we summarize research progress regarding genetic ancestry, demographic history, the adaptive process, and the archaic identification of multiple ethnic minorities in different Chinese frontier regions. Finally, we discuss the gaps and opportunities in genomic studies of Chinese populations and the need for a more comprehensive understanding of genomic diversity and the evolution of populations of East Asian ancestry in the post-genomic era.
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Affiliation(s)
- Hao Chen
- Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Shuhua Xu
- Center for Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China.
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4
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Wei X, Zhang M, Min R, Jiang Z, Xue J, Zhu Z, Yuan H, Li X, Zhao D, Cao P, Liu F, Dai Q, Feng X, Yang R, Wu X, Hu C, Ma M, Liu X, Wan Y, Yang F, Zhou R, Kang L, Dong G, Ping W, Wang T, Miao B, Bai F, Zheng Y, Liu Y, Yang MA, Wang W, Bennett EA, Fu Q. Neolithic to Bronze Age human maternal genetic history in Yunnan, China. J Genet Genomics 2025; 52:483-493. [PMID: 39343094 DOI: 10.1016/j.jgg.2024.09.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2024] [Revised: 09/23/2024] [Accepted: 09/23/2024] [Indexed: 10/01/2024]
Abstract
Yunnan in southwest China is a geographically and ethnically complex region at the intersection of southern China and Southeast Asia, and a focal point for human migrations. To clarify its maternal genetic history, we generated 152 complete mitogenomes from 17 Yunnan archaeological sites. Our results reveal distinct genetic histories segregated by geographical regions. Maternal lineages of ancient populations from northwestern and northern Yunnan exhibit closer affinities with past and present-day populations from northern East Asia and Xizang, providing important genetic evidence for the migration and interaction of populations along the Tibetan-Yi corridor since the Neolithic. Between 5500 and 1800 years ago, central Yunnan populations maintained their internal genetic relationships, including a 7000-year-old basal lineage of the rare and widely dispersed haplogroup M61. At the Xingyi site, changes in mitochondrial DNA haplogroups occurred between the Late Neolithic and Bronze Age, with haplogroups shifting from those predominant in the Yellow River region to those predominant in coastal southern China. These results highlight the high diversity of Yunnan populations during the Neolithic to Bronze Age.
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Affiliation(s)
- Xinyu Wei
- China-Central Asia "the Belt and Road" Joint Laboratory on Human and Environment Research, Key Laboratory of Cultural Heritage Research and Conservation, School of Cultural Heritage, Northwest University, Xi'an, Shaanxi 710127, China; Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China
| | - Ming Zhang
- China-Central Asia "the Belt and Road" Joint Laboratory on Human and Environment Research, Key Laboratory of Cultural Heritage Research and Conservation, School of Cultural Heritage, Northwest University, Xi'an, Shaanxi 710127, China; Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China
| | - Rui Min
- Yunnan Institute of Cultural Relics and Archaeology, Kunming, Yunnan 650118, China
| | - Zhilong Jiang
- Yunnan Institute of Cultural Relics and Archaeology, Kunming, Yunnan 650118, China
| | - Jiayang Xue
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China; College of Earth and Planetary Sciences, University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Zhonghua Zhu
- Yunnan Institute of Cultural Relics and Archaeology, Kunming, Yunnan 650118, China
| | - Haibing Yuan
- Center for Archaeological Science, Sichuan University, Chengdu, Sichuan 610064, China
| | - Xiaorui Li
- Yunnan Institute of Cultural Relics and Archaeology, Kunming, Yunnan 650118, China
| | - Dongyue Zhao
- China-Central Asia "the Belt and Road" Joint Laboratory on Human and Environment Research, Key Laboratory of Cultural Heritage Research and Conservation, School of Cultural Heritage, Northwest University, Xi'an, Shaanxi 710127, China
| | - Peng Cao
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China
| | - Feng Liu
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China
| | - Qingyan Dai
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China
| | - Xiaotian Feng
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China
| | - Ruowei Yang
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China
| | - Xiaohong Wu
- School of Archaeology and Museology, Peking University, Beijing 100871, China
| | - Changcheng Hu
- Yunnan Institute of Cultural Relics and Archaeology, Kunming, Yunnan 650118, China
| | - Minmin Ma
- Key Laboratory of Western China's Environmental Systems (Ministry of Education), College of Earth and Environmental Sciences, Lanzhou University, Lanzhou, Gansu 730000, China
| | - Xu Liu
- Yunnan Museum, Kunming, Yunnan 650206, China
| | - Yang Wan
- Yunnan Institute of Cultural Relics and Archaeology, Kunming, Yunnan 650118, China
| | - Fan Yang
- Yunnan Institute of Cultural Relics and Archaeology, Kunming, Yunnan 650118, China
| | - Ranchao Zhou
- Yunnan Institute of Cultural Relics and Archaeology, Kunming, Yunnan 650118, China
| | - Lihong Kang
- Yunnan Institute of Cultural Relics and Archaeology, Kunming, Yunnan 650118, China
| | - Guanghui Dong
- Key Laboratory of Western China's Environmental Systems (Ministry of Education), College of Earth and Environmental Sciences, Lanzhou University, Lanzhou, Gansu 730000, China
| | - Wanjing Ping
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China
| | - Tianyi Wang
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China; College of Earth and Planetary Sciences, University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Bo Miao
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China; College of Life Sciences, Northwest University, Xi'an, Shaanxi 710069, China
| | - Fan Bai
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China; College of Earth and Planetary Sciences, University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Yuxin Zheng
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China; College of Life Sciences, Northwest University, Xi'an, Shaanxi 710069, China
| | - Yuxiao Liu
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China; Sino-Danish Center, University of the Chinese Academy of Sciences, Beijing 100049, China; College of Earth and Planetary Sciences, University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Melinda A Yang
- Department of Biology, University of Richmond, Richmond, VA 23173, USA.
| | - Wenjun Wang
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China; Science and Technology Archaeology, National Centre for Archaeology, Beijing 100013, China.
| | - E Andrew Bennett
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China.
| | - Qiaomei Fu
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China; College of Earth and Planetary Sciences, University of the Chinese Academy of Sciences, Beijing 100049, China.
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5
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Qiao X, Shi J, Xu H, Liu K, Pu Y, Xue X, Zheng W, Guo Y, Ma H, Wang CC, Bitsue HK, Xu X, Wang S, Zhao J, Guo X, Hou X, Wang X, Peng L, Qiu Z, Su B, Tang W, He Y, Guo J, Yang Z. Genetic diversity and dietary adaptations of the Central Plains Han Chinese population in East Asia. Commun Biol 2025; 8:291. [PMID: 39987348 PMCID: PMC11846999 DOI: 10.1038/s42003-025-07760-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2024] [Accepted: 02/17/2025] [Indexed: 02/24/2025] Open
Abstract
The Central Plains Han Chinese (CPHC) is the typical agricultural population of East Asia. Investigating the genome of the CPHC is crucial to understanding the genetic structure and adaptation of the modern humans in East Asia. Here, we perform whole genome sequencing of 492 CPHC individuals and obtained 22.65 million SNPs, 4.26 million INDELs and 41,959 SVs. We found the CPHC has a higher level of genetic diversity and the glycolipid metabolic genes show strong selection signals, e.g. LONP2, FADS2, FGF21 and SLC19A2. Ancient DNA analyses suggest that the domestication of crops, which drove the emergence of the candidate mutations. Notably, East Asian-specific SVs, e.g., DEL_21699 (LINC01749) and DEL_38406 (FAM102A) may be associated with the high prevalence of esophageal squamous carcinoma and primary angle-closure glaucoma. Our results provide an important genetic resource and show that dietary adaptations play an important role in phenotypic evolution in East Asian populations.
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Affiliation(s)
- Xiaoyang Qiao
- Tianjian Laboratory of Advanced Biomedical Sciences, Academy of Medical Science, Zhengzhou University, Zhengzhou, China
| | - Jianxiang Shi
- Tianjian Laboratory of Advanced Biomedical Sciences, Academy of Medical Science, Zhengzhou University, Zhengzhou, China
| | - Hongen Xu
- Tianjian Laboratory of Advanced Biomedical Sciences, Academy of Medical Science, Zhengzhou University, Zhengzhou, China
| | - Kai Liu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Youwei Pu
- Tianjian Laboratory of Advanced Biomedical Sciences, Academy of Medical Science, Zhengzhou University, Zhengzhou, China
| | - Xia Xue
- Tianjian Laboratory of Advanced Biomedical Sciences, Academy of Medical Science, Zhengzhou University, Zhengzhou, China
| | - Wangshan Zheng
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Yongbo Guo
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Hao Ma
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China
| | - Chuan-Chao Wang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China
| | - Habtom K Bitsue
- Tianjian Laboratory of Advanced Biomedical Sciences, Academy of Medical Science, Zhengzhou University, Zhengzhou, China
| | - Xiaoyu Xu
- Tianjian Laboratory of Advanced Biomedical Sciences, Academy of Medical Science, Zhengzhou University, Zhengzhou, China
| | - Shanshan Wang
- Tianjian Laboratory of Advanced Biomedical Sciences, Academy of Medical Science, Zhengzhou University, Zhengzhou, China
| | - Jingru Zhao
- Tianjian Laboratory of Advanced Biomedical Sciences, Academy of Medical Science, Zhengzhou University, Zhengzhou, China
| | - Xiangqian Guo
- Zhongyuan Intelligent Medical Laboratory, School of Basic Medical Sciences, Henan University, Kaifeng, China
| | - Xinyue Hou
- Tianjian Laboratory of Advanced Biomedical Sciences, Academy of Medical Science, Zhengzhou University, Zhengzhou, China
| | - Xinwei Wang
- Tianjian Laboratory of Advanced Biomedical Sciences, Academy of Medical Science, Zhengzhou University, Zhengzhou, China
| | - Lei Peng
- Tianjian Laboratory of Advanced Biomedical Sciences, Academy of Medical Science, Zhengzhou University, Zhengzhou, China
| | - Zan Qiu
- Tianjian Laboratory of Advanced Biomedical Sciences, Academy of Medical Science, Zhengzhou University, Zhengzhou, China
| | - Bing Su
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Wenxue Tang
- The Research and Application Center of Precision Medicine, Departments of Otolaryngology, The Second Affiliated Hospital of Zhengzhou University, Zhengzhou, China.
| | - Yaoxi He
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.
| | - Jiancheng Guo
- The Research and Application Center of Precision Medicine, The Second Affiliated Hospital of Zhengzhou University, Zhengzhou, China.
| | - Zhaohui Yang
- Tianjian Laboratory of Advanced Biomedical Sciences, Academy of Medical Science, Zhengzhou University, Zhengzhou, China.
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6
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Wang M, Duan S, Sun Q, Liu K, Liu Y, Wang Z, Li X, Wei L, Liu Y, Nie S, Zhou K, Ma Y, Yuan H, Liu B, Hu L, Liu C, He G. YHSeqY3000 panel captures all founding lineages in the Chinese paternal genomic diversity database. BMC Biol 2025; 23:18. [PMID: 39838386 PMCID: PMC11752814 DOI: 10.1186/s12915-025-02122-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Accepted: 01/07/2025] [Indexed: 01/23/2025] Open
Abstract
BACKGROUND The advancements in second-/third-generation sequencing technologies, alongside computational innovations, have significantly enhanced our understanding of the genomic structure of Y-chromosomes and their unique phylogenetic characteristics. These researches, despite the challenges posed by the lack of population-scale genomic databases, have the potential to revolutionize our approach to high-resolution, population-specific Y-chromosome panels and databases for anthropological and forensic applications. OBJECTIVES This study aimed to develop the highest-resolution Y-targeted sequencing panel, utilizing time-stamped, core phylogenetic informative mutations identified from high-coverage sequences in the YanHuang cohort. This panel is intended to provide a new tool for forensic complex pedigree search and paternal biogeographical ancestry inference, as well as explore the general patterns of the fine-scale paternal evolutionary history of ethnolinguistically diverse Chinese populations. RESULTS The sequencing performance of the East Asian-specific Y-chromosomal panel, including 2999-core SNP variants, was found to be robust and reliable. The YHSeqY3000 panel was designed to capture the genetic diversity of Chinese paternal lineages from 3500 years ago, identifying 408 terminal lineages in 2097 individuals across 41 genetically and geographically distinct populations. We identified a fine-scale paternal substructure that was correlating with ancient population migrations and expansions. New evidence was provided for extensive gene flow events between minority ethnic groups and Han Chinese people, based on the integrative Chinese Paternal Genomic Diversity Database. CONCLUSIONS This work successfully integrated Y-chromosome-related basic genomic science with forensic and anthropological translational applications, emphasizing the necessity of comprehensively characterizing Y-chromosome genomic diversity from genomically under-representative populations. This is particularly important in the second phase of our population-specific medical or anthropological genomic cohorts, where dense sampling strategies are employed.
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Affiliation(s)
- Mengge Wang
- Institute of Rare Diseases, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, 610000, Sichuan, China.
- Center for Archaeological Science, Sichuan University, Chengdu, 610000, China.
- Anti-Drug Technology Center of Guangdong Province, Guangzhou, 510230, China.
- Department of Oto-Rhino-Laryngology, West China Hospital of Sichuan University, Chengdu, 610000, China.
| | - Shuhan Duan
- Institute of Rare Diseases, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, 610000, Sichuan, China
- Center for Archaeological Science, Sichuan University, Chengdu, 610000, China
- School of Basic Medical Sciences, North Sichuan Medical College, Nanchong, 637100, China
- Department of Oto-Rhino-Laryngology, West China Hospital of Sichuan University, Chengdu, 610000, China
| | - Qiuxia Sun
- Institute of Rare Diseases, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, 610000, Sichuan, China
- Center for Archaeological Science, Sichuan University, Chengdu, 610000, China
- Department of Forensic Medicine, College of Basic Medicine, Chongqing Medical University, Chongqing, 400331, China
| | - Kaijun Liu
- School of International Tourism and Culture, Guizhou Normal University, Guiyang, 550025, China
- MoFang Human Genome Research Institute, Tianfu Software Park, Chengdu, 610042, Sichuan, China
| | - Yan Liu
- Institute of Rare Diseases, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, 610000, Sichuan, China
- School of Basic Medical Sciences, North Sichuan Medical College, Nanchong, 637100, China
| | - Zhiyong Wang
- Institute of Rare Diseases, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, 610000, Sichuan, China
- Center for Archaeological Science, Sichuan University, Chengdu, 610000, China
- School of Forensic Medicine, Kunming Medical University, Kunming, 650500, China
| | - Xiangping Li
- Institute of Rare Diseases, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, 610000, Sichuan, China
- Center for Archaeological Science, Sichuan University, Chengdu, 610000, China
- School of Forensic Medicine, Kunming Medical University, Kunming, 650500, China
| | - Lanhai Wei
- School of Ethnology and Anthropology, Inner Mongolia Normal University, Hohhot, 010028, Inner Mongolia, China
| | - Yunhui Liu
- Institute of Rare Diseases, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, 610000, Sichuan, China
- Center for Archaeological Science, Sichuan University, Chengdu, 610000, China
- Department of Forensic Medicine, College of Basic Medicine, Chongqing Medical University, Chongqing, 400331, China
| | - Shengjie Nie
- School of Forensic Medicine, Kunming Medical University, Kunming, 650500, China
| | - Kun Zhou
- MoFang Human Genome Research Institute, Tianfu Software Park, Chengdu, 610042, Sichuan, China
| | - Yongxin Ma
- Department of Medical Genetics, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Huijun Yuan
- Institute of Rare Diseases, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, 610000, Sichuan, China
- Center for Archaeological Science, Sichuan University, Chengdu, 610000, China
| | - Bing Liu
- Institute of Forensic Science, Ministry of Public Security, Beijing, 100038, China
| | - Lan Hu
- Institute of Forensic Science, Ministry of Public Security, Beijing, 100038, China
| | - Chao Liu
- Anti-Drug Technology Center of Guangdong Province, Guangzhou, 510230, China.
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, 510515, China.
| | - Guanglin He
- Institute of Rare Diseases, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, 610000, Sichuan, China.
- Center for Archaeological Science, Sichuan University, Chengdu, 610000, China.
- Anti-Drug Technology Center of Guangdong Province, Guangzhou, 510230, China.
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7
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Wang B, Hao D, Xu Y, Zhu K, Wang R, Yang X, Shen Q, Xu M, Bai T, Ma H, Zheng J, Wang X, Zou X, Zhou H, Mao X, Tang J, Peng Y, Tao L, He H, Chen H, Guo J, Ji Z, Liu Y, Wen S, Jin L, Zhang Q, Wang CC. Population expansion from central plain to northern coastal China inferred from ancient human genomes. iScience 2024; 27:111405. [PMID: 39697594 PMCID: PMC11652891 DOI: 10.1016/j.isci.2024.111405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Revised: 08/06/2024] [Accepted: 11/13/2024] [Indexed: 12/20/2024] Open
Abstract
The population history of the northern coastal Chinese is largely unknown due to the lack of ancient human genomes from the Neolithic to historical periods. In this study, we reported 14 newly generated ancient genomes from Linzi, one of China's densely populated and economically prosperous cities from the Zhou to Han Dynasties. The ancient samples in this study were dated to the Warring States period to the Eastern Han Dynasty (∼2,000 BP). We found the samples derived all their ancestry from Late Bronze Age to Iron Age Middle Yellow River farmers rather than local Neolithic populations. They were genetically homogeneous with present-day Han Chinese of Shandong, suggesting 2,000 years of genetic stability. Our results highlight the role of the eastward migration of Yellow River farmers in the Central Plain to northern coastal China in forming the present-day genetic structure of Han Chinese.
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Affiliation(s)
- Baitong Wang
- Department of Anthropology and Ethnology, Institute of Anthropology, Fujian Provincial Key Laboratory of Philosophy and Social Sciences in Bioanthropology, School of Sociology and Anthropology, Xiamen University Xiamen 361005, China
| | - Daohua Hao
- Shandong Provincial Institute of Cultural Relics and Archaeology, Jinan 250012, China
| | - Yu Xu
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China
| | - Kongyang Zhu
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China
| | - Rui Wang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China
| | - Xiaomin Yang
- Department of Anthropology and Ethnology, Institute of Anthropology, Fujian Provincial Key Laboratory of Philosophy and Social Sciences in Bioanthropology, School of Sociology and Anthropology, Xiamen University Xiamen 361005, China
| | - Qu Shen
- Department of Anthropology and Ethnology, Institute of Anthropology, Fujian Provincial Key Laboratory of Philosophy and Social Sciences in Bioanthropology, School of Sociology and Anthropology, Xiamen University Xiamen 361005, China
| | - Mengting Xu
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China
| | - Tianyou Bai
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China
| | - Hao Ma
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China
| | - Jiajing Zheng
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China
| | - Xinyi Wang
- Department of Anthropology and Ethnology, Institute of Anthropology, Fujian Provincial Key Laboratory of Philosophy and Social Sciences in Bioanthropology, School of Sociology and Anthropology, Xiamen University Xiamen 361005, China
| | - Xinyue Zou
- Department of Anthropology and Ethnology, Institute of Anthropology, Fujian Provincial Key Laboratory of Philosophy and Social Sciences in Bioanthropology, School of Sociology and Anthropology, Xiamen University Xiamen 361005, China
| | - Hongming Zhou
- Department of Anthropology and Ethnology, Institute of Anthropology, Fujian Provincial Key Laboratory of Philosophy and Social Sciences in Bioanthropology, School of Sociology and Anthropology, Xiamen University Xiamen 361005, China
| | - Xiaolu Mao
- Department of Anthropology and Ethnology, Institute of Anthropology, Fujian Provincial Key Laboratory of Philosophy and Social Sciences in Bioanthropology, School of Sociology and Anthropology, Xiamen University Xiamen 361005, China
| | - Jiaxin Tang
- Department of Anthropology and Ethnology, Institute of Anthropology, Fujian Provincial Key Laboratory of Philosophy and Social Sciences in Bioanthropology, School of Sociology and Anthropology, Xiamen University Xiamen 361005, China
| | - Yanying Peng
- Department of Anthropology and Ethnology, Institute of Anthropology, Fujian Provincial Key Laboratory of Philosophy and Social Sciences in Bioanthropology, School of Sociology and Anthropology, Xiamen University Xiamen 361005, China
| | - Le Tao
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China
| | - Haifeng He
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China
| | - Haodong Chen
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China
| | - Jianxin Guo
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650201, China
| | - Zhi Ji
- Department of Anthropology and Ethnology, Institute of Anthropology, Fujian Provincial Key Laboratory of Philosophy and Social Sciences in Bioanthropology, School of Sociology and Anthropology, Xiamen University Xiamen 361005, China
| | - Yilan Liu
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China
| | - Shaoqing Wen
- Institute of Archaeological Science, Fudan University, Shanghai 200438, China
| | - Li Jin
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences and Human Phenome Institute, Fudan University, Shanghai 200433, China
- Ministry of Education Key Laboratory of Contemporary Anthropology, Department of Anthropology and Human Genetics, School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Qun Zhang
- Department of Archaeology, School of History, Wuhan University, Wuhan, China
| | - Chuan-Chao Wang
- Department of Anthropology and Ethnology, Institute of Anthropology, Fujian Provincial Key Laboratory of Philosophy and Social Sciences in Bioanthropology, School of Sociology and Anthropology, Xiamen University Xiamen 361005, China
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China
- Ministry of Education Key Laboratory of Contemporary Anthropology, Department of Anthropology and Human Genetics, School of Life Sciences, Fudan University, Shanghai 200433, China
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8
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Wang M, Liu Y, Luo L, Feng Y, Wang Z, Yang T, Yuan H, Liu C, He G. Genomic insights into Neolithic founding paternal lineages around the Qinghai-Xizang Plateau using integrated YanHuang resource. iScience 2024; 27:111456. [PMID: 39759003 PMCID: PMC11696643 DOI: 10.1016/j.isci.2024.111456] [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: 09/16/2024] [Revised: 10/16/2024] [Accepted: 11/19/2024] [Indexed: 01/07/2025] Open
Abstract
Indigenous populations of the Qinghai-Xizang Plateau exhibit unique high-altitude adaptations, especially within Tibeto-Burman (TB) groups. However, the paternal genetic heritage of eastern Plateau regions remains less explored. We present one integrative Y chromosome dataset of 9,901 modern and ancient individuals, including whole Y chromosome sequences from 1,297 individuals and extensive Y-SNP/STR genotype data. We reveal the Paleolithic common origin and following divergence of Qinghai-Xizang Plateau ancestors from East Asian lowlands, marked by subsequent isolation and Holocene expansion involving local hunter-gatherers and millet-farming communities. We identified two key TB-related founding lineages, D-Z31591 and O-CTS4658, which underwent significant expansions around 5,000 years ago on the Qinghai-Xizang Plateau and its eastern Tibetan-Yi Corridor. The genetic legacy of these TB lineages highlights crucial migration pathways linking the Plateau and lowland southwestern China. Our findings align paternal genetic structures with East Asian geography and linguistic groups, underscoring the utility of Y chromosome analyses in unraveling complex paternal histories.
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Affiliation(s)
- Mengge Wang
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu 610000, China
- Center for Archaeological Science, Sichuan University, Chengdu 610000, China
- Department of Forensic Medicine, College of Basic Medicine, Chongqing Medical University, Chongqing 400331, China
- Anti-Drug Technology Center of Guangdong Province, Guangzhou 510230, China
| | - Yunhui Liu
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu 610000, China
- Center for Archaeological Science, Sichuan University, Chengdu 610000, China
- Department of Forensic Medicine, College of Basic Medicine, Chongqing Medical University, Chongqing 400331, China
| | - Lintao Luo
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu 610000, China
- Center for Archaeological Science, Sichuan University, Chengdu 610000, China
- Department of Forensic Medicine, College of Basic Medicine, Chongqing Medical University, Chongqing 400331, China
| | - Yuhang Feng
- 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
- Center for Archaeological Science, Sichuan University, Chengdu 610000, China
- Department of Forensic Medicine, College of Basic Medicine, Chongqing Medical University, Chongqing 400331, China
| | - Ting Yang
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu 610000, China
- Center for Archaeological Science, Sichuan University, Chengdu 610000, China
| | - Huijun Yuan
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu 610000, China
- Center for Archaeological Science, Sichuan University, Chengdu 610000, China
| | - Chao Liu
- Anti-Drug Technology Center of Guangdong Province, Guangzhou 510230, China
| | - Guanglin He
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu 610000, China
- Center for Archaeological Science, Sichuan University, Chengdu 610000, China
- Department of Forensic Medicine, College of Basic Medicine, Chongqing Medical University, Chongqing 400331, China
- Anti-Drug Technology Center of Guangdong Province, Guangzhou 510230, China
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9
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Wang F, Wang R, Ma H, Zeng W, Zhao Y, Wu H, Tang Z, He H, Fang H, Wang CC. Neolithization of Dawenkou culture in the lower Yellow River involved the demic diffusion from the Central Plain. Sci Bull (Beijing) 2024; 69:3677-3681. [PMID: 39198092 DOI: 10.1016/j.scib.2024.08.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2024] [Revised: 07/31/2024] [Accepted: 08/01/2024] [Indexed: 09/01/2024]
Affiliation(s)
- Fen Wang
- School of Archaeology, Shandong University, Jinan 250100, China.
| | - Rui Wang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen 361102, China
| | - Hao Ma
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen 361102, China
| | - Wen Zeng
- School of Archaeology, Shandong University, Jinan 250100, China
| | - Yongsheng Zhao
- School of Archaeology, Shandong University, Jinan 250100, China
| | - Hao Wu
- School of Archaeology, Shandong University, Jinan 250100, China
| | - Zhongming Tang
- School of Archaeology, Shandong University, Jinan 250100, China
| | - Haifeng He
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen 361102, China
| | - Hui Fang
- School of Archaeology, Shandong University, Jinan 250100, China
| | - Chuan-Chao Wang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen 361102, China; Department of Anthropology and Ethnology, Institute of Anthropology, Fujian Provincial Key Laboratory of Philosophy and Social Sciences in Bioanthropology, School of Sociology and Anthropology, Xiamen University, Xiamen 361005, China.
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10
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Zhu K, Hu C, Yang M, Zhang X, Guo J, Xie M, Yang X, Ma H, Wang R, Zhao J, Tao L, He H, Wan W, Zhang Q, Jin L, Zuo Y, Zhou B, Huang J, Wang CC. The demic diffusion of Han culture into the Yunnan-Guizhou plateau inferred from ancient genomes. Natl Sci Rev 2024; 11:nwae387. [PMID: 39687206 PMCID: PMC11647586 DOI: 10.1093/nsr/nwae387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Revised: 10/27/2024] [Accepted: 10/28/2024] [Indexed: 12/18/2024] Open
Affiliation(s)
- Kongyang Zhu
- Key Laboratory of Environmental Pollution Monitoring and Disease Control, Ministry of Education, Department of Forensic Medicine, Guizhou Medical University, China
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, China
| | - Changguo Hu
- Guizhou Provincial Institute of Cultural Relics and Archaeology, China
| | - Meiqing Yang
- Key Laboratory of Environmental Pollution Monitoring and Disease Control, Ministry of Education, Department of Forensic Medicine, Guizhou Medical University, China
| | - Xinglong Zhang
- Guizhou Provincial Institute of Cultural Relics and Archaeology, China
| | - Jianxin Guo
- Department of Anthropology and Ethnology, Institute of Anthropology, Fujian Provincial Key Laboratory of Philosophy and Social Sciences in Bioanthropology, School of Sociology and Anthropology, Xiamen University, China
| | - Mingxia Xie
- Key Laboratory of Environmental Pollution Monitoring and Disease Control, Ministry of Education, Department of Forensic Medicine, Guizhou Medical University, China
| | - Xiaomin Yang
- Department of Anthropology and Ethnology, Institute of Anthropology, Fujian Provincial Key Laboratory of Philosophy and Social Sciences in Bioanthropology, School of Sociology and Anthropology, Xiamen University, China
| | - Hao Ma
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, China
| | - Rui Wang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, China
| | - Jing Zhao
- Department of Anthropology and Ethnology, Institute of Anthropology, Fujian Provincial Key Laboratory of Philosophy and Social Sciences in Bioanthropology, School of Sociology and Anthropology, Xiamen University, China
| | - Le Tao
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, China
| | - Haifeng He
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, China
| | - Wen Wan
- Key Laboratory of Environmental Pollution Monitoring and Disease Control, Ministry of Education, Department of Forensic Medicine, Guizhou Medical University, China
| | - Qun Zhang
- Department of Archaeology, School of History, Wuhan University, China
| | - Li Jin
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences and Human Phenome Institute, Fudan University, China
- Ministry of Education Key Laboratory of Contemporary Anthropology, Department of Anthropology and Human Genetics, School of Life Sciences, Fudan University, China
| | - Yunjie Zuo
- Guizhou Provincial Institute of Cultural Relics and Archaeology, China
| | - Bisu Zhou
- Guizhou Provincial Institute of Cultural Relics and Archaeology, China
| | - Jiang Huang
- Key Laboratory of Environmental Pollution Monitoring and Disease Control, Ministry of Education, Department of Forensic Medicine, Guizhou Medical University, China
| | - Chuan-Chao Wang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, China
- Department of Anthropology and Ethnology, Institute of Anthropology, Fujian Provincial Key Laboratory of Philosophy and Social Sciences in Bioanthropology, School of Sociology and Anthropology, Xiamen University, China
- Ministry of Education Key Laboratory of Contemporary Anthropology, Department of Anthropology and Human Genetics, School of Life Sciences, Fudan University, China
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11
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Li S, Wang R, Ma H, Tu Z, Qiu L, Chen H, Jiang L, Geng Y, Liu H, Wang J, Shen Q, Jin L, Li C, Wang CC, Wei X. Ancient genomic time transect unravels the population dynamics of Neolithic middle Yellow River farmers. Sci Bull (Beijing) 2024; 69:3365-3370. [PMID: 39277520 DOI: 10.1016/j.scib.2024.09.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Revised: 07/02/2024] [Accepted: 07/29/2024] [Indexed: 09/17/2024]
Affiliation(s)
- Shiwei Li
- Henan Provincial Institute of Cultural Heritage and Archaeology, Zhengzhou 450000, China
| | - Rui Wang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen 361102, China
| | - Hao Ma
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen 361102, China
| | - Zheng Tu
- National Engineering Laboratory for Forensic Science, Key Laboratory of Forensic Genetics of Ministry of Public Security, Beijing Engineering Research Center of Crime Scene Evidence Examination, Institute of Forensic Science, Beijing 100038, China
| | - Limin Qiu
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen 361102, China
| | - Haodong Chen
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen 361102, China
| | - Li Jiang
- National Engineering Laboratory for Forensic Science, Key Laboratory of Forensic Genetics of Ministry of Public Security, Beijing Engineering Research Center of Crime Scene Evidence Examination, Institute of Forensic Science, Beijing 100038, China
| | - Yuezu Geng
- National Engineering Laboratory for Forensic Science, Key Laboratory of Forensic Genetics of Ministry of Public Security, Beijing Engineering Research Center of Crime Scene Evidence Examination, Institute of Forensic Science, Beijing 100038, China
| | - Hai Liu
- Henan Provincial Public Security Forensic Science Centre, Zhengzhou 450003, China
| | - Jifeng Wang
- Henan Provincial Public Security Forensic Science Centre, Zhengzhou 450003, China
| | - Qu Shen
- Department of Anthropology and Ethnology, Institute of Anthropology, Fujian Provincial Key Laboratory of Philosophy and Social Sciences in Bioanthropology, School of Sociology and Anthropology, Xiamen University, Xiamen 361005, China
| | - Li Jin
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences and Human Phenome Institute, Fudan University, Shanghai 200433, China; Ministry of Education Key Laboratory of Contemporary Anthropology, Department of Anthropology and Human Genetics, School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Caixia Li
- National Engineering Laboratory for Forensic Science, Key Laboratory of Forensic Genetics of Ministry of Public Security, Beijing Engineering Research Center of Crime Scene Evidence Examination, Institute of Forensic Science, Beijing 100038, China.
| | - Chuan-Chao Wang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen 361102, China; Department of Anthropology and Ethnology, Institute of Anthropology, Fujian Provincial Key Laboratory of Philosophy and Social Sciences in Bioanthropology, School of Sociology and Anthropology, Xiamen University, Xiamen 361005, China; Ministry of Education Key Laboratory of Contemporary Anthropology, Department of Anthropology and Human Genetics, School of Life Sciences, Fudan University, Shanghai 200433, China; State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen 361102, China.
| | - Xingtao Wei
- Henan Provincial Institute of Cultural Heritage and Archaeology, Zhengzhou 450000, China.
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12
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Zhu K, He H, Tao L, Ma H, Yang X, Wang R, Guo J, Wang CC. Protocol for a comprehensive pipeline to study ancient human genomes. STAR Protoc 2024; 5:102985. [PMID: 38691462 PMCID: PMC11070629 DOI: 10.1016/j.xpro.2024.102985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Revised: 11/19/2023] [Accepted: 03/11/2024] [Indexed: 05/03/2024] Open
Abstract
Ancient genomics has revolutionized our understanding of human evolution and migration history in recent years. Here, we present a protocol to prepare samples for ancient genomics research. We describe steps for releasing DNA from human remains, DNA library construction, hybridization capture, quantification, and sequencing. We then detail procedures for mapping sequence reads and population genetics analysis. This protocol also outlines challenges in extracting ancient DNA samples and authenticating ancient DNA to uncover the genetic history and diversity of ancient populations. For complete details on the use and execution of this protocol, please refer to Tao et al.1.
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Affiliation(s)
- Kongyang Zhu
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen 361102, China
| | - Haifeng He
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen 361102, China
| | - Le Tao
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen 361102, China
| | - Hao Ma
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen 361102, China
| | - Xiaomin Yang
- Department of Anthropology and Ethnology, Institute of Anthropology, School of Sociology and Anthropology, Xiamen University Xiamen 361005, China
| | - Rui Wang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen 361102, China
| | - Jianxin Guo
- Department of Anthropology and Ethnology, Institute of Anthropology, School of Sociology and Anthropology, Xiamen University Xiamen 361005, China; State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650201, China.
| | - Chuan-Chao Wang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen 361102, China; Department of Anthropology and Ethnology, Institute of Anthropology, School of Sociology and Anthropology, Xiamen University Xiamen 361005, China; Ministry of Education Key Laboratory of Contemporary Anthropology, Department of Anthropology and Human Genetics, School of Life Sciences, Fudan University, Shanghai 200433, China; State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, Fujian 361102, China; Institute of Artificial Intelligence, Xiamen University, Xiamen, Fujian 361005, China.
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13
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Bellwood P. Archaeogenetics: Tracing ancient migrations from the Yellow River. Curr Biol 2024; 34:R18-R20. [PMID: 38194921 DOI: 10.1016/j.cub.2023.11.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2024]
Abstract
Migration from the Yellow River homeland of Sino-Tibetan languages and people has impacted humans in East Asia for more than 6,000 years. A new study of ancient DNA from southwest China reveals an important component of this migration history.
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Affiliation(s)
- Peter Bellwood
- School of Archaeology and Anthropology, Australian National University, Canberra, ACT 2600, Australia.
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