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Zhang M, Song Y, Wang C, Sun G, Zhuang L, Guo M, Ren L, Wangdue S, Dong G, Dai Q, Cao P, Yang R, Liu F, Feng X, Bennett EA, Zhang X, Chen X, Wang F, Luan F, Dong W, Lu G, Hao D, Hou H, Wang H, Qiao H, Wang Z, Hu X, He W, Xi L, Wang W, Shao J, Sun Z, Yue L, Ding Y, Tashi N, Tsho Y, Tong Y, Yang Y, Zhu S, Miao B, Wang W, Zhang L, Hu S, Ni X, Fu Q. Ancient Mitogenomes Reveal the Maternal Genetic History of East Asian Dogs. Mol Biol Evol 2024; 41:msae062. [PMID: 38507661 PMCID: PMC11003542 DOI: 10.1093/molbev/msae062] [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: 07/22/2023] [Revised: 02/27/2024] [Accepted: 03/11/2024] [Indexed: 03/22/2024] Open
Abstract
Recent studies have suggested that dogs were domesticated during the Last Glacial Maximum (LGM) in Siberia, which contrasts with previous proposed domestication centers (e.g. Europe, the Middle East, and East Asia). Ancient DNA provides a powerful resource for the study of mammalian evolution and has been widely used to understand the genetic history of domestic animals. To understand the maternal genetic history of East Asian dogs, we have made a complete mitogenome dataset of 120 East Asian canids from 38 archaeological sites, including 102 newly sequenced from 12.9 to 1 ka BP (1,000 years before present). The majority (112/119, 94.12%) belonged to haplogroup A, and half of these (55/112, 49.11%) belonged to sub-haplogroup A1b. Most existing mitochondrial haplogroups were present in ancient East Asian dogs. However, mitochondrial lineages in ancient northern dogs (northeastern Eurasia and northern East Asia) were deeper and older than those in southern East Asian dogs. Results suggests that East Asian dogs originated from northeastern Eurasian populations after the LGM, dispersing in two possible directions after domestication. Western Eurasian (Europe and the Middle East) dog maternal ancestries genetically influenced East Asian dogs from approximately 4 ka BP, dramatically increasing after 3 ka BP, and afterwards largely replaced most primary maternal lineages in northern East Asia. Additionally, at least three major mitogenome sub-haplogroups of haplogroup A (A1a, A1b, and A3) reveal at least two major dispersal waves onto the Qinghai-Tibet Plateau in ancient times, indicating eastern (A1b and A3) and western (A1a) Eurasian origins.
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Affiliation(s)
- 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 Culture Heritage, Northwest University, Xi’an, China
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing, China
| | - Yanbo Song
- School of Archaeology, Shandong University, Jinan, China
| | - Caihui Wang
- China-Central Asia “the Belt and Road” Joint Laboratory on Human and Environment Research, Key Laboratory of Cultural Heritage Research and Conservation, School of Culture Heritage, Northwest University, Xi’an, China
| | - Guoping Sun
- Zhejiang Provincial Institute of Cultural Relics and Archaeology, Hangzhou, China
| | | | | | - Lele Ren
- School of History and Culture, Lanzhou University, Lanzhou, China
| | - Shargan Wangdue
- Tibet Institute for Conservation and Research of Cultural Relics, Lhasa, China
| | - Guanghui Dong
- Key Laboratory of Western China's Environmental Systems (Ministry of Education), College of Earth and Environmental Sciences, Lanzhou University, Lanzhou, China
| | - Qingyan Dai
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing, China
| | - Peng Cao
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing, China
| | - Ruowei Yang
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing, China
| | - Feng Liu
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing, China
| | - Xiaotian Feng
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing, China
| | - E Andrew Bennett
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing, China
| | - Xiaoling Zhang
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing, China
| | - Xi Chen
- Department of Cultural Heritage and Museology, Nanjing Normal University, Nanjing, China
| | - Fen Wang
- School of Archaeology, Shandong University, Jinan, China
| | - Fengshi Luan
- School of Archaeology, Shandong University, Jinan, China
| | - Wenbin Dong
- Shandong Provincial Institute of Cultural Relics and Archaeology, Jinan, China
| | - Guoquan Lu
- School of Archaeology, Shandong University, Jinan, China
| | - Daohua Hao
- Shandong Provincial Institute of Cultural Relics and Archaeology, Jinan, China
| | - Hongwei Hou
- Gansu Provincial Institute of Cultural Relics and Archaeology, Lanzhou, China
| | - Hui Wang
- Gansu Provincial Institute of Cultural Relics and Archaeology, Lanzhou, China
- Fudan Archaeological Science Institute, Fudan University, Shanghai, China
| | - Hong Qiao
- Qinghai Provincial Cultural Relics and Archaeology Institute, Xining, China
| | - Zhongxin Wang
- Qinghai Provincial Cultural Relics and Archaeology Institute, Xining, China
| | - Xiaojun Hu
- Qinghai Provincial Cultural Relics and Archaeology Institute, Xining, China
| | - Wei He
- Tibet Institute for Conservation and Research of Cultural Relics, Lhasa, China
| | - Lin Xi
- Shaanxi Academy of Archaeology, Xi’an, China
| | - Weilin Wang
- School of Archaeology and Museology, Shanxi University, Taiyuan, China
| | - Jing Shao
- Shaanxi Academy of Archaeology, Xi’an, China
| | | | | | - Yan Ding
- Shaanxi Academy of Archaeology, Xi’an, China
| | - Norbu Tashi
- Tibet Institute for Conservation and Research of Cultural Relics, Lhasa, China
| | - Yang Tsho
- Tibet Institute for Conservation and Research of Cultural Relics, Lhasa, China
| | - Yan Tong
- Tibet Institute for Conservation and Research of Cultural Relics, Lhasa, China
| | - Yangheshan Yang
- School of Ecological and Environmental Sciences, East China Normal University, Shanghai, China
| | - Shilun Zhu
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing, China
- University of the Chinese Academy of Sciences, Beijing, China
| | - Bo Miao
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing, China
| | - Wenjun Wang
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing, China
- Science and Technology Archaeology, National Centre for Archaeology, Beijing, China
| | - Lizhao Zhang
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing, China
| | - Songmei Hu
- Joint International Research Laboratory of Environmental and Social Archaeology, Shandong University, Qingdao, China
- Shaanxi Academy of Archaeology, Xi’an, China
| | - Xijun Ni
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing, China
- University of the Chinese Academy of Sciences, Beijing, China
| | - Qiaomei Fu
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing, China
- University of the Chinese Academy of Sciences, Beijing, China
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Ávila-Arcos MC, Raghavan M, Schlebusch C. Going local with ancient DNA: A review of human histories from regional perspectives. Science 2023; 382:53-58. [PMID: 37797024 DOI: 10.1126/science.adh8140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2023] [Accepted: 09/05/2023] [Indexed: 10/07/2023]
Abstract
Ancient DNA (aDNA) has added a wealth of information about our species' history, including insights on genetic origins, migrations and gene flow, genetic admixture, and health and disease. Much early work has focused on continental-level questions, leaving many regional questions, especially those relevant to the Global South, comparatively underexplored. A few success stories of aDNA studies from smaller laboratories involve more local aspects of human histories and health in the Americas, Africa, Asia, and Oceania. In this Review, we cover some of these contributions by synthesizing finer-scale questions of importance to the archaeogenetics field, as well as to Indigenous and Descendant communities. We further highlight the potential of aDNA to uncover past histories in regions where colonialism has neglected the oral histories of oppressed peoples.
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Affiliation(s)
- María C Ávila-Arcos
- International Laboratory for Human Genome Research, Universidad Nacional Autónoma de México, Querétaro, Mexico
| | - Maanasa Raghavan
- Department of Human Genetics, University of Chicago, Chicago, IL, USA
| | - Carina Schlebusch
- Human Evolution, Department of Organismal Biology, Uppsala University, Uppsala, Sweden
- Palaeo-Research Institute, University of Johannesburg, Johannesburg, South Africa
- SciLifeLab, Uppsala, Sweden
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Lin Z, Zhu Z, Zhuang M, Wang Z, Zhang Y, Gao F, Niu Q, Ji T. Effects of local domestication warrant attention in honey bee population genetics. SCIENCE ADVANCES 2023; 9:eade7917. [PMID: 37134176 PMCID: PMC10156114 DOI: 10.1126/sciadv.ade7917] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Honey bees, Apis mellifera, have for millennia been managed and exploited by humans and introduced into most suitable regions worldwide. However, given the lack of records for many introduction events, treating A. mellifera populations as native would predictably bias genetic studies regarding origin and evolution. Here, we used the Dongbei bee, a well-documented population, introduced beyond the natural distribution range approximately 100 years ago, to elucidate the effects of local domestication on animal population genetic analyses. Strong domestication pressure was detected in this population, and the genetic divergence between Dongbei bee and its ancestral subspecies was found to have occurred at the lineage level. Results of phylogenetic and time divergence analyses could consequently be misinterpreted. Proposing new subspecies or lineages and performing analyses of origin should thus strive to eliminate anthropogenic effects. We highlight the need for definitions of landrace and breed in honey bee sciences and make preliminary suggestions.
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Affiliation(s)
- Zheguang Lin
- Apicultural Research Institute, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Zhongxu Zhu
- Department of Biomedical Sciences, City University of Hong Kong, Hong Kong SAR, China
| | - Mingliang Zhuang
- Apiculture Science Institute of Jilin Province, Jilin 132108, China
| | - Zhi Wang
- Apiculture Science Institute of Jilin Province, Jilin 132108, China
| | - Yi Zhang
- Apicultural Research Institute, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Fuchao Gao
- Mudanjiang Branch of Heilongjiang Academy of Agricultural Sciences, Mudanjiang 157043, China
| | - Qingsheng Niu
- Apiculture Science Institute of Jilin Province, Jilin 132108, China
| | - Ting Ji
- Apicultural Research Institute, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
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Wang Y, Kahaer A, Shi W, Guo H, Rexiti P. Morphometric measurement of lumbar pedicle in different regions: a systematic review. J Orthop Surg Res 2023; 18:30. [PMID: 36631862 PMCID: PMC9832728 DOI: 10.1186/s13018-023-03499-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 01/01/2023] [Indexed: 01/13/2023] Open
Abstract
OBJECTIVE To collect the data of pedicle width and height in different areas, and to investigate the difference and variation rule of pedicle width and height. METHODS Comprehensive search of PubMed, Ovid Medline, and Web of science databases was performed. Collected data were imported into SPSS, and one-way ANOVA test and post hoc test were used to determine whether there were statistical differences in pedicle width and height between the different regions. RESULTS Oceania had the largest pedicle width and height, followed by Americans. West Asian had the largest pedicle width in Asia, followed by East and Southeast Asian, and Chinese and South Asian had similar pedicle width. Different from the variation pattern of pedicle width, the pedicle height of Chinese, East and Southeast Asian and West Asian in Asian range is similar, but the pedicle height of South Asian is significantly smaller than the first three, and has statistical significance. CONCLUSIONS People in different regions have similar patterns of variation in pedicle width and height even though they belong to different ethnic groups. This phenomenon is particularly prominent and pronounced in populations in geographically close areas, which may be related to inter-ethnic integration due to population movement between adjacent areas. There is a relationship between the morphological characteristics of the human lumbar pedicle and geographical location.
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Affiliation(s)
- Yixi Wang
- grid.13394.3c0000 0004 1799 3993First Clinical Medical College, Xinjiang Medical University, Urumqi, China
| | - Alafate Kahaer
- grid.412631.3Departments of Spine Surgery, Xinjiang Uygur Autonomous Region, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, 830054 China
| | - Wenjie Shi
- grid.13394.3c0000 0004 1799 3993First Clinical Medical College, Xinjiang Medical University, Urumqi, China
| | - Hailong Guo
- grid.412631.3Departments of Spine Surgery, Xinjiang Uygur Autonomous Region, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, 830054 China
| | - Paerhati Rexiti
- grid.412631.3Departments of Spine Surgery, Xinjiang Uygur Autonomous Region, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, 830054 China
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5
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Fu Q. Insights into evolutionary dynamics of East Asians through Ancient DNA. CHINESE SCIENCE BULLETIN-CHINESE 2022. [DOI: 10.1360/tb-2022-0569] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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6
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The genomic history of southwestern Chinese populations demonstrated massive population migration and admixture among proto-Hmong-Mien speakers and incoming migrants. Mol Genet Genomics 2022; 297:241-262. [PMID: 35031862 DOI: 10.1007/s00438-021-01837-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 11/10/2021] [Indexed: 10/19/2022]
Abstract
Southwest China was the crossroad for the initial settler people of East Asia, which shows the highest diversity in languages and genetics. This region played a significant role in the formation of the genetic makeup of the proto-Hmong-Mien-speaking people and in the north-to-south human expansion during the Neolithic-to-historic transformation. Their genetic history covering migration events and the admixture processes still needs to be further explored. Therefore, in the current study, we have generated genome-wide data from three genomic aspects covering autosomal, mitochondrial and Y-chromosomal regions in 260 Hmong-Mien, Tibeto-Burman, and Sinitic people from 29 different southwestern Chinese groups, and further analyzed them with 2676 published modern and ancient Eurasian genomes. Here, we have noticed a new southwestern East Asian genetic cline composed of the Hmong-Mien-specific ancestry enriched in modern Hmong and Pathen. This newly identified southern inland East Asian lineage contributed to a great extent of the gene pool in the modern southern East Asians. We also have observed genetic substructure among Hmong-Mien-speaking populations. The southern Hmong-Mien-speaking people showed more genetic affinity with modern Tai-Kadai/Austroasiatic people, while the northern Hmong-Mien speakers expressed a closer genetic connection with the Neolithic-to-modern northern East Asians. Moreover, southwestern Sinitic populations had a strong genomic affinity with the adjacent Hmong-Mien-speaking populations and the lowlander Tibeto-Burman-speaking populations, which suggested the large-scale genetic admixture occurred between them. Allele-sharing-based qpAdm/qpGraph results further confirmed that all included southwestern Chinese populations could be modeled as a mixed result of the major ancestry component from the northern millet farmers in the Yellow River basin and the minor ancestry component from the southern rice farmers in the Yangtze River basin. Usually, this newly identified Hmong-Mien-associated southern East Asian ancestry could improve our understanding of the full-scale genetic landscape of the evolutionary and admixture history of southwestern East Asians. Further ancient genomic studies from southeastern China are required to shed deeper light on our established phylogeny context.
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Liu Y, Wang T, Wu X, Fan X, Wang W, Xie G, Li Z, Yang Q, Cao P, Yang R, Liu F, Dai Q, Feng X, Ping W, Miao B, Wu Y, Liu Y, Fu Q. Maternal genetic history of southern East Asians over the past 12,000 years. J Genet Genomics 2021; 48:899-907. [PMID: 34419425 DOI: 10.1016/j.jgg.2021.06.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 06/04/2021] [Accepted: 06/05/2021] [Indexed: 12/13/2022]
Abstract
Southern East Asia, including Guangxi and Fujian provinces in China, is home to diverse ethnic groups, languages, and cultures. Previous studies suggest a high complexity regarding population dynamics and the history of southern East Asians. However, large-scale genetic studies on ancient populations in this region are hindered by limited sample preservation. Here, using highly efficient DNA capture techniques, we obtain 48 complete mitochondrial genomes of individuals from Guangxi and Fujian in China and reconstruct their maternal genetic history over the past 12,000 years. We find a strong connection between southern East Asians dating to ~12,000-6000 years ago and present-day Southeast Asians. In addition, stronger genetic affinities to northern East Asians are observed in historical southern East Asians than Neolithic southern East Asians, suggesting increased interactions between northern and southern East Asians over time. Overall, we reveal dynamic connections between ancient southern East Asians and populations located in surrounding regions, as well as a shift in maternal genetic structure within the populations over time.
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Affiliation(s)
- Yalin Liu
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing 100044, China; Sino-Danish Center, University of the Chinese Academy of Sciences, Beijing 100049, China; University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Tianyi Wang
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing 100044, China; University of the Chinese Academy of Sciences, Beijing 100049, China; Northwest University, Xi'an 710069, China
| | - Xichao Wu
- Fujian Longyan Museum, Longyan 364000, China
| | - Xuechun Fan
- International Research Center for Austronesian Archaeology, Pingtan 350000, China; Fujian Museum, Fuzhou 350001, China
| | - Wei Wang
- Institute of Cultural Heritage, Shandong University, Qingdao 266237, China
| | - Guangmao Xie
- Guangxi Institute of Cultural Relic Protection and Archaeology, Nanning 530022, China; College of History, Culture and Tourism, Guangxi Normal University, Guilin 541001, China
| | - Zhen Li
- Guangxi Institute of Cultural Relic Protection and Archaeology, Nanning 530022, China
| | - Qingping Yang
- Guangxi Institute of Cultural Relic Protection and Archaeology, Nanning 530022, China
| | - Peng Cao
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing 100044, China
| | - Ruowei Yang
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing 100044, China
| | - Feng Liu
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing 100044, China
| | - Qingyan Dai
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing 100044, China
| | - Xiaotian Feng
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing 100044, China
| | - Wanjing Ping
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing 100044, China
| | - Bo Miao
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing 100044, China; Northwest University, Xi'an 710069, China
| | - Yun Wu
- Yunnan Institute of Cultural Relics and Archaeology, Kunming 650118, China; Archaeological Institute for Yangtze Civilization, Wuhan University, Wuhan 430072, China
| | - Yichen Liu
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing 100044, China.
| | - Qiaomei Fu
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing 100044, China; University of the Chinese Academy of Sciences, Beijing 100049, China.
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Zhang X, Sun A, Ge J. Origin and Spread of the ALDH2 Glu504Lys Allele. PHENOMICS (CHAM, SWITZERLAND) 2021; 1:222-228. [PMID: 36939783 PMCID: PMC9590465 DOI: 10.1007/s43657-021-00017-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 04/28/2021] [Accepted: 05/19/2021] [Indexed: 01/14/2023]
Abstract
Gene polymorphism of acetaldehyde dehydrogenase 2 (ALDH2), a key enzyme for alcohol metabolism in humans, can affect catalytic activity. The ALDH2 Glu504Lys mutant allele has a high-frequency distribution in East Asian populations and has been demonstrated to be associated with an increased risk of cardiovascular disease, stroke, and tumors. Available evidence suggests that the evolution of the ALDH2 gene has been influenced by multiple factors. Random mutations produce Glu504Lys, and genetic drift alters the frequency of this allele; additionally, environmental factors such as hepatitis B virus infection and high-elevation hypoxia affect its frequency through selective effects, ultimately resulting in a high frequency of this allele in East Asian populations. Here, the origin, selection, and spread of the ALDH2 Glu504Lys allele are discussed, and an outlook for further research is proposed to realize a precision medical strategy based on the genetic and environmental variations in ALDH2.
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Affiliation(s)
- Xiaokai Zhang
- Department of Cardiology, Zhongshan Hospital, Fudan University, Shanghai Institute of Cardiovascular Diseases, Shanghai 200032, China
| | - Aijun Sun
- Department of Cardiology, Zhongshan Hospital, Fudan University, Shanghai Institute of Cardiovascular Diseases, Shanghai 200032, China
- Institute of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Junbo Ge
- Department of Cardiology, Zhongshan Hospital, Fudan University, Shanghai Institute of Cardiovascular Diseases, Shanghai 200032, China
- Institute of Biomedical Sciences, Fudan University, Shanghai 200032, China
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Yousaf A, Liu J, Ye S, Chen H. Current Progress in Evolutionary Comparative Genomics of Great Apes. Front Genet 2021; 12:657468. [PMID: 34456962 PMCID: PMC8385753 DOI: 10.3389/fgene.2021.657468] [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: 01/22/2021] [Accepted: 07/15/2021] [Indexed: 12/04/2022] Open
Abstract
The availability of high-quality genome sequences of great ape species provides unprecedented opportunities for genomic analyses. Herein, we reviewed the recent progress in evolutionary comparative genomic studies of the existing great ape species, including human, chimpanzee, bonobo, gorilla, and orangutan. We elaborate discovery on evolutionary history, natural selection, structural variations, and new genes of these species, which is informative for understanding the origin of human-specific phenotypes.
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Affiliation(s)
- Aisha Yousaf
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.,China National Center for Bioinformation, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Junfeng Liu
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.,China National Center for Bioinformation, Beijing, China
| | - Sicheng Ye
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.,China National Center for Bioinformation, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Hua Chen
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.,China National Center for Bioinformation, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China.,CAS Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
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10
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Chen J, He G, Ren Z, Wang Q, Liu Y, Zhang H, Yang M, Zhang H, Ji J, Zhao J, Guo J, Zhu K, Yang X, Wang R, Ma H, Wang CC, Huang J. Genomic Insights Into the Admixture History of Mongolic- and Tungusic-Speaking Populations From Southwestern East Asia. Front Genet 2021; 12:685285. [PMID: 34239544 PMCID: PMC8258170 DOI: 10.3389/fgene.2021.685285] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Accepted: 05/05/2021] [Indexed: 12/17/2022] Open
Abstract
As a major part of the modern Trans-Eurasian or Altaic language family, most of the Mongolic and Tungusic languages were mainly spoken in northern China, Mongolia, and southern Siberia, but some were also found in southern China. Previous genetic surveys only focused on the dissection of genetic structure of northern Altaic-speaking populations; however, the ancestral origin and genomic diversification of Mongolic and Tungusic-speaking populations from southwestern East Asia remain poorly understood because of the paucity of high-density sampling and genome-wide data. Here, we generated genome-wide data at nearly 700,000 single-nucleotide polymorphisms (SNPs) in 26 Mongolians and 55 Manchus collected from Guizhou province in southwestern China. We applied principal component analysis (PCA), ADMIXTURE, f statistics, qpWave/qpAdm analysis, qpGraph, TreeMix, Fst, and ALDER to infer the fine-scale population genetic structure and admixture history. We found significant genetic differentiation between northern and southern Mongolic and Tungusic speakers, as one specific genetic cline of Manchu and Mongolian was identified in Guizhou province. Further results from ADMIXTURE and f statistics showed that the studied Guizhou Mongolians and Manchus had a strong genetic affinity with southern East Asians, especially for inland southern East Asians. The qpAdm-based estimates of ancestry admixture proportion demonstrated that Guizhou Mongolians and Manchus people could be modeled as the admixtures of one northern ancestry related to northern Tungusic/Mongolic speakers or Yellow River farmers and one southern ancestry associated with Austronesian, Tai-Kadai, and Austroasiatic speakers. The qpGraph-based phylogeny and neighbor-joining tree further confirmed that Guizhou Manchus and Mongolians derived approximately half of the ancestry from their northern ancestors and the other half from southern Indigenous East Asians. The estimated admixture time ranged from 600 to 1,000 years ago, which further confirmed the admixture events were mediated via the Mongolians Empire expansion during the formation of the Yuan dynasty.
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Affiliation(s)
- Jing Chen
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, China
| | - Guanglin He
- State Key Laboratory of Cellular Stress Biology, State Key Laboratory of Marine Environmental Science, Department of Anthropology and Ethnology, Institute of Anthropology, National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, China
| | - Zheng Ren
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, China
| | - Qiyan Wang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, China
| | - Yubo Liu
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, China
| | - Hongling Zhang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, China
| | - Meiqing Yang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, China
| | - Han Zhang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, China
| | - Jingyan Ji
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, China
| | - Jing Zhao
- State Key Laboratory of Cellular Stress Biology, State Key Laboratory of Marine Environmental Science, Department of Anthropology and Ethnology, Institute of Anthropology, National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, China
| | - Jianxin Guo
- State Key Laboratory of Cellular Stress Biology, State Key Laboratory of Marine Environmental Science, Department of Anthropology and Ethnology, Institute of Anthropology, National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, China
| | - Kongyang Zhu
- State Key Laboratory of Cellular Stress Biology, State Key Laboratory of Marine Environmental Science, Department of Anthropology and Ethnology, Institute of Anthropology, National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, China
| | - Xiaomin Yang
- State Key Laboratory of Cellular Stress Biology, State Key Laboratory of Marine Environmental Science, Department of Anthropology and Ethnology, Institute of Anthropology, National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, China
| | - Rui Wang
- State Key Laboratory of Cellular Stress Biology, State Key Laboratory of Marine Environmental Science, Department of Anthropology and Ethnology, Institute of Anthropology, National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, China
| | - Hao Ma
- State Key Laboratory of Cellular Stress Biology, State Key Laboratory of Marine Environmental Science, Department of Anthropology and Ethnology, Institute of Anthropology, National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, China
| | - Chuan-Chao Wang
- State Key Laboratory of Cellular Stress Biology, State Key Laboratory of Marine Environmental Science, Department of Anthropology and Ethnology, Institute of Anthropology, National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, China
- School of Basic Medical Sciences, Zhejiang University School of Medicine, Hangzhou, China
| | - Jiang Huang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, China
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11
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Liu J, Zeng W, Sun B, Mao X, Zhao Y, Wang F, Li Z, Luan F, Guo J, Zhu C, Wang Z, Wei C, Zhang M, Cao P, Liu F, Dai Q, Feng X, Yang R, Hou W, Ping W, Wu X, Andrew Bennett E, Liu Y, Fu Q. Maternal genetic structure in ancient Shandong between 9500 and 1800 years ago. Sci Bull (Beijing) 2021; 66:1129-1135. [PMID: 36654346 DOI: 10.1016/j.scib.2021.01.029] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2020] [Revised: 08/06/2020] [Accepted: 09/28/2020] [Indexed: 01/20/2023]
Abstract
Archaeological and ancient DNA studies revealed that Shandong, a multi-culture center in northern coastal China, was home to ancient populations having ancestry related to both northern and southern East Asian populations. However, the limited temporal and geographical range of previous studies have been insufficient to describe the population history of this region in greater detail. Here, we report the analysis of 86 complete mitochondrial genomes from the remains of 9500 to 1800-year-old humans from 12 archaeological sites across Shandong. For samples older than 4600 years before present (BP), we found haplogroups D4, D5, B4c1, and B5b2, which are observed in present-day northern and southern East Asians. For samples younger than 4600 BP, haplogroups C (C7a1 and C7b), M9 (M9a1), and F (F1a1, F2a, and F4a1) begin to appear, indicating changes in the Shandong maternal genetic structure starting from the beginning of the Longshan cultural period. Within Shandong, the genetic exchange is possible between the coastal and inland regions after 3100 BP. We also discovered the B5b2 lineage in Shandong populations, with the oldest Bianbian individual likely related to the ancestors of some East Asians and North Asians. By reconstructing a maternal genetic structure of Shandong populations, we provide greater resolution of the population dynamics of the northern coastal East Asia over the past nine thousand years.
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Affiliation(s)
- Juncen Liu
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China; Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing 100044, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wen Zeng
- Institute of Cultural Heritage, Shandong University, Qingdao 266237, China
| | - Bo Sun
- Shandong Provincial Institute of Cultural Relics and Archaeology, Jinan 250012, China
| | - Xiaowei Mao
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China; Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing 100044, China
| | - Yongsheng Zhao
- Institute of Cultural Heritage, Shandong University, Qingdao 266237, China
| | - Fen Wang
- School of History and Culture, Shandong University, Jinan 250100, China
| | - Zhenguang Li
- Shandong Provincial Institute of Cultural Relics and Archaeology, Jinan 250012, China
| | - Fengshi Luan
- School of History and Culture, Shandong University, Jinan 250100, China
| | - Junfeng Guo
- Jinan Municipal Institute of Archaeology, Jinan 250062, China
| | - Chao Zhu
- Shandong Provincial Institute of Cultural Relics and Archaeology, Jinan 250012, China
| | - Zimeng Wang
- Shandong Provincial Institute of Cultural Relics and Archaeology, Jinan 250012, China
| | - Chengmin Wei
- Shandong Provincial Institute of Cultural Relics and Archaeology, Jinan 250012, China
| | - Ming Zhang
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China; Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing 100044, China; University of Chinese Academy of Sciences, Beijing 100049, 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
| | - Weihong Hou
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China; Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing 100044, China
| | - Wanjing Ping
- 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
| | - E Andrew Bennett
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China; Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing 100044, China
| | - Yichen Liu
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China; Center for Excellence in Life and Paleoenvironment, 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; Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing 100044, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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12
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Yao H, Wang M, Zou X, Li Y, Yang X, Li A, Yeh HY, Wang P, Wang Z, Bai J, Guo J, Chen J, Ding X, Zhang Y, Lin B, Wang CC, He G. New insights into the fine-scale history of western-eastern admixture of the northwestern Chinese population in the Hexi Corridor via genome-wide genetic legacy. Mol Genet Genomics 2021; 296:631-651. [PMID: 33650010 DOI: 10.1007/s00438-021-01767-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2020] [Accepted: 02/08/2021] [Indexed: 02/06/2023]
Abstract
Trans-Eurasian cultural and genetic exchanges have significantly influenced the demographic dynamics of Eurasian populations. The Hexi Corridor, located along the southeastern edge of the Eurasian steppe, served as an important passage of the ancient Silk Road in Northwest China and intensified the transcontinental exchange and interaction between populations on the Central Plain and in Western Eurasia. Historical and archeological records indicate that the Western Eurasian cultural elements were largely brought into North China via this geographical corridor, but there is debate on the extent to which the spread of barley/wheat agriculture into North China and subsequent Bronze Age cultural and technological mixture/shifts were achieved by the movement of people or dissemination of ideas. Here, we presented higher-resolution genome-wide autosomal and uniparental Y/mtDNA SNP or STR data for 599 northwestern Han Chinese individuals and conducted 2 different comprehensive genetic studies among Neolithic-to-present-day Eurasians. Genetic studies based on lower-resolution STR markers via PCA, STRUCTURE, and phylogenetic trees showed that northwestern Han Chinese individuals had increased genetic homogeneity relative to northern Mongolic/Turkic/Tungusic speakers and Tibeto-Burman groups. The genomic signature constructed based on modern/ancient DNA further illustrated that the primary ancestry of the northwestern Han was derived from northern millet farmer ancestors, which was consistent with the hypothesis of Han origin in North China and more recent northwestward population expansion. This was subsequently confirmed via excess shared derived alleles in f3/f4 statistical analyses and by more northern East Asian-related ancestry in the qpAdm/qpGraph models. Interestingly, we identified one western Eurasian admixture signature that was present in northwestern Han but absent from southern Han, with an admixture time dated to approximately 1000 CE (Tang and Song dynasties). Generally, we provided supporting evidence that historic Trans-Eurasian communication was primarily maintained through population movement, not simply cultural diffusion. The observed population dynamics in northwestern Han Chinese not only support the North China origin hypothesis but also reflect the multiple sources of the genetic diversity observed in this population.
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Affiliation(s)
- Hongbin Yao
- Belt and Road Research Center for Forensic Molecular Anthropology Gansu University of Political Science and Law, Lanzhou, 730000, China.
| | - Mengge Wang
- Institute of Forensic Medicine, West China School of Basic Science and Forensic Medicine, Sichuan University, Chengdu, 610065, China
| | - Xing Zou
- Institute of Forensic Medicine, West China School of Basic Science and Forensic Medicine, Sichuan University, Chengdu, 610065, China
| | - Yingxiang Li
- Department of Anthropology and Ethnology, Institute of Anthropology, National Institute for Data Science in Health and Medicine, School of Life Sciences, Xiamen University, Xiamen, 361005, China.,AnLan AI, Shenzhen, China
| | - Xiaomin Yang
- Department of Anthropology and Ethnology, Institute of Anthropology, National Institute for Data Science in Health and Medicine, School of Life Sciences, Xiamen University, Xiamen, 361005, China
| | - Ailin Li
- Belt and Road Research Center for Forensic Molecular Anthropology Gansu University of Political Science and Law, Lanzhou, 730000, China
| | - Hui-Yuan Yeh
- School of Humanities, Nanyang Technological University, Nanyang, Singapore, 639798, Singapore
| | - Peixin Wang
- College of Medical Information, Chongqing Medical University, Chongqing, 400331, China
| | - Zheng Wang
- Institute of Forensic Medicine, West China School of Basic Science and Forensic Medicine, Sichuan University, Chengdu, 610065, China
| | - Jingya Bai
- Department of Medicine, Northwest Minzu University, Lanzhou, 730000, Gansu, China.,Key Laboratory for Physique and Health of the Minorities, Northwest Minzu University, Lanzhou, 730000, Gansu, China
| | - Jianxin Guo
- Department of Anthropology and Ethnology, Institute of Anthropology, National Institute for Data Science in Health and Medicine, School of Life Sciences, Xiamen University, Xiamen, 361005, China
| | - Jinwen Chen
- Department of Anthropology and Ethnology, Institute of Anthropology, National Institute for Data Science in Health and Medicine, School of Life Sciences, Xiamen University, Xiamen, 361005, China
| | - Xiao Ding
- Belt and Road Research Center for Forensic Molecular Anthropology Gansu University of Political Science and Law, Lanzhou, 730000, China
| | - Yan Zhang
- Belt and Road Research Center for Forensic Molecular Anthropology Gansu University of Political Science and Law, Lanzhou, 730000, China
| | - Baoquan Lin
- Belt and Road Research Center for Forensic Molecular Anthropology Gansu University of Political Science and Law, Lanzhou, 730000, China
| | - Chuan-Chao Wang
- Department of Anthropology and Ethnology, Institute of Anthropology, National Institute for Data Science in Health and Medicine, School of Life Sciences, Xiamen University, Xiamen, 361005, China.
| | - Guanglin He
- Belt and Road Research Center for Forensic Molecular Anthropology Gansu University of Political Science and Law, Lanzhou, 730000, China. .,Department of Anthropology and Ethnology, Institute of Anthropology, National Institute for Data Science in Health and Medicine, School of Life Sciences, Xiamen University, Xiamen, 361005, China.
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13
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OSADA NAOKI, KAWAI YOSUKE. Exploring models of human migration to the Japanese archipelago using genome-wide genetic data. ANTHROPOL SCI 2021. [DOI: 10.1537/ase.201215] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Affiliation(s)
- NAOKI OSADA
- Faculty of Information Science and Technology, Hokkaido University, Sapporo
| | - YOSUKE KAWAI
- Genome Medical Science Project, National Center for Global Health and Medicine, Tokyo
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