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1
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D'Amato ME, Ristow P, Livesey M, Heynes K, Huber N, Bravi C, Hansen AJ, Parson W. Persistence of Ancestral KhoeSan Mitochondrial Patterns in Contemporary South African Populations. Ann Hum Genet 2025:e12589. [PMID: 39775598 DOI: 10.1111/ahg.12589] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Revised: 11/27/2024] [Accepted: 12/10/2024] [Indexed: 01/11/2025]
Abstract
INTRODUCTION Southern Africa has been inhabited by hunter-gatherers for at least 20,000 years and has received diverse immigration flows in the last 2000 years. The original inhabitants have interacted with the pastoralist migrants from Eastern Africa (∼2000 ybp), followed by the southern Bantu migration arriving some 1000 ybp, and more recently with the European and Asian settlers after the 17th century. Many of the original Khoekhoe and San inhabitants have either become extinct or have disappeared through admixture in South Africa (SA), in a sex-biased manner involving KhoeSan women. METHODS In this study, we generated mitochondrial DNA (mtDNA) control region (CR) sequences for 247 South African individuals. The sampling effort was concentrated in regions and populations with historical links to the KhoeSan population groups: admixed (Coloured, Griqua), Nama (Khoekhoe) and Bantu in three provinces. Here we evaluate the composition and extent of connectivity between population groups and regions, and to assess the distribution of haplotypes for the practical application of mtDNA CR data in forensic identifications. RESULTS The analysis of the newly generated sequences revealed 142 distinct haplotypes, of which 122 were unique. Haplogroup L0 was predominant (overall 71.7%). A high-frequency L0d2a haplotype dominated the pool of the admixed groups with 10%-12.5% incidence overall or per region. Comparative analysis with 545 extant mtDNA CR sequences from South African KhoeSan and admixed descendants revealed extensive population structure and high within-group haplotype sharing. CONCLUSION The observed population and regional variations, combined with the prevalence of high-frequency haplotypes, align with patterns of matrilocality. These findings highlight the limitations of using mtDNA control region analysis for forensic applications in South Africa.
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Affiliation(s)
- Maria Eugenia D'Amato
- Forensic DNA Laboratory, Department of Biotechnology, Faculty of Natural Sciences, University of the Western Cape, Cape Town, South Africa
| | - Peter Ristow
- Forensic DNA Laboratory, Department of Biotechnology, Faculty of Natural Sciences, University of the Western Cape, Cape Town, South Africa
| | - Michelle Livesey
- Forensic DNA Laboratory, Department of Biotechnology, Faculty of Natural Sciences, University of the Western Cape, Cape Town, South Africa
| | - Kirsty Heynes
- Forensic DNA Laboratory, Department of Biotechnology, Faculty of Natural Sciences, University of the Western Cape, Cape Town, South Africa
| | - Nicole Huber
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria
| | - Claudio Bravi
- Laboratorio de Genética Molecular Poblacional, Instituto Multidisciplinario de Biología Celular, Comisión de Investigaciones Científicas de la Provincia de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas, La Plata, Argentina
| | - Anders J Hansen
- Section for GeoGenetics, Globe Institute, University of Copenhagen, Kobenhavn, Denmark
| | - Walther Parson
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria
- Forensic Science Program, The Pennsylvania State University, University Park, Pennsylvania, USA
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2
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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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3
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Zhai Y, Zhou T, Wei Y, Zou Q, Wang Y. ReAlign-N: an integrated realignment approach for multiple nucleic acid sequence alignment, combining global and local realignments. NAR Genom Bioinform 2024; 6:lqae170. [PMID: 39703429 PMCID: PMC11655299 DOI: 10.1093/nargab/lqae170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2024] [Revised: 10/05/2024] [Accepted: 11/19/2024] [Indexed: 12/21/2024] Open
Abstract
Ensuring accurate multiple sequence alignment (MSA) is essential for comprehensive biological sequence analysis. However, the complexity of evolutionary relationships often results in variations that generic alignment tools may not adequately address. Realignment is crucial to remedy this issue. Currently, there is a lack of realignment methods tailored for nucleic acid sequences, particularly for lengthy sequences. Thus, there's an urgent need for the development of realignment methods better suited to address these challenges. This study presents ReAlign-N, a realignment method explicitly designed for multiple nucleic acid sequence alignment. ReAlign-N integrates both global and local realignment strategies for improved accuracy. In the global realignment phase, ReAlign-N incorporates K-Band and innovative memory-saving technology into the dynamic programming approach, ensuring high efficiency and minimal memory requirements for large-scale realignment tasks. The local realignment stage employs full matching and entropy scoring methods to identify low-quality regions and conducts realignment through MAFFT. Experimental results demonstrate that ReAlign-N consistently outperforms initial alignments on simulated and real datasets. Furthermore, compared to ReformAlign, the only existing multiple nucleic acid sequence realignment tool, ReAlign-N, exhibits shorter running times and occupies less memory space. The source code and test data for ReAlign-N are available on GitHub (https://github.com/malabz/ReAlign-N).
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Affiliation(s)
- Yixiao Zhai
- Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, No.2006, Xiyuan Avenue, Pidu Zone, Chengdu 610054, China
- Institute of Digital Health, Yangtze Delta Region Institute (Quzhou), University of Electronic Science and Technology of China, No.1, Chengdian Road, Kecheng Zone, Quzhou 324003, China
| | - Tong Zhou
- Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, No.2006, Xiyuan Avenue, Pidu Zone, Chengdu 610054, China
- Institute of Digital Health, Yangtze Delta Region Institute (Quzhou), University of Electronic Science and Technology of China, No.1, Chengdian Road, Kecheng Zone, Quzhou 324003, China
| | - Yanming Wei
- Institute of Digital Health, Yangtze Delta Region Institute (Quzhou), University of Electronic Science and Technology of China, No.1, Chengdian Road, Kecheng Zone, Quzhou 324003, China
- School of Computer Science and Technology, Xidian University, No.266, Xifeng Road, Chang'an Zone, Xi’an 710071, China
| | - Quan Zou
- Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, No.2006, Xiyuan Avenue, Pidu Zone, Chengdu 610054, China
- Institute of Digital Health, Yangtze Delta Region Institute (Quzhou), University of Electronic Science and Technology of China, No.1, Chengdian Road, Kecheng Zone, Quzhou 324003, China
| | - Yansu Wang
- Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, No.2006, Xiyuan Avenue, Pidu Zone, Chengdu 610054, China
- Institute of Digital Health, Yangtze Delta Region Institute (Quzhou), University of Electronic Science and Technology of China, No.1, Chengdian Road, Kecheng Zone, Quzhou 324003, China
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4
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Biddanda A, Bandyopadhyay E, de la Fuente Castro C, Witonsky D, Urban Aragon JA, Pasupuleti N, Moots HM, Fonseca R, Freilich S, Stanisavic J, Willis T, Menon A, Mustak MS, Kodira CD, Naren AP, Sikdar M, Rai N, Raghavan M. Distinct positions of genetic and oral histories: Perspectives from India. HGG ADVANCES 2024; 5:100305. [PMID: 38720459 PMCID: PMC11153255 DOI: 10.1016/j.xhgg.2024.100305] [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: 01/05/2024] [Revised: 05/04/2024] [Accepted: 05/04/2024] [Indexed: 05/16/2024] Open
Abstract
Over the past decade, genomic data have contributed to several insights on global human population histories. These studies have been met both with interest and critically, particularly by populations with oral histories that are records of their past and often reference their origins. While several studies have reported concordance between oral and genetic histories, there is potential for tension that may stem from genetic histories being prioritized or used to confirm community-based knowledge and ethnography, especially if they differ. To investigate the interplay between oral and genetic histories, we focused on the southwestern region of India and analyzed whole-genome sequence data from 156 individuals identifying as Bunt, Kodava, Nair, and Kapla. We supplemented limited anthropological records on these populations with oral history accounts from community members and historical literature, focusing on references to non-local origins such as the ancient Scythians in the case of Bunt, Kodava, and Nair, members of Alexander the Great's army for the Kodava, and an African-related source for Kapla. We found these populations to be genetically most similar to other Indian populations, with the Kapla more similar to South Indian tribal populations that maximize a genetic ancestry related to Ancient Ancestral South Indians. We did not find evidence of additional genetic sources in the study populations than those known to have contributed to many other present-day South Asian populations. Our results demonstrate that oral and genetic histories may not always provide consistent accounts of population origins and motivate further community-engaged, multi-disciplinary investigations of non-local origin stories in these communities.
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Affiliation(s)
- Arjun Biddanda
- Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA
| | - Esha Bandyopadhyay
- Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA
| | - Constanza de la Fuente Castro
- Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA; Programa de Genética Humana, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - David Witonsky
- Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA
| | | | - Nagarjuna Pasupuleti
- Department of Applied Zoology, Mangalore University, Mangalagangothri, Karnataka 574199, India
| | - Hannah M Moots
- Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA; Institute for the Study of Ancient Cultures Museum, University of Chicago, Chicago, IL, USA
| | - Renée Fonseca
- Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA
| | - Suzanne Freilich
- Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA; Department of Evolutionary Anthropology, University of Vienna, Vienna 1090, Austria
| | - Jovan Stanisavic
- Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA
| | - Tabitha Willis
- Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA
| | - Anoushka Menon
- Department of Archaeology, University of Cambridge, Cambridge CB2 3DZ, UK
| | - Mohammed S Mustak
- Department of Applied Zoology, Mangalore University, Mangalagangothri, Karnataka 574199, India
| | | | - Anjaparavanda P Naren
- Division of Pulmonary Medicine, Cystic Fibrosis Research Center, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Mithun Sikdar
- Anthropological Survey of India, Mysore, Karnataka 570026, India
| | - Niraj Rai
- Birbal Sahni Institute of Palaeosciences, Uttar Pradesh, Lucknow, Uttar Pradesh 226007, India.
| | - Maanasa Raghavan
- Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA.
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5
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Borisova TV, Cherdonova AM, Pshennikova VG, Teryutin FM, Morozov IV, Bondar AA, Baturina OA, Kabilov MR, Romanov GP, Solovyev AV, Fedorova SA, Barashkov NA. High prevalence of m.1555A > G in patients with hearing loss in the Baikal Lake region of Russia as a result of founder effect. Sci Rep 2024; 14:15342. [PMID: 38961196 PMCID: PMC11222474 DOI: 10.1038/s41598-024-66254-z] [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: 03/25/2024] [Accepted: 07/01/2024] [Indexed: 07/05/2024] Open
Abstract
Mitochondrial forms account approximately 1-2% of all nonsyndromic cases of hearing loss (HL). One of the most common causative variants of mtDNA is the m.1555A > G variant of the MT-RNR1 gene (OMIM 561000). Currently the detection of the m.1555A > G variant of the MT-RNR1 gene is not included in all research protocols. In this study this variant was screened among 165 patients with HL from the Republic of Buryatia, located in the Baikal Lake region of Russia. In our study, the total contribution of the m.1555A > G variant to the etiology of HL was 12.7% (21/165), while the update global prevalence of this variant is 1.8% (863/47,328). The m.1555A > G variant was notably more prevalent in Buryat (20.2%) than in Russian patients (1.3%). Mitogenome analysis in 14 unrelated Buryat families carrying the m.1555A > G variant revealed a predominant lineage: in 13 families, a cluster affiliated with sub-haplogroup A5b (92.9%) was identified, while one family had the D5a2a1 lineage (7.1%). In a Russian family with the m.1555A > G variant the lineage affiliated with sub-haplogroup F1a1d was found. Considering that more than 90% of Buryat families with the m.1555A > G variant belong to the single maternal lineage cluster we conclude that high prevalence of this variant in patients with HL in the Baikal Lake region can be attributed to a founder effect.
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Affiliation(s)
- Tuyara V Borisova
- Laboratory of Molecular Biology, Institute of Natural Sciences, M.K. Ammosov North-Eastern Federal University, Kulakovskogo 46, 677013, Yakutsk, Russia
| | - Aleksandra M Cherdonova
- Laboratory of Molecular Biology, Institute of Natural Sciences, M.K. Ammosov North-Eastern Federal University, Kulakovskogo 46, 677013, Yakutsk, Russia
| | - Vera G Pshennikova
- Laboratory of Molecular Biology, Institute of Natural Sciences, M.K. Ammosov North-Eastern Federal University, Kulakovskogo 46, 677013, Yakutsk, Russia
- Laboratory of Molecular Genetics, Yakut Science Centre of Complex Medical Problems, Yaroslavskogo 6/3, 677000, Yakutsk, Russia
| | - Fedor M Teryutin
- Laboratory of Molecular Biology, Institute of Natural Sciences, M.K. Ammosov North-Eastern Federal University, Kulakovskogo 46, 677013, Yakutsk, Russia
- Laboratory of Molecular Genetics, Yakut Science Centre of Complex Medical Problems, Yaroslavskogo 6/3, 677000, Yakutsk, Russia
| | - Igor V Morozov
- SB RAS Genomics Core Facility, Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Prospekt Akademika Lavrentieva 8, 630090, Novosibirsk, Russia
- Novosibirsk State University, 630090, Novosibirsk, Russia
| | - Alexander A Bondar
- SB RAS Genomics Core Facility, Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Prospekt Akademika Lavrentieva 8, 630090, Novosibirsk, Russia
| | - Olga A Baturina
- SB RAS Genomics Core Facility, Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Prospekt Akademika Lavrentieva 8, 630090, Novosibirsk, Russia
| | - Marsel R Kabilov
- SB RAS Genomics Core Facility, Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Prospekt Akademika Lavrentieva 8, 630090, Novosibirsk, Russia
| | - Georgii P Romanov
- Laboratory of Molecular Biology, Institute of Natural Sciences, M.K. Ammosov North-Eastern Federal University, Kulakovskogo 46, 677013, Yakutsk, Russia
| | - Aisen V Solovyev
- Laboratory of Molecular Biology, Institute of Natural Sciences, M.K. Ammosov North-Eastern Federal University, Kulakovskogo 46, 677013, Yakutsk, Russia
| | - Sardana A Fedorova
- Laboratory of Molecular Biology, Institute of Natural Sciences, M.K. Ammosov North-Eastern Federal University, Kulakovskogo 46, 677013, Yakutsk, Russia
- Laboratory of Molecular Genetics, Yakut Science Centre of Complex Medical Problems, Yaroslavskogo 6/3, 677000, Yakutsk, Russia
| | - Nikolay A Barashkov
- Laboratory of Molecular Biology, Institute of Natural Sciences, M.K. Ammosov North-Eastern Federal University, Kulakovskogo 46, 677013, Yakutsk, Russia.
- Laboratory of Molecular Genetics, Yakut Science Centre of Complex Medical Problems, Yaroslavskogo 6/3, 677000, Yakutsk, Russia.
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Childebayeva A, Fricke F, Rohrlach AB, Huang L, Schiffels S, Vesakoski O, Mannermaa K, Semerau L, Aron F, Solodovnikov K, Rykun M, Moiseyev V, Khartanovich V, Kovtun I, Krause J, Kuzminykh S, Haak W. Bronze age Northern Eurasian genetics in the context of development of metallurgy and Siberian ancestry. Commun Biol 2024; 7:723. [PMID: 38862782 PMCID: PMC11166947 DOI: 10.1038/s42003-024-06343-x] [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: 09/20/2023] [Accepted: 05/16/2024] [Indexed: 06/13/2024] Open
Abstract
The Eurasian Bronze Age (BA) has been described as a period of substantial human migrations, the emergence of pastoralism, horse domestication, and development of metallurgy. This study focuses on two north Eurasian sites sharing Siberian genetic ancestry. One of the sites, Rostovka, is associated with the Seima-Turbino (ST) phenomenon (~2200-1900 BCE) that is characterized by elaborate metallurgical objects found throughout Northern Eurasia. The genetic profiles of Rostovka individuals vary widely along the forest-tundra Siberian genetic cline represented by many modern Uralic-speaking populations, and the genetic heterogeneity observed is consistent with the current understanding of the ST being a transcultural phenomenon. Individuals from the second site, Bolshoy Oleni Ostrov in Kola, in comparison form a tighter cluster on the Siberian ancestry cline. We further explore this Siberian ancestry profile and assess the role of the ST phenomenon and other contemporaneous BA cultures in the spread of Uralic languages and Siberian ancestry.
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Affiliation(s)
- Ainash Childebayeva
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, D-04103, Leipzig, Germany.
- Department of Anthropology, University of Texas at Austin, Austin, TX, 78712, USA.
- Department of Anthropology, University of Kansas, Lawrence, KS, 66044, USA.
| | - Fabian Fricke
- German Archaeological Institute, Eurasia Department, Berlin, 14195, Germany
| | - Adam Benjamin Rohrlach
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, D-04103, Leipzig, Germany
- School of Computer and Mathematical Sciences, University of Adelaide, Adelaide, SA, 5005, Australia
| | - Lei Huang
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, D-04103, Leipzig, Germany
| | - Stephan Schiffels
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, D-04103, Leipzig, Germany
| | - Outi Vesakoski
- Department of Finnish and Finno-Ugric Languages, University of Turku, Turku, 20014, Finland
| | - Kristiina Mannermaa
- Department of Cultures, University of Helsinki, Yliopistonkatu 4, 00100, Helsinki, Finland
| | - Lena Semerau
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, D-04103, Leipzig, Germany
| | - Franziska Aron
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, 07745, Germany
| | - Konstantin Solodovnikov
- Institute of Problems of Northern Development, Tyumen Scientific Center of the Siberian Branch of Russian Academy of Sciences, Tyumen, 625008, Russia
| | - Marina Rykun
- Department of Anthropology and Ethnology, National Research Tomsk State University, Tomsk, 634050, Russia
| | - Vyacheslav Moiseyev
- Peter the Great Museum of Anthropology and Ethnography (Kunstkamera), Russian Academy of Sciences, University Embankment, 3, Saint Petersburg, 199034, Russia
| | - Valery Khartanovich
- Peter the Great Museum of Anthropology and Ethnography (Kunstkamera), Russian Academy of Sciences, University Embankment, 3, Saint Petersburg, 199034, Russia
| | - Igor Kovtun
- Igor V. Kovtun, Independent Researcher, Kemerovo, 650000, Russia
| | - Johannes Krause
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, D-04103, Leipzig, Germany
| | - Sergey Kuzminykh
- Russian Academy of Sciences, Institute of Archaeology, Laboratory of Natural Scientific Methods, Moscow, 117292, Russia
| | - Wolfgang Haak
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, D-04103, Leipzig, Germany.
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7
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Zhai Y, Chao J, Wang Y, Zhang P, Tang F, Zou Q. TPMA: A two pointers meta-alignment tool to ensemble different multiple nucleic acid sequence alignments. PLoS Comput Biol 2024; 20:e1011988. [PMID: 38557416 PMCID: PMC11008887 DOI: 10.1371/journal.pcbi.1011988] [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: 11/28/2023] [Revised: 04/11/2024] [Accepted: 03/11/2024] [Indexed: 04/04/2024] Open
Abstract
Accurate multiple sequence alignment (MSA) is imperative for the comprehensive analysis of biological sequences. However, a notable challenge arises as no single MSA tool consistently outperforms its counterparts across diverse datasets. Users often have to try multiple MSA tools to achieve optimal alignment results, which can be time-consuming and memory-intensive. While the overall accuracy of certain MSA results may be lower, there could be local regions with the highest alignment scores, prompting researchers to seek a tool capable of merging these locally optimal results from multiple initial alignments into a globally optimal alignment. In this study, we introduce Two Pointers Meta-Alignment (TPMA), a novel tool designed for the integration of nucleic acid sequence alignments. TPMA employs two pointers to partition the initial alignments into blocks containing identical sequence fragments. It selects blocks with the high sum of pairs (SP) scores to concatenate them into an alignment with an overall SP score superior to that of the initial alignments. Through tests on simulated and real datasets, the experimental results consistently demonstrate that TPMA outperforms M-Coffee in terms of aSP, Q, and total column (TC) scores across most datasets. Even in cases where TPMA's scores are comparable to M-Coffee, TPMA exhibits significantly lower running time and memory consumption. Furthermore, we comprehensively assessed all the MSA tools used in the experiments, considering accuracy, time, and memory consumption. We propose accurate and fast combination strategies for small and large datasets, which streamline the user tool selection process and facilitate large-scale dataset integration. The dataset and source code of TPMA are available on GitHub (https://github.com/malabz/TPMA).
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Affiliation(s)
- Yixiao Zhai
- Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu, China
- Quzhou People’s Hospital, Quzhou Affiliated Hospital of Wenzhou Medical University, Quzhou, China
- Yangtze Delta Region Institute (Quzhou), University of Electronic Science and Technology of China, Quzhou, China
| | - Jiannan Chao
- Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu, China
- Yangtze Delta Region Institute (Quzhou), University of Electronic Science and Technology of China, Quzhou, China
| | - Yizheng Wang
- Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu, China
- Yangtze Delta Region Institute (Quzhou), University of Electronic Science and Technology of China, Quzhou, China
| | - Pinglu Zhang
- Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu, China
- Yangtze Delta Region Institute (Quzhou), University of Electronic Science and Technology of China, Quzhou, China
| | - Furong Tang
- Quzhou People’s Hospital, Quzhou Affiliated Hospital of Wenzhou Medical University, Quzhou, China
- Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing, China
| | - Quan Zou
- Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu, China
- Yangtze Delta Region Institute (Quzhou), University of Electronic Science and Technology of China, Quzhou, China
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8
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Sturk-Andreaggi K, Bodner M, Ring JD, Ameur A, Gyllensten U, Parson W, Marshall C, Allen M. Complete Mitochondrial DNA Genome Variation in the Swedish Population. Genes (Basel) 2023; 14:1989. [PMID: 38002932 PMCID: PMC10671102 DOI: 10.3390/genes14111989] [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: 09/03/2023] [Revised: 10/04/2023] [Accepted: 10/19/2023] [Indexed: 11/26/2023] Open
Abstract
The development of complete mitochondrial genome (mitogenome) reference data for inclusion in publicly available population databases is currently underway, and the generation of more high-quality mitogenomes will only enhance the statistical power of this forensically useful locus. To characterize mitogenome variation in Sweden, the mitochondrial DNA (mtDNA) reads from the SweGen whole genome sequencing (WGS) dataset were analyzed. To overcome the interference from low-frequency nuclear mtDNA segments (NUMTs), a 10% variant frequency threshold was applied for the analysis. In total, 934 forensic-quality mitogenome haplotypes were characterized. Almost 45% of the SweGen haplotypes belonged to haplogroup H. Nearly all mitogenome haplotypes (99.1%) were assigned to European haplogroups, which was expected based on previous mtDNA studies of the Swedish population. There were signature northern Swedish and Finnish haplogroups observed in the dataset (e.g., U5b1, W1a), consistent with the nuclear DNA analyses of the SweGen data. The complete mitogenome analysis resulted in high haplotype diversity (0.9996) with a random match probability of 0.15%. Overall, the SweGen mitogenomes provide a large mtDNA reference dataset for the Swedish population and also contribute to the effort to estimate global mitogenome haplotype frequencies.
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Affiliation(s)
- Kimberly Sturk-Andreaggi
- Department of Immunology Genetics and Pathology, Uppsala University, 751 08 Uppsala, Sweden; (A.A.); (U.G.)
- Armed Forces Medical Examiner System’s Armed Forces DNA Identification Laboratory (AFMES-AFDIL), Dover Air Force Base, DE 19902, USA (C.M.)
- SNA International, LLC, Alexandria, VI 22314, USA
| | - Martin Bodner
- Institute of Legal Medicine, Medical University of Innsbruck, 6020 Innsbruck, Austria; (M.B.); (W.P.)
| | - Joseph D. Ring
- Armed Forces Medical Examiner System’s Armed Forces DNA Identification Laboratory (AFMES-AFDIL), Dover Air Force Base, DE 19902, USA (C.M.)
- SNA International, LLC, Alexandria, VI 22314, USA
| | - Adam Ameur
- Department of Immunology Genetics and Pathology, Uppsala University, 751 08 Uppsala, Sweden; (A.A.); (U.G.)
| | - Ulf Gyllensten
- Department of Immunology Genetics and Pathology, Uppsala University, 751 08 Uppsala, Sweden; (A.A.); (U.G.)
| | - Walther Parson
- Institute of Legal Medicine, Medical University of Innsbruck, 6020 Innsbruck, Austria; (M.B.); (W.P.)
- Forensic Science Program, The Pennsylvania State University, University Park, State College, PA 16801, USA
| | - Charla Marshall
- Armed Forces Medical Examiner System’s Armed Forces DNA Identification Laboratory (AFMES-AFDIL), Dover Air Force Base, DE 19902, USA (C.M.)
- Forensic Science Program, The Pennsylvania State University, University Park, State College, PA 16801, USA
| | - Marie Allen
- Department of Immunology Genetics and Pathology, Uppsala University, 751 08 Uppsala, Sweden; (A.A.); (U.G.)
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9
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Uricoechea Patiño D, Collins A, García OJR, Santos Vecino G, Cuenca JVR, Bernal JE, Benavides Benítez E, Vergara Muñoz S, Briceño Balcázar I. High Mitochondrial Haplotype Diversity Found in Three Pre-Hispanic Groups from Colombia. Genes (Basel) 2023; 14:1853. [PMID: 37895202 PMCID: PMC10606881 DOI: 10.3390/genes14101853] [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: 08/09/2023] [Revised: 08/30/2023] [Accepted: 09/18/2023] [Indexed: 10/29/2023] Open
Abstract
The analysis of mitochondrial DNA (mtDNA) hypervariable region (HVR) sequence data from ancient human remains provides valuable insights into the genetic structure and population dynamics of ancient populations. mtDNA is particularly useful in studying ancient populations, because it is maternally inherited and has a higher mutation rate compared to nuclear DNA. To determine the genetic structure of three Colombian pre-Hispanic populations and compare them with current populations, we determined the haplotypes from human bone remains by sequencing several mitochondrial DNA segments. A wide variety of mitochondrial polymorphisms were obtained from 33 samples. Our results support a high population heterogeneity among pre-Hispanic populations in Colombia.
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Affiliation(s)
- Daniel Uricoechea Patiño
- Doctoral Program in Biosciences, Human Genetics Group, Faculty of Medicine, University of La Sabana, Chía 250001, Colombia;
| | - Andrew Collins
- Human Genetics & Genomic Medicine, Faculty of Medicine, University of Southampton, Southampton SO16 6YD, UK;
| | | | - Gustavo Santos Vecino
- Department of Anthropology, Faculty of Social and Human Science, Universidad de Antioquia, Medellín 050010, Colombia;
| | | | - Jaime E. Bernal
- Faculty of Medicine, University of Sinú, Cartagena de Indias 130011, Colombia; (J.E.B.); (E.B.B.); (S.V.M.)
| | - Escilda Benavides Benítez
- Faculty of Medicine, University of Sinú, Cartagena de Indias 130011, Colombia; (J.E.B.); (E.B.B.); (S.V.M.)
| | - Saray Vergara Muñoz
- Faculty of Medicine, University of Sinú, Cartagena de Indias 130011, Colombia; (J.E.B.); (E.B.B.); (S.V.M.)
| | - Ignacio Briceño Balcázar
- Doctoral Program in Biosciences, Human Genetics Group, Faculty of Medicine, University of La Sabana, Chía 250001, Colombia;
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10
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Zhao D, Chen Y, Xie G, Ma P, Wen Y, Zhang F, Wang Y, Cui Y, Gao S. A multidisciplinary study on the social customs of the Tang Empire in the Medieval Ages. PLoS One 2023; 18:e0288128. [PMID: 37494335 PMCID: PMC10370703 DOI: 10.1371/journal.pone.0288128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 06/20/2023] [Indexed: 07/28/2023] Open
Abstract
Multidisciplinary research on human remains can provide important information about population dynamics, culture diffusion, as well as social organization and customs in history. In this study, multidisciplinary analyses were undertaken on a joint burial (M56) in the Shuangzhao cemetery of the Tang Dynasty (618-907 AD), one of the most prosperous dynasties in Chinese history, to shed light on the genetic profile and sociocultural aspects of this dynasty. The archaeological investigation suggested that this burial belonged to the Mid-Tang period and was used by common civilians. The osteological analysis identified the sex, age, and health status of the three individuals excavated from M56, who shared a similar diet inferred from the stable isotopic data. Genomic evidence revealed that these co-buried individuals had no genetic kinship but all belonged to the gene pool of the ancient populations in the Central Plains, represented by Yangshao and Longshan individuals, etc. Multiple lines of evidence, including archaeology, historic records, as well as chemical and genetic analyses, have indicated a very probable familial joint burial of husband and wives. Our study provides insights into the burial customs and social organization of the Tang Dynasty and reconstructs a scenario of civilian life in historic China.
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Affiliation(s)
- Dongyue Zhao
- School of Cultural Heritage, Northwest University, Xi'an, China
| | - Yang Chen
- School of Pharmaceutical Sciences, Jilin University, Changchun, China
| | - Gaowen Xie
- Xianyang Institute of Cultural Relics and Archaeology, Xianyang, China
| | - Pengcheng Ma
- School of Life Sciences, Jilin University, Changchun, China
| | - Yufeng Wen
- School of Life Sciences, Jilin University, Changchun, China
| | - Fan Zhang
- School of Life Sciences, Jilin University, Changchun, China
| | - Yafei Wang
- Xianyang Institute of Cultural Relics and Archaeology, Xianyang, China
| | - Yinqiu Cui
- School of Life Sciences, Jilin University, Changchun, China
| | - Shizhu Gao
- School of Pharmaceutical Sciences, Jilin University, Changchun, China
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11
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Tran HL, Mai HP, Le Thi D, Thi ND, Le Tung L, Thanh TP, Manh HT, Mau HN, Chu HH, Hoang H. The first maternal genetic study of hunter-gatherers from Vietnam. Mol Genet Genomics 2023:10.1007/s00438-023-02050-0. [PMID: 37438447 DOI: 10.1007/s00438-023-02050-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 06/22/2023] [Indexed: 07/14/2023]
Abstract
The current limitation of ancient DNA data from Vietnam led to the controversy surrounding the prehistory of people in this region. The combination of high heat and humidity damaged ancient bones that challenged the study of human evolution, especially when using DNA as study materials. So far, only 4 k years of history have been recorded despite the 65 k years of history of anatomically modern human occupations in Vietnam. Here we report, to our knowledge, the oldest mitogenomes of two hunter-gatherers from Vietnam. We extracted DNA from the femurs of two individuals aged 6.2 k cal BP from the Con Co Ngua (CCN) site in Thanh Hoa, Vietnam. This archeological site is the largest cemetery of the hunter-gatherer population in Southeast Asia (SEA) that was discovered, but their genetics have not been explored until the present. We indicated that the CCN haplotype belongs to a rare haplogroup that was not detected in any present-day Vietnamese individuals. Further matrilineal analysis on CCN mitogenomes showed a close relationship with ancient farmers and present-day populations in SEA. The mitogenomes of hunter-gatherers from Vietnam debate the "two layers" model of peopling history in SEA and provide an alternative solution for studying challenging ancient human samples from Vietnam.
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Affiliation(s)
- Huyen Linh Tran
- Institute of Biotechnology, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay District, Hanoi, Vietnam
- University of Science and Technology of Hanoi, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Huong Pham Mai
- Institute of Biotechnology, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay District, Hanoi, Vietnam
| | - Dung Le Thi
- Institute of Biotechnology, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay District, Hanoi, Vietnam
- University of Science and Technology of Hanoi, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Nhung Doan Thi
- Institute of Biotechnology, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay District, Hanoi, Vietnam
| | - Lam Le Tung
- Institute of Biotechnology, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay District, Hanoi, Vietnam
| | - Tung Pham Thanh
- Institute of Biotechnology, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay District, Hanoi, Vietnam
| | - Ha Tran Manh
- Institute of Biotechnology, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay District, Hanoi, Vietnam
| | - Hung Nguyen Mau
- Institute of Biotechnology, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay District, Hanoi, Vietnam
| | - Hoang Ha Chu
- Institute of Biotechnology, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay District, Hanoi, Vietnam
- University of Science and Technology of Hanoi, Vietnam Academy of Science and Technology, Hanoi, Vietnam
- Graduate University of Science and Technology, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Ha Hoang
- Institute of Biotechnology, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay District, Hanoi, Vietnam.
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12
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Lam XJ, Xu B, Yeo PL, Cheah PS, Ling KH. Mitochondria dysfunction and bipolar disorder: From pathology to therapy. IBRO Neurosci Rep 2023; 14:407-418. [PMID: 37388495 PMCID: PMC10300489 DOI: 10.1016/j.ibneur.2023.04.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2022] [Accepted: 04/08/2023] [Indexed: 07/01/2023] Open
Abstract
Bipolar disorder (BD) is one of the major psychiatric diseases in which the impairment of mitochondrial functions has been closely connected or associated with the disease pathologies. Different lines of evidence of the close connection between mitochondria dysfunction and BD were discussed with a particular focus on (1) dysregulation of energy metabolism, (2) effect of genetic variants, (3) oxidative stress, cell death and apoptosis, (4) dysregulated calcium homeostasis and electrophysiology, and (5) current as well as potential treatments targeting at restoring mitochondrial functions. Currently, pharmacological interventions generally provide limited efficacy in preventing relapses or recovery from mania or depression episodes. Thus, understanding mitochondrial pathology in BD will lead to novel agents targeting mitochondrial dysfunction and formulating new effective therapy for BD.
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Affiliation(s)
- Xin-Jieh Lam
- Department of Human Anatomy, Faculty of Medicine and Health Sciences, Unversiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia
| | - Bingzhe Xu
- School of Biomedical Engineering, Sun Yat-sen University, 132 Daxuecheng Outer Ring E Rd, Panyu Qu, Guangzhou Shi, Guangdong 511434, People's Republic of China
| | - Pei-Ling Yeo
- School of Postgraduate Studies and Research, International Medical University, 126, Jalan Jalil Perkasa 19, 57000 Bukit Jalil, Kuala Lumpur, Malaysia
| | - Pike-See Cheah
- Department of Human Anatomy, Faculty of Medicine and Health Sciences, Unversiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia
| | - King-Hwa Ling
- Department of Biomedical Science, Faculty of Medicine and Health Sciences, Unversiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia
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13
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Jing P, Mei X, Zhang YY, Zheng FJ, Luo XM, Liu LJ, Yu HH, Zhang XB. Major depressive disorder is correlated with the mitochondrial ND1 T3394C mutation in two Han Chinese families: Two case reports. World J Psychiatry 2023; 13:75-83. [PMID: 36925947 PMCID: PMC10011944 DOI: 10.5498/wjp.v13.i2.75] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 12/09/2022] [Accepted: 01/16/2023] [Indexed: 02/17/2023] Open
Abstract
BACKGROUND Major depressive disorder (MDD) is the most frequent reason of disabled people in the world, as reported by the World Health Organization. However, the diagnosis of MDD is mainly based on clinical symptoms. CASE SUMMARY The clinical, genetic, and molecular characteristics of two Chinese families with MDD are described in this study. There were variable ages of onset and severity in depression among the families. Both Chinese families had a very low pre-valence of MDD. The mitochondrial genomes of these pedigrees were sequenced and indicated a homoplasmic T3394C (Y30H) mutation, with the polymorphism located at a highly conserved tyrosine at position 30 of ND1. The analysis also revealed unique sets of mitochondrial DNA (mtDNA) polymorphisms orig-inating from haplogroups M9a3 and M9a. CONCLUSION This finding of the T3394C mutation in two unrelated depressed patients provides strong evidence that this mutation may have a part in the etiology of MDD. However, In these two Chinese families having the T3394C mutation, no functional mtDNA mutation was observed. Therefore, T3394C mutations are related with MDD, and the phenotypic manifestation of these mutations may be affected by changes in nuclear genes or environmental factors.
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Affiliation(s)
- Pan Jing
- Department of Psychiatric, Ningbo Kangning Hospital, Ningbo 315201, Zhejiang Province, China
| | - Xi Mei
- Department of Psychiatric, Ningbo Kangning Hospital, Ningbo 315201, Zhejiang Province, China
| | - Yuan-Yuan Zhang
- Department of Psychiatric, Ningbo Kangning Hospital, Ningbo 315201, Zhejiang Province, China
| | - Fei-Jie Zheng
- Department of Psychiatric, Ningbo Kangning Hospital, Ningbo 315201, Zhejiang Province, China
| | - Xiao-Min Luo
- Department of Psychiatric, Ningbo Kangning Hospital, Ningbo 315201, Zhejiang Province, China
| | - Ling-Jiang Liu
- Department of Psychiatric, Ningbo Kangning Hospital, Ningbo 315201, Zhejiang Province, China
| | - Hai-Hang Yu
- Department of Psychiatric, Ningbo Kangning Hospital, Ningbo 315201, Zhejiang Province, China
| | - Xiao-Bin Zhang
- Department of Psychiatry, Suzhou Guangji Hospital, Suzhou 215003, Jiangsu Province, China
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14
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Lin M, Trejaut JA. Diversity and distribution of mitochondrial DNA in non-Austronesian-speaking Taiwanese individuals. Hum Genome Var 2023; 10:2. [PMID: 36653363 PMCID: PMC9849472 DOI: 10.1038/s41439-022-00228-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 11/12/2022] [Accepted: 11/22/2022] [Indexed: 01/19/2023] Open
Abstract
Many studies have described the diversity of Austronesian-speaking Taiwanese people to shed more light on their origin and their connection with the "Out of Taiwan" migrations. However, the genetic relationship between the non-Austronesian-speaking groups of Taiwan and the populations of continental Asia is still unclear. Here, we studied the diversity of mtDNA in 767 non-Austronesian speakers from 16 locations in Taiwan using partial sequencing obtained from the hypervariable segment I (HVS-I) and coding regions 8,001-9,000 and 9.801-10,900 and 85 complete mtDNA genome sequences. Bayesian analysis of population structure was used to examine their relationship with over 3662 individuals representing indigenous groups of Taiwan, continental East Asia, Japan, and Island Southeast Asia. The whole analysis identified 278 haplotypes. Complete genomes revealed 62 novel subhaplogroups, of which 31 were exclusive to Taiwan. Estimates of coalescence times of all subhaplogroups showed peaks of diversification greater than 5.0 kya, likely characterizing gene flow from continental East Asian groups but not excluding in situ Taiwanese ancestry. Furthermore, a significant number of clades exclusive to non-Austronesian speakers of Taiwan (NAN_Tw) showed coalescence peaks between 1.0 and 2.6 kya, suggesting possible late Neolithic to early metal age settlements of NAN_Tw and local expansion in Taiwan.
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Affiliation(s)
- Marie Lin
- Molecular Anthropology and Transfusion Medicine Research Laboratory, Mackay Memorial Hospital, Taipei, Taiwan.
| | - Jean A Trejaut
- Molecular Anthropology and Transfusion Medicine Research Laboratory, Mackay Memorial Hospital, Taipei, Taiwan.
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15
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Inoue Y, Igarashi T, Hasebe Y, Kawagishi-Hotta M, Okuno R, Yamada T, Hasegawa S. Identification of mitochondrial genetic variants associated with human corneocyte size in Japanese women. Exp Dermatol 2022; 31:1944-1948. [PMID: 36067013 DOI: 10.1111/exd.14673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 08/23/2022] [Accepted: 09/02/2022] [Indexed: 12/14/2022]
Abstract
Mitochondria have their own DNA (mtDNA). Genetic variants are likely to accumulate in mtDNA, and its base substitution rate is known to be very fast, 10-20 times faster than that of nuclear DNA. For this reason, mtSNPs (mitochondrial genome single nucleotide polymorphisms) are frequently detected in mtDNA. Several thousands of copies of mtDNA are considered to be present in a cell, and variants that have occurred in mtDNA are expected to markedly affect the intracellular energy production system and ROS (reactive oxygen species) kinetics. Therefore, recently, mtSNPs have come to be considered very important as a determinant of the individual constitution such as the life-span and disease susceptibility. In this study, we searched for mtSNPs that affect the individual corneocyte size using samples from 358 Japanese women. As a result, mtSNPs 10609C and 12406A were found to be significantly related to the corneocyte size in the outermost layer of the epidermis. There have been a large number of reports concerning the association between mtSNPs and individual constitution, but little evaluation of their relationships with epidermal properties has been made. The results of the present study first suggested that mtSNPs may affect the epidermal properties in Japanese women.
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Affiliation(s)
- Yu Inoue
- Research Laboratories, Nippon Menard Cosmetic Co., Ltd, Nagoya, Japan.,Nagoya University-MENARD Collaborative Research Chair, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Toshio Igarashi
- Research Laboratories, Nippon Menard Cosmetic Co., Ltd, Nagoya, Japan
| | - Yuichi Hasebe
- Research Laboratories, Nippon Menard Cosmetic Co., Ltd, Nagoya, Japan.,Nagoya University-MENARD Collaborative Research Chair, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Mika Kawagishi-Hotta
- Research Laboratories, Nippon Menard Cosmetic Co., Ltd, Nagoya, Japan.,Nagoya University-MENARD Collaborative Research Chair, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Ryosuke Okuno
- Research Laboratories, Nippon Menard Cosmetic Co., Ltd, Nagoya, Japan.,Nagoya University-MENARD Collaborative Research Chair, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Takaaki Yamada
- Research Laboratories, Nippon Menard Cosmetic Co., Ltd, Nagoya, Japan
| | - Seiji Hasegawa
- Research Laboratories, Nippon Menard Cosmetic Co., Ltd, Nagoya, Japan.,Nagoya University-MENARD Collaborative Research Chair, Nagoya University Graduate School of Medicine, Nagoya, Japan
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16
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Askapuli A, Vilar M, Garcia-Ortiz H, Zhabagin M, Sabitov Z, Akilzhanova A, Ramanculov E, Schamiloglu U, Martinez-Hernandez A, Contreras-Cubas C, Barajas-Olmos F, Schurr TG, Zhumadilov Z, Flores-Huacuja M, Orozco L, Hawks J, Saitou N. Kazak mitochondrial genomes provide insights into the human population history of Central Eurasia. PLoS One 2022; 17:e0277771. [PMID: 36445929 PMCID: PMC9707748 DOI: 10.1371/journal.pone.0277771] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 11/03/2022] [Indexed: 11/30/2022] Open
Abstract
As a historical nomadic group in Central Asia, Kazaks have mainly inhabited the steppe zone from the Altay Mountains in the East to the Caspian Sea in the West. Fine scale characterization of the genetic profile and population structure of Kazaks would be invaluable for understanding their population history and modeling prehistoric human expansions across the Eurasian steppes. With this mind, we characterized the maternal lineages of 200 Kazaks from Jetisuu at mitochondrial genome level. Our results reveal that Jetisuu Kazaks have unique mtDNA haplotypes including those belonging to the basal branches of both West Eurasian (R0, H, HV) and East Eurasian (A, B, C, D) lineages. The great diversity observed in their maternal lineages may reflect pivotal geographic location of Kazaks in Eurasia and implies a complex history for this population. Comparative analyses of mitochondrial genomes of human populations in Central Eurasia reveal a common maternal genetic ancestry for Turko-Mongolian speakers and their expansion being responsible for the presence of East Eurasian maternal lineages in Central Eurasia. Our analyses further indicate maternal genetic affinity between the Sherpas from the Tibetan Plateau with the Turko-Mongolian speakers.
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Affiliation(s)
- Ayken Askapuli
- School of Sciences and Humanities, Nazarbayev University, Astana, Kazakhstan
- National Center for Biotechnology, Astana, Kazakhstan
- National Laboratory Astana, Nazarbayev University, Astana, Kazakhstan
- Department of Integrative Biology, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Miguel Vilar
- The Genographic Project, National Geographic Society, Washington, DC, United States of America
- Department of Anthropology, University of Maryland, College Park, Maryland, United States of America
| | - Humberto Garcia-Ortiz
- Immunogenomics and Metabolic Diseases Laboratory, National Institute of Genomic Medicine, Mexico City, Mexico
| | - Maxat Zhabagin
- School of Sciences and Humanities, Nazarbayev University, Astana, Kazakhstan
- National Center for Biotechnology, Astana, Kazakhstan
- National Laboratory Astana, Nazarbayev University, Astana, Kazakhstan
| | | | - Ainur Akilzhanova
- National Laboratory Astana, Nazarbayev University, Astana, Kazakhstan
| | - Erlan Ramanculov
- School of Sciences and Humanities, Nazarbayev University, Astana, Kazakhstan
- National Center for Biotechnology, Astana, Kazakhstan
| | - Uli Schamiloglu
- School of Sciences and Humanities, Nazarbayev University, Astana, Kazakhstan
| | - Angelica Martinez-Hernandez
- Immunogenomics and Metabolic Diseases Laboratory, National Institute of Genomic Medicine, Mexico City, Mexico
| | - Cecilia Contreras-Cubas
- Immunogenomics and Metabolic Diseases Laboratory, National Institute of Genomic Medicine, Mexico City, Mexico
| | - Francisco Barajas-Olmos
- Immunogenomics and Metabolic Diseases Laboratory, National Institute of Genomic Medicine, Mexico City, Mexico
| | - Theodore G. Schurr
- Department of Anthropology, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Zhaxybay Zhumadilov
- National Laboratory Astana, Nazarbayev University, Astana, Kazakhstan
- School of Medicine, Nazarbayev University, Astana, Kazakhstan
| | - Marlen Flores-Huacuja
- Immunogenomics and Metabolic Diseases Laboratory, National Institute of Genomic Medicine, Mexico City, Mexico
| | - Lorena Orozco
- Immunogenomics and Metabolic Diseases Laboratory, National Institute of Genomic Medicine, Mexico City, Mexico
| | - John Hawks
- Department of Integrative Biology, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Department of Anthropology, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Naruya Saitou
- Population Genetics Laboratory, National Institute of Genetics, Mishima, Shizuoka, Japan
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, Tokyo, Japan
- Advanced Medical Research Center, Faculty of Medicine, University of the Ryukyus, Okinawa Ken, Japan
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17
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Mitochondrial DNA population variation is not associated with Alzheimer's in the Japanese population: A consistent finding across global populations. PLoS One 2022; 17:e0276169. [PMID: 36264923 PMCID: PMC9584534 DOI: 10.1371/journal.pone.0276169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Accepted: 10/02/2022] [Indexed: 11/06/2022] Open
Abstract
Several mitochondrial DNA (mtDNA) haplogroup association studies have suggested that common mtDNA variants are associated with multifactorial diseases, including Alzheimer’s disease (AD). However, such studies have also produced conflicting results. A new mtDNA association model, the ‘variant load model’ (VLM), has been applied to multiple disease phenotypes. Application of the VLM in a 2017 study failed to find different variant loads in AD patients compared to controls, in two cohorts of European origin. The study also suggested a lower variant load in healthy elderly individuals, but could offer no replicate cohort to support this observation. Here, the VLM is applied to Japanese mtDNA sequences; in doing so, we explored the role of mtDNA variation in AD and ageing in a different global population. Consistent with the previous findings using the VLM in two populations of European origin, we found no evidence for an association between rarer, non-haplogroup associated variation and the development of AD. However, the result in the context of ageing that suggested those with fewer mildly deleterious mutations might undergo healthier ageing, was not replicated. In contrast to our previous study, our present results suggest that those living to advanced old age may harbour more mildly deleterious mtDNA variations. Importantly our analysis showed this finding is not primarily being driven by many rare population variants dispersed across the mtDNA, but by a few more frequent variants with high MutPred scores. It is suggested the variants in question do not exert a mildly deleterious effect in their most frequent haplogroup context.
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Cultural transmission of traditional songs in the Ryukyu Archipelago. PLoS One 2022; 17:e0270354. [PMID: 35749479 PMCID: PMC9231793 DOI: 10.1371/journal.pone.0270354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 06/08/2022] [Indexed: 11/19/2022] Open
Abstract
Geographic patterns of cultural variations are affected by how cultural traits are transmitted within and between populations. It has been argued that cultural traits are transmitted in different manners depending on their characteristics; for example, words for basic concepts are less liable to horizontal transmission between populations (i.e., borrowing) than other words. Here we examine the geographic variation of traditional songs in the Ryukyu Archipelago, southwestern islands of Japan, to explore cultural evolution of music with a focus on different social contexts in which songs are sung. Published scores of 1,342 traditional songs are coded using the CantoCore song classification scheme and distances between the songs are calculated from the codings. Neighbor-Net graphs of regions/islands are generated on the basis of the musical distances, and delta scores are obtained to examine the treelikeness of the networks. We also perform analysis of molecular variance (AMOVA) to evaluate the extent of musical diversification among regions/islands. Our results suggest that horizontal transmission between populations has played a greater role in the formation of musical diversity than that of linguistic diversity in the Ryukyu Archipelago and that the social context in which songs are sung has an effect on how they are transmitted within and between populations. In addition, we compare the observed patterns of song diversity among regions/islands with those of lexical and mitochondrial-DNA (mtDNA) diversity, showing that the variation of songs sung in the "work" context are associated with the linguistic variation, whereas no association is found between the musical and genetic variation.
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Hou L, Hu C, Ji L, Wang Q, Liang M. The Mitochondrial tRNA Phe 625G>A Mutation in Three Han Chinese Families With Cholecystolithiasis. Front Genet 2022; 13:814729. [PMID: 35719381 PMCID: PMC9198646 DOI: 10.3389/fgene.2022.814729] [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: 11/18/2021] [Accepted: 04/19/2022] [Indexed: 11/16/2022] Open
Abstract
In this study, we assessed three Chinese families with inherited cholecystolithiasis and conducted the clinical, genetic, and molecular characterization of these subjects. Eight of eighteen matrilineal relatives had a clinical phenotype in these three families. Sequence analysis of complete mitochondrial genomes in these probands identified the homoplasmic tRNAPhe 625 G > A mutation and distinct sets of mtDNA polymorphisms belonging to haplogroups H2, F4b, and M10a. The 625G > A mutation disturbed the classic G-C base-pairings at a highly conserved position 49 in the T-stem of mitochondrial tRNAs. Molecular dynamics simulation showed that the structure of tRNAphe with 625 G > A mutation was noticeably remodeled while compared with the isoform of the wild type. The occurrence of tRNAPhe 625 G > A mutation in these various genetically unrelated subjects strongly indicates that this mutation is involved in the pathogenesis of cholecystolithiasis. This is the first evidence that tRNA mutations are associated with cholecystolithiasis, and it provided more insights into the genetic mechanism of cholecystolithiasis.
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Affiliation(s)
- Lingling Hou
- Department of Medical Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Cuifang Hu
- Attardi Institute of Mitochondrial Biomedicine, Wenzhou Medical University, Wenzhou, China
| | - Lili Ji
- Department of Medical Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Qiongdan Wang
- Department of Medical Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Min Liang
- Department of Medical Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China.,Attardi Institute of Mitochondrial Biomedicine, Wenzhou Medical University, Wenzhou, China
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20
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Sato T, Goto-Inoue N, Kimishima M, Toyoharu J, Minei R, Ogura A, Nagoya H, Mori T. A novel ND1 mitochondrial DNA mutation is maternally inherited in growth hormone transgenesis in amago salmon (Oncorhynchus masou ishikawae). Sci Rep 2022; 12:6720. [PMID: 35469048 PMCID: PMC9038734 DOI: 10.1038/s41598-022-10521-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Accepted: 03/22/2022] [Indexed: 11/12/2022] Open
Abstract
Growth hormone (GH) transgenesis can be used to manipulate the growth performance of fish and mammals. In this study, homozygous and hemizygous GH-transgenic amago salmon (Oncorhynchus masou ishikawae) derived from a single female exhibited hypoglycemia. Proteomic and signal network analyses using iTRAQ indicated a decreased NAD+/NADH ratio in transgenic fish, indicative of reduced mitochondrial ND1 function and ROS levels. Mitochondrial DNA sequencing revealed that approximately 28% of the deletion mutations in the GH homozygous- and hemizygous-female-derived mitochondrial DNA occurred in ND1. These fish also displayed decreased ROS levels. Our results indicate that GH transgenesis in amago salmon may induce specific deletion mutations that are maternally inherited over generations and alter energy production.
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Affiliation(s)
- Tomohiko Sato
- Department of Marine Science and Resources, Nihon University College of Bioresource Sciences, Kameino 1866, Fujisawa, 252-0880, Japan
| | - Naoko Goto-Inoue
- Department of Marine Science and Resources, Nihon University College of Bioresource Sciences, Kameino 1866, Fujisawa, 252-0880, Japan
| | - Masaya Kimishima
- Department of Marine Science and Resources, Nihon University College of Bioresource Sciences, Kameino 1866, Fujisawa, 252-0880, Japan
| | - Jike Toyoharu
- Research Institute of Medical Research Support Center Electron Microscope Laboratory, School of Medicine, Nihon University, Tokyo, 173-8610, Japan
| | - Ryuhei Minei
- Department of Computer Bioscience, Nagahama Institute of Bio-Science and Technology, Nagahama, 526-0829, Japan
| | - Atsushi Ogura
- Department of Computer Bioscience, Nagahama Institute of Bio-Science and Technology, Nagahama, 526-0829, Japan
| | - Hiroyuki Nagoya
- National Research Institute of Aquaculture, Fisheries Research and Education Agency, Minamiise, 516-0193, Japan
| | - Tsukasa Mori
- Department of Marine Science and Resources, Nihon University College of Bioresource Sciences, Kameino 1866, Fujisawa, 252-0880, Japan.
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21
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Hayashi A, Pietrusewsky M. Discriminant function analysis of craniometric data for distinguishing Japanese and Filipino crania. AUST J FORENSIC SCI 2022. [DOI: 10.1080/00450618.2022.2057589] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Atsuko Hayashi
- Social Welfare and War Victims’ Relief Bureau, Ministry of Labour, Health, and Welfare, Chiyoda-ku, Tokyo, Japan
| | - Michael Pietrusewsky
- Department of Anthropology, University of Hawai‘i at Mānoa, Honolulu, Hawai‘i, USA
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22
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Gubina MA, Babenko VN, Batsevich VA, Leibova NA, Zabiyako AP. Polymorphism of Mitochondrial DNA and Six Nuclear Genes in the Amur Evenk Population. RUSS J GENET+ 2022. [DOI: 10.1134/s1022795422010033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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23
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Miura S, Sasaki A, Kasai S, Sugawara T, Maeda Y, Goto S, Kasai T, Shimizume N, Jung S, Iwane T, Itoh K, Matsubara A. Association of mitochondrial DNA haplogroup and hearing impairment with aging in Japanese general population of the Iwaki Health Promotion Project. J Hum Genet 2022; 67:369-375. [PMID: 35034960 PMCID: PMC9130095 DOI: 10.1038/s10038-022-01011-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2021] [Revised: 12/20/2021] [Accepted: 01/01/2022] [Indexed: 11/09/2022]
Abstract
Age-related hearing loss (ARHL) is a complex multifactorial disorder. Studies in animals, including mitochondria-mutator mice, and in human suggest that oxidative stress and mitochondrial disturbance play an important role in the pathoetiology of ARHL. Mitochondrial DNA (mtDNA) haplogroups are populations with genetically similar traits, and they have been reported to affect the mitochondrial function of oxidative phosphorylation. To gain further insights into the relationships between mitochondrial haplotypes and the susceptibility to cochlear aging, in this study, we aimed to elucidate how the differences in mtDNA haplogroups may affect ARHL development in Japanese general population. We focused on early onset ARHL, as the same mtDNA haplogroup can show either a negative or positive effect on systemic co-morbidities of ARHL that appear later in life. A total of 1167 participants of the Iwaki Health Promotion Project were surveyed in 2014, and 12 major haplotype groups (D4a, D4b, D5, G1, G2, M7a, M7b, A, B4, B5, N9, and F) were selected for the analysis. A total of 698 subjects aged 30 to 65 years were included in the statistical analysis, and the hearing loss group consisted of 112 males (40.3%) and 111 females (26.4%). Multiple logistic regression analysis showed that the male subjects belonging to haplogroup A had a significantly increased risk of hearing loss, whereas the female subjects belonging to haplogroup N9 had a significantly decreased risk of hearing loss. These results suggested that the mtDNA haplogroup may be an indicator for future risk of morbidity associated with ARHL.
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Affiliation(s)
- Shiori Miura
- Department of Otorhinolaryngology, Hirosaki University Graduate School of Medicine, Hirosaki, Japan
| | - Akira Sasaki
- Department of Otorhinolaryngology, Hirosaki University Graduate School of Medicine, Hirosaki, Japan.
| | - Shuya Kasai
- Department of Stress Response Science, Hirosaki University Graduate School of Medicine, Hirosaki, Japan
| | - Takayuki Sugawara
- Research Institute of Bio-System Informatics, Tohoku Chemical Co., Ltd, Morioka, Japan.,Center of Innovation Research Initiatives Organization, Hirosaki University, Hirosaki, Japan
| | - Yasunori Maeda
- Department of Otorhinolaryngology, Hirosaki University Graduate School of Medicine, Hirosaki, Japan
| | - Shinichi Goto
- Department of Otorhinolaryngology, Hirosaki University Graduate School of Medicine, Hirosaki, Japan
| | - Takashi Kasai
- Department of Otorhinolaryngology, Hirosaki University Graduate School of Medicine, Hirosaki, Japan
| | - Nami Shimizume
- Department of Otorhinolaryngology, Hirosaki University Graduate School of Medicine, Hirosaki, Japan
| | - Songee Jung
- Department of Digital Nutrition, Graduate School of Medicine, Hirosaki University, Hirosaki, Japan
| | - Takuro Iwane
- Hirosaki University COI Research Initiative Organization, Hirosaki University, Hirosaki, Japan
| | - Ken Itoh
- Department of Stress Response Science, Hirosaki University Graduate School of Medicine, Hirosaki, Japan
| | - Atsushi Matsubara
- Department of Otorhinolaryngology, Hirosaki University Graduate School of Medicine, Hirosaki, Japan
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Pham VH, Nguyen VL, Jung HE, Cho YS, Shin JG. The frequency of the known mitochondrial variants associated with drug-induced toxicity in a Korean population. BMC Med Genomics 2022; 15:3. [PMID: 34980117 PMCID: PMC8722126 DOI: 10.1186/s12920-021-01153-0] [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: 10/14/2021] [Accepted: 12/16/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Few studies have annotated the whole mitochondrial DNA (mtDNA) genome associated with drug responses in Asian populations. This study aimed to characterize mtDNA genetic profiles, especially the distribution and frequency of well-known genetic biomarkers associated with diseases and drug-induced toxicity in a Korean population. METHOD Whole mitochondrial genome was sequenced for 118 Korean subjects by using a next-generation sequencing approach. The bioinformatic pipeline was constructed for variant calling, haplogroup classification and annotation of mitochondrial mutation. RESULTS A total of 681 variants was identified among all subjects. The MT-TRNP gene and displacement loop showed the highest numbers of variants (113 and 74 variants, respectively). The m.16189T > C allele, which is known to reduce the mtDNA copy number in human cells was detected in 25.4% of subjects. The variants (m.2706A > G, m.3010A > G, and m.1095T > C), which are associated with drug-induced toxicity, were observed with the frequency of 99.15%, 30.51%, and 0.08%, respectively. The m.2150T > A, a genotype associated with highly disruptive effects on mitochondrial ribosomes, was identified in five subjects. The D and M groups were the most dominant groups with the frequency of 34.74% and 16.1%, respectively. CONCLUSIONS Our finding was consistent with Korean Genome Project and well reflected the unique profile of mitochondrial haplogroup distribution. It was the first study to annotate the whole mitochondrial genome with drug-induced toxicity to predict the ADRs event in clinical implementation for Korean subjects. This approach could be extended for further study for validation of the potential ethnic-specific mitochondrial genetic biomarkers in the Korean population.
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Affiliation(s)
- Vinh Hoa Pham
- Department of Pharmacology and Pharmacogenomics Research Center, Inje University, College of Medicine, 633-165 Gaegum-Dong, Jin-Gu, Busan, Republic of Korea
| | - Van Lam Nguyen
- Department of Pharmacology and Pharmacogenomics Research Center, Inje University, College of Medicine, 633-165 Gaegum-Dong, Jin-Gu, Busan, Republic of Korea
| | - Hye-Eun Jung
- Department of Pharmacology and Pharmacogenomics Research Center, Inje University, College of Medicine, 633-165 Gaegum-Dong, Jin-Gu, Busan, Republic of Korea.,Department of Precision Medicine, SPMED Co., Ltd., Busan, 46508, Republic of Korea
| | - Yong-Soon Cho
- Department of Pharmacology and Pharmacogenomics Research Center, Inje University, College of Medicine, 633-165 Gaegum-Dong, Jin-Gu, Busan, Republic of Korea.,Department of Pharmacology and Clinical Pharmacology, PharmacoGenomics Research Center, Inje University College of Medicine, Busan, 47392, Republic of Korea.,Center for Personalized Precision Medicine of Tuberculosis, Inje University College of Medicine, Busan, Republic of Korea
| | - Jae-Gook Shin
- Department of Pharmacology and Pharmacogenomics Research Center, Inje University, College of Medicine, 633-165 Gaegum-Dong, Jin-Gu, Busan, Republic of Korea. .,Department of Pharmacology and Clinical Pharmacology, PharmacoGenomics Research Center, Inje University College of Medicine, Busan, 47392, Republic of Korea. .,Center for Personalized Precision Medicine of Tuberculosis, Inje University College of Medicine, Busan, Republic of Korea.
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25
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Li M, Gong S, Han X, Zhou L, Zhang S, Ren Q, Cai X, Luo Y, Liu W, Zhu Y, Zhou X, Li Y, Ji L. Contribution of mitochondrial gene variants in diabetes and diabetic kidney disease. Front Endocrinol (Lausanne) 2022; 13:953631. [PMID: 36313763 PMCID: PMC9597463 DOI: 10.3389/fendo.2022.953631] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 08/04/2022] [Indexed: 11/18/2022] Open
Abstract
OBJECTIVES Mitochondrial DNA (mtDNA) plays an important role in the pathogenesis of diabetes. Variants in mtDNA have been reported in diabetes, but studies on the whole mtDNA variants were limited. Our study aims to explore the association of whole mtDNA variants with diabetes and diabetic kidney disease (DKD). METHODS The whole mitochondrial genome was screened by next-generation sequencing in cohort 1 consisting of 50 early-onset diabetes (EOD) patients with a maternally inherited diabetes (MID) family history. A total of 42 variants possibly associated with mitochondrial diseases were identified according to the filtering strategy. These variants were sequenced in cohort 2 consisting of 90 EOD patients with MID. The association between the clinical phenotype and these variants was analyzed. Then, these variants were genotyped in cohort 3 consisting of 1,571 type 2 diabetes mellitus patients and 496 subjects with normal glucose tolerance (NGT) to analyze the association between variants with diabetes and DKD. RESULTS Patients with variants in the non-coding region had a higher percentage of obesity and levels of fasting insulin (62.1% vs. 24.6%, P = 0.001; 80.0% vs. 26.5% P < 0.001). The patients with the variants in rRNA had a higher prevalence of obesity (71.4% vs. 30.3%, P = 0.007), and the patients with the variants in mitochondrial complex I had a higher percentage of the upper tertile of FINS (64.3% vs. 34.3%, P = 0.049). Among 20 homogeneous variants successfully captured, two known variants (m.A3943G, m.A10005G) associated with other mitochondrial diseases were only in the diabetic group, but not in the NGT group, which perhaps indicated its possible association with diabetes. The prevalence of DKD was significantly higher in the group with the 20 variants than those without these variants (18.7% vs. 14.6%, P = 0.049) in the participants with diabetes of cohort 3. CONCLUSION MtDNA variants are associated with MID and DKD, and our findings advance our understanding of mtDNA in diabetes and DKD. It will have important implications for the individual therapy of mitochondrial diabetes.
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Affiliation(s)
- Meng Li
- Department of Endocrinology and Metabolism, Peking University People’s Hospital, Peking University Diabetes Center, Beijing, China
| | - Siqian Gong
- Department of Endocrinology and Metabolism, Peking University People’s Hospital, Peking University Diabetes Center, Beijing, China
| | - Xueyao Han
- Department of Endocrinology and Metabolism, Peking University People’s Hospital, Peking University Diabetes Center, Beijing, China
| | - Lingli Zhou
- Department of Endocrinology and Metabolism, Peking University People’s Hospital, Peking University Diabetes Center, Beijing, China
| | - Simin Zhang
- Department of Endocrinology and Metabolism, Peking University People’s Hospital, Peking University Diabetes Center, Beijing, China
| | - Qian Ren
- Department of Endocrinology and Metabolism, Peking University People’s Hospital, Peking University Diabetes Center, Beijing, China
| | - Xiaoling Cai
- Department of Endocrinology and Metabolism, Peking University People’s Hospital, Peking University Diabetes Center, Beijing, China
| | - Yingying Luo
- Department of Endocrinology and Metabolism, Peking University People’s Hospital, Peking University Diabetes Center, Beijing, China
| | - Wei Liu
- Department of Endocrinology and Metabolism, Peking University People’s Hospital, Peking University Diabetes Center, Beijing, China
| | - Yu Zhu
- Department of Endocrinology and Metabolism, Peking University People’s Hospital, Peking University Diabetes Center, Beijing, China
| | - Xianghai Zhou
- Department of Endocrinology and Metabolism, Peking University People’s Hospital, Peking University Diabetes Center, Beijing, China
| | - Yufeng Li
- Department of Endocrinology, Pinggu Teaching Hospital, Capital Medical University, Beijing, China
| | - Linong Ji
- Department of Endocrinology and Metabolism, Peking University People’s Hospital, Peking University Diabetes Center, Beijing, China
- *Correspondence: Linong Ji,
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An J, Min KI, Ju YS. Identifying Somatic Mitochondrial DNA Mutations. Methods Mol Biol 2022; 2493:153-165. [PMID: 35751814 DOI: 10.1007/978-1-0716-2293-3_10] [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] [Indexed: 06/15/2023]
Abstract
Mitochondria are cellular organelles that play an essential role in eukaryotes, producing the energy needed for a cell to survive. Beyond the ~3.2 Gb of nuclear genomic DNA, each human cell has hundreds of mitochondria which carry one or a few copies of the 16.5 kb circular mitochondria DNA (mtDNA). Despite its small size, the circular genome encodes 37 genes, including 13 proteins that generate respiratory chain complexes together with other proteins of nuclear origin. Similar to nuclear genome, mtDNA in cancer cells frequently harbor somatically acquired alterations. Whole-genome or whole-exome sequencing of the tumor and its matched normal tissues (frequently blood or adjacent non-tumor tissues) enables sensitive and efficient detection of somatic mtDNA mutations. Because each cancer cell commonly carries hundreds to thousands of mtDNA copies, detection of mtDNA mutations is dependent on the heteroplasmic level of each mutation. Here, we describe strategies to accurately identify somatic mtDNA mutations in cancer genome studies.
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Affiliation(s)
- Jisong An
- Graduate School of Medical Science and Engineering (GSMSE), Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
| | - Kyoung Il Min
- Graduate School of Medical Science and Engineering (GSMSE), Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
| | - Young Seok Ju
- Graduate School of Medical Science and Engineering (GSMSE), Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea.
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27
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Xin Y, Jia R, Zhang S, Guo F. Mitochondrial genome sequencing with short overlapping amplicons on MiSeq FGx system. Forensic Sci Res 2021; 7:142-153. [PMID: 35784421 PMCID: PMC9246037 DOI: 10.1080/20961790.2021.1963514] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 07/22/2021] [Accepted: 07/29/2021] [Indexed: 11/03/2022] Open
Abstract
With the development and maturation of massively parallel sequencing (MPS) technology, the mitochondrial genome (mitogenome) sequencing is increasingly applied in the forensic field. In this study, we employed the strategy of short overlapping amplicons for the whole mitogenome, library preparation with tagmentation using the Nextera® XT DNA Library Preparation Kit, sequencing on the MiSeq FGxTM Forensic Genomics System and analyzing data using the mitochondrial(mtDNA) MSR Plug-in and the mtDNA Variant Analyzer. A total of 27 libraries and 56 libraries were sequenced in a run using MiSeq Reagent Kit v2 and v3, respectively. Results showed more than 1800 × of averaged depth of coverage (DoC) at each position. Concordant haplotypes of 9947 A and 2800 M were obtained at 32 variants. Cross-reactivity was observed with 1 ng primate DNA and 10 ng non-primate DNA but could be easily distinguished. Full and accurate variants were obtained from at least 50 pg input DNA and from minor contributors between 19:1 and 1:19 mixed ratios with known reference profiles. More than 86% variants were detected from ≥200-bp degraded samples but its haplotype was assigned to more ancestral haplogroup. Further, a total of 3 962 variants were observed at 613 nucleotide positions from 103 Xibe mitogenomes with 25:1 ratio of transitions to transversions. Two new transversions (C13735A and A14755C) and two tri-alleles at nps 9824 and 16092 were identified. There were 103 unique mitogenome haplotypes from 103 Chinese Xibe that were assigned to 79 haplogroups. Haplogroup D was the preponderant top-level haplogroup in Xibe followed by F, B, M, A, N, G, C, Z, Y, HV and J. Random match probability (RMP) and haplotype diversity (HD) of the whole mitogenome was calculated as 0.0097 and 1.0000, respectively. Compared with HVS-I only, RMP decreased 33.56%, while the number of haplotypes and HD increased 15.73% and 0.49%, respectively. Principal component analysis (PCA) showed that Xibe was clustered to East and Southeast Asian. As a whole, this MPS strategy is suitable for the whole mitogenome sequencing especially for degraded samples and can facilitate generating mitogenome data to support the routine application in forensic sciences. EMP00726 is the first whole mitogenome dataset from Xibe contributed to the EMPOP. Supplemental data for this article are available online at.
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Affiliation(s)
- Yang Xin
- Forensic Science College, Criminal Investigation Police University of China, Shenyang, China
| | - Rulin Jia
- Forensic Science College, Criminal Investigation Police University of China, Shenyang, China
| | - Suhua Zhang
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Science, Ministry of Justice, Shanghai, China
| | - Fei Guo
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Science, Ministry of Justice, Shanghai, China
- Forensic Science College, Criminal Investigation Police University of China, Shenyang, China
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Association of m.5178C>A variant with serum lipid levels: a systematic review and meta-analysis. Biosci Rep 2021; 41:230366. [PMID: 34859818 PMCID: PMC8685646 DOI: 10.1042/bsr20212246] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 11/23/2021] [Accepted: 11/24/2021] [Indexed: 01/01/2023] Open
Abstract
Background: Emerging evidence shows that m.5178C>A variant is associated with a lower risk of coronary artery disease (CAD). However, the specific mechanisms remain elusive. Since dyslipidemia is one of the most critical risk factors for CAD and accounts for at least 50% of the population-attributable risk, it is tempting to speculate that the reduced CAD risk caused by the m.5178C>A variant may stem from an improved lipid profile. In order to verify this hypothesis, we conducted the present study to clarify the association of m.5178C>A variant with lipid levels. Methods: By searching ten databases for studies published before 30 June 2021. Thirteen East Asian populations (7587 individuals) were included for the analysis. Results: The present study showed that m.5178C>A variant was associated with higher high-density lipoprotein cholesterol (HDL-C) [standardized mean difference (SMD) = 0.12, 95% confidence interval (CI) = 0.06–0.17, P<0.001] and total cholesterol (TC) (SMD = 0.08, 95% CI = 0.02–0.14, P=0.01) levels. In subgroup analysis, the association of m.5178C>A variant with higher HDL-C levels were observed in Japanese (SMD = 0.09, 95% CI = 0.01–0.17, P=0.03) and Chinese populations (SMD = 0.13, 95% CI = 0.07–0.20, P<0.001). However, the association of m.5178C>A variant with lower low-density lipoprotein cholesterol (LDL-C) levels were only observed in Japanese populations (SMD = −0.11, 95% CI = −0.22 to 0.00, P=0.04). Conclusions: The m.5178C>A variant was associated with higher HDL-C and lower LDL-C levels in Japanese populations, which may contribute to decreased CAD risk and longevity of Japanese.
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Liou CW, Chen SH, Lin TK, Tsai MH, Chang CC. Oxidative Stress Biomarkers and Mitochondrial DNA Copy Number Associated with APOE4 Allele and Cholinesterase Inhibitor Therapy in Patients with Alzheimer's Disease. Antioxidants (Basel) 2021; 10:antiox10121971. [PMID: 34943074 PMCID: PMC8750673 DOI: 10.3390/antiox10121971] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Revised: 12/02/2021] [Accepted: 12/08/2021] [Indexed: 11/16/2022] Open
Abstract
Studies of the oxidative/anti-oxidative status in patients with Alzheimer’s disease (AD) carrying different alleles of the apolipoprotein E (APOE) gene are currently inconclusive; meanwhile, data regarding mitochondrial DNA copy number (mtCN) remain limited. We herein determined the thiobarbituric acid reactive substances (TBARS), thiols, and mtCN in blood samples of 600 AD patients and 601 controls. A significantly higher oxidative TBARS (1.64 μmol/L), lower antioxidative thiols (1.60 μmol/L), and lower mtCN (2.34 log Delta Ct) were found in the AD cohort as compared to the non-AD cohort (1.54 μmol/L, 1.71 μmol/L, 2.46 log Delta Ct). We further identified the ε4 alleles (APOE4) and separated subjects into three groups according to the number of APOE4. A significant trend was noted in the TBARS levels of both AD and non-AD cohorts, highest in the homozygous two alleles (1.86 and 1.80 μmol/L), followed by heterozygous one allele (1.70 and 1.74 μmol/L), and lowest in the no APOE4 allele (1.56 and 1.48 μmol/L). Similar trends of lower thiols and mtCN were also found in the AD cohort. In our study of the influence of cholinesterase inhibitor therapy, we found significantly reduced TBARS levels, and elevated mtCN in AD patients receiving rivastigmine and galantamine therapy. Our study demonstrates associations between the APOE4 allele and oxidative stress biomarkers and mtCN. Using cholinesterase inhibitor therapy may benefit AD patients through attenuation of oxidative stress and manipulation of the mtCN.
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Affiliation(s)
- Chia-Wei Liou
- Department of Neurology, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung 83301, Taiwan; (C.-W.L.); (S.-H.C.); (T.-K.L.)
- Center for Mitochondrial Research and Medicine, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung 83301, Taiwan
| | - Shih-Hsuan Chen
- Department of Neurology, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung 83301, Taiwan; (C.-W.L.); (S.-H.C.); (T.-K.L.)
| | - Tsu-Kung Lin
- Department of Neurology, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung 83301, Taiwan; (C.-W.L.); (S.-H.C.); (T.-K.L.)
- Center for Mitochondrial Research and Medicine, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung 83301, Taiwan
| | - Meng-Han Tsai
- Department of Neurology, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung 83301, Taiwan; (C.-W.L.); (S.-H.C.); (T.-K.L.)
- Correspondence: (M.-H.T.); (C.-C.C.); Tel.: +886-7-7317123 (ext. 2285) (M.-H.T.); +886-7-7318762 (C.-C.C.)
| | - Chiung-Chih Chang
- Department of Neurology, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung 83301, Taiwan; (C.-W.L.); (S.-H.C.); (T.-K.L.)
- Cognition and Aging Center and Institute for Translational Research in Biomedicine, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung 83301, Taiwan
- Correspondence: (M.-H.T.); (C.-C.C.); Tel.: +886-7-7317123 (ext. 2285) (M.-H.T.); +886-7-7318762 (C.-C.C.)
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30
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Nishikawa Y, Ishida T. Genetic lineage of the Amami islanders inferred from classical genetic markers. Meta Gene 2021. [DOI: 10.1016/j.mgene.2021.100956] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
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31
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Guo J, Wang W, Zhao K, Li G, He G, Zhao J, Yang X, Chen J, Zhu K, Wang R, Ma H, Xu B, Wang C. Genomic insights into
Neolithic
farming‐related migrations in the junction of east and southeast
Asia. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2021. [DOI: 10.1002/ajpa.24434] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Jianxin Guo
- Department of Anthropology and Ethnology, Institute of Anthropology, School of Sociology and Anthropology, State Key Laboratory of Cellular Stress Biology, School of Life Sciences, State Key Laboratory of Marine Environmental Science Xiamen University Xiamen China
| | - Weitao Wang
- Yunnan Modern Forensic Institute Kunming China
| | - Kai Zhao
- Yunnan Modern Forensic Institute Kunming China
| | | | - Guanglin He
- Department of Anthropology and Ethnology, Institute of Anthropology, School of Sociology and Anthropology, State Key Laboratory of Cellular Stress Biology, School of Life Sciences, State Key Laboratory of Marine Environmental Science Xiamen University Xiamen China
| | - Jing Zhao
- Department of Anthropology and Ethnology, Institute of Anthropology, School of Sociology and Anthropology, State Key Laboratory of Cellular Stress Biology, School of Life Sciences, State Key Laboratory of Marine Environmental Science Xiamen University Xiamen China
| | - Xiaomin Yang
- Department of Anthropology and Ethnology, Institute of Anthropology, School of Sociology and Anthropology, State Key Laboratory of Cellular Stress Biology, School of Life Sciences, State Key Laboratory of Marine Environmental Science Xiamen University Xiamen China
| | - Jinwen Chen
- Department of Anthropology and Ethnology, Institute of Anthropology, School of Sociology and Anthropology, State Key Laboratory of Cellular Stress Biology, School of Life Sciences, State Key Laboratory of Marine Environmental Science Xiamen University Xiamen China
| | - Kongyang Zhu
- Department of Anthropology and Ethnology, Institute of Anthropology, School of Sociology and Anthropology, State Key Laboratory of Cellular Stress Biology, School of Life Sciences, State Key Laboratory of Marine Environmental Science Xiamen University Xiamen China
| | - Rui Wang
- Department of Anthropology and Ethnology, Institute of Anthropology, School of Sociology and Anthropology, State Key Laboratory of Cellular Stress Biology, School of Life Sciences, State Key Laboratory of Marine Environmental Science Xiamen University Xiamen China
| | - Hao Ma
- Department of Anthropology and Ethnology, Institute of Anthropology, School of Sociology and Anthropology, State Key Laboratory of Cellular Stress Biology, School of Life Sciences, State Key Laboratory of Marine Environmental Science Xiamen University Xiamen China
| | - Bingying Xu
- Research Center of Biomedical Engineering Kunming Medical University Kunming China
| | - Chuan‐Chao Wang
- Department of Anthropology and Ethnology, Institute of Anthropology, School of Sociology and Anthropology, State Key Laboratory of Cellular Stress Biology, School of Life Sciences, State Key Laboratory of Marine Environmental Science Xiamen University Xiamen China
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32
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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: 0.5] [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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33
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Cooke NP, Mattiangeli V, Cassidy LM, Okazaki K, Stokes CA, Onbe S, Hatakeyama S, Machida K, Kasai K, Tomioka N, Matsumoto A, Ito M, Kojima Y, Bradley DG, Gakuhari T, Nakagome S. Ancient genomics reveals tripartite origins of Japanese populations. SCIENCE ADVANCES 2021; 7:eabh2419. [PMID: 34533991 PMCID: PMC8448447 DOI: 10.1126/sciadv.abh2419] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Accepted: 07/29/2021] [Indexed: 06/13/2023]
Abstract
Prehistoric Japan underwent rapid transformations in the past 3000 years, first from foraging to wet rice farming and then to state formation. A long-standing hypothesis posits that mainland Japanese populations derive dual ancestry from indigenous Jomon hunter-gatherer-fishers and succeeding Yayoi farmers. However, the genomic impact of agricultural migration and subsequent sociocultural changes remains unclear. We report 12 ancient Japanese genomes from pre- and postfarming periods. Our analysis finds that the Jomon maintained a small effective population size of ~1000 over several millennia, with a deep divergence from continental populations dated to 20,000 to 15,000 years ago, a period that saw the insularization of Japan through rising sea levels. Rice cultivation was introduced by people with Northeast Asian ancestry. Unexpectedly, we identify a later influx of East Asian ancestry during the imperial Kofun period. These three ancestral components continue to characterize present-day populations, supporting a tripartite model of Japanese genomic origins.
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Affiliation(s)
- Niall P. Cooke
- School of Medicine, Trinity College Dublin, Dublin, Ireland
| | | | - Lara M. Cassidy
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland
| | - Kenji Okazaki
- Department of Anatomy, Faculty of Medicine, Tottori University, Japan
| | | | - Shin Onbe
- Kumakogen Board of Education, Kumakogen, Japan
| | | | - Kenichi Machida
- Toyama Prefectural Research Office for Archaeological Heritage, Toyama, Japan
| | - Kenji Kasai
- Toyama Prefectural Center for Archaeological Operations, Toyama, Japan
| | | | | | - Masafumi Ito
- Foundation of Ishikawa Archaeological Artifacts Center, Kanazawa, Japan
| | - Yoshitaka Kojima
- Center for the Study of Ancient Civilizations and Cultural Resources, College of Human and Social Sciences, Kanazawa University, Kanazawa, Japan
| | - Daniel G. Bradley
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland
| | - Takashi Gakuhari
- Center for the Study of Ancient Civilizations and Cultural Resources, College of Human and Social Sciences, Kanazawa University, Kanazawa, Japan
| | - Shigeki Nakagome
- School of Medicine, Trinity College Dublin, Dublin, Ireland
- Center for the Study of Ancient Civilizations and Cultural Resources, College of Human and Social Sciences, Kanazawa University, Kanazawa, Japan
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34
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Yang XY, Rakha A, Chen W, Hou J, Qi XB, Shen QK, Dai SS, Sulaiman X, Abdulloevich NT, Afanasevna ME, Ibrohimovich KB, Chen X, Yang WK, Adnan A, Zhao RH, Yao YG, Su B, Peng MS, Zhang YP. Tracing the Genetic Legacy of the Tibetan Empire in the Balti. Mol Biol Evol 2021; 38:1529-1536. [PMID: 33283852 PMCID: PMC8042757 DOI: 10.1093/molbev/msaa313] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The rise and expansion of Tibetan Empire in the 7th to 9th centuries AD affected the course of history across East Eurasia, but the genetic impact of Tibetans on surrounding populations remains undefined. We sequenced 60 genomes for four populations from Pakistan and Tajikistan to explore their demographic history. We showed that the genomes of Balti people from Baltistan comprised 22.6–26% Tibetan ancestry. We inferred a single admixture event and dated it to about 39–21 generations ago, a period that postdated the conquest of Baltistan by the ancient Tibetan Empire. The analyses of mitochondrial DNA, Y, and X chromosome data indicated that both ancient Tibetan males and females were involved in the male-biased dispersal. Given the fact that the Balti people adopted Tibetan language and culture in history, our study suggested the impact of Tibetan Empire on Baltistan involved dominant cultural and minor demic diffusion.
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Affiliation(s)
- Xing-Yan Yang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, School of Life Sciences, Yunnan University, Kunming, China
| | - Allah Rakha
- Department of Forensic Sciences, University of Health Sciences, Lahore, Pakistan.,Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Wei Chen
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, China.,State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China
| | - Juzhi Hou
- Key Laboratory of Alpine Ecology (LAE), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing, China
| | - Xue-Bin Qi
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Quan-Kuan Shen
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China
| | - Shan-Shan Dai
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China
| | - Xierzhatijiang Sulaiman
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | | | - Manilova Elena Afanasevna
- E.N. Pavlovsky Institute of Zoology and Parasitology, Academy of Sciences of Republic of Tajikistan, Dushanbe, Tajikistan
| | | | - Xi Chen
- Research Center for Ecology and Environment of Central Asia, Chinese Academy of Sciences, Urumqi, China.,Key Laboratory of Biogeography and Bioresource in Arid Land, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China
| | - Wei-Kang Yang
- Research Center for Ecology and Environment of Central Asia, Chinese Academy of Sciences, Urumqi, China.,Key Laboratory of Biogeography and Bioresource in Arid Land, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China
| | - Atif Adnan
- Department of Human Anatomy, School of Basic Medicine, China Medical University, Shenyang, China
| | - Ruo-Han Zhao
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Yong-Gang Yao
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China.,KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Bing Su
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China.,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
| | - Min-Sheng Peng
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China.,KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Ya-Ping Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, School of Life Sciences, Yunnan University, Kunming, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China.,KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
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35
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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: 1.5] [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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36
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Mizuno F, Gojobori J, Kumagai M, Baba H, Taniguchi Y, Kondo O, Matsushita M, Matsushita T, Matsuda F, Higasa K, Hayashi M, Wang L, Kurosaki K, Ueda S. Population dynamics in the Japanese Archipelago since the Pleistocene revealed by the complete mitochondrial genome sequences. Sci Rep 2021; 11:12018. [PMID: 34121089 PMCID: PMC8200360 DOI: 10.1038/s41598-021-91357-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Accepted: 05/25/2021] [Indexed: 12/14/2022] Open
Abstract
The Japanese Archipelago is widely covered with acidic soil made of volcanic ash, an environment which is detrimental to the preservation of ancient biomolecules. More than 10,000 Palaeolithic and Neolithic sites have been discovered nationwide, but few skeletal remains exist and preservation of DNA is poor. Despite these challenging circumstances, we succeeded in obtaining a complete mitogenome (mitochondrial genome) sequence from Palaeolithic human remains. We also obtained those of Neolithic (the hunting-gathering Jomon and the farming Yayoi cultures) remains, and over 2,000 present-day Japanese. The Palaeolithic mitogenome sequence was not found to be a direct ancestor of any of Jomon, Yayoi, and present-day Japanese people. However, it was an ancestral type of haplogroup M, a basal group of the haplogroup M. Therefore, our results indicate continuity in the maternal gene pool from the Palaeolithic to present-day Japanese. We also found that a vast increase of population size happened and has continued since the Yayoi period, characterized with paddy rice farming. It means that the cultural transition, i.e. rice agriculture, had significant impact on the demographic history of Japanese population.
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Affiliation(s)
- Fuzuki Mizuno
- Department of Legal Medicine, Toho University School of Medicine, Tokyo, Japan.
| | - Jun Gojobori
- Department of Evolutionary Studies of Biosystems, SOKENDAI (The Graduate University for Advanced Studies), Hayama, Japan.
| | - Masahiko Kumagai
- Advanced Analysis Center, National Agriculture and Food Research Organization, Tsukuba, Japan
| | - Hisao Baba
- Department of Anthropology, National Museum of Nature and Science, Tokyo, Japan
| | - Yasuhiro Taniguchi
- Department of Archaeology, Faculty of Letters, Kokugakuin University, Tokyo, Japan
| | - Osamu Kondo
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | | | | | | | - Koichiro Higasa
- Department of Genome Analysis, Institute of Biomedical Science, Kansai Medical University, Hirakata, Japan
| | - Michiko Hayashi
- Department of Legal Medicine, Toho University School of Medicine, Tokyo, Japan
| | - Li Wang
- School of Medicine, Hangzhou Normal University, Hangzhou, China.
| | - Kunihiko Kurosaki
- Department of Legal Medicine, Toho University School of Medicine, Tokyo, Japan
| | - Shintaroh Ueda
- Department of Legal Medicine, Toho University School of Medicine, Tokyo, Japan.,Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
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Obesity associated with a novel mitochondrial tRNACys 5802A>G mutation in a Chinese family. Biosci Rep 2021; 40:221715. [PMID: 31868206 PMCID: PMC6944677 DOI: 10.1042/bsr20192153] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Revised: 12/18/2019] [Accepted: 12/19/2019] [Indexed: 01/07/2023] Open
Abstract
A Chinese family with matrilineally inherited obesity was assessed and its clinical, genetic, and molecular profiling was conducted. Obesity was observed in matrilineal relatives (3 out of 7) of a single generation (of 3 alive generations) in this family. On pedigree analysis and sequencing of their mitochondrial DNA (mtDNA), a novel homoplasmic mutation of the mitochondrial tRNACys gene (5802A>G) was identified in these individuals. This mutation correlated with a destabilized conserved base pair in this tRNA anticodon stem. Position 30 is known to be crucial for carrying out effective codon recognition and stability of tRNA. In accordance with the importance of this conserved site, we observed that the predicted structure of tRNACys with the mutation was noticeably remodeled in a molecular dynamics simulation when compared with the isoform of the wild-type. All other 46 mutations observed in the individual’s mtDNA were known variants belonging to haplogroup D4. Thus, this is the first report that provides evidence of the association between a mutation in tRNA and an enhanced risk of maternally transmissible obesity, offering more insights into obesity and its underlying nature.
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38
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Sun CB, Bai HX, Xu DN, Xiao Q, Liu Z. Mitochondrial 13513G>A Mutation With Low Mutant Load Presenting as Isolated Leber's Hereditary Optic Neuropathy Assessed by Next Generation Sequencing. Front Neurol 2021; 12:601307. [PMID: 33746872 PMCID: PMC7970004 DOI: 10.3389/fneur.2021.601307] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 02/10/2021] [Indexed: 11/13/2022] Open
Abstract
Objective: Mitochondrial 13513G>A mutation presenting as isolated Leber's hereditary optic neuropathy (LHON) without any extraocular pathology has not been reported in literature. We herein evaluate the clinical characteristics and heteroplasmy of m.13513G>A mutation manifesting as isolated LHON. Methods: Seven members of a Chinese family were enrolled in this study. All subjects underwent detailed systemic and ophthalmic examinations. Mitochondrial DNA in their blood was assessed by targeted PCR amplifications, next generation sequencing (NGS), and pyrosequencing. One hundred of blood samples from ethnic-matched healthy volunteers were tested by NGS and pyrosequencing as normal controls. Results: Isolated LHON without any other ocular or extraocular pathology was identified in a 16 year old patient in this family. Heteroplasmic m.13513G>A mutation was detected by NGS of the full mtDNA genome in the patient with mutant load of 33.56%, and of 26% 3 months and 3 years after the onset of LHON, respectively. No m.13513G>A mutation was detected in all his relatives by NGS. Pyrosequencing revealed the mutant load of m.13513G>A mutation of the LHON patient, his mother, father and sister were 22.4, 1.9, 0, and 0%, respectively. None of 100 healthy control subjects was detected to harbor m.13513G>A mutation either by NGS or by pyrosequencing of the full mt DNA genome. Conclusions: We first report m.13513G>A mutation with low mutant load presenting as isolated LHON. NGS of the full mitochondrial DNA genome is highly recommended for LHON suspects when targeted PCR amplification for main primary point mutations of LHON was negative.
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Affiliation(s)
- Chuan-bin Sun
- Eye Center, Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, China
| | - Hai-xia Bai
- Eye Center, Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, China
| | - Dan-ni Xu
- Eye Center, Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, China
| | - Qing Xiao
- Eye Center, Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, China
| | - Zhe Liu
- Department of Ophthalmology, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, Hangzhou, China
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Wang Q, Zhao J, Ren Z, Sun J, He G, Guo J, Zhang H, Ji J, Liu Y, Yang M, Yang X, Chen J, Zhu K, Wang R, Li Y, Chen G, Huang J, Wang CC. Male-Dominated Migration and Massive Assimilation of Indigenous East Asians in the Formation of Muslim Hui People in Southwest China. Front Genet 2021; 11:618614. [PMID: 33505437 PMCID: PMC7834311 DOI: 10.3389/fgene.2020.618614] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2020] [Accepted: 12/10/2020] [Indexed: 12/11/2022] Open
Abstract
The origin and diversification of Muslim Hui people in China via demic or simple cultural diffusion is a long-going debate. We here generated genome-wide data at nearly 700,000 single nucleotide polymorphisms (SNPs) from 45 Hui and 14 Han Chinese individuals collected from Guizhou province in southwest China. We applied principal component analysis (PCA), ADMIXTURE, f-statistics, qpWave, and qpAdm analysis to infer the population genetic structure and admixture history. Our results revealed the Guizhou Hui people have a limited amount of West Eurasian related ancestry at a proportion of 6%, but show massive genetic assimilation with indigenous southern Han Chinese and Tibetan or Tungusic/Mongolic related northern East Asians. We also detected a high frequency of North Asia or Central Asia related paternal Y-chromosome but not maternal mtDNA lineages in Guizhou Hui. Our observation supports the cultural diffusion has played a vital role in the formation of Hui people and the migration of Hui people to southwest China was probably a sex-biased male-driven process.
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Affiliation(s)
- Qiyan Wang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, China
| | - Jing Zhao
- Department of Anthropology and Ethnology, Institute of Anthropology, School of Life Sciences, Xiamen University, Xiamen, China
| | - Zheng Ren
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, China
| | - Jin Sun
- Department of Anthropology and Ethnology, Institute of Anthropology, School of Life Sciences, Xiamen University, Xiamen, China
| | - Guanglin He
- Department of Anthropology and Ethnology, Institute of Anthropology, School of Life Sciences, Xiamen University, Xiamen, China
| | - Jianxin Guo
- Department of Anthropology and Ethnology, Institute of Anthropology, School of Life Sciences, Xiamen University, Xiamen, China
| | - Hongling Zhang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, China
| | - Jingyan Ji
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, China
| | - Yubo Liu
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, China
| | - Meiqing Yang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, China
| | - Xiaomin Yang
- Department of Anthropology and Ethnology, Institute of Anthropology, School of Life Sciences, Xiamen University, Xiamen, China
| | - Jinwen Chen
- Department of Anthropology and Ethnology, Institute of Anthropology, School of Life Sciences, Xiamen University, Xiamen, China
| | - Kongyang Zhu
- Department of Anthropology and Ethnology, Institute of Anthropology, School of Life Sciences, Xiamen University, Xiamen, China
| | - Rui Wang
- Department of Anthropology and Ethnology, Institute of Anthropology, School of Life Sciences, Xiamen University, Xiamen, China
| | - Yingxiang Li
- Department of Anthropology and Ethnology, Institute of Anthropology, School of Life Sciences, Xiamen University, Xiamen, China
| | | | - Jiang Huang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, China
| | - Chuan-Chao Wang
- Department of Anthropology and Ethnology, Institute of Anthropology, School of Life Sciences, Xiamen University, Xiamen, China
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40
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JINAM TIMOTHYA, KAWAI YOSUKE, SAITOU NARUYA. Modern human DNA analyses with special reference to the inner dual-structure model of Yaponesian. ANTHROPOL SCI 2021. [DOI: 10.1537/ase.201217] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Affiliation(s)
- TIMOTHY A. JINAM
- Population Genetics Laboratory, National Institute of Genetics, Mishima
- Department of Genetics, School of Life Science, Graduate University for Advanced Studies (SOKENDAI), Mishima
| | - YOSUKE KAWAI
- Genome Medical Science Project, National Center for Global Health and Medicine, Tokyo
| | - NARUYA SAITOU
- Population Genetics Laboratory, National Institute of Genetics, Mishima
- Department of Genetics, School of Life Science, Graduate University for Advanced Studies (SOKENDAI), Mishima
- Faculty of Medicine, University of The Ryukyus, Nishihara
- Department of Biological Sciences, Graduate School of Science, the University of Tokyo, Tokyo
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41
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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: 0.8] [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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42
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He W, Chen C, Xiang K, Wang J, Zheng P, Tembrock LR, Jin D, Wu Z. The History and Diversity of Rice Domestication as Resolved From 1464 Complete Plastid Genomes. FRONTIERS IN PLANT SCIENCE 2021; 12:781793. [PMID: 34868182 PMCID: PMC8637288 DOI: 10.3389/fpls.2021.781793] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Accepted: 10/27/2021] [Indexed: 05/19/2023]
Abstract
The plastid is an essential organelle in autotrophic plant cells, descending from free-living cyanobacteria and acquired by early eukaryotic cells through endosymbiosis roughly one billion years ago. It contained a streamlined genome (plastome) that is uniparentally inherited and non-recombinant, which makes it an ideal tool for resolving the origin and diversity of plant species and populations. In the present study, a large dataset was amassed by de novo assembling plastomes from 295 common wild rice (Oryza rufipogon Griff.) and 1135 Asian cultivated rice (Oryza sativa L.) accessions, supplemented with 34 plastomes from other Oryza species. From this dataset, the phylogenetic relationships and biogeographic history of O. rufipogon and O. sativa were reconstructed. Our results revealed two major maternal lineages across the two species, which further diverged into nine well supported genetic clusters. Among them, the Or-wj-I/II/III and Or-wi-I/II genetic clusters were shared with cultivated (percentage for each cluster ranging 54.9%∼99.3%) and wild rice accessions. Molecular dating, phylogeographic analyses and reconstruction of population historical dynamics indicated an earlier origin of the Or-wj-I/II genetic clusters from East Asian with at least two population expansions, and later origins of other genetic clusters from multiple regions with one or more population expansions. These results supported a single origin of japonica rice (mainly in Or-wj-I/II) and multiple origins of indica rice (in all five clusters) for the history of rice domestication. The massive plastomic data set presented here provides an important resource for understanding the history and evolution of rice domestication as well as a genomic resources for use in future breeding and conservation efforts.
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Affiliation(s)
- Wenchuang He
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- MOA Key Laboratory of Crop Ecophysiology and Farming System in the Middle Reaches of the Yangtze River, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Caijin Chen
- MOA Key Laboratory of Crop Ecophysiology and Farming System in the Middle Reaches of the Yangtze River, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
- Institute of Biological and Environmental Sciences, University of Aberdeen, Aberdeen, United Kingdom
| | - Kunli Xiang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Jie Wang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- School of Landscape and Architecture, Zhejiang A&F University, Hangzhou, China
| | - Ping Zheng
- Department of Horticulture, Washington State University, Pullman, WA, United States
| | - Luke R. Tembrock
- Department of Agricultural Biology, Colorado State University, Fort Collins, CO, United States
- Luke R. Tembrock,
| | - Deming Jin
- MOA Key Laboratory of Crop Ecophysiology and Farming System in the Middle Reaches of the Yangtze River, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
- Deming Jin,
| | - Zhiqiang Wu
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- *Correspondence: Zhiqiang Wu,
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43
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Scott GR, Stull KE, Sbei AN, McKinney M, Boling SR, Irish JD. Rocker jaw: Global context for a Polynesian characteristic. Anat Rec (Hoboken) 2020; 304:1776-1791. [PMID: 33159494 DOI: 10.1002/ar.24566] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2020] [Revised: 10/26/2020] [Accepted: 10/27/2020] [Indexed: 11/11/2022]
Abstract
Our goal is to describe the global distribution of the "rocker jaw" variant in human populations. Rocker jaw refers to mandibles that lack the antegonial notch, making them unstable on a flat surface. Data were collected by C.G. Turner II on 9,207 individuals from Asia, Europe, the Pacific, and the Americas, and by J.D. Irish on 3,526 individuals from North and South Africa. With a focus on Polynesia, where the trait is most common, frequencies are presented for subdivisions of Oceania, Australasia, Eurasia, the Americas, and Africa. While the rocker jaw is a Polynesian characteristic, the trait is found throughout the world. Within major geographic regions, there are interesting contrasts, for example, (a) the similarity of Jomon and Ainu and their difference from modern Japanese; (b) Aleuts and Northwest Coast Indians are similar and both are distinct from the Inuit and other Native Americans; and (c) North and Sub-Saharan Africans show a regional difference that parallels genetic and dental distinctions. Skeletons in South America that exhibit the rocker jaw have been interpreted as Polynesian voyagers who ventured to the west coast of South America. The rarity of rocker jaw in South American natives supports this view. The rocker jaw can be attributed to the unique basicranium morphology and large upper facial height of Polynesians, which highlights the integrated growth of a functional module (i.e., mastication) of the craniofacial complex. The unusually high frequency of the trait in Polynesians is a product of both function and founder effect/genetic drift.
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Affiliation(s)
| | - Kyra E Stull
- Department of Anthropology, University of Nevada Reno, Reno, Nevada, USA
| | - Andrea N Sbei
- Department of Anthropology, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | - Mason McKinney
- Department of Anthropology, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | - Scarlett R Boling
- Department of Anthropology, University of Nevada Reno, Reno, Nevada, USA
| | - Joel D Irish
- Research Centre in Evolutionary Anthropology and Palaeoecology, School of Biological and Environmental Sciences, Liverpool John Moores University, Liverpool, UK
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44
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Mizuno F, Taniguchi Y, Kondo O, Hayashi M, Kurosaki K, Ueda S. A study of 8,300-year-old Jomon human remains in Japan using complete mitogenome sequences obtained by next-generation sequencing. Ann Hum Biol 2020; 47:555-559. [PMID: 32674620 DOI: 10.1080/03014460.2020.1797164] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Ancient human remains have been assigned to their mitochondrial DNA (mtDNA) haplogroups. To obtain efficiently deep and reliable nucleotide sequences of ancient DNA of interest, we achieved target enrichment followed by next-generation sequencing (NGS). Complete mitochondrial genome (mitogenome) sequences were obtained for three human remains from the Iyai rock-shelter site of the Initial Jomon Period in Japan. All the Jomon mitogenomes belong to haplogroup N9b, but no sequences among them were identical. High genetic diversity was clarified even among the Jomon human remains belonging to haplogroup N9b, which has been described as a haplogroup representing the Jomon people.
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Affiliation(s)
- Fuzuki Mizuno
- Department of Legal Medicine, Toho University School of Medicine, Tokyo, Japan
| | - Yasuhiro Taniguchi
- Department of Archaeology, Faculty of Letters, Kokugakuin University, Tokyo, Japan
| | - Osamu Kondo
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Michiko Hayashi
- Department of Legal Medicine, Toho University School of Medicine, Tokyo, Japan
| | - Kunihiko Kurosaki
- Department of Legal Medicine, Toho University School of Medicine, Tokyo, Japan
| | - Shintaroh Ueda
- Department of Legal Medicine, Toho University School of Medicine, Tokyo, Japan.,Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
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45
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Ischemic Stroke Risk Associated with Mitochondrial Haplogroup F in the Asian Population. Cells 2020; 9:cells9081885. [PMID: 32796743 PMCID: PMC7463505 DOI: 10.3390/cells9081885] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 08/06/2020] [Accepted: 08/06/2020] [Indexed: 12/22/2022] Open
Abstract
Mitochondrial dysfunction is involved in the pathogenesis of atherosclerosis, the primary risk factor for ischemic stroke. This study aims to explore the role of mitochondrial genomic variations in ischemic stroke, and to uncover the nuclear genes involved in this relationship. Eight hundred and thirty Taiwanese patients with a history of ischemic stroke and 966 normal controls were genotyped for their mitochondrial haplogroup (Mthapg). Cytoplasmic hybrid cells (cybrids) harboring different Mthapgs were used to observe functional differences under hypoxia-ischemia. RNA sequencing (RNASeq) was conducted to identify the particularly elevated mRNA. The patient study identified an association between Mthapg F1 and risk of ischemic stroke (OR 1.72:1.27-2.34, p = 0.001). The cellular study further demonstrated an impeded induction of hypoxic inducible factor 1α in the Mthapg F1 cybrid after hypoxia-ischemia. Additionally, the study demonstrated that Mthapg F cybrids were associated with an altered mitochondrial function, including decreased oxygen consumption, higher mitochondrial ROS production, and lower mitochondrial membrane potential. Mthapg F cybrids were also noted to be prone to inflammation, with increased expression of several inflammatory cytokines and elevated matrix metalloproteinase 9. The RNASeq identified significantly elevated expressions of angiopoietin-like 4 in Mthapg F1 cybrids after hypoxia-ischemia. Our study demonstrates an association between Mthapg F and susceptibility to ischemic stroke.
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46
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Nishida Y, Hara M, Fuku N, Taguchi N, Horita M, Shimanoe C, Higaki Y, Tanaka K. The interaction between mitochondrial haplogroups (M7a/D) and physical activity on adiponectin in a Japanese population. Mitochondrion 2020; 53:234-242. [PMID: 32565400 DOI: 10.1016/j.mito.2020.06.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Revised: 05/09/2020] [Accepted: 06/10/2020] [Indexed: 11/24/2022]
Abstract
Mitochondrial haplogroups F, A, and M7a are associated with increased risks of lifestyle diseases, while haplogroups N9 and D are associated with decreased risks of lifestyle diseases or with longevity. The current study determined the existence of interactions between 5 selected haplogroups and physical activity (PA) on total and high-molecular-weight (HMW) adiponectin in 3,994 men and 6,014 women. The interactions between haplogroups (M7a/D) and PA on adiponectin were significant in men (total and HMW: P-interaction = 0.041 and 0.011). The positive association of PA with adiponectin in men carrying haplogroup M7a is attenuated in comparison to men carrying haplogroup D.
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Affiliation(s)
- Yuichiro Nishida
- Department of Preventive Medicine, Faculty of Medicine, Saga University, Nabeshima 5-1-1, Saga 849-8501, Japan.
| | - Megumi Hara
- Department of Preventive Medicine, Faculty of Medicine, Saga University, Nabeshima 5-1-1, Saga 849-8501, Japan
| | - Noriyuki Fuku
- Graduate School of Health and Sports Science, Juntendo University, Hiraka-Gakuendai 1-1, Inzai-Shi, Chiba 270-1695, Japan
| | - Naoto Taguchi
- Department of Preventive Medicine, Faculty of Medicine, Saga University, Nabeshima 5-1-1, Saga 849-8501, Japan
| | - Mikako Horita
- Department of Preventive Medicine, Faculty of Medicine, Saga University, Nabeshima 5-1-1, Saga 849-8501, Japan
| | - Chisato Shimanoe
- Clinical Research Center, Saga University Hospital, Nabeshima 5-1-1, Saga 849-8501, Japan
| | - Yasuki Higaki
- Laboratory of Exercise Physiology, Faculty of Sports and Health Science, Fukuoka University, Nanakuma 8-19-1, Jonan-Ku, Fukuoka 814-0180, Japan
| | - Keitaro Tanaka
- Department of Preventive Medicine, Faculty of Medicine, Saga University, Nabeshima 5-1-1, Saga 849-8501, Japan
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Chaubey G, van Driem G. Munda languages are father tongues, but Japanese and Korean are not. EVOLUTIONARY HUMAN SCIENCES 2020; 2:e19. [PMID: 37588351 PMCID: PMC10427457 DOI: 10.1017/ehs.2020.14] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
Over two decades ago, it was observed that the linguistic affinity of the language spoken by a particular population tended to correlate with the predominant paternal, i.e. Y-chromosomal, lineage found in that population. Such correlations were found to be ubiquitous but not universal, and the striking exceptions to such conspicuous patterns of correlation between linguistic and genetic phylogeography elicit particular interest and beg for clarification. Within the Austroasiatic language family, the Munda languages are a clear-cut case of father tongues, whereas Japanese and Korean are manifestly not. In this study, the cases of Munda and Japanese are juxtaposed. A holistic understanding of these contrasting cases of ethnolinguistic prehistory with respect to the father tongue correlation will first necessitate a brief exposition of the phylogeography of the Y chromosomal lineage O. Then triangulation discloses some contours and particulars of both long lost episodes of ethnolinguistic prehistory.
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Affiliation(s)
- Gyaneshwer Chaubey
- Department of Zoology, Benaras Hindu University, Varanasi, Uttar Pradesh221005, India
| | - George van Driem
- Linguistics Institute, University of Bern, Länggassstrasse 49, CH 3012Bern, Switzerland
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48
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de Boer E, Yang MA, Kawagoe A, Barnes GL. Japan considered from the hypothesis of farmer/language spread. EVOLUTIONARY HUMAN SCIENCES 2020; 2:e13. [PMID: 37588377 PMCID: PMC10427481 DOI: 10.1017/ehs.2020.7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Formally, the Farming/Language Dispersal hypothesis as applied to Japan relates to the introduction of agriculture and spread of the Japanese language (between ca. 500 BC-AD 800). We review current data from genetics, archaeology, and linguistics in relation to this hypothesis. However, evidence bases for these disciplines are drawn from different periods. Genetic data have primarily been sampled from present-day Japanese and prehistoric Jōmon peoples (14,000-300 BC), preceding the introduction of rice agriculture. The best archaeological evidence for agriculture comes from western Japan during the Yayoi period (ca. 900 BC-AD 250), but little is known about northeastern Japan, which is a focal point here. And despite considerable hypothesizing about prehistoric language, the spread of historic languages/ dialects through the islands is more accessible but difficult to relate to prehistory. Though the lack of Yayoi skeletal material available for DNA analysis greatly inhibits direct study of how the pre-agricultural Jōmon peoples interacted with rice agriculturalists, our review of Jōmon genetics sets the stage for further research into their relationships. Modern linguistic research plays an unexpected role in bringing Izumo (Shimane Prefecture) and the Japan Sea coast into consideration in the populating of northeastern Honshu by agriculturalists beyond the Kantō region.
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Affiliation(s)
- Elisabeth de Boer
- Faculty of East Asian Studies, Ruhr-Universität Bochum, Bochum, Germany
| | - Melinda A. Yang
- Department of Biology, University of Richmond, Richmond, Virginia, USA
| | - Aileen Kawagoe
- Department of Social Studies, New International School of Japan, Tokyo, Japan
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Jeon S, Bhak Y, Choi Y, Jeon Y, Kim S, Jang J, Jang J, Blazyte A, Kim C, Kim Y, Shim J, Kim N, Kim YJ, Park SG, Kim J, Cho YS, Park Y, Kim HM, Kim BC, Park NH, Shin ES, Kim BC, Bolser D, Manica A, Edwards JS, Church G, Lee S, Bhak J. Korean Genome Project: 1094 Korean personal genomes with clinical information. SCIENCE ADVANCES 2020; 6:eaaz7835. [PMID: 32766443 PMCID: PMC7385432 DOI: 10.1126/sciadv.aaz7835] [Citation(s) in RCA: 71] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Accepted: 03/19/2020] [Indexed: 05/30/2023]
Abstract
We present the initial phase of the Korean Genome Project (Korea1K), including 1094 whole genomes (sequenced at an average depth of 31×), along with data of 79 quantitative clinical traits. We identified 39 million single-nucleotide variants and indels of which half were singleton or doubleton and detected Korean-specific patterns based on several types of genomic variations. A genome-wide association study illustrated the power of whole-genome sequences for analyzing clinical traits, identifying nine more significant candidate alleles than previously reported from the same linkage disequilibrium blocks. Also, Korea1K, as a reference, showed better imputation accuracy for Koreans than the 1KGP panel. As proof of utility, germline variants in cancer samples could be filtered out more effectively when the Korea1K variome was used as a panel of normals compared to non-Korean variome sets. Overall, this study shows that Korea1K can be a useful genotypic and phenotypic resource for clinical and ethnogenetic studies.
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Affiliation(s)
- Sungwon Jeon
- Korean Genomics Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
- Department of Biomedical Engineering, School of Life Sciences, UNIST, Ulsan 44919, Republic of Korea
| | - Youngjune Bhak
- Korean Genomics Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
- Department of Biomedical Engineering, School of Life Sciences, UNIST, Ulsan 44919, Republic of Korea
- Clinomics Inc., Ulsan 44919, Republic of Korea
| | - Yeonsong Choi
- Korean Genomics Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
- Department of Biomedical Engineering, School of Life Sciences, UNIST, Ulsan 44919, Republic of Korea
| | - Yeonsu Jeon
- Korean Genomics Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
- Department of Biomedical Engineering, School of Life Sciences, UNIST, Ulsan 44919, Republic of Korea
| | - Seunghoon Kim
- Korean Genomics Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
- Department of Biomedical Engineering, School of Life Sciences, UNIST, Ulsan 44919, Republic of Korea
| | - Jaeyoung Jang
- Korean Genomics Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Jinho Jang
- Korean Genomics Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
- Department of Biomedical Engineering, School of Life Sciences, UNIST, Ulsan 44919, Republic of Korea
| | - Asta Blazyte
- Korean Genomics Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Changjae Kim
- Korean Genomics Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
- Clinomics Inc., Ulsan 44919, Republic of Korea
| | - Yeonkyung Kim
- Korean Genomics Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Jungae Shim
- Korean Genomics Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Nayeong Kim
- Korean Genomics Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Yeo Jin Kim
- Korean Genomics Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Seung Gu Park
- Korean Genomics Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Jungeun Kim
- Personal Genomics Institute (PGI), Genome Research Foundation (GRF), Osong 28160, Republic of Korea
| | | | - Yeshin Park
- Clinomics Inc., Ulsan 44919, Republic of Korea
| | - Hak-Min Kim
- Korean Genomics Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
- Department of Biomedical Engineering, School of Life Sciences, UNIST, Ulsan 44919, Republic of Korea
- Clinomics Inc., Ulsan 44919, Republic of Korea
| | | | - Neung-Hwa Park
- Department of Internal Medicine, University of Ulsan College of Medicine, Ulsan University Hospital, Ulsan 44033, Republic of Korea
- Biomedical Research Center, University of Ulsan College of Medicine, Ulsan University Hospital, Ulsan 44033, Republic of Korea
| | - Eun-Seok Shin
- Division of Cardiology, Department of Internal Medicine, Ulsan Medical Center, Ulsan 44686, Republic of Korea
| | | | - Dan Bolser
- Clinomics Inc., Ulsan 44919, Republic of Korea
| | - Andrea Manica
- Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK
| | - Jeremy S. Edwards
- Department of Chemistry and Chemical Biology, University of New Mexico and University of New Mexico Comprehensive Cancer Center, Albuquerque, NM 87106, USA
| | - George Church
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Semin Lee
- Korean Genomics Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
- Department of Biomedical Engineering, School of Life Sciences, UNIST, Ulsan 44919, Republic of Korea
| | - Jong Bhak
- Korean Genomics Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
- Department of Biomedical Engineering, School of Life Sciences, UNIST, Ulsan 44919, Republic of Korea
- Clinomics Inc., Ulsan 44919, Republic of Korea
- Personal Genomics Institute (PGI), Genome Research Foundation (GRF), Osong 28160, Republic of Korea
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Zhang X, Li C, Zhou Y, Huang J, Yu T, Liu X, Shi H, Liu H, Chia S, Huang S, Guo Y, Shoocongdej R, Ji X, Su B. A Matrilineal Genetic Perspective of Hanging Coffin Custom in Southern China and Northern Thailand. iScience 2020; 23:101032. [PMID: 32304863 PMCID: PMC7163074 DOI: 10.1016/j.isci.2020.101032] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Revised: 02/06/2020] [Accepted: 03/30/2020] [Indexed: 01/16/2023] Open
Abstract
Hanging Coffin is a unique and ancient burial custom that has been practiced in southern China, Southeast Asia, and near Oceania regions for more than 3,000 years. Here, we conducted mitochondrial whole-genome analyses of 41 human remains sampled from 13 Hanging Coffin sites in southern China and northern Thailand, which were dated between ∼2,500 and 660 years before present. We found that there were genetic connections between the Hanging Coffin people living in different geographic regions. Notably, the matrilineal genetic diversity of the Hanging Coffin people from southern China is much higher than those from northern Thailand, consistent with the hypothesized single origin of the Hanging Coffin custom in southern China about 3,600 years ago, followed by its dispersal in southern China through demic diffusion, whereas the major dispersal pattern in Southeast Asia is cultural assimilation in the past 2,000 years.
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Affiliation(s)
- Xiaoming Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China; Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China
| | - Chunmei Li
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China; Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China
| | - Yanan Zhou
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jiahui Huang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Tengsong Yu
- Zhaotong Institute of Cultural Relics Protection and Archaeology, Zhaoyang, Yunnan 657200, China
| | - Xu Liu
- Yunnan Institute of Cultural Relics and Archaeology, Kunming 650118, China
| | - Hong Shi
- Yunnan Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming 650500, China; Yunnan Provincial Academy of Science and Technology, Kunming 650228, China
| | - Hong Liu
- International Joint Research Center for Karstology, Yunnan University, Kunming, 650223, China
| | - Stephen Chia
- Center for Global Archaeological Research, University of Science Malaysia, Penang, Malaysia
| | - Shenmin Huang
- Key Laboratory of Environmental Change and Resources Use in Baibu Gulf, Ministry of Education, Nanning Normal University, Nanning, Guangxi 530001, China
| | - Yaozheng Guo
- Youjiang Nationalities Museum, Baise, Guangxi 533000, China
| | - Rasmi Shoocongdej
- Department of Archaeology, Faculty of Archaeology, Silpakorn University, Bangkok 10200, Thailand.
| | - Xueping Ji
- Yunnan Institute of Cultural Relics and Archaeology, Kunming 650118, China; School of Geoscience, Yunnan University, Kunming 650091, China.
| | - Bing Su
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China; Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China.
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