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Feng Y, Chen L, Wang X, Zhang H, Wang Q, Liu Y, Jin X, Yang M, Huang J, Ren Z. Analysis of maternal genetic structure of mitochondrial DNA control region from Tai-Kadai-speaking Buyei population in southwestern China. BMC Genomics 2024; 25:50. [PMID: 38212691 PMCID: PMC10782584 DOI: 10.1186/s12864-023-09941-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: 10/17/2023] [Accepted: 12/26/2023] [Indexed: 01/13/2024] Open
Abstract
BACKGROUND Even though the Buyei are a recognised ethnic group in southwestern China, there hasn't been much work done on forensic population genetics, notably using mitochondrial DNA. The sequences and haplogroups of mitochondrial DNA control regions of the Buyei peoples were studied to provide support for the establishment of a reference database for forensic DNA analysis in East Asia. METHODS AND RESULTS The mitochondrial DNA control region sequences of 200 Buyei individuals in Guizhou were investigated. The haplotype frequencies and haplogroup distribution of the Buyei nationality in Guizhou were calculated. At the same time, the paired Fst values of the study population and other populations around the world were computed, to explore their genetic polymorphism and population relationship. A total of 179 haplotypes were detected in the Buyei population, with frequencies of 0.005-0.015. All haplotypes were assigned to 89 different haplogroups. The haplotype diversity and random matching probability were 0.999283 and 0.0063, respectively. The paired Fst genetic distances and correlation p-values among the 54 populations revealed that the Guizhou Buyei was most closely related to the Henan Han and the Guizhou Miao, and closer to the Hazara population in Pakistan and the Chiang Mai population. CONCLUSIONS The study of mitochondrial DNA based on the maternal genetic structure of the Buyei nationality in Guizhou will benefit the establishment of an East Asian forensic DNA reference database and provide a reference for anthropological research in the future.
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Grants
- KY No. [2021]065 Guizhou Province Education Department, Characteristic Region Project, Qian Education
- [2020] 4Y057 Guizhou Scientific Support Project, Qian Science Support
- No. 82160324 National Natural Science Foundation of China
- No. 82160324 National Natural Science Foundation of China
- [2020]6012 Guizhou "Hundred" High-level Innovative Talent Project, Qian Science Platform Talents
- KF202009 Shanghai Key Lab of Forensic Medicine, Key Lab of Forensic Science, Ministry of Justice, China (Academy of Forensic Science), Open Project
- NO. [2016] 1345 Guizhou Engineering Technology Research Center Project, Qian High-Tech of Development and Reform Commission, NO. [2016] 1345
- [2020] 1Y353 Guizhou Science Project, Qian Science Foundation
- [2018] 5779-X Guizhou Scientific Cultivation Project, Qian Science Platform Talent
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Affiliation(s)
- Yuhang Feng
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, 550004, Guizhou, China
| | - Li Chen
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, 550004, Guizhou, China
| | - Xiaoxue Wang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, 550004, Guizhou, China
| | - Hongling Zhang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, 550004, Guizhou, China
| | - Qiyan Wang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, 550004, Guizhou, China
| | - Yubo Liu
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, 550004, Guizhou, China
| | - Xiaoye Jin
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, 550004, Guizhou, China
| | - Meiqing Yang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, 550004, Guizhou, China
| | - Jiang Huang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, 550004, Guizhou, China.
| | - Zheng Ren
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, 550004, Guizhou, China.
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Ren Z, Feng Y, Zhang H, Wang Q, Yang M, Liu Y, Le C, Wang J, Huang J. Genetic analysis of the mitochondrial DNA control region in Tai-Kadai-speaking Dong population in southwest China. Ann Hum Biol 2022; 49:354-360. [PMID: 36190920 DOI: 10.1080/03014460.2022.2131334] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Abstract
BACKGROUND Dong people in Southwest China are officially recognised as an ethnic group, but there has been a lack of population genetic research on this group, especially based on mitochondrial DNA data. AIM To study the sequences and haplogroups of the mitochondrial DNA control region in a typical Dong population, and to provide help for the construction of a forensic mitochondrial DNA analysis reference database in East Asia. SUBJECTS AND METHODS The sequences of the mitochondrial DNA control region were analysed in 200 individuals of Dong in Guizhou. The haplotype frequencies, haplogroup distribution and paired Fst values of Guizhou Dong and 51 other populations in the world were calculated and explained to explore the genetic polymorphism and population relationships. RESULTS A total of 180 haplotypes were detected, with frequencies of 0.005-0.02. All haplotypes were assigned to 97 different haplogroups. The haplotype diversity and random matching probability were 0.998643 and 0.00635, respectively. The paired Fst values and correlation p values of 52 populations showed that the Guizhou Dong had the closest genetic relationship with the Henan Han and the Guizhou Miao in China, and were closest to the Punjab population in Pakistan and the Kashmiri population when compared with the world populations. CONCLUSIONS Our study was based on the matrilineal genetic structure of Guizhou Dong to study mitochondrial DNA, which was helpful to promote the establishment of the forensic DNA reference database in East Asia and provide reference for anthropological research.
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Affiliation(s)
- Zheng Ren
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, P. R. China
| | - Yuhang Feng
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, P. R. China
| | - Hongling Zhang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, P. R. China
| | - Qiyan Wang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, P. R. China
| | - Meiqing Yang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, P. R. China
| | - Yubo Liu
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, P. R. China
| | - Cuiyun Le
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, P. R. China
| | - Jie Wang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, P. R. China
| | - Jiang Huang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, P. R. China
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Connell JR, Benton MC, Lea RA, Sutherland HG, Haupt LM, Wright KM, Griffiths LR. Evaluating the suitability of current mitochondrial DNA interpretation guidelines for multigenerational whole mitochondrial genome comparisons. J Forensic Sci 2022; 67:1766-1775. [PMID: 35855536 PMCID: PMC9543078 DOI: 10.1111/1556-4029.15097] [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: 04/21/2022] [Revised: 06/06/2022] [Accepted: 06/30/2022] [Indexed: 12/03/2022]
Abstract
Sanger sequencing of the mitochondrial DNA (mtDNA) control region was previously the only method available for forensic casework involving degraded samples from skeletal remains. The introduction of Next Generation Sequencing (NGS) has transformed genetic data generation and human identification using mtDNA. Whole mitochondrial genome (mtGenome) analysis is now being introduced into forensic laboratories around the world to analyze historical remains. Research into large pedigrees using the mtGenome is critical to evaluate currently available interpretation guidelines for mtDNA analysis, which were developed for comparisons using the control region. This study included mtGenomes from 225 individuals from the last four generations of the Norfolk Island (NI) genetic isolate pedigree consisting of 49 distinct maternal lineages. The data from these individuals were arranged into 2339 maternally related pairs separated by up to 18 meioses. Our results show that 97.3% of maternally related pairs were concordant at all nucleotide positions, resulting in the correct interpretation of “Cannot Exclude”; 2.7% of pairs produced an “Inconclusive” result, and there were no instances of false exclusion. While these results indicate that existing guidelines are suitable for multigenerational whole mtGenome analysis, we recommend caution be taken when classifying heteroplasmic changes as differences for human identification. Our data showed the classification of heteroplasmic changes as differences increases the prevalence of inconclusive identification by 6%, with false exclusions observed in 0.34% of pairs examined. Further studies of multigenerational pedigrees, however, are needed to validate mtGenome interpretation guidelines for historical case work to more fully utilize emerging advancements.
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Affiliation(s)
- Jasmine R Connell
- Queensland University of Technology (QUT), Centre for Genomics and Personalised Health, Genomics Research Centre, School of Biomedical Sciences, Kelvin Grove, Qld, Australia
| | - Miles C Benton
- Queensland University of Technology (QUT), Centre for Genomics and Personalised Health, Genomics Research Centre, School of Biomedical Sciences, Kelvin Grove, Qld, Australia.,Human Genomics, Kenepuru Science Centre, Institute of Environmental Science and Research, Wellington, New Zealand
| | - Rodney A Lea
- Queensland University of Technology (QUT), Centre for Genomics and Personalised Health, Genomics Research Centre, School of Biomedical Sciences, Kelvin Grove, Qld, Australia
| | - Heidi G Sutherland
- Queensland University of Technology (QUT), Centre for Genomics and Personalised Health, Genomics Research Centre, School of Biomedical Sciences, Kelvin Grove, Qld, Australia
| | - Larisa M Haupt
- Queensland University of Technology (QUT), Centre for Genomics and Personalised Health, Genomics Research Centre, School of Biomedical Sciences, Kelvin Grove, Qld, Australia
| | - Kirsty M Wright
- Queensland University of Technology (QUT), Centre for Genomics and Personalised Health, Genomics Research Centre, School of Biomedical Sciences, Kelvin Grove, Qld, Australia.,Unrecovered War Casualties-Army, Australian Defence Force, Russell Offices, Russell, ACT, Australia.,Royal Australian Air Force (RAAF), Headquarters History and Heritage, Unrecovered War Casualties-Air Force, Russell, ACT, Australia
| | - Lyn R Griffiths
- Queensland University of Technology (QUT), Centre for Genomics and Personalised Health, Genomics Research Centre, School of Biomedical Sciences, Kelvin Grove, Qld, Australia
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4
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Feng Y, Zhang H, Wang Q, Yang M, Liu Y, Wang Jie, Huang J, Ren Z. The mitochondrial DNA control region sequences from the Chinese Sui population of southwestern China. Ann Hum Biol 2021; 48:635-640. [PMID: 34663140 DOI: 10.1080/03014460.2021.1994649] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
BACKGROUND Sui people are officially recognised people living in southwest China, but there has been a lack of genetic research, especially based on mitochondrial DNA data. AIM To study the sequences and haplogroups of the mitochondrial DNA control region in a typical Sui population, with the aim of helping to promote the establishment of a forensic DNA analysis reference database in East Asia. SUBJECTS AND METHODS We analysed 201 Sui individuals and observed the sequences of the mitochondrial DNA control region. We calculated and explained the haplotype frequencies, haplogroup distribution and pairwise Fst values between the Sui and 47 other populations in the world, in order to explore genetic polymorphisms and population relationships. RESULTS 161 haplotypes were found in the Sui population, with frequencies of 0.0049-0.0199. All samples were assigned to 80 different haplogroups. The haplotype diversity and random matching probability were 0.999938 and 0.024729, respectively. The pairwise Fst values and correlation p-values of 48 populations showed that the Sui population was most closely related to the Miao population in Guizhou and the Han population in Henan, and closer to the Punjab population and Pukhtunkhwa population in Pakistan, and was significantly different from the other 43 groups. Compared with the other 43 groups, it is relatively isolated. CONCLUSION Our results show that the study of mitochondrial DNA based on the analysis of matrilineal genetic structure of the Sui population can help to promote the establishment of a forensic DNA reference database in East Asia and provide reference for future anthropological research.
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Affiliation(s)
- Yuhang Feng
- Department of Forensic Medicine, Guizhou Medical University, Guiyang 550004, Guizhou, China
| | - Hongling Zhang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang 550004, Guizhou, China
| | - Qiyan Wang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang 550004, Guizhou, China
| | - Meiqing Yang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang 550004, Guizhou, China
| | - Yubo Liu
- Department of Forensic Medicine, Guizhou Medical University, Guiyang 550004, Guizhou, China
| | - Wang Jie
- Department of Forensic Medicine, Guizhou Medical University, Guiyang 550004, Guizhou, China
| | - Jiang Huang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang 550004, Guizhou, China
| | - Zheng Ren
- Department of Forensic Medicine, Guizhou Medical University, Guiyang 550004, Guizhou, China
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5
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Genetic characterization of a collection of Tsantsas from Ecuadorian museums. Forensic Sci Int 2021; 325:110879. [PMID: 34174769 DOI: 10.1016/j.forsciint.2021.110879] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2021] [Revised: 05/17/2021] [Accepted: 06/11/2021] [Indexed: 11/22/2022]
Abstract
Tsantsas are shrunken human heads originally made for ceremonial purposes by Amazonian indigenous groups of the Shuar and Achuar family, previously called Jivaroan tribes. A significant demand of these objects during the first half of the 20th century led to the manufacture of counterfeit shrunken heads for commercial purposes. For museums where these collections are held, as well as for the indigenous groups who claim their ownership, it is important to identify the origin and authenticity of these tsantsas. We hypothesized that a collection of 14 tsantsas from 3 different museum collections in Ecuador are human and aimed to characterize their sex and potential origin. We amplified the amelogenin gene and performed a high resolution melting analysis to determine their human origin and characterize their sex. We also analyzed a fragment (16209-16402) from the HVR-1 region to identify the mtDNA haplogroups present in the tsantsa collection. Our exploratory results show that all the tsantsas are human and that the collection is comprised of 13 males and 1 female. A total of seven mtDNA haplogroups were found among the tsantsa collection using the mtDNA EMPOP database. These results show a predominance of the Amerindian mtDNA haplogroups B, C and D. Additional principal component analysis, genetic distance tree and haplotype network analyses suggest a relationship between the tsantsa specimens and Native American groups.
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Mitochondrial DNA Profiles of Individuals from a 12th Century Necropolis in Feldioara (Transylvania). Genes (Basel) 2021; 12:genes12030436. [PMID: 33808521 PMCID: PMC8003334 DOI: 10.3390/genes12030436] [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: 01/25/2021] [Revised: 02/26/2021] [Accepted: 03/17/2021] [Indexed: 11/17/2022] Open
Abstract
The genetic signature of modern Europeans is the cumulated result of millennia of discrete small-scale exchanges between multiple distinct population groups that performed a repeated cycle of movement, settlement, and interactions with each other. In this study we aimed to highlight one such minute genetic cycle in a sea of genetic interactions by reconstructing part of the genetic story of the migration, settlement, interaction, and legacy of what is today the Transylvanian Saxon. The analysis of the mitochondrial DNA control region of 13 medieval individuals from Feldioara necropolis (Transylvania region, Romania) reveals a genetically heterogeneous group where all identified haplotypes are different. Most of the perceived maternal lineages are of Western Eurasian origin, except for the Central Asiatic haplogroup C seen in only one sample. Comparisons with historical and modern populations describe the contribution of the investigated Saxon settlers to the genetic history of this part of Europe.
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7
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The shaping of immunological responses through natural selection after the Roma Diaspora. Sci Rep 2020; 10:16134. [PMID: 32999407 PMCID: PMC7528012 DOI: 10.1038/s41598-020-73182-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Accepted: 09/02/2020] [Indexed: 01/20/2023] Open
Abstract
The Roma people are the largest transnational ethnic minority in Europe and can be considered the last human migration of South Asian origin into the continent. They left Northwest India approximately 1,000 years ago, reaching the Balkan Peninsula around the twelfth century and Romania in the fourteenth century. Here, we analyze whole-genome sequencing data of 40 Roma and 40 non-Roma individuals from Romania. We performed a genome-wide scan of selection comparing Roma, their local host population, and a Northwestern Indian population, to identify the selective pressures faced by the Roma mainly after they settled in Europe. We identify under recent selection several pathways implicated in immune responses, among them cellular metabolism pathways known to be rewired after immune stimulation. We validated the interaction between PIK3-mTOR-HIF-1α and cytokine response influenced by bacterial and fungal infections. Our results point to a significant role of these pathways for host defense against the most prevalent pathogens in Europe during the last millennium.
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Melchionda F, Stanciu F, Buscemi L, Pesaresi M, Tagliabracci A, Turchi C. Searching the undetected mtDNA variants in forensic MPS data. Forensic Sci Int Genet 2020; 49:102399. [PMID: 33038616 DOI: 10.1016/j.fsigen.2020.102399] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 08/27/2020] [Accepted: 09/21/2020] [Indexed: 10/23/2022]
Abstract
The efficiency of MPS in forensic mtDNA analysis has been thoroughly proven, although a reliable and well established data evaluation still remains a critical point. Numerous bioinformatics tools have been developed, but most of them require specific operating systems and high costs, while free open-source programs with user-friendly interfaces are few. In this study, 43 full mtGenomes were sequenced using the Ion Personal Genome Machine™ (PGM™) System and analyzed utilizing the plug-in Variant Caller (TVC) of the Ion Torrent Software Suite and the mtDNA-Server (mDS), a free web-based mitochondrial analysis tool for MPS data. The outcomes of these two different analysis tools were compared to variants noted after manual inspection of the aligned reads performed using Integrative Genomics Viewer (IGV). The comparison highlighted the presence of thirty-nine discordant variant calls, which were resolved by Sanger sequencing that confirmed the presence of all variants, except for 7 deletions. The combined adoption of IGV and Sanger type sequencing confirmatory steps, in addition of TVC and mDS analysis, resulted in a more accurate variants assignment with the detection of 32 additional true polymorphisms, which were noted in the final dataset. Regarding the heteroplasmy issue, out of a total of thirty heteroplasmic variants, twenty-eight were detected by the TVC, while the mDS detected twenty-two. Overall, none of the used bioinformatics tools were the perfect choice and a secondary analysis with an expert's opinion in complete mtGenome MPS data evaluation is still required in forensic genetic analysis.
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Affiliation(s)
- Filomena Melchionda
- Section of Legal Medicine, Department of Excellence of Biomedical Sciences and Public Health, Polytechnic University of Marche, Ancona, Italy - Via Tronto, 60126 Torrette Ancona, Italy.
| | - Florin Stanciu
- Romanian National DNA Database, National Forensic Science Institute, General Inspectorate of Romanian Police, Bucharest, Romania.
| | - Loredana Buscemi
- Section of Legal Medicine, Department of Excellence of Biomedical Sciences and Public Health, Polytechnic University of Marche, Ancona, Italy - Via Tronto, 60126 Torrette Ancona, Italy.
| | - Mauro Pesaresi
- Section of Legal Medicine, Department of Excellence of Biomedical Sciences and Public Health, Polytechnic University of Marche, Ancona, Italy - Via Tronto, 60126 Torrette Ancona, Italy.
| | - Adriano Tagliabracci
- Section of Legal Medicine, Department of Excellence of Biomedical Sciences and Public Health, Polytechnic University of Marche, Ancona, Italy - Via Tronto, 60126 Torrette Ancona, Italy.
| | - Chiara Turchi
- Section of Legal Medicine, Department of Excellence of Biomedical Sciences and Public Health, Polytechnic University of Marche, Ancona, Italy - Via Tronto, 60126 Torrette Ancona, Italy.
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9
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Mengge W, Guanglin H, Yongdong S, Shouyu W, Xing Z, Jing L, Zheng W, Hou Y. Massively parallel sequencing of mitogenome sequences reveals the forensic features and maternal diversity of tai-kadai-speaking hlai islanders. Forensic Sci Int Genet 2020; 47:102303. [PMID: 32361554 DOI: 10.1016/j.fsigen.2020.102303] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2019] [Revised: 03/30/2020] [Accepted: 04/16/2020] [Indexed: 12/11/2022]
Abstract
As a single maternally inherited locus, human mitochondrial DNA (mtDNA) is geographically arranged and plays a key role in forensic applications. Hlai population has been evidenced as the most typical and unmixed representative of the Tai-Kadai-speaking populations via genome-wide analyses. However, forensic features and maternal diversity of the complete mitogenomes in this Tai-Kadai ancestrally related population are scarce. Thus, we sequenced the complete mitogenomes in 127 Hainan Hlais and found 109 distinct haplotypes belonging to 43 terminal haplogroups resulting in the haplotype diversity of 0.9970. Our results of comprehensive population comparisons showed that Hlai islanders had a close genetic affinity with Tai-Kadai-speaking populations from Southeast Asia, which is consistent with the back-migration of Chinese Neolithic farmers into this region via the inland route. Besides, maternally genetic evidence further revealed a close genetic relationship between Tai-Kadai-speaking and Austronesian-speaking populations when only East Asian dataset was considered, which is consistent with the common origin from Yangtze rice farmers and then spread southward along the inland and coastal routes, respectively. In the reconstructed phylogenetic tree and median-joining networks, the vast majority of Hlais were clustered in exclusive clades, which demonstrated that Hlai people probably had undergone founder effect or genetic bottleneck in their history, and remained genetically isolated for a long time. Collectively, Hainan Hlai did not exhibit detectable maternal gene flow from surrounding or incoming populations. Mitogenome information generated in this study is a contribution in mitigating the underrepresentation of Chinese data in forensic mitogenetics and will assist geography-, metapopulation-, as well as phylogeny-based queries.
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Affiliation(s)
- Wang Mengge
- Institute of Forensic Medicine, West China School of Basic Science & Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - He Guanglin
- Institute of Forensic Medicine, West China School of Basic Science & Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Su Yongdong
- Forensic Identification Center, Public Security Bureau of Tibet Tibetan Autonomous Region, Lhasa, Tibet Tibetan Autonomous Region, 850000, China
| | - Wang Shouyu
- Institute of Forensic Medicine, West China School of Basic Science & Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Zou Xing
- Institute of Forensic Medicine, West China School of Basic Science & Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Liu Jing
- Institute of Forensic Medicine, West China School of Basic Science & Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Wang Zheng
- Institute of Forensic Medicine, West China School of Basic Science & Forensic Medicine, Sichuan University, Chengdu 610041, China.
| | - Yiping Hou
- Institute of Forensic Medicine, West China School of Basic Science & Forensic Medicine, Sichuan University, Chengdu 610041, China.
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10
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Sensitivity of mitochondrial DNA heteroplasmy detection using Next Generation Sequencing. Mitochondrion 2020; 50:88-93. [DOI: 10.1016/j.mito.2019.10.006] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Accepted: 10/10/2019] [Indexed: 01/03/2023]
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11
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Le C, Ren Z, Zhang H, Wang Q, Yang M, Liu Y, Huang J, Wang J. The mitochondrial DNA control region sequences from the Chinese Miao population of southeastern China. Ann Hum Biol 2019; 46:606-609. [PMID: 31775532 DOI: 10.1080/03014460.2019.1694701] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Background: Miao people are an officially recognised ethnic group living in southwest China, but have seldom been studied genetically, especially with respect to mtDNA data.Aim: To investigate the sequences and haplogroups of the mtDNA control region in a typical Miao population, with the aim of providing a good start for the expansion of the East Asian mtDNA reference database for forensic DNA analysis.Subjects and methods: We analysed 203 Miao individuals, looking at mtDNA control region sequences. We calculated and illustrated the haplotype frequencies, haplogroup distribution and pairwise Fst values between the Miao and six other worldwide populations to explore genetic polymorphisms and population relationships.Results: We observed 121 haplotypes with corresponding frequencies ranging from 0.0049 to 0.0690 in the Miao population. All the samples were assigned to 71 different haplogroups. The haplotype diversity and the random match probability were estimated to be 0.9844 and 0.0204, respectively. The pairwise Fst values and associated p values among seven populations suggest that the Miao population has significant differences to the other six populations, and is relatively isolated compared with them.Conclusions: Our results suggest that frequency estimates for mtDNA haplotypes in Miao ethnic groups should be determined independently rather than being pooled with other populations.
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Affiliation(s)
- Cuiyun Le
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, PR China
| | - Zheng Ren
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, PR China
| | - Hongling Zhang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, PR China
| | - Qiyan Wang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, PR China
| | - Meiqing Yang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, PR China
| | - Yubo Liu
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, PR China
| | - Jiang Huang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, PR China
| | - Jie Wang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, PR China
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Rusu I, Radu C, Țentea O, Popescu O, Kelemen B. A probable case of infantile cortical hyperostosis in 2nd-4th centuries AD Romania. INTERNATIONAL JOURNAL OF PALEOPATHOLOGY 2019; 26:8-13. [PMID: 31153087 DOI: 10.1016/j.ijpp.2019.05.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Revised: 05/08/2019] [Accepted: 05/21/2019] [Indexed: 06/09/2023]
Abstract
OBJECTIVE This study aims to discuss the differential diagnosis for the pathological alterations displayed on an infant skeleton from Romania. MATERIALS One infant skeleton retrieved form the bathhouse of an abandoned Roman fort and dated between the 2nd and the 4th centuries AD. METHODS All available skeletal elements were analyzed macroscopically. In addition, the isotopic signatures (δ13C and δ15N) and the control region of the human mitochondrial genome for this archaeological sample were analyzed. RESULTS Based on dental development and long bone length, the skeleton was aged between birth and 2 months of age. Pathological lesions were noted on the mandible and diaphyses of long bones, but spared the metaphyses. CONCLUSIONS The perinatal age of the individual, along with lesion morphology and location, suggests a diagnosis of infantile cortical hyperostosis. LIMITATIONS The analysis would benefit from further stable isotope and mitochondrial genome analyses, which was limited due to the absence of comparative human and faunal remains from the site. SUGGESTIONS FOR FURTHER RESEARCH Further multidisciplinary research on human archaeological remains from Romania would provide a clearer image of past disease and life histories in this geographic area.
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Affiliation(s)
- Ioana Rusu
- Molecular Biology Center, Interdisciplinary Research Institute on Bio-Nano-Sciences, Babeș-Bolyai University, 400271, Cluj-Napoca, Romania; Department of Molecular Biology and Biotechnology, Faculty of Biology and Geology, Babeș-Bolyai University, 400006, Cluj-Napoca, Romania.
| | - Claudia Radu
- Molecular Biology Center, Interdisciplinary Research Institute on Bio-Nano-Sciences, Babeș-Bolyai University, 400271, Cluj-Napoca, Romania; Department of Ancient History and Archaeology, Faculty of History and Philosophy, Babeș-Bolyai University, 400084, Cluj-Napoca, Romania
| | - Ovidiu Țentea
- Department of Archaeology, National Museum of Romanian History, 030026, Bucharest, Romania
| | - Octavian Popescu
- Molecular Biology Center, Interdisciplinary Research Institute on Bio-Nano-Sciences, Babeș-Bolyai University, 400271, Cluj-Napoca, Romania; Department of Molecular Biology and Biotechnology, Faculty of Biology and Geology, Babeș-Bolyai University, 400006, Cluj-Napoca, Romania; Institute of Biology Bucharest, Romanian Academy, 060031, Bucharest, Romania
| | - Beatrice Kelemen
- Molecular Biology Center, Interdisciplinary Research Institute on Bio-Nano-Sciences, Babeș-Bolyai University, 400271, Cluj-Napoca, Romania; Department of Molecular Biology and Biotechnology, Faculty of Biology and Geology, Babeș-Bolyai University, 400006, Cluj-Napoca, Romania
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Amorim A, Fernandes T, Taveira N. Mitochondrial DNA in human identification: a review. PeerJ 2019; 7:e7314. [PMID: 31428537 PMCID: PMC6697116 DOI: 10.7717/peerj.7314] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Accepted: 06/18/2019] [Indexed: 11/21/2022] Open
Abstract
Mitochondrial DNA (mtDNA) presents several characteristics useful for forensic studies, especially related to the lack of recombination, to a high copy number, and to matrilineal inheritance. mtDNA typing based on sequences of the control region or full genomic sequences analysis is used to analyze a variety of forensic samples such as old bones, teeth and hair, as well as other biological samples where the DNA content is low. Evaluation and reporting of the results requires careful consideration of biological issues as well as other issues such as nomenclature and reference population databases. In this work we review mitochondrial DNA profiling methods used for human identification and present their use in the main cases of humanidentification focusing on the most relevant issues for forensics.
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Affiliation(s)
- António Amorim
- Instituto Nacional de Medicina Legal e Ciências Forenses, Lisboa, Portugal
- Faculdade de Ciências da Universidade de Lisboa, Lisboa, Portugal
| | - Teresa Fernandes
- Escola de Ciências e Tecnologias, Universidade de Évora, Évora, Portugal
- Research Center for Anthropology and Health (CIAS), Universidade de Coimbra, Coimbra, Portugal
| | - Nuno Taveira
- Instituto Universitário Egas Moniz (IUEM), Almada, Portugal
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Lisbon, Portugal
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Asari M, Isozaki S, Hoshina C, Okuda K, Tanaka H, Horioka K, Shiono H, Shimizu K. Discrimination of haplotype in mitochondrial DNA mixtures using LNA-mediated PCR clamping. Forensic Sci Int Genet 2019; 41:58-63. [PMID: 30974414 DOI: 10.1016/j.fsigen.2019.03.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Revised: 03/20/2019] [Accepted: 03/20/2019] [Indexed: 10/27/2022]
Abstract
Locked nucleic acid (LNA) has been widely used for various genetic analyses, and has many benefits, in terms of the specificity or sensitivity of amplification, because LNA-containing primers/probes form more stable duplexes with template DNA than probes lacking LNA. Here, we developed a new method for discriminating HV1 haplotypes from mitochondrial DNA (mtDNA) mixtures by applying PCR clamping using LNA. PCR clamping is based on the selective inhibition of amplification using LNA-containing probes, which can discriminate single-nucleotide differences. Before designing probes, we selected 171 sequences with single-nucleotide variations from the HV1 region, and evaluated the specificity of LNA-containing probes for them by predicting Tm values. The differences of Tm between mismatched and exactly matched probe-template duplexes depended markedly on the type of LNA nucleotides for discriminating single-nucleotide differences, and the cytosine LNA nucleotide at the site of variations in the probes was most effective to discriminate these differences. For mixture analysis, each probe targeted one or two variations (16209C, 16217C, 16257A/16261T, 16297C/16298C, 16304C, 16362C, or 16362T) that are particularly common in the Japanese population, and seven designed probes completely inhibited the amplification of exactly matched templates. We prepared mixed samples by mixing DNA from two individuals at a ratio of 1:9, 1:4, 1:1, 4:1, or 9:1, and then performed Sanger sequencing analysis after PCR clamping with each probe. Our method distinguished each haplotype at lower ratios from two-person mixtures, and enabled sensitive detection at 12 pg of total DNA including 600 copies of mtDNA. Moreover, we analyzed three-person mixtures with representative sequences, and detected the minor haplotype of one individual present at a rate of 10% by adding two selected probes. The ability to discriminate haplotypes in mixed samples by using LNA-mediated PCR clamping indicates the potential value of mtDNA analysis in criminal investigations.
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Affiliation(s)
- Masaru Asari
- Department of Legal Medicine, Asahikawa Medical University, Asahikawa 078-8510, Japan.
| | - Shotaro Isozaki
- Department of Legal Medicine, Asahikawa Medical University, Asahikawa 078-8510, Japan
| | - Chisato Hoshina
- Department of Legal Medicine, Asahikawa Medical University, Asahikawa 078-8510, Japan
| | - Katsuhiro Okuda
- Department of Legal Medicine, Asahikawa Medical University, Asahikawa 078-8510, Japan
| | - Hiroki Tanaka
- Department of Legal Medicine, Asahikawa Medical University, Asahikawa 078-8510, Japan
| | - Kie Horioka
- Department of Legal Medicine, Asahikawa Medical University, Asahikawa 078-8510, Japan
| | - Hiroshi Shiono
- Department of Legal Medicine, Asahikawa Medical University, Asahikawa 078-8510, Japan
| | - Keiko Shimizu
- Department of Legal Medicine, Asahikawa Medical University, Asahikawa 078-8510, Japan
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Benvisto A, Messina F, Finocchio A, Popa L, Stefan M, Stefanescu G, Mironeanu C, Novelletto A, Rapone C, Berti A. A genetic portrait of the South-Eastern Carpathians based on autosomal short tandem repeats loci used in forensics. Am J Hum Biol 2018; 30:e23139. [PMID: 30099799 DOI: 10.1002/ajhb.23139] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2018] [Revised: 04/02/2018] [Accepted: 05/17/2018] [Indexed: 11/09/2022] Open
Abstract
OBJECTIVES This work aimed to describe the genetic landscape of the Balkan Peninsula, as revealed by STR markers commonly used in forensics and spatial methods specifically developed for genetic data. METHODS We generated and analyzed 16 short tandem repeats (STRs) autosomal genotypes in 287 subjects from ten administrative/geographical regions of Eastern Europe (Romania and the Republic of Moldova). We report estimates of the allele frequencies in these sub-populations, their fixation indexes, and use these results to complement previous spatial analyses of Southern Europe. RESULTS In seven out of ten analyzed regional samples the heterozygosity, averaged across loci, was lower than expected. The average Fis was 0.011. Among the 16 loci, five returned a significant fixation index Fst. The composite Fst across the 16 loci, among the 10 regional samples, was 0.00417, a figure twice as large as that obtained with the same markers across the entire Northern Mediterranean. The first spatial principal component (sPC1) returned the picture of a Central-European pattern of frequencies for the Carpathians, which extended to the Southern boundary of the Balkan Peninsula. However, the 8 alleles extracted by sPC1 returned a picture of a strong reduction of the migration rate in the Carpathian region, mostly between the inner locations. CONCLUSIONS Our results revealed an unexpected heterogeneity in the area. We believe that populations from some regions will require treatment as distinct entities when considered in forensic applications.
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Affiliation(s)
- Alessandro Benvisto
- Reparto Carabinieri Investigazioni Scientifiche - Sezione di Biologia, Rome, 00191, Italy
| | - Francesco Messina
- Department of Biology, University of Rome Tor Vergata, Rome, 00133, Italy
| | - Andrea Finocchio
- Department of Biology, University of Rome Tor Vergata, Rome, 00133, Italy
| | - Luis Popa
- "Grigore Antipa" National Museum of Natural History, Bucharest, 011341, Romania
| | - Mihaela Stefan
- Department of Genetics, University of Bucharest, Bucharest, 76258, Romania
| | | | | | - Andrea Novelletto
- Department of Biology, University of Rome Tor Vergata, Rome, 00133, Italy
| | - Cesare Rapone
- Reparto Carabinieri Investigazioni Scientifiche - Sezione di Biologia, Rome, 00191, Italy
| | - Andrea Berti
- Reparto Carabinieri Investigazioni Scientifiche - Sezione di Biologia, Rome, 00191, Italy
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Rusu I, Modi A, Vai S, Pilli E, Mircea C, Radu C, Urduzia C, Pinter ZK, Bodolică V, Dobrinescu C, Hervella M, Popescu O, Lari M, Caramelli D, Kelemen B. Maternal DNA lineages at the gate of Europe in the 10th century AD. PLoS One 2018. [PMID: 29538439 PMCID: PMC5851556 DOI: 10.1371/journal.pone.0193578] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Given the paucity of archaeogenetic data available for medieval European populations in comparison to other historical periods, the genetic landscape of this age appears as a puzzle of dispersed, small, known pieces. In particular, Southeastern Europe has been scarcely investigated to date. In this paper, we report the study of mitochondrial DNA in 10th century AD human samples from Capidava necropolis, located in Dobruja (Southeastern Romania, Southeastern Europe). This geographical region is particularly interesting because of the extensive population flux following diverse migration routes, and the complex interactions between distinct population groups during the medieval period. We successfully amplified and typed the mitochondrial control region of 10 individuals. For five of them, we also reconstructed the complete mitochondrial genomes using hybridization-based DNA capture combined with Next Generation Sequencing. We have portrayed the genetic structure of the Capidava medieval population, represented by 10 individuals displaying 8 haplotypes (U5a1c2a, V1a, R0a2’3, H1, U3a, N9a9, H5e1a1, and H13a1a3). Remarkable for this site is the presence of both Central Asiatic (N9a) and common European mtDNA haplotypes, establishing Capidava as a point of convergence between East and West. The distribution of mtDNA lineages in the necropolis highlighted the existence of two groups of two individuals with close maternal relationships as they share the same haplotypes. We also sketch, using comparative statistical and population genetic analyses, the genetic relationships between the investigated dataset and other medieval and modern Eurasian populations.
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Affiliation(s)
- Ioana Rusu
- Molecular Biology Center, Interdisciplinary Research Institute on Bio-Nano-Sciences, Babeș-Bolyai University, Cluj-Napoca, Romania
- Department of Molecular Biology and Biotechnology, Faculty of Biology and Geology, Babeș-Bolyai University, Cluj-Napoca, Romania
- * E-mail: (IR); (AM)
| | - Alessandra Modi
- Dipartimento di Biologia, Università di Firenze, Florence, Italy
- * E-mail: (IR); (AM)
| | - Stefania Vai
- Dipartimento di Biologia, Università di Firenze, Florence, Italy
| | - Elena Pilli
- Dipartimento di Biologia, Università di Firenze, Florence, Italy
| | - Cristina Mircea
- Molecular Biology Center, Interdisciplinary Research Institute on Bio-Nano-Sciences, Babeș-Bolyai University, Cluj-Napoca, Romania
- Department of Molecular Biology and Biotechnology, Faculty of Biology and Geology, Babeș-Bolyai University, Cluj-Napoca, Romania
| | - Claudia Radu
- Molecular Biology Center, Interdisciplinary Research Institute on Bio-Nano-Sciences, Babeș-Bolyai University, Cluj-Napoca, Romania
- Faculty of History and Philosophy, Babeș-Bolyai University, Cluj-Napoca, Romania
| | | | - Zeno Karl Pinter
- Department of History, Heritage and Protestant Theology, Lucian Blaga University of Sibiu, Sibiu, Romania
- Institute of Social Sciences and Humanities, Romanian Academy, Sibiu, Romania
| | - Vitalie Bodolică
- Department of Research-Development and Projects, Museum of National History and Archeology, Constanța, Romania
| | - Cătălin Dobrinescu
- Department of Research-Development and Projects, Museum of National History and Archeology, Constanța, Romania
| | - Montserrat Hervella
- Department of Genetics, Physical Anthropology and Animal Physiology, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), Bizkaia, Spain
| | - Octavian Popescu
- Molecular Biology Center, Interdisciplinary Research Institute on Bio-Nano-Sciences, Babeș-Bolyai University, Cluj-Napoca, Romania
- Department of Molecular Biology and Biotechnology, Faculty of Biology and Geology, Babeș-Bolyai University, Cluj-Napoca, Romania
| | - Martina Lari
- Dipartimento di Biologia, Università di Firenze, Florence, Italy
| | - David Caramelli
- Dipartimento di Biologia, Università di Firenze, Florence, Italy
| | - Beatrice Kelemen
- Molecular Biology Center, Interdisciplinary Research Institute on Bio-Nano-Sciences, Babeș-Bolyai University, Cluj-Napoca, Romania
- Department of Molecular Biology and Biotechnology, Faculty of Biology and Geology, Babeș-Bolyai University, Cluj-Napoca, Romania
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Cocoş R, Schipor S, Hervella M, Cianga P, Popescu R, Bănescu C, Constantinescu M, Martinescu A, Raicu F. Genetic affinities among the historical provinces of Romania and Central Europe as revealed by an mtDNA analysis. BMC Genet 2017; 18:20. [PMID: 28270115 PMCID: PMC5341396 DOI: 10.1186/s12863-017-0487-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Accepted: 03/02/2017] [Indexed: 01/17/2023] Open
Abstract
Background As a major crossroads between Asia and Europe, Romania has experienced continuous migration and invasion episodes. The precise routes may have been shaped by the topology of the territory and had diverse impacts on the genetic structure of mitochondrial DNA (mtDNA) in historical Romanian provinces. We studied 714 Romanians from all historical provinces, Wallachia, Dobrudja, Moldavia, and Transylvania, by analyzing the mtDNA control region and coding markers to encompass the complete landscape of mtDNA haplogroups. Results We observed a homogenous distribution of the majority of haplogroups among the Romanian provinces and a clear association with the European populations. A principal component analysis and multidimensional scaling analysis supported the genetic similarity of the Wallachia, Moldavia, and Dobrudja groups with the Balkans, while the Transylvania population was closely related to Central European groups. These findings could be explained by the topology of the Romanian territory, where the Carpathian Arch played an important role in migration patterns. Signals of Asian maternal lineages were observed in all Romanian historical provinces, indicating gene flow along the migration routes through East Asia and Europe. Conclusions Our current findings based on the mtDNA analysis of populations in historical provinces of Romania suggest similarity between populations in Transylvania and Central Europe, supported both by the observed clines in haplogroup frequencies for several European and Asian maternal lineages and MDS analyses. Electronic supplementary material The online version of this article (doi:10.1186/s12863-017-0487-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Relu Cocoş
- "Carol Davila" University of Medicine and Pharmacy, Chair of Medical Genetics, 19-21, Prof. dr. Dimitrie Gerota St., 020032, Bucharest, Romania.,Genome Life Research Center, Bucharest, Romania
| | - Sorina Schipor
- National Institute of Endocrinology "C. I. Parhon", Bucharest, Romania
| | - Montserrat Hervella
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU), Bizkaia, Spain
| | - Petru Cianga
- Department of Immunology, Grigore T. Popa University of Medicine and Pharmacy, Iasi, Romania
| | - Roxana Popescu
- "Victor Babeş" University of Medicine and Pharmacy, Timişoara, Romania
| | - Claudia Bănescu
- Department of Medical Genetics, University of Medicine and Pharmacy Tîrgu Mureş, Tîrgu Mureş, Romania
| | - Mihai Constantinescu
- "Francisc I. Rainer" Institute of Anthropology, Romanian Academy, Bucharest, Romania
| | - Alina Martinescu
- Department of Medical Genetics, Ovidius University, Faculty of Medicine, Constanța, Romania
| | - Florina Raicu
- "Carol Davila" University of Medicine and Pharmacy, Chair of Medical Genetics, 19-21, Prof. dr. Dimitrie Gerota St., 020032, Bucharest, Romania. .,"Francisc I. Rainer" Institute of Anthropology, Romanian Academy, Bucharest, Romania.
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