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Eliopoulos C, Moraitis K, Borrini M, Irish J, Kallis X, Manoli P, Chimonas M, Cariolou M. Fatal gunshot trauma of a child: A case from colonial Cyprus. MEDICINE, SCIENCE, AND THE LAW 2024; 64:169-172. [PMID: 37743624 PMCID: PMC10938475 DOI: 10.1177/00258024231202563] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
Forensic science has made some significant contributions to the investigation of human rights abuses related to armed conflicts, especially in the last 40 years. Some investigations are aimed at the collection of evidence in order to prosecute those responsible, while others are humanitarian in nature. This paper presents the multidisciplinary effort to recover and identify the remains of a 7-year-old child who was shot by British colonial forces in Cyprus in 1956. An investigation led to the discovery of the burial site, and archaeological methods were used to recover the remains. The anthropological examination provided information about the age of the child, as well as the nature of the skeletal trauma present. DNA results confirmed the identity of the victim, and the remains were released to the surviving family members for burial.
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Affiliation(s)
- Constantine Eliopoulos
- School of Biological and Environmental Sciences, Liverpool John Moores University, Liverpool, UK
| | - Konstantinos Moraitis
- Department of Forensic Medicine and Toxicology, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece
| | - Matteo Borrini
- School of Biological and Environmental Sciences, Liverpool John Moores University, Liverpool, UK
| | - Joel Irish
- School of Biological and Environmental Sciences, Liverpool John Moores University, Liverpool, UK
| | - Xenophon Kallis
- Office of the Presidential Commissioner for Humanitarian Affairs, The Republic of Cyprus, Nicosia, Cyprus
| | - Panayiotis Manoli
- Laboratory of Forensic Genetics, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Marios Chimonas
- Laboratory of Forensic Genetics, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Marios Cariolou
- Laboratory of Forensic Genetics, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
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Moutsouri I, Manoli P, Christofi V, Bashiardes E, Keravnou A, Xenophontos S, Cariolou MA. Deciphering the maternal ancestral lineage of Greek Cypriots, Armenian Cypriots and Maronite Cypriots. PLoS One 2024; 19:e0292790. [PMID: 38315645 PMCID: PMC10843121 DOI: 10.1371/journal.pone.0292790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 09/28/2023] [Indexed: 02/07/2024] Open
Abstract
Cyprus was conquered from several populations because of its special geographical location. In this study, 406 unrelated Cypriot samples were tested based on their mitochondrial DNA. In more detail, 185 were Greek Cypriots, 114 Armenian Cypriots and 107 Maronite Cypriots. This is the first time where the mitochondrial DNA of Greek Cypriots, Armenian Cypriots and Maronite Cypriots is compared with the aim of characterizing the maternal ancestry of Cypriots. The control region of the mtDNA is the most informative in terms of studying maternal ancestry and consists of three hypervariable regions (HVS-I, HVS-II, HVS-III). The hypervariable regions can provide important information regarding the maternal ancestor of the tested samples. The entire control region of the mtDNA was used to determine the mitotypes and subsequently the haplogroups of all the Cypriot DNA samples. Based on the aforementioned analyses, Greek Cypriots were found to be genetically closer to Armenian Cypriots, while Greek Cypriots and Armenian Cypriots showed moderate genetic differentiation with Maronite Cypriots. The most prevalent haplogroups among Cypriots were haplogroups H and U, while R0 is common but in different frequencies for Greek Cypriots, Armenian Cypriots and Maronite Cypriots. It is proposed that the maternal ancestor may have originated during the Neolithic period and/or the Bronze age.
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Affiliation(s)
- Irene Moutsouri
- Department of Cardiovascular Genetics and The Laboratory of Forensic Genetics, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Panayiotis Manoli
- Department of Cardiovascular Genetics and The Laboratory of Forensic Genetics, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Vasilis Christofi
- Department of Cardiovascular Genetics and The Laboratory of Forensic Genetics, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Evy Bashiardes
- Department of Cardiovascular Genetics and The Laboratory of Forensic Genetics, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Anna Keravnou
- Department of Cardiovascular Genetics and The Laboratory of Forensic Genetics, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Stavroulla Xenophontos
- Department of Cardiovascular Genetics and The Laboratory of Forensic Genetics, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Marios A Cariolou
- Department of Cardiovascular Genetics and The Laboratory of Forensic Genetics, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
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Silva NM, Kreutzer S, Souleles A, Triantaphyllou S, Kotsakis K, Urem-Kotsou D, Halstead P, Efstratiou N, Kotsos S, Karamitrou-Mentessidi G, Adaktylou F, Chondroyianni-Metoki A, Pappa M, Ziota C, Sampson A, Papathanasiou A, Vitelli K, Cullen T, Kyparissi-Apostolika N, Lanz AZ, Peters J, Rio J, Wegmann D, Burger J, Currat M, Papageorgopoulou C. Ancient mitochondrial diversity reveals population homogeneity in Neolithic Greece and identifies population dynamics along the Danubian expansion axis. Sci Rep 2022; 12:13474. [PMID: 35931723 PMCID: PMC9356035 DOI: 10.1038/s41598-022-16745-8] [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: 02/25/2022] [Accepted: 07/14/2022] [Indexed: 11/09/2022] Open
Abstract
The aim of the study is to investigate mitochondrial diversity in Neolithic Greece and its relation to hunter-gatherers and farmers who populated the Danubian Neolithic expansion axis. We sequenced 42 mitochondrial palaeogenomes from Greece and analysed them together with European set of 328 mtDNA sequences dating from the Early to the Final Neolithic and 319 modern sequences. To test for population continuity through time in Greece, we use an original structured population continuity test that simulates DNA from different periods by explicitly considering the spatial and temporal dynamics of populations. We explore specific scenarios of the mode and tempo of the European Neolithic expansion along the Danubian axis applying spatially explicit simulations coupled with Approximate Bayesian Computation. We observe a striking genetic homogeneity for the maternal line throughout the Neolithic in Greece whereas population continuity is rejected between the Neolithic and present-day Greeks. Along the Danubian expansion axis, our best-fitting scenario supports a substantial decrease in mobility and an increasing local hunter-gatherer contribution to the gene-pool of farmers following the initial rapid Neolithic expansion. Οur original simulation approach models key demographic parameters rather than inferring them from fragmentary data leading to a better understanding of this important process in European prehistory.
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Affiliation(s)
- Nuno M Silva
- Department of Genetics & Evolution, University of Geneva, Geneva, Switzerland
| | - Susanne Kreutzer
- Palaeogenetics Group, Institute of Organismic and Molecular Evolution (iomE), Johannes Gutenberg University of Mainz, 55099, Mainz, Germany.,Functional Genomics Center Zurich/GEML, Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Angelos Souleles
- Laboratory of Physical Anthropology, Department of History & Ethnology, Democritus University of Thrace, 69100, Komotini, Greece
| | - Sevasti Triantaphyllou
- Faculty of Philosophy, School of History and Archaeology, Aristotle University of Thessaloniki, 54124, Thessaloniki, Greece
| | - Kostas Kotsakis
- Faculty of Philosophy, School of History and Archaeology, Aristotle University of Thessaloniki, 54124, Thessaloniki, Greece
| | - Dushka Urem-Kotsou
- Department of History & Ethnology, Democritus University of Thrace, 69100, Komotini, Greece
| | - Paul Halstead
- Emeritus, Department of Archaeology, University of Sheffield, Sheffield, S1 3NJ, UK
| | - Nikos Efstratiou
- Faculty of Philosophy, School of History and Archaeology, Aristotle University of Thessaloniki, 54124, Thessaloniki, Greece
| | - Stavros Kotsos
- Ephorate of Antiquities of Thessaloniki City, Hellenic Ministry of Culture and Sports, 54003, Thessaloniki, Greece
| | | | - Fotini Adaktylou
- Ephorate of Antiquities of Chalcidice and Mount Athos, Hellenic Ministry of Culture and Sports, 63100, Poligiros Chalcidice, Greece
| | | | - Maria Pappa
- Ephorate of Antiquities of Thessaloniki Region, Hellenic Ministry of Culture and Sports, 54646, Thessaloniki, Greece
| | - Christina Ziota
- Ephorate of Antiquities of Florina, Hellenic Ministry of Culture and Sports, 53100, Florina, Greece
| | - Adamantios Sampson
- Department of Mediterranean Studies, University of Aegean, 85132, Rhodes, Greece
| | - Anastasia Papathanasiou
- Ephorate of Paleoanthropology and Speleology, Hellenic Ministry of Culture and Sports, 11636, Athens, Greece
| | - Karen Vitelli
- Prof. Emerita, Department of Anthropology, Franchthi Cave Project, Indiana University Bloomington, Bloomington, USA
| | - Tracey Cullen
- American School of Classical Studies at Athens, Princeton, NJ, USA
| | - Nina Kyparissi-Apostolika
- Ephor Emerita of the Ephorate of Paleoanthropology and Speleology, Hellenic Ministry of Culture and Sports, 11636, Athens, Greece
| | - Andrea Zeeb Lanz
- General Direction for Cultural Heritage of Rhineland-Palatinate, Speyer, Germany
| | - Joris Peters
- Institute of Palaeoanatomy, Domestication Research and the History of Veterinary Medicine, LMU Munich, Munich, Germany.,SNSB, State Collection of Palaeoanatomy Munich, Munich, Germany
| | - Jérémy Rio
- Department of Genetics & Evolution, University of Geneva, Geneva, Switzerland
| | - Daniel Wegmann
- Department of Biology, University of Fribourg, 1700, Fribourg, Switzerland.,Swiss Institute of Bioinformatics, 1700, Fribourg, Switzerland
| | - Joachim Burger
- Palaeogenetics Group, Institute of Organismic and Molecular Evolution (iomE), Johannes Gutenberg University of Mainz, 55099, Mainz, Germany.,Functional Genomics Center Zurich/GEML, Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Mathias Currat
- Department of Genetics & Evolution, University of Geneva, Geneva, Switzerland. .,Institute of Genetics and Genomics in Geneva (IGE3), University of Geneva, Geneva, Switzerland.
| | - Christina Papageorgopoulou
- Laboratory of Physical Anthropology, Department of History & Ethnology, Democritus University of Thrace, 69100, Komotini, Greece.
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Frequency distribution of mitochondrial DNA haplogroups within the Kalash population of Pakistan. Meta Gene 2021. [DOI: 10.1016/j.mgene.2021.100893] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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Mitochondrial DNA (hypervariable region I) diversity in Basrah population - Iraq. Genomics 2020; 112:3560-3564. [PMID: 32289467 DOI: 10.1016/j.ygeno.2020.04.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2020] [Revised: 03/24/2020] [Accepted: 04/06/2020] [Indexed: 10/24/2022]
Abstract
In attempt to investigate the origin of Basrah, we examined the mitochondrial DNA(mt-DNA) variations by hypervariable segment 1(HVS1) Sequencing and determination of specific site haplogroups. In Basrah, no significant differences diversity among Iraqis' HVS1 compared with other countries. The values were within the range of gene diversity across the Middle East and exhibited the unimodal pattern of differences in the pairwise sequence. Given the small genetic differences between people living in this area, phylogenetic analysis showed a large variability of the communities of Basrah; they didn't cluster on the phylogenetic tree.
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Zimmermann B, Sturk-Andreaggi K, Huber N, Xavier C, Saunier J, Tahir M, Chouery E, Jalkh N, Megarbane A, Bodner M, Coble M, Irwin J, Parsons T, Parson W. Mitochondrial DNA control region variation in Lebanon, Jordan, and Bahrain. Forensic Sci Int Genet 2019; 42:99-102. [DOI: 10.1016/j.fsigen.2019.06.020] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Revised: 06/06/2019] [Accepted: 06/25/2019] [Indexed: 10/26/2022]
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Ethnogenetic analysis reveals that Kohistanis of Pakistan were genetically linked to west Eurasians by a probable ancestral genepool from Eurasian steppe in the bronze age. Mitochondrion 2019; 47:82-93. [PMID: 31103559 DOI: 10.1016/j.mito.2019.05.004] [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: 10/19/2018] [Revised: 04/06/2019] [Accepted: 05/15/2019] [Indexed: 12/13/2022]
Abstract
Despite the unique geographic, ethnic, social and cultural features of Kohistan in Pakistan, the origin and descent of Kohistanis remain still obscure. In an effort to address questions concerning the genetic structure, origin and genetic affinities of Kohistanis, we herein applied an ethnogenetic approach consisting on mitochondrial DNA (mtDNA) analysis and dental morphology analysis. We sequenced HVS1 of mtDNA, observed 14 haplotypes and assigned a total of 9 haplogroups belonging to macrolineages M (17%) and N (83%). Genetic diversity estimates in Kohistanis (Hd = 0.910 ± 0.014; Pi = 0.019 ± 0.001; θw = 0.019 ± 0.006) were similar to that of previous studies in other Pakistani populations. Overall, the analyses of dental morphology and mtDNA profile of Kohistanis resulted in similar findings. All the analyses indicate that Kohistanis share affinities to populations from Europe, Near East, Central Asia and South Asia. The Kohistani HVS1 haplotype 2 shares 100% identity to HVS1 haplotypes across the Europe. These results in light of recent insights into ancient genomics lead us to conclude that ancestry from Eurasian Steppe genetically linked Kohistanis to all these populations in the Bronze Age. This is consistent with linguistic evidence and also with the Indo-Aryan migration model for the peopling of South Asia.
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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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Simão F, Ferreira AP, de Carvalho EF, Parson W, Gusmão L. Defining mtDNA origins and population stratification in Rio de Janeiro. Forensic Sci Int Genet 2018; 34:97-104. [PMID: 29433058 DOI: 10.1016/j.fsigen.2018.02.003] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Revised: 01/29/2018] [Accepted: 02/02/2018] [Indexed: 10/18/2022]
Abstract
The genetic composition of the Brazilian population was shaped by interethnic admixture between autochthonous Native Americans, Europeans settlers and African slaves. This structure, characteristic of most American populations, implies the need for large population forensic databases to capture the high diversity that is usually associated with admixed populations. In the present work, we sequenced the control region of mitochondrial DNA from 205 non-related individuals living in the Rio de Janeiro metropolitan region. Overall high haplotype diversity (0.9994 ± 0.0006) was observed, and pairwise comparisons showed a high proportion of haplotype pairs with more than one-point differences. When ignoring homopolymeric tracts, pairwise comparisons showed no differences 0.18% of the time, and differences in a single position were found with a frequency of 0.32%. A high percentage of African mtDNA was found (42%), with lineages showing a major South West origin. For the West Eurasian and Native American haplogroups (representing 32% and 26%, respectively) it was not possible to evaluate a clear geographic or linguistic affiliation. When grouping the mtDNA lineages according to their continental origin (Native American, European and African), differences were observed for the ancestry proportions estimated with autosomal ancestry-informative markers, suggesting some level of genetic substructure. The results from this study are in accordance with historical data where admixture processes are confirmed with a strong maternal contribution of African maternal ancestry and a relevant contribution of Native American maternal ancestry. Moreover, the evidence for some degree of association between mtDNA and autosomal information should be considered when combining these types of markers in forensic analysis.
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Affiliation(s)
- Filipa Simão
- DNA Diagnostic Laboratory (LDD), State University of Rio de Janeiro (UERJ), Rio de Janeiro, Brazil
| | - Ana Paula Ferreira
- DNA Diagnostic Laboratory (LDD), State University of Rio de Janeiro (UERJ), Rio de Janeiro, Brazil
| | | | - Walther Parson
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria; Forensic Science Program, The Pennsylvania State University,University Park, PA, USA.
| | - Leonor Gusmão
- DNA Diagnostic Laboratory (LDD), State University of Rio de Janeiro (UERJ), Rio de Janeiro, Brazil
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Yaka R, Birand A, Yılmaz Y, Caner C, Açan SC, Gündüzalp S, Parvizi P, Erim Özdoğan A, Togan İ, Somel M. Archaeogenetics of Late Iron Age Çemialo Sırtı, Batman: Investigating maternal genetic continuity in north Mesopotamia since the Neolithic. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2018; 166:196-207. [PMID: 29399779 DOI: 10.1002/ajpa.23423] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Revised: 12/13/2017] [Accepted: 01/12/2018] [Indexed: 01/25/2023]
Abstract
OBJECTIVES North Mesopotamia has witnessed dramatic social change during the Holocene, but the impact of these events on its demographic history is poorly understood. Here, we study this question by analysing genetic data from the recently excavated Late Iron Age settlement of Çemialo Sırtı in Batman, southeast Turkey. Archaeological and radiocarbon evidence indicate that the site was inhabited during the second and first millennia BCE. Çemialo Sırtı reveals nomadic items of the Early Iron Age, as well as items associated with the Late Achaemenid and subsequent Hellenistic Periods. We compare Çemialo Sırtı mitochondrial DNA profiles with earlier and later populations from west Eurasia to describe genetic continuity patterns in the region. MATERIALS AND METHODS A total of 16 Çemialo Sırtı individuals' remains were studied. PCR and Sanger sequencing were used to obtain mitochondrial DNA HVRI-HVRII sequences. We studied haplotype diversity and pairwise genetic distances using FST , comparing the Çemialo Sırtı population with ancient and modern-day populations from west Eurasia. Coalescent simulations were carried out to test continuity for specific population comparisons. RESULTS Mitochondrial DNA (mtDNA) haplotypes from 12 Çemialo Sırtı individuals reveal high haplotype diversity in this population, conspicuously higher than early Holocene west Eurasian populations, which supports the notion of increasing population admixture in west Eurasia through the Holocene. In its mtDNA composition, Çemialo Sırtı shows highest affinity to Neolithic north Syria and Neolithic Anatolia among ancient populations studied, and to modern-day southwest Asian populations. Based on population genetic simulations we cannot reject continuity between Neolithic and Iron Age, or between Iron Age and present-day populations of the region. DISCUSSION Despite the region's complex sociopolitical history and indication for increased genetic diversity over time, we find no evidence for sharp shifts in north Mesopotamian maternal genetic composition within the last 10,000 years.
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Affiliation(s)
- Reyhan Yaka
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
| | - Ayşegül Birand
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
| | - Yasemin Yılmaz
- Department of Archaeology, Düzce University, Düzce, Turkey
| | - Ceren Caner
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
| | - Sinan Can Açan
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
| | - Sidar Gündüzalp
- Department of Prehistory, İstanbul University, İstanbul, Turkey
| | - Poorya Parvizi
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
| | - Aslı Erim Özdoğan
- Department of Archaeology, Çanakkale Onsekiz Mart University, Çanakkale, Turkey
| | - İnci Togan
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
| | - Mehmet Somel
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
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Ben Halim N, Hsouna S, Lasram K, Chargui M, Khemira L, Saidane R, Abdelhak S, Kefi R. Mitochondrial DNA structure of an isolated Tunisian Berber population and its relationship with Mediterranean populations. Ann Hum Biol 2018; 45:86-97. [DOI: 10.1080/03014460.2017.1414875] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Nizar Ben Halim
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur in Tunis, Tunis, Tunisia
- University of Tunis El Manar, Tunis, Tunisia
| | - Sana Hsouna
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur in Tunis, Tunis, Tunisia
- University of Tunis El Manar, Tunis, Tunisia
| | - Khaled Lasram
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur in Tunis, Tunis, Tunisia
- University of Tunis El Manar, Tunis, Tunisia
| | - Mariem Chargui
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur in Tunis, Tunis, Tunisia
- University of Tunis El Manar, Tunis, Tunisia
| | - Laaroussi Khemira
- Association de Sauvegarde de la Nature et de Protection de l’Environnement à Douiret (ASNAPED), Tunis, Tunisia
| | - Rachid Saidane
- Association de Sauvegarde de la Nature et de Protection de l’Environnement à Douiret (ASNAPED), Tunis, Tunisia
| | - Sonia Abdelhak
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur in Tunis, Tunis, Tunisia
- University of Tunis El Manar, Tunis, Tunisia
| | - Rym Kefi
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur in Tunis, Tunis, Tunisia
- University of Tunis El Manar, Tunis, Tunisia
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Elkamel S, Boussetta S, Khodjet-El-Khil H, Benammar Elgaaied A, Cherni L. Ancient and recent Middle Eastern maternal genetic contribution to North Africa as viewed by mtDNA diversity in Tunisian Arab populations. Am J Hum Biol 2018; 30:e23100. [PMID: 29359455 DOI: 10.1002/ajhb.23100] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Revised: 12/06/2017] [Accepted: 12/29/2017] [Indexed: 11/07/2022] Open
Abstract
OBJECTIVES Through previous mitochondrial DNA studies, the Middle Eastern maternal genetic contribution to Tunisian populations appears limited. In fact, most of the studied communities were cosmopolitan, or of Berber or Andalusian origin. To provide genetic evidence for the actual contribution of Middle Eastern mtDNA lineages to Tunisia, we focused on two Arab speaking populations from Kairouan and Wesletia known to belong to an Arab genealogical lineage. MATERIALS AND METHODS A total of 114 samples were sequenced for the mtDNA HVS-I and HVS-II regions. Using these data, we evaluated the distribution of Middle Eastern haplogroups in the study populations, constructed interpolation maps, and established phylogenetic networks allowing estimation of the coalescence time for three specific Middle Eastern subclades (R0a, J1b, and T1). RESULTS Both studied populations displayed North African genetic structure and Middle Eastern lineages with a frequency of 12% and 28.12% in Kairouan and Wesletia, respectively. TMRCA estimates for haplogroups T1a, R0a, and J1b in Tunisian Arabian samples were around 15 000 YBP, 9000 to 5000 YBP, and 960 to 600 YBP, respectively. CONCLUSIONS The Middle Eastern maternal genetic contribution to Tunisian populations, as to other North African populations, occurred mostly in deep prehistory. They were brought in different migration waves during the Upper Paleolithic, probably with the expansion of Iberomaurusian culture, and during Epipaleolithic and Early Neolithic periods, which are concomitant with the Capsian civilization. Middle Eastern lineages also came to Tunisia during the recent Islamic expansion of the 7th CE and the subsequent massive Bedouin migration during the 11th CE.
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Affiliation(s)
- Sarra Elkamel
- Laboratory of Genetics, Immunology and Human Pathology, Faculté des Sciences de Tunis, Université de Tunis El Manar, Tunis, 2092, Tunisia
| | - Sami Boussetta
- Laboratory of Genetics, Immunology and Human Pathology, Faculté des Sciences de Tunis, Université de Tunis El Manar, Tunis, 2092, Tunisia
| | - Houssein Khodjet-El-Khil
- Laboratory of Genetics, Immunology and Human Pathology, Faculté des Sciences de Tunis, Université de Tunis El Manar, Tunis, 2092, Tunisia
| | - Amel Benammar Elgaaied
- Laboratory of Genetics, Immunology and Human Pathology, Faculté des Sciences de Tunis, Université de Tunis El Manar, Tunis, 2092, Tunisia
| | - Lotfi Cherni
- Laboratory of Genetics, Immunology and Human Pathology, Faculté des Sciences de Tunis, Université de Tunis El Manar, Tunis, 2092, Tunisia.,High Institute of Biotechnology, University of Monastir, Monastir, 5000, Tunisia
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Georgiou A, Demetriou CA, Heraclides A, Christou YP, Leonidou E, Loukaides P, Yiasoumi E, Panagiotou D, Manoli P, Thomson P, Loizidou MA, Hadjisavvas A, Zamba-Papanicolaou E. Mitochondrial superclusters influence age of onset of Parkinson's disease in a gender specific manner in the Cypriot population: A case-control study. PLoS One 2017; 12:e0183444. [PMID: 28877188 PMCID: PMC5587277 DOI: 10.1371/journal.pone.0183444] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Accepted: 08/06/2017] [Indexed: 01/25/2023] Open
Abstract
Background Despite evidence supporting an involvement of mitochondrial dysfunction in the pathogenesis of some neurodegenerative disorders, there are inconsistent findings concerning mitochondrial haplogroups and their association to neurodegenerative disorders, including idiopathic Parkinson’s disease (PD). Methods To test this hypothesis for the Greek-Cypriot population, a cohort of 230 PD patients and 457 healthy matched controls were recruited. Mitochondrial haplogroup distributions for cases and controls were determined. Association tests were carried out between mitochondrial haplogroups and PD. Results Mitochondrial haplogroup U was associated with a reduced PD risk in the Cypriot population. After pooling mitochondrial haplogroups together into haplogroup clusters and superclusters, association tests demonstrated a significantly protective effect of mitochondrial haplogroup cluster N (xR) and supercluster LMN for PD risk only in females. In addition, for female PD cases belonging to UKJT and R (xH, xUKJT) haplogroup, the odds of having a later age of onset of PD were 13 and 15 times respectively higher than the odds for female cases with an H haplogroup. Conclusion Statistically significant associations regarding PD risk and PD age of onset were mostly detected for females thus suggesting that gender is a risk modifier between mitochondrial haplogroups and PD status / PD age of onset. The biological mechanisms behind this gender specificity remain to be determined.
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Affiliation(s)
- Andrea Georgiou
- Neurology Clinic D, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
- The Cyprus School of Molecular Medicine, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Christiana A. Demetriou
- Neurology Clinic D, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
- The Cyprus School of Molecular Medicine, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Alexandros Heraclides
- Department of Primary Care and Population Health, University of Nicosia Medical School, Nicosia, Cyprus
| | - Yiolanda P. Christou
- Neurology Clinic D, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
- Neurology Clinic B, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Eleni Leonidou
- Neurology Clinic C, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | | | | | | | - Panayiotis Manoli
- Department of Cardiovascular Genetics and the Laboratory of Forensic Genetics, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Pippa Thomson
- Centre for Genomic and Experimental Medicine, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Maria A. Loizidou
- The Cyprus School of Molecular Medicine, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
- Electron Microscopy and Molecular Pathology Department, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Andreas Hadjisavvas
- The Cyprus School of Molecular Medicine, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
- Electron Microscopy and Molecular Pathology Department, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Eleni Zamba-Papanicolaou
- Neurology Clinic D, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
- The Cyprus School of Molecular Medicine, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
- * E-mail:
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Rakha A, Fatima, Peng MS, Adan A, Bi R, Yasmin M, Yao YG. mtDNA sequence diversity of Hazara ethnic group from Pakistan. Forensic Sci Int Genet 2017; 30:e1-e5. [DOI: 10.1016/j.fsigen.2017.07.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2017] [Revised: 07/02/2017] [Accepted: 07/08/2017] [Indexed: 10/19/2022]
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Kefi R, Hechmi M, Naouali C, Jmel H, Hsouna S, Bouzaid E, Abdelhak S, Beraud-Colomb E, Stevanovitch A. On the origin of Iberomaurusians: new data based on ancient mitochondrial DNA and phylogenetic analysis of Afalou and Taforalt populations. Mitochondrial DNA A DNA Mapp Seq Anal 2016; 29:147-157. [PMID: 28034339 DOI: 10.1080/24701394.2016.1258406] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The Western North African population was characterized by the presence of Iberomaurusian civilization at the Epiplaeolithic period (around 20,000 years before present (YBP) to 10,000 YBP). The origin of this population is still not clear: they may come from Europe, Near East, sub-Saharan Africa or they could have evolved in situ in North Africa. With the aim to contribute to a better knowledge of the settlement of North Africa we analysed the mitochondrial DNA extracted from Iberomaurusian skeletons exhumed from the archaeological site of Afalou (AFA) (15,000-11,000 YBP) in Algeria and from the archaeological site of Taforalt (TAF) (23,000-10,800 YBP) in Morocco. Then, we carried out a phylogenetic analysis relating these Iberomaurusians to 61 current Mediterranean populations. The genetic structure of TAF and AFA specimens contains only North African and Eurasian maternal lineages. These finding demonstrate the presence of these haplotypes in North Africa from at least 20,000 YBP. The very low contribution of a Sub-Saharan African haplotype in the Iberomaurusian samples is confirmed. We also highlighted the existence of genetic flows between Southern and Northern coast of the Mediterranean.
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Affiliation(s)
- Rym Kefi
- a Laboratory of Biomedical Genomics and Oncogenetics , Institut Pasteur de Tunis , Tunis , Tunisia.,b University Tunis El Manar , Tunis , Tunisia
| | - Meriem Hechmi
- a Laboratory of Biomedical Genomics and Oncogenetics , Institut Pasteur de Tunis , Tunis , Tunisia
| | - Chokri Naouali
- a Laboratory of Biomedical Genomics and Oncogenetics , Institut Pasteur de Tunis , Tunis , Tunisia.,b University Tunis El Manar , Tunis , Tunisia
| | - Haifa Jmel
- a Laboratory of Biomedical Genomics and Oncogenetics , Institut Pasteur de Tunis , Tunis , Tunisia
| | - Sana Hsouna
- a Laboratory of Biomedical Genomics and Oncogenetics , Institut Pasteur de Tunis , Tunis , Tunisia.,b University Tunis El Manar , Tunis , Tunisia
| | - Eric Bouzaid
- c Institut National de Police Scientifique Laboratoire de Marseille , Marseille , France
| | - Sonia Abdelhak
- a Laboratory of Biomedical Genomics and Oncogenetics , Institut Pasteur de Tunis , Tunis , Tunisia.,b University Tunis El Manar , Tunis , Tunisia
| | | | - Alain Stevanovitch
- c Institut National de Police Scientifique Laboratoire de Marseille , Marseille , France
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Serin A, Canan H, Alper B, Korkut Gulmen M, Zimmermann B, Parson W. Mitochondrial DNA control region haplotype and haplogroup diversity in South Eastern Turkey. Forensic Sci Int Genet 2016; 24:176-179. [DOI: 10.1016/j.fsigen.2016.07.011] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2016] [Revised: 07/12/2016] [Accepted: 07/23/2016] [Indexed: 10/21/2022]
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17
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Turchi C, Stanciu F, Paselli G, Buscemi L, Parson W, Tagliabracci A. The mitochondrial DNA makeup of Romanians: A forensic mtDNA control region database and phylogenetic characterization. Forensic Sci Int Genet 2016; 24:136-142. [DOI: 10.1016/j.fsigen.2016.06.013] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Revised: 05/26/2016] [Accepted: 06/18/2016] [Indexed: 01/13/2023]
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18
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Gurkan C, Sevay H, Demirdov DK, Hossoz S, Ceker D, Teralı K, Erol AS. Turkish Cypriot paternal lineages bear an autochthonous character and closest resemblance to those from neighbouring Near Eastern populations. Ann Hum Biol 2016; 44:164-174. [DOI: 10.1080/03014460.2016.1207805] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Cemal Gurkan
- Turkish Cypriot DNA Laboratory, Committee on Missing Persons in Cyprus Turkish Cypriot Member Office, Nicosia (North Cyprus), Turkey
| | - Huseyin Sevay
- Department of Information Systems Engineering, Near East University, Nicosia (North Cyprus), Turkey
| | - Damla Kanliada Demirdov
- Turkish Cypriot DNA Laboratory, Committee on Missing Persons in Cyprus Turkish Cypriot Member Office, Nicosia (North Cyprus), Turkey
| | - Sinem Hossoz
- Department of Anthropology, Ankara University, Ankara, Turkey
| | - Deren Ceker
- Department of Anthropology, Ankara University, Ankara, Turkey
| | - Kerem Teralı
- Turkish Cypriot DNA Laboratory, Committee on Missing Persons in Cyprus Turkish Cypriot Member Office, Nicosia (North Cyprus), Turkey
| | - Ayla Sevim Erol
- Department of Anthropology, Ankara University, Ankara, Turkey
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Messina F, Scano G, Contini I, Martínez-Labarga C, De Stefano GF, Rickards O. Linking between genetic structure and geographical distance: Study of the maternal gene pool in the Ethiopian population. Ann Hum Biol 2016; 44:53-69. [PMID: 26883569 DOI: 10.3109/03014460.2016.1155646] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Background The correlation between genetics and geographical distance has already been examined through the study of the dispersion of human populations, especially in terms of uniparental genetic markers. Aim The present work characterises, at the level of the mitochondrial DNA (mtDNA), two new samples of Amhara and Oromo populations from Ethiopia to evaluate the possible pattern of distribution for mtDNA variation and to test the hypothesis of the Isolation-by-Distance (IBD) model among African, European and Middle-Eastern populations. Subjects and methods This study analysed 173 individuals belonging to two ethnic groups of Ethiopia, Amhara and Oromo, by assaying HVS-I and HVS-II of mtDNA D-loop and informative coding region SNPs of mtDNA. Results The analysis suggests a relationship between genetic and geographic distances, affirming that the mtDNA pool of Africa, Europe and the Middle East might be coherent with the IBD model. Moreover, the mtDNA gene pools of the Sub-Saharan African and Mediterranean populations were very different. Conclusion In this study the pattern of mtDNA distribution, beginning with the Ethiopian plateau, was tested in the IBD model. It could be affirmed that, on a continent scale, the mtDNA pool of Africa, Europe and the Middle East might fall under the IBD model.
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Affiliation(s)
- Francesco Messina
- a Center of Molecular Anthropology for Ancient DNA Study, Department of Biology , University of Rome 'Tor Vergata' , Via della Ricerca Scientifica n. 1 , 00133 Rome , Italy
| | - Giuseppina Scano
- a Center of Molecular Anthropology for Ancient DNA Study, Department of Biology , University of Rome 'Tor Vergata' , Via della Ricerca Scientifica n. 1 , 00133 Rome , Italy
| | - Irene Contini
- a Center of Molecular Anthropology for Ancient DNA Study, Department of Biology , University of Rome 'Tor Vergata' , Via della Ricerca Scientifica n. 1 , 00133 Rome , Italy
| | - Cristina Martínez-Labarga
- a Center of Molecular Anthropology for Ancient DNA Study, Department of Biology , University of Rome 'Tor Vergata' , Via della Ricerca Scientifica n. 1 , 00133 Rome , Italy
| | - Gian Franco De Stefano
- a Center of Molecular Anthropology for Ancient DNA Study, Department of Biology , University of Rome 'Tor Vergata' , Via della Ricerca Scientifica n. 1 , 00133 Rome , Italy
| | - Olga Rickards
- a Center of Molecular Anthropology for Ancient DNA Study, Department of Biology , University of Rome 'Tor Vergata' , Via della Ricerca Scientifica n. 1 , 00133 Rome , Italy
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Coevolution of genes and languages and high levels of population structure among the highland populations of Daghestan. J Hum Genet 2015; 61:181-91. [PMID: 26607180 DOI: 10.1038/jhg.2015.132] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2015] [Revised: 08/11/2015] [Accepted: 10/08/2015] [Indexed: 01/29/2023]
Abstract
As a result of the combination of great linguistic and cultural diversity, the highland populations of Daghestan present an excellent opportunity to test the hypothesis of language-gene coevolution at a fine geographic scale. However, previous genetic studies generally have been restricted to uniparental markers and have not included many of the key populations of the region. To improve our understanding of the genetic structure of Daghestani populations and to investigate possible correlations between genetic and linguistic variation, we analyzed ~550,000 autosomal single nucleotide polymorphisms, phylogenetically informative Y chromosome markers and mtDNA haplotypes in 21 ethnic Daghestani groups. We found high levels of population structure in Daghestan consistent with the hypothesis of long-term isolation among populations of the highland Caucasus. Highland Daghestani populations exhibit extremely high levels of between-population diversity for all genetic systems tested, leading to some of the highest FST values observed for any region of the world. In addition, we find a significant positive correlation between gene and language diversity, suggesting that these two aspects of human diversity have coevolved as a result of historical patterns of social interaction among highland farmers at the community level. Finally, our data are consistent with the hypothesis that most Daghestanian-speaking groups descend from a common ancestral population (~6000-6500 years ago) that spread to the Caucasus by demic diffusion followed by population fragmentation and low levels of gene flow.
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Hsouna S, Ben Halim N, Lasram K, Meiloud G, Arfa I, Kerkeni E, Romdhane L, Jamoussi H, Bahri S, Ben Ammar S, Abid A, Barakat A, Houmeida A, Abdelhak S, Kefi R. Study of the T16189C variant and mitochondrial lineages in Tunisian and overall Mediterranean region. Mitochondrial DNA A DNA Mapp Seq Anal 2015; 27:1558-63. [PMID: 25208176 DOI: 10.3109/19401736.2014.953136] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The mitochondrial DNA (mtDNA) variant T16189C has been investigated in several metabolic diseases. In this study, we aimed to estimate the frequency of the T16189C variant in Tunisian and other Mediterranean populations and to evaluate the impact of this variant on the phylogeny of Mediterranean populations. Blood sample of 240 unrelated Tunisian subjects were recruited from several Tunisian localities. The hypervariable region 1 of the mtDNA were amplified and sequenced. Additional sequences (N = 4921) from Mediterranean populations were compiled from previous studies. The average frequency of T16189C variant in Tunisia (29%) is similar to that observed in North African and Near Eastern populations. Our findings showed positive correlation of the T16189C variant with Sub-Saharan and North African lineages, while a negative correlation was found with the Eurasian haplogroups, reaching its maximum with the Eurasian haplogroup H. The principal component analyses showed a high internal heterogeneity between Tunisian localities. At the Mediterranean scale, Tunisians are closer to North African (Algerian and Moroccan) and Near Eastern populations (Syrians and Palestinians) than to Europeans.
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Affiliation(s)
- Sana Hsouna
- a Biomedical Genomics and Oncogenetics laboratory (LR 11 IPT 05), Institut Pasteur de Tunis, Université El Manar de Tunis , Tunis , Tunisia
| | - Nizar Ben Halim
- a Biomedical Genomics and Oncogenetics laboratory (LR 11 IPT 05), Institut Pasteur de Tunis, Université El Manar de Tunis , Tunis , Tunisia
| | - Khaled Lasram
- a Biomedical Genomics and Oncogenetics laboratory (LR 11 IPT 05), Institut Pasteur de Tunis, Université El Manar de Tunis , Tunis , Tunisia
| | - Ghlana Meiloud
- b Laboratoire de Biochimie et Biologie Moléculaire , Faculté des Sciences et Techniques , Nouakchott , Mauritania
| | - Imen Arfa
- a Biomedical Genomics and Oncogenetics laboratory (LR 11 IPT 05), Institut Pasteur de Tunis, Université El Manar de Tunis , Tunis , Tunisia
| | - Emna Kerkeni
- c Genetics Laboratory, Faculté de Médecine de Monastir , Monastir , Tunisia
| | - Lilia Romdhane
- a Biomedical Genomics and Oncogenetics laboratory (LR 11 IPT 05), Institut Pasteur de Tunis, Université El Manar de Tunis , Tunis , Tunisia
| | - Henda Jamoussi
- a Biomedical Genomics and Oncogenetics laboratory (LR 11 IPT 05), Institut Pasteur de Tunis, Université El Manar de Tunis , Tunis , Tunisia
| | - Sonia Bahri
- e Department of Biochemistry , Institut Pasteur de Tunis , Tunis , Tunisia , and
| | - Slim Ben Ammar
- e Department of Biochemistry , Institut Pasteur de Tunis , Tunis , Tunisia , and
| | - Abdelmajid Abid
- a Biomedical Genomics and Oncogenetics laboratory (LR 11 IPT 05), Institut Pasteur de Tunis, Université El Manar de Tunis , Tunis , Tunisia .,d Service de Consultation Externe et Exploration Fonctionnelle, Institut National de Nutrition , Tunis , Tunisia
| | - Abdelhamid Barakat
- f Laboratoire de Génétique Moléculaire Humaine, Département de Recherche Scientifique , Institut Pasteur du Maroc , Casablanca , Morocco
| | - Ahmed Houmeida
- b Laboratoire de Biochimie et Biologie Moléculaire , Faculté des Sciences et Techniques , Nouakchott , Mauritania
| | - Sonia Abdelhak
- a Biomedical Genomics and Oncogenetics laboratory (LR 11 IPT 05), Institut Pasteur de Tunis, Université El Manar de Tunis , Tunis , Tunisia
| | - Rym Kefi
- a Biomedical Genomics and Oncogenetics laboratory (LR 11 IPT 05), Institut Pasteur de Tunis, Université El Manar de Tunis , Tunis , Tunisia
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Messina F, Finocchio A, Rolfo MF, De Angelis F, Rapone C, Coletta M, Martínez-Labarga C, Biondi G, Berti A, Rickards O. Traces of forgotten historical events in mountain communities in Central Italy: A genetic insight. Am J Hum Biol 2015; 27:508-19. [PMID: 25728801 DOI: 10.1002/ajhb.22677] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2014] [Revised: 11/20/2014] [Accepted: 12/20/2014] [Indexed: 01/16/2023] Open
Abstract
OBJECTIVES Analysis of human genetic variation in mountain communities can shed light on the peopling of mountainous regions, perhaps revealing whether the remote geographic location spared them from outside invasion and preserved their gene pool from admixture. In this study, we created a model to assess genetic traces of historical events by reconstructing the paternal and maternal genetic history of seven small mountain villages in inland valleys of Central Italy. METHODS The communities were selected for their geographic isolation, attested biodemographic stability, and documented history prior to the Roman conquest. We studied the genetic structure by analyzing two hypervariable segments (HVS-I and HVS-II) of the mtDNA D-loop and several informative single nucleotide polymorphisms (SNPs) of the mtDNA coding region in 346 individuals, in addition to 17 short tandem repeats (STRs) and Y-chromosome SNPs in 237 male individuals. RESULTS For both uniparental markers, most of the haplogroups originated in Western Europe while some Near Eastern haplogroups were identified at low frequencies. However, there was an evident genetic similarity between the Central Italian samples and Near Eastern populations mainly in the male genetic pool. CONCLUSIONS The samples highlight an overall European genetic pattern both for mtDNA and Y chromosome. Notwithstanding this scenario, Y chromosome haplogroup Q, a common paternal lineage in Central/Western Asia but almost Europe-wide absent, was found, suggesting that Central Italy could have hosted a settlement from Anatolia that might be supported by cultural, topographic and genetic evidence.
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Affiliation(s)
- Francesco Messina
- Department of Biology, Center of Molecular Anthropology for ancient DNA study, University of Rome 'Tor Vergata', Via della Ricerca Scientifica n. 1, 00133, Rome, Italy
| | - Andrea Finocchio
- Department of Biology, Center of Molecular Anthropology for ancient DNA study, University of Rome 'Tor Vergata', Via della Ricerca Scientifica n. 1, 00133, Rome, Italy
| | - Mario Federico Rolfo
- Department of Historical, Philosophical and Social Sciences, Cultural and Territory Heritage, University of Rome 'Tor Vergata', Via Columbia n. 1, 00173, Rome, Italy
| | - Flavio De Angelis
- Department of Biology, Center of Molecular Anthropology for ancient DNA study, University of Rome 'Tor Vergata', Via della Ricerca Scientifica n. 1, 00133, Rome, Italy
| | - Cesare Rapone
- Carabinieri, Scientific Investigation Department, Viale di Tor di Quinto 151, 00191, Rome, Italy
| | - Martina Coletta
- Department of Biology, Center of Molecular Anthropology for ancient DNA study, University of Rome 'Tor Vergata', Via della Ricerca Scientifica n. 1, 00133, Rome, Italy
| | - Cristina Martínez-Labarga
- Department of Biology, Center of Molecular Anthropology for ancient DNA study, University of Rome 'Tor Vergata', Via della Ricerca Scientifica n. 1, 00133, Rome, Italy
| | - Gianfranco Biondi
- Department of Environmental Sciences, University of L'Aquila, Via Vetoio, 67010, L'Aquila, Italy
| | - Andrea Berti
- Carabinieri, Scientific Investigation Department, Viale di Tor di Quinto 151, 00191, Rome, Italy
| | - Olga Rickards
- Department of Biology, Center of Molecular Anthropology for ancient DNA study, University of Rome 'Tor Vergata', Via della Ricerca Scientifica n. 1, 00133, Rome, Italy
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Davidovic S, Malyarchuk B, Aleksic JM, Derenko M, Topalovic V, Litvinov A, Stevanovic M, Kovacevic-Grujicic N. Mitochondrial DNA perspective of Serbian genetic diversity. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2014; 156:449-65. [PMID: 25418795 DOI: 10.1002/ajpa.22670] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2014] [Accepted: 11/04/2014] [Indexed: 11/08/2022]
Abstract
Although south-Slavic populations have been studied to date from various aspects, the population of Serbia, occupying the central part of the Balkan Peninsula, is still genetically understudied at least at the level of mitochondrial DNA (mtDNA) variation. We analyzed polymorphisms of the first and the second mtDNA hypervariable segments (HVS-I and HVS-II) and informative coding-region markers in 139 Serbians to shed more light on their mtDNA variability, and used available data on other Slavic and neighboring non-Slavic populations to assess their interrelations in a broader European context. The contemporary Serbian mtDNA profile is consistent with the general European maternal landscape having a substantial proportion of shared haplotypes with eastern, central, and southern European populations. Serbian population was characterized as an important link between easternmost and westernmost south-Slavic populations due to the observed lack of genetic differentiation with all other south-Slavic populations and its geographical positioning within the Balkan Peninsula. An increased heterogeneity of south Slavs, most likely mirroring turbulent demographic events within the Balkan Peninsula over time (i.e., frequent admixture and differential introgression of various gene pools), and a marked geographical stratification of Slavs to south-, east-, and west-Slavic groups, were also found. A phylogeographic analyses of 20 completely sequenced Serbian mitochondrial genomes revealed not only the presence of mtDNA lineages predominantly found within the Slavic gene pool (U4a2a*, U4a2a1, U4a2c, U4a2g, HV10), supporting a common Slavic origin, but also lineages that may have originated within the southern Europe (H5*, H5e1, H5a1v) and the Balkan Peninsula in particular (H6a2b and L2a1k).
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Affiliation(s)
- Slobodan Davidovic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, 11010, Belgrade, Serbia
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Jankova-Ajanovska R, Zimmermann B, Huber G, Röck AW, Bodner M, Jakovski Z, Janeska B, Duma A, Parson W. Mitochondrial DNA control region analysis of three ethnic groups in the Republic of Macedonia. Forensic Sci Int Genet 2014; 13:1-2. [PMID: 25051224 PMCID: PMC4234079 DOI: 10.1016/j.fsigen.2014.06.013] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2014] [Revised: 06/21/2014] [Accepted: 06/23/2014] [Indexed: 11/17/2022]
Abstract
A total of 444 individuals representing three ethnic groups (Albanians, Turks and Romanies) in the Republic of Macedonia were sequenced in the mitochondrial control region. The mtDNA haplogroup composition differed between the three groups. Our results showed relatively high frequencies of haplogroup H12 in Albanians (8.8%) and less in Turks (3.3%), while haplogroups M5a1 and H7a1a were dominant in Romanies (13.7% and 10.3%, respectively) but rare in the former two. This highlights the importance of regional sampling for forensic mtDNA databasing purposes. These population data will be available on EMPOP under accession numbers EMP00644 (Albanians), EMP00645 (Romanies) and EMP00646 (Turks).
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Affiliation(s)
- Renata Jankova-Ajanovska
- Institute of Forensic Medicine, Criminalistic and Medical Deontology, Medical Faculty, University "Ss. Cyril and Methodius", Skopje, Macedonia
| | - Bettina Zimmermann
- Institute of Legal Medicine, Innsbruck Medical University, Innsbruck, Austria
| | - Gabriela Huber
- Institute of Legal Medicine, Innsbruck Medical University, Innsbruck, Austria
| | - Alexander W Röck
- Institute of Legal Medicine, Innsbruck Medical University, Innsbruck, Austria
| | - Martin Bodner
- Institute of Legal Medicine, Innsbruck Medical University, Innsbruck, Austria
| | - Zlatko Jakovski
- Institute of Forensic Medicine, Criminalistic and Medical Deontology, Medical Faculty, University "Ss. Cyril and Methodius", Skopje, Macedonia
| | - Biljana Janeska
- Institute of Forensic Medicine, Criminalistic and Medical Deontology, Medical Faculty, University "Ss. Cyril and Methodius", Skopje, Macedonia
| | - Aleksej Duma
- Institute of Forensic Medicine, Criminalistic and Medical Deontology, Medical Faculty, University "Ss. Cyril and Methodius", Skopje, Macedonia
| | - Walther Parson
- Institute of Legal Medicine, Innsbruck Medical University, Innsbruck, Austria; Penn State Eberly College of Science, University Park, PA, USA.
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Kefi R, Hsouna S, Ben Halim N, Lasram K, Romdhane L, Messai H, Abdelhak S. Phylogeny and genetic structure of Tunisians and their position within Mediterranean populations. ACTA ACUST UNITED AC 2014; 26:593-604. [PMID: 24491098 DOI: 10.3109/19401736.2013.879649] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Tunisia is located at the crossroads of Europe, the Middle East and Sub-Saharan Africa. This position might lead to numerous waves of migrations, contributing to the current genetic landscape of Tunisians. In this study, we analyzed 815 mitochondrial DNA (mtDNA) sequences from Tunisia in order to characterize the mitochondrial DNA genetic structure of this region, to construct the processes for its composition and to compare it to other Mediterranean populations. To that end, additional 4206 mtDNA sequences were compiled from previous studies performed in African (1237), Near Eastern (231) and European (2738) populations. Both phylogenetic and statistical analyses were performed. This study confirmed the mosaic genetic structure of the Tunisian population with the predominance of the Eurasian lineages, followed by the Sub-Saharan and North African lineages. Among Tunisians, the highest haplogroup and haplotype diversity were observed in particular in the Capital Tunis. No significant differentiation was observed between both geographical (Northern versus Southern Tunisia) and different ethnic groups in Tunisia. Our results highlight the presence of outliers and most frequent unique sequences in Tunisia (10.2%) compared to 45 Mediterranean populations. Phylogenetic analysis showed that the majority of Tunisian localities were closer to North Africans and Near Eastern populations than to Europeans. The exception was found for Berbers from Jerba which are clustered with Sardinians and Valencians.
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Affiliation(s)
- Rym Kefi
- Biomedical Genomics and Oncogenetics Laboratory (LR 11 IPT 05), Institut Pasteur de Tunis, Université El Manar de Tunis , Tunis , Tunisia and
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Investigation of mtDNA control region sequences in an Egyptian population sample. Leg Med (Tokyo) 2013; 15:338-41. [DOI: 10.1016/j.legalmed.2013.06.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2013] [Revised: 06/17/2013] [Accepted: 06/24/2013] [Indexed: 10/26/2022]
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Badro DA, Douaihy B, Haber M, Youhanna SC, Salloum A, Ghassibe-Sabbagh M, Johnsrud B, Khazen G, Matisoo-Smith E, Soria-Hernanz DF, Wells RS, Tyler-Smith C, Platt DE, Zalloua PA. Y-chromosome and mtDNA genetics reveal significant contrasts in affinities of modern Middle Eastern populations with European and African populations. PLoS One 2013; 8:e54616. [PMID: 23382925 PMCID: PMC3559847 DOI: 10.1371/journal.pone.0054616] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2012] [Accepted: 12/13/2012] [Indexed: 11/21/2022] Open
Abstract
The Middle East was a funnel of human expansion out of Africa, a staging area for the Neolithic Agricultural Revolution, and the home to some of the earliest world empires. Post LGM expansions into the region and subsequent population movements created a striking genetic mosaic with distinct sex-based genetic differentiation. While prior studies have examined the mtDNA and Y-chromosome contrast in focal populations in the Middle East, none have undertaken a broad-spectrum survey including North and sub-Saharan Africa, Europe, and Middle Eastern populations. In this study 5,174 mtDNA and 4,658 Y-chromosome samples were investigated using PCA, MDS, mean-linkage clustering, AMOVA, and Fisher exact tests of FST's, RST's, and haplogroup frequencies. Geographic differentiation in affinities of Middle Eastern populations with Africa and Europe showed distinct contrasts between mtDNA and Y-chromosome data. Specifically, Lebanon's mtDNA shows a very strong association to Europe, while Yemen shows very strong affinity with Egypt and North and East Africa. Previous Y-chromosome results showed a Levantine coastal-inland contrast marked by J1 and J2, and a very strong North African component was evident throughout the Middle East. Neither of these patterns were observed in the mtDNA. While J2 has penetrated into Europe, the pattern of Y-chromosome diversity in Lebanon does not show the widespread affinities with Europe indicated by the mtDNA data. Lastly, while each population shows evidence of connections with expansions that now define the Middle East, Africa, and Europe, many of the populations in the Middle East show distinctive mtDNA and Y-haplogroup characteristics that indicate long standing settlement with relatively little impact from and movement into other populations.
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Affiliation(s)
| | | | - Marc Haber
- The Lebanese American University, Chouran, Beirut, Lebanon
- Institut de Biologia Evolutiva (CSIC-UPF), Departament de Ciències de la Salut i de la Vida, Universitat Pompeu Fabra, Barcelona, Spain
| | | | | | | | - Brian Johnsrud
- Modern Thought and Literature, Stanford University, Stanford, California, United States of America
| | - Georges Khazen
- The Lebanese American University, Chouran, Beirut, Lebanon
| | - Elizabeth Matisoo-Smith
- Allan Wilson Centre for Molecular Ecology and Evolution, University of Otago, Dunedin, New Zealand
| | - David F. Soria-Hernanz
- Institut de Biologia Evolutiva (CSIC-UPF), Departament de Ciències de la Salut i de la Vida, Universitat Pompeu Fabra, Barcelona, Spain
- The Genographic Project, National Geographic Society, Washington, DC, United States of America
| | - R. Spencer Wells
- The Genographic Project, National Geographic Society, Washington, DC, United States of America
| | - Chris Tyler-Smith
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, United Kingdom
| | - Daniel E. Platt
- Computational Biology Centre, IBM TJ Watson Research Centre, Yorktown Heights, New York, United States of America
| | - Pierre A. Zalloua
- The Lebanese American University, Chouran, Beirut, Lebanon
- Harvard School of Public Health, Boston, Massachusetts, United States of America
- * E-mail:
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Connor TMF, Oygar DD, Gale DP, Steenkamp R, Nitsch D, Neild GH, Maxwell PH. Incidence of end-stage renal disease in the Turkish-Cypriot population of Northern Cyprus: a population based study. PLoS One 2013; 8:e54394. [PMID: 23349874 PMCID: PMC3547872 DOI: 10.1371/journal.pone.0054394] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2012] [Accepted: 12/11/2012] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND This is the first report of the incidence and causes of end-stage renal disease (ESRD) of the Turkish-Cypriot population in Northern Cyprus. METHODS Data were collected over eight consecutive years (2004-2011) from all those starting renal replacement therapy (RRT) in this population. Crude and age-standardised incidence at 90 days was calculated and comparisons made with other national registries. We collected DNA from the entire prevalent population. As an initial experiment we looked for two genetic causes of ESRD that have been reported in Greek Cypriots. RESULTS Crude and age-standardised incidence at 90 days was 234 and 327 per million population (pmp) per year, respectively. The mean age was 63, and 62% were male. The age-adjusted prevalence of RRT in Turkish-Cypriots was 1543 pmp on 01/01/2011. The incidence of RRT is higher than other countries reporting to the European Renal Association - European Dialysis and Transplant Association, with the exception of Turkey. Diabetes is a major cause of ESRD in those under 65, accounting for 36% of incident cases followed by 30% with uncertain aetiology. 18% of the incident population had a family history of ESRD. We identified two families with thin basement membrane nephropathy caused by a mutation in COL4A3, but no new cases of CFHR5 nephropathy. CONCLUSIONS This study provides the first estimate of RRT incidence in the Turkish-Cypriot population, describes the contribution of different underlying diagnoses to ESRD, and provides a basis for healthcare policy planning.
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Affiliation(s)
- Thomas M F Connor
- UCL Division of Medicine and Centre for Nephrology, University College London, London, United Kingdom.
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Pardiñas AF, Roca A, García-Vazquez E, López B. Assessing the genetic influence of ancient sociopolitical structure: micro-differentiation patterns in the population of Asturias (Northern Spain). PLoS One 2012; 7:e50206. [PMID: 23209673 PMCID: PMC3507697 DOI: 10.1371/journal.pone.0050206] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2012] [Accepted: 10/16/2012] [Indexed: 11/18/2022] Open
Abstract
The human populations of the Iberian Peninsula are the varied result of a complex mixture of cultures throughout history, and are separated by clear social, cultural, linguistic or geographic barriers. The stronger genetic differences between closely related populations occur in the northern third of Spain, a phenomenon commonly known as "micro-differentiation". It has been argued and discussed how this form of genetic structuring can be related to both the rugged landscape and the ancient societies of Northern Iberia, but this is difficult to test in most regions due to the intense human mobility of previous centuries. Nevertheless, the Spanish autonomous community of Asturias shows a complex history which hints of a certain isolation of its population. This, joined together with a difficult terrain full of deep valleys and steep mountains, makes it suitable for performing a study of genetic structure, based on mitochondrial DNA and Y-Chromosome markers. Our analyses do not only show that there are micro-differentiation patterns inside the Asturian territory, but that these patterns are strikingly similar between both uniparental markers. The inference of barriers to gene flow also indicates that Asturian populations from the coastal north and the mountainous south seem to be relatively isolated from the rest of the territory. These findings are discussed in light of historic and geographic data and, coupled with previous evidence, show that the origin of the current genetic patterning might indeed lie in Roman and Pre-Roman sociopolitical divisions.
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Affiliation(s)
- Antonio F. Pardiñas
- Departamento de Biología de Organismos y Sistemas, Universidad de Oviedo, Asturias, Spain
| | - Agustín Roca
- Departamento de Biología Funcional, Universidad de Oviedo, Asturias, Spain
| | - Eva García-Vazquez
- Departamento de Biología Funcional, Universidad de Oviedo, Asturias, Spain
| | - Belén López
- Departamento de Biología de Organismos y Sistemas, Universidad de Oviedo, Asturias, Spain
- * E-mail:
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Balanovsky OP, Koshel SM, Zaporozhchenko VV, Pshenichnov AS, Frolova SA, Kuznetsova MA, Baranova EE, Teuchezh IE, Kuznetsova AA, Romashkina MV, Utevska OM, Churnosov ML, Villems R, Balanovska EV. Genetic ecological monitoring in human populations: Heterozygosity, mtDNA haplotype variation, and genetic load. RUSS J GENET+ 2011. [DOI: 10.1134/s1022795411110056] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Salihović MP, Barešić A, Klarić IM, Cukrov S, Lauc LB, Janićijević B. The role of the Vlax Roma in shaping the European Romani maternal genetic history. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2011; 146:262-70. [DOI: 10.1002/ajpa.21566] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2011] [Accepted: 05/09/2011] [Indexed: 11/07/2022]
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Lao O, Vallone PM, Coble MD, Diegoli TM, van Oven M, van der Gaag KJ, Pijpe J, de Knijff P, Kayser M. Evaluating self-declared ancestry of U.S. Americans with autosomal, Y-chromosomal and mitochondrial DNA. Hum Mutat 2011; 31:E1875-93. [PMID: 20886636 PMCID: PMC3051415 DOI: 10.1002/humu.21366] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The current U.S. population represents an amalgam of individuals originating mainly from four continental regions (Africa, Europe, Asia and America). To study the genetic ancestry and compare with self-declared ancestry we have analyzed paternally, maternally and bi-parentally inherited DNA markers sensitive for indicating continental genetic ancestry in all four major U.S. American groups. We found that self-declared U.S. Hispanics and U.S. African Americans tend to show variable degrees of continental genetic admixture among the three genetic systems, with evidence for a marked sex-biased admixture history. Moreover, for these two groups we observed significant regional variation across the country in genetic admixture. In contrast, self-declared U.S. European and U.S. Asian Americans were genetically more homogeneous at the continental ancestry level. Two autosomal ancestry-sensitive markers located in skin pigmentation candidate genes showed significant differences in self-declared U.S. African Americans or U.S. European Americans, relative to their assumed parental populations from Africa or Europe. This provides genetic support for the importance of skin color in the complex process of ancestry identification.
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Affiliation(s)
- Oscar Lao
- Department of Forensic Molecular Biology, Erasmus MC University Medical Center Rotterdam, Rotterdam, The Netherlands
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Palanichamy MG, Zhang CL, Mitra B, Malyarchuk B, Derenko M, Chaudhuri TK, Zhang YP. Mitochondrial haplogroup N1a phylogeography, with implication to the origin of European farmers. BMC Evol Biol 2010; 10:304. [PMID: 20939899 PMCID: PMC2964711 DOI: 10.1186/1471-2148-10-304] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2010] [Accepted: 10/12/2010] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Tracing the genetic origin of central European farmer N1a lineages can provide a unique opportunity to assess the patterns of the farming technology spread into central Europe in the human prehistory. Here, we have chosen twelve N1a samples from modern populations which are most similar with the farmer N1a types and performed the complete mitochondrial DNA genome sequencing analysis. To assess the genetic and phylogeographic relationship, we performed a detailed survey of modern published N1a types from Eurasian and African populations. RESULTS The geographic origin and expansion of farmer lineages related N1a subclades have been deduced from combined analysis of 19 complete sequences with 166 N1a haplotypes. The phylogeographic analysis revealed that the central European farmer lineages have originated from different sources: from eastern Europe, local central Europe, and from the Near East via southern Europe. CONCLUSIONS The results obtained emphasize that the arrival of central European farmer lineages did not occur via a single demic diffusion event from the Near East at the onset of the Neolithic spread of agriculture into Europe. Indeed these results indicate that the Neolithic transition process was more complex in central Europe and possibly the farmer N1a lineages were a result of a 'leapfrog' colonization process.
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Affiliation(s)
- Malliya Gounder Palanichamy
- Laboratory for Conservation and Utilization of Bio-resources, Yunnan University, 2 North Green Lake Street, Kunming 650091, China.
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Zoossmann-Diskin A. The origin of Eastern European Jews revealed by autosomal, sex chromosomal and mtDNA polymorphisms. Biol Direct 2010; 5:57. [PMID: 20925954 PMCID: PMC2964539 DOI: 10.1186/1745-6150-5-57] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2010] [Accepted: 10/06/2010] [Indexed: 12/24/2022] Open
Abstract
Background This study aims to establish the likely origin of EEJ (Eastern European Jews) by genetic distance analysis of autosomal markers and haplogroups on the X and Y chromosomes and mtDNA. Results According to the autosomal polymorphisms the investigated Jewish populations do not share a common origin, and EEJ are closer to Italians in particular and to Europeans in general than to the other Jewish populations. The similarity of EEJ to Italians and Europeans is also supported by the X chromosomal haplogroups. In contrast according to the Y-chromosomal haplogroups EEJ are closest to the non-Jewish populations of the Eastern Mediterranean. MtDNA shows a mixed pattern, but overall EEJ are more distant from most populations and hold a marginal rather than a central position. The autosomal genetic distance matrix has a very high correlation (0.789) with geography, whereas the X-chromosomal, Y-chromosomal and mtDNA matrices have a lower correlation (0.540, 0.395 and 0.641 respectively). Conclusions The close genetic resemblance to Italians accords with the historical presumption that Ashkenazi Jews started their migrations across Europe in Italy and with historical evidence that conversion to Judaism was common in ancient Rome. The reasons for the discrepancy between the biparental markers and the uniparental markers are discussed. Reviewers This article was reviewed by Damian Labuda (nominated by Jerzy Jurka), Kateryna Makova and Qasim Ayub (nominated by Dan Graur).
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Affiliation(s)
- Avshalom Zoossmann-Diskin
- Department of Haematology and Genetic Pathology, School of Medicine, Flinders University, Adelaide, Australia.
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Palencia L, Valverde L, Alvarez A, Cainé LM, Cardoso S, Alfonso-Sánchez MA, Pinheiro MF, de Pancorbo MM. Mitochondrial DNA diversity in a population from Santa Catarina (Brazil): predominance of the European input. Int J Legal Med 2010; 124:331-6. [PMID: 20480173 DOI: 10.1007/s00414-010-0464-2] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2010] [Accepted: 04/29/2010] [Indexed: 12/16/2022]
Abstract
The state of Santa Catarina (Brazil) is known to have represented a cultural crossroads in South America due to several historic migrations mainly from Europe and Africa. We set out to scrutinize whether the genetic imprint of these migrations could be traced through analysis of the matrilineal gene pool of the Catarinenses. The entire control region of the mitochondrial DNA was studied in 80 healthy and maternally unrelated individuals. The analysis of haplogroup distribution revealed that this population is extremely heterogeneous, showing the coexistence of matrilineal lineages with three different phylogeographic origins. European lineages are the most frequent due mainly to the impact of relatively recent migratory waves from Europe. In spite of this, Native American lineages and African lineages incorporated with the slave trade are also present in noticeable proportions. The strikingly high variability generated by intense gene flow is mirrored in a high sequence diversity (0.9930) and power of discrimination (0.9806). Thus, analysis of the entire mitochondrial DNA control region emerges as a valuable tool for forensic genetic purposes in this highly admixed population, an attribute common to several present-day Latin American populations.
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Affiliation(s)
- Leire Palencia
- BIOMICs Research Group, Centro de Investigación y Estudios Avanzados Lucio Lascaray, Universidad del País Vasco UPV/EHU, Miguel de Unamuno 3, 01006 Vitoria-Gasteiz, Spain
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Population genetics of Y-chromosome STRs in a population of Northern Greeks. Forensic Sci Int Genet 2009; 4:e21-2. [DOI: 10.1016/j.fsigen.2009.01.001] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2008] [Accepted: 01/02/2009] [Indexed: 11/23/2022]
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Tillmar AO, Coble MD, Wallerström T, Holmlund G. Homogeneity in mitochondrial DNA control region sequences in Swedish subpopulations. Int J Legal Med 2009; 124:91-8. [PMID: 19590886 DOI: 10.1007/s00414-009-0354-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2008] [Accepted: 05/12/2009] [Indexed: 11/24/2022]
Abstract
In order to promote mitochondrial DNA (mtDNA) testing in Sweden we have typed 296 Swedish males, which will serve as a Swedish mtDNA frequency database. The tested males were taken from seven geographically different regions representing the contemporary Swedish population. The complete mtDNA control region was typed and the Swedish population was shown to have high haplotype diversity with a random match probability of 0.5%. Almost 47% of the tested samples belonged to haplogroup H and further haplogroup comparison with worldwide populations clustered the Swedish mtDNA data together with other European populations. AMOVA analysis of the seven Swedish subregions displayed no significant maternal substructure in Sweden (F (ST) = 0.002). Our conclusion from this study is that the typed Swedish individuals serve as good representatives for a Swedish forensic mtDNA database. Some caution should, however, be taken for individuals from the northernmost part of Sweden (provinces of Norrbotten and Lapland) due to specific demographic conditions. Furthermore, our analysis of a small sample set of a Swedish Saami population confirmed earlier findings that the Swedish Saami population is an outlier among European populations.
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Affiliation(s)
- Andreas O Tillmar
- Department of Forensic Genetics and Forensic Toxicology, National Board of Forensic Medicine, Artillerigatan 12, Linköping, Sweden.
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Saunier JL, Irwin JA, Strouss KM, Ragab H, Sturk KA, Parsons TJ. Mitochondrial control region sequences from an Egyptian population sample. Forensic Sci Int Genet 2009; 3:e97-103. [DOI: 10.1016/j.fsigen.2008.09.004] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2008] [Accepted: 09/15/2008] [Indexed: 10/21/2022]
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Saunier JL, Irwin JA, Just RS, O'Callaghan J, Parsons TJ. Mitochondrial control region sequences from a U.S. "Hispanic" population sample. Forensic Sci Int Genet 2008; 2:e19-23. [PMID: 19083798 DOI: 10.1016/j.fsigen.2007.11.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2007] [Revised: 10/17/2007] [Accepted: 11/06/2007] [Indexed: 11/28/2022]
Abstract
Entire mitochondrial control region data was generated for 128 "Hispanics" from the United States. These samples have been previously typed for 15 autosomal STRs [J.M. Butler, R. Schoske, P.M. Vallone, J.W. Redman, M.C. Kline, Allele frequencies for 15 autosomal STR loci on U.S. Caucasian, African American, and Hispanic populations, J. Forensic Sci. 48 (2003) 908-911]. High-throughput robotics, a redundant sequencing approach, and several quality control checks were implemented to generate a high-quality database. The data presented here will augment Hispanic reference data available for forensic mtDNA comparisons.
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Affiliation(s)
- Jessica L Saunier
- Armed Forces DNA Identification Laboratory, Rockville, MD 20850, United States
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Brandstätter A, Egyed B, Zimmermann B, Duftner N, Padar Z, Parson W. Migration rates and genetic structure of two Hungarian ethnic groups in Transylvania, Romania. Ann Hum Genet 2007; 71:791-803. [PMID: 17532745 DOI: 10.1111/j.1469-1809.2007.00371.x] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Transylvania's ethnic mosaic is composed of Romanians, German Saxons and Hungarians. The ethnic groups of the Hungarian minority that settled in Romania show differences in dialects, customs and religious affiliations. In this study entire mtDNA control region sequences from 360 individuals of Hungarian ethnicity from two populations (the Csángó and the Székely), settled in the historical region of Transylvania in Romania, were generated and analyzed following high quality sequencing standards. Phylogenetic analyses were used for haplogroup determination, quasi-median network analyses were applied for the visualization of character conflicts, and median joining reconstructions were used for depicting haplotype structures. Affiliation of haplotypes to major west Eurasian haplogroups was confirmed using coding region SNPs. Gene flow between the two populations was low and biased towards a higher migration rate from the Csángó to the Székely than vice versa. Phylogeographic analyses revealed effects of genetic isolation within the Csángó population, which is, in its genetic structure, clearly different from the Székely population. The pronounced genetic divergence between the two populations is in sharp contrast to the expectation of high genetic similarity due to the close geographic proximity of their native homelands. The population data will be incorporated in the EMPOP database (http://www.empop.org).
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Affiliation(s)
- A Brandstätter
- Institute of Legal Medicine, Innsbruck Medical University, Austria
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