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Resutik P, Schneider J, Aeschbacher S, Vigeland MD, Gysi M, Moser C, Barbieri C, Widmer P, Currat M, Kratzer A, Krützen M, Haas C, Arora N. Uncovering genetic signatures of the Walser migration in the Alps: Patterns of diversity and differentiation. Forensic Sci Int Genet 2025; 76:103206. [PMID: 39674091 DOI: 10.1016/j.fsigen.2024.103206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2024] [Revised: 11/20/2024] [Accepted: 12/06/2024] [Indexed: 12/16/2024]
Abstract
Since leaving Africa, human populations have gone through a series of range expansions. While the genomic signatures of these expansions are well detectable on a continental scale, the genomic consequences of small-scale expansions over shorter time spans are more challenging to disentangle. The medieval migration of the Walser people from their homeland in ssouthern Switzerland (Upper Valais) into other regions of the Alps is a good example of such a comparatively recent geographic and demographic expansion in humans. While several studies from the 1980s, based on allozyme markers, assessed levels of isolation and inbreeding in individual Walser communities, they mostly did so by focusing on a single community at a time. Here, we provide a comprehensive overview of genetic diversity and differentiation based on samples from multiple Walser, Walser-homeland, and non-Walser Alpine communities, along with an idealized (simulated) Swiss reference population (Ref-Pop). To explore genetic signals of the Walser migration in the genomes of their descendants, we use a set of forensic autosomal STRs as well as uniparental markers. Estimates of pairwise FST based on autosomal STRs reveal that the Walser-homeland and Walser communities show low to moderate genetic differentiation from the non-Walser Alpine communities and the idealized Ref-Pop. The geographically more remote and likely more isolated Walser-homeland community of Lötschental and the Walser communities of Vals and Gressoney appear genetically more strongly differentiated than other communities. Analyses of mitochondrial DNA revealed the presence of haplogroup W6 among the Walser communities, a haplogroup that is otherwise rare in central Europe. Our study contributes to the understanding of genetic diversity in the Walser-homeland and Walser people, but also highlights the need for a more comprehensive study of the population genetic structure and evolutionary history of European Alpine populations using genome-wide data.
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Affiliation(s)
- Peter Resutik
- Zurich Institute of Forensic Medicine, University of Zurich, Zurich, Switzerland.
| | - Joëlle Schneider
- Zurich Institute of Forensic Medicine, University of Zurich, Zurich, Switzerland
| | - Simon Aeschbacher
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
| | | | - Mario Gysi
- Zurich Institute of Forensic Medicine, University of Zurich, Zurich, Switzerland
| | - Corinne Moser
- Zurich Institute of Forensic Medicine, University of Zurich, Zurich, Switzerland
| | - Chiara Barbieri
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland; Department of Life and Environmental Sciences, University of Cagliari, Cagliari, Italy
| | - Paul Widmer
- Department of Comparative Language Science, University of Zurich, Zurich, Switzerland
| | - Mathias Currat
- AGP lab, Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland; Institute of Genetics and Genomics in Geneva (IGE3), University of Geneva, Geneva, Switzerland
| | - Adelgunde Kratzer
- Zurich Institute of Forensic Medicine, University of Zurich, Zurich, Switzerland
| | - Michael Krützen
- Department of Evolutionary Anthropology, University of Zurich, Zurich, Switzerland
| | - Cordula Haas
- Zurich Institute of Forensic Medicine, University of Zurich, Zurich, Switzerland
| | - Natasha Arora
- Zurich Institute of Forensic Medicine, University of Zurich, Zurich, Switzerland.
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Mayordomo AC, Gagliardi F, Simão F, Rabitti L, Fernandez RL, Samsonowicz T, Canteros MS, Velez CP, Catoira LM, Buono NS, Furman N, Piñero MH, Gusmão L. Using uniparental genetic profiles to unravel the complexity of Argentine admixed populations. Forensic Sci Int Genet 2025; 76:103216. [PMID: 39732109 DOI: 10.1016/j.fsigen.2024.103216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2024] [Accepted: 12/22/2024] [Indexed: 12/30/2024]
Abstract
Latin American countries are distinguished by their highly admixed populations, characterized by a significant preservation of Native American matrilineal ancestry. This contrasts with the paternal lineages, which exhibit different patterns due to pronounced sex-biased mating practices during the colonial period. Uniparental genetic markers have been instrumental in population genetics, facilitating the reconstruction of human settlement histories and serving forensic identification purposes. The primary objective of this study was to investigate the diversity and structure of lineage markers in Argentina and compare them with other admixed populations in South America. For this study, we analyzed Y-STR and mtDNA haplotypes from 5202 unrelated individuals, providing a detailed description of the observed variability in both markers. Additionally, we conducted a genetic distance analysis, incorporating data from bibliographic sources across Argentina and South America. In pairwise comparisons among provinces, higher FST values were found in mtDNA haplotypes than in Y-STR haplotypes. This allows for more provinces to be grouped by similarity when using Y-STR data. These differences were also evident in the multidimensional scaling (MDS) analysis between South American countries. Y-STR haplotypes showed greater similarity to European haplotypes, whereas mtDNA haplotypes exhibited greater dispersion. Thus, the comprehensive compilation of haplotypes in this study, including those integrated from our research and those cited in existing literature, provides an in-depth understanding of the inherent genetic complexities within Argentina.
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Affiliation(s)
- Andrea C Mayordomo
- Banco Nacional de Datos Genéticos, Avda. Córdoba 831, Buenos Aires C1054AAH, Argentina.
| | - Florencia Gagliardi
- Banco Nacional de Datos Genéticos, Avda. Córdoba 831, Buenos Aires C1054AAH, Argentina
| | - Filipa Simão
- DNA Diagnostic Laboratory, Institute of Biology Roberto Alcantara Gomes, State University of Rio de, Rio de Janeiro 20550-900, Brazil
| | - Luciana Rabitti
- Banco Nacional de Datos Genéticos, Avda. Córdoba 831, Buenos Aires C1054AAH, Argentina
| | - Rocio L Fernandez
- Banco Nacional de Datos Genéticos, Avda. Córdoba 831, Buenos Aires C1054AAH, Argentina
| | - Tamara Samsonowicz
- Banco Nacional de Datos Genéticos, Avda. Córdoba 831, Buenos Aires C1054AAH, Argentina
| | - Malena S Canteros
- Banco Nacional de Datos Genéticos, Avda. Córdoba 831, Buenos Aires C1054AAH, Argentina
| | - Cecilia P Velez
- Banco Nacional de Datos Genéticos, Avda. Córdoba 831, Buenos Aires C1054AAH, Argentina
| | - Leila M Catoira
- Banco Nacional de Datos Genéticos, Avda. Córdoba 831, Buenos Aires C1054AAH, Argentina
| | - Natalia S Buono
- Banco Nacional de Datos Genéticos, Avda. Córdoba 831, Buenos Aires C1054AAH, Argentina
| | - Nicolas Furman
- Banco Nacional de Datos Genéticos, Avda. Córdoba 831, Buenos Aires C1054AAH, Argentina
| | | | - Leonor Gusmão
- DNA Diagnostic Laboratory, Institute of Biology Roberto Alcantara Gomes, State University of Rio de, Rio de Janeiro 20550-900, Brazil
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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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Helena's Many Daughters: More Mitogenome Diversity behind the Most Common West Eurasian mtDNA Control Region Haplotype in an Extended Italian Population Sample. Int J Mol Sci 2022; 23:ijms23126725. [PMID: 35743173 PMCID: PMC9223851 DOI: 10.3390/ijms23126725] [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: 05/24/2022] [Revised: 06/13/2022] [Accepted: 06/14/2022] [Indexed: 01/27/2023] Open
Abstract
The high number of matching haplotypes of the most common mitochondrial (mt)DNA lineages are considered to be the greatest limitation for forensic applications. This study investigates the potential to solve this constraint by massively parallel sequencing a large number of mitogenomes that share the most common West Eurasian mtDNA control region (CR) haplotype motif (263G 315.1C 16519C). We augmented a pilot study on 29 to a total of 216 Italian mitogenomes that represents the largest set of the most common CR haplotype compiled from a single country. The extended population sample confirmed and extended the huge coding region diversity behind the most common CR motif. Complete mitogenome sequencing allowed for the detection of 163 distinct haplotypes, raising the power of discrimination from 0 (CR) to 99.6% (mitogenome). The mtDNAs were clustered into 61 named clades of haplogroup H and did not reveal phylogeographic trends within Italy. Rapid individualization approaches for investigative purposes are limited to the most frequent H clades of the dataset, viz. H1, H3, and H7.
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Sarno S, Petrilli R, Abondio P, De Giovanni A, Boattini A, Sazzini M, De Fanti S, Cilli E, Ciani G, Gentilini D, Pettener D, Romeo G, Giuliani C, Luiselli D. Genetic history of Calabrian Greeks reveals ancient events and long term isolation in the Aspromonte area of Southern Italy. Sci Rep 2021; 11:3045. [PMID: 33542324 PMCID: PMC7862261 DOI: 10.1038/s41598-021-82591-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Accepted: 01/15/2021] [Indexed: 01/30/2023] Open
Abstract
Calabrian Greeks are an enigmatic population that have preserved and evolved a unique variety of language, Greco, survived in the isolated Aspromonte mountain area of Southern Italy. To understand their genetic ancestry and explore possible effects of geographic and cultural isolation, we genome-wide genotyped a large set of South Italian samples including both communities that still speak Greco nowadays and those that lost the use of this language earlier in time. Comparisons with modern and ancient populations highlighted ancient, long-lasting genetic links with Eastern Mediterranean and Caucasian/Near-Eastern groups as ancestral sources of Southern Italians. Our results suggest that the Aspromonte communities might be interpreted as genetically drifted remnants that departed from such ancient genetic background as a consequence of long-term isolation. Specific patterns of population structuring and higher levels of genetic drift were indeed observed in these populations, reflecting geographic isolation amplified by cultural differences in the groups that still conserve the Greco language. Isolation and drift also affected the current genetic differentiation at specific gene pathways, prompting for future genome-wide association studies aimed at exploring trait-related loci that have drifted up in frequency in these isolated groups.
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Affiliation(s)
- Stefania Sarno
- grid.6292.f0000 0004 1757 1758Department of Biological, Geological and Environmental Sciences, University of Bologna, Bologna, Italy
| | - Rosalba Petrilli
- grid.6292.f0000 0004 1757 1758Department of Biological, Geological and Environmental Sciences, University of Bologna, Bologna, Italy
| | - Paolo Abondio
- grid.6292.f0000 0004 1757 1758Department of Biological, Geological and Environmental Sciences, University of Bologna, Bologna, Italy
| | - Andrea De Giovanni
- grid.6292.f0000 0004 1757 1758Department of Biological, Geological and Environmental Sciences, University of Bologna, Bologna, Italy ,grid.6292.f0000 0004 1757 1758Department of Cultural Heritage, University of Bologna, Ravenna, Italy
| | - Alessio Boattini
- grid.6292.f0000 0004 1757 1758Department of Biological, Geological and Environmental Sciences, University of Bologna, Bologna, Italy
| | - Marco Sazzini
- grid.6292.f0000 0004 1757 1758Department of Biological, Geological and Environmental Sciences, University of Bologna, Bologna, Italy ,grid.6292.f0000 0004 1757 1758Interdepartmental Centre Alma Mater Research Institute on Global Challenges and Climate Change, University of Bologna, Bologna, Italy
| | - Sara De Fanti
- grid.6292.f0000 0004 1757 1758Department of Biological, Geological and Environmental Sciences, University of Bologna, Bologna, Italy ,grid.6292.f0000 0004 1757 1758Interdepartmental Centre Alma Mater Research Institute on Global Challenges and Climate Change, University of Bologna, Bologna, Italy
| | - Elisabetta Cilli
- grid.6292.f0000 0004 1757 1758Department of Cultural Heritage, University of Bologna, Ravenna, Italy
| | - Graziella Ciani
- grid.6292.f0000 0004 1757 1758Department of Biological, Geological and Environmental Sciences, University of Bologna, Bologna, Italy
| | - Davide Gentilini
- grid.8982.b0000 0004 1762 5736Department of Brain and Behavioral Sciences, University of Pavia, Pavia, Italy ,Italian Auxologic Institute IRCCS, Cusano Milanino, Milan, Italy
| | - Davide Pettener
- grid.6292.f0000 0004 1757 1758Department of Biological, Geological and Environmental Sciences, University of Bologna, Bologna, Italy
| | - Giovanni Romeo
- grid.412311.4Medical Genetics Unit, Sant’Orsola-Malpighi University Hospital, Bologna, Italy ,European School of Genetic Medicine, Bologna, Italy
| | - Cristina Giuliani
- grid.6292.f0000 0004 1757 1758Department of Biological, Geological and Environmental Sciences, University of Bologna, Bologna, Italy ,grid.6292.f0000 0004 1757 1758Interdepartmental Centre Alma Mater Research Institute on Global Challenges and Climate Change, University of Bologna, Bologna, Italy
| | - Donata Luiselli
- grid.6292.f0000 0004 1757 1758Department of Cultural Heritage, University of Bologna, Ravenna, Italy
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ElHefnawi M, Hegazy E, Elfiky A, Jeon Y, Jeon S, Bhak J, Mohamed Metwally F, Sugano S, Horiuchi T, Kazumi A, Blazyte A. Complete genome sequence and bioinformatics analysis of nine Egyptian females with clinical information from different geographic regions in Egypt. Gene 2020; 769:145237. [PMID: 33127537 DOI: 10.1016/j.gene.2020.145237] [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] [Received: 11/25/2019] [Revised: 08/03/2020] [Accepted: 10/11/2020] [Indexed: 10/23/2022]
Abstract
Egyptians are at a crossroad between Africa and Eurasia, providing useful genomic resources for analyzing both genetic and environmental factors for future personalized medicine. Two personal Egyptian whole genomes have been published previously by us and here nine female whole genome sequences with clinical information have been added to expand the genomic resource of Egyptian personal genomes. Here we report the analysis of whole genomes of nine Egyptian females from different regions using Illumina short-read sequencers. At 30x sequencing coverage, we identified 12 SNPs that were shared in most of the subjects associated with obesity which are concordant with their clinical diagnosis. Also, we found mtDNA mutation A4282G is common in all the samples and this is associated with chronic progressive external ophthalmoplegia (CPEO). Haplogroup and Admixture analyses revealed that most Egyptian samples are close to the other north Mediterranean, Middle Eastern, and European, respectively, possibly reflecting the into-Africa influx of human migration. In conclusion, we present whole-genome sequences of nine Egyptian females with personal clinical information that cover the diverse regions of Egypt. Although limited in sample size, the whole genomes data provides possible geno-phenotype candidate markers that are relevant to the region's diseases.
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Affiliation(s)
- Mahmoud ElHefnawi
- School of Information Technology and Computer Science, Nile University, Giza 12588, Egypt; Informatics & Systems Department, the National Research Centre, Cairo, Egypt; Biomedical Informatics and Chemoinformatics Group, Center of Excellence for Medical Research, National Research Centre, Cairo, Egypt.
| | - Elsayed Hegazy
- School of Information Technology and Computer Science, Nile University, Giza 12588, Egypt
| | - Asmaa Elfiky
- Environmental and Occupational Medicine Department, Environmental Research Division, National Research Centre, Cairo, Egypt
| | - Yeonsu Jeon
- Korean Genomics Center (KOGIC), UNIST, Republic of Korea; Department of Biomedical Engineering, School of Life Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan, Republic of Korea
| | - Sungwon Jeon
- Korean Genomics Center (KOGIC), UNIST, Republic of Korea; Department of Biomedical Engineering, School of Life Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan, Republic of Korea
| | - Jong Bhak
- Korean Genomics Center (KOGIC), UNIST, Republic of Korea; Department of Biomedical Engineering, School of Life Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan, Republic of Korea; Personal Genomics Institute, Genome Research Foundation, Osong, Republic of Korea
| | - Fateheya Mohamed Metwally
- Environmental and Occupational Medicine Department, Environmental Research Division, National Research Centre, Cairo, Egypt
| | - Sumio Sugano
- The Institute of Medical Science, University of Tokyo, Japan
| | - Terumi Horiuchi
- Graduate School of Frontier Sciences, University of Tokyo, Chiba, Japan
| | - Abe Kazumi
- The Institute of Medical Science, University of Tokyo, Japan
| | - Asta Blazyte
- Korean Genomics Center (KOGIC), UNIST, Republic of Korea; Department of Biomedical Engineering, School of Life Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan, Republic of Korea
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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: 0.2] [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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dos Reis RS, Simão F, dos Santos Stange V, Garcia FM, Spinassé Dettogni R, Stur E, da Silva AMÁ, de Carvalho EF, Gusmão L, Drumond Louro I. A view of the maternal inheritance of Espírito Santo populations: The contrast between the admixed and Pomeranian descent groups. Forensic Sci Int Genet 2019; 40:175-181. [DOI: 10.1016/j.fsigen.2019.03.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Revised: 02/22/2019] [Accepted: 03/05/2019] [Indexed: 11/28/2022]
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9
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Boattini A, Sarno S, Fiorani O, Lisa A, Luiselli D, Pettener D. Ripples on the surface. Surnames and genes in Sicily and Southern Italy. Ann Hum Biol 2018; 45:57-65. [PMID: 29183201 DOI: 10.1080/03014460.2017.1411525] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
BACKGROUND Southern Italy and Sicily played a key role in the peopling history of the Mediterranean. While genetic research showed the remarkable homogeneity of these regions, surname-based studies instead suggested low population mobility, hence potential structuring. AIM In order to better understand these different patterns, this study (1) thoroughly analysed the surname structure of Sicily and Southern Italy and (2) tested its relationships with a wide set of molecular markers. SUBJECTS AND METHODS Surname data were collected from 1213 municipalities and compared to uniparental and autosomal genetic markers typed in ∼300 individuals from 8-10 populations. Surname analyses were performed using different multivariate methods, while comparisons with genetic data relied on correlation tests. RESULTS Surnames were clearly structured according to regional geographic patterns, which likely emerged because of recent isolation-by-distance-like population dynamics. In general, genetic markers, hinting at a pervasive homogeneity, did not correlate with surname distribution. However, long autosomal haplotypes (>5 cM) that compared to genotypic (SNPs) data identify more "recent" relatedness, showing a clear association with surname patterns. CONCLUSION The apparent contradiction between surname structure and genetic homogeneity was resolved by figuring surnames as recent "ripples" deposited on a vast and ancient homogeneous genetic "surface".
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Affiliation(s)
- Alessio Boattini
- a Department of Biological, Geological and Environmental Sciences , University of Bologna , Bologna , Italy
| | - Stefania Sarno
- a Department of Biological, Geological and Environmental Sciences , University of Bologna , Bologna , Italy
| | - Ornella Fiorani
- b Institute of Molecular Genetics (IGM) , Consiglio Nazionale delle Ricerche (CNR) , Pavia , Italy
| | - Antonella Lisa
- b Institute of Molecular Genetics (IGM) , Consiglio Nazionale delle Ricerche (CNR) , Pavia , Italy
| | - Donata Luiselli
- a Department of Biological, Geological and Environmental Sciences , University of Bologna , Bologna , Italy
| | - Davide Pettener
- a Department of Biological, Geological and Environmental Sciences , University of Bologna , Bologna , Italy
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Evaluation of the precision ID whole MtDNA genome panel for forensic analyses. Forensic Sci Int Genet 2018; 35:21-25. [PMID: 29626805 DOI: 10.1016/j.fsigen.2018.03.013] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2018] [Revised: 02/20/2018] [Accepted: 03/28/2018] [Indexed: 12/18/2022]
Abstract
Mitochondrial DNA (mtDNA) amplification and Massively Parallel Sequencing (MPS) using an early access version of the Precision ID Whole MtDNA Genome Panel (Thermo Fisher Scientific) and the Ion Personal Genome Machine (PGM) were evaluated using 15 forensically relevant samples. Samples were selected to represent typical forensic specimens for mtDNA analysis including hairs, hair shafts, swabs and ancient solid tissue samples (bones and teeth) that were stored in the freezer for up to several years after having been typed with conventional Sanger-type Sequencing and Capillary Electrophoresis. The MPS haplotypes confirmed the earlier results in all samples and provided additional sequence information that improved discrimination power and haplogroup estimation. The results raised the appetite for further experiments to validate and apply the new technology in forensic practice.
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11
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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: 2.6] [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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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: 1.9] [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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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: 0.8] [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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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: 0.8] [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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Vai S, Ghirotto S, Pilli E, Tassi F, Lari M, Rizzi E, Matas-Lalueza L, Ramirez O, Lalueza-Fox C, Achilli A, Olivieri A, Torroni A, Lancioni H, Giostra C, Bedini E, Baricco LP, Matullo G, Di Gaetano C, Piazza A, Veeramah K, Geary P, Caramelli D, Barbujani G. Genealogical relationships between early medieval and modern inhabitants of Piedmont. PLoS One 2015; 10:e0116801. [PMID: 25635682 PMCID: PMC4312042 DOI: 10.1371/journal.pone.0116801] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2014] [Accepted: 12/16/2014] [Indexed: 11/18/2022] Open
Abstract
In the period between 400 to 800 AD, also known as the period of the Barbarian invasions, intense migration is documented in the historical record of Europe. However, little is known about the demographic impact of these historical movements, potentially ranging from negligible to substantial. As a pilot study in a broader project on Medieval Europe, we sampled 102 specimens from 5 burial sites in Northwestern Italy, archaeologically classified as belonging to Lombards or Longobards, a Germanic people ruling over a vast section of the Italian peninsula from 568 to 774. We successfully amplified and typed the mitochondrial hypervariable region I (HVR-I) of 28 individuals. Comparisons of genetic diversity with other ancient populations and haplotype networks did not suggest that these samples are heterogeneous, and hence allowed us to jointly compare them with three isolated contemporary populations, and with a modern sample of a large city, representing a control for the effects of recent immigration. We then generated by serial coalescent simulations 16 millions of genealogies, contrasting a model of genealogical continuity with one in which the contemporary samples are genealogically independent from the medieval sample. Analyses by Approximate Bayesian Computation showed that the latter model fits the data in most cases, with one exception, Trino Vercellese, in which the evidence was compatible with persistence up to the present time of genetic features observed among this early medieval population. We conclude that it is possible, in general, to detect evidence of genealogical ties between medieval and specific modern populations. However, only seldom did mitochondrial DNA data allow us to reject with confidence either model tested, which indicates that broader analyses, based on larger assemblages of samples and genetic markers, are needed to understand in detail the effects of medieval migration.
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Affiliation(s)
- Stefania Vai
- Dipartimento di Biologia Evoluzionistica, Università di Firenze, 50122 Florence, Italy
| | - Silvia Ghirotto
- Dipartimento di Scienze della Vita e Biotecnologie, Università di Ferrara, 44121 Ferrara, Italy
| | - Elena Pilli
- Dipartimento di Biologia Evoluzionistica, Università di Firenze, 50122 Florence, Italy
| | - Francesca Tassi
- Dipartimento di Scienze della Vita e Biotecnologie, Università di Ferrara, 44121 Ferrara, Italy
| | - Martina Lari
- Dipartimento di Biologia Evoluzionistica, Università di Firenze, 50122 Florence, Italy
| | - Ermanno Rizzi
- Institute for Biomedical Technologies, National Research Council, 20090 Segrate, Milan, Italy
| | | | - Oscar Ramirez
- Institut de Biologia Evolutiva, CSIC-UPF, Barcelona 08003, Spain
| | | | - Alessandro Achilli
- Dipartimento di Chimica, Biologia e Biotecnologie, Università di Perugia, 06123 Perugia, Italy
| | - Anna Olivieri
- Dipartimento di Biologia e Biotecnologie “L. Spallanzani”, Università di Pavia, 27100,Pavia,Italy
| | - Antonio Torroni
- Dipartimento di Biologia e Biotecnologie “L. Spallanzani”, Università di Pavia, 27100,Pavia,Italy
| | - Hovirag Lancioni
- Dipartimento di Chimica, Biologia e Biotecnologie, Università di Perugia, 06123 Perugia, Italy
| | - Caterina Giostra
- Dipartimento di Storia, Archeologia e Storia dell’arte, Università Cattolica del Sacro Cuore, 20123 Milano, Italy
| | - Elena Bedini
- Anthropozoologica L.B.A. s.n.c., 57123 Livorno, Italy
| | | | | | | | | | - Krishna Veeramah
- Department of Ecology and Evolution, State University of New York, Stony Brook, New York 11794–5245, United States of America
| | - Patrick Geary
- School of Historical Studies, Institute for Advanced Study, Princeton, New Jersey 08540, United States of America
| | - David Caramelli
- Dipartimento di Biologia Evoluzionistica, Università di Firenze, 50122 Florence, Italy
| | - Guido Barbujani
- Dipartimento di Scienze della Vita e Biotecnologie, Università di Ferrara, 44121 Ferrara, Italy
- * E-mail:
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Bodner M, Iuvaro A, Strobl C, Nagl S, Huber G, Pelotti S, Pettener D, Luiselli D, Parson W. Helena, the hidden beauty: Resolving the most common West Eurasian mtDNA control region haplotype by massively parallel sequencing an Italian population sample. Forensic Sci Int Genet 2014; 15:21-6. [PMID: 25303789 DOI: 10.1016/j.fsigen.2014.09.012] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2014] [Accepted: 09/16/2014] [Indexed: 01/24/2023]
Abstract
The analysis of mitochondrial (mt)DNA is a powerful tool in forensic genetics when nuclear markers fail to give results or maternal relatedness is investigated. The mtDNA control region (CR) contains highly condensed variation and is therefore routinely typed. Some samples exhibit an identical haplotype in this restricted range. Thus, they convey only weak evidence in forensic queries and limited phylogenetic information. However, a CR match does not imply that also the mtDNA coding regions are identical or samples belong to the same phylogenetic lineage. This is especially the case for the most frequent West Eurasian CR haplotype 263G 315.1C 16519C, which is observed in various clades within haplogroup H and occurs at a frequency of 3-4% in many European populations. In this study, we investigated the power of massively parallel complete mtGenome sequencing in 29 Italian samples displaying the most common West Eurasian CR haplotype - and found an unexpected high diversity. Twenty-eight different haplotypes falling into 19 described sub-clades of haplogroup H were revealed in the samples with identical CR sequences. This study demonstrates the benefit of complete mtGenome sequencing for forensic applications to enforce maximum discrimination, more comprehensive heteroplasmy detection, as well as highest phylogenetic resolution.
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Affiliation(s)
- Martin Bodner
- Institute of Legal Medicine, Innsbruck Medical University, Innsbruck, Austria
| | - Alessandra Iuvaro
- Institute of Legal Medicine, Innsbruck Medical University, Innsbruck, Austria; Department of Medical and Surgical Sciences, Institute of Legal Medicine, University of Bologna, Bologna, Italy
| | - Christina Strobl
- Institute of Legal Medicine, Innsbruck Medical University, Innsbruck, Austria
| | - Simone Nagl
- Institute of Legal Medicine, Innsbruck Medical University, Innsbruck, Austria
| | - Gabriela Huber
- Institute of Legal Medicine, Innsbruck Medical University, Innsbruck, Austria
| | - Susi Pelotti
- Department of Medical and Surgical Sciences, Institute of Legal Medicine, University of Bologna, Bologna, Italy
| | - Davide Pettener
- Department of Biological, Geological and Environmental Science, Laboratory of Molecular Anthropology, University of Bologna, Bologna, Italy
| | - Donata Luiselli
- Department of Biological, Geological and Environmental Science, Laboratory of Molecular Anthropology, University of Bologna, Bologna, Italy.
| | - 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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Zimmermann B, Rock AW, Dur A, Parson W. Improved visibility of character conflicts in quasi-median networks with the EMPOP NETWORK software. Croat Med J 2014; 55:115-20. [PMID: 24778097 PMCID: PMC4020147 DOI: 10.3325/cmj.2014.55.115] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Aim To provide a valuable tool for graphical representation of mitochondrial DNA (mtDNA) data that enables visual emphasis on complex substructures within the network to highlight possible ambiguities and errors. Method We applied the new NETWORK graphical user interface, available via EMPOP (European DNA Profiling Group Mitochondrial DNA Population Database; www.empop.org) by means of two mtDNA data sets that were submitted for quality control. Results The quasi-median network torsi of the two data sets resulted in complex reticulations, suggesting ambiguous data. To check the corresponding raw data, accountable nodes and connecting branches of the network could be identified by highlighting induced subgraphs with concurrent dimming of their complements. This is achieved by accentuating the relevant substructures in the network: mouse clicking on a node displays a list of all mtDNA haplotypes included in that node; the selection of a branch specifies the mutation(s) connecting two nodes. It is indicated to evaluate these mutations by means of the raw data. Conclusion Inspection of the raw data confirmed the presence of phantom mutations due to suboptimal electrophoresis conditions and data misinterpretation. The network software proved to be a powerful tool to highlight problematic data and guide quality control of mtDNA data tables.
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Affiliation(s)
| | | | | | - Walther Parson
- Walther Parson, Institute of Legal Medicine, Medical University, Mullerstrasse 44, A-6020 Innsbruck, Austria,
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Pardiñas AF, Martínez JL, Roca A, García-Vazquez E, López B. Over the sands and far away: interpreting an Iberian mitochondrial lineage with ancient Western African origins. Am J Hum Biol 2014; 26:777-83. [PMID: 25130626 DOI: 10.1002/ajhb.22601] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2013] [Revised: 07/11/2014] [Accepted: 07/17/2014] [Indexed: 12/29/2022] Open
Abstract
OBJECTIVES There is an ongoing effort to characterize the genetic links between Africa and Europe, mostly using lineages and haplotypes that are specific to one continent but had an ancient origin in the other. Mitochondrial DNA has been proven to be a very useful tool for this purpose since a high number of putatively European-specific variants of the African L* lineages have been defined over the years. Due to their geographic locations, Spain and Portugal seem to be ideal places for searching for these lineages. METHODS Five members of a minor branch of haplogroup L3f were found in recent DNA samplings in the region of Asturias (Northern Spain), which is known for its historical isolation. The frequency of L3f in this population (≈1%) is unexpectedly high in comparison with other related lineages in Europe. Complete mitochondrial DNA sequencing of these L3f lineages, as well phylogenetic and phylogeographic comparative analyses have been performed. RESULTS The L3f variant found in Asturias seems to constitute an Iberian-specific haplogroup, distantly related to lineages in Northern Africa and with a deep ancestry in Western Africa. Coalescent algorithms estimate the minimum arrival time as 8,000 years ago, and a possible route through the Gibraltar Strait. CONCLUSIONS Results are concordant with a previously proposed Neolithic connection between Southern Europe and Western Africa, which might be key to the proper understanding of the ancient links between these two continents.
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Affiliation(s)
- Antonio F Pardiñas
- Departamento de Biología de Organismos y Sistemas, Universidad de Oviedo, Asturias, 33071, Spain
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Mitochondrial DNA control region diversity in a population from Espirito Santo state, Brazil. Mol Biol Rep 2014; 41:6645-8. [DOI: 10.1007/s11033-014-3547-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2013] [Accepted: 06/20/2014] [Indexed: 10/25/2022]
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An ancient Mediterranean melting pot: investigating the uniparental genetic structure and population history of sicily and southern Italy. PLoS One 2014; 9:e96074. [PMID: 24788788 PMCID: PMC4005757 DOI: 10.1371/journal.pone.0096074] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2013] [Accepted: 04/03/2014] [Indexed: 11/19/2022] Open
Abstract
Due to their strategic geographic location between three different continents, Sicily and Southern Italy have long represented a major Mediterranean crossroad where different peoples and cultures came together over time. However, its multi-layered history of migration pathways and cultural exchanges, has made the reconstruction of its genetic history and population structure extremely controversial and widely debated. To address this debate, we surveyed the genetic variability of 326 accurately selected individuals from 8 different provinces of Sicily and Southern Italy, through a comprehensive evaluation of both Y-chromosome and mtDNA genomes. The main goal was to investigate the structuring of maternal and paternal genetic pools within Sicily and Southern Italy, and to examine their degrees of interaction with other Mediterranean populations. Our findings show high levels of within-population variability, coupled with the lack of significant genetic sub-structures both within Sicily, as well as between Sicily and Southern Italy. When Sicilian and Southern Italian populations were contextualized within the Euro-Mediterranean genetic space, we observed different historical dynamics for maternal and paternal inheritances. Y-chromosome results highlight a significant genetic differentiation between the North-Western and South-Eastern part of the Mediterranean, the Italian Peninsula occupying an intermediate position therein. In particular, Sicily and Southern Italy reveal a shared paternal genetic background with the Balkan Peninsula and the time estimates of main Y-chromosome lineages signal paternal genetic traces of Neolithic and post-Neolithic migration events. On the contrary, despite showing some correspondence with its paternal counterpart, mtDNA reveals a substantially homogeneous genetic landscape, which may reflect older population events or different demographic dynamics between males and females. Overall, both uniparental genetic structures and TMRCA estimates confirm the role of Sicily and Southern Italy as an ancient Mediterranean melting pot for genes and cultures.
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Boattini A, Martinez-Cruz B, Sarno S, Harmant C, Useli A, Sanz P, Yang-Yao D, Manry J, Ciani G, Luiselli D, Quintana-Murci L, Comas D, Pettener D, the Genographic Consortium. Uniparental markers in Italy reveal a sex-biased genetic structure and different historical strata. PLoS One 2013; 8:e65441. [PMID: 23734255 PMCID: PMC3666984 DOI: 10.1371/journal.pone.0065441] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2013] [Accepted: 04/24/2013] [Indexed: 11/18/2022] Open
Abstract
Located in the center of the Mediterranean landscape and with an extensive coastal line, the territory of what is today Italy has played an important role in the history of human settlements and movements of Southern Europe and the Mediterranean Basin. Populated since Paleolithic times, the complexity of human movements during the Neolithic, the Metal Ages and the most recent history of the two last millennia (involving the overlapping of different cultural and demic strata) has shaped the pattern of the modern Italian genetic structure. With the aim of disentangling this pattern and understanding which processes more importantly shaped the distribution of diversity, we have analyzed the uniparentally-inherited markers in ∼900 individuals from an extensive sampling across the Italian peninsula, Sardinia and Sicily. Spatial PCAs and DAPCs revealed a sex-biased pattern indicating different demographic histories for males and females. Besides the genetic outlier position of Sardinians, a North West–South East Y-chromosome structure is found in continental Italy. Such structure is in agreement with recent archeological syntheses indicating two independent and parallel processes of Neolithisation. In addition, date estimates pinpoint the importance of the cultural and demographic events during the late Neolithic and Metal Ages. On the other hand, mitochondrial diversity is distributed more homogeneously in agreement with older population events that might be related to the presence of an Italian Refugium during the last glacial period in Europe.
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Affiliation(s)
- Alessio Boattini
- Laboratorio di Antropologia Molecolare, Dipartimento di Scienze Biologiche, Geologiche e Ambientali, Università di Bologna, Bologna, Italy
| | - Begoña Martinez-Cruz
- Institut de Biologia Evolutiva (CSIC-UPF), Departament de Ciències de la Salut i de la Vida, Universitat Pompeu Fabra, Barcelona, Spain
| | - Stefania Sarno
- Laboratorio di Antropologia Molecolare, Dipartimento di Scienze Biologiche, Geologiche e Ambientali, Università di Bologna, Bologna, Italy
| | - Christine Harmant
- Institut Pasteur, Human Evolutionary Genetics Unit, Department of Genomes and Genetics, Paris, France
- Centre National de la Recherche Scientifique, Paris, France
| | - Antonella Useli
- Dipartimento di Scienze della Natura e del Territorio, Università di Sassari, Sassari, Italy
| | - Paula Sanz
- Institut de Biologia Evolutiva (CSIC-UPF), Departament de Ciències de la Salut i de la Vida, Universitat Pompeu Fabra, Barcelona, Spain
| | - Daniele Yang-Yao
- Laboratorio di Antropologia Molecolare, Dipartimento di Scienze Biologiche, Geologiche e Ambientali, Università di Bologna, Bologna, Italy
| | - Jeremy Manry
- Institut Pasteur, Human Evolutionary Genetics Unit, Department of Genomes and Genetics, Paris, France
- Centre National de la Recherche Scientifique, Paris, France
| | - Graziella Ciani
- Laboratorio di Antropologia Molecolare, Dipartimento di Scienze Biologiche, Geologiche e Ambientali, Università di Bologna, Bologna, Italy
| | - Donata Luiselli
- Laboratorio di Antropologia Molecolare, Dipartimento di Scienze Biologiche, Geologiche e Ambientali, Università di Bologna, Bologna, Italy
| | - Lluis Quintana-Murci
- Institut Pasteur, Human Evolutionary Genetics Unit, Department of Genomes and Genetics, Paris, France
- Centre National de la Recherche Scientifique, Paris, France
| | - David Comas
- Institut de Biologia Evolutiva (CSIC-UPF), Departament de Ciències de la Salut i de la Vida, Universitat Pompeu Fabra, Barcelona, Spain
- * E-mail: (DC); (DP)
| | - Davide Pettener
- Laboratorio di Antropologia Molecolare, Dipartimento di Scienze Biologiche, Geologiche e Ambientali, Università di Bologna, Bologna, Italy
- * E-mail: (DC); (DP)
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Ghirotto S, Tassi F, Fumagalli E, Colonna V, Sandionigi A, Lari M, Vai S, Petiti E, Corti G, Rizzi E, De Bellis G, Caramelli D, Barbujani G. Origins and evolution of the Etruscans' mtDNA. PLoS One 2013; 8:e55519. [PMID: 23405165 PMCID: PMC3566088 DOI: 10.1371/journal.pone.0055519] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2012] [Accepted: 12/24/2012] [Indexed: 11/25/2022] Open
Abstract
The Etruscan culture is documented in Etruria, Central Italy, from the 8th to the 1st century BC. For more than 2,000 years there has been disagreement on the Etruscans’ biological origins, whether local or in Anatolia. Genetic affinities with both Tuscan and Anatolian populations have been reported, but so far all attempts have failed to fit the Etruscans’ and modern populations in the same genealogy. We extracted and typed the hypervariable region of mitochondrial DNA of 14 individuals buried in two Etruscan necropoleis, analyzing them along with other Etruscan and Medieval samples, and 4,910 contemporary individuals from the Mediterranean basin. Comparing ancient (30 Etruscans, 27 Medieval individuals) and modern DNA sequences (370 Tuscans), with the results of millions of computer simulations, we show that the Etruscans can be considered ancestral, with a high degree of confidence, to the current inhabitants of Casentino and Volterra, but not to the general contemporary population of the former Etruscan homeland. By further considering two Anatolian samples (35 and 123 individuals) we could estimate that the genetic links between Tuscany and Anatolia date back to at least 5,000 years ago, strongly suggesting that the Etruscan culture developed locally, and not as an immediate consequence of immigration from the Eastern Mediterranean shores.
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Affiliation(s)
- Silvia Ghirotto
- Department of Biology and Evolution, University of Ferrara, Ferrara, Italy
| | - Francesca Tassi
- Department of Biology and Evolution, University of Ferrara, Ferrara, Italy
| | - Erica Fumagalli
- Department of Biology and Evolution, University of Ferrara, Ferrara, Italy
- Department of Biotechnologies and Biosciences, University of Milano-Bicocca, Milan, Italy
| | - Vincenza Colonna
- Department of Biology and Evolution, University of Ferrara, Ferrara, Italy
- Institute of Genetics e Biophysics “Adriano Buzzati-Traverso”, National Research Council, Naples, Italy
| | - Anna Sandionigi
- Department of Evolutionary Biology, University of Florence, Florence, Italy
| | - Martina Lari
- Department of Evolutionary Biology, University of Florence, Florence, Italy
| | - Stefania Vai
- Department of Evolutionary Biology, University of Florence, Florence, Italy
| | - Emmanuele Petiti
- Department of Evolutionary Biology, University of Florence, Florence, Italy
| | - Giorgio Corti
- Institute for Biomedical Technologies, National Research Council, Segrate, Milan, Italy
| | - Ermanno Rizzi
- Institute for Biomedical Technologies, National Research Council, Segrate, Milan, Italy
| | - Gianluca De Bellis
- Institute for Biomedical Technologies, National Research Council, Segrate, Milan, Italy
| | - David Caramelli
- Department of Evolutionary Biology, University of Florence, Florence, Italy
| | - Guido Barbujani
- Department of Biology and Evolution, University of Ferrara, Ferrara, Italy
- * E-mail:
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A cautionary note on switching mitochondrial DNA reference sequences in forensic genetics. Forensic Sci Int Genet 2012; 6:e182-4. [PMID: 22840856 DOI: 10.1016/j.fsigen.2012.06.015] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2012] [Revised: 06/27/2012] [Accepted: 06/29/2012] [Indexed: 11/24/2022]
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24
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Montesino M, Prieto L. Capillary electrophoresis of Big-Dye terminator sequencing reactions for human mtDNA Control Region haplotyping in the identification of human remains. Methods Mol Biol 2012; 830:267-281. [PMID: 22139667 DOI: 10.1007/978-1-61779-461-2_19] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Cycle sequencing reaction with Big-Dye terminators provides the methodology to analyze mtDNA Control Region amplicons by means of capillary electrophoresis. DNA sequencing with ddNTPs or terminators was developed by (1). The progressive automation of the method by combining the use of fluorescent-dye terminators with cycle sequencing has made it possible to increase the sensibility and efficiency of the method and hence has allowed its introduction into the forensic field. PCR-generated mitochondrial DNA products are the templates for sequencing reactions. Different set of primers can be used to generate amplicons with different sizes according to the quality and quantity of the DNA extract providing sequence data for different ranges inside the Control Region.
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Affiliation(s)
- Marta Montesino
- Comisaría General de Policía Científica, Servicio de Analítica, Laboratorio de ADN, Instituto Universitario de Investigación en Ciencias Policiales (IUICP), Madrid, Spain.
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Preliminary results of mitochondrial DNA sequence variation in Jujuy population (Argentina). FORENSIC SCIENCE INTERNATIONAL GENETICS SUPPLEMENT SERIES 2011. [DOI: 10.1016/j.fsigss.2011.08.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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26
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Vanek D, Silerova M, Urbanova V, Saskova L, Dubska J, Beran M. Mitochondrial control region sequences of the Czech Republic population and a comparison to other populations. FORENSIC SCIENCE INTERNATIONAL GENETICS SUPPLEMENT SERIES 2011. [DOI: 10.1016/j.fsigss.2011.09.069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
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Abstract
A rare combination of mutations within mitochondrial DNA subhaplogroup T2e is identified as affiliated with Sephardic Jews, a group that has received relatively little attention. Four investigations were pursued: Search of the motif in 250 000 control region records across 8 databases, comparison of frequencies of T subhaplogroups (T1, T2b, T2c, T2e, T4, T(*)) across 11 diverse populations, creation of a phylogenic median-joining network from public T2e control region entries, and analysis of one Sephardic mitochondrial full genomic sequence with the motif. It was found that the rare motif belonged only to Sephardic descendents (Turkey, Bulgaria), to inhabitants of North American regions known for secret Spanish-Jewish colonization, or were consistent with Sephardic ancestry. The incidence of subhaplogroup T2e decreased from the Western Arabian Peninsula to Italy to Spain and into Western Europe. The ratio of sister subhaplogroups T2e to T2b was found to vary 40-fold across populations from a low in the British Isles to a high in Saudi Arabia with the ratio in Sephardim more similar to Saudi Arabia, Egypt, and Italy than to hosts Spain and Portugal. Coding region mutations of 2308G and 14499T may locate the Sephardic signature within T2e, but additional samples and reworking of current T2e phylogenetic branch structure is needed. The Sephardic Turkish community has a less pronounced founder effect than some Ashkenazi groups considered singly (eg, Polish), but other comparisons of interest await comparable averaging. Registries of signatures will benefit the study of populations with a large number of smaller-size founders.
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Paneto GG, Köhnemann S, Martins JA, Cicarelli RMB, Pfeiffer H. A single multiplex PCR and SNaPshot minisequencing reaction of 42 SNPs to classify admixture populations into mitochondrial DNA haplogroups. Mitochondrion 2010; 11:296-302. [PMID: 21172459 DOI: 10.1016/j.mito.2010.12.010] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2010] [Revised: 11/02/2010] [Accepted: 12/03/2010] [Indexed: 11/24/2022]
Abstract
SNaPshot minisequencing reaction is in increasing use because of its fast detection of many polymorphisms in a single assay. In this work we described a highly sensitive single nucleotide polymorphisms (SNPs) typing method with detection of 42 mitochondrial DNA (mtDNA) SNPs in a single PCR and SNaPshot multiplex reaction, in order to allow haplogroup classification in Latin American admixture population. We validated the panel typing 160 Brazilian individuals. Complete SNP profiles were obtained from 10 pg of total DNA. We conclude that it is possible to build and genotype more than forty mtDNA SNPs in a single multiplex PCR and SNaPshot reaction, with sensitivity and reliability, resolving haplogroup classification in admixture populations.
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Affiliation(s)
- Greiciane G Paneto
- Faculdade de Ciências Farmacêuticas, Unesp-Univ Estadual Paulista, Araraquara, SP, Brazil.
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Prieto L, Zimmermann B, Goios A, Rodriguez-Monge A, Paneto GG, Alves C, Alonso A, Fridman C, Cardoso S, Lima G, Anjos MJ, Whittle MR, Montesino M, Cicarelli RMB, Rocha AM, Albarrán C, de Pancorbo MM, Pinheiro MF, Carvalho M, Sumita DR, Parson W. The GHEP-EMPOP collaboration on mtDNA population data--A new resource for forensic casework. Forensic Sci Int Genet 2010; 5:146-51. [PMID: 21075696 PMCID: PMC3065011 DOI: 10.1016/j.fsigen.2010.10.013] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Mitochondrial DNA (mtDNA) population data for forensic purposes are still scarce for some populations, which may limit the evaluation of forensic evidence especially when the rarity of a haplotype needs to be determined in a database search. In order to improve the collection of mtDNA lineages from the Iberian and South American subcontinents, we here report the results of a collaborative study involving nine laboratories from the Spanish and Portuguese Speaking Working Group of the International Society for Forensic Genetics (GHEP-ISFG) and EMPOP. The individual laboratories contributed population data that were generated throughout the past 10 years, but in the majority of cases have not been made available to the scientific community. A total of 1019 haplotypes from Iberia (Basque Country, 2 general Spanish populations, 2 North and 1 Central Portugal populations), and Latin America (3 populations from São Paulo) were collected, reviewed and harmonized according to defined EMPOP criteria. The majority of data ambiguities that were found during the reviewing process (41 in total) were transcription errors confirming that the documentation process is still the most error-prone stage in reporting mtDNA population data, especially when performed manually. This GHEP–EMPOP collaboration has significantly improved the quality of the individual mtDNA datasets and adds mtDNA population data as valuable resource to the EMPOP database (www.empop.org).
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Affiliation(s)
- L Prieto
- Comisaría General de Policía Científica, University Institute of Research in Forensic Sciences (IUICP), Madrid, Spain
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Messina F, Scorrano G, Labarga CM, Rolfo MF, Rickards O. Mitochondrial DNA variation in an isolated area of Central Italy. Ann Hum Biol 2010; 37:385-402. [PMID: 20377493 DOI: 10.3109/03014461003720304] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
BACKGROUND The genetic variation in Italy is the result of ancient population movement, demographic change, and geography. The increasing possibility of studying the maternal genetic structure of selected Italian population samples at a high level of phylogenetic resolution provides a particularly useful model to assess the presence of genetic traces of the ancient people who lived in Italy in pre-Roman times in present populations AIM In this study we reconstructed the genetic maternal history of Jenne and Vallepietra, two mountain communities in the Aniene Valley in the Simbruini Mountains near Rome. Both communities have been spared external invasion due to their geographic location, which very likely preserved the genetic pool of these autochthonous populations. SUBJECTS AND METHODS The study population (124 individuals from Jenne and Vallepietra) were investigated for D-loop mtDNA hypervariable segments I (HVS-I) and II (HVS-II) and for informative single nucleotide polymorphisms (SNPs) within the coding region. The detected haplotypes were then compared with those of other Italian, European and Mediterranean populations. RESULTS The distribution of mtDNA diversity in Jenne and Vallepietra, although similar to that found in other European populations, shows a basic variability and the typical signs of a certain degree of isolation between them and other populations analysed; in particular, the Vallepietra sample showed an unusually high frequency (71.3%) of mtDNA haplogroups which are typical of Near Eastern and South-Western Asian populations. CONCLUSION The high degree of differentiation between the two villages is intriguing, since it suggests a low level of gene flow between them, despite their close geographic proximity and shared linguistic features. The degree of their genetic isolation, also in comparison to other Italian, European and Mediterranean populations, is consistent with isolation among geographically separated populations.
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Affiliation(s)
- Francesco Messina
- Dipartimento di Biologia, Università di Roma Tor Vergata, Via della Ricerca Scientifica n. 1, 00173 Rome, Italy
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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: 1.6] [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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Ottoni C, Martinez-Labarga C, Vitelli L, Scano G, Fabrini E, Contini I, Biondi G, Rickards O. Human mitochondrial DNA variation in Southern Italy. Ann Hum Biol 2010; 36:785-811. [PMID: 19852679 DOI: 10.3109/03014460903198509] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
BACKGROUND Since prehistoric times Southern Italy has been a cultural crossroads of the Mediterranean basin. Genetic data on the peoples of Basilicata and Calabria are scarce and, particularly, no records on mtDNA variability have been published. AIM In this study mtDNA haplotypes of populations from Basilicata, Calabria and Sicily are compared with those of other Italian and Mediterranean populations, so as to investigate their genetic relationships. SUBJECTS AND METHODS A total of 341 individuals was analysed for mtDNA in order to provide their classification into haplogroups. Multivariate analysis was used to compare the studied populations with other Mediterranean samples; median-joining network analysis was applied to observe the relationship between the major lineages of the Southern Italians. RESULTS The haplogroup distribution in the Southern Italian samples falls within the typical pattern of mtDNA variability of Western Eurasia. The comparison with other Mediterranean countries showed a substantial homogeneity of the area, which is probably related to the historic contact through the Mediterranean Sea. CONCLUSION The mtDNA analysis demonstrated that Southern Italy displays a typical pattern of Mediterranean basin variability, even though it appears plausible that Southern Italy was less affected by the effects of the Late Glacial Maximum, which reduced genetic diversity in Europe.
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Affiliation(s)
- Claudio Ottoni
- Department of Biology, University of Rome 'Tor Vergata' Via della Ricerca Scientifica, n. 1, 00173, Rome, Italy
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Anjum GM, Du W, Klein R, Amara U, Huber-Lang M, Schneider EM, Wiegand P. Pyrosequencing-based strategy for a successful SNP detection in two hypervariable regions: HV-I/HV-II of the human mitochondrial displacement loop. Electrophoresis 2010; 31:309-14. [PMID: 20084631 DOI: 10.1002/elps.200900325] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Ghulam Murtza Anjum
- Sektion Experimentelle Anaesthesiologie, Universitaetsklinikum Ulm, Ulm, Germany
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Preliminary results of mitochondrial DNA sequence variation in Spanish Pyrenean populations. FORENSIC SCIENCE INTERNATIONAL GENETICS SUPPLEMENT SERIES 2009. [DOI: 10.1016/j.fsigss.2009.08.061] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Grignani P, Turchi C, Achilli A, Peloso G, Alù M, Ricci U, Robino C, Pelotti S, Carnevali E, Boschi I, Tagliabracci A, Previderè C. Multiplex mtDNA coding region SNP assays for molecular dissection of haplogroups U/K and J/T. Forensic Sci Int Genet 2009; 4:21-5. [DOI: 10.1016/j.fsigen.2009.04.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2008] [Revised: 03/23/2009] [Accepted: 04/02/2009] [Indexed: 11/28/2022]
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Guardado-Estrada M, Juarez-Torres E, Medina-Martinez I, Wegier A, Macías A, Gomez G, Cruz-Talonia F, Roman-Bassaure E, Piñero D, Kofman-Alfaro S, Berumen J. A great diversity of Amerindian mitochondrial DNA ancestry is present in the Mexican mestizo population. J Hum Genet 2009; 54:695-705. [DOI: 10.1038/jhg.2009.98] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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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: 0.8] [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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Pala M, Achilli A, Olivieri A, Kashani BH, Perego UA, Sanna D, Metspalu E, Tambets K, Tamm E, Accetturo M, Carossa V, Lancioni H, Panara F, Zimmermann B, Huber G, Al-Zahery N, Brisighelli F, Woodward SR, Francalacci P, Parson W, Salas A, Behar DM, Villems R, Semino O, Bandelt HJ, Torroni A. Mitochondrial haplogroup U5b3: a distant echo of the epipaleolithic in Italy and the legacy of the early Sardinians. Am J Hum Genet 2009; 84:814-21. [PMID: 19500771 PMCID: PMC2694970 DOI: 10.1016/j.ajhg.2009.05.004] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2009] [Revised: 05/15/2009] [Accepted: 05/15/2009] [Indexed: 11/16/2022] Open
Abstract
There are extensive data indicating that some glacial refuge zones of southern Europe (Franco-Cantabria, Balkans, and Ukraine) were major genetic sources for the human recolonization of the continent at the beginning of the Holocene. Intriguingly, there is no genetic evidence that the refuge area located in the Italian Peninsula contributed to this process. Here we show, through phylogeographic analyses of mitochondrial DNA (mtDNA) variation performed at the highest level of molecular resolution (52 entire mitochondrial genomes), that the most likely homeland for U5b3-a haplogroup present at a very low frequency across Europe-was the Italian Peninsula. In contrast to mtDNA haplogroups that expanded from other refugia, the Holocene expansion of haplogroup U5b3 toward the North was restricted by the Alps and occurred only along the Mediterranean coasts, mainly toward nearby Provence (southern France). From there, approximately 7,000-9,000 years ago, a subclade of this haplogroup moved to Sardinia, possibly as a result of the obsidian trade that linked the two regions, leaving a distinctive signature in the modern people of the island. This scenario strikingly matches the age, distribution, and postulated geographic source of a Sardinian Y chromosome haplogroup (I2a2-M26), a paradigmatic case in the European context of a founder event marking both female and male lineages.
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Affiliation(s)
- Maria Pala
- Dipartimento di Genetica e Microbiologia, Università di Pavia, Pavia 27100, Italy
| | - Alessandro Achilli
- Dipartimento di Genetica e Microbiologia, Università di Pavia, Pavia 27100, Italy
- Dipartimento di Biologia Cellulare e Ambientale, Università di Perugia, Perugia 06123, Italy
| | - Anna Olivieri
- Dipartimento di Genetica e Microbiologia, Università di Pavia, Pavia 27100, Italy
| | | | - Ugo A. Perego
- Dipartimento di Genetica e Microbiologia, Università di Pavia, Pavia 27100, Italy
- Sorenson Molecular Genealogy Foundation, Salt Lake City, UT 84115, USA
| | - Daria Sanna
- Dipartimento di Zoologia e Genetica Evoluzionistica, Università di Sassari, Sassari 07100, Italy
| | - Ene Metspalu
- Department of Evolutionary Biology, University of Tartu and Estonian Biocentre, Tartu 51010, Estonia
| | - Kristiina Tambets
- Department of Evolutionary Biology, University of Tartu and Estonian Biocentre, Tartu 51010, Estonia
| | - Erika Tamm
- Department of Evolutionary Biology, University of Tartu and Estonian Biocentre, Tartu 51010, Estonia
| | - Matteo Accetturo
- Dipartimento di Genetica e Microbiologia, Università di Pavia, Pavia 27100, Italy
| | - Valeria Carossa
- Dipartimento di Genetica e Microbiologia, Università di Pavia, Pavia 27100, Italy
| | - Hovirag Lancioni
- Dipartimento di Biologia Cellulare e Ambientale, Università di Perugia, Perugia 06123, Italy
| | - Fausto Panara
- Dipartimento di Biologia Cellulare e Ambientale, Università di Perugia, Perugia 06123, Italy
| | - Bettina Zimmermann
- Institute of Legal Medicine, Innsbruck Medical University, Innsbruck A-6020, Austria
| | - Gabriela Huber
- Institute of Legal Medicine, Innsbruck Medical University, Innsbruck A-6020, Austria
| | - Nadia Al-Zahery
- Dipartimento di Genetica e Microbiologia, Università di Pavia, Pavia 27100, Italy
- Department of Biotechnology, College of Science, University of Baghdad, Iraq
| | - Francesca Brisighelli
- Unidade de Xenética, Departamento de Anatomía Patolóxica e Ciencias Forenses; and Instituto de Medicina Legal, Facultade de Medicina, Universidade de Santiago de Compostela, Santiago de Compostela, Galicia 15782, Spain
| | - Scott R. Woodward
- Sorenson Molecular Genealogy Foundation, Salt Lake City, UT 84115, USA
| | - Paolo Francalacci
- Dipartimento di Zoologia e Genetica Evoluzionistica, Università di Sassari, Sassari 07100, Italy
| | - Walther Parson
- Institute of Legal Medicine, Innsbruck Medical University, Innsbruck A-6020, Austria
| | - Antonio Salas
- Unidade de Xenética, Departamento de Anatomía Patolóxica e Ciencias Forenses; and Instituto de Medicina Legal, Facultade de Medicina, Universidade de Santiago de Compostela, Santiago de Compostela, Galicia 15782, Spain
| | - Doron M. Behar
- Molecular Medicine Laboratory, Rambam Health Care Campus, Haifa 31096, Israel
| | - Richard Villems
- Department of Evolutionary Biology, University of Tartu and Estonian Biocentre, Tartu 51010, Estonia
| | - Ornella Semino
- Dipartimento di Genetica e Microbiologia, Università di Pavia, Pavia 27100, Italy
| | | | - Antonio Torroni
- Dipartimento di Genetica e Microbiologia, Università di Pavia, Pavia 27100, Italy
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Turchi C, Buscemi L, Giacchino E, Onofri V, Fendt L, Parson W, Tagliabracci A. Polymorphisms of mtDNA control region in Tunisian and Moroccan populations: An enrichment of forensic mtDNA databases with Northern Africa data. Forensic Sci Int Genet 2009; 3:166-72. [DOI: 10.1016/j.fsigen.2009.01.014] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Affiliation(s)
- T. A. Brettell
- Department of Chemical and Physical Sciences, Cedar Crest College, 100 College Drive, Allentown, Pennsylvania 18104-6196
| | - J. M. Butler
- Biochemical Science Division, National Institute of Standards and Technology, Gaithersburg, Maryland 20899-8312
| | - J. R. Almirall
- Department of Chemistry and Biochemistry and International Forensic Research Institute, Florida International University, University Park, Miami, Florida 33199
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41
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Phylogenetic classification of Japanese mtDNA assisted by complete mitochondrial DNA sequences. Int J Legal Med 2008; 124:7-12. [DOI: 10.1007/s00414-008-0308-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2008] [Accepted: 11/20/2008] [Indexed: 01/27/2023]
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Populationsgenetische mitochondriale DNA-Daten. MED GENET-BERLIN 2008. [DOI: 10.1007/s11825-008-0118-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Zusammenfassung
Der populationsgenetische Aspekt der Nutzung mitochondrialer DNA in der Forensik und medizinischen Genetik bezieht sich implizit auf die gesamte Datengrundlage und die mtDNA-Phylogenie, von der in Hinblick auf die zu untersuchenden Fragestellungen gezielt Teile ausgesondert werden. Wir heben besonders jene Aspekte hervor, die in der Vergangenheit bei vielen Untersuchungen nicht adäquat berücksichtigt wurden.
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Köhnemann S, Sibbing U, Pfeiffer H, Hohoff C. A rapid mtDNA assay of 22 SNPs in one multiplex reaction increases the power of forensic testing in European Caucasians. Int J Legal Med 2008; 122:517-23. [PMID: 18712405 DOI: 10.1007/s00414-008-0267-x] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2008] [Accepted: 06/20/2008] [Indexed: 11/28/2022]
Abstract
We have developed a multiplex mitochondrial (mtDNA) assay of 21 coding region single nucleotide polymorphisms (SNPs) and one control region SNP outside hypervariable region 1 (HVR1) and hypervariable region 2 (HVR2) that can be amplified in a single reverse touchdown polymerase chain reaction. Single base extension using the SNaPshot technique is also carried out as one multiplex. Besides the nine major European haplogroups (i.e. H, I, J, K, T, U, V, W, and X), 16 additional subclades (i.e. N1, X2, X2b, U2'-4/7'-9', J/T, J1, J1c, HV, H1, H1a1, H1c, H3, H4, H6a, H7a H10) can be detected and classified into a phylogenetic mtDNA tree. By analyzing 130 Caucasoid samples from Germany, 36 different haplotypes were found resulting in a power of discrimination of 93.2%. Although 49% of all samples belonged to superhaplogroup H, the most common haplotype, i.e., haplogroup-specific SNPs plus haplogroup unspecific SNPs, had a frequency of only 18%. This assay is applicable for high-throughput mtDNA analysis and forensic mass screening. It will give additional information to the common control region sequencing of HVR1 and HVR2.
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Affiliation(s)
- S Köhnemann
- Institut für Rechtsmedizin, Universitätsklinikum Münster, Röntgenstr. 23, Münster, 48149, Germany
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