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Sensitivity of mitochondrial DNA heteroplasmy detection using Next Generation Sequencing. Mitochondrion 2020; 50:88-93. [DOI: 10.1016/j.mito.2019.10.006] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Accepted: 10/10/2019] [Indexed: 01/03/2023]
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Pimenta J, Lopes AM, Carracedo A, Arenas M, Amorim A, Comas D. Spatially explicit analysis reveals complex human genetic gradients in the Iberian Peninsula. Sci Rep 2019; 9:7825. [PMID: 31127131 PMCID: PMC6534591 DOI: 10.1038/s41598-019-44121-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Accepted: 05/09/2019] [Indexed: 12/17/2022] Open
Abstract
The Iberian Peninsula is a well-delimited geographic region with a rich and complex human history. However, the causes of its genetic structure and past migratory dynamics are not yet fully understood. In order to shed light on them, here we evaluated the gene flow and genetic structure throughout the Iberian Peninsula with spatially explicit modelling applied to a georeferenced genetic dataset composed of genome-wide SNPs from 746 individuals belonging to 17 different regions of the Peninsula. We found contrasting patterns of genetic structure throughout Iberia. In particular, we identified strong patterns of genetic differentiation caused by relevant barriers to gene flow in northern regions and, on the other hand, a large genetic similarity in central and southern regions. In addition, our results showed a preferential north to south migratory dynamics and suggest a sex-biased dispersal in Mediterranean and southern regions. The estimated genetic patterns did not fit with the geographical relief of the Iberian landscape and they rather seem to follow political and linguistic territorial boundaries.
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Affiliation(s)
- João Pimenta
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- Institute of Molecular Pathology and Immunology of the University of Porto, Porto, Portugal
- Institute of Evolutionary Biology (CSIC-UPF). Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona, Spain
- Faculty of Sciences, University of Porto, Porto, Portugal
- Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Vairão, Portugal
| | - Alexandra M Lopes
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- Institute of Molecular Pathology and Immunology of the University of Porto, Porto, Portugal
| | - Angel Carracedo
- Instituto de Ciencias Forenses, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
- Grupo de Medicina Xenómica, CIBERER, Santiago de Compostela, Spain
| | - Miguel Arenas
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- Institute of Molecular Pathology and Immunology of the University of Porto, Porto, Portugal
- Department of Biochemistry, Genetics and Immunology, University of Vigo, Vigo, Spain
- Biomedical Research Center (CINBIO), University of Vigo, 36310, Vigo, Spain
| | - António Amorim
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- Institute of Molecular Pathology and Immunology of the University of Porto, Porto, Portugal
- Faculty of Sciences, University of Porto, Porto, Portugal
| | - David Comas
- Institute of Evolutionary Biology (CSIC-UPF). Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona, Spain.
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Varano S, Gaspari L, De Angelis F, Scano G, Contini I, Martínez-Labarga C, Rickards O. Mitochondrial characterisation of two Spanish populations from the Vera and Bejar valleys (Central Spain). Ann Hum Biol 2019; 45:531-539. [DOI: 10.1080/03014460.2018.1559355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- Sara Varano
- Centre of Molecular Anthropology for Ancient DNA Studies, Department of Biology, University of Rome “Tor Vergata”, Rome, Italy
| | - Luca Gaspari
- Centre of Molecular Anthropology for Ancient DNA Studies, Department of Biology, University of Rome “Tor Vergata”, Rome, Italy
| | - Flavio De Angelis
- Centre of Molecular Anthropology for Ancient DNA Studies, Department of Biology, University of Rome “Tor Vergata”, Rome, Italy
| | - Giuseppina Scano
- Centre of Molecular Anthropology for Ancient DNA Studies, Department of Biology, University of Rome “Tor Vergata”, Rome, Italy
| | - Irene Contini
- Centre of Molecular Anthropology for Ancient DNA Studies, Department of Biology, University of Rome “Tor Vergata”, Rome, Italy
| | - Cristina Martínez-Labarga
- Centre of Molecular Anthropology for Ancient DNA Studies, Department of Biology, University of Rome “Tor Vergata”, Rome, Italy
| | - Olga Rickards
- Centre of Molecular Anthropology for Ancient DNA Studies, Department of Biology, University of Rome “Tor Vergata”, Rome, Italy
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Barral-Arca R, Pischedda S, Gómez-Carballa A, Pastoriza A, Mosquera-Miguel A, López-Soto M, Martinón-Torres F, Álvarez-Iglesias V, Salas A. Meta-Analysis of Mitochondrial DNA Variation in the Iberian Peninsula. PLoS One 2016; 11:e0159735. [PMID: 27441366 PMCID: PMC4956223 DOI: 10.1371/journal.pone.0159735] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Accepted: 07/07/2016] [Indexed: 12/14/2022] Open
Abstract
The Iberian Peninsula has been the focus of attention of numerous studies dealing with mitochondrial DNA (mtDNA) variation, most of them targeting the control region segment. In the present study we sequenced the control region of 3,024 Spanish individuals from areas where available data were still limited. We also compiled mtDNA haplotypes from the literature involving 4,588 sequences and 28 population groups or small regions. We meta-analyzed all these data in order to shed further light on patterns of geographic variation, taking advantage of the large sample size and geographic coverage, in contrast with the atomized sampling strategy of previous work. The results indicate that the main mtDNA haplogroups show primarily clinal geographic patterns across the Iberian geography, roughly along a North-South axis. Haplogroup HV0 (where haplogroup U is nested) is more prevalent in the Franco Cantabrian region, in good agreement with previous findings that identified this area as a climate refuge during the Last Glacial Maximum (LGM), prior to a subsequent demographic re-expansion towards Central Europe and the Mediterranean. Typical sub-Saharan and North African lineages are slightly more prevalent in South Iberia, although at low frequencies; this pattern has been shaped mainly by the transatlantic slave trade and the Arab invasion of the Iberian Peninsula. The results also indicate that summary statistics that aim to measure molecular variation, or AMOVA, have limited sensitivity to detect population substructure, in contrast to patterns revealed by phylogeographic analysis. Overall, the results suggest that mtDNA variation in Iberia is substantially stratified. These patterns might be relevant in biomedical studies given that stratification is a common cause of false positives in case-control mtDNA association studies, and should be also considered when weighting the DNA evidence in forensic casework, which is strongly dependent on haplotype frequencies.
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Affiliation(s)
- Ruth Barral-Arca
- Unidade de Xenética, Departamento de Anatomía Patolóxica e Ciencias Forenses, Instituto de Ciencias Forenses, Facultade de Medicina, Universidade de Santiago de Compostela, Galicia, Spain
- GenPop Research Group, Instituto de Investigaciones Sanitarias (IDIS), Hospital Clínico Universitario de Santiago, Galicia, Spain
| | - Sara Pischedda
- Unidade de Xenética, Departamento de Anatomía Patolóxica e Ciencias Forenses, Instituto de Ciencias Forenses, Facultade de Medicina, Universidade de Santiago de Compostela, Galicia, Spain
- GenPop Research Group, Instituto de Investigaciones Sanitarias (IDIS), Hospital Clínico Universitario de Santiago, Galicia, Spain
| | - Alberto Gómez-Carballa
- Unidade de Xenética, Departamento de Anatomía Patolóxica e Ciencias Forenses, Instituto de Ciencias Forenses, Facultade de Medicina, Universidade de Santiago de Compostela, Galicia, Spain
- GenPop Research Group, Instituto de Investigaciones Sanitarias (IDIS), Hospital Clínico Universitario de Santiago, Galicia, Spain
- Grupo de Investigación en Genética, Vacunas, Infecciones y Pediatría (GENVIP), Hospital Clínico Universitario and Universidade de Santiago de Compostela (USC), Galicia, Spain
| | - Ana Pastoriza
- Unidade de Xenética, Departamento de Anatomía Patolóxica e Ciencias Forenses, Instituto de Ciencias Forenses, Facultade de Medicina, Universidade de Santiago de Compostela, Galicia, Spain
| | - Ana Mosquera-Miguel
- Unidade de Xenética, Departamento de Anatomía Patolóxica e Ciencias Forenses, Instituto de Ciencias Forenses, Facultade de Medicina, Universidade de Santiago de Compostela, Galicia, Spain
| | - Manuel López-Soto
- Servicio de Biología, Instituto Nacional de Toxicología y Ciencias Forenses, Departamento de Sevilla, Sevilla, Spain
| | - Federico Martinón-Torres
- Grupo de Investigación en Genética, Vacunas, Infecciones y Pediatría (GENVIP), Hospital Clínico Universitario and Universidade de Santiago de Compostela (USC), Galicia, Spain
- Pediatric Emergency and Critical Care Division, Department of Pediatrics, Hospital Clínico Universitario de Santiago, Santiago de Compostela, Galicia, Spain
| | - Vanesa Álvarez-Iglesias
- Unidade de Xenética, Departamento de Anatomía Patolóxica e Ciencias Forenses, Instituto de Ciencias Forenses, Facultade de Medicina, Universidade de Santiago de Compostela, Galicia, Spain
| | - Antonio Salas
- Unidade de Xenética, Departamento de Anatomía Patolóxica e Ciencias Forenses, Instituto de Ciencias Forenses, Facultade de Medicina, Universidade de Santiago de Compostela, Galicia, Spain
- GenPop Research Group, Instituto de Investigaciones Sanitarias (IDIS), Hospital Clínico Universitario de Santiago, Galicia, Spain
- * E-mail:
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Messina F, Scano G, Contini I, Martínez-Labarga C, De Stefano GF, Rickards O. Linking between genetic structure and geographical distance: Study of the maternal gene pool in the Ethiopian population. Ann Hum Biol 2016; 44:53-69. [PMID: 26883569 DOI: 10.3109/03014460.2016.1155646] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Background The correlation between genetics and geographical distance has already been examined through the study of the dispersion of human populations, especially in terms of uniparental genetic markers. Aim The present work characterises, at the level of the mitochondrial DNA (mtDNA), two new samples of Amhara and Oromo populations from Ethiopia to evaluate the possible pattern of distribution for mtDNA variation and to test the hypothesis of the Isolation-by-Distance (IBD) model among African, European and Middle-Eastern populations. Subjects and methods This study analysed 173 individuals belonging to two ethnic groups of Ethiopia, Amhara and Oromo, by assaying HVS-I and HVS-II of mtDNA D-loop and informative coding region SNPs of mtDNA. Results The analysis suggests a relationship between genetic and geographic distances, affirming that the mtDNA pool of Africa, Europe and the Middle East might be coherent with the IBD model. Moreover, the mtDNA gene pools of the Sub-Saharan African and Mediterranean populations were very different. Conclusion In this study the pattern of mtDNA distribution, beginning with the Ethiopian plateau, was tested in the IBD model. It could be affirmed that, on a continent scale, the mtDNA pool of Africa, Europe and the Middle East might fall under the IBD model.
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Affiliation(s)
- Francesco Messina
- a Center of Molecular Anthropology for Ancient DNA Study, Department of Biology , University of Rome 'Tor Vergata' , Via della Ricerca Scientifica n. 1 , 00133 Rome , Italy
| | - Giuseppina Scano
- a Center of Molecular Anthropology for Ancient DNA Study, Department of Biology , University of Rome 'Tor Vergata' , Via della Ricerca Scientifica n. 1 , 00133 Rome , Italy
| | - Irene Contini
- a Center of Molecular Anthropology for Ancient DNA Study, Department of Biology , University of Rome 'Tor Vergata' , Via della Ricerca Scientifica n. 1 , 00133 Rome , Italy
| | - Cristina Martínez-Labarga
- a Center of Molecular Anthropology for Ancient DNA Study, Department of Biology , University of Rome 'Tor Vergata' , Via della Ricerca Scientifica n. 1 , 00133 Rome , Italy
| | - Gian Franco De Stefano
- a Center of Molecular Anthropology for Ancient DNA Study, Department of Biology , University of Rome 'Tor Vergata' , Via della Ricerca Scientifica n. 1 , 00133 Rome , Italy
| | - Olga Rickards
- a Center of Molecular Anthropology for Ancient DNA Study, Department of Biology , University of Rome 'Tor Vergata' , Via della Ricerca Scientifica n. 1 , 00133 Rome , Italy
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Messina F, Finocchio A, Rolfo MF, De Angelis F, Rapone C, Coletta M, Martínez-Labarga C, Biondi G, Berti A, Rickards O. Traces of forgotten historical events in mountain communities in Central Italy: A genetic insight. Am J Hum Biol 2015; 27:508-19. [PMID: 25728801 DOI: 10.1002/ajhb.22677] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2014] [Revised: 11/20/2014] [Accepted: 12/20/2014] [Indexed: 01/16/2023] Open
Abstract
OBJECTIVES Analysis of human genetic variation in mountain communities can shed light on the peopling of mountainous regions, perhaps revealing whether the remote geographic location spared them from outside invasion and preserved their gene pool from admixture. In this study, we created a model to assess genetic traces of historical events by reconstructing the paternal and maternal genetic history of seven small mountain villages in inland valleys of Central Italy. METHODS The communities were selected for their geographic isolation, attested biodemographic stability, and documented history prior to the Roman conquest. We studied the genetic structure by analyzing two hypervariable segments (HVS-I and HVS-II) of the mtDNA D-loop and several informative single nucleotide polymorphisms (SNPs) of the mtDNA coding region in 346 individuals, in addition to 17 short tandem repeats (STRs) and Y-chromosome SNPs in 237 male individuals. RESULTS For both uniparental markers, most of the haplogroups originated in Western Europe while some Near Eastern haplogroups were identified at low frequencies. However, there was an evident genetic similarity between the Central Italian samples and Near Eastern populations mainly in the male genetic pool. CONCLUSIONS The samples highlight an overall European genetic pattern both for mtDNA and Y chromosome. Notwithstanding this scenario, Y chromosome haplogroup Q, a common paternal lineage in Central/Western Asia but almost Europe-wide absent, was found, suggesting that Central Italy could have hosted a settlement from Anatolia that might be supported by cultural, topographic and genetic evidence.
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Affiliation(s)
- Francesco Messina
- Department of Biology, Center of Molecular Anthropology for ancient DNA study, University of Rome 'Tor Vergata', Via della Ricerca Scientifica n. 1, 00133, Rome, Italy
| | - Andrea Finocchio
- Department of Biology, Center of Molecular Anthropology for ancient DNA study, University of Rome 'Tor Vergata', Via della Ricerca Scientifica n. 1, 00133, Rome, Italy
| | - Mario Federico Rolfo
- Department of Historical, Philosophical and Social Sciences, Cultural and Territory Heritage, University of Rome 'Tor Vergata', Via Columbia n. 1, 00173, Rome, Italy
| | - Flavio De Angelis
- Department of Biology, Center of Molecular Anthropology for ancient DNA study, University of Rome 'Tor Vergata', Via della Ricerca Scientifica n. 1, 00133, Rome, Italy
| | - Cesare Rapone
- Carabinieri, Scientific Investigation Department, Viale di Tor di Quinto 151, 00191, Rome, Italy
| | - Martina Coletta
- Department of Biology, Center of Molecular Anthropology for ancient DNA study, University of Rome 'Tor Vergata', Via della Ricerca Scientifica n. 1, 00133, Rome, Italy
| | - Cristina Martínez-Labarga
- Department of Biology, Center of Molecular Anthropology for ancient DNA study, University of Rome 'Tor Vergata', Via della Ricerca Scientifica n. 1, 00133, Rome, Italy
| | - Gianfranco Biondi
- Department of Environmental Sciences, University of L'Aquila, Via Vetoio, 67010, L'Aquila, Italy
| | - Andrea Berti
- Carabinieri, Scientific Investigation Department, Viale di Tor di Quinto 151, 00191, Rome, Italy
| | - Olga Rickards
- Department of Biology, Center of Molecular Anthropology for ancient DNA study, University of Rome 'Tor Vergata', Via della Ricerca Scientifica n. 1, 00133, Rome, Italy
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Alvarez L, Ciria E, Marques SL, Santos C, Aluja MP. Y-chromosome analysis in a Northwest Iberian population: unraveling the impact of Northern African lineages. Am J Hum Biol 2014; 26:740-6. [PMID: 25123837 DOI: 10.1002/ajhb.22602] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2013] [Revised: 06/03/2014] [Accepted: 06/15/2014] [Indexed: 11/09/2022] Open
Abstract
OBJECTIVES To provide new clues about the genetic origin, composition and structure of the population of the Spanish province of Zamora, with an emphasis on the genetic impact of the period of Islamic rule in the Iberian Peninsula. METHODS Polymorphisms in the paternally inherited Y-chromosome, Single Nucleotide Polymorphisms and Short Tandem Repeats, were analyzed in 235 unrelated males born in six different regions in the Zamora province. RESULTS A relatively homogenous Y-chromosome haplogroup composition was observed in the Zamora province. Haplogroups R1b1-P25 and I-M170, widespread in European populations, accounted for 64.9% of the total sample. Moreover, all of the observed African lineages, accounting for 10.2% of the total variability, belonged to haplogroups having Northwest African origin (E1b1b1b-M81, E1b1b1a-β-M78, and J1-M267). CONCLUSIONS No differences between regions or sub-structure due to geographical boundaries were detected. The specific Northwest African male lineages observed contrast with the mitochondrial DNA data, where the majority of African lineages were found to be sub-Saharan. This work made it possible to study the impact of recent historical events in the male gene pool in the province of Zamora in Spain.
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Affiliation(s)
- Luis Alvarez
- Unitat Antropologia Biològica, Universitat Autònoma de Barcelona, 08193, Bellaterra, Barcelona, Spain; IPATIMUP, Institute of Molecular Pathology and Immunology of the University of Porto, 4200-465, Porto, Portugal
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Pinto JC, Pereira V, Marques SL, Amorim A, Alvarez L, Prata MJ. Mirandese language and genetic differentiation in Iberia: a study using X chromosome markers. Ann Hum Biol 2014; 42:20-5. [DOI: 10.3109/03014460.2014.944215] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- J. C. Pinto
- Faculty of Sciences, University of Porto, Porto, Portugal,
- IPATIMUP, Institute of Molecular Pathology and Immunology, University of Porto, Porto, Portugal,
- CIBIO, Research Center in Biodiversity and Genetic Resources, University of Porto, Vairão, Portugal, and
| | - V. Pereira
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - S. L. Marques
- Faculty of Sciences, University of Porto, Porto, Portugal,
- IPATIMUP, Institute of Molecular Pathology and Immunology, University of Porto, Porto, Portugal,
| | - A. Amorim
- Faculty of Sciences, University of Porto, Porto, Portugal,
- IPATIMUP, Institute of Molecular Pathology and Immunology, University of Porto, Porto, Portugal,
| | - L. Alvarez
- IPATIMUP, Institute of Molecular Pathology and Immunology, University of Porto, Porto, Portugal,
| | - M. J. Prata
- Faculty of Sciences, University of Porto, Porto, Portugal,
- IPATIMUP, Institute of Molecular Pathology and Immunology, University of Porto, Porto, Portugal,
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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: 0.6] [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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Echoes from Sepharad: signatures on the maternal gene pool of crypto-Jewish descendants. Eur J Hum Genet 2014; 23:693-9. [PMID: 25074462 DOI: 10.1038/ejhg.2014.140] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2014] [Revised: 06/11/2014] [Accepted: 06/20/2014] [Indexed: 11/08/2022] Open
Abstract
The majority of genetic studies on Jewish populations have been focused on Ashkenazim, and genetic data from the Sephardic original source, the Iberian Peninsula, are particularly scarce. Regarding the mitochondrial genome, the available information is limited to a single Portuguese village, Belmonte, where just two different lineages (a single one corresponding to 93.3%) were found in 30 individuals. Aiming at disclosing the ancestral maternal background of the Portuguese Jewry, we enlarged the sampling to other crypto-Jewish descendants in the Bragança district (NE Portugal). Fifty-seven complete mtDNA genomes were newly sequenced and - in contrast with Belmonte - a high level of diversity was found, with five haplogroups (HV0b, N1, T2b11, T2e and U2e) being putatively identified as Sephardic founding lineages. Therefore - in sharp contrast with Belmonte - these communities have managed to escape the expected inbreeding effects caused by centuries of religious repression and have kept a significant proportion of the Sephardic founder gene pool. This deeper analysis of the surviving Sephardic maternal lineages allowed a much more comprehensive and detailed perspective on the origins and survival of the Sephardic genetic heritage. In line with previously published results on Sephardic paternal lineages, our findings also show a surprising resistance to the erosion of genetic diversity in the maternal lineages.
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Hernández CL, Reales G, Dugoujon JM, Novelletto A, Rodríguez JN, Cuesta P, Calderón R. Human maternal heritage in Andalusia (Spain): its composition reveals high internal complexity and distinctive influences of mtDNA haplogroups U6 and L in the western and eastern side of region. BMC Genet 2014; 15:11. [PMID: 24460736 PMCID: PMC3905667 DOI: 10.1186/1471-2156-15-11] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2013] [Accepted: 01/17/2014] [Indexed: 12/03/2022] Open
Abstract
Background The archeology and history of the ancient Mediterranean have shown that this sea has been a permeable obstacle to human migration. Multiple cultural exchanges around the Mediterranean have taken place with presumably population admixtures. A gravitational territory of those migrations has been the Iberian Peninsula. Here we present a comprehensive analysis of the maternal gene pool, by means of control region sequencing and PCR-RFLP typing, of autochthonous Andalusians originating from the coastal provinces of Huelva and Granada, located respectively in the west and the east of the region. Results The mtDNA haplogroup composition of these two southern Spanish populations has revealed a wide spectrum of haplogroups from different geographical origins. The registered frequencies of Eurasian markers, together with the high incidence and diversification of African maternal lineages (15% of the total mitochondrial variability) among Huelva Andalusians when compared to its eastwards relatives of Granada and other Iberian populations, constitute relevant findings unknown up-to-date on the characteristics of mtDNA within Andalusia that testifies a female population substructure. Therefore, Andalusia must not be considered a single, unique population. Conclusions The maternal legacy among Andalusians reflects distinctive local histories, pointing out the role of the westernmost territory of Peninsular Spain as a noticeable recipient of multiple and diverse human migrations. The obtained results underline the necessity of further research on genetic relationships in both sides of the western Mediterranean, using carefully collected samples from autochthonous individuals. Many studies have focused on recent North African gene flow towards Iberia, yet scientific attention should be now directed to thoroughly study the introduction of European genes in northwest Africa across the sea, in order to determine its magnitude, timescale and methods, and to compare them to those terrestrial movements from eastern Africa and southwestern Asia.
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Affiliation(s)
| | | | | | | | | | | | - Rosario Calderón
- Departamento de Zoología y Antropología Física, Facultad de Biología, Universidad Complutense, Madrid, Spain.
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Pardiñas AF, Roca A, García-Vazquez E, López B. Evaluation of large-scale genetic structure in complex demographic and historical scenarios: the mitochondrial DNA and Y-chromosome pools of the Iberian Atlantic façade. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2014; 153:617-26. [PMID: 24375152 DOI: 10.1002/ajpa.22461] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2013] [Accepted: 12/12/2013] [Indexed: 11/11/2022]
Abstract
Genetic structural patterns of human populations are usually a combination of long-term evolutionary forces and short-term social, cultural, and demographic processes. Recently, using mitochondrial DNA and Y-chromosome loci, various studies in northern Spain have found evidence that the geographical distribution of Iron Age tribal peoples might have influenced current patterns of genetic structuring in several autochthonous populations. Using the wealth of data that are currently available from the whole territory of the Iberian Peninsula, we have evaluated its genetic structuring in the spatial scale of the Atlantic façade. Hierarchical tree modeling procedures, combined with a classic analysis of molecular variance (AMOVA), were used to model known sociocultural divisions from the third century BCE to the eighth century CE, contrasting them with uniparental marker data. Our results show that, while mountainous and abrupt areas of the Iberian North bear the signals of long-term isolation in their maternal and paternal gene pools, the makeup of the Atlantic façade as a whole can be related to tribal population groups that predate the Roman conquest of the Peninsula. The maintenance through time of such a structure can be related to the numerous geographic barriers of the Iberian mainland, which have historically conditioned its settlement patterns and the occurrence of genetic drift processes.
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Affiliation(s)
- Antonio F Pardiñas
- Departamento de Biología de Organismos y Sistemas, Universidad de Oviedo, Asturias, Spain
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Frequency and pattern of heteroplasmy in the complete human mitochondrial genome. PLoS One 2013; 8:e74636. [PMID: 24098342 PMCID: PMC3788774 DOI: 10.1371/journal.pone.0074636] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2013] [Accepted: 08/03/2013] [Indexed: 11/19/2022] Open
Abstract
Determining the levels of human mitochondrial heteroplasmy is of utmost importance in several fields. In spite of this, there are currently few published works that have focused on this issue. In order to increase the knowledge of mitochondrial DNA (mtDNA) heteroplasmy, the main goal of this work is to investigate the frequency and the mutational spectrum of heteroplasmy in the human mtDNA genome. To address this, a set of nine primer pairs designed to avoid co-amplification of nuclear DNA (nDNA) sequences of mitochondrial origin (NUMTs) was used to amplify the mitochondrial genome in 101 individuals. The analysed individuals represent a collection with a balanced representation of genders and mtDNA haplogroup distribution, similar to that of a Western European population. The results show that the frequency of heteroplasmic individuals exceeds 61%. The frequency of point heteroplasmy is 28.7%, with a widespread distribution across the entire mtDNA. In addition, an excess of transitions in heteroplasmy were detected, suggesting that genetic drift and/or selection may be acting to reduce its frequency at population level. In fact, heteroplasmy at highly stable positions might have a greater impact on the viability of mitochondria, suggesting that purifying selection must be operating to prevent their fixation within individuals. This study analyses the frequency of heteroplasmy in a healthy population, carrying out an evolutionary analysis of the detected changes and providing a new perspective with important consequences in medical, evolutionary and forensic fields.
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Linguistic isolates in Portugal: insights from the mitochondrial DNA pattern. Forensic Sci Int Genet 2013; 7:618-623. [PMID: 24041913 DOI: 10.1016/j.fsigen.2013.08.009] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2013] [Revised: 08/15/2013] [Accepted: 08/21/2013] [Indexed: 11/23/2022]
Abstract
Miranda do Douro, located in the northeastern region of Portugal, has notable characteristics not only from a geographic or naturalistic point of view, but also from a cultural perspective. A remarkable one is the coexistence of two different languages: Portuguese and Mirandese, the second being an Astur-Leonese dialect. The current persistence of the Astur-Leonese dialect in this population falls on the singularity of the region: relative isolation, implying difficulties to communicate with other Portuguese regions, while the same location facilitated the establishment of social and commercial relationships with adjacent Spanish territories, origin of the Astur-Leonese language. The objective of this study was to characterize the population from Miranda through the analysis of maternal lineages in order to evaluate whether its mitochondrial DNA diversity fitted the patterns previously reported for other populations from the Iberian Peninsula. Viewing that, the entire control region of mitochondrial DNA from 121 individuals was examined. Miranda showed a haplogroup composition usual for a Western European population, in the sense that as high as 63.6% of sequences belonged to macro-haplogroup R0. Lineages ascribed to have an African (L2a and L1b) origin, were detected, but reaching an amount commonly found in Portugal. Miranda also presented a few haplogroups typically found in Jewish populations, while rarely observed in other Iberian populations. The finding can be explained by gene flow with crypto-Jew communities that since long are known to be established in the region where Miranda is located. In Miranda, both genetic and nucleotide diversities presented low values (0.9292 ± 0.0180 and 0.01101 ± 0.00614 respectively) when compared to populations from its micro-geographical framework, which constitute a sign of population isolation that certainly provided conditions for the survival of the Astur-Leonese dialect in the region.
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Pardiñas AF, Roca A, Garcia-Vazquez E, Lopez B. Mitochondrial diversity patterns and the Magdalenian resettlement of Europe: new insights from the edge of the Franco-Cantabrian refuge. J Hum Genet 2012; 57:717-26. [PMID: 22895249 DOI: 10.1038/jhg.2012.100] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Phylogeography of the mitochondrial lineages commonly found in Western Europe can be interpreted in the light of a postglacial resettlement of the continent. The center of this proposal lies in the Franco-Cantabrian glacial refuge, located in the northern Iberian Peninsula and Southwestern France. Recently, this interpretation has been confronted by the unexpected patterns of diversity found in some European haplogroups. To shed new lights on this issue, research on Iberian populations is crucial if events behind the actual genetics of the European continent are to be untangled. In this regard, the region of Asturias has not been extensively studied, despite its convoluted history with prolonged periods of isolation. As mitochondrial DNA is a kind of data that has been commonly used in human population genetics, we conducted a thorough regional study in which we collected buccal swabs from 429 individuals with confirmed Asturian ancestry. The joint analysis of these sequences with a large continent-wide database and previously published diversity patterns allowed us to discuss a new explanation for the population dynamics inside the Franco-Cantabrian area, based on range expansion theory. This approximation to previously contradictory findings has made them compatible with most proposals about the postglacial resettlement of Western Europe.
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Affiliation(s)
- Antonio F Pardiñas
- Departamento de Biología de Organismos y Sistemas, Universidad de Oviedo, Oviedo, Spain
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Sans M, Figueiro G, Ackermann E, Barreto I, Egaña A, Bertoni B, Poittevin-Gilmet E, Maytia D, Hidalgo PC. Mitochondrial DNA in Basque descendants from the city of Trinidad, Uruguay: Uruguayan- or Basque-like population? Hum Biol 2011; 83:55-70. [PMID: 21453004 DOI: 10.3378/027.083.0104] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Like other countries in the Americas, during its colonization Uruguay was the recipient of immigrants from several ethnic groups from Europe, as well as of enslaved Africans. After its independence in 1830, Basques were the first group of Europeans to arrive in the country. In this paper, we aim to contribute to the understanding of the process of integration of these migratory waves into the Uruguayan society. For that purpose, individuals of Basque origin from the city of Trinidad, Uruguay, were chosen to participate in this study. Particularly, we wanted to determine if Basque descendants in Uruguay remained relatively isolated or if they mixed with other ethnic groups. Mitochondrial DNA (mtDNA) of 60 self-identified Basque descendants, taken from a larger sample of subjects with Basque ancestors, was analyzed. The origin of mtDNA haplogroups was 77.8% European, 20.4% Amerindian, and 1.8% African, showing similar frequencies to other Uruguayan regions. Very few sequences showed a clear Basque origin, although other sources such as the Canary Islands are likely. Moreover, genetic distances clearly show that Basque descendants are genetically closer to other Uruguayan groups than to European populations, including Basques. It is possible to conclude that Basques and their descendants in the region of Trinidad did not remain isolated and that their marriage behavior was similar to that of other Uruguayan populations. However, to have a more accurate picture of the way Basques intermarried with other populations in Uruguay, new analyses are needed that take into account paternal lineages as well as biparental genetic markers.
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Affiliation(s)
- M Sans
- Department of Biological Anthropology, Facultad de Humanidades y Ciencias de la Educación, Universidad de la República, 11200 Montevideo, Uruguay
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Davis MC, Novak SJ, Hampikian G. Mitochondrial DNA analysis of an immigrant Basque population: loss of diversity due to founder effects. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2010; 144:516-25. [PMID: 21404229 DOI: 10.1002/ajpa.21432] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2010] [Accepted: 09/27/2010] [Indexed: 01/21/2023]
Abstract
The Basques have a well-documented history of migration and settlement in the Americas, and they often retain cultural identity across generations. Numerous genetic studies have been carried out on European Basques; thus, immigrant Basques are an ideal population for investigating the genetic consequences of a recent human migration event. We have sampled 53 unrelated individuals with Basque ancestry in Boise, Idaho and determined the mitochondrial DNA (mtDNA) sequence variation of the first and second hypervariable regions. Thirty-six mtDNA haplotypes were detected in our sample. We found evidence of genetic changes consistent with founder effects, which is compatible with the known history of migration. Compared with the European Basque population, the immigrant Basques are significantly different in terms of haplogroup frequency distribution and diversity. They have a lower measure of weighted intralineage mean pairwise diversity (WIMP) and greater genetic distance from other European populations. These data indicate that this immigrant Basque population has experienced a reduction in genetic diversity compared with the putative source population. However, this loss of diversity is not detectable using indices of demographic history such as Tajima's D and Fu's F. This study represents the first description of mtDNA diversity in an immigrant Basque population, and our findings indicate that founder effects accompanying this relatively recent migration event have shaped the genetic diversity of this population.
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Affiliation(s)
- Michael C Davis
- Department of Biological Sciences, Boise State University, Boise, ID 83725, USA
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