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Fibla J, Maceda I, Laplana M, Guerrero M, Álvarez MM, Burgueño J, Camps A, Fàbrega J, Felisart J, Grané J, Remón JL, Serra J, Moral P, Lao O. The power of geohistorical boundaries for modeling the genetic background of human populations: The case of the rural catalan Pyrenees. Front Genet 2023; 13:1100440. [PMID: 36704333 PMCID: PMC9871830 DOI: 10.3389/fgene.2022.1100440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Accepted: 12/12/2022] [Indexed: 01/11/2023] Open
Abstract
The genetic variation of the European population at a macro-geographic scale follows genetic gradients which reflect main migration events. However, less is known about factors affecting mating patterns at a micro-geographic scale. In this study we have analyzed 726,718 autosomal single nucleotide variants in 435 individuals from the catalan Pyrenees covering around 200 km of a vast and abrupt region in the north of the Iberian Peninsula, for which we have information about the geographic origin of all grand-parents and parents. At a macro-geographic scale, our analyses recapitulate the genetic gradient observed in Spain. However, we also identified the presence of micro-population substructure among the sampled individuals. Such micro-population substructure does not correlate with geographic barriers such as the expected by the orography of the considered region, but by the bishoprics present in the covered geographic area. These results support that, on top of main human migrations, long ongoing socio-cultural factors have also shaped the genetic diversity observed at rural populations.
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Affiliation(s)
- Joan Fibla
- Department of Basic Medical Sciences, University of Lleida, Lleida, Spain,Institute of Biomedical Research of Lleida (IRBLleida), Lleida, Spain,*Correspondence: Joan Fibla, ; Oscar Lao,
| | - Iago Maceda
- CNAG-CRG, Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Marina Laplana
- Department of Basic Medical Sciences, University of Lleida, Lleida, Spain
| | - Montserrat Guerrero
- Department of Geography and Sociology, University of Lleida. Pl. Víctor Siurana, Lleida, Spain
| | - Miguel Martín Álvarez
- Genome Data Science, Institute for Research in Biomedicine (IRB Barcelona), Barcelona Institute for Science and Technology, Barcelona, Spain
| | - Jesús Burgueño
- Department of Geography and Sociology, University of Lleida. Pl. Víctor Siurana, Lleida, Spain
| | | | - Jordi Fàbrega
- Fundació Sant Hospital La Seu d’Urgell, La Seu d'Urgell, Spain
| | | | - Joan Grané
- Hospital de Campdevànol, Campdevànol, Girona, Spain
| | - José Luis Remón
- Servei d’atenció primària Lleida Nord, Gerència Territorial Alt Pirineu i Aran, Institut Català de la Salut, Tremp, Spain
| | - Jordi Serra
- Laboratori d’Anàlisis Clíniques, Hospital Comarcal del Pallars, Tremp, Spain
| | - Pedro Moral
- Department of Evolutionary Biology, Ecology and Environmental Sciences, Faculty of Biology, Biodiversity Research Institute, University of Barcelona, Barcelona, Spain
| | - Oscar Lao
- CNAG-CRG, Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, Barcelona, Spain,*Correspondence: Joan Fibla, ; Oscar Lao,
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Resano M, Zanetti D, Esteban EM, Moral P. X-Chromosome Alu Insertions in Bahía Blanca, Argentina: Assessment of Population Information from Varied Genetic Markers and Usefulness of X-Chromosome Markers to Trace Sex-Biased Parental Contributions. Hum Biol 2022. [DOI: 10.1353/hub.2017.0002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Novillo A, Gaibar M, Romero-Lorca A, Chaabani H, Amir N, Moral P, Esteban ME, Fernández-Santander A. UDP-glucuronosyltransferase genetic variation in North African populations: a comparison with African and European data. Ann Hum Biol 2019; 45:516-523. [PMID: 30616396 DOI: 10.1080/03014460.2018.1559354] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
BACKGROUND Genetic variation in glucuronosyltransferases (UGT) is crucial in drug metabolism and risk of some diseases. AIM To examine genetic variation in UGT in North African populations. SUBJECTS AND METHODS Allele frequencies of SNPs UGT1A424Thr, UGT1A448Val, UGT2B1585Tyr, UGT2B15523Thr and UGT2B17 CNV deletion from Morocco, Algeria, Tunisia and Libya were compared to European and Sub-Saharan populations. RESULTS North Africans are the group with the highest genetic heterogeneity given by internal differences in the occurrence of UGT2B17 deletion, UGT1A448Val and UGT1A4 haplotypes. UGT2B15 SNPs differentiate Sub-Saharans from the rest of the populations. CONCLUSION North African populations show a high frequency of carriers of UGT2B15523Thr, a variant linked to an increased risk of prostate cancer. High Atlas Moroccans and Algerians show low frequency of UGT2B17del, a variant associated with high concentrations of testosterone and oestradiol.
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Affiliation(s)
- Apolonia Novillo
- a Basic Biomedical Sciences Department , Universidad Europea de Madrid , Madrid , Spain
| | - María Gaibar
- a Basic Biomedical Sciences Department , Universidad Europea de Madrid , Madrid , Spain
| | - Alicia Romero-Lorca
- a Basic Biomedical Sciences Department , Universidad Europea de Madrid , Madrid , Spain
| | - Hassen Chaabani
- b Faculty of Pharmacy , University of Monastir , Monastir , Tunisia
| | - Nadir Amir
- c Laboratoire de Biochimie Appliquée, 5 Faculté des Sciences de la Nature et de la Vie , Université de Bejaia , Bejaia , Algeria
| | - Pedro Moral
- d Section of Zoology and Biological Anthropology, Department of Evolutionary Biology, Ecology and Environmental Sciences, Faculty of Biology , Universitat de Barcelona , Barcelona , Spain.,e Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona , Barcelona , Spain
| | - M Esther Esteban
- d Section of Zoology and Biological Anthropology, Department of Evolutionary Biology, Ecology and Environmental Sciences, Faculty of Biology , Universitat de Barcelona , Barcelona , Spain.,e Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona , Barcelona , Spain
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Chacón-Duque JC, Adhikari K, Fuentes-Guajardo M, Mendoza-Revilla J, Acuña-Alonzo V, Barquera R, Quinto-Sánchez M, Gómez-Valdés J, Everardo Martínez P, Villamil-Ramírez H, Hünemeier T, Ramallo V, Silva de Cerqueira CC, Hurtado M, Villegas V, Granja V, Villena M, Vásquez R, Llop E, Sandoval JR, Salazar-Granara AA, Parolin ML, Sandoval K, Peñaloza-Espinosa RI, Rangel-Villalobos H, Winkler CA, Klitz W, Bravi C, Molina J, Corach D, Barrantes R, Gomes V, Resende C, Gusmão L, Amorim A, Xue Y, Dugoujon JM, Moral P, González-José R, Schuler-Faccini L, Salzano FM, Bortolini MC, Canizales-Quinteros S, Poletti G, Gallo C, Bedoya G, Rothhammer F, Balding D, Hellenthal G, Ruiz-Linares A. Latin Americans show wide-spread Converso ancestry and imprint of local Native ancestry on physical appearance. Nat Commun 2018; 9:5388. [PMID: 30568240 PMCID: PMC6300600 DOI: 10.1038/s41467-018-07748-z] [Citation(s) in RCA: 90] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Accepted: 11/19/2018] [Indexed: 12/15/2022] Open
Abstract
Historical records and genetic analyses indicate that Latin Americans trace their ancestry mainly to the intermixing (admixture) of Native Americans, Europeans and Sub-Saharan Africans. Using novel haplotype-based methods, here we infer sub-continental ancestry in over 6,500 Latin Americans and evaluate the impact of regional ancestry variation on physical appearance. We find that Native American ancestry components in Latin Americans correspond geographically to the present-day genetic structure of Native groups, and that sources of non-Native ancestry, and admixture timings, match documented migratory flows. We also detect South/East Mediterranean ancestry across Latin America, probably stemming mostly from the clandestine colonial migration of Christian converts of non-European origin (Conversos). Furthermore, we find that ancestry related to highland (Central Andean) versus lowland (Mapuche) Natives is associated with variation in facial features, particularly nose morphology, and detect significant differences in allele frequencies between these groups at loci previously associated with nose morphology in this sample.
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Affiliation(s)
- Juan-Camilo Chacón-Duque
- Department of Genetics, Evolution and Environment and UCL Genetics Institute, University College London, London, WC1E 6BT, UK
| | - Kaustubh Adhikari
- Department of Genetics, Evolution and Environment and UCL Genetics Institute, University College London, London, WC1E 6BT, UK
| | - Macarena Fuentes-Guajardo
- Department of Genetics, Evolution and Environment and UCL Genetics Institute, University College London, London, WC1E 6BT, UK
- Departamento de Tecnología Médica, Facultad de Ciencias de la Salud, Universidad de Tarapacá, Arica, 1000009, Chile
| | - Javier Mendoza-Revilla
- Department of Genetics, Evolution and Environment and UCL Genetics Institute, University College London, London, WC1E 6BT, UK
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, 31, Peru
| | - Victor Acuña-Alonzo
- Department of Genetics, Evolution and Environment and UCL Genetics Institute, University College London, London, WC1E 6BT, UK
- Molecular Genetics Laboratory, Escuela Nacional de Antropología e Historia, Mexico City, 14030, Mexico
| | - Rodrigo Barquera
- Molecular Genetics Laboratory, Escuela Nacional de Antropología e Historia, Mexico City, 14030, Mexico
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, 07745, Germany
| | - Mirsha Quinto-Sánchez
- Ciencia Forense, Facultad de Medicina, Universidad Nacional Autónoma de México, Mexico City, 04510, Mexico
| | - Jorge Gómez-Valdés
- Posgrado en Antropología Física, Escuela Nacional de Antropología e Historia, Mexico City, 14030, Mexico
| | - Paola Everardo Martínez
- Posgrado en Antropología, Universidad Nacional Autónoma de México, Mexico City, 04510, Mexico
| | - Hugo Villamil-Ramírez
- Unidad de Genómica de Poblaciones Aplicada a la Salud, Facultad de Química, Universidad Nacional Autónoma de México e Instituto Nacional de Medicina Genómica, Mexico City, 04510, Mexico
| | - Tábita Hünemeier
- Departamento de Genética e Biología Evolutiva, Instituto de Biociências, Universidade de São Paulo, Sao Paulo, 05508-090, Brazil
| | - Virginia Ramallo
- Instituto Patagónico de Ciencias Sociales y Humanas-Centro Nacional Patagónico, CONICET, Puerto Madryn, U912OACD, Argentina
- Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, 91501-970, Brazil
| | - Caio C Silva de Cerqueira
- Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, 91501-970, Brazil
| | - Malena Hurtado
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, 31, Peru
| | - Valeria Villegas
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, 31, Peru
| | - Vanessa Granja
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, 31, Peru
| | - Mercedes Villena
- Instituto Boliviano de Biología de Altura (IBBA), Universidad Mayor de San Andrés (UMSA), La Paz, 2070, Bolivia
| | - René Vásquez
- Instituto Boliviano de Biología de Altura (IBBA), Universidad Autónoma Tomás Frías, Potosí, 53820, Bolivia
| | - Elena Llop
- Programa de Genetica Humana, ICBM, Facultad de Medicina, Universidad de Chile, Santiago, 1027, Chile
| | - José R Sandoval
- Facultad de Medicina Humana, Universidad de San Martín de Porres, Lima, 12, Peru
| | | | - Maria-Laura Parolin
- Instituto de Diversidad y Evolución Austral (IDEAus), Centro Nacional Patagónico, CONICET, Puerto Madryn, U912OACD, Argentina
| | - Karla Sandoval
- National Laboratory of Genomics and Biodiversity (LANGEBIO), CINVESTAV, Irapuato, 36821, Mexico
| | - Rosenda I Peñaloza-Espinosa
- Department of Biological Systems, Division of Biological and Health Sciences, Universidad Autónoma Metropolitana-Xochimilco, Mexico City, 04960, Mexico
| | - Hector Rangel-Villalobos
- Instituto de Investigación en Genética Molecular, Universidad de Guadalajara, Ocotlán, 1115, Mexico
| | - Cheryl A Winkler
- Basic Research Laboratory, National Cancer Institute, Frederick National Laboratory, Frederick, MD, 21702, USA
| | - William Klitz
- Integrative Biology, University of California, Berkeley, CA, 94720, USA
| | - Claudio Bravi
- Instituto Multidisciplinario de Biología Celular, CONICET, La Plata, B1906APO, Argentina
| | - Julio Molina
- Centro de Investigaciones Biomédicas de Guatemala, Ciudad de Guatemala, 01011, Guatemala
| | - Daniel Corach
- Servicio de Huellas Digitales Genéticas and CONICET, Universidad de Buenos Aires, Buenos Aires, C1113AAD, Argentina
| | - Ramiro Barrantes
- Escuela de Biología, Universidad de Costa Rica, San José, 2060, Costa Rica
| | - Verónica Gomes
- Instituto de Patologia e Imunologia Molecular da Universidade do Porto (IPATIMUP), Porto, 4200-135, Portugal
- Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto, Porto, 4200-135, Portugal
| | - Carlos Resende
- Instituto de Patologia e Imunologia Molecular da Universidade do Porto (IPATIMUP), Porto, 4200-135, Portugal
- Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto, Porto, 4200-135, Portugal
| | - Leonor Gusmão
- Instituto de Patologia e Imunologia Molecular da Universidade do Porto (IPATIMUP), Porto, 4200-135, Portugal
- Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto, Porto, 4200-135, Portugal
- DNA Diagnostic Laboratory (LDD), Universidade do Estado do Rio de Janeiro, Rio de Janeiro, 23968-000, Brazil
| | - Antonio Amorim
- Instituto de Patologia e Imunologia Molecular da Universidade do Porto (IPATIMUP), Porto, 4200-135, Portugal
- Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto, Porto, 4200-135, Portugal
- Faculdade de Ciências, Universidade do Porto, Porto, 4169-007, Portugal
| | - Yali Xue
- The Wellcome Trust Sanger Institute, Hinxton, CB10 1SA, UK
| | - Jean-Michel Dugoujon
- Centre National de la Recherche Scientifique, Université Toulouse 3 Paul Sabatier, Toulouse, 31330, France
| | - Pedro Moral
- Departamento de Biología Evolutiva, Ecología y Ciencias Ambientales, Universitat de Barcelona, Barcelona, 08007, Spain
| | - Rolando González-José
- Instituto Patagónico de Ciencias Sociales y Humanas-Centro Nacional Patagónico, CONICET, Puerto Madryn, U912OACD, Argentina
| | - Lavinia Schuler-Faccini
- Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, 91501-970, Brazil
| | - Francisco M Salzano
- Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, 91501-970, Brazil
| | - Maria-Cátira Bortolini
- Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, 91501-970, Brazil
| | - Samuel Canizales-Quinteros
- Unidad de Genómica de Poblaciones Aplicada a la Salud, Facultad de Química, Universidad Nacional Autónoma de México e Instituto Nacional de Medicina Genómica, Mexico City, 04510, Mexico
| | - Giovanni Poletti
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, 31, Peru
| | - Carla Gallo
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, 31, Peru
| | - Gabriel Bedoya
- Genética Molecular (GENMOL), Universidad de Antioquia, Medellín, 5001000, Colombia
| | - Francisco Rothhammer
- Programa de Genetica Humana, ICBM, Facultad de Medicina, Universidad de Chile, Santiago, 1027, Chile
- Instituto de Alta Investigación, Universidad de Tarapacá, Arica, 1000009, Chile
| | - David Balding
- Department of Genetics, Evolution and Environment and UCL Genetics Institute, University College London, London, WC1E 6BT, UK
- Schools of BioSciences and Mathematics & Statistics, University of Melbourne, Melbourne, VIC, 3010, Australia
| | - Garrett Hellenthal
- Department of Genetics, Evolution and Environment and UCL Genetics Institute, University College London, London, WC1E 6BT, UK.
| | - Andrés Ruiz-Linares
- Ministry of Education Key Laboratory of Contemporary Anthropology and Collaborative Innovation Center of Genetics and Development, School of Life Sciences and Human Phenome Institute, Fudan University, Shanghai, 200433, China.
- Aix-Marseille Univ, CNRS, EFS, ADES, Marseille, 13007, France.
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Gutiérrez JC, Merino S, de la Calle P, Perrino C, Represa M, Moral P. Correlation of preoperative findings in computed axial tomography with the presence of difficult airway in patients undergoing head and neck otorhinolaryngological surgery. ACTA ACUST UNITED AC 2018; 65:252-257. [PMID: 29502798 DOI: 10.1016/j.redar.2018.01.013] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Revised: 01/18/2018] [Accepted: 01/19/2018] [Indexed: 11/28/2022]
Abstract
OBJECTIVES To establish a correlation between 4 measurements made on preoperative computed axial tomography and the presence of difficult airway, as well as its clinical prediction in patients undergoing otorhinolaryngological surgery. MATERIAL AND METHODS A retrospective, observational study was carried out using the information gathered from the clinical notes of 104 patients undergoing general anaesthesia and endotracheal intubation for oncological otorhinolaryngological surgery over a period of 36 months. Based on the findings in the preoperative imaging tests, a multivariate logistic regression analysis was performed, where the dependent variable was the presence of extreme grades of visualization of the glottis visualisation (Cormack III-IV) or the presence of predictors of difficult intubation (Mallampati III-IV). This resulted in a total of 4 tomographic and clinical factors of difficult airway being introduced in this model. RESULTS In the Cormack III-IV group, the results were not statistically significant in the multivariate model when compared to the tomography predictors, distance from epiglottis to posterior pharyngeal wall (95% CI; 0.030 - 2.31, P<.05), and the distance from the base of the tongue to the posterior pharyngeal wall (95% CI; 0.018-1.37, P<.05). In the Mallampati III-IV group, in the multivariate model only the distance from the vocal cords to the posterior pharyngeal wall showed clinically significant results (95% CI; 0.104 - 8.53, P<.05). CONCLUSIONS In the approach to the airway, reliance on predictors is based on physical examination to anticipate situations that put oxygenation and ventilation of the patients at risk. There are still insufficient data to recommend imaging tests in this area, however it seems that in the future they may be added to the diagnostic performance of physical examination as predictors of difficult airway.
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Affiliation(s)
- J C Gutiérrez
- Servicio de Anestesiología y Reanimación, Hospital Clínico San Carlos, Madrid, España.
| | - S Merino
- Servicio de Radiodiagnóstico, Hospital Clínico San Carlos, Madrid, España
| | - P de la Calle
- Servicio de Anestesiología y Reanimación, Hospital Clínico San Carlos, Madrid, España
| | - C Perrino
- Servicio de Anestesiología y Reanimación, Hospital Clínico San Carlos, Madrid, España
| | - M Represa
- Servicio de Anestesiología y Reanimación, Hospital Clínico San Carlos, Madrid, España
| | - P Moral
- Servicio de Anestesiología y Reanimación, Hospital Clínico San Carlos, Madrid, España
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D’Atanasio E, Trombetta B, Bonito M, Finocchio A, Di Vito G, Seghizzi M, Romano R, Russo G, Paganotti GM, Watson E, Coppa A, Anagnostou P, Dugoujon JM, Moral P, Sellitto D, Novelletto A, Cruciani F. The peopling of the last Green Sahara revealed by high-coverage resequencing of trans-Saharan patrilineages. Genome Biol 2018; 19:20. [PMID: 29433568 PMCID: PMC5809971 DOI: 10.1186/s13059-018-1393-5] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2017] [Accepted: 01/19/2018] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND Little is known about the peopling of the Sahara during the Holocene climatic optimum, when the desert was replaced by a fertile environment. RESULTS In order to investigate the role of the last Green Sahara in the peopling of Africa, we deep-sequence the whole non-repetitive portion of the Y chromosome in 104 males selected as representative of haplogroups which are currently found to the north and to the south of the Sahara. We identify 5,966 mutations, from which we extract 142 informative markers then genotyped in about 8,000 subjects from 145 African, Eurasian and African American populations. We find that the coalescence age of the trans-Saharan haplogroups dates back to the last Green Sahara, while most northern African or sub-Saharan clades expanded locally in the subsequent arid phase. CONCLUSIONS Our findings suggest that the Green Sahara promoted human movements and demographic expansions, possibly linked to the adoption of pastoralism. Comparing our results with previously reported genome-wide data, we also find evidence for a sex-biased sub-Saharan contribution to northern Africans, suggesting that historical events such as the trans-Saharan slave trade mainly contributed to the mtDNA and autosomal gene pool, whereas the northern African paternal gene pool was mainly shaped by more ancient events.
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Affiliation(s)
- Eugenia D’Atanasio
- Dipartimento di Biologia e Biotecnologie “C. Darwin”, Sapienza Università di Roma, Rome, Italy
- Istituto Pasteur-Fondazione Cenci Bolognetti, Sapienza Università di Roma, Rome, Italy
| | - Beniamino Trombetta
- Dipartimento di Biologia e Biotecnologie “C. Darwin”, Sapienza Università di Roma, Rome, Italy
| | - Maria Bonito
- Dipartimento di Biologia e Biotecnologie “C. Darwin”, Sapienza Università di Roma, Rome, Italy
| | - Andrea Finocchio
- Dipartimento di Biologia, Università di Roma “Tor Vergata”, Rome, Italy
| | - Genny Di Vito
- Dipartimento di Biologia e Biotecnologie “C. Darwin”, Sapienza Università di Roma, Rome, Italy
| | - Mara Seghizzi
- Dipartimento di Biologia e Biotecnologie “C. Darwin”, Sapienza Università di Roma, Rome, Italy
| | - Rita Romano
- Dipartimento di Sanità Pubblica e Malattie Infettive, Sapienza Università di Roma, Rome, Italy
| | - Gianluca Russo
- Dipartimento di Sanità Pubblica e Malattie Infettive, Sapienza Università di Roma, Rome, Italy
| | - Giacomo Maria Paganotti
- Botswana-University of Pennsylvania Partnership, Gaborone, Botswana
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA USA
| | | | - Alfredo Coppa
- Dipartimento di Biologia Ambientale, Sapienza Università di Roma, Rome, Italy
| | - Paolo Anagnostou
- Dipartimento di Biologia Ambientale, Sapienza Università di Roma, Rome, Italy
- Istituto Italiano di Antropologia, Rome, Italy
| | - Jean-Michel Dugoujon
- Centre National de la Recherche Scientifique (CNRS), Université Toulouse-3–Paul-Sabatier, Toulouse, France
| | - Pedro Moral
- Department of Animal Biology-Anthropology, Biodiversity Research Institute, University of Barcelona, Barcelona, Spain
| | | | - Andrea Novelletto
- Dipartimento di Biologia, Università di Roma “Tor Vergata”, Rome, Italy
| | - Fulvio Cruciani
- Dipartimento di Biologia e Biotecnologie “C. Darwin”, Sapienza Università di Roma, Rome, Italy
- Istituto di Biologia e Patologia Molecolari, CNR, Rome, Italy
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Santamaría J, Álvarez-Álvarez MM, Esteban ME, Ramon-Gurrea E, Moral P. Dinucleotide (CA)n tandem repeats on the human X-chromosome and the history of the Mediterranean populations. Ann Hum Biol 2018; 45:72-76. [PMID: 29382285 DOI: 10.1080/03014460.2017.1414877] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
BACKGROUND Tandem repeats (STRs) are genomic markers of particular interest in forensic and population genetics. Most of the population data currently available correspond to the variation of STRs of forensic panels, which barely include dinucleotide tandem repeats. AIMS The aim of the study is to test the usefulness of a battery of dinucleotide STRs on the X chromosome for population and forensic studies. SUBJECTS AND METHODS A total of 672 individuals from 12 Mediterranean populations and two external references were analysed for 15 X-STR following the instructions of the commercial company and using control DNA from the CEPH centre whose sequences are published in GenBank. Genotypic results were analysed using standard population genetics methods including estimates of linkage disequilibrium, population structure and gene flow. Common forensic efficiency parameters were calculated. RESULTS The analysed X-STRs show high values of genetic diversity, comparable to other STRs of more common use. No significant associations between markers were found. A slight population structure was detected between the two shores of the Mediterranean. The X-STRs studied here present a similar degree of variability to that of other X-STRs used in forensics. CONCLUSION Tandem-repeated dinucleotides are a good tool for evidencing population differences here. Forensic parameters indicate that the dinucleotide X-STRs are suitable for forensic use.
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Affiliation(s)
- Josep Santamaría
- a Departamento de Biologia Evolutiva, Ecología y Ciencias Ambientales , Universitat de Barcelona , Barcelona , Spain
| | - Miguel M Álvarez-Álvarez
- a Departamento de Biologia Evolutiva, Ecología y Ciencias Ambientales , Universitat de Barcelona , Barcelona , Spain
| | - M Esther Esteban
- a Departamento de Biologia Evolutiva, Ecología y Ciencias Ambientales , Universitat de Barcelona , Barcelona , Spain
| | - Elies Ramon-Gurrea
- a Departamento de Biologia Evolutiva, Ecología y Ciencias Ambientales , Universitat de Barcelona , Barcelona , Spain
| | - Pedro Moral
- a Departamento de Biologia Evolutiva, Ecología y Ciencias Ambientales , Universitat de Barcelona , Barcelona , Spain
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Halima AB, Bahri R, Esteban E, Moral P, Chaabani H. Variation of Rhesus Haplotype Frequencies in North Africans and in Worldwide Population Analyses. INT J HUM GENET 2017. [DOI: 10.1080/09723757.2015.11886247] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Abir Ben Halima
- Laboratory of Human Genetics and Anthropology, Faculty of Pharmacy, University of Monastir, 5000 Monastir, Tunisia
| | - Raoudha Bahri
- Laboratory of Human Genetics and Anthropology, Faculty of Pharmacy, University of Monastir, 5000 Monastir, Tunisia
| | - Esther Esteban
- Secció d’Antropologia, Departament de Biologia Animal, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain
| | - Pedro Moral
- Secció d’Antropologia, Departament de Biologia Animal, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain
| | - Hassen Chaabani
- Laboratory of Human Genetics and Anthropology, Faculty of Pharmacy, University of Monastir, 5000 Monastir, Tunisia
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Resano M, Zanetti D, Esteban EM, Moral P. X-Chromosome Alu Insertions in Bahía Blanca, Argentina: Assessment of Population Information from Varied Genetic Markers and Usefulness of X-Chromosome Markers to Trace Sex-Biased Parental Contributions. Hum Biol 2017; 88:275-286. [PMID: 28826322 DOI: 10.13110/humanbiology.88.4.0275] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Bahía Blanca is an urban city in a historically and geographically strategic location for the mixture of different populations in Argentina. In the present study, 10 Alu elements from the X chromosome are analyzed to characterize the genetic composition of the city's population, to compare it with other worldwide populations, and to explore the usefulness of X-chromosome markers for human population genetics purposes. In the Bahía Blanca sample, 7 of 10 Alu insertion frequencies are polymorphic. X-chromosome Alu results in Bahía Blanca are compared with eight different populations from Africa, Europe, and America. Genetic distance analysis indicates that the Bahía Blanca sample is closer to the European and North African samples (average distances of 0.106 and 0.113) than to the Native American (0.163) and sub-Saharan African samples (0.247). Genetic relationships shown by multidimensional scaling illustrate the intermediate position of Bahía Blanca compared with groups in other regions (European, Native American, and African). Admixture results of the Bahía Blanca sample for X-chromosome markers indicate similar proportions of Native American (0.472) and European parental contributions (0.479) and a minor sub-Saharan African contribution (0.049). These results are consistent with the past decade's genetic studies of Argentinean populations that reported higher Native American and sub-Saharan African contributions than previous data.
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Affiliation(s)
- Magdalena Resano
- 1 Unitat d'Antropologia, Departament de Biologia Evolutiva, Ecologia i Ciències Ambientals, Universitat de Barcelona, Barcelona, Spain
| | - Daniela Zanetti
- 1 Unitat d'Antropologia, Departament de Biologia Evolutiva, Ecologia i Ciències Ambientals, Universitat de Barcelona, Barcelona, Spain
| | - Esther M Esteban
- 1 Unitat d'Antropologia, Departament de Biologia Evolutiva, Ecologia i Ciències Ambientals, Universitat de Barcelona, Barcelona, Spain.,2 Institut de Recerca de la Biodiversitat, Universitat de Barcelona, Barcelona, Spain
| | - Pedro Moral
- 1 Unitat d'Antropologia, Departament de Biologia Evolutiva, Ecologia i Ciències Ambientals, Universitat de Barcelona, Barcelona, Spain.,2 Institut de Recerca de la Biodiversitat, Universitat de Barcelona, Barcelona, Spain
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10
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Álvarez-Álvarez MM, Zanetti D, Carreras-Torres R, Moral P, Athanasiadis G. A survey of sub-Saharan gene flow into the Mediterranean at risk loci for coronary artery disease. Eur J Hum Genet 2017; 25:472-476. [PMID: 28098150 DOI: 10.1038/ejhg.2016.200] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Revised: 11/24/2016] [Accepted: 12/14/2016] [Indexed: 12/31/2022] Open
Abstract
This study tries to find detectable signals of gene flow of Sub-Saharan origin into the Mediterranean in four genomic regions previously associated with coronary artery disease. A total of 366 single-nucleotide polymorphisms were genotyped in 772 individuals from 10 Mediterranean countries. Population structure analyses were performed, in which a noticeable Sub-Saharan component was found in the studied samples. The overall percentage of this Sub-Saharan component presents differences between the two Mediterranean coasts. D-statistics suggest possible Sub-Saharan introgression into one of the studied genomic regions (10q11). We also found differences in linkage disequilibrium patterns between the two Mediterranean coasts, possibly attributable to differential Sub-Saharan admixture. Our results confirm the potentially important role of human demographic history when performing epidemiological studies.
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Affiliation(s)
- Miguel M Álvarez-Álvarez
- Faculty of Biology, Department of Evolutionary Biology, Ecology and Environmental Sciences, Biodiversity Research Institute, University of Barcelona,Barcelona, Spain
| | - Daniela Zanetti
- Faculty of Biology, Department of Evolutionary Biology, Ecology and Environmental Sciences, Biodiversity Research Institute, University of Barcelona,Barcelona, Spain
| | - Robert Carreras-Torres
- Faculty of Biology, Department of Evolutionary Biology, Ecology and Environmental Sciences, Biodiversity Research Institute, University of Barcelona,Barcelona, Spain
| | - Pedro Moral
- Faculty of Biology, Department of Evolutionary Biology, Ecology and Environmental Sciences, Biodiversity Research Institute, University of Barcelona,Barcelona, Spain
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11
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Carreras-Torres R, Ferran A, Zanetti D, Esteban E, Varesi L, Pojskic N, Coia V, Chaabani H, Via M, Moral P. Population structure from NOS genes correlates with geographical differences in coronary incidence across Europe. Am J Phys Anthropol 2016; 161:634-645. [PMID: 27500977 DOI: 10.1002/ajpa.23063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2015] [Revised: 06/19/2016] [Accepted: 07/26/2016] [Indexed: 11/05/2022]
Abstract
OBJECTIVES The population analysis of cardiovascular risk and non-risk genetic variation can help to identify adaptive or random demographic processes that shaped coronary incidence variation across geography. MATERIAL AND METHODS In this study, 114 single nucleotide polymorphisms and 17 tandem repeat polymorphisms from Nitric Oxide Synthases (NOS) regions were analyzed in 1686 individuals from 35 populations from Europe, North Africa, and the Middle East. NOS genes encode for key enzymes on nitric oxide availability, which is involved in several cardiovascular processes. These genetic variations were used to test for selection and to infer the population structure of NOS regions. Moreover, we tested whether the variation in the incidence of coronary events and in the levels of classical risk factors in 11 of these European populations could be explained by the population structure estimates. RESULTS Our results supported, first, the absence of clear signs of selection for NOS genetic variants associated with cardiovascular diseases, and second, the presence of a continuous genetic pattern of variation across European and North African populations without a Mediterranean barrier for gene flow. Finally, population structure estimates from NOS regions are closely correlated with coronary event rates and classical risk parameters (explaining 39-98%) among European populations. CONCLUSION Our results reinforce the hypothesis that genetic bases of cardiovascular diseases and associated complex phenotypes could be geographically shaped by random demographic processes.
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Affiliation(s)
- Robert Carreras-Torres
- Departament Biologia Animal, Unitat d'Antropologia, Facultat de Biologia, Universitat de Barcelona, Spain
| | - Albert Ferran
- Departament Biologia Animal, Unitat d'Antropologia, Facultat de Biologia, Universitat de Barcelona, Spain
| | - Daniela Zanetti
- Departament Biologia Animal, Unitat d'Antropologia, Facultat de Biologia, Universitat de Barcelona, Spain
| | - Esther Esteban
- Departament Biologia Animal, Unitat d'Antropologia, Facultat de Biologia, Universitat de Barcelona, Spain.,Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Spain
| | - Laurent Varesi
- Laboratoire de virologie, Faculté des Sciences et Techniques, Université de Corse, France
| | - Naris Pojskic
- Laboratory for Molecular Genetics of Natural Resources, Institute for Genetic Engineering and Biotechnology, University of Sarajevo, Bosnia and Herzegovina
| | - Valentina Coia
- Accademia Europea di Bolzano (EURAC), Istituto per le Mummie e l'Iceman, Bolzano, Italy
| | - Hassen Chaabani
- Laboratory of Human Genetics and Anthropology, Faculty of Pharmacy, University of Monastir, Tunisia
| | - Marc Via
- Departament Psicologia Clínica i Psicobiologia and Institute of Neurosciences (UBNEURO), Universitat de Barcelona, Spain.,Institut de Recerca Pediàtrica Hospital Sant Joan de Déu (IRP_HSJD), Barcelona, Spain
| | - Pedro Moral
- Departament Biologia Animal, Unitat d'Antropologia, Facultat de Biologia, Universitat de Barcelona, Spain.,Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Spain
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12
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Fernández-Santander A, Novillo A, Gaibar M, Romero-Lorca A, Moral P, Sánchez-Cuenca D, Amir N, Chaabani H, Harich N, Esteban ME. Cytochrome and sulfotransferase gene variation in north African populations. Pharmacogenomics 2016; 17:1415-23. [PMID: 27471773 DOI: 10.2217/pgs-2016-0016] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
AIM To describe the diversity of four cytochrome and four sulfotransferase polymorphisms in six north African samples. Scarce data have been compiled for these samples despite the rich genetic background of north African populations. MATERIALS & METHODS CYP3A4*1B, CYP3A4*17, CYP3A4*3, CYP3A5*3, SULT1A1*2, SULT1A2*2, SULT1A2*3 and SULT1E1*2 polymorphisms were explored in 556 individuals from Morocco, Algeria, Tunisia and Libya. RESULTS Allele frequencies in our samples largely exceeded the variation ranges described for European populations, especially for CYP3A4*1B, SULT1A1*2 and SULT1A2*3. CONCLUSION North African populations are heterogeneous, genetically diverse and show a considerable sub-Saharan African contribution for markers associated with increased risk of prostate cancer and with differential drug metabolism.
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Affiliation(s)
| | - Apolonia Novillo
- Basic Biomedical Sciences Department, Universidad Europea de Madrid, Madrid, Spain
| | - María Gaibar
- Basic Biomedical Sciences Department, Universidad Europea de Madrid, Madrid, Spain
| | - Alicia Romero-Lorca
- Basic Biomedical Sciences Department, Universidad Europea de Madrid, Madrid, Spain
| | - Pedro Moral
- Section of Zoology and Anthropology, Department of Evolutive Biology, Ecology and Environmental Sciences, Faculty of Biology, University of Barcelona, Barcelona, Spain.,Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain
| | - David Sánchez-Cuenca
- Departamento de Genética, Antropología Física y Fisiología Animal (UPV/EHU), Leioa, Spain
| | - Nadir Amir
- Laboratoire de Biochimie Appliquée, Faculté des Sciences de la Nature et de la Vie, Université de Bejaia, Algeria
| | - Hassen Chaabani
- Faculty of Pharmacy, University of Monastir, Monastir, Tunisia
| | - Nourdin Harich
- Départément de Biologie, Faculté des Sciences, Université Chouaib Doukkali, El Jadida, Morocco
| | - Maria Esther Esteban
- Section of Zoology and Anthropology, Department of Evolutive Biology, Ecology and Environmental Sciences, Faculty of Biology, University of Barcelona, Barcelona, Spain.,Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain
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13
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Álvarez-Álvarez MM, Carreras-Torres R, Zanetti D, Vegas E, Moral P. Population variation of LIN28B in the Mediterranean: Novel markers for microgeographic discrimination. Am J Hum Biol 2016; 28:905-912. [PMID: 27338933 DOI: 10.1002/ajhb.22887] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2015] [Revised: 04/11/2016] [Accepted: 06/06/2016] [Indexed: 11/09/2022] Open
Abstract
OBJECTIVES The aim of this study is to determine whether the LIN28B gene is differentially distributed in the Mediterranean region through the analysis of the allele distribution of three single nucleotide polymorphisms (SNPs), namely rs7759938, rs314277, and rs221639, in 24 populations. These SNPs have been recently related to the age at menarche, pubertal height growth, peripubertal body mass index, levels of prenatal testosterone exposure, and cancer survival. METHODS A total of 1,197 DNA samples were genotyped. The allele frequencies were used to determine the relationship between populations, with data from the 1000 Genomes Project being used for external comparisons. The genotype distributions and the population structure between populations and groups of populations were determined. RESULTS The population results indicate a significant degree of variation (FST = 0.043, P < 0.0001). Allele frequencies show significant differences among populations. A hierarchical variance analysis is consistent with a primary differentiation between populations on the North and South coasts of the Mediterranean. This difference is especially evident in the unexpected distribution of the SNP rs221639, which shows one of the highest FST (11.5%, P < 0.0001) values described in the Mediterranean region thus far. CONCLUSION The population differentiation and the structuring of the genetic variance, in agreement with previous studies, indicate that the SNPs in question are good tools for the study of human populations, even at a microgeographic level. Am. J. Hum. Biol. 28:905-912, 2016. © 2016Wiley Periodicals, Inc.
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Affiliation(s)
- Miguel M Álvarez-Álvarez
- Anthropology Unit, Department of Animal Biology, Faculty of Biology, University of Barcelona, Barcelona, Spain. Biodiversity Research Institute (IRBio)
| | - Robert Carreras-Torres
- Anthropology Unit, Department of Animal Biology, Faculty of Biology, University of Barcelona, Barcelona, Spain. Biodiversity Research Institute (IRBio)
| | - Daniela Zanetti
- Anthropology Unit, Department of Animal Biology, Faculty of Biology, University of Barcelona, Barcelona, Spain. Biodiversity Research Institute (IRBio)
| | - Esteban Vegas
- Department of Statistics, Faculty of Biology, University of Barcelona, Barcelona, Spain
| | - Pedro Moral
- Anthropology Unit, Department of Animal Biology, Faculty of Biology, University of Barcelona, Barcelona, Spain. Biodiversity Research Institute (IRBio)
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14
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Zanetti D, Via M, Carreras-Torres R, Esteban E, Chaabani H, Anaibar F, Harich N, Habbal R, Ghalim N, Moral P. Analysis of Genomic Regions Associated With Coronary Artery Disease Reveals Continent-Specific Single Nucleotide Polymorphisms in North African Populations. J Epidemiol 2016; 26:264-71. [PMID: 26780859 PMCID: PMC4848325 DOI: 10.2188/jea.je20150034] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Background In recent years, several genomic regions have been robustly associated with coronary artery disease (CAD) in different genome-wide association studies (GWASs) conducted mainly in people of European descent. These kinds of data are lacking in African populations, even though heart diseases are a major cause of premature death and disability. Methods Here, 384 single nucleotide polymorphisms (SNPs) in the top four CAD risk regions (1p13, 1q41, 9p21, and 10q11) were genotyped in 274 case-control samples from Morocco and Tunisia, with the aim of analyzing for the first time if the associations found in European populations were transferable to North Africans. Results The results indicate that, as in Europe, these four genetic regions are also important for CAD risk in North Africa. However, the individual SNPs associated with CAD in Africa are different from those identified in Europe in most cases (1p13, 1q41, and 9p21). Moreover, the seven risk variants identified in North Africans are efficient in discriminating between cases and controls in North African populations, but not in European populations. Conclusions This study indicates a disparity in markers associated to CAD susceptibility between North Africans and Europeans that may be related to population differences in the chromosomal architecture of these risk regions.
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Affiliation(s)
- Daniela Zanetti
- Department of Animal Biology-Anthropology, University of Barcelona
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15
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Zanetti D, Sadiq M, Carreras-Torres R, Khabour O, Alkaraki A, Esteban E, Via M, Moral P. Human diversity in Jordan: polymorphic Alu insertions in general Jordanian and Bedouin groups. Hum Biol 2015; 86:131-8. [PMID: 25397703 DOI: 10.3378/027.086.0201] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/03/2014] [Indexed: 11/05/2022]
Abstract
Jordan, located in the Levant region, is an area crucial for the investigation of human migration between Africa and Eurasia. However, the genetic history of Jordanians has yet to be clarified, including the origin of the Bedouins today resident in Jordan. Here, we provide new genetic data on autosomal independent markers in two Jordanian population samples (Bedouins and the general population) to begin to examine the genetic diversity inside this country and to provide new information about the genetic position of these populations in the context of the Mediterranean and Middle East area. The markers analyzed were 18 Alu polymorphic insertions characterized by their identity by descent, known ancestral state (lack of insertion), and apparent selective neutrality. The results indicate significant genetic diffferences between Bedouins and general Jordanians (p = 0.038). Whereas Bedouins show a close genetic proximity to North Africans, general Jordanians appear genetically more similar to other Middle East populations. In general, these data are consistent with the hypothesis that Bedouins had an important role in the peopling of Jordan and constitute the original substrate of the current population. However, migration into Jordan in recent years likely has contributed to the diversity among current Jordanian population groups.
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Affiliation(s)
- Daniela Zanetti
- Department of Animal Biology-Anthropology, University of Barcelona, Barcelona, Spain
| | - May Sadiq
- Department of Biological Sciences, Yarmouk University, Irbid, Jordan
| | | | - Omar Khabour
- Department of Medical Laboratory Sciences, Jordan University of Science and Technology, Irbid, Jordan, and Department of Biology, Faculty of Science, Taibah University, Saudi Arabia
| | | | - Esther Esteban
- Department of Animal Biology-Anthropology, University of Barcelona, Barcelona, Spain
| | - Marc Via
- Department of Psychiatry and Clinical Psychobiology, University of Barcelona, Barcelona, Spain
| | - Pedro Moral
- Department of Animal Biology-Anthropology, University of Barcelona, Barcelona, Spain
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Zanetti D, Carreras-Torres R, Esteban E, Via M, Moral P. Potential Signals of Natural Selection in the Top Risk Loci for Coronary Artery Disease: 9p21 and 10q11. PLoS One 2015; 10:e0134840. [PMID: 26252781 PMCID: PMC4529309 DOI: 10.1371/journal.pone.0134840] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2015] [Accepted: 07/15/2015] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Coronary artery disease (CAD) is a complex disease and the leading cause of death in the world. Populations of different ancestry do not always share the same risk markers. Natural selective processes may be the cause of some of the population differences detected for specific risk mutations. OBJECTIVE In this study, 384 single nucleotide polymorphisms (SNPs) located in four genomic regions associated with CAD (1p13, 1q41, 9p21 and 10q11) are analysed in a set of 19 populations from Europe, Middle East and North Africa and also in Asian and African samples from the 1000 Genomes Project. The aim of this survey is to explore for the first time whether the genetic variability in these genomic regions is better explained by demography or by natural selection. RESULTS The results indicate significant differences in the structure of genetic variation and in the LD patterns among populations that probably explain the population disparities found in markers of susceptibility to CAD. CONCLUSIONS The results are consistent with potential signature of positive selection in the 9p21 region and of balancing selection in the 9p21 and 10q11. Specifically, in Europe three CAD risk markers in the 9p21 region (rs9632884, rs1537371 and rs1333042) show consistent signals of positive selection. The results of this study are consistent with a potential selective role of CAD in the configuration of genetic diversity in current human populations.
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Affiliation(s)
- Daniela Zanetti
- Department of Animal Biology-Anthropology, University of Barcelona, Barcelona, Spain
| | | | - Esther Esteban
- Department of Animal Biology-Anthropology, University of Barcelona, Barcelona, Spain
- Biodiversity Research Institute, University of Barcelona, Spain
| | - Marc Via
- Department of Psychiatry and Clinical Psychobiology and Institute for Brain, Cognition and Behavior (IR3C), University of Barcelona, Barcelona, Spain
| | - Pedro Moral
- Department of Animal Biology-Anthropology, University of Barcelona, Barcelona, Spain
- Biodiversity Research Institute, University of Barcelona, Spain
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De Fanti S, Sazzini M, Giuliani C, Frazzoni F, Sarno S, Boattini A, Marasco E, Mantovani V, Franceschi C, Moral P, Garagnani P, Luiselli D. Inferring the genetic history of lactase persistence along the Italian peninsula from a large genomic interval surrounding theLCTgene. Am J Phys Anthropol 2015; 158:708-18. [DOI: 10.1002/ajpa.22814] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2015] [Revised: 06/19/2015] [Accepted: 07/03/2015] [Indexed: 12/15/2022]
Affiliation(s)
- Sara De Fanti
- Laboratory of Molecular Anthropology, Department of Biological, Geological and Environmental Sciences (BiGeA); University of Bologna; Bologna 40126 Italy
- Department of Biological, Geological and Environmental Sciences (BiGeA), Centre for Genome Biology; University of Bologna; Bologna 40126 Italy
| | - Marco Sazzini
- Laboratory of Molecular Anthropology, Department of Biological, Geological and Environmental Sciences (BiGeA); University of Bologna; Bologna 40126 Italy
- Department of Biological, Geological and Environmental Sciences (BiGeA), Centre for Genome Biology; University of Bologna; Bologna 40126 Italy
| | - Cristina Giuliani
- Laboratory of Molecular Anthropology, Department of Biological, Geological and Environmental Sciences (BiGeA); University of Bologna; Bologna 40126 Italy
- Department of Biological, Geological and Environmental Sciences (BiGeA), Centre for Genome Biology; University of Bologna; Bologna 40126 Italy
| | - Federica Frazzoni
- Laboratory of Molecular Anthropology, Department of Biological, Geological and Environmental Sciences (BiGeA); University of Bologna; Bologna 40126 Italy
| | - Stefania Sarno
- Laboratory of Molecular Anthropology, Department of Biological, Geological and Environmental Sciences (BiGeA); University of Bologna; Bologna 40126 Italy
| | - Alessio Boattini
- Laboratory of Molecular Anthropology, Department of Biological, Geological and Environmental Sciences (BiGeA); University of Bologna; Bologna 40126 Italy
| | - Elena Marasco
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES); University of Bologna; Bologna 40126 Italy
| | - Vilma Mantovani
- Center for Applied Biomedical Research (CRBA); St. Orsola-Malpighi University Hospital; Bologna 40138 Italy
| | - Claudio Franceschi
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES); University of Bologna; Bologna 40126 Italy
| | - Pedro Moral
- Department of Animal Biology-Anthropology; University of Barcelona; Barcelona 08028 Spain
| | - Paolo Garagnani
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES); University of Bologna; Bologna 40126 Italy
| | - Donata Luiselli
- Laboratory of Molecular Anthropology, Department of Biological, Geological and Environmental Sciences (BiGeA); University of Bologna; Bologna 40126 Italy
- Department of Biological, Geological and Environmental Sciences (BiGeA), Centre for Genome Biology; University of Bologna; Bologna 40126 Italy
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Trombetta B, D'Atanasio E, Massaia A, Ippoliti M, Coppa A, Candilio F, Coia V, Russo G, Dugoujon JM, Moral P, Akar N, Sellitto D, Valesini G, Novelletto A, Scozzari R, Cruciani F. Phylogeographic Refinement and Large Scale Genotyping of Human Y Chromosome Haplogroup E Provide New Insights into the Dispersal of Early Pastoralists in the African Continent. Genome Biol Evol 2015; 7:1940-50. [PMID: 26108492 PMCID: PMC4524485 DOI: 10.1093/gbe/evv118] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Haplogroup E, defined by mutation M40, is the most common human Y chromosome clade within Africa. To increase the level of resolution of haplogroup E, we disclosed the phylogenetic relationships among 729 mutations found in 33 haplogroup DE Y-chromosomes sequenced at high coverage in previous studies. Additionally, we dissected the E-M35 subclade by genotyping 62 informative markers in 5,222 samples from 118 worldwide populations. The phylogeny of haplogroup E showed novel features compared with the previous topology, including a new basal dichotomy. Within haplogroup E-M35, we resolved all the previously known polytomies and assigned all the E-M35* chromosomes to five new different clades, all belonging to a newly identified subhaplogroup (E-V1515), which accounts for almost half of the E-M35 chromosomes from the Horn of Africa. Moreover, using a Bayesian phylogeographic analysis and a single nucleotide polymorphism-based approach we localized and dated the origin of this new lineage in the northern part of the Horn, about 12 ka. Time frames, phylogenetic structuring, and sociogeographic distribution of E-V1515 and its subclades are consistent with a multistep demic spread of pastoralism within north-eastern Africa and its subsequent diffusion to subequatorial areas. In addition, our results increase the discriminative power of the E-M35 haplogroup for use in forensic genetics through the identification of new ancestry-informative markers.
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Affiliation(s)
- Beniamino Trombetta
- Dipartimento di Biologia e Biotecnologie "C. Darwin," Sapienza Università di Roma, Italy
| | - Eugenia D'Atanasio
- Dipartimento di Biologia e Biotecnologie "C. Darwin," Sapienza Università di Roma, Italy
| | - Andrea Massaia
- Dipartimento di Biologia e Biotecnologie "C. Darwin," Sapienza Università di Roma, Italy Present address: The Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, United Kingdom
| | - Marco Ippoliti
- Dipartimento di Biologia e Biotecnologie "C. Darwin," Sapienza Università di Roma, Italy
| | - Alfredo Coppa
- Dipartimento di Biologia Ambientale, Sapienza Università di Roma, Italy
| | | | - Valentina Coia
- Accademia Europea di Bolzano (EURAC), Istituto per le Mummie e l'Iceman, Bolzano, Italy
| | - Gianluca Russo
- Dipartimento di Sanità Pubblica e Malattie Infettive, Sapienza Università di Roma, Italy
| | - Jean-Michel Dugoujon
- Laboratoire d'Anthropologie Moléculaire et Imagerie de Synthèse, UMR 5288, Centre National de la Recherche Scientifique (CNRS), Université Toulouse-3-Paul-Sabatier, Toulouse, France
| | - Pedro Moral
- Department of Animal Biology-Anthropology, Biodiversity Research Institute, University of Barcelona, Spain
| | - Nejat Akar
- Pediatrics Department, TOBB-Economy and Technology University Hospital, Ankara, Turkey
| | | | - Guido Valesini
- Dipartimento di Medicina Interna e Specialità Mediche, Sapienza Università di Roma, Italy
| | - Andrea Novelletto
- Dipartimento di Biologia e Biotecnologie "C. Darwin," Sapienza Università di Roma, Italy
| | - Rosaria Scozzari
- Dipartimento di Biologia e Biotecnologie "C. Darwin," Sapienza Università di Roma, Italy
| | - Fulvio Cruciani
- Dipartimento di Biologia e Biotecnologie "C. Darwin," Sapienza Università di Roma, Italy Istituto di Biologia e Patologia Molecolari, CNR, Rome Italy
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Luna F, Camargo AM, Alonso V, Moral P. Effects of parental reproductive behavior on offspring sex ratio in a pre-industrial western Mediterranean population (La Alpujarra, 1900–1950, SE Spain). anthranz 2014; 71:303-12. [DOI: 10.1127/0003-5548/2014/0398] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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Bachis V, Calò CM, Vona G, Corrias L, Carreras-Torres R, Moral P. Analysis of 16 STRs of NOS gene regions and around in six sardinian populations (Italy). Am J Hum Biol 2014; 26:401-6. [DOI: 10.1002/ajhb.22533] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2013] [Revised: 02/12/2014] [Accepted: 02/14/2014] [Indexed: 01/09/2023] Open
Affiliation(s)
- Valeria Bachis
- Department of Science of Life and Environment; University of Cagliari; Monserrato 09042 Italy
| | - Carla Maria Calò
- Department of Science of Life and Environment; University of Cagliari; Monserrato 09042 Italy
| | - Giuseppe Vona
- Department of Science of Life and Environment; University of Cagliari; Monserrato 09042 Italy
| | - Laura Corrias
- Department of Science of Life and Environment; University of Cagliari; Monserrato 09042 Italy
| | - Robert Carreras-Torres
- Department of Animal Biology and Anthropology; Institute of Biodiversity; University of Barcelona; Barcelona 08028 Spain
| | - Pedro Moral
- Department of Animal Biology and Anthropology; Institute of Biodiversity; University of Barcelona; Barcelona 08028 Spain
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Rocañín-Arjó A, Rodríguez-Botigué L, Esteban E, Theves C, Evdokimova LE, Fedorova SA, Gibert M, Crubezy E, Moral P. Close genetic relationships in vast territories: autosomal and X chromosome Alu diversity in Yakuts from Siberia. Anthropol Anz 2014; 70:309-17. [PMID: 24466640 DOI: 10.1127/0003-5548/2013/0296] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Twelve autosomal and 8 X chromosome Alu markers were genotyped for the first time in 161 Central and West Yakuts to test their ability to reconstruct the genetic history of these populations, the northernmost Turkic-speaker ethnic group living in Siberia. Autosomal data revealed that both groups showed extremely close genetic distances to other populations of Siberian origins that occupied areas from Lake Baikal, the ancestral place of origin of Yakuts, to North Siberia, their current territories. Autosomal and X chromosome data revealed some discrepancies on the genetic differentiation and the effective sizes of Central and West Yakuts. Such discrepancies could be related to the patrilineal and occasionally polygamous structure of these populations. Autosomal and X Alu markers are informative markers to reconstruct population past demography and history, but their utility is limited by the available data. This study represents a contribution for further investigations on these populations.
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Affiliation(s)
- Ares Rocañín-Arjó
- Secció d'Antropologia, Departament de Biologia Animal, Universitat de Barcelona, Barcelona, Spain
| | - Laura Rodríguez-Botigué
- Institut de Biologia Evolutiva (CSIC-UPF), Department de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona, Spain
| | - Esther Esteban
- Secció d'Antropologia, Departament de Biologia Animal, Universitat de Barcelona, Barcelona, Spain
| | - Catherine Theves
- Laboratory AMIS, UMR 5288, CNRS-Université de Toulouse III-Paul Sabatier, Université de Strasbourg, France
| | | | - Sardana A Fedorova
- North-Eastern Federal University and Yakut Research Centre of Complex Medical Problems, Russian Academy of Medical Sciences, Republic of Sakha, Russian Federation
| | - Morgane Gibert
- Laboratory AMIS, UMR 5288, CNRS-Université de Toulouse III-Paul Sabatier, Université de Strasbourg, France
| | - Eric Crubezy
- Laboratory AMIS, UMR 5288, CNRS-Université de Toulouse III-Paul Sabatier, Université de Strasbourg, France
| | - Pedro Moral
- Secció d'Antropologia, Departament de Biologia Animal, Universitat de Barcelona, Barcelona, Spain
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Halima AB, Bahri R, Esteban E, Aribia MHB, Moral P, Chaabani H. Ethnic composition and genetic differentiation of the Libyan population: insights onAlupolymorphisms. Ann Hum Biol 2013; 41:229-37. [DOI: 10.3109/03014460.2013.850112] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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Cutrona MB, Beznoussenko GV, Fusella A, Martella O, Moral P, Mironov AA. Silencing of mammalian Sar1 isoforms reveals COPII-independent protein sorting and transport. Traffic 2013; 14:691-708. [PMID: 23433038 DOI: 10.1111/tra.12060] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2012] [Revised: 02/16/2013] [Accepted: 02/21/2013] [Indexed: 01/01/2023]
Abstract
The Sar1 GTPase coordinates the assembly of coat protein complex-II (COPII) at specific sites of the endoplasmic reticulum (ER). COPII is required for ER-to-Golgi transport, as it provides a structural and functional framework to ship out protein cargoes produced in the ER. To investigate the requirement of COPII-mediated transport in mammalian cells, we used small interfering RNA (siRNA)-mediated depletion of Sar1A and Sar1B. We report that depletion of these two mammalian forms of Sar1 disrupts COPII assembly and the cells fail to organize transitional elements that coordinate classical ER-to-Golgi protein transfer. Under these conditions, minimal Golgi stacks are seen in proximity to juxtanuclear ER membranes that contain elements of the intermediate compartment, and from which these stacks coordinate biosynthetic transport of protein cargo, such as the vesicular stomatitis virus G protein and albumin. Here, transport of procollagen-I is inhibited. These data provide proof-of-principle for the contribution of alternative mechanisms that support biosynthetic trafficking in mammalian cells, providing evidence of a functional boundary associated with a bypass of COPII.
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Affiliation(s)
- Meritxell B Cutrona
- Department of Cellular and Translational Pharmacology, Consorzio Mario Negri Sud, Via Nazionale 8/A, 66030 Santa Maria Imbaro, Chieti, Italy.
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Bahri R, Halima AB, Ayadi I, Esteban E, Alfadhli SM, Rebai A, Moral P, Chaabani H. Genetic position of Bahrain natives among wider Middle East populations according to Alu insertion polymorphisms. Ann Hum Biol 2012; 40:35-40. [DOI: 10.3109/03014460.2012.728622] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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Gayà-Vidal M, Athanasiadis G, Carreras-Torres R, Via M, Esteban E, Villena M, Vasquez R, Dugoujon JM, Moral P. Apolipoprotein E/C1/C4/C2 gene cluster diversity in two native Andean populations: Aymaras and Quechuas. Ann Hum Genet 2012; 76:283-95. [PMID: 22681517 DOI: 10.1111/j.1469-1809.2012.00712.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The APOE/C1/C4/C2 gene cluster presents high relevance in lipid metabolism and, therefore, has important epidemiological implications. Here, we study for the first time the variation patterns of 25 polymorphisms (10 short tandem repeats, STRs, and 15 single nucleotide polymorphismas, SNPs) in two native Andean samples from Bolivia (45 Aymaras and 45 Quechuas) as well as one European sample (n = 41) as external reference. We estimated diversity parameters, linkage disequilibrium patterns, population structure, and possible selective effects. In general, diversity was low and could be partly attributed to selection (probably due to its physiological importance), since the APOE/C1/C4/C2 region was highly conserved compared to the flanking genes in both Bolivians and Europeans. Moreover, the lower gene diversity in Bolivians compared to Europeans for some markers might indicate different demographic histories. Regarding the APOE isoforms, in addition to ɛ3 (94%) and ɛ4 (5%), isoform ɛ2 (1%) was also detected in Bolivians. In relation to previous hypotheses, our results support that genetic drift or founder effects rather than selection for increased cholesterol absorption are the main factors that have shaped the distribution of APOE isoforms observed in South America.
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Affiliation(s)
- Magdalena Gayà-Vidal
- Biologia Animal, Facultat de Biologia, Universitat de Barcelona, Barcelona 08028, Spain
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Bahri R, El Moncer W, Al-Batayneh K, Sadiq M, Esteban E, Moral P, Chaabani H. Genetic differentiation and origin of the Jordanian population: an analysis of Alu insertion polymorphisms. Genet Test Mol Biomarkers 2011; 16:324-9. [PMID: 22106835 DOI: 10.1089/gtmb.2011.0197] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
AIM Although much of Jordan is covered by desert, its north-western region forms part of the Fertile Crescent region that had given a rich past to Jordanians. This past, scarcely described by historians, is not yet clarified by sufficient genetic data. Thus in this paper we aim to determine the genetic differentiation of the Jordanian population and to discuss its origin. METHODS A total of 150 unrelated healthy Jordanians were investigated for ten Alu insertion polymorphisms. Genetic relationships among populations were estimated by a principal component (PC) plot based on the analyses of the R-matrix software. RESULTS Statistical analysis showed that the Jordanian population is not significantly different from the United Arab Emirates population or the North Africans. This observation, well represented in PC plot, suggests a common origin of these populations belonging respectively to ancient Mesopotamia, Arabia, and North Africa. CONCLUSION Our results are compatible with ancient peoples' movements from Arabia to ancient Mesopotamia and North Africa as proposed by historians and supported by previous genetic results. The original genetic profile of the Jordanian population, very likely Arabian Semitic, has not been subject to significant change despite the succession of several civilizations.
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Affiliation(s)
- Raoudha Bahri
- Laboratory of Human Genetics and Anthropology, Faculty of Pharmacy, University of Monastir, Monastir, Tunisia
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El Moncer W, Bahri R, Esteban E, Abdenni-Guenounou B, Moral P, Ben Chibani J, Chaabani H. Research of the origin of a particular Tunisian group using a physical marker and Alu insertion polymorphisms. Genet Mol Biol 2011; 34:371-6. [PMID: 21931506 PMCID: PMC3168174 DOI: 10.1590/s1415-47572011005000021] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2010] [Accepted: 03/23/2011] [Indexed: 11/22/2022] Open
Abstract
The aim of this study was to show how, in some particular circumstances, a physical marker can be used along with molecular markers in the research of an ancient people movement. A set of five Alu insertions was analysed in 42 subjects from a particular Tunisian group (El Hamma) that has, unlike most of the Tunisian population, a very dark skin, similar to that of sub-Saharans, and in 114 Tunisian subjects (Gabes sample) from the same governorate, but outside the group. Our results showed that the El Hamma group is genetically midway between sub-Saharan populations and North Africans, whereas the Gabes sample is clustered among North Africans. In addition, The A25 Alu insertion, considered characteristic to sub-Saharan Africans, was present in the El Hamma group at a relatively high frequency. This frequency was similar to that found in sub-Saharans from Nigeria, but significantly different from those found in the Gabes sample and in other North African populations. Our molecular results, consistent with the skin color status, suggest a sub-Saharan origin of this particular Tunisian group.
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Affiliation(s)
- Wifak El Moncer
- Laboratory of Human Genetics and Anthropology, Faculty of Pharmacy, University of Monastir, Monastir, Tunisia
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Gayà-Vidal M, Moral P, Saenz-Ruales N, Gerbault P, Tonasso L, Villena M, Vasquez R, Bravi CM, Dugoujon JM. mtDNA and Y-chromosome diversity in Aymaras and Quechuas from Bolivia: Different stories and special genetic traits of the Andean Altiplano populations. Am J Phys Anthropol 2011; 145:215-30. [DOI: 10.1002/ajpa.21487] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2010] [Accepted: 12/09/2010] [Indexed: 11/11/2022]
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Carreras-Torres R, Athanasiadis G, Via M, Trenchs J, Gayà-Vidal M, Santamaria J, Esteban E, Moral P. Allele-allele interaction within the F13A1 gene: a risk factor for ischaemic heart disease in Spanish population. Thromb Res 2010; 126:e241-5. [PMID: 20553949 DOI: 10.1016/j.thromres.2010.04.021] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2010] [Revised: 04/30/2010] [Accepted: 04/30/2010] [Indexed: 12/01/2022]
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Piras I, Falchi A, Moral P, Paoli G, Calò CM, Vona G, Varesi L. A gradient of NOS1 overproduction alleles in European and Mediterranean populations. Genet Test Mol Biomarkers 2010; 14:673-6. [PMID: 20818978 DOI: 10.1089/gtmb.2010.0041] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
AIM A (CA)n repeat located in the 3' UTR region of exon 29 of the NOS1 gene (encoding for neuronal nitric oxide synthase) has been shown to affect the size of mRNA. NOS1 mRNA is highly diverse, contributing to changes in transcript generation, degradation, processing, or subcellular targeting. In the present work, we analyzed allele frequencies of this (CA)n repeat in nine populations of the Mediterranean area and Middle Europe. We aimed at testing the presence of a north-south positive gradient of frequencies of ≤17 allele repeats, compatible with the hypothesis of positive selection suggested in two of our previous works, related to the past prevalence of malaria infection in Europe. RESULTS Results show significant negative correlations of latitude with frequencies of alleles S and genotypes S/S and S/L (p < 0.01). CONCLUSIONS In conclusion, the north-south gradient of S alleles found in the present work would confirm our previous observation about the NOS1 gene, reinforcing the hypothesis of a selective action of malaria infection. This hypothesis is strengthened by the role of nitric oxide in the immunity system.
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Affiliation(s)
- Ignazio Piras
- Faculty of Science, University of Corsica, Corsica, France.
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Gibert M, Theves C, Ricaut FX, Dambueva I, Bazarov B, Moral P, Crubezy E, Perrucho M, Felix-Sanchez M, Sevin A. mtDNA variation in the Buryat population of the Barguzin Valley: New insights into the micro-evolutionary history of the Baikal area. Ann Hum Biol 2010; 37:501-23. [DOI: 10.3109/03014460903433828] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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González-Pérez E, Esteban E, Via M, Gayà-Vidal M, Athanasiadis G, Dugoujon JM, Luna F, Mesa MS, Fuster V, Kandil M, Harich N, Bissar-Tadmouri N, Saetta A, Moral P. Population relationships in the Mediterranean revealed by autosomal genetic data (Alu and Alu/STR compound systems). Am J Phys Anthropol 2010; 141:430-9. [PMID: 19918993 DOI: 10.1002/ajpa.21161] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
The variation of 18 Alu polymorphisms and 3 linked STRs was determined in 1,831 individuals from 15 Mediterranean populations to analyze the relationships between human groups in this geographical region and provide a complementary perspective to information from studies based on uniparental markers. Patterns of population diversity revealed by the two kinds of markers examined were different from one another, likely in relation to their different mutation rates. Therefore, while the Alu biallelic variation underlies general heterogeneity throughout the whole Mediterranean region, the combined use of Alu and STR points to a considerable genetic differentiation between the two Mediterranean shores, presumably strengthened by a considerable sub-Saharan African genetic contribution in North Africa (around 13% calculated from Alu markers). Gene flow analysis confirms the permeability of the Sahara to human passage along with the existence of trans-Mediterranean interchanges. Two specific Alu/STR combinations-CD4 110(-) and DM 107(-)-detected in all North African samples, the Iberian Peninsula, Greece, Turkey, and some Mediterranean islands suggest an ancient genetic background of current Mediterranean peoples.
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Affiliation(s)
- Emili González-Pérez
- Secció d'Antropologia, Departament de Biologia Animal, Universitat de Barcelona, Barcelona, Spain
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Gayà-Vidal M, Dugoujon JM, Esteban E, Athanasiadis G, Rodríguez A, Villena M, Vasquez R, Moral P. Autosomal and X chromosome Alu insertions in Bolivian Aymaras and Quechuas: two languages and one genetic pool. Am J Hum Biol 2010; 22:154-62. [PMID: 19593738 DOI: 10.1002/ajhb.20967] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Thirty-two polymorphic Alu insertions (18 autosomal and 14 from the X chromosome) were studied in 192 individuals from two Amerindian populations of the Bolivian Altiplano (Aymara and Quechua speakers: the two main Andean linguistic groups), to provide relevant information about their genetic relationships and demographic processes. The main objective was to determine from genetic data whether the expansion of the Quechua language into Bolivia could be associated with demographic (Inca migration of Quechua-speakers from Peru into Bolivia) or cultural (language imposition by the Inca Empire) processes. Allele frequencies were used to assess the genetic relationships between these two linguistic groups. Our results indicated that the two Bolivian samples showed a high genetic similarity for both sets of markers and were clearly differentiated from the two Peruvian Quechua samples available in the literature. Additionally, our data were compared with the available literature to determine the genetic and linguistic structure, and East-West differentiation in South America. The close genetic relationship between the two Bolivian samples and their differentiation from the Quechua-speakers from Peru suggests that the Quechua language expansion in Bolivia took place without any important demographic contribution. Moreover, no clear geographical or linguistic structure was found for the Alu variation among South Amerindians.
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Affiliation(s)
- Magdalena Gayà-Vidal
- Unitat d'Antropologia, Biologia Animal, Universitat de Barcelona, Barcelona, Spain
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Díaz R, Moral P, Fonfría M, de Juan M, Mancheño N, Tormo A. Multimodality management of a locally advanced primary oesophageal melanoma with radical surgery and adjuvant chemoimmunoradiotherapy. Clin Transl Oncol 2010; 12:306-9. [DOI: 10.1007/s12094-010-0509-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Athanasiadis G, González-Pérez E, Esteban E, Dugoujon JM, Stoneking M, Moral P. The Mediterranean Sea as a barrier to gene flow: evidence from variation in and around the F7 and F12 genomic regions. BMC Evol Biol 2010; 10:84. [PMID: 20346176 PMCID: PMC2853540 DOI: 10.1186/1471-2148-10-84] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2009] [Accepted: 03/27/2010] [Indexed: 11/30/2022] Open
Abstract
Background The Mediterranean has a long history of interactions among different peoples. In this study, we investigate the genetic relationships among thirteen population samples from the broader Mediterranean region together with three other groups from the Ivory Coast and Bolivia with a particular focus on the genetic structure between North Africa and South Europe. Analyses were carried out on a diverse set of neutral and functional polymorphisms located in and around the coagulation factor VII and XII genomic regions (F7 and F12). Results Principal component analysis revealed a significant clustering of the Mediterranean samples into North African and South European groups consistent with the results from the hierarchical AMOVA, which showed a low but significant differentiation between groups from the two shores. For the same range of geographic distances, populations from each side of the Mediterranean were found to differ genetically more than populations within the same side. To further investigate this differentiation, we carried out haplotype analyses, which provided partial evidence that sub-Saharan gene flow was higher towards North Africa than South Europe. Conclusions As there is no consensus between the two genomic regions regarding gene flow through the Sahara, it is hard to reach a solid conclusion about its role in the differentiation between the two Mediterranean shores and more data are necessary to reach a definite conclusion. However our data suggest that the Mediterranean Sea was at least partially a barrier to gene flow between the two shores.
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Affiliation(s)
- Georgios Athanasiadis
- Unitat d'Antropologia, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain
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Athanasiadis G, Esteban E, Gayà -Vidal M, Dugoujon JM, Moschonas N, Chaabani H, Bissar-Tadmouri N, Harich N, Stoneking M, Moral P. Different Evolutionary Histories of the Coagulation Factor VII Gene in Human Populations? Ann Hum Genet 2010; 74:34-45. [DOI: 10.1111/j.1469-1809.2009.00557.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Gaibar M, Esteban E, Moral P, Gómez-Gallego F, Santiago C, Bandrés F, Luna F, Fernández-Santander A. STR genetic diversity in a Mediterranean population from the south of the Iberian Peninsula. Ann Hum Biol 2009; 37:253-66. [DOI: 10.3109/03014460903341851] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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Athanasiadis G, Esteban E, Vidal MG, Torres RC, Bahri R, Moral P. Polymorphism FXII 46C>T and cardiovascular risk: additional data from Spanish and Tunisian patients. BMC Res Notes 2009; 2:154. [PMID: 19646235 PMCID: PMC2732920 DOI: 10.1186/1756-0500-2-154] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2009] [Accepted: 07/31/2009] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Previous studies showed an association between Coagulation Factor XII 46C>T polymorphism and variation in FXII plasma levels, as 46C>T seems to affect the translation efficiency. Case-control studies in Spanish samples indicated that genotype T/T is an independent risk factor for venous thrombosis, ischemic stroke and acute coronary artery disease. In this study, we tried to reaffirm the importance of 46C>T in two samples from Spain and Tunisia. FINDINGS A Transmission Disequilibrium Test (TDT) based on 101 family trios from Barcelona with one offspring affected by ischemic heart disease and a classical case-control study based on 76 patients with IHD and 118 healthy individuals from North and Centre-South Tunisia were conducted. Subjects were genotyped for 46C>T and data were analyzed accordingly, revealing no association in any of the two samples (TDT: P = 0.16, relative risk 1.17; case-control study: P = 0.59, odds ratio 1.36). CONCLUSION The results suggest that 46C>T is not a risk factor for ischemic heart disease in any of the two analyzed samples and therefore the polymorphism seems not to be a universal risk factor for cardiovascular diseases.
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Affiliation(s)
- Georgios Athanasiadis
- Unitat d'Antropologia, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain.
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Ennafaa H, Amor MB, Yacoubi-Loueslati B, Khodjet el-khil H, Gonzalez-Perez E, Moral P, Maca-Meyer N, Elgaaied A. Alu polymorphisms in Jerba Island population (Tunisia): Comparative study in Arab and Berber groups. Ann Hum Biol 2009; 33:634-40. [PMID: 17381061 DOI: 10.1080/03014460600931087] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Jerba Island represents an interesting area because four distinct ethnic groups have been cohabiting there until now: Arabs, Berbers, dark-skinned people of sub-Saharan origin and Jews. Religious and cultural differences seem to have constituted an obstacle to their intermixing. Our aim is to provide further information on the genetic structure of the Arab and Berber groups for whom previous data based on haploid markers confirmed their reproductive isolation. Five polymorphic Alu markers (HS 4.69, Sb 19.3, TPA-25, ACE and APO-A1) were analysed in a sample of 43 Arabs and 48 Berbers of Jerba. The genetic relationships among these groups and several populations from North Africa, sub-Saharan Africa and Europe were analysed using genetic distances based on allele frequencies. The results showed a homogeneous distribution of Alu insertions in the two geographically close groups, reflecting ancient relationships between them. This study also revealed that Arabs from Jerba present close genetic distances to other North African populations, whilst Berbers of Jerba occupy an intermediate position among Mediterranean populations.
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Affiliation(s)
- Hajer Ennafaa
- Laboratory of Genetics, Immunology and Human Pathologies, Faculty of Sciences of Tunis, Tunis, Tunisia.
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Bahri R, Esteban E, Moral P, Chaabani H. New insights into the genetic history of Tunisians: Data from Alu insertion and apolipoprotein E gene polymorphisms. Ann Hum Biol 2009; 35:22-33. [DOI: 10.1080/03014460701753729] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Bahri R, Esteban E, Moral P, Hassine M, Ben Hamda K, Chaabani H. Apolipoprotein gene polymorphisms and plasma levels in healthy Tunisians and patients with coronary artery disease. Lipids Health Dis 2008; 7:46. [PMID: 19014618 PMCID: PMC2615423 DOI: 10.1186/1476-511x-7-46] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2008] [Accepted: 11/17/2008] [Indexed: 12/30/2022] Open
Abstract
Aim To analyze apolipoprotein gene polymorphisms in the Tunisian population and to check the relation of these polymorphisms and homocysteine, lipid and apolipoprotein levels to the coronary artery disease (CAD). Methods In healthy blood donors and in patients with CAD complicated by myocardial infarction (MI) four apolipoprotein gene polymorphisms [APO (a) PNR, APO E, APO CI and APO CII] were determined and plasma levels of total homocysteine, total cholesterol (TC), triglycerides (TG), HDL-cholesterol (HLD-C) and apolipoproteins (apo A-I, Apo B, Apo E) were measured. Results Analysis of the four apolipoprotein gene polymorphisms shows a relative genetic homogeneity between Tunisian population and those on the other side of Mediterranean basin. Compared to controls, CAD patients have significantly higher main concentrations of TC, TG, LDL-C, apo B and homocysteine, and significantly lower ones of HDL-C, apo A-I and apo E. The four apolipoprotein gene polymorphisms have not showed any significant differences between patients and controls. However, the APO E4 allele appears to be associated to the severity of CAD and to high levels of atherogenic parameters and low level of apo E, which has very likely an anti-atherogenic role. Conclusion Although APO (a) PNR, APO CI and APO CII genes are analyzed in only few populations, they show a frequency distribution, which is not at variance with that of APO E gene and other widely studied genetic markers. In the Tunisian population the APO E 4 appears to be only indirectly involved in the severity of CAD. In the routine practice, in addition of classic parameters, it will be useful to measure the concentration of apo E and that of Homocysteine and if possible to determine the APO E gene polymorphism.
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Affiliation(s)
- Raoudha Bahri
- Laboratoire de Génétique Humaine, Faculté de Pharmacie de Monastir, Université de Monastir 5000 Monastir, Tunisia.
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Piras I, Falchi A, Moral P, Melis A, Giovannoni L, Paoli G, Calò C, Vona G, Varesi L. Frequencies of promoter pentanucleotide (TTTTA)n of CYP11A gene in European and North African populations. ACTA ACUST UNITED AC 2008; 12:93-6. [PMID: 18307388 DOI: 10.1089/gte.2007.0060] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
The present work attempts to determine the distribution of CYP11A (TTTTA)n genotype and allele frequencies in 10 European and North African populations. This polymorphism has been associated with hyperandrogenism by several association studies. To our knowledge, this is the first study investigating the ethnic variation of this polymorphism. DNA was extracted from 868 whole-blood samples with the standard phenol-chloroform technique, and PCR reactions were carried out using fluorescent primers as described previously. PCR products were analyzed by an ABI 3,730 DNA Analyzer. A total of six alleles were identified, ranging from 220 bp (4 repeats [4R]) to 250 bp (10R). The most frequent allelic fragment size in all populations was 4R, with frequencies ranging from 47.9% (Sicily) to 62.8% (Tuscany and Germany). Allelic frequencies showed high heterogeneity between analyzed populations. We detected a significant gradient for alleles 4R and 8R. In this study, we report the allele frequency distribution of CYP11A (TTTTA)n showing a north-south geographic gradient. This result could be useful for epidemiological studies about hyperandrogenism.
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Affiliation(s)
- Ignazio Piras
- Department of Experimental Biology, University of Cagliari, Cagliari, Italy
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Resano M, Esteban E, González-Pérez E, Vía M, Athanasiadis G, Avena S, Goicoechea A, Bartomioli M, Fernández V, Cabrera A, Dejean C, Carnese F, Moral P. How many populations set foot through the Patagonian door? Genetic composition of the current population of Bahía Blanca (Argentina) based on data from 19 Alu polymorphisms. Am J Hum Biol 2008; 19:827-35. [PMID: 17876811 DOI: 10.1002/ajhb.20648] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The city of Bahía Blanca occupies a strategic place in Argentina south of the Pampean region in the north-east corner of the Patagonia. Since 1828, this city has been the historical and political border between Amerindian lands in the south, and the lands of European colonists. Nowadays, Bahía Blanca is an urban population mainly composed by descendents of immigrants from Spain and other European countries with apparently low admixture with Amerindians. In view of the unexpectedly high Amerindian admixture levels (about 46.7%) suggested by mtDNA data, and protein markers (19.5%), we analyzed a set of 19 Alu polymorphisms (18 autosomal, 1 of Chromosome Y) in a well-documented genealogical sample from Bahía Blanca. The genotyped sample was made up of 119 unrelated healthy individuals whose birth place and grandparent origins were fully documented. According to available genealogical records, the total sample has been subdivided into two groups: Bahía Blanca Original (64 individuals with all 4 gandparents born in Argentina) and Bahía Blanca Mix (55 individuals with one to three grandparents born out of Argentina). Allele frequencies and gene diversity values in Bahía Blanca fit well into the European ranges. Population relationships have been tested for 8 Alu markers, whose variation has been described in several Amerindian and European samples. Reynolds genetic distances underline the significant genetic similarity of Bahía Blanca to Europeans (mean distance 0.044) and their differentiation from Amerindians (0.146). Interestingly enough, when the general sample is divided, Bahía Blanca Original appears slightly closer to Amerindians (0.127) in contrast to Bahía Blanca Mix (0.161). Furthermore, the genetic relationships depicted through a principal components analysis emphasize the relative similarity of Bahía Blanca Original to Amerindians. A thorough knowledge of the sample origins has allowed us to make a subtle distinction of the genetic composition of Bahía Blanca.
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Affiliation(s)
- M Resano
- Unitat d'Antropologia, Departament de Biologia Animal, Universitat de Barcelona, Barcelona, Spain
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Ghiani ME, Moral P, Mitchell RJ, Hernández M, García-Moro C, Vona G. Y-chromosome-Specific STR haplotype data on the Rapanui population (Easter Island). Hum Biol 2007; 78:565-78. [PMID: 17506287 DOI: 10.1353/hub.2007.0005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Located in the south Pacific Ocean, Rapanui is one of the most isolated inhabited islands in the world. Cultural and biological data suggest that the initial Rapanui population originated from central Polynesia, although the presence of foreign or exotic genes in the contemporary population, as a result of admixture with Europeans and/or South Americans during the last two centuries, also has to be considered. To estimate the genetic affinities of the Rapanui population with neighboring populations, we analyzed seven microsatellite polymorphisms of the Y chromosome that recently have been indicated as useful in the study of local population structure and recent demographic history. Phylogenetic analysis of Rapanui Y-chromosome haplotypes identified two clusters. The largest cluster contained 60% of all haplotypes and is characterized, in particular, by the presence of the DYS19*16, DYS390*20, and DYS393*14 alleles, a combination found frequently in Western Samoa. The second cluster is characterized by the presence of the DYS19*14, DYS390*24, and DYS393*13 alleles, and these have a relatively high frequency in European and European-derived populations but are either infrequent or absent in native Pacific populations. In addition to the two clusters, one male is of haplogroup Q*, which is indicative of native American ancestry. The genetic structure of the current male population of Rapanui is most likely a product of some genetic contribution from European and South American invaders who mated with the indigenous Polynesian women. However, analysis of Rapanui's relationships with other Pacific and Asian populations indicates that, as in Western Samoa and Samoa, the population has experienced extreme drift and founder events.
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Affiliation(s)
- Maria Elena Ghiani
- Section of Anthropology, Department of Experimental Biology, University of Cagliari, Monserrato-Cagliari 09042, Italy
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45
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Cruciani F, La Fratta R, Trombetta B, Santolamazza P, Sellitto D, Colomb EB, Dugoujon JM, Crivellaro F, Benincasa T, Pascone R, Moral P, Watson E, Melegh B, Barbujani G, Fuselli S, Vona G, Zagradisnik B, Assum G, Brdicka R, Kozlov AI, Efremov GD, Coppa A, Novelletto A, Scozzari R. Tracing Past Human Male Movements in Northern/Eastern Africa and Western Eurasia: New Clues from Y-Chromosomal Haplogroups E-M78 and J-M12. Mol Biol Evol 2007; 24:1300-11. [PMID: 17351267 DOI: 10.1093/molbev/msm049] [Citation(s) in RCA: 119] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Detailed population data were obtained on the distribution of novel biallelic markers that finely dissect the human Y-chromosome haplogroup E-M78. Among 6,501 Y chromosomes sampled in 81 human populations worldwide, we found 517 E-M78 chromosomes and assigned them to 10 subhaplogroups. Eleven microsatellite loci were used to further evaluate subhaplogroup internal diversification. The geographic and quantitative analyses of haplogroup and microsatellite diversity is strongly suggestive of a northeastern African origin of E-M78, with a corridor for bidirectional migrations between northeastern and eastern Africa (at least 2 episodes between 23.9-17.3 ky and 18.0-5.9 ky ago), trans-Mediterranean migrations directly from northern Africa to Europe (mainly in the last 13.0 ky), and flow from northeastern Africa to western Asia between 20.0 and 6.8 ky ago. A single clade within E-M78 (E-V13) highlights a range expansion in the Bronze Age of southeastern Europe, which is also detected by haplogroup J-M12. Phylogeography pattern of molecular radiation and coalescence estimates for both haplogroups are similar and reveal that the genetic landscape of this region is, to a large extent, the consequence of a recent population growth in situ rather than the result of a mere flow of western Asian migrants in the early Neolithic. Our results not only provide a refinement of previous evolutionary hypotheses but also well-defined time frames for past human movements both in northern/eastern Africa and western Eurasia.
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Affiliation(s)
- Fulvio Cruciani
- Dipartimento di Genetica e Biologia Molecolare, Sapienza Università di Roma, Rome, Italy, and Laboratoire d'Immunologie, Hôpital de Sainte-Marguerite, Marseille, France
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Athanasiadis G, Esteban E, Via M, Dugoujon JM, Moschonas N, Chaabani H, Moral P. The X chromosome Alu insertions as a tool for human population genetics: data from European and African human groups. Eur J Hum Genet 2007; 15:578-83. [PMID: 17327877 DOI: 10.1038/sj.ejhg.5201797] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Alu elements are the most abundant mobile elements in the human genome (approximately 1,100,000 copies). Polymorphic Alu elements have been proved to be useful in studies of human origins and relationships owing to two important advantages: identity by descent and absence of the Alu element known to be the ancestral state. Alu variation in the X chromosome has been described previously in human populations but, as far as we know, these elements have not been used in population relationship studies. Here, we describe the allele frequencies of 13 'young' Alu elements of the X chromosome (Ya5DP62, Ya5DP57, Yb8DP49, Ya5a2DP1, Yb8DP2, Ya5DP3, Ya5NBC37, Yd3JX437, Ya5DP77, Ya5NBC491, Yb8NBC578, Ya5DP4 and Ya5DP13) in six human populations from sub-Saharan Africa (the Ivory Coast), North Africa (Moroccan High Atlas, Siwa oasis in Egypt, Tunisia), Greece (Crete Island) and Spain (Basque Country). Eight out of 13 Alu elements have shown remarkably high gene diversity values in all groups (average heterozygosities: 0.342 in the Ivory Coast, 0.250 in North Africa, 0.209 in Europe). Genetic relationships agree with a geographical pattern of differentiation among populations, with some peculiar features observed in North Africans. Crete Island and the Basque Country show the lowest genetic distance (0.0163) meanwhile Tunisia, in spite of its geographical location, lies far from the other two North African samples. The results of our work demonstrate that X chromosome Alu elements comprise a reliable set of genetic markers useful to describe human population relationships for fine-scale geographical studies.
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Affiliation(s)
- Georgios Athanasiadis
- Unitat d'Antropologia, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain
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47
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Falchi A, Piras IS, Giovannoni L, Moral P, Vona G, Varesi L. Population genetic data on four STR loci, PAI (CA)n, GpIIIa (CT)n, PLAT (TG)14 (CA)12, and NOS2A (CCTTT)n, in Mediterranean populations. Leg Med (Tokyo) 2007; 9:218-20. [PMID: 17320454 DOI: 10.1016/j.legalmed.2007.01.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2006] [Revised: 11/28/2006] [Accepted: 01/05/2007] [Indexed: 10/23/2022]
Abstract
In the present study, we have analyzed four highly polymorphic regions (STRs) chosen from four candidate genes involved in: (1) Platelet aggregation: alpha subunit of the platelet GpIIb/GpIIIa integrin complex (GpIIIa (CT)n; 17q21.31), (2) Coagulation fibrinolysis: Plasminogen Activator Tissue (PLAT5 (TG)14(TA)12; 8p12-q11.2) and Plasminogen Activator Inhibitor-1 (PAI-1 (CA)n; 7q21.3-q22), (3) Oxidative metabolism: the inducible nitric oxide (NO) synthase (iNOS) gene (NOS2A (CCTTT)n; 17cen-q11.2). Allele frequencies for these four STR loci were investigated in several Mediterranean populations. The population data deviate from the Hardy-Weinberg equilibrium in all populations for GpIIIa (CT)n polymorphism.
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Affiliation(s)
- Alessandra Falchi
- Department of Human Genetics, Faculty of Science, University of Corsica, BP52 20250 Corte Corsica, France.
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Luna F, Moral P, Alonso V, Fernandez-Santander A. Factors Influencing Prereproductive Mortality in the Isolated and Preindustrial Western Mediterranean Population of La Alpujarra, 1900–1950. Hum Biol 2007; 79:381-94. [DOI: 10.1353/hub.2007.0051] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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González-Pérez E, Esteban E, Via M, García-Moro C, Hernández M, Moral P. Genetic change in the polynesian population of Easter Island: evidence from Alu insertion polymorphisms. Ann Hum Genet 2006; 70:829-40. [PMID: 17044858 DOI: 10.1111/j.1469-1809.2006.00293.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The origin of Pacific islanders is still an open issue in human population genetics. To address this topic we analyzed a set of 18 Alu insertion polymorphisms in a total of 176 chromosomes from native Easter Island inhabitants (Rapanui). Available genealogical records allowed us to subdivide the total island sample into two groups, representative of the native population living in the island around 1900, and another formed by individuals with some ancestors of non-Rapanui origin. Significant genetic differentiation was found between these groups, allowing us to make some biodemographic and historical inferences about the origin and evolution of this geographically isolated island population. Our data are consistent with equivalent and recent contributions from Amerindian and European migrants to the 1900s Rapanui population, with an accelerated increase in the European gene flow during the 20(th) century, especially since the 1960s. Comparative analysis of our results with other available Alu variation data on neighbouring populations supports the "Voyaging Corridor" model of Polynesian human settlement, which indicates that pre-Polynesians are mainly derived from Southeast Asian and Wallacean populations rather than from Taiwan or the Philippines. This study underlines the importance of sampling and taking into account historical information in genetic studies to unravel the recent evolution of human populations.
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Affiliation(s)
- E González-Pérez
- Unitat d'Antropologia, Departament de Biologia Animal, Universitat de Barcelona, Avda. Diagonal 645, 08028-Barcelona, Spain
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Piras I, Melis A, Ghiani ME, Falchi A, Luiselli D, Moral P, Varesi L, Calò CM, Vona G. Human CHIT1 gene distribution: new data from Mediterranean and European populations. J Hum Genet 2006; 52:110. [PMID: 17106626 DOI: 10.1007/s10038-006-0086-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2006] [Accepted: 10/24/2006] [Indexed: 10/23/2022]
Abstract
A 24 bp duplication in the CHIT1 gene (H allele) is associated with a deficiency in the activity of chitotriosidase, an enzyme with the capability to hydrolyse chitin. A recent study in European and two sub-Saharan populations suggested a relationship between the presence of the mutation, improved environmental conditions, and the disappearance of parasitic diseases, including Plasmodium falciparum malaria. This result was not supported by the high frequency of the 24 bp duplication in a sample from Taiwan, an area with high malaria endemicity until 40 years ago. In this study, we analysed the frequency variability of the H allele in Mediterranean populations and its internal variability in Sardinia (Italy) with respect to malaria, which had been endemic on the island until its eradication during 1946-1950. The pattern of H frequency distributions is not consistent with the hypothesis of selective pressures acting on CHIT1 gene. The Moran's index coefficient and correlogram seem to indicate, indeed, that allele distribution was determined by random factors. The pattern of frequency distribution suggests a possible Asiatic origin of the H allele, but it could be possible also that the mutant allele had diffused out of Africa, and was subsequently lost from African populations.
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Affiliation(s)
- Ignazio Piras
- Department of Experimental Biology, University of Cagliari, SS 554, km 4,500, 09042, Monserrato (CA), Italy.
| | - Alessandra Melis
- Department of Experimental Biology, University of Cagliari, SS 554, km 4,500, 09042, Monserrato (CA), Italy
| | - Maria Elena Ghiani
- Department of Experimental Biology, University of Cagliari, SS 554, km 4,500, 09042, Monserrato (CA), Italy
| | | | - Donata Luiselli
- Department of Experimental Evolutionistic Biology, University of Bologna, Bologna, Italy
| | - Pedro Moral
- Department of Animal Biology, University of Barcelona, Barcelona, Spain
| | - Laurent Varesi
- Department of Human Genetics, University of Corsica, Corte, France
| | - Carla Maria Calò
- Department of Experimental Biology, University of Cagliari, SS 554, km 4,500, 09042, Monserrato (CA), Italy
| | - Giuseppe Vona
- Department of Experimental Biology, University of Cagliari, SS 554, km 4,500, 09042, Monserrato (CA), Italy
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