154 results on '"Dugoujon JM"'
Search Results
2. PopAffiliator: online calculator for individual affiliation to a major population group based on 17 autosomal STR genotype profile
- Author
-
Pereira, L, Alshamali, F, Andreassen, R, Ballard, R, Chantratita, W, Cho, NS, Coudray, C, Dugoujon, JM, Espinoza, M, González-Andrade, F, Hadi, S, Immel, U-D, Marian, C, Gonzalez-Martin, A, Mertens, G, Parson, W, Perone, C, Prieto, L, Takeshita, H, Villalobos, HR, Zeng, Z, Zhivotovsky, L, Camacho, R, Fonseca, NA, and Instituto de Investigação e Inovação em Saúde
- Subjects
Individual affiliation ,Autosomal STRs ,Online calculator ,Genotype profile - Abstract
Because of their sensitivity and high level of discrimination, short tandem repeat (STR) maker systems are currently the method of choice in routine forensic casework and data banking, usually in multiplexes up to 15-17 loci. Constraints related to sample amount and quality, frequently encountered in forensic casework, will not allow to change this picture in the near future, notwithstanding the technological developments. In this study, we present a free online calculator named PopAffiliator ( http://cracs.fc.up.pt/popaffiliator ) for individual population affiliation in the three main population groups, Eurasian, East Asian and sub-Saharan African, based on genotype profiles for the common set of STRs used in forensics. This calculator performs affiliation based on a model constructed using machine learning techniques. The model was constructed using a data set of approximately fifteen thousand individuals collected for this work. The accuracy of individual population affiliation is approximately 86%, showing that the common set of STRs routinely used in forensics provide a considerable amount of information for population assignment, in addition to being excellent for individual identification. IPATIMUP is an Associate Laboratory of the Portuguese Ministry of Science, Technology and Higher Education and is partially supported by FCT, the Portuguese Foundation for Science and Technology. CRACS-INESC Porto is supported by Programa Operacional Ciência, Tecnologia e Inovação (POCTI) e Quadro Comunitário de Apoio III. NJ and DH were supported by grant 196-1962766-2751. LZh received grants from the Russian Academy of Science for Mol & Cell Biol and FSM.
- Published
- 2011
3. Phylogeography of Y chromosome in Northern Africa
- Author
-
Cruciani, Fulvio, LA FRATTA, R, Santolamazza, P, Sellitto, D, Cefali', Me, BERAUD COLOMB, E, Dugoujon, Jm, and Scozzari, Rosaria
- Published
- 2006
4. Northern and eastern Africa: a Y-chromosome-based phylogeographic analysis
- Author
-
Cruciani, Fulvio, LA FRATTA, R, Trombetta, Beniamino, Santolamazza, P, Sellitto, D, BERAUD COLOMB, E, Dugoujon, Jm, and Scozzari, Rosaria
- Published
- 2006
5. PHYLOGEOGRAPHY OF Y CHROMOSOME IN NORTHERN AND EASTERN AFRICA
- Author
-
Cruciani, Fulvio, LA FRATTA, R, Santolamazza, P, Sellitto, D, Cefali', Me, BERAUD COLOMB, E, Dugoujon, Jm, and Scozzari, Rosaria
- Published
- 2006
6. Alu Insertions in the Iberian Peninsula and North West Africa – Genetic Boundaries or Melting Pot?
- Author
-
Gonzalez-Perez, E., Via, M., Esteban, E., Lopez-Alomar, A., Stephane Mazieres, Harich, N., Kandil, M., Dugoujon, Jm, and Moral, P.
- Subjects
Alu elements ,polymorphisms ,Iberian populations ,Berber populations ,humanities - Abstract
The Western Mediterranean Basin joins a set of ethnically different populations as Iberians and Basques in the North shore and Berbers and Arab-speakers in the South one. In spite of this differentiation, they have maintained historical contacts since ancient times. The existence of a possible common genetic background (specially for Berbers and Iberians) together with the genetic impact of the Islamic occupation of the Iberian Peninsula during 7 centuries are some of the intriguing anthropological questions that have been studied in this area using several classical and DNA markers. The aim of this work is to present the results on a survey of polymorphic Alu elements in 10 human populations of the Western Mediterranean. Recent Alu subfamilies include a significant number of polymorphic Alu insertions in humans. The polymorphic Alu elements are neutral genetic markers of identical descent with known ancestral states. This fact turns Alu insertions into useful markers for the study of human population genetics. A total number of 14 Alu insertions were analyzed in 5 Iberian populations, 3 Berber groups from North-Western Africa, an Arab-speaker population from Morocco and a sub-Saharan ethnic group from Ivory Coast. The results of this study allow the genetic characterization of Berber populations, which show a certain degree of differentiation from Arab-speaking groups of the same geographic area. Furthermore, a closer genetic distance between South Spain and Moroccan Berbers as compared with other Spanish samples supports a major genetic influx consistent with some (but not all) previous genetic studies on populations from the two shores of the Gibraltar Straits.
- Published
- 2003
7. Immunoglobulin allotypes and hepatitis C virus (HCV) infection
- Author
-
Rat, C., Goria, O., Doffoel, M., Vinel, JP, Daveau, M, Dugoujon, JM, and Lerebours, E.
- Published
- 1998
- Full Text
- View/download PDF
8. Ancient human genomes suggest three ancestral populations for present-day Europeans
- Author
-
Joanna L. Mountain, Michael F. Hammer, Ruslan Ruizbakiev, Cesare de Filippo, Kumarasamy Thangaraj, David E. C. Cole, Haim Ben-Ami, Leila Laredj, Mark Lipson, Jüri Parik, Valentino Romano, Andres Ruiz-Linares, Fouad Berrada, Dominique Delsate, Ugur Hodoglugil, Antti Sajantila, Olga Utevska, Shahlo Turdikulova, Tor Hervig, Ludmila P. Osipova, Hovhannes Sahakyan, Robert W. Mahley, Ramiro Barrantes, Kirsten I. Bos, Stanislav Dryomov, Peter H. Sudmant, Nadin Rohland, Heng Li, Gabriel Renaud, Mikhail Voevoda, Claudio M. Bravi, Jean-Michel Guinet, Rem I. Sukernik, Joachim Wahl, Matthias Meyer, Christos Economou, Kay Prüfer, Graciela Bailliet, Mait Metspalu, Mikhail Churnosov, Iosif Lazaridis, Johannes Krause, Bonnie Berger, Levon Yepiskoposyan, Francesca Brisighelli, Francesco Calì, Irene Gallego Romero, Oleg Balanovsky, George Ayodo, Alan Cooper, Alissa Mittnik, Julio Molina, George van Driem, Jean-Michel Dugoujon, Larissa Damba, Fedor Platonov, Nick Patterson, David Reich, Thomas B. Nyambo, David Comas, Olga L. Posukh, Béla Melegh, Draga Toncheva, Alena Kushniarevich, Brenna M. Henn, Montgomery Slatkin, René Vasquez, Elena B. Starikovskaya, Joachim Burger, Ayele Tarekegn, Tatijana Zemunik, Ene Metspalu, Sena Karachanak-Yankova, Lalji Singh, Wolfgang Haak, Susanna Sawyer, Rick A. Kittles, Cheryl A. Winkler, Svante Pääbo, Francisco Rothhammer, Marina Gubina, Pierre Zalloua, Aashish R. Jha, Swapan Mallick, Sergi Castellano, Qiaomei Fu, Desislava Nesheva, Sergey Litvinov, Ingrida Uktveryte, Michael Francken, Cosimo Posth, Theologos Loukidis, Cristian Capelli, Janet Kelso, Sarah A. Tishkoff, Toomas Kivisild, Mark G. Thomas, Elin Fornander, Mercedes Villena, Fredrik Hallgren, Vaidutis Kučinskas, Daniel Corach, George B.J. Busby, Judit Bene, William Klitz, Hamza A. Babiker, Karola Kirsanow, Ruth Bollongino, Rita Khusainova, Evan E. Eichler, Sardana A. Fedorova, Klemetti Näkkäläjärvi, Igor Rudan, Susanne Nordenfelt, Joshua G. Schraiber, Elena Balanovska, Antonio Salas, Richard Villems, Gabriel Bedoya, Elza Khusnutdinova, Massachusetts Institute of Technology. Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology. Department of Mathematics, Lipson, Mark, Berger Leighton, Bonnie, Lazaridis,I, Patterson,P, Mittnik,A, Renaud,G, Mallick,S, Kirsanow,K, Sudmant,PH, Schraiber,JG, Castellano,S, Lipson,M, Berger,B, Economou,C, Bollongino,R, Fu,Q, Bos,KI, Nordenfelt,S, Li,H, De Filippo,C, Pruefer,K, Sawyer, Posth,C, Haak1,H, Hallgren,F, Fornander,E, Rohland,N, Delsate,D, Francken,M, Guinet,JM, Wah,J, Ayodo,G, Babiker,HA, Bailliet,G, Balanovska,E, Balanovsky,O, Barrantes,R, Bedoya,G, Ben-Ami,H, Bene,J, Berrada,F, Bravi,CM, Brisighelli,F, Busby,GBJ, Cali,F, Churnosov,M, Cole,DEC, Corach,D, Damba,L, van Driem,G, Dryomov,S, Dugoujon,JM, Fedorova,SA, Gallego Romero,I, Gubina,M, Hammer,M, Henn,BM, Hervig,T, Hodoglugi,U, Jha,AR, Karachanak-Yankova,S, Khusainova,R, Khusnutdinova,E, Kittles,R:Kivisild,T, Klitz,W, Kucˇinskas,V, Kushniarevich,A, Laredj,L, Litvinov,S, Loukidis,T, Mahley,RW, Melegh,B, Metspalu,E, Molina,J, Mountain,J, Na¨kka¨la¨ja¨rvi,K, Nesheva,D, Nyambo,T, Osipova,L, Parik,J, Platonov,F, Posukh,O, Romano,V, Rothhammer,F, Rudan,I, Ruizbakiev,R, Sahakyan,H, Sajantila,A, Salas,A, Starikovskaya,EB, Tarekegn,A, Toncheva,D, Turdikulova,S, Uktveryte,I, Utevska,O, Vasquez,R, Villena,M, Voevoda,M, Winkler,CA, Yepiskoposyan,L, Zalloua,P, Zemunik,T, Cooper, Capelli,C, Thomas,MG, Ruiz-inares,A, Tishkoff,SA, Singh,L, Thangaraj,K, Villems,R, Comas,D, Sukernik,R, Metspalu,M, Meyer,M, Eichler,EE, Burger,J, Slatkin,M, Pa¨a¨bo,S, Kelso,J, Reich,D, and Krause,J
- Subjects
History ,Neanderthal ,Biología ,Population Dynamics ,Present day ,Genoma humà ,Genome ,purl.org/becyt/ford/1 [https] ,Basal (phylogenetics) ,Settore BIO/13 - Biologia Applicata ,History, Ancient ,Genetics ,Principal Component Analysis ,education.field_of_study ,0303 health sciences ,Multidisciplinary ,Ancient DNA ,030305 genetics & heredity ,food and beverages ,Agriculture ,Genomics ,3. Good health ,Europe ,Workforce ,CIENCIAS NATURALES Y EXACTAS ,Human ,Archaeogenetics ,Asia ,Lineage (genetic) ,EUROPE ,Otras Ciencias Biológicas ,European Continental Ancestry Group ,Population ,Settore BIO/08 - ANTROPOLOGIA ,evolution ,Europeans ,Biology ,Article ,White People ,Ancient ,Genètica de poblacions humanes ,Human origins ,Ciencias Biológicas ,03 medical and health sciences ,HUMAN ORIGINS ,biology.animal ,Humans ,ANCIENT DNA ,purl.org/becyt/ford/1.6 [https] ,education ,Quantitative Biology - Populations and Evolution ,Denisovan ,030304 developmental biology ,Genetic diversity ,ancient DNA, modern DNA, Europeans, prehistory ,Genome, Human ,Populations and Evolution (q-bio.PE) ,biology.organism_classification ,Evolutionary biology ,FOS: Biological sciences ,Upper Paleolithic ,Human genome ,GENOMICS - Abstract
We sequenced the genomes of a ∼7,000-year-old farmer from Germany and eight ∼8,000-year-old hunter-gatherers from Luxembourg and Sweden. We analysed these and other ancient genomes1,2,3,4 with 2,345 contemporary humans to show that most present-day Europeans derive from at least three highly differentiated populations: west European hunter-gatherers, who contributed ancestry to all Europeans but not to Near Easterners; ancient north Eurasians related to Upper Palaeolithic Siberians3, who contributed to both Europeans and Near Easterners; and early European farmers, who were mainly of Near Eastern origin but also harboured west European hunter-gatherer related ancestry. We model these populations’ deep relationships and show that early European farmers had ∼44% ancestry from a ‘basal Eurasian’ population that split before the diversification of other non-African lineages., Instituto Multidisciplinario de Biología Celular
- Published
- 2014
9. Naturally acquired antibodies from Beninese infants promote Plasmodium falciparum merozoite-phagocytosis by human blood leukocytes: implications for control of asymptomatic malaria infections.
- Author
-
Fall AKDJ, Kana IH, Dechavanne C, Garcia-Senosiain A, Guitard E, Milet J, Massougbodji A, Garcia A, Dugoujon JM, Migot-Nabias F, Theisen M, and Courtin D
- Subjects
- Child, Infant, Animals, Humans, Merozoites, Plasmodium falciparum, Asymptomatic Infections, Longitudinal Studies, Phagocytosis, Leukocytes, Immunoglobulin G, Malaria, Malaria, Falciparum
- Abstract
Background: Immunoglobulin G (IgG) antibodies are thought to play important roles in the protection against Plasmodium falciparum (P. falciparum) malaria. A longitudinal cohort study performed in the Southern part of Benin, identified a group of infants who were able to control asymptomatic malaria infections (CAIG)., Methods: IgG antibodies against distinct merozoite antigens were quantified in plasma from Beninese infants. Functionality of these antibodies was assessed by the merozoite-phagocytosis assay using THP-1 cells and primary neutrophils as effector cells. Gm allotypes were determined by a serological method of haemagglutination inhibition., Results: Purified IgG from infants in CAIG promoted higher levels of merozoite-phagocytosis than did IgG from children who were unable to control asymptomatic infections (Ologit multivariate regression model, Coef. = 0.06, 95% CI 0.02;0.10, P = 0.002). High level of merozoite-phagocytosis activity was significantly associated with high levels of IgG against AMA1 (Coef. = 1.76, 95% CI 0.39;3.14, P = 0.012) and GLURP-R2 (Coef. = 12.24, 95% CI 1.35;23.12, P = 0.028). Moreover, infants of the G3m5,6,10,11,13,14,24 phenotype showed higher merozoite-phagocytosis activity (Generalized linear model multivariate regression, Coef. = 7.46, 95% CI 0.31;14.61, P = 0.041) than those presenting other G3m phenotypes., Conclusion: The results of the present study confirm the importance of antibodies to merozoite surface antigens in the control of asymptomatic malaria infection in Beninese infants. The study also demonstrated that G3m phenotypes impact the functional activity of IgG. This last point could have a considerable impact in the research of candidate vaccines against malaria parasites or other pathogens., (© 2022. The Author(s).)
- Published
- 2022
- Full Text
- View/download PDF
10. Genetic variation patterns of β-thalassemia in Western Andalusia (Spain) reveal a structure of specific mutations within the Iberian Peninsula.
- Author
-
Sánchez-Martínez LJ, Hernández CL, Rodríguez JN, Dugoujon JM, Novelletto A, Ropero P, Pereira L, and Calderón R
- Subjects
- Alleles, Humans, Mutation, Spain epidemiology, beta-Globins genetics, beta-Thalassemia epidemiology, beta-Thalassemia genetics
- Abstract
Background: Analyses of the genomic variation in the western Mediterranean population are being used to reveal its evolutionary history and to understand the molecular basis of particular diseases., Aim: To observe the β-thalassemia mutational spectrum in western Andalusia, Spain, in the context of the Mediterranean. In addition, associations between disease and neutral gene variants within the β-globin gene (HBB) were also evaluated., Subjects and Methods: This study included 63 unrelated individuals diagnosed with β-thalassemia. In addition, 97 unrelated, healthy subjects of the same territory were also analysed as proxies of the normal genetic background. Allele associations and population genetic structure analyses were performed using different methodologies., Results: Data have revealed a rather restricted spectrum of β-thalassemia mutations in the analysed sample. Although the detected variants fit well with the Mediterranean pattern, certain singularities support a structure of some specific β-thalassemia alleles. The IVSI-1 (G > A) shows a strong regionalisation. The spatial correlogram revealed a typically narrow wave structure, presumably linked to genetic isolation and genetic drift., Conclusions: The long history of endemic malaria in the study territory, the rather high consanguinity rates among its autochthonous population, and other demographic features have been used here to understand the western Andalusian β-thalassemia molecular portrait.
- Published
- 2021
- Full Text
- View/download PDF
11. Susceptibility to Plasmodium falciparum Malaria: Influence of Combined Polymorphisms of IgG3 Gm Allotypes and Fc Gamma Receptors IIA, IIIA, and IIIB.
- Author
-
Fall AKDJ, Dechavanne C, Sabbagh A, Guitard E, Milet J, Garcia A, Dugoujon JM, Courtin D, and Migot-Nabias F
- Subjects
- Benin, Female, GPI-Linked Proteins genetics, Genes, Immunoglobulin Heavy Chain, Genetic Association Studies, Genetic Predisposition to Disease, Host-Pathogen Interactions, Humans, Immunoglobulin Constant Regions, Immunoglobulin G blood, Infant, Infant, Newborn, Malaria, Falciparum diagnosis, Malaria, Falciparum immunology, Malaria, Falciparum parasitology, Male, Phenotype, Plasmodium falciparum immunology, Risk Assessment, Risk Factors, Immunoglobulin G genetics, Malaria, Falciparum genetics, Plasmodium falciparum pathogenicity, Polymorphism, Genetic, Receptors, IgG genetics
- Abstract
The binding of immunoglobulin (Ig) to Fc gamma receptors (FcgR) at the immune cell surface is an important step to initiate immunological defense against malaria. However, polymorphisms in receptors and/or constant regions of the IgG heavy chains may modulate this binding. Here, we investigated whether polymorphisms located in FcgR and constant regions of the heavy chain of IgG are associated with susceptibility to P. falciparum malaria. For this purpose, a clinical and parasitological follow-up on malaria was conducted among 656 infants in southern Benin. G3m allotypes (from total IgG3) were determined by a serological method of hemagglutination inhibition. FcgRIIA 131R/H and FcgRIIIA 176F/V genotypes were determined using the TaqMan method and FcgRIIIB NA1/NA2 genotypes were assessed by polymerase chain reaction using allele-specific primers. Association analyses between the number of malaria infections during the follow-up and polymorphisms in IgG G3m allotypes and FcgR were studied independently by zero inflated binomial negative regression. The influence of combinations of G3m allotypes and FcgRIIA/FcgRIIIA/FcgRIIIB polymorphisms on the number of P. falciparum infections, and their potential interaction with environmental exposure to malaria was assessed by using the generalized multifactor dimensionality reduction (GMDR) method. Results showed that individual carriage of G3m24 single allotype and of G3m5,6,10,11,13,14,24 phenotype was independently associated with a high risk of malaria infection. A risk effect for G3m6 was observed only under high environmental exposure. FcgRIIIA 176VV single genotype and combined carriage of FcgRIIA 131RH/FcgRIIIA 176VV/FcgRIIIB NA1NA2, FcgRIIA 131HH/FcgRIIIA 176FF/FcgRIIIB NA1NA1, FcgRIIA 131HH/FcgRIIIA 176VV/FcgRIIIB NA2NA2 and FcgRIIA 131HH/FcgRIIIA 176VV/FcgRIIIB NA1NA2 genotypes were related to a high number of malaria infections. The risk was accentuated for FcgRIIIA 176VV when considering the influence of environmental exposure to malaria. Finally, the GMDR analysis including environmental exposure showed strengthened associations with a malaria risk when FcgRIIA/FcgRIIIA/FcgRIIIB genotypes were combined to G3m5,6,11,24 and G3m5,6,10,11,13,15,24 phenotypes or G3m10 and G3m13 single allotypes. Our results highlight the relevance of studying IgG heavy chain and FcgR polymorphisms, independently as well as in combination, in relation to the individual susceptibility to P. falciparum infection. The intensity of individual exposure to mosquito bites was demonstrated to impact the relationships found., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2020 Fall, Dechavanne, Sabbagh, Guitard, Milet, Garcia, Dugoujon, Courtin and Migot-Nabias.)
- Published
- 2020
- Full Text
- View/download PDF
12. Predicting haplogroups using a versatile machine learning program (PredYMaLe) on a new mutationally balanced 32 Y-STR multiplex (CombYplex): Unlocking the full potential of the human STR mutation rate spectrum to estimate forensic parameters.
- Author
-
Bouakaze C, Delehelle F, Saenz-Oyhéréguy N, Moreira A, Schiavinato S, Croze M, Delon S, Fortes-Lima C, Gibert M, Bujan L, Huyghe E, Bellis G, Calderon R, Hernández CL, Avendaño-Tamayo E, Bedoya G, Salas A, Mazières S, Charioni J, Migot-Nabias F, Ruiz-Linares A, Dugoujon JM, Thèves C, Mollereau-Manaute C, Noûs C, Poulet N, King T, D'Amato ME, and Balaresque P
- Subjects
- DNA Fingerprinting, Humans, Male, Multiplex Polymerase Chain Reaction, Polymorphism, Single Nucleotide, Chromosomes, Human, Y, Forensic Genetics methods, Haplotypes, Machine Learning, Microsatellite Repeats, Mutation Rate
- Abstract
We developed a new mutationally well-balanced 32 Y-STR multiplex (CombYplex) together with a machine learning (ML) program PredYMaLe to assess the impact of STR mutability on haplogourp prediction, while respecting forensic community criteria (high DC/HD). We designed CombYplex around two sub-panels M1 and M2 characterized by average and high-mutation STR panels. Using these two sub-panels, we tested how our program PredYmale reacts to mutability when considering basal branches and, moving down, terminal branches. We tested first the discrimination capacity of CombYplex on 996 human samples using various forensic and statistical parameters and showed that its resolution is sufficient to separate haplogroup classes. In parallel, PredYMaLe was designed and used to test whether a ML approach can predict haplogroup classes from Y-STR profiles. Applied to our kit, SVM and Random Forest classifiers perform very well (average 97 %), better than Neural Network (average 91 %) and Bayesian methods (< 90 %). We observe heterogeneity in haplogroup assignation accuracy among classes, with most haplogroups having high prediction scores (99-100 %) and two (E1b1b and G) having lower scores (67 %). The small sample sizes of these classes explain the high tendency to misclassify the Y-profiles of these haplogroups; results were measurably improved as soon as more training data were added. We provide evidence that our ML approach is a robust method to accurately predict haplogroups when it is combined with a sufficient number of markers, well-balanced mutation rate Y-STR panels, and large ML training sets. Further research on confounding factors (such as CNV-STR or gene conversion) and ideal STR panels in regard to the branches analysed can be developed to help classifiers further optimize prediction scores., (Copyright © 2020 Elsevier B.V. All rights reserved.)
- Published
- 2020
- Full Text
- View/download PDF
13. Human Genomic Diversity Where the Mediterranean Joins the Atlantic.
- Author
-
Hernández CL, Pita G, Cavadas B, López S, Sánchez-Martínez LJ, Dugoujon JM, Novelletto A, Cuesta P, Pereira L, and Calderón R
- Subjects
- Africa, Northern, Humans, Mediterranean Region, Phylogeography, Polymorphism, Single Nucleotide, Genetic Variation, Genome, Human, Human Migration
- Abstract
Throughout the past few years, a lively debate emerged about the timing and magnitude of the human migrations between the Iberian Peninsula and the Maghreb. Several pieces of evidence, including archaeological, anthropological, historical, and genetic data, have pointed to a complex and intermingled evolutionary history in the western Mediterranean area. To study to what extent connections across the Strait of Gibraltar and surrounding areas have shaped the present-day genomic diversity of its populations, we have performed a screening of 2.5 million single-nucleotide polymorphisms in 142 samples from southern Spain, southern Portugal, and Morocco. We built comprehensive data sets of the studied area and we implemented multistep bioinformatic approaches to assess population structure, demographic histories, and admixture dynamics. Both local and global ancestry inference showed an internal substructure in the Iberian Peninsula, mainly linked to a differential African ancestry. Western Iberia, from southern Portugal to Galicia, constituted an independent cluster within Iberia characterized by an enriched African genomic input. Migration time modeling showed recent historic dates for the admixture events occurring both in Iberia and in the North of Africa. However, an integrative vision of both paleogenomic and modern DNA data allowed us to detect chronological transitions and population turnovers that could be the result of transcontinental migrations dating back from Neolithic times. The present contribution aimed to fill the gaps in the modern human genomic record of a key geographic area, where the Mediterranean and the Atlantic come together., (© The Author(s) 2019. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.)
- Published
- 2020
- Full Text
- View/download PDF
14. A multivariate statistical approach for the estimation of the ethnic origin of unknown genetic profiles in forensic genetics.
- Author
-
Alladio E, Della Rocca C, Barni F, Dugoujon JM, Garofano P, Semino O, Berti A, Novelletto A, Vincenti M, and Cruciani F
- Subjects
- Discriminant Analysis, Forensic Genetics methods, Genetic Markers, Genetics, Population, Genotype, Humans, Least-Squares Analysis, Principal Component Analysis, Support Vector Machine, DNA Fingerprinting methods, Genetic Profile, Microsatellite Repeats, Racial Groups genetics
- Abstract
DNA typing and genetic profile data interpretation are among the most relevant topics in forensic science; among other applications, genetic profile's capability to distinguish biogeographic information about population groups, subgroups and affiliations have been largely explored in the last decade. In fact, for investigative and intelligence purposes, it is extremely useful to identify subjects and estimate their biogeographic origins by examining the recovered DNA profiles from evidence on a crime scene. Current approaches for BiogeoGraphic Ancestry (BGA) estimation using STRs profiles are usually based on Bayesian methods, which quantify the evidence in terms of likelihood ratio, supporting or not the hypothesis that a certain profile belongs to a specific ethnic group. The present study provides an alternative approach to the likelihood ratio method that involves multivariate data analysis strategies for the estimation of multiple populations. Starting from the well-known NIST US autosomal STRs dataset involving African-American, Asian, and Caucasian individuals, and moving towards further and more geographically restricted populations (such as Northern Africans vs sub-Saharan Africans, Afghans vs Iraqis and Italians vs Romanians), powerful multivariate techniques such as Sparse and Logistic Principal Component Analysis (SL-PCA), Sparse Partial Least Squares-Discriminant Analysis (sPLS-DA) and Support Vector Machines (SVM) were employed and their discriminating power was also compared. Both sPLS-DA and SVM techniques provided robust classifications, yielding high sensitivity and specificity models capable of discriminating populations on ethnic basis. This application may represent a powerful and dynamic tool for law enforcement agencies whenever a standard autosomal STR profile is obtained from the biological evidence collected at a crime scene or recovered during mass-disaster and missing person investigations., (Copyright © 2019 Elsevier B.V. All rights reserved.)
- Published
- 2020
- Full Text
- View/download PDF
15. Population structure of modern-day Italians reveals patterns of ancient and archaic ancestries in Southern Europe.
- Author
-
Raveane A, Aneli S, Montinaro F, Athanasiadis G, Barlera S, Birolo G, Boncoraglio G, Di Blasio AM, Di Gaetano C, Pagani L, Parolo S, Paschou P, Piazza A, Stamatoyannopoulos G, Angius A, Brucato N, Cucca F, Hellenthal G, Mulas A, Peyret-Guzzon M, Zoledziewska M, Baali A, Bycroft C, Cherkaoui M, Chiaroni J, Di Cristofaro J, Dina C, Dugoujon JM, Galan P, Giemza J, Kivisild T, Mazieres S, Melhaoui M, Metspalu M, Myers S, Pereira L, Ricaut FX, Brisighelli F, Cardinali I, Grugni V, Lancioni H, Pascali VL, Torroni A, Semino O, Matullo G, Achilli A, Olivieri A, and Capelli C
- Subjects
- Animals, Genome-Wide Association Study, History, Ancient, Human Genetics, Humans, Italy, Neanderthals genetics, DNA, Ancient, Databases, Genetic, Genetic Drift, Genome, Human, White People genetics
- Abstract
European populations display low genetic differentiation as the result of long-term blending of their ancient founding ancestries. However, it is unclear how the combination of ancient ancestries related to early foragers, Neolithic farmers, and Bronze Age nomadic pastoralists can explain the distribution of genetic variation across Europe. Populations in natural crossroads like the Italian peninsula are expected to recapitulate the continental diversity, but have been systematically understudied. Here, we characterize the ancestry profiles of Italian populations using a genome-wide dataset representative of modern and ancient samples from across Italy, Europe, and the rest of the world. Italian genomes capture several ancient signatures, including a non-steppe contribution derived ultimately from the Caucasus. Differences in ancestry composition, as the result of migration and admixture, have generated in Italy the largest degree of population structure detected so far in the continent, as well as shaping the amount of Neanderthal DNA in modern-day populations.
- Published
- 2019
- Full Text
- View/download PDF
16. Paternal lineages in southern Iberia provide time frames for gene flow from mainland Europe and the Mediterranean world.
- Author
-
Hernández CL, Dugoujon JM, Sánchez-Martínez LJ, Cuesta P, Novelletto A, and Calderón R
- Subjects
- Humans, Male, Microsatellite Repeats, Phylogeny, Phylogeography, Spain, Chromosomes, Human, Y genetics, Gene Flow, Human Migration
- Abstract
Background: The geography of southern Iberia and an abundant archaeological record of human occupation are ideal conditions for a full understanding of scenarios of genetic history in the area. Recent advances in the phylogeography of Y-chromosome lineages offer the opportunity to set upper bounds for the appearance of different genetic components., Aim: To provide a global knowledge on the Y haplogroups observed in Andalusia with their Y microsatellite variation. Preferential attention is given to the vehement debate about the age, origin and expansion of R1b-M269 clade and sub-lineages., Subject and Methods: Four hundred and fourteen male DNA samples from western and eastern autochthonous Andalusians were genotyped for a set of Y-SNPs and Y-STRs. Gene diversity, potential population genetic structures and coalescent times were assessed., Results: Most of the analysed samples belong to the European haplogroup R1b1a1a2-M269, whereas haplogroups E, J, I, G and T show lower frequencies. A phylogenetic dissection of the R1b-M269 was performed and younger time frames than those previously reported in the literature were obtained for its sub-lineages., Conclusion: The particular Andalusian R1b-M269 assemblage confirms the shallow topology of the clade. Moreover, the sharing of lineages with the rest of Europe indicates the impact in Iberia of an amount of pre-existing diversity, with the possible exception of R1b-DF27. Lineages such as J2-M172 and G-M201 highlight the importance of maritime travels of early farmers who reached the Iberian Peninsula.
- Published
- 2019
- Full Text
- View/download PDF
17. Rapidly mutating Y-STRs in rapidly expanding populations: Discrimination power of the Yfiler Plus multiplex in northern Africa.
- Author
-
D'Atanasio E, Iacovacci G, Pistillo R, Bonito M, Dugoujon JM, Moral P, El-Chennawi F, Melhaoui M, Baali A, Cherkaoui M, Sellitto D, Trombetta B, Berti A, and Cruciani F
- Subjects
- Africa, Northern, Black People genetics, DNA Fingerprinting, Genotype, Haplotypes, Humans, Male, Chromosomes, Human, Y, Genetics, Population, Microsatellite Repeats, Polymerase Chain Reaction instrumentation, Polymorphism, Single Nucleotide
- Abstract
The male-specific northern African genetic pool is characterised by a high frequency of the E-M81 haplogroup, which expanded in very recent times (2-3 kiloyears ago). As a consequence of their recent coalescence, E-M81 chromosomes often cannot be completely distinguished on the basis of their Y-STR profiles, unless rapidly-mutating Y-STRs (RM Y-STRs) are analysed. In this study, we used the Yfiler® Plus kit, which includes 7 RM Y-STRs and 20 standard Y-STR, to analyse 477 unrelated males coming from 11 northern African populations sampled from Morocco, Algeria, Libya and Egypt. The Y chromosomes were assigned to monophyletic lineages after the analysis of 72 stable biallelic polymorphisms and, as expected, we found a high proportion of E-M81 subjects (about 46%), with frequencies decreasing from west to east. We found low intra-population diversity indexes, in particular in the populations that experienced long-term isolation. The AMOVA analysis showed significant differences between the countries and between most of the 11 populations, with a rough differentiation between northwestern Africa and northeastern Africa, where the Egyptians Berbers from Siwa represented an outlier population. The comparison between the Yfiler® and the Yfiler® Plus network of the E-M81 Y chromosomes confirmed the high power of discrimination of the latter kit, thanks to higher variability of the RM Y-STRs: indeed, the number of chromosomes sharing the same haplotype was drastically reduced from 201 to 81 and limited, in the latter case, to subjects from the same population., (Copyright © 2018. Published by Elsevier B.V.)
- Published
- 2019
- Full Text
- View/download PDF
18. Latin Americans show wide-spread Converso ancestry and imprint of local Native ancestry on physical appearance.
- Author
-
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, and Ruiz-Linares A
- Subjects
- Haplotypes, Humans, Mexico, Nose anatomy & histology, South America, Human Migration, Indians, North American genetics, Indians, South American genetics
- 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.
- Published
- 2018
- Full Text
- View/download PDF
19. The peopling of the last Green Sahara revealed by high-coverage resequencing of trans-Saharan patrilineages.
- Author
-
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, and Cruciani F
- Subjects
- Africa, Northern, Chromosomes, Human, Y, Humans, Male, Phylogeny, Population Dynamics, High-Throughput Nucleotide Sequencing
- 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.
- Published
- 2018
- Full Text
- View/download PDF
20. Reconstructing an African haploid genome from the 18th century.
- Author
-
Jagadeesan A, Gunnarsdóttir ED, Ebenesersdóttir SS, Guðmundsdóttir VB, Thordardottir EL, Einarsdóttir MS, Jónsson H, Dugoujon JM, Fortes-Lima C, Migot-Nabias F, Massougbodji A, Bellis G, Pereira L, Másson G, Kong A, Stefánsson K, and Helgason A
- Subjects
- Humans, Male, Family Characteristics history, Genome-Wide Association Study methods, History, 18th Century, Iceland, Polymorphism, Single Nucleotide, Sequence Analysis, DNA methods, Transients and Migrants, West Indies, Black People genetics, Enslaved Persons, Genome, Human, Haploidy, Pedigree
- Abstract
A genome is a mosaic of chromosome fragments from ancestors who existed some arbitrary number of generations earlier. Here, we reconstruct the genome of Hans Jonatan (HJ), born in the Caribbean in 1784 to an enslaved African mother and European father. HJ migrated to Iceland in 1802, married and had two children. We genotyped 182 of his 788 descendants using single-nucleotide polymorphism (SNP) chips and whole-genome sequenced (WGS) 20 of them. Using these data, we reconstructed 38% of HJ's maternal genome and inferred that his mother was from the region spanned by Benin, Nigeria and Cameroon.
- Published
- 2018
- Full Text
- View/download PDF
21. Genome-wide Ancestry and Demographic History of African-Descendant Maroon Communities from French Guiana and Suriname.
- Author
-
Fortes-Lima C, Gessain A, Ruiz-Linares A, Bortolini MC, Migot-Nabias F, Bellis G, Moreno-Mayar JV, Restrepo BN, Rojas W, Avendaño-Tamayo E, Bedoya G, Orlando L, Salas A, Helgason A, Gilbert MTP, Sikora M, Schroeder H, and Dugoujon JM
- Subjects
- Africa, Brazil, Female, French Guiana, Gene Flow genetics, Genetics, Population, Genome-Wide Association Study methods, Haplotypes, Hispanic or Latino genetics, Humans, Male, Polymorphism, Single Nucleotide genetics, Suriname, White People genetics, Black People genetics
- Abstract
The transatlantic slave trade was the largest forced migration in world history. However, the origins of the enslaved Africans and their admixture dynamics remain unclear. To investigate the demographic history of African-descendant Marron populations, we generated genome-wide data (4.3 million markers) from 107 individuals from three African-descendant populations in South America, as well as 124 individuals from six west African populations. Throughout the Americas, thousands of enslaved Africans managed to escape captivity and establish lasting communities, such as the Noir Marron. We find that this population has the highest proportion of African ancestry (∼98%) of any African-descendant population analyzed to date, presumably because of centuries of genetic isolation. By contrast, African-descendant populations in Brazil and Colombia harbor substantially more European and Native American ancestry as a result of their complex admixture histories. Using ancestry tract-length analysis, we detect different dates for the European admixture events in the African-Colombian (1749 CE; confidence interval [CI]: 1737-1764) and African-Brazilian (1796 CE; CI: 1789-1804) populations in our dataset, consistent with the historically attested earlier influx of Africans into Colombia. Furthermore, we find evidence for sex-specific admixture patterns, resulting from predominantly European paternal gene flow. Finally, we detect strong genetic links between the African-descendant populations and specific source populations in Africa on the basis of haplotype sharing patterns. Although the Noir Marron and African-Colombians show stronger affinities with African populations from the Bight of Benin and the Gold Coast, the African-Brazilian population from Rio de Janeiro has greater genetic affinity with Bantu-speaking populations from the Bight of Biafra and west central Africa., (Copyright © 2017 American Society of Human Genetics. Published by Elsevier Inc. All rights reserved.)
- Published
- 2017
- Full Text
- View/download PDF
22. The distribution of mitochondrial DNA haplogroup H in southern Iberia indicates ancient human genetic exchanges along the western edge of the Mediterranean.
- Author
-
Hernández CL, Dugoujon JM, Novelletto A, Rodríguez JN, Cuesta P, and Calderón R
- Subjects
- Europe, Evolution, Molecular, Gene Flow, Genetic Variation, Humans, Mediterranean Region, Racial Groups, DNA, Mitochondrial genetics, Genetics, Population, Haplotypes, Human Migration
- Abstract
Background: The structure of haplogroup H reveals significant differences between the western and eastern edges of the Mediterranean, as well as between the northern and southern regions. Human populations along the westernmost Mediterranean coasts, which were settled by individuals from two continents separated by a relatively narrow body of water, show the highest frequencies of mitochondrial haplogroup H. These characteristics permit the analysis of ancient migrations between both shores, which may have occurred via primitive sea crafts and early seafaring. We collected a sample of 750 autochthonous people from the southern Iberian Peninsula (Andalusians from Huelva and Granada provinces). We performed a high-resolution analysis of haplogroup H by control region sequencing and coding SNP screening of the 337 individuals harboring this maternal marker. Our results were compared with those of a wide panel of populations, including individuals from Iberia, the Maghreb, and other regions around the Mediterranean, collected from the literature., Results: Both Andalusian subpopulations showed a typical western European profile for the internal composition of clade H, but eastern Andalusians from Granada also revealed interesting traces from the eastern Mediterranean. The basal nodes of the most frequent H sub-haplogroups, H1 and H3, harbored many individuals of Iberian and Maghrebian origins. Derived haplotypes were found in both regions; haplotypes were shared far more frequently between Andalusia and Morocco than between Andalusia and the rest of the Maghreb. These and previous results indicate intense, ancient and sustained contact among populations on both sides of the Mediterranean., Conclusions: Our genetic data on mtDNA diversity, combined with corresponding archaeological similarities, provide support for arguments favoring prehistoric bonds with a genetic legacy traceable in extant populations. Furthermore, the results presented here indicate that the Strait of Gibraltar and the adjacent Alboran Sea, which have often been assumed to be an insurmountable geographic barrier in prehistory, served as a frequently traveled route between continents.
- Published
- 2017
- Full Text
- View/download PDF
23. Dispersals and genetic adaptation of Bantu-speaking populations in Africa and North America.
- Author
-
Patin E, Lopez M, Grollemund R, Verdu P, Harmant C, Quach H, Laval G, Perry GH, Barreiro LB, Froment A, Heyer E, Massougbodji A, Fortes-Lima C, Migot-Nabias F, Bellis G, Dugoujon JM, Pereira JB, Fernandes V, Pereira L, Van der Veen L, Mouguiama-Daouda P, Bustamante CD, Hombert JM, and Quintana-Murci L
- Subjects
- Africa, Central, Human Migration, Humans, North America, Polymorphism, Single Nucleotide, Rainforest, Speech, Adaptation, Physiological genetics, Black or African American genetics, Genetic Loci, HLA Antigens genetics, Lactase genetics, Language
- Abstract
Bantu languages are spoken by about 310 million Africans, yet the genetic history of Bantu-speaking populations remains largely unexplored. We generated genomic data for 1318 individuals from 35 populations in western central Africa, where Bantu languages originated. We found that early Bantu speakers first moved southward, through the equatorial rainforest, before spreading toward eastern and southern Africa. We also found that genetic adaptation of Bantu speakers was facilitated by admixture with local populations, particularly for the HLA and LCT loci. Finally, we identified a major contribution of western central African Bantu speakers to the ancestry of African Americans, whose genomes present no strong signals of natural selection. Together, these results highlight the contribution of Bantu-speaking peoples to the complex genetic history of Africans and African Americans., (Copyright © 2017, American Association for the Advancement of Science.)
- Published
- 2017
- Full Text
- View/download PDF
24. Human Immunoglobulin Heavy Gamma Chain Polymorphisms: Molecular Confirmation Of Proteomic Assessment.
- Author
-
Dambrun M, Dechavanne C, Emmanuel A, Aussenac F, Leduc M, Giangrande C, Vinh J, Dugoujon JM, Lefranc MP, Guillonneau F, and Migot-Nabias F
- Subjects
- Alleles, Child, Child, Preschool, Databases, Protein, Female, Humans, Immunoglobulin Gm Allotypes, Male, Mass Spectrometry, Peptides metabolism, Sequence Analysis, DNA, Immunoglobulin gamma-Chains genetics, Polymorphism, Genetic, Proteomics methods
- Abstract
Immunoglobulin G (IgG) proteins are known for the huge diversity of the variable domains of their heavy and light chains, aimed at protecting each individual against foreign antigens. The IgG also harbor specific polymorphism concentrated in the CH2 and CH3-CHS constant regions located on the Fc fragment of their heavy chains. But this individual particularity relies only on a few amino acids among which some could make accurate sequence determination a challenge for mass spectrometry-based techniques.The purpose of the study was to bring a molecular validation of proteomic results by the sequencing of encoding DNA fragments. It was performed using ten individual samples (DNA and sera) selected on the basis of their Gm (gamma marker) allotype polymorphism in order to cover the main immunoglobulin heavy gamma (IGHG) gene diversity. Gm allotypes, reflecting part of this diversity, were determined by a serological method. On its side, the IGH locus comprises four functional IGHG genes totalizing 34 alleles and encoding the four IgG subclasses. The genomic study focused on the nucleotide polymorphism of the CH2 and CH3-CHS exons and of the intron. Despite strong sequence identity, four pairs of specific gene amplification primers could be designed. Additional primers were identified to perform the subsequent sequencing. The nucleotide sequences obtained were first assigned to a specific IGHG gene, and then IGHG alleles were deduced using a home-made decision tree reading of the nucleotide sequences. IGHG amino acid (AA) alleles were determined by mass spectrometry. Identical results were found at 95% between alleles identified by proteomics and those deduced from genomics. These results validate the proteomic approach which could be used for diagnostic purposes, namely for a mother-and-child differential IGHG detection in a context of suspicion of congenital infection., (© 2017 by The American Society for Biochemistry and Molecular Biology, Inc.)
- Published
- 2017
- Full Text
- View/download PDF
25. Genetic population study of Y-chromosome markers in Benin and Ivory Coast ethnic groups.
- Author
-
Fortes-Lima C, Brucato N, Croze M, Bellis G, Schiavinato S, Massougbodji A, Migot-Nabias F, and Dugoujon JM
- Subjects
- Benin, Cote d'Ivoire, Haplotypes, Humans, Microsatellite Repeats genetics, Polymorphism, Single Nucleotide, Chromosomes, Human, Y, Ethnicity genetics, Genetic Markers, Genetics, Population
- Abstract
Ninety-six single nucleotide polymorphisms (SNPs) and seventeen short tandem repeat (STRs) were investigated on the Y-chromosome of 288 unrelated healthy individuals from populations in Benin (Bariba, Yoruba, and Fon) and the Ivory Coast (Ahizi and Yacouba). We performed a multidimensional scaling analysis based on FST and RST genetic distances using a large extensive database of sub-Saharan African populations. There is more genetic homogeneity in Ivory Coast populations compared with populations from Benin. Notably, the Beninese Yoruba are significantly differentiated from neighbouring groups, but also from the Yoruba from Nigeria (FST>0.05; P<0.01). The Y-chromosome dataset presented here provides new valuable data to understand the complex genetic diversity and human male demographic events in West Africa., (Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.)
- Published
- 2015
- Full Text
- View/download PDF
26. Early Holocenic and Historic mtDNA African Signatures in the Iberian Peninsula: The Andalusian Region as a Paradigm.
- Author
-
Hernández CL, Soares P, Dugoujon JM, Novelletto A, Rodríguez JN, Rito T, Oliveira M, Melhaoui M, Baali A, Pereira L, and Calderón R
- Subjects
- Africa, Asia, Emigration and Immigration, Europe, Female, Gene Frequency genetics, Genetic Variation genetics, Genetics, Population, Haplotypes genetics, Humans, Male, DNA, Mitochondrial genetics
- Abstract
Determining the timing, identity and direction of migrations in the Mediterranean Basin, the role of "migratory routes" in and among regions of Africa, Europe and Asia, and the effects of sex-specific behaviors of population movements have important implications for our understanding of the present human genetic diversity. A crucial component of the Mediterranean world is its westernmost region. Clear features of transcontinental ancient contacts between North African and Iberian populations surrounding the maritime region of Gibraltar Strait have been identified from archeological data. The attempt to discern origin and dates of migration between close geographically related regions has been a challenge in the field of uniparental-based population genetics. Mitochondrial DNA (mtDNA) studies have been focused on surveying the H1, H3 and V lineages when trying to ascertain north-south migrations, and U6 and L in the opposite direction, assuming that those lineages are good proxies for the ancestry of each side of the Mediterranean. To this end, in the present work we have screened entire mtDNA sequences belonging to U6, M1 and L haplogroups in Andalusians--from Huelva and Granada provinces--and Moroccan Berbers. We present here pioneer data and interpretations on the role of NW Africa and the Iberian Peninsula regarding the time of origin, number of founders and expansion directions of these specific markers. The estimated entrance of the North African U6 lineages into Iberia at 10 ky correlates well with other L African clades, indicating that U6 and some L lineages moved together from Africa to Iberia in the Early Holocene. Still, founder analysis highlights that the high sharing of lineages between North Africa and Iberia results from a complex process continued through time, impairing simplistic interpretations. In particular, our work supports the existence of an ancient, frequently denied, bridge connecting the Maghreb and Andalusia.
- Published
- 2015
- Full Text
- View/download PDF
27. Genetic Variations in the TP53 Pathway in Native Americans Strongly Suggest Adaptation to the High Altitudes of the Andes.
- Author
-
Jacovas VC, Rovaris DL, Peréz O, de Azevedo S, Macedo GS, Sandoval JR, Salazar-Granara A, Villena M, Dugoujon JM, Bisso-Machado R, Petzl-Erler ML, Salzano FM, Ashton-Prolla P, Ramallo V, and Bortolini MC
- Subjects
- Altitude, Humans, Acclimatization genetics, Indians, North American genetics, Polymorphism, Single Nucleotide, Tumor Suppressor Protein p53 genetics
- Abstract
The diversity of the five single nucleotide polymorphisms located in genes of the TP53 pathway (TP53, rs1042522; MDM2, rs2279744; MDM4, rs1563828; USP7, rs1529916; and LIF, rs929271) were studied in a total of 282 individuals belonging to Quechua, Aymara, Chivay, Cabanaconde, Yanke, Taquile, Amantani, Anapia, Uros, Guarani Ñandeva, and Guarani Kaiowá populations, characterized as Native American or as having a high level (> 90%) of Native American ancestry. In addition, published data pertaining to 100 persons from five other Native American populations (Surui, Karitiana, Maya, Pima, and Piapoco) were analyzed. The populations were classified as living in high altitude (≥ 2,500 m) or in lowlands (< 2,500 m). Our analyses revealed that alleles USP7-G, LIF-T, and MDM2-T showed significant evidence that they were selected for in relation to harsh environmental variables related to high altitudes. Our results show for the first time that alleles of classical TP53 network genes have been evolutionary co-opted for the successful human colonization of the Andes.
- Published
- 2015
- Full Text
- View/download PDF
28. 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.
- Author
-
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, and Cruciani F
- Subjects
- Africa, Evolution, Molecular, Genotyping Techniques, Human Migration, Humans, Male, Mutation, Phylogeny, Phylogeography, Polymorphism, Single Nucleotide, Chromosomes, Human, Y classification, Haplotypes
- 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., (© The Author(s) 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.)
- Published
- 2015
- Full Text
- View/download PDF
29. Surnames and Y-chromosomal markers reveal low relationships in Southern Spain.
- Author
-
Calderón R, Hernández CL, Cuesta P, and Dugoujon JM
- Subjects
- Genetics, Population, Geography, Haplotypes, Humans, Male, Polymorphism, Single Nucleotide, Spain, Chromosomes, Human, Y, Genetic Markers, Names
- Abstract
A sample of 416 males from western and eastern Andalusia has been jointly analyzed for surnames and Y-chromosome haplogroups and haplotypes. The observed number of different surnames was 222 (353 when the second surname of the Spanish system of naming is considered). The great majority of recorded surnames have a Castilian-Leonese origin, while Catalan or Basque surnames have not been found. A few Arab-related surnames appear but none discernible of Sephardic-Jewish descent. Low correlation among surnames with different population frequencies and Y-chromosome markers, at different levels of genetic resolution, has been observed in Andalusia. This finding could be explained mainly by the very low rate of monophyletic surnames because of the historical process of surname ascription and the resulting high frequencies of the most common Spanish surnames. The introduction of surnames in Spain during the Middle Ages coincided with Reconquest of the territories under Islamic rule, and Muslims and Jews progressively adopted the present male line surname system. Sampled surnames and Y-chromosome lineages fit well a power-law distribution and observed isonymy is very close to that of the general population. Besides, our data and results show that the reliability of the isonymy method should be questioned because of the high rate of polyphyletic surnames, even in small geographic regions and autochthonous populations. Random isonymy would be consistently dependent of the most common surname frequencies in the population.
- Published
- 2015
- Full Text
- View/download PDF
30. Determined about sex: sex-testing in 45 primate species using a 2Y/1X sex-typing assay.
- Author
-
Cadamuro VC, Bouakaze C, Croze M, Schiavinato S, Tonasso L, Gérard P, Fausser JL, Gibert M, Dugoujon JM, Braga J, and Balaresque P
- Subjects
- Animals, Base Sequence, DNA genetics, Female, Humans, Male, Molecular Sequence Data, Multiplex Polymerase Chain Reaction, Primates classification, Sequence Homology, Nucleic Acid, Primates genetics, Sex Determination Processes, X Chromosome, Y Chromosome
- Abstract
Sex-testing using molecular genetic technique is routinely used in the fields of forensics, population genetics and conservation biology. However, none of the assay used so far allows a non-ambiguous and successful sex determination for human and non-human primate species. The most widely used method, AMELY/X, and its alternatives suffer from a set of drawbacks in humans and can rarely be used in New World primate species. Here, we designed a new sex-typing assay using a multiplexed PCR amplification of UTX and UTY-homologous loci and combined male-specific SRY locus. This method was successfully tested on 1048 samples, including 82 non-human primates from 45 Anthropoidea and Lemuriformes species and 966 human samples from 24 populations (Africans, Europeans, and South Americans). This sex-typing method is applicable across all primate species tested from Hominoidea to Indriidae, and also on various populations with different background origins; it represents a robust and cheap sex-typing assay to be used both by the anthropologist and primatologist communities., (Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.)
- Published
- 2015
- Full Text
- View/download PDF
31. Immunoglobulin genes in Andalusia (Spain). Genetic diversity in the Mediterranean space.
- Author
-
Fortes-Lima C, Dugoujon JM, Hernández CL, Reales G, and Calderón R
- Subjects
- Africa, Europe, Gene Frequency, Genotype, Haplotypes, Humans, Immunoglobulin G genetics, Immunoglobulin Heavy Chains genetics, Mediterranean Region, Polymorphism, Genetic genetics, Spain, Genes, Immunoglobulin genetics, Genetic Variation genetics
- Abstract
Andalusia is the most densely populated region of Spain since ancient times, and has a rich history of contacts across the Mediterranean. Earlier studies have underlined the relatively high frequency of the Sub-Saharan GM 1,17 5* haplotype in western Andalusia (Huelva province, n=252) and neighbouring Atlantic regions. Here, we provide novel data on GM/KM markers in eastern Andalusians (n=195) from Granada province, where African GM*1,17 5* frequency is relatively high (0.044). The most frequent GM haplotypes in Andalusia parallel the most common in Europe. Altogether, these data allow us to gain insight into the genetic diversity of southern Iberia. Additionally, we assess population structure by comparing our Iberian samples with 41 Mediterranean populations. GM haplotype variation across the Mediterranean reflects intense and complex interactions between North Africans and South Europeans along human history, highlighting that African influence over the Iberian Peninsula does not follow an isotropic pattern., (Copyright © 2014 Académie des sciences. Published by Elsevier SAS. All rights reserved.)
- Published
- 2014
- Full Text
- View/download PDF
32. Ancient human genomes suggest three ancestral populations for present-day Europeans.
- Author
-
Lazaridis I, Patterson N, Mittnik A, Renaud G, Mallick S, Kirsanow K, Sudmant PH, Schraiber JG, Castellano S, Lipson M, Berger B, Economou C, Bollongino R, Fu Q, Bos KI, Nordenfelt S, Li H, de Filippo C, Prüfer K, Sawyer S, Posth C, Haak W, Hallgren F, Fornander E, Rohland N, Delsate D, Francken M, Guinet JM, Wahl J, Ayodo G, Babiker HA, Bailliet G, Balanovska E, Balanovsky O, Barrantes R, Bedoya G, Ben-Ami H, Bene J, Berrada F, Bravi CM, Brisighelli F, Busby GB, Cali F, Churnosov M, Cole DE, Corach D, Damba L, van Driem G, Dryomov S, Dugoujon JM, Fedorova SA, Gallego Romero I, Gubina M, Hammer M, Henn BM, Hervig T, Hodoglugil U, Jha AR, Karachanak-Yankova S, Khusainova R, Khusnutdinova E, Kittles R, Kivisild T, Klitz W, Kučinskas V, Kushniarevich A, Laredj L, Litvinov S, Loukidis T, Mahley RW, Melegh B, Metspalu E, Molina J, Mountain J, Näkkäläjärvi K, Nesheva D, Nyambo T, Osipova L, Parik J, Platonov F, Posukh O, Romano V, Rothhammer F, Rudan I, Ruizbakiev R, Sahakyan H, Sajantila A, Salas A, Starikovskaya EB, Tarekegn A, Toncheva D, Turdikulova S, Uktveryte I, Utevska O, Vasquez R, Villena M, Voevoda M, Winkler CA, Yepiskoposyan L, Zalloua P, Zemunik T, Cooper A, Capelli C, Thomas MG, Ruiz-Linares A, Tishkoff SA, Singh L, Thangaraj K, Villems R, Comas D, Sukernik R, Metspalu M, Meyer M, Eichler EE, Burger J, Slatkin M, Pääbo S, Kelso J, Reich D, and Krause J
- Subjects
- Agriculture history, Asia ethnology, Europe, History, Ancient, Humans, Population Dynamics, Principal Component Analysis, Workforce, Genome, Human genetics, White People classification, White People genetics
- Abstract
We sequenced the genomes of a ∼7,000-year-old farmer from Germany and eight ∼8,000-year-old hunter-gatherers from Luxembourg and Sweden. We analysed these and other ancient genomes with 2,345 contemporary humans to show that most present-day Europeans derive from at least three highly differentiated populations: west European hunter-gatherers, who contributed ancestry to all Europeans but not to Near Easterners; ancient north Eurasians related to Upper Palaeolithic Siberians, who contributed to both Europeans and Near Easterners; and early European farmers, who were mainly of Near Eastern origin but also harboured west European hunter-gatherer related ancestry. We model these populations' deep relationships and show that early European farmers had ∼44% ancestry from a 'basal Eurasian' population that split before the diversification of other non-African lineages.
- Published
- 2014
- Full Text
- View/download PDF
33. New insights into the distribution of APOE polymorphism in the Iberian Peninsula. The case of Andalusia (Spain).
- Author
-
Reales G, Hernández CL, Dugoujon JM, Novelletto A, Cuesta P, Fortes-Lima C, Rodríguez JN, and Calderón R
- Subjects
- Female, Humans, Male, Real-Time Polymerase Chain Reaction, Spain, Apolipoproteins E genetics, Gene Frequency, Polymorphism, Single Nucleotide
- Abstract
Background: The APOE gene has received much attention due to the remarkable spatial variation patterns of some of its genotypes and alleles in human populations and to its relevance in biomedicine., Aim: This work was addressed to investigate the extent of APOE polymorphism between autochthonous Andalusians originating from Huelva and Granada provinces. No data on this marker in these southern Spanish coastal populations are available up to date., Subjects and Methods: This study used genomic DNA from healthy, unrelated Andalusians of both sexes (n = 322). All samples were genotyped for two SNPs, rs429358 and rs7412, which determine the three APOE alleles: ε2, ε3 and ε4. For analyses, a TaqMan-based technique was applied using a RT-PCR. Comparisons with other Mediterranean populations were performed based on multivariate analysis., Results: A relatively high frequency of ε4 in Granada (eastern Andalusia), as well as a low ε2 frequency in Huelva (western Andalusia) were observed. The finding that ε4 allele in Southern Spain and Portugal is higher than expected given its geographical location poses an interesting question for this study, given the well-established APOE-ε4 gradient in Europe., Conclusion: This population study may represent useful information for further prospective anthropological and molecular genetic studies focused on unravelling the relationship between population genetic composition and specific human diseases.
- Published
- 2014
- Full Text
- View/download PDF
34. Human maternal heritage in Andalusia (Spain): its composition reveals high internal complexity and distinctive influences of mtDNA haplogroups U6 and L in the western and eastern side of region.
- Author
-
Hernández CL, Reales G, Dugoujon JM, Novelletto A, Rodríguez JN, Cuesta P, and Calderón R
- Subjects
- Evolution, Molecular, Gene Flow, Gene Pool, Human Migration, Humans, Models, Genetic, Spain, DNA, Mitochondrial genetics, Genetics, Population, Haplotypes
- Abstract
Background: The archeology and history of the ancient Mediterranean have shown that this sea has been a permeable obstacle to human migration. Multiple cultural exchanges around the Mediterranean have taken place with presumably population admixtures. A gravitational territory of those migrations has been the Iberian Peninsula. Here we present a comprehensive analysis of the maternal gene pool, by means of control region sequencing and PCR-RFLP typing, of autochthonous Andalusians originating from the coastal provinces of Huelva and Granada, located respectively in the west and the east of the region., Results: The mtDNA haplogroup composition of these two southern Spanish populations has revealed a wide spectrum of haplogroups from different geographical origins. The registered frequencies of Eurasian markers, together with the high incidence and diversification of African maternal lineages (15% of the total mitochondrial variability) among Huelva Andalusians when compared to its eastwards relatives of Granada and other Iberian populations, constitute relevant findings unknown up-to-date on the characteristics of mtDNA within Andalusia that testifies a female population substructure. Therefore, Andalusia must not be considered a single, unique population., Conclusions: The maternal legacy among Andalusians reflects distinctive local histories, pointing out the role of the westernmost territory of Peninsular Spain as a noticeable recipient of multiple and diverse human migrations. The obtained results underline the necessity of further research on genetic relationships in both sides of the western Mediterranean, using carefully collected samples from autochthonous individuals. Many studies have focused on recent North African gene flow towards Iberia, yet scientific attention should be now directed to thoroughly study the introduction of European genes in northwest Africa across the sea, in order to determine its magnitude, timescale and methods, and to compare them to those terrestrial movements from eastern Africa and southwestern Asia.
- Published
- 2014
- Full Text
- View/download PDF
35. Subtle adjustments of the glucose-6-phosphate dehydrogenase (G6PD) mutation database and reference sequence.
- Author
-
Mazières S, Petit F, Dugoujon JM, Iriart X, Berry A, Carme B, Nacher M, Bailly P, and Chiaroni J
- Subjects
- Humans, Databases, Genetic, Glucosephosphate Dehydrogenase genetics, Mutation
- Published
- 2014
- Full Text
- View/download PDF
36. Tracing Arab-Islamic inheritance in Madagascar: study of the Y-chromosome and mitochondrial DNA in the Antemoro.
- Author
-
Capredon M, Brucato N, Tonasso L, Choesmel-Cadamuro V, Ricaut FX, Razafindrazaka H, Rakotondrabe AB, Ratolojanahary MA, Randriamarolaza LP, Champion B, and Dugoujon JM
- Subjects
- Databases, Genetic, Female, Geography, Haplotypes genetics, Humans, Madagascar, Male, Microsatellite Repeats genetics, Principal Component Analysis, Recombination, Genetic genetics, Arabs genetics, Chromosomes, Human, Y genetics, DNA, Mitochondrial genetics, Ethnicity genetics, Inheritance Patterns genetics, Islam
- Abstract
Madagascar is located at the crossroads of the Asian and African worlds and is therefore of particular interest for studies on human population migration. Within the large human diversity of the Great Island, we focused our study on a particular ethnic group, the Antemoro. Their culture presents an important Arab-Islamic influence, but the question of an Arab biological inheritance remains unresolved. We analyzed paternal (n=129) and maternal (n=135) lineages of this ethnic group. Although the majority of Antemoro genetic ancestry comes from sub-Saharan African and Southeast Asian gene pools, we observed in their paternal lineages two specific haplogroups (J1 and T1) linked to Middle Eastern origins. This inheritance was restricted to some Antemoro sub-groups. Statistical analyses tended to confirm significant Middle Eastern genetic contribution. This study gives a new perspective to the large human genetic diversity in Madagascar.
- Published
- 2013
- Full Text
- View/download PDF
37. The Hmong Diaspora: preserved South-East Asian genetic ancestry in French Guianese Asians.
- Author
-
Brucato N, Mazières S, Guitard E, Giscard PH, Bois E, Larrouy G, and Dugoujon JM
- Subjects
- Asia, Southeastern, Chromosomes, Human, X genetics, DNA, Mitochondrial genetics, Data Interpretation, Statistical, Ethnicity genetics, French Guiana, Gene Frequency, Gene Pool, Genetic Variation, Haplotypes, Human Migration, Humans, Immunoglobulin G genetics, Immunoglobulin G immunology, Polymorphism, Single Nucleotide, Population, Tandem Repeat Sequences, Asian People genetics
- Abstract
The Hmong Diaspora is one of the widest modern human migrations. Mainly localised in South-East Asia, the United States of America, and metropolitan France, a small community has also settled the Amazonian forest of French Guiana. We have biologically analysed 62 individuals of this unique Guianese population through three complementary genetic markers: mitochondrial DNA (HVS-I/II and coding region SNPs), Y-chromosome (SNPs and STRs), and the Gm allotypic system. All genetic systems showed a high conservation of the Asian gene pool (Asian ancestry: mtDNA=100.0%; NRY=99.1%; Gm=96.6%), without a trace of founder effect. When compared across various Asian populations, the highest correlations were observed with Hmong-Mien groups still living in South-East Asia (Fst<0.05; P-value<0.05). Despite a long history punctuated by exodus, the French Guianese Hmong have maintained their original genetic diversity., (Copyright © 2012 Académie des sciences. Published by Elsevier SAS. All rights reserved.)
- Published
- 2012
- Full Text
- View/download PDF
38. Reconstructing Native American population history.
- Author
-
Reich D, Patterson N, Campbell D, Tandon A, Mazieres S, Ray N, Parra MV, Rojas W, Duque C, Mesa N, García LF, Triana O, Blair S, Maestre A, Dib JC, Bravi CM, Bailliet G, Corach D, Hünemeier T, Bortolini MC, Salzano FM, Petzl-Erler ML, Acuña-Alonzo V, Aguilar-Salinas C, Canizales-Quinteros S, Tusié-Luna T, Riba L, Rodríguez-Cruz M, Lopez-Alarcón M, Coral-Vazquez R, Canto-Cetina T, Silva-Zolezzi I, Fernandez-Lopez JC, Contreras AV, Jimenez-Sanchez G, Gómez-Vázquez MJ, Molina J, Carracedo A, Salas A, Gallo C, Poletti G, Witonsky DB, Alkorta-Aranburu G, Sukernik RI, Osipova L, Fedorova SA, Vasquez R, Villena M, Moreau C, Barrantes R, Pauls D, Excoffier L, Bedoya G, Rothhammer F, Dugoujon JM, Larrouy G, Klitz W, Labuda D, Kidd J, Kidd K, Di Rienzo A, Freimer NB, Price AL, and Ruiz-Linares A
- Subjects
- Americas, Asia, Cluster Analysis, Emigration and Immigration statistics & numerical data, Gene Flow, Genetics, Population, History, Ancient, Humans, Models, Genetic, Polymorphism, Single Nucleotide genetics, Siberia, Emigration and Immigration history, Indians, North American genetics, Indians, North American history, Phylogeny
- Abstract
The peopling of the Americas has been the subject of extensive genetic, archaeological and linguistic research; however, central questions remain unresolved. One contentious issue is whether the settlement occurred by means of a single migration or multiple streams of migration from Siberia. The pattern of dispersals within the Americas is also poorly understood. To address these questions at a higher resolution than was previously possible, we assembled data from 52 Native American and 17 Siberian groups genotyped at 364,470 single nucleotide polymorphisms. Here we show that Native Americans descend from at least three streams of Asian gene flow. Most descend entirely from a single ancestral population that we call 'First American'. However, speakers of Eskimo-Aleut languages from the Arctic inherit almost half their ancestry from a second stream of Asian gene flow, and the Na-Dene-speaking Chipewyan from Canada inherit roughly one-tenth of their ancestry from a third stream. We show that the initial peopling followed a southward expansion facilitated by the coast, with sequential population splits and little gene flow after divergence, especially in South America. A major exception is in Chibchan speakers on both sides of the Panama isthmus, who have ancestry from both North and South America.
- Published
- 2012
- Full Text
- View/download PDF
39. Apolipoprotein E/C1/C4/C2 gene cluster diversity in two native Andean populations: Aymaras and Quechuas.
- Author
-
Gayà-Vidal M, Athanasiadis G, Carreras-Torres R, Via M, Esteban E, Villena M, Vasquez R, Dugoujon JM, and Moral P
- Subjects
- Bolivia, Demography, Ethnicity genetics, Female, Gene Frequency, Humans, Linkage Disequilibrium, Male, Microsatellite Repeats, Polymorphism, Single Nucleotide, White People, Apolipoproteins E genetics, Multigene Family, Polymorphism, Genetic
- 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., (© 2012 The Authors Annals of Human Genetics © 2012 Blackwell Publishing Ltd/University College London.)
- Published
- 2012
- Full Text
- View/download PDF
40. The Arabo-Islamic migrations in Madagascar: first genetic study of the GM system in three Malagasy populations.
- Author
-
Capredon M, Sanchez-Mazas A, Guitard E, Razafindrazaka H, Chiaroni J, Champion B, and Dugoujon JM
- Subjects
- Computational Biology, Databases, Factual, Gene Frequency, Genetic Testing, Genetic Variation, Haplotypes, Humans, Immunoglobulin Gm Allotypes blood, Madagascar ethnology, Phenotype, Population Surveillance, Arabs genetics, Emigration and Immigration, Genetics, Population, Immunoglobulin Gm Allotypes genetics
- Abstract
The Antemoro are an ethnic group from the southeast coast of Madagascar who claims an Arab origin. Cultural signatures of an Arabo-Islamic influence have been found in this region. Nevertheless, their origins are very contentious. Through this study, we want to determine whether this ethnic group had a particular GM profile that differentiated it from other Malagasy populations, and whether there were detectable genetic traces of the Arabo-Islamic migration. The Gm polymorphisms of IgG immunoglobulins was analysed in a population of Antemoro (N = 85), two other Malagasy populations from northern Fihereňa (N = 82) and southern Fihereňa (N = 50) and in a Comorian population (N = 171). This last group was used to enlarge the database for genetic comparisons. Results revealed significant contributions from Africa (60%, 0.092 ≤F(ST) ≤ 0.280) and Southeast Asia (40%, 0.043 ≤ F(ST) ≤ 0.590) to the Antemoro genetic pool. No direct genetic relationships with the Middle East. These results bring new insights into the population history of Madagascar., (© 2011 Blackwell Publishing Ltd.)
- Published
- 2012
- Full Text
- View/download PDF
41. Y-STR genetic diversity in autochthonous Andalusians from Huelva and Granada provinces (Spain).
- Author
-
Ambrosio B, Novelletto A, Hernandez C, Dugoujon JM, Fortes-Lima C, Rodriguez JN, and Calderon R
- Subjects
- DNA Fingerprinting, Haplotypes, Humans, Male, Polymerase Chain Reaction, Spain, Chromosomes, Human, Y, Ethnicity genetics, Genetic Variation, Genetics, Population, Microsatellite Repeats
- Abstract
Seventeen Y-chromosomal short tandem repeats (STRs) were analyzed in 347 healthy, unrelated, autochthonous males from the Andalusian provinces of Huelva (N=167) and Granada (N=180). AmpFlSTR Y-filer PCR Amplification kit (Applied Biosystems) was used to type the Y-STR markers. A total of 156 and 166 different haplotypes for the 17 Y-STR set were detected in Huelva, and Granada, respectively. The same haplotype diversity was found for both samples (0.998±0.001), and the overall discrimination capacity was 0.904. The most common minimal haplotype (DYS19, DYS389 I, DYS389 II, DYS390, DYS391, DYS392, DYS393) in both subpopulations was 14-13-16-24-11-13-13, which is also the most frequent haplotype among Atlantic European populations. Comparison analysis using pairwise R(ST) values and Analysis of Molecular Variance (AMOVA) revealed a significant genetic distance between our Andalusian samples and other ones from the northern Iberian fringe (including Basque and Pyrenean populations). However, results from the multi-dimensional scaling analysis (MDS) yielded a well-defined group of Iberian populations separated from the other Mediterranean clusters observed., (Copyright © 2011 Elsevier Ireland Ltd. All rights reserved.)
- Published
- 2012
- Full Text
- View/download PDF
42. Mass spectrometry detection of G3m and IGHG3 alleles and follow-up of differential mother and neonate IgG3.
- Author
-
Dechavanne C, Guillonneau F, Chiappetta G, Sago L, Lévy P, Salnot V, Guitard E, Ehrenmann F, Broussard C, Chafey P, Le Port A, Vinh J, Mayeux P, Dugoujon JM, Lefranc MP, and Migot-Nabias F
- Subjects
- Alleles, Female, Humans, Immunoglobulin G blood, Immunoglobulin G genetics, Immunoglobulin Gm Allotypes blood, Immunoglobulin Gm Allotypes chemistry, Immunoglobulin Gm Allotypes genetics, Infant, Infant, Newborn, Male, Immunoglobulin G chemistry, Mass Spectrometry methods
- Abstract
Mass spectrometry (MS) analysis for detection of immunoglobulins (IG) of the human IgG3 subclass is described that relies on polymorphic amino acids of the heavy gamma3 chains. IgG3 is the most polymorphic human IgG subclass with thirteen G3m allotypes located on the constant CH2 and CH3 domains of the gamma3 chain, the combination of which leads to six major G3m alleles. Amino acid changes resulting of extensive sequencing previously led to the definition of 19 IGHG3 alleles that have been correlated to the G3m alleles. As a proof of concept, MS proteotypic peptides were defined which encompass discriminatory amino acids for the identification of the G3m and IGHG3 alleles. Plasma samples originating from ten individuals either homozygous or heterozygous for different G3m alleles, and including one mother and her baby (drawn sequentially from birth to 9 months of age), were analyzed. Total IgG3 were purified using affinity chromatography and then digested by a combination of AspN and trypsin proteases, and peptides of interest were detected by mass spectrometry. The sensitivity of the method was assessed by mixing variable amounts of two plasma samples bearing distinct G3m allotypes. A label-free approach using the high-performance liquid chromatography (HPLC) retention time of peptides and their MS mass analyzer peak intensity gave semi-quantitative information. Quantification was realized by selected reaction monitoring (SRM) using synthetic peptides as internal standards. The possibility offered by this new methodology to detect and quantify neo-synthesized IgG in newborns will improve knowledge on the first acquisition of antibodies in infants and constitutes a promising diagnostic tool for vertically-transmitted diseases.
- Published
- 2012
- Full Text
- View/download PDF
43. Evolutionary responses to a constructed niche: ancient Mesoamericans as a model of gene-culture coevolution.
- Author
-
Hünemeier T, Amorim CE, Azevedo S, Contini V, Acuña-Alonzo V, Rothhammer F, Dugoujon JM, Mazières S, Barrantes R, Villarreal-Molina MT, Paixão-Côrtes VR, Salzano FM, Canizales-Quinteros S, Ruiz-Linares A, and Bortolini MC
- Subjects
- Agriculture, Alleles, Gene Frequency genetics, Genetic Association Studies, Genetic Loci genetics, Genetics, Population, Genotype, Geography, Humans, Pollen growth & development, Polymorphism, Single Nucleotide genetics, Radiometric Dating, Regression Analysis, Zea mays growth & development, Biological Evolution, Culture, Ecosystem, Indians, North American genetics, Models, Biological
- Abstract
Culture and genetics rely on two distinct but not isolated transmission systems. Cultural processes may change the human selective environment and thereby affect which individuals survive and reproduce. Here, we evaluated whether the modes of subsistence in Native American populations and the frequencies of the ABCA1*Arg230Cys polymorphism were correlated. Further, we examined whether the evolutionary consequences of the agriculturally constructed niche in Mesoamerica could be considered as a gene-culture coevolution model. For this purpose, we genotyped 229 individuals affiliated with 19 Native American populations and added data for 41 other Native American groups (n = 1905) to the analysis. In combination with the SNP cluster of a neutral region, this dataset was then used to unravel the scenario involved in 230Cys evolutionary history. The estimated age of 230Cys is compatible with its origin occurring in the American continent. The correlation of its frequencies with the archeological data on Zea pollen in Mesoamerica/Central America, the neutral coalescent simulations, and the F(ST)-based natural selection analysis suggest that maize domestication was the driving force in the increase in the frequencies of 230Cys in this region. These results may represent the first example of a gene-culture coevolution involving an autochthonous American allele.
- Published
- 2012
- Full Text
- View/download PDF
44. PopAffiliator: online calculator for individual affiliation to a major population group based on 17 autosomal short tandem repeat genotype profile.
- Author
-
Pereira L, Alshamali F, Andreassen R, Ballard R, Chantratita W, Cho NS, Coudray C, Dugoujon JM, Espinoza M, González-Andrade F, Hadi S, Immel UD, Marian C, Gonzalez-Martin A, Mertens G, Parson W, Perone C, Prieto L, Takeshita H, Rangel Villalobos H, Zeng Z, Zhivotovsky L, Camacho R, and Fonseca NA
- Subjects
- Artificial Intelligence, Gene Frequency genetics, Humans, Computers legislation & jurisprudence, Forensic Genetics instrumentation, Forensic Genetics legislation & jurisprudence, Genetic Markers genetics, Genetics, Population legislation & jurisprudence, Genotype, Microsatellite Repeats genetics, Population Groups genetics
- Abstract
Because of their sensitivity and high level of discrimination, short tandem repeat (STR) maker systems are currently the method of choice in routine forensic casework and data banking, usually in multiplexes up to 15-17 loci. Constraints related to sample amount and quality, frequently encountered in forensic casework, will not allow to change this picture in the near future, notwithstanding the technological developments. In this study, we present a free online calculator named PopAffiliator ( http://cracs.fc.up.pt/popaffiliator ) for individual population affiliation in the three main population groups, Eurasian, East Asian and sub-Saharan African, based on genotype profiles for the common set of STRs used in forensics. This calculator performs affiliation based on a model constructed using machine learning techniques. The model was constructed using a data set of approximately fifteen thousand individuals collected for this work. The accuracy of individual population affiliation is approximately 86%, showing that the common set of STRs routinely used in forensics provide a considerable amount of information for population assignment, in addition to being excellent for individual identification.
- Published
- 2011
- Full Text
- View/download PDF
45. Combined effects of Gm or Km immunoglobulin allotypes and age on antibody responses to Plasmodium falciparum VarO rosetting variant in Benin.
- Author
-
Migot-Nabias F, Lokossou AG, Vigan-Womas I, Guitard E, Guillotte M, Noukpo JM, Mercereau-Puijalon O, Dugoujon JM, and Garcia A
- Subjects
- Adolescent, Age Factors, Analysis of Variance, Benin epidemiology, Chi-Square Distribution, Child, Child, Preschool, Cohort Studies, Humans, Immunoglobulin Gm Allotypes classification, Immunoglobulin Km Allotypes classification, Infant, Linear Models, Malaria, Falciparum epidemiology, Antibodies, Protozoan immunology, Immunoglobulin Gm Allotypes immunology, Immunoglobulin Km Allotypes immunology, Malaria, Falciparum immunology, Plasmodium falciparum immunology, Protozoan Proteins immunology
- Abstract
Clinical protection of Beninese children against Plasmodium falciparum malaria was shown to be influenced by immunoglobulin (IG) Gm and Km allotypes, and related to seroreactivity with the rosette-forming VarO-antigenic variant. IgG to the VarO-infected erythrocyte surface, IgG1 and IgG3 to PfEMP1-NTS-DBL1α(1)-VarO were higher in the under 4-year-old children carrying the Gm 5,6,13,14;1,17 phenotype. In contrast, surface-reactive IgG, total IgG, IgG1 and IgG3 to NTS-DBL1α(1)- and DBL2βC2-VarO domains were lower in the above 4-year-old children harbouring the Km1 allotype. These data outline an age-related association of antibodies against malaria antigens and IG allotype distribution., (Copyright © 2011 Institut Pasteur. Published by Elsevier SAS. All rights reserved.)
- Published
- 2011
- Full Text
- View/download PDF
46. mtDNA and Y-chromosome diversity in Aymaras and Quechuas from Bolivia: different stories and special genetic traits of the Andean Altiplano populations.
- Author
-
Gayà-Vidal M, Moral P, Saenz-Ruales N, Gerbault P, Tonasso L, Villena M, Vasquez R, Bravi CM, and Dugoujon JM
- Subjects
- Analysis of Variance, Bolivia, Female, Genetic Markers genetics, Genetics, Population, Haplotypes, Humans, Language, Male, Polymorphism, Single Nucleotide, Chromosomes, Human, Y, DNA, Mitochondrial genetics, Indians, South American genetics, Microsatellite Repeats
- Abstract
Two Bolivian samples belonging to the two main Andean linguistic groups (Aymaras and Quechuas) were studied for mtDNA and Y-chromosome uniparental markers to evaluate sex-specific differences and give new insights into the demographic processes of the Andean region. mtDNA-coding polymorphisms, HVI-HVII control regions, 17 Y-STRs, and three SNPs were typed in two well-defined populations with adequate size samples. The two Bolivian samples showed more genetic differences for the mtDNA than for the Y-chromosome. For the mtDNA, 81% of Aymaras and 61% of Quechuas presented haplogroup B2. Native American Y-chromosomes were found in 97% of Aymaras (89% hg Q1a3a and 11% hg Q1a3*) and 78% of Quechuas (100% hg Q1a3a). Our data revealed high diversity values in the two populations, in agreement with other Andean studies. The comparisons with the available literature for both sets of markers indicated that the central Andean area is relatively homogeneous. For mtDNA, the Aymaras seemed to have been more isolated throughout time, maintaining their genetic characteristics, while the Quechuas have been more permeable to the incorporation of female foreigners and Peruvian influences. On the other hand, male mobility would have been widespread across the Andean region according to the homogeneity found in the area. Particular genetic characteristics presented by both samples support a past common origin of the Altiplano populations in the ancient Aymara territory, with independent, although related histories, with Peruvian (Quechuas) populations., (Copyright © 2011 Wiley-Liss, Inc.)
- Published
- 2011
- Full Text
- View/download PDF
47. Immunogenetics as a tool in anthropological studies.
- Author
-
Sanchez-Mazas A, Fernandez-Viña M, Middleton D, Hollenbach JA, Buhler S, Di D, Rajalingam R, Dugoujon JM, Mack SJ, and Thorsby E
- Subjects
- Genetic Variation, HLA Antigens genetics, Humans, Polymorphism, Genetic, Anthropology methods, Immunogenetics
- Abstract
The genes coding for the main molecules involved in the human immune system--immunoglobulins, human leucocyte antigen (HLA) molecules and killer-cell immunoglobulin-like receptors (KIR)--exhibit a very high level of polymorphism that reveals remarkable frequency variation in human populations. 'Genetic marker' (GM) allotypes located in the constant domains of IgG antibodies have been studied for over 40 years through serological typing, leading to the identification of a variety of GM haplotypes whose frequencies vary sharply from one geographic region to another. An impressive diversity of HLA alleles, which results in amino acid substitutions located in the antigen-binding region of HLA molecules, also varies greatly among populations. The KIR differ between individuals according to both gene content and allelic variation, and also display considerable population diversity. Whereas the molecular evolution of these polymorphisms has most likely been subject to natural selection, principally driven by host-pathogen interactions, their patterns of genetic variation worldwide show significant signals of human geographic expansion, demographic history and cultural diversification. As current developments in population genetic analysis and computer simulation improve our ability to discriminate among different--either stochastic or deterministic--forces acting on the genetic evolution of human populations, the study of these systems shows great promise for investigating both the peopling history of modern humans in the time since their common origin and human adaptation to past environmental (e.g. pathogenic) changes. Therefore, in addition to mitochondrial DNA, Y-chromosome, microsatellites, single nucleotide polymorphisms and other markers, immunogenetic polymorphisms represent essential and complementary tools for anthropological studies., (© 2011 The Authors. Immunology © 2011 Blackwell Publishing Ltd.)
- Published
- 2011
- Full Text
- View/download PDF
48. French Guiana Amerindian demographic history as revealed by autosomal and Y-chromosome STRs.
- Author
-
Mazieres S, Callegari-Jacques SM, Crossetti SG, Dugoujon JM, Larrouy G, Bois E, Crubezy E, Hutz MH, and Salzano FM
- Subjects
- Brazil, Demography, Female, French Guiana, Gene Flow, Gene Frequency, Genetic Markers, Genetic Variation, Geography, Haplotypes, Humans, Male, Pedigree, Peru, Polymerase Chain Reaction, Polymorphism, Genetic, Statistics, Nonparametric, Chromosomes, Human genetics, Chromosomes, Human, Y genetics, Indians, South American genetics, Microsatellite Repeats
- Abstract
Background: Previous investigations of French Guiana Amerindians performed by this group included blood group and protein genetic markers, mitochondrial DNA and Y-chromosome investigations. Molecular autosomal data and more extensive Y-chromosome determinations were lacking., Subjects and Methods: The genetic variability of 15 autosome (ASTRs) and 17 Y-chromosome (YSTRs) microsatellite loci was studied in four French Guiana (Emerillon, Palikur, Wayampi, Kali'na) and one Brazilian (Apalai) Amerindian populations. A sixth group, the Peruvian Matsiguenga of the Maipurean linguistic family, was included in the data analysis since they could provide information about the past migration of people from that linguistic stock into northeastern Amazonia., Results: Marked ASTR and YSTR variability was found, with 96% of the YSTR haplotypes being found in one population only. There was excellent agreement between the present and previous autosomal or uniparental results. Multidimensional scaling based on F(ST) genetic distances and population structure analysis revealed heterogeneity in gene distribution, with a clear difference between the Matsiguenga and Emerillon and the other groups. In the latter, Wilcoxon sign-rank test between observed and expected heterozygosity and the mode of allele frequency distribution revealed clues of a significant past genetic bottleneck. The Wayampi stand genetically closer to the Apalai, Palikur and Kali'na when examined for the autosome but not the Y-chromosome panel of markers, suggesting preferential female gene flow., Conclusion: The new data provided additional important information about the biological history of people from a remote South American region, indicating how gene diversity analyses can be used to increase understanding of human microevolutionary processes.
- Published
- 2011
- Full Text
- View/download PDF
49. Searching the peopling of the Iberian Peninsula from the perspective of two andalusian subpopulations: a study based on Y-chromosome haplogroups J and E.
- Author
-
Ambrosio B, Hernández C, Novelletto A, Dugoujon JM, Rodríguez JN, Cuesta P, Fortes-Lima C, and Calderón R
- Subjects
- Humans, Jews, Spain, Chromosomes, Human, Y, Emigration and Immigration, Haplotypes
- Abstract
This study aims at a high-resolution analysis of Y-chromosome J and E haplogroups among Andalusians to reconstruct Neolithic, protohistorical and historical migrations in the Mediterranean region. Genotyping of two samples from Granada (n=250 males) and Huelva (n=167 males) (Spain) with Y-chromosome binary and microsatellite markers was performed, and the results compared with other Mediterranean populations. The two samples showed genetic differences that can be associated with different evolutionary processes. Migrations toward Andalusia probably originated in the Arabian Peninsula, Fertile Crescent, Balkan region and North Africa, and they would have predominantly occurred in protohistoric and historic times. Maritime travel would have notably contributed to recent gene flow into Iberia. This survey highlight the complexity of the Mediterranean migration processes and demonstrate the impact of the different population sources on the genetic composition of the Spanish population. The main in-migrations to Iberia most likely did not occur through intermediate stages or, if such stages did occur, they would have been very few.
- Published
- 2010
50. Contrasting patterns of nuclear and mtDNA diversity in Native American populations.
- Author
-
Yang NN, Mazières S, Bravi C, Ray N, Wang S, Burley MW, Bedoya G, Rojas W, Parra MV, Molina JA, Gallo C, Poletti G, Hill K, Hurtado AM, Petzl-Erler ML, Tsuneto LT, Klitz W, Barrantes R, Llop E, Rothhammer F, Labuda D, Salzano FM, Bortolini MC, Excoffier L, Dugoujon JM, and Ruiz-Linares A
- Subjects
- Chromosomes, Human, X genetics, Chromosomes, Human, Y genetics, Female, Humans, Male, Microsatellite Repeats, Sequence Analysis, DNA methods, DNA, Mitochondrial genetics, Emigration and Immigration, Indians, North American genetics, Indians, South American genetics
- Abstract
We report an integrated analysis of nuclear (autosomal, X- and Y-chromosome) short tandem repeat (STR) data and mtDNA D-loop sequences obtained in the same set of 22 Native populations from across the Americas. A north to south gradient of decreasing population diversity was observed, in agreement with a settlement of the Americas from the extreme northwest of the continent. This correlation is stronger with "least cost distances," which consider the coasts as facilitators of migration. Continent-wide estimates of population structure are highest for the Y-chromosome and lowest for the autosomes, consistent with the effective size of the different marker systems examined. Population differentiation is highest in East South America and lowest in Meso America and the Andean region. Regional analyses suggest a deviation from mutation-drift equilibrium consistent with population expansion in Meso America and the Andes and population contraction in Northwest and East South America. These data hint at an early divergence of Andean and non-Andean South Americans and at a contrasting demographic history for populations from these regions., (© 2010 The Authors Annals of Human Genetics © 2010 Blackwell Publishing Ltd/University College London.)
- Published
- 2010
- Full Text
- View/download PDF
Catalog
Discovery Service for Jio Institute Digital Library
For full access to our library's resources, please sign in.