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Abeid SN, Motrane M, Farhane H, Harich N. Human population genetics of Comoros islanders: Alu polymorphisms and the peopling of the three major islands. GENE REPORTS 2021. [DOI: 10.1016/j.genrep.2020.100927] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Abdeli A, Benhassine T. Genetic diversity of 15 autosomal STRs in a sample of Berbers from Aurès region in the Northeast of Algeria and genetic relationships with other neighbouring samples. Ann Hum Biol 2020; 47:284-293. [PMID: 32183545 DOI: 10.1080/03014460.2020.1736628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Background: The history of the Aurès mountains and neighbouring areas, a large region of the East of Algeria, was part of the history of the ancient independent Berber kingdoms supposed to be the ancestors of the current Berber people. The genetic background of this region has not yet been clarified.Aim: The aims of our study were to investigate the genetic characteristics of 15 autosomal short tandem repeats (STRs) in a sample from these regions, to determine the degree of heterogeneity among Algerian and North African samples and to analyse the genetic relationships with other populations.Subjects and methods: Allele frequencies, forensic parameters and Hardy-Weinberg equilibrium (HWE) of 15 autosomal STRs included in the PowerPlex® ESI 16 System were obtained from 308 individuals. Allele frequencies were used to determine the relationships with other populations.Results: All loci were highly polymorphic and no significant deviation from HWE was detected. Allele frequencies showed that the samples of Aurès region share genetic affinities with other Algerian, North African and Middle Eastern samples, with the exception of samples from Iran and Matmata.Conclusions: These markers revealed a genetic homogeneity between the Algerian and North African samples. The genetic affinities indicate that this sample could share a common ancestor with the Middle Eastern samples.
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Affiliation(s)
- Amine Abdeli
- Laboratoire de Biologie Cellulaire et Moléculaire, Faculté des Sciences Biologiques, Université des Sciences et de la Technologie Houari Boumediene, Alger, Algeria.,Institut National de Criminalistique et de Criminologie de la Gendarmerie Nationale, Alger, Algeria
| | - Traki Benhassine
- Laboratoire de Biologie Cellulaire et Moléculaire, Faculté des Sciences Biologiques, Université des Sciences et de la Technologie Houari Boumediene, Alger, Algeria
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Abeid SN, Motrane M, Farhane H, Harich N. Alu elements within the human major histocompatibility class I region in the Comoros Islands: genetic variation and population relationships. Ann Hum Biol 2019; 46:169-174. [PMID: 31116034 DOI: 10.1080/03014460.2019.1620854] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/06/2022]
Abstract
Background: Alu elements are attractive markers for population genetics, disease, forensics and paternity analyses, due to their particular characteristics. Five polymorphic Alu insertions within the MHC class I region have been little examined in human populations. Aim: The analysis of the genetic diversity of autochthonous Comorians from the three major islands of the archipelago by these polymorphic MHC Alus and to assess their relationships together and with other populations. Subjects and methods: Two hundred and fifty-seven unrelated participants from the Comoros archipelago, Grande Comore (86), Anjouan (93) and Moheli (78), were examined for five MHC Alu insertions. The data were analysed for intra- and inter-population genetic variation. Results: All MHC Alu were polymorphic in the three samples and only one significant differentiation was observed between Anjouan and Moheli. According to the MDS and AMOVA results, the populations included in the inter-population analyses were grouped in three major clusters according to their genetic ancestry. The haplotype diversity showed by the Comorians is higher than in previously studied African populations and occupies an intermediate position between African and Asian clusters. Conclusion: MHC Alu insertions are useful markers to study micro-geographical genetic variations. Using these polymorphisms, new insights have been obtained about the biological history and evolution of the Comoros.
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Affiliation(s)
- Said Nassor Abeid
- a Equipe des Sciences Anthropogénétiques et Biotechnologies, Département de Biologie , Faculté des Sciences, Université Chouaïb Doukkali , El Jadida , Morocco
| | - Majida Motrane
- a Equipe des Sciences Anthropogénétiques et Biotechnologies, Département de Biologie , Faculté des Sciences, Université Chouaïb Doukkali , El Jadida , Morocco
| | - Hamid Farhane
- a Equipe des Sciences Anthropogénétiques et Biotechnologies, Département de Biologie , Faculté des Sciences, Université Chouaïb Doukkali , El Jadida , Morocco
| | - Nourdin Harich
- a Equipe des Sciences Anthropogénétiques et Biotechnologies, Département de Biologie , Faculté des Sciences, Université Chouaïb Doukkali , El Jadida , Morocco
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Abdeli A, Benhassine T. Paternal lineage of the Berbers from Aurès in Algeria: estimate of their genetic variation. Ann Hum Biol 2019; 46:160-168. [PMID: 30939942 DOI: 10.1080/03014460.2019.1602166] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Background: Aurès is a vast territory in the east of Algeria, characterised by its traditional Berber settlement which has preserved its language and its rich history; its name goes back to antiquity and before the Roman conquest it was part of the territory of ancient Numidia. The Chaoui people in this region are one of Algeria's largest Berber groups. Aim: The aims were to investigate the level of genetic diversity of the Berbers of Aurès through the analysis of the paternal gene pool and to estimate the percentage of genetic variation among different geographical regions and linguistic groups from Algeria. Subjects and methods: Twenty-three Y-STRs were genotyped in a sample of 218 unrelated males of the Berbers of Aurès. Algorithms were used to estimate the Y-chromosome haplogroups. Genetic distance, non-metric MDS and AMOVA were used to analyse the genetic relationships between sample groups. Results: The paternal lineage of this sample of the Aurès region did not exhibit strong signals of differentiation with other samples from North-central, Northwest, and South Algeria. However, significant differences were found within this sample, demonstrating a high degree of heterogeneity. Conclusion: The results demonstrate that Aurès people are isolated and closed, but nevertheless have quite different genetic profiles.
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Affiliation(s)
- Amine Abdeli
- a Laboratoire de Biologie Cellulaire et Moléculaire, Faculté des Sciences Biologiques , Université des Sciences et de la Technologie Houari Boumediene , Algiers , Algeria.,b Institut National de Criminalistique et de Criminologie de la Gendarmerie Nationale , Algiers , Algeria
| | - Traki Benhassine
- a Laboratoire de Biologie Cellulaire et Moléculaire, Faculté des Sciences Biologiques , Université des Sciences et de la Technologie Houari Boumediene , Algiers , Algeria
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Badache H, Boussetta S, Elgaaeid AB, Cherni L, El-khil HK. Investigation of the genetic structure of Kabyle and Chaouia Algerian populations through the polymorphism of Alu insertion markers. Ann Hum Biol 2019; 46:150-159. [DOI: 10.1080/03014460.2019.1588994] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- Hocine Badache
- Laboratory of Genetics, Immunology and Human Pathology, Faculty of Sciences of Tunis, University of Tunis El Manar, Tunisia
| | - Sami Boussetta
- Laboratory of Genetics, Immunology and Human Pathology, Faculty of Sciences of Tunis, University of Tunis El Manar, Tunisia
| | - Amel Benammar Elgaaeid
- Laboratory of Genetics, Immunology and Human Pathology, Faculty of Sciences of Tunis, University of Tunis El Manar, Tunisia
| | - Lotfi Cherni
- Laboratory of Genetics, Immunology and Human Pathology, Faculty of Sciences of Tunis, University of Tunis El Manar, Tunisia
- Higher Institute of Biotechnology, University of Monastir, Tunisia
| | - Houssein Khodjet El-khil
- Laboratory of Genetics, Immunology and Human Pathology, Faculty of Sciences of Tunis, University of Tunis El Manar, Tunisia
- Higher Institute of Biotechnology, University of Monastir, Tunisia
- Department of Biomedical Sciences, College of Health Sciences Qatar University, Doha, Qatar
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Genetic structure in the paternal lineages of South East Spain revealed by the analysis of 17 Y-STRs. Sci Rep 2019; 9:5234. [PMID: 30914710 PMCID: PMC6435739 DOI: 10.1038/s41598-019-41580-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Accepted: 02/08/2019] [Indexed: 11/09/2022] Open
Abstract
The genetic data of 17 Y chromosome short tandem repeats in 146 unrelated donor residents in the provinces of Granada, Málaga, and Almería (GMA) were analyzed to determine the genetic legacy of the male inhabitants of the former Kingdom of Granada. A total of 139 unique haplotypes were identified. Observed allele frequencies and haplogroup frequencies were also analyzed. By AMOVA and STRUCTURE analysis, the populations of the 3 provinces could be treated genetically as a single population. The most frequent haplogroup was R1b1b2 (58.22%). By network analysis of all individuals, we observed a distribution according to haplogroup assignment. To improve the characterization of GMA population, it was compared with those of North Africa, the Iberian Peninsula, and southern Europe. In our analysis of allele frequencies and genetic distances, the GMA population lay within the Spanish population group. Further, in the STRUCTURE analysis, there was no African component in the GMA population, confirming that, based on our genetic markers, the GMA population does not reflect any male genetic influence of the North African people. The presence of African haplogroups in the GMA population is irrelevant when their frequency is compared with those in other European populations.
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Novillo A, Gaibar M, Romero-Lorca A, Chaabani H, Amir N, Moral P, Esteban ME, Fernández-Santander A. UDP-glucuronosyltransferase genetic variation in North African populations: a comparison with African and European data. Ann Hum Biol 2019; 45:516-523. [PMID: 30616396 DOI: 10.1080/03014460.2018.1559354] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
BACKGROUND Genetic variation in glucuronosyltransferases (UGT) is crucial in drug metabolism and risk of some diseases. AIM To examine genetic variation in UGT in North African populations. SUBJECTS AND METHODS Allele frequencies of SNPs UGT1A424Thr, UGT1A448Val, UGT2B1585Tyr, UGT2B15523Thr and UGT2B17 CNV deletion from Morocco, Algeria, Tunisia and Libya were compared to European and Sub-Saharan populations. RESULTS North Africans are the group with the highest genetic heterogeneity given by internal differences in the occurrence of UGT2B17 deletion, UGT1A448Val and UGT1A4 haplotypes. UGT2B15 SNPs differentiate Sub-Saharans from the rest of the populations. CONCLUSION North African populations show a high frequency of carriers of UGT2B15523Thr, a variant linked to an increased risk of prostate cancer. High Atlas Moroccans and Algerians show low frequency of UGT2B17del, a variant associated with high concentrations of testosterone and oestradiol.
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Affiliation(s)
- Apolonia Novillo
- a Basic Biomedical Sciences Department , Universidad Europea de Madrid , Madrid , Spain
| | - María Gaibar
- a Basic Biomedical Sciences Department , Universidad Europea de Madrid , Madrid , Spain
| | - Alicia Romero-Lorca
- a Basic Biomedical Sciences Department , Universidad Europea de Madrid , Madrid , Spain
| | - Hassen Chaabani
- b Faculty of Pharmacy , University of Monastir , Monastir , Tunisia
| | - Nadir Amir
- c Laboratoire de Biochimie Appliquée, 5 Faculté des Sciences de la Nature et de la Vie , Université de Bejaia , Bejaia , Algeria
| | - Pedro Moral
- d Section of Zoology and Biological Anthropology, Department of Evolutionary Biology, Ecology and Environmental Sciences, Faculty of Biology , Universitat de Barcelona , Barcelona , Spain.,e Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona , Barcelona , Spain
| | - M Esther Esteban
- d Section of Zoology and Biological Anthropology, Department of Evolutionary Biology, Ecology and Environmental Sciences, Faculty of Biology , Universitat de Barcelona , Barcelona , Spain.,e Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona , Barcelona , Spain
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Santamaría J, Álvarez-Álvarez MM, Esteban ME, Ramon-Gurrea E, Moral P. Dinucleotide (CA)n tandem repeats on the human X-chromosome and the history of the Mediterranean populations. Ann Hum Biol 2018; 45:72-76. [PMID: 29382285 DOI: 10.1080/03014460.2017.1414877] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
BACKGROUND Tandem repeats (STRs) are genomic markers of particular interest in forensic and population genetics. Most of the population data currently available correspond to the variation of STRs of forensic panels, which barely include dinucleotide tandem repeats. AIMS The aim of the study is to test the usefulness of a battery of dinucleotide STRs on the X chromosome for population and forensic studies. SUBJECTS AND METHODS A total of 672 individuals from 12 Mediterranean populations and two external references were analysed for 15 X-STR following the instructions of the commercial company and using control DNA from the CEPH centre whose sequences are published in GenBank. Genotypic results were analysed using standard population genetics methods including estimates of linkage disequilibrium, population structure and gene flow. Common forensic efficiency parameters were calculated. RESULTS The analysed X-STRs show high values of genetic diversity, comparable to other STRs of more common use. No significant associations between markers were found. A slight population structure was detected between the two shores of the Mediterranean. The X-STRs studied here present a similar degree of variability to that of other X-STRs used in forensics. CONCLUSION Tandem-repeated dinucleotides are a good tool for evidencing population differences here. Forensic parameters indicate that the dinucleotide X-STRs are suitable for forensic use.
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Affiliation(s)
- Josep Santamaría
- a Departamento de Biologia Evolutiva, Ecología y Ciencias Ambientales , Universitat de Barcelona , Barcelona , Spain
| | - Miguel M Álvarez-Álvarez
- a Departamento de Biologia Evolutiva, Ecología y Ciencias Ambientales , Universitat de Barcelona , Barcelona , Spain
| | - M Esther Esteban
- a Departamento de Biologia Evolutiva, Ecología y Ciencias Ambientales , Universitat de Barcelona , Barcelona , Spain
| | - Elies Ramon-Gurrea
- a Departamento de Biologia Evolutiva, Ecología y Ciencias Ambientales , Universitat de Barcelona , Barcelona , Spain
| | - Pedro Moral
- a Departamento de Biologia Evolutiva, Ecología y Ciencias Ambientales , Universitat de Barcelona , Barcelona , Spain
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Čížková M, Hofmanová Z, Mokhtar MG, Janoušek V, Diallo I, Munclinger P, Černý V. Alu insertion polymorphisms in the African Sahel and the origin of Fulani pastoralists. Ann Hum Biol 2017; 44:537-545. [PMID: 28502204 DOI: 10.1080/03014460.2017.1328073] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
BACKGROUND The origin of Western African pastoralism, represented today by the Fulani nomads, has been a highly debated issue for the past decades, and has not yet been conclusively resolved. AIM This study focused on Alu polymorphisms in sedentary and nomadic populations across the African Sahel to investigate patterns of diversity that can complement the existing results and contribute to resolving issues concerning the origin of West African pastoralism. SUBJECTS AND METHODS A new dataset of 21 Alu biallelic markers covering a substantial part of the African Sahel has been analysed jointly with several published North African populations. RESULTS Interestingly, with regard to Alu variation, the relationship of Fulani pastoralists to North Africans is not as evident as was earlier revealed by studies of uniparental loci such as mtDNA and NRY. Alu insertions point rather to an affinity of Fulani pastoralists to Eastern Africans also leading a pastoral lifestyle. CONCLUSIONS It is suggested that contemporary Fulani pastoralists might be descendants of an ancestral Eastern African population that, while crossing the Sahara in the Holocene, admixed slightly with a population of Eurasian (as evidenced by uniparental polymorphisms) ancestry. It seems that, in the Fulani pastoralists, Alu elements reflect more ancient genetic relationships than do uniparental genetic systems.
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Affiliation(s)
- Martina Čížková
- a Department of Anthropology and Human Genetics, Faculty of Science , Charles University , Prague , Czech Republic
| | - Zuzana Hofmanová
- a Department of Anthropology and Human Genetics, Faculty of Science , Charles University , Prague , Czech Republic.,b Palaeogenetics Group , Johannes Gutenberg University Mainz , Mainz , Germany
| | - Mohammed G Mokhtar
- c Arabic Department, Faculty of Arts , University of Kordofan , Al-Ubayyid , Sudan
| | - Václav Janoušek
- d Department of Zoology, Faculty of Science , Charles University , Prague , Czech Republic
| | - Issa Diallo
- e Département de Linguistique et Langues Nationales , Institut des Sciences des Sociétés, CNRST , Ouagadougou , Burkina Faso
| | - Pavel Munclinger
- d Department of Zoology, Faculty of Science , Charles University , Prague , Czech Republic
| | - Viktor Černý
- f Department of the Archaeology of Landscape and Archaeobiology, Archaeogenetics Laboratory , Institute of Archaeology of the Academy of Sciences of the Czech Republic , Prague , Czech Republic
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Álvarez-Álvarez MM, Zanetti D, Carreras-Torres R, Moral P, Athanasiadis G. A survey of sub-Saharan gene flow into the Mediterranean at risk loci for coronary artery disease. Eur J Hum Genet 2017; 25:472-476. [PMID: 28098150 DOI: 10.1038/ejhg.2016.200] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Revised: 11/24/2016] [Accepted: 12/14/2016] [Indexed: 12/31/2022] Open
Abstract
This study tries to find detectable signals of gene flow of Sub-Saharan origin into the Mediterranean in four genomic regions previously associated with coronary artery disease. A total of 366 single-nucleotide polymorphisms were genotyped in 772 individuals from 10 Mediterranean countries. Population structure analyses were performed, in which a noticeable Sub-Saharan component was found in the studied samples. The overall percentage of this Sub-Saharan component presents differences between the two Mediterranean coasts. D-statistics suggest possible Sub-Saharan introgression into one of the studied genomic regions (10q11). We also found differences in linkage disequilibrium patterns between the two Mediterranean coasts, possibly attributable to differential Sub-Saharan admixture. Our results confirm the potentially important role of human demographic history when performing epidemiological studies.
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Affiliation(s)
- Miguel M Álvarez-Álvarez
- Faculty of Biology, Department of Evolutionary Biology, Ecology and Environmental Sciences, Biodiversity Research Institute, University of Barcelona,Barcelona, Spain
| | - Daniela Zanetti
- Faculty of Biology, Department of Evolutionary Biology, Ecology and Environmental Sciences, Biodiversity Research Institute, University of Barcelona,Barcelona, Spain
| | - Robert Carreras-Torres
- Faculty of Biology, Department of Evolutionary Biology, Ecology and Environmental Sciences, Biodiversity Research Institute, University of Barcelona,Barcelona, Spain
| | - Pedro Moral
- Faculty of Biology, Department of Evolutionary Biology, Ecology and Environmental Sciences, Biodiversity Research Institute, University of Barcelona,Barcelona, Spain
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Álvarez-Álvarez MM, Carreras-Torres R, Zanetti D, Vegas E, Moral P. Population variation of LIN28B in the Mediterranean: Novel markers for microgeographic discrimination. Am J Hum Biol 2016; 28:905-912. [PMID: 27338933 DOI: 10.1002/ajhb.22887] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2015] [Revised: 04/11/2016] [Accepted: 06/06/2016] [Indexed: 11/09/2022] Open
Abstract
OBJECTIVES The aim of this study is to determine whether the LIN28B gene is differentially distributed in the Mediterranean region through the analysis of the allele distribution of three single nucleotide polymorphisms (SNPs), namely rs7759938, rs314277, and rs221639, in 24 populations. These SNPs have been recently related to the age at menarche, pubertal height growth, peripubertal body mass index, levels of prenatal testosterone exposure, and cancer survival. METHODS A total of 1,197 DNA samples were genotyped. The allele frequencies were used to determine the relationship between populations, with data from the 1000 Genomes Project being used for external comparisons. The genotype distributions and the population structure between populations and groups of populations were determined. RESULTS The population results indicate a significant degree of variation (FST = 0.043, P < 0.0001). Allele frequencies show significant differences among populations. A hierarchical variance analysis is consistent with a primary differentiation between populations on the North and South coasts of the Mediterranean. This difference is especially evident in the unexpected distribution of the SNP rs221639, which shows one of the highest FST (11.5%, P < 0.0001) values described in the Mediterranean region thus far. CONCLUSION The population differentiation and the structuring of the genetic variance, in agreement with previous studies, indicate that the SNPs in question are good tools for the study of human populations, even at a microgeographic level. Am. J. Hum. Biol. 28:905-912, 2016. © 2016Wiley Periodicals, Inc.
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Affiliation(s)
- Miguel M Álvarez-Álvarez
- Anthropology Unit, Department of Animal Biology, Faculty of Biology, University of Barcelona, Barcelona, Spain. Biodiversity Research Institute (IRBio)
| | - Robert Carreras-Torres
- Anthropology Unit, Department of Animal Biology, Faculty of Biology, University of Barcelona, Barcelona, Spain. Biodiversity Research Institute (IRBio)
| | - Daniela Zanetti
- Anthropology Unit, Department of Animal Biology, Faculty of Biology, University of Barcelona, Barcelona, Spain. Biodiversity Research Institute (IRBio)
| | - Esteban Vegas
- Department of Statistics, Faculty of Biology, University of Barcelona, Barcelona, Spain
| | - Pedro Moral
- Anthropology Unit, Department of Animal Biology, Faculty of Biology, University of Barcelona, Barcelona, Spain. Biodiversity Research Institute (IRBio)
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Zanetti D, Sadiq M, Carreras-Torres R, Khabour O, Alkaraki A, Esteban E, Via M, Moral P. Human diversity in Jordan: polymorphic Alu insertions in general Jordanian and Bedouin groups. Hum Biol 2015; 86:131-8. [PMID: 25397703 DOI: 10.3378/027.086.0201] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/03/2014] [Indexed: 11/05/2022]
Abstract
Jordan, located in the Levant region, is an area crucial for the investigation of human migration between Africa and Eurasia. However, the genetic history of Jordanians has yet to be clarified, including the origin of the Bedouins today resident in Jordan. Here, we provide new genetic data on autosomal independent markers in two Jordanian population samples (Bedouins and the general population) to begin to examine the genetic diversity inside this country and to provide new information about the genetic position of these populations in the context of the Mediterranean and Middle East area. The markers analyzed were 18 Alu polymorphic insertions characterized by their identity by descent, known ancestral state (lack of insertion), and apparent selective neutrality. The results indicate significant genetic diffferences between Bedouins and general Jordanians (p = 0.038). Whereas Bedouins show a close genetic proximity to North Africans, general Jordanians appear genetically more similar to other Middle East populations. In general, these data are consistent with the hypothesis that Bedouins had an important role in the peopling of Jordan and constitute the original substrate of the current population. However, migration into Jordan in recent years likely has contributed to the diversity among current Jordanian population groups.
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Affiliation(s)
- Daniela Zanetti
- Department of Animal Biology-Anthropology, University of Barcelona, Barcelona, Spain
| | - May Sadiq
- Department of Biological Sciences, Yarmouk University, Irbid, Jordan
| | | | - Omar Khabour
- Department of Medical Laboratory Sciences, Jordan University of Science and Technology, Irbid, Jordan, and Department of Biology, Faculty of Science, Taibah University, Saudi Arabia
| | | | - Esther Esteban
- Department of Animal Biology-Anthropology, University of Barcelona, Barcelona, Spain
| | - Marc Via
- Department of Psychiatry and Clinical Psychobiology, University of Barcelona, Barcelona, Spain
| | - Pedro Moral
- Department of Animal Biology-Anthropology, University of Barcelona, Barcelona, Spain
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Tadmouri GO, Sastry KS, Chouchane L. Arab gene geography: From population diversities to personalized medical genomics. Glob Cardiol Sci Pract 2014; 2014:394-408. [PMID: 25780794 PMCID: PMC4355514 DOI: 10.5339/gcsp.2014.54] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2014] [Accepted: 12/11/2014] [Indexed: 12/20/2022] Open
Abstract
Genetic disorders are not equally distributed over the geography of the Arab region. While a number of disorders have a wide geographical presence encompassing 10 or more Arab countries, almost half of these disorders occur in a single Arab country or population. Nearly, one-third of the genetic disorders in Arabs result from congenital malformations and chromosomal abnormalities, which are also responsible for a significant proportion of neonatal and perinatal deaths in Arab populations. Strikingly, about two-thirds of these diseases in Arab patients follow an autosomal recessive mode of inheritance. High fertility rates together with increased consanguineous marriages, generally noticed in Arab populations, tend to increase the rates of genetic and congenital abnormalities. Many of the nearly 500 genes studied in Arab people revealed striking spectra of heterogeneity with many novel and rare mutations causing large arrays of clinical outcomes. In this review we provided an overview of Arab gene geography, and various genetic abnormalities in Arab populations, including disorders of blood, metabolic, circulatory and neoplasm, and also discussed their associated molecules or genes responsible for the cause of these disorders. Although studying Arab-specific genetic disorders resulted in a high value knowledge base, approximately 35% of genetic diseases in Arabs do not have a defined molecular etiology. This is a clear indication that comprehensive research is required in this area to understand the molecular pathologies causing diseases in Arab populations.
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Affiliation(s)
| | - Konduru S Sastry
- Laboratory of Genetic Medicine and Immunology, Weill Cornell Medical College in Qatar, Qatar Foundation, Doha, Qatar
| | - Lotfi Chouchane
- Laboratory of Genetic Medicine and Immunology, Weill Cornell Medical College in Qatar, Qatar Foundation, Doha, Qatar
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BAHRI RAOUDHA, ESTEBAN ESTHER, BEN HALIMA ABIR, MORAL PEDRO, CHAABANI HASSEN. Distinctive genetic signatures of Alu/STR compound systems revealed by analyses of Mediterranean and Middle East populations. ANTHROPOL SCI 2014. [DOI: 10.1537/ase.140602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Affiliation(s)
- RAOUDHA BAHRI
- Laboratory of Human Genetics and Anthropology, Faculty of Pharmacy, University of Monastir
| | - ESTHER ESTEBAN
- Secció d’Antropologia, Departament de Biologia Animal, Facultat de Biologia, Universitat de Barcelona, Barcelona
| | - ABIR BEN HALIMA
- Laboratory of Human Genetics and Anthropology, Faculty of Pharmacy, University of Monastir
| | - PEDRO MORAL
- Secció d’Antropologia, Departament de Biologia Animal, Facultat de Biologia, Universitat de Barcelona, Barcelona
| | - HASSEN CHAABANI
- Laboratory of Human Genetics and Anthropology, Faculty of Pharmacy, University of Monastir
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Halima AB, Bahri R, Esteban E, Aribia MHB, Moral P, Chaabani H. Ethnic composition and genetic differentiation of the Libyan population: insights onAlupolymorphisms. Ann Hum Biol 2013; 41:229-37. [DOI: 10.3109/03014460.2013.850112] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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Salem AH, Bahri R, Jarjanazi H, Chaabani H. Geographical and social influences on genetic diversity within the Egyptian population: analyses ofAluinsertion polymorphisms. Ann Hum Biol 2013; 41:61-6. [DOI: 10.3109/03014460.2013.826734] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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Spatial principal component analysis points at global genetic structure in the Western Mediterranean. J Hum Genet 2013; 58:762-5. [PMID: 24005895 DOI: 10.1038/jhg.2013.94] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2013] [Revised: 08/02/2013] [Accepted: 08/09/2013] [Indexed: 11/08/2022]
Abstract
Many studies have tackled the existence of a genetic barrier in the Strait of Gibraltar between Iberian and North African populations, often with controversial conclusions. Here, we address this issue using a collection of Western Mediterranean populations and two dimensionality reduction methods: principal component analysis (PCA) and spatial PCA (sPCA). Our four different data sets consisted of (i) 16 polymorphic Alu insertions in 12 populations; (ii) 35 single-nucleotide polymorphisms in 13 populations; (iii) 13 short tandem repeats in 11 populations; and (iv) all 64 markers in 9 populations. In all PCA plots, South European and North African samples were visually distinguishable along the first PC. Several smaller clusters were also identifiable, especially on the African side of our geographical setting. sPCA indicated a single global structure for each of the marker sets and no local structures. These results are more compatible with a clinal distribution of allele frequencies rather than with abrupt changes, suggesting that isolation-by-distance, rather than a barrier to gene flow, is a more likely mechanism of genetic differentiation in the Western Mediterranean. An alternative/complementary explanation is progressive introgression from North African to Southwestern European populations.
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Pojskic N, Silajdzic E, Kalamujic B, Kapur-Pojskic L, Lasic L, Tulic U, Hadziselimovic R. Polymorphic Alu insertions in human populations of Bosnia and Herzegovina. Ann Hum Biol 2013; 40:181-5. [DOI: 10.3109/03014460.2012.756063] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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Gaibar M, Esteban ME, Via M, Harich N, Kandil M, Fernández-Santander A. Usefulness of autosomal STR polymorphisms beyond forensic purposes: data on Arabic- and Berber-speaking populations from central Morocco. Ann Hum Biol 2013; 39:297-304. [PMID: 22747069 DOI: 10.3109/03014460.2012.697578] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
BACKGROUND This work describes, for the first time, the profile of Middle Atlas Berbers and Arabic-speaking central Moroccans for 15 autosomal STR loci widely used in forensic sciences. AIM The main objectives were to determine the degree of heterogeneity among different Moroccan samples to identify geographic or linguistic patterns and to evaluate the usefulness of forensic STRs in anthropological studies. SUBJECTS AND METHODS Blood samples were collected from 71 Arabic-speakers and 75 Berbers from the regions of Doukkala (central-west coast) and Khenifra (Middle Atlas), respectively. The AmpFlSTR Identifier kit was used to genotype 15 autosomal STR in both samples. RESULTS Middle Atlas Berbers showed slightly higher genetic variation values compared to Arabic-speakers, both in the number of alleles and heterozygosity. In order to assess population relationships, data from Morocco, Algeria, Tunisia, Libya, Egypt, Kuwait, Qatar, Palestine, Syria, South-Spain and Turkey were included in the analysis. Within Morocco, genetic distances followed a clear geographic pattern. In the Arabic-speaking sample the genetic proportion of 'Arabian' admixture was estimated in 13%. CONCLUSION The low value of admixture suggests that the Arabization of Morocco had a reduced demographic impact, which should be taken with caution because it is based on autosomal STRs with low inter-population variation levels.
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Affiliation(s)
- Maria Gaibar
- Departamento de CC. Biomédicas Básicas, Universidad Europea de Madrid, 28670 Villaviciosa de Odón, Madrid, Spain
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Bahri R, Halima AB, Ayadi I, Esteban E, Alfadhli SM, Rebai A, Moral P, Chaabani H. Genetic position of Bahrain natives among wider Middle East populations according to Alu insertion polymorphisms. Ann Hum Biol 2012; 40:35-40. [DOI: 10.3109/03014460.2012.728622] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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Fernández-Santander A, Valveny N, Harich N, Kandil M, Luna F, Martín MÁ, Rubio JC, Lucia A, Gaibar M. Polymorphisms influencing muscle phenotypes in North-African and Spanish populations. Ann Hum Biol 2012; 39:166-9. [PMID: 22324844 DOI: 10.3109/03014460.2012.657243] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
AIM The purpose of this study was to determine the allelic and genotypic frequency distribution of the C34T mutation in the muscle isoform of the adenosine monophosphate deaminase 1 (AMPD1) gene and of the missense substitution K153R in the myostatin (GDF8) gene in one Spanish and two North African populations. METHOD One sample of 98 individuals was genotyped from the South of Spain (Alpujarra) and two samples from Morocco (77 Berbers and 78 Arabs). RESULTS The frequency of the AMPD1 C34T mutation was lower in Berbers (0.071) compared with the Alpujarra cohort (0.153, p = 0.018). The GDF8 K153R substitution showed little variability among the three cohorts. CONCLUSIONS Studies with larger cohorts and other ethnic groups are needed to corroborate that there does not exist any major variability in the genotype distribution of genes associated with muscle phenotypes in the South-Eastern Mediterranean area.
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Bahri R, El Moncer W, Al-Batayneh K, Sadiq M, Esteban E, Moral P, Chaabani H. Genetic differentiation and origin of the Jordanian population: an analysis of Alu insertion polymorphisms. Genet Test Mol Biomarkers 2011; 16:324-9. [PMID: 22106835 DOI: 10.1089/gtmb.2011.0197] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
AIM Although much of Jordan is covered by desert, its north-western region forms part of the Fertile Crescent region that had given a rich past to Jordanians. This past, scarcely described by historians, is not yet clarified by sufficient genetic data. Thus in this paper we aim to determine the genetic differentiation of the Jordanian population and to discuss its origin. METHODS A total of 150 unrelated healthy Jordanians were investigated for ten Alu insertion polymorphisms. Genetic relationships among populations were estimated by a principal component (PC) plot based on the analyses of the R-matrix software. RESULTS Statistical analysis showed that the Jordanian population is not significantly different from the United Arab Emirates population or the North Africans. This observation, well represented in PC plot, suggests a common origin of these populations belonging respectively to ancient Mesopotamia, Arabia, and North Africa. CONCLUSION Our results are compatible with ancient peoples' movements from Arabia to ancient Mesopotamia and North Africa as proposed by historians and supported by previous genetic results. The original genetic profile of the Jordanian population, very likely Arabian Semitic, has not been subject to significant change despite the succession of several civilizations.
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Affiliation(s)
- Raoudha Bahri
- Laboratory of Human Genetics and Anthropology, Faculty of Pharmacy, University of Monastir, Monastir, Tunisia
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El Moncer W, Bahri R, Esteban E, Abdenni-Guenounou B, Moral P, Ben Chibani J, Chaabani H. Research of the origin of a particular Tunisian group using a physical marker and Alu insertion polymorphisms. Genet Mol Biol 2011; 34:371-6. [PMID: 21931506 PMCID: PMC3168174 DOI: 10.1590/s1415-47572011005000021] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2010] [Accepted: 03/23/2011] [Indexed: 11/22/2022] Open
Abstract
The aim of this study was to show how, in some particular circumstances, a physical marker can be used along with molecular markers in the research of an ancient people movement. A set of five Alu insertions was analysed in 42 subjects from a particular Tunisian group (El Hamma) that has, unlike most of the Tunisian population, a very dark skin, similar to that of sub-Saharans, and in 114 Tunisian subjects (Gabes sample) from the same governorate, but outside the group. Our results showed that the El Hamma group is genetically midway between sub-Saharan populations and North Africans, whereas the Gabes sample is clustered among North Africans. In addition, The A25 Alu insertion, considered characteristic to sub-Saharan Africans, was present in the El Hamma group at a relatively high frequency. This frequency was similar to that found in sub-Saharans from Nigeria, but significantly different from those found in the Gabes sample and in other North African populations. Our molecular results, consistent with the skin color status, suggest a sub-Saharan origin of this particular Tunisian group.
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Affiliation(s)
- Wifak El Moncer
- Laboratory of Human Genetics and Anthropology, Faculty of Pharmacy, University of Monastir, Monastir, Tunisia
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Ottoni C, Primativo G, Hooshiar Kashani B, Achilli A, Martínez-Labarga C, Biondi G, Torroni A, Rickards O. Mitochondrial haplogroup H1 in north Africa: an early holocene arrival from Iberia. PLoS One 2010; 5:e13378. [PMID: 20975840 PMCID: PMC2958834 DOI: 10.1371/journal.pone.0013378] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2010] [Accepted: 09/22/2010] [Indexed: 12/12/2022] Open
Abstract
The Tuareg of the Fezzan region (Libya) are characterized by an extremely high frequency (61%) of haplogroup H1, a mitochondrial DNA (mtDNA) haplogroup that is common in all Western European populations. To define how and when H1 spread from Europe to North Africa up to the Central Sahara, in Fezzan, we investigated the complete mitochondrial genomes of eleven Libyan Tuareg belonging to H1. Coalescence time estimates suggest an arrival of the European H1 mtDNAs at about 8,000–9,000 years ago, while phylogenetic analyses reveal three novel H1 branches, termed H1v, H1w and H1x, which appear to be specific for North African populations, but whose frequencies can be extremely different even in relatively close Tuareg villages. Overall, these findings support the scenario of an arrival of haplogroup H1 in North Africa from Iberia at the beginning of the Holocene, as a consequence of the improvement in climate conditions after the Younger Dryas cold snap, followed by in situ formation of local H1 sub-haplogroups. This process of autochthonous differentiation continues in the Libyan Tuareg who, probably due to isolation and recent founder events, are characterized by village-specific maternal mtDNA lineages.
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Affiliation(s)
- Claudio Ottoni
- Department of Biology, University of Rome Tor Vergata, Rome, Italy
- Laboratory of Forensic Genetics and Molecular Archaeology, Universitaire Ziekenhuizen, Leuven, Belgium
- Center for Archaeological Sciences, Katholieke Universiteit Leuven, Leuven, Belgium
- Center for Human Genetics, Katholieke Universiteit Leuven, Leuven, Belgium
| | | | | | - Alessandro Achilli
- Dipartimento di Genetica e Microbiologia, Università di Pavia, Pavia, Italy
- Dipartimento di Biologia Cellulare e Ambientale, Università di Perugia, Perugia, Italy
| | | | - Gianfranco Biondi
- Dipartimento di Scienze Ambientali, Università dell'Aquila, L'Aquila, Italy
| | - Antonio Torroni
- Dipartimento di Genetica e Microbiologia, Università di Pavia, Pavia, Italy
| | - Olga Rickards
- Department of Biology, University of Rome Tor Vergata, Rome, Italy
- * E-mail:
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Mixed origin of the current Tunisian population from the analysis of Alu and Alu/STR compound systems. J Hum Genet 2010; 55:827-33. [DOI: 10.1038/jhg.2010.120] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Gaibar M, Esteban E, Harich N, Kandil M, Fernández-Santander A. Genetic differences among North African Berber and Arab-speaking populations revealed by Y-STR diversity. Ann Hum Biol 2010; 38:228-36. [PMID: 20854231 DOI: 10.3109/03014460.2010.514862] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Y-chromosome STR polymorphisms are inherited in a haploid state which makes them a powerful tool for easy tracing of paternal lineage and for use in human population evolutionary studies. North-African Y chromosomal diversity has traditionally been studied in order to find genetic and geographic associations as well as to test how natural and cultural barriers have affected the degree of genetic flow not only within North Africa but also in a wider Mediterranean context. The degree of Berber/Arab genetic differentiation in the Moroccan population has been tested for a complete set of forensic markers as sixteen Y-chromosomal short tandem repeats (STRs) (DYS19, DYS385, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS437, DYS438, DYS439, DYS448, DYS456, DYS458, DYS635 and GATA H4.1). The results suggest considerable population heterogeneity in North Africa.
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Affiliation(s)
- Maria Gaibar
- Departamento de Ciencias Biomédicas Básicas, Universidad Europea de Madrid, Villaviciosa de Odón, Spain
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Currat M, Poloni ES, Sanchez-Mazas A. Human genetic differentiation across the Strait of Gibraltar. BMC Evol Biol 2010; 10:237. [PMID: 20682051 PMCID: PMC3020631 DOI: 10.1186/1471-2148-10-237] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2010] [Accepted: 08/03/2010] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND The Strait of Gibraltar is a crucial area in the settlement history of modern humans because it represents a possible connection between Africa and Europe. So far, genetic data were inconclusive about the fact that this strait constitutes a barrier to gene flow, as previous results were highly variable depending on the genetic locus studied. The present study evaluates the impact of the Gibraltar region in reducing gene flow between populations from North-Western Africa and South-Western Europe, by comparing formally various genetic loci. First, we compute several statistics of population differentiation. Then, we use an original simulation approach in order to infer the most probable evolutionary scenario for the settlement of the area, taking into account the effects of both demography and natural selection at some loci. RESULTS We show that the genetic patterns observed today in the region of the Strait of Gibraltar may reflect an ancient population genetic structure which has not been completely erased by more recent events such as Neolithic migrations. Moreover, the differences observed among the loci (i.e. a strong genetic boundary revealed by the Y-chromosome polymorphism and, at the other extreme, no genetic differentiation revealed by HLA-DRB1 variation) across the strait suggest specific evolutionary histories like sex-mediated migration and natural selection. By considering a model of balancing selection for HLA-DRB1, we here estimate a coefficient of selection of 2.2% for this locus (although weaker in Europe than in Africa), which is in line with what was estimated from synonymous versus non-synonymous substitution rates. Selection at this marker thus appears strong enough to leave a signature not only at the DNA level, but also at the population level where drift and migration processes were certainly relevant. CONCLUSIONS Our multi-loci approach using both descriptive analyses and Bayesian inferences lead to better characterize the role of the Strait of Gibraltar in the evolution of modern humans. We show that gene flow across the Strait of Gibraltar occurred at relatively high rates since pre-Neolithic times and that natural selection and sex-bias migrations distorted the demographic signal at some specific loci of our genome.
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Affiliation(s)
- Mathias Currat
- Laboratory of Anthropology, Genetics and Peopling history (AGP), Department of Anthropology, University of Geneva, Geneva, Switzerland.
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Athanasiadis G, González-Pérez E, Esteban E, Dugoujon JM, Stoneking M, Moral P. The Mediterranean Sea as a barrier to gene flow: evidence from variation in and around the F7 and F12 genomic regions. BMC Evol Biol 2010; 10:84. [PMID: 20346176 PMCID: PMC2853540 DOI: 10.1186/1471-2148-10-84] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2009] [Accepted: 03/27/2010] [Indexed: 11/30/2022] Open
Abstract
Background The Mediterranean has a long history of interactions among different peoples. In this study, we investigate the genetic relationships among thirteen population samples from the broader Mediterranean region together with three other groups from the Ivory Coast and Bolivia with a particular focus on the genetic structure between North Africa and South Europe. Analyses were carried out on a diverse set of neutral and functional polymorphisms located in and around the coagulation factor VII and XII genomic regions (F7 and F12). Results Principal component analysis revealed a significant clustering of the Mediterranean samples into North African and South European groups consistent with the results from the hierarchical AMOVA, which showed a low but significant differentiation between groups from the two shores. For the same range of geographic distances, populations from each side of the Mediterranean were found to differ genetically more than populations within the same side. To further investigate this differentiation, we carried out haplotype analyses, which provided partial evidence that sub-Saharan gene flow was higher towards North Africa than South Europe. Conclusions As there is no consensus between the two genomic regions regarding gene flow through the Sahara, it is hard to reach a solid conclusion about its role in the differentiation between the two Mediterranean shores and more data are necessary to reach a definite conclusion. However our data suggest that the Mediterranean Sea was at least partially a barrier to gene flow between the two shores.
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Affiliation(s)
- Georgios Athanasiadis
- Unitat d'Antropologia, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain
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