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Jones RJ, Tay GK, Mawart A, Alsafar H. Y-Chromosome haplotypes reveal relationships between populations of the Arabian Peninsula, North Africa and South Asia. Ann Hum Biol 2017; 44:738-746. [PMID: 28948851 DOI: 10.1080/03014460.2017.1384508] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
BACKGROUND The United Arab Emirates (UAE) is positioned at the crossroads of human migration out of Africa and through to Asia and Europe. AIM To compare the degree of genetic diversity of the Arabian UAE population with populations in other countries from the Middle East, South Asia and North Africa. SUBJECTS AND METHODS Twenty-seven Y-STR were analysed in 217 individuals. Y-STR haplotypes from this study were compared to population data stored in YHRD, using MDS and AMOVA. RESULTS Two hundred and twelve haplotypes were observed in the 217 individuals studied. Although the reduction in Y-STR loci from 27 to 17 resulted in a decrease in discriminatory power, comparisons of populations were possible. The UAE population clustered closer with other populations of the Middle East. The South Asian and North African populations were separated by Middle Eastern populations in between both clusters. CONCLUSION This is the first study to report the diversity of a population of the Arabian Peninsula using 27 Y-STR. MDS plots show that Middle Eastern populations are positioned in the centre, with African, Asian and European populations around the Arab population cluster. The findings of this study are consistent with this region being at the epicentre of human migration between continents.
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Affiliation(s)
- Rebecca J Jones
- a School of Anatomy, Physiology and Human Biology , University of Western Australia , Crawley , WA , Australia
| | - Guan K Tay
- b School of Psychiatry and Clinical Neurosciences , University of Western Australia , Crawley , WA , Australia.,c School of Medical and Health Sciences , Edith Cowan University , Joondalup , WA , Australia.,d Center for Biotechnology , Khalifa University of Science, Technology and Research , Abu Dhabi , United Arab Emirates
| | - Aurélie Mawart
- d Center for Biotechnology , Khalifa University of Science, Technology and Research , Abu Dhabi , United Arab Emirates
| | - Habiba Alsafar
- d Center for Biotechnology , Khalifa University of Science, Technology and Research , Abu Dhabi , United Arab Emirates.,e Faculty of Biomedical Engineering , Khalifa University of Science, Technology and Research , Abu Dhabi , United Arab Emirates
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Ambrosio B, Novelletto A, Hernandez C, Dugoujon JM, Fortes-Lima C, Rodriguez JN, Calderon R. Y-STR genetic diversity in autochthonous Andalusians from Huelva and Granada provinces (Spain). Forensic Sci Int Genet 2011; 6:e66-71. [PMID: 21664894 DOI: 10.1016/j.fsigen.2011.05.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2011] [Revised: 05/10/2011] [Accepted: 05/11/2011] [Indexed: 10/18/2022]
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.
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Affiliation(s)
- Beatriz Ambrosio
- Departamento de Zoología y Antropología Física, Facultad de Biología, Universidad Complutense, Ciudad Universitaria, 28040 Madrid, Spain
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3
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Y-STR genetic diversity in Moroccans from the Figuig oasis. Forensic Sci Int Genet 2010; 4:e139-41. [DOI: 10.1016/j.fsigen.2010.02.006] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2009] [Revised: 02/08/2010] [Accepted: 02/11/2010] [Indexed: 11/20/2022]
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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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Nuñez C, Baeta M, Sosa C, Casalod Y, Ge J, Budowle B, Martínez-Jarreta B. Reconstructing the population history of Nicaragua by means of mtDNA, Y-chromosome STRs, and autosomal STR markers. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2010; 143:591-600. [PMID: 20721944 DOI: 10.1002/ajpa.21355] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2010] [Accepted: 05/15/2010] [Indexed: 11/12/2022]
Abstract
Before the arrival of the Spaniards in Nicaragua, diverse Native American groups inhabited the territory. In colonial times, Native Nicaraguan populations interacted with Europeans and slaves from Africa. To ascertain the extent of this genetic admixture and provide genetic evidence about the origin of the Nicaraguan ancestors, we analyzed the mitochondrial control region (HVSI and HVSII), 17 Y chromosome STRs, and 15 autosomal STRs in 165 Mestizo individuals from Nicaragua. To carry out interpopulation comparisons, HVSI sequences from 29 American populations were compiled from the literature. The results reveal a close relationship between Oto-manguean, Uto-Aztecan, Mayan groups from Mexico, and a Chibchan group to Nicaraguan lineages. The Native American contribution to present-day Nicaraguan Mestizos accounts for most of the maternal lineages, whereas the majority of Nicaraguan Y chromosome haplogroups can be traced back to a West Eurasian origin. Pairwise Fst distances based on Y-STRs between Nicaragua and European, African and Native American populations show that Nicaragua is much closer to Europeans than the other populations. Additionally, admixture proportions based on autosomal STRs indicate a predominantly Spanish contribution. Our study reveals that the Nicaraguan Mestizo population harbors a high proportion of European male and Native American female substrate. Finally, the amount of African ancestry is also interesting, probably because of the contribution of Spanish conquerors with North African genetic traces or that of West African slaves.
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Affiliation(s)
- Carolina Nuñez
- Laboratory of Forensic Genetics, Faculty of Medicine, University of Zaragoza, 50009 Zaragoza, 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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Moors and Saracens in Europe: estimating the medieval North African male legacy in southern Europe. Eur J Hum Genet 2009; 17:848-52. [PMID: 19156170 DOI: 10.1038/ejhg.2008.258] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
To investigate the male genetic legacy of the Arab rule in southern Europe during medieval times, we focused on specific Northwest African haplogroups and identified evolutionary close STR-defined haplotypes in Iberia, Sicily and the Italian peninsula. Our results point to a higher recent Northwest African contribution in Iberia and Sicily in agreement with historical data. southern Italian regions known to have experienced long-term Arab presence also show an enrichment of Northwest African types. The forensic and genomic implications of these findings are discussed.
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Castrì L, Otárola F, Blell M, Ruiz E, Barrantes R, Luiselli D, Pettener D, Madrigal L. Indentured migration and differential gender gene flow: the origin and evolution of the East-Indian community of Limón, Costa Rica. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2007; 134:175-89. [PMID: 17568447 DOI: 10.1002/ajpa.20652] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
After the emancipation of African slaves in the Caribbean, the labor void left by out-migrating former slaves was filled by in-migrating indentured servants from prepartition India and China. In some areas of the Caribbean such as Trinidad, Suriname, and Guyana, the East-Indian migrants formed large communities. In this article, we report a study based on mtDNA and Y-chromosomal markers of a small East-Indian community from Limón, Costa Rica. The purpose of the project is to determine the place of origin in the Indian subcontinent of the ancestors of our group and the contributions to its gene pool through gene flow by members of other ethnic groups. Both Y-chromosome and mtDNA suggest that the Indo-Costa Ricans descend from migrants primarily from Central India. While both paternal and maternal markers indicate that this group is overwhelmingly of Indian origin, they also indicate that males and females of African, European, and Amerindian origin contributed to it differently. We discuss our results in the historical context of the virtual extinction of Amerindian Caribbean groups, the forced migration of African slaves to the Caribbean, and the gene flow between Amerindians, Europeans, East-Indians, and Africans that eventually produced the Caribbean's currently diverse gene pool.
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Affiliation(s)
- Loredana Castrì
- Dipartimento di Biologia Evoluzionistica Sperimentale, Area di Antropologia, Università di Bologna, Via Selmi 3, 40126 Bologna, Italy
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Robino C, Crobu F, Di Gaetano C, Bekada A, Benhamamouch S, Cerutti N, Piazza A, Inturri S, Torre C. Analysis of Y-chromosomal SNP haplogroups and STR haplotypes in an Algerian population sample. Int J Legal Med 2007; 122:251-5. [PMID: 17909833 DOI: 10.1007/s00414-007-0203-5] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2007] [Accepted: 08/31/2007] [Indexed: 11/28/2022]
Abstract
The distribution of Y-chromosomal single nucleotide polymorphism (SNP) haplogroups and short tandem repeat (STR) haplotypes was determined in a sample of 102 unrelated men of Arab origin from northwestern Algeria (Oran area). A total of nine different haplogroups were identified by a panel of 22 binary markers. The most common haplogroups observed in the Algerian population were E3b2 (45.1%) and J1 (22.5%). Y-STR typing by a 17-loci multiplex system allowed 93 haplotypes to be defined (88 were unique). Striking differences in the allele distribution and gene diversity of Y-STR markers between haplogroups could be found. In particular, intermediate alleles at locus DYS458 specifically characterized the haplotypes of individuals carrying haplogroup J1. All the intermediate alleles shared a common repeat sequence structure, supporting the hypothesis that the variant originated from a single mutational event.
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Affiliation(s)
- C Robino
- Department of Anatomy, Pharmacology and Legal Medicine, University of Turin, Turin, Italy.
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Gonçalves R, Freitas A, Branco M, Rosa A, Fernandes AT, Zhivotovsky LA, Underhill PA, Kivisild T, Brehm A. Y-chromosome lineages from Portugal, Madeira and Açores record elements of Sephardim and Berber ancestry. Ann Hum Genet 2006; 69:443-54. [PMID: 15996172 DOI: 10.1111/j.1529-8817.2005.00161.x] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A total of 553 Y-chromosomes were analyzed from mainland Portugal and the North Atlantic Archipelagos of Açores and Madeira, in order to characterize the genetic composition of their male gene pool. A large majority (78-83% of each population) of the male lineages could be classified as belonging to three basic Y chromosomal haplogroups, R1b, J, and E3b. While R1b, accounting for more than half of the lineages in any of the Portuguese sub-populations, is a characteristic marker of many different West European populations, haplogroups J and E3b consist of lineages that are typical of the circum-Mediterranean region or even East Africa. The highly diverse haplogroup E3b in Portuguese likely combines sub-clades of distinct origins. The present composition of the Y chromosomes in Portugal in this haplogroup likely reflects a pre-Arab component shared with North African populations or testifies, at least in part, to the influence of Sephardic Jews. In contrast to the marginally low sub-Saharan African Y chromosome component in Portuguese, such lineages have been detected at a moderately high frequency in our previous survey of mtDNA from the same samples, indicating the presence of sex-related gene flow, most likely mediated by the Atlantic slave trade.
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Affiliation(s)
- Rita Gonçalves
- Human Genetics Laboratory, University of Madeira, Campus of Penteada, 9000-390 Funchal, Portugal
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11
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Rosa A, Ornelas C, Brehm A, Villems R. Population data on 11 Y-chromosome STRs from Guiné-Bissau. Forensic Sci Int 2006; 157:210-7. [PMID: 15885946 DOI: 10.1016/j.forsciint.2005.04.005] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2005] [Indexed: 11/18/2022]
Abstract
The forensic value of Y-STR markers in Guiné-Bissau was accessed by typing of 215 males. Allele and haplotype frequencies, determined for loci DYS19, DYS389-I, DYS389-II, DYS390, DYS391, DYS392, DYS393, DYS437, DYS438, DYS439 and the duplicated locus DYS385, are within the limits of variation found in other populations south of the Sahara. The level of discrimination achieved is Guineans is higher than for European or other African populations with comparable data. The haplotype diversity of 0.9995 is reduced to 0.9981 when the minimal haplotype is considered thus revealing the importance of increasing the number of typed loci.
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Affiliation(s)
- Alexandra Rosa
- Department of Biology, Universidade da Madeira, Campus Universitário da Penteada, 9000-390 Funchal, Portugal.
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12
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Cherni L, Pereira L, Goios A, Loueslati BY, Khodjet el Khil H, Gomes I, Gusmão L, Alves C, Slama A, Amorim A, Elgaaied AB. Y-chromosomal STR haplotypes in three ethnic groups and one cosmopolitan population from Tunisia. Forensic Sci Int 2005; 152:95-9. [PMID: 15939181 DOI: 10.1016/j.forsciint.2005.02.007] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2004] [Accepted: 02/16/2005] [Indexed: 10/25/2022]
Abstract
The 11 Y-chromosomal short tandem repeats (STRs) included in the Promega Corporation PowerPlex Y System (DYS19, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS385, DYS437, DYS438 and DYS439) were typed in three ethnic groups ("Andalusians", Berber and Arab) and one cosmopolitan population (Tunis) from Tunisia, summing up 247 individuals, and 139 different haplotypes. Focusing the analysis on the seven Y-STRs of the YHRD Minimal Haplotype Core (DYS385 excepted), "Andalusians" showed no differences from the Cosmopolitan and the Arab samples previously published (our Arab sample presented an extremely low haplotype diversity), but were different from the Berbers. The Berbers from Tunisia were not different from those from Morocco.
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Affiliation(s)
- Lotfi Cherni
- Laboratory of Molecular Genetic Immunology and Biotechnology, Faculty of Sciences of Tunis, Tunisia
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Hallenberg C, Simonsen B, Sanchez J, Morling N. Y-chromosome STR haplotypes in Somalis. Forensic Sci Int 2005; 151:317-21. [PMID: 15939170 DOI: 10.1016/j.forsciint.2005.01.011] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2004] [Revised: 01/10/2005] [Accepted: 01/15/2005] [Indexed: 10/25/2022]
Abstract
A total of 201 males from Somalia were typed for the Y-chromosome STRs DYS19, DYS385a/b, DYS389-I, DYS389-II, DYS390, DYS391, DYS392, DYS393, DYS437, DYS438 and DYS439 with the PowerPlex Y kit (Promega). A total of 96 different haplotypes were observed and the haplotype diversity was 0.9715. The number of unique haplotypes was 71 while the most common haplotype was observed 24 times.
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Affiliation(s)
- Charlotte Hallenberg
- Department of Forensic Genetics, Institute of Forensic Medicine, University of Copenhagen, Frederik V's Vej 11, 2100 Copenhagen Ø, Denmark.
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Zurita AI, Hernandez A, Sanchez JJ, Cuellas JA. Y-chromosome STR haplotypes in the Canary Islands population (Spain). Forensic Sci Int 2005; 148:233-8. [PMID: 15639620 DOI: 10.1016/j.forsciint.2004.05.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2004] [Revised: 05/07/2004] [Accepted: 05/15/2004] [Indexed: 11/20/2022]
Abstract
Haplotype frequencies of eight Y-chromosome STR loci (DYS19, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393 and DYS385) were determined from a sample of 285 unrelated males from Canary Islands.
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Affiliation(s)
- Ada I Zurita
- Instituto Nacional de Toxicologia y Ciencias Forenses, Delegación de Canarias, Tenerife, Spain
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