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Genetic insight into Nigerian population groups using an X-chromosome decaplex system. FORENSIC SCIENCE INTERNATIONAL GENETICS SUPPLEMENT SERIES 2019. [DOI: 10.1016/j.fsigss.2019.10.067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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Fortes-Lima C, Brucato N, Croze M, Bellis G, Schiavinato S, Massougbodji A, Migot-Nabias F, Dugoujon JM. Genetic population study of Y-chromosome markers in Benin and Ivory Coast ethnic groups. Forensic Sci Int Genet 2015; 19:232-237. [PMID: 26275614 DOI: 10.1016/j.fsigen.2015.07.021] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2015] [Revised: 07/17/2015] [Accepted: 07/31/2015] [Indexed: 11/29/2022]
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.
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Affiliation(s)
- Cesar Fortes-Lima
- Evolutionary Medicine Group, Laboratoire d'Anthropologie Moléculaire et Imagerie de Synthèse, UMR 5288, Centre National de la Recherche Scientifique (CNRS), Université Toulouse 3-Paul-Sabatier, Toulouse, France
| | - Nicolas Brucato
- Leiden University Center for Linguistics, Leiden, the Netherlands
| | - Myriam Croze
- Section of Evolutionary Biology, Department of Biology II, University of Munich, 82152 Planegg-Martinsried, Germany
| | - Gil Bellis
- Institut National d'Etudes Démographiques, Paris, France
| | - Stephanie Schiavinato
- Evolutionary Medicine Group, Laboratoire d'Anthropologie Moléculaire et Imagerie de Synthèse, UMR 5288, Centre National de la Recherche Scientifique (CNRS), Université Toulouse 3-Paul-Sabatier, Toulouse, France
| | - Achille Massougbodji
- Centre d'Etude et de Recherche sur le Paludisme Associé à la Grossesse et à l'Enfance, Faculté des Sciences de la Santé, Université d'Abomey-Calavi, Cotonou, Bénin
| | - Florence Migot-Nabias
- Centre d'Etude et de Recherche sur le Paludisme Associé à la Grossesse et à l'Enfance, Faculté des Sciences de la Santé, Université d'Abomey-Calavi, Cotonou, Bénin; Institut de Recherche pour le Développement, UMR 216 Mère et enfant face aux infections tropicales, 4 avenue de l'Observatoire, 75006 Paris, France; COMUE Sorbonne Paris Cité, Université Paris Descartes, Faculté des Sciences Pharmaceutiques et Biologiques, Paris, France
| | - Jean-Michel Dugoujon
- Evolutionary Medicine Group, Laboratoire d'Anthropologie Moléculaire et Imagerie de Synthèse, UMR 5288, Centre National de la Recherche Scientifique (CNRS), Université Toulouse 3-Paul-Sabatier, Toulouse, France.
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Anagnostou P, Battaggia C, Capocasa M, Boschi I, Brisighelli F, Batini C, Spedini G, Destro-Bisol G. Reevaluating a model of gender-biased gene flow among Sub-Saharan Hunter-gatherers and farmers. Hum Biol 2014; 85:597-606. [PMID: 25019191 DOI: 10.3378/027.085.0406] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/13/2013] [Indexed: 11/05/2022]
Abstract
In a previous study, we proposed a model for genetic admixture between African hunter-gatherers and food producers, in which we integrated demographic and genetic aspects together with ethnographic knowledge (Destro-Bisol et al. 2004b). In that study it was possible to test the model only using genetic information from widely dispersed and genetically heterogeneous populations. Here we reevaluate the congruence between the model and patterns of genetic variation using an anthropologically and geographically more homogeneous data set that includes Pygmies and farmers from Cameroon, Congo, and the Central African Republic. As implied by the model, the ratios of mtDNA to Y chromosome Nm estimates (effective population size, N, times the migration rate, m; 0.154 in Pygmies and 6.759 in farmers), support an asymmetric gene flow, with a higher Bantu-to-Pygmy gene flow for paternal than for maternal lineages, and vice versa for farmers. Analyses of intra- and interpopulation genetic variation further support the above observation, showing a prevailing effect of genetic drift on maternal lineages and gene flow on paternal lineages among Pygmies, and an opposite pattern among farmers. We also detected differences between patterns for classical and molecular measures of Y chromosome intrapopulation variation, which likely represent signatures of the introgression of Bantu lineages into the gene pool of Pygmy populations. On the whole, our results seem to reflect differences in the demographic history and the degree of patrilocality and polygyny between the two population groups, thus providing further support to our microevolutionary model in an anthropologically coherent framework.
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Affiliation(s)
- Paolo Anagnostou
- Università di Roma "La Sapienza," Dipartimento di Biologia Ambientale, Rome, Italy and Istituto Italiano di Antropologia, Rome, Italy
| | - Cinzia Battaggia
- Università di Roma "La Sapienza," Dipartimento di Biologia Ambientale, Rome, Italy
| | - Marco Capocasa
- Istituto Italiano di Antropologia, Rome, Italy and Università di Roma, "La Sapienza," Dipartimento Biologia e Biotecnologie "Charles Darwin," Rome, Italy
| | - Ilaria Boschi
- Istituto di Medicina Legale, Università Cattolica del Sacro Cuore, Rome, Italy
| | | | - Chiara Batini
- Department of Genetics, University of Leicester, Leicester, UK
| | - Gabriella Spedini
- Università di Roma "La Sapienza," Dipartimento di Biologia Ambientale, Rome, Italy and Istituti Italiano di Antropologia, Rome, Italy
| | - Giovanni Destro-Bisol
- Università di Roma "La Sapienza," Dipartimento di Biologia Ambientale, Rome, Italy and Istituti Italiano di Antropologia, Rome, Italy
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Brucato N, Cassar O, Tonasso L, Tortevoye P, Migot-Nabias F, Plancoulaine S, Guitard E, Larrouy G, Gessain A, Dugoujon JM. The imprint of the Slave Trade in an African American population: mitochondrial DNA, Y chromosome and HTLV-1 analysis in the Noir Marron of French Guiana. BMC Evol Biol 2010; 10:314. [PMID: 20958967 PMCID: PMC2973943 DOI: 10.1186/1471-2148-10-314] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2010] [Accepted: 10/19/2010] [Indexed: 11/17/2022] Open
Abstract
Background Retracing the genetic histories of the descendant populations of the Slave Trade (16th-19th centuries) is particularly challenging due to the diversity of African ethnic groups involved and the different hybridisation processes with Europeans and Amerindians, which have blurred their original genetic inheritances. The Noir Marron in French Guiana are the direct descendants of maroons who escaped from Dutch plantations in the current day Surinam. They represent an original ethnic group with a highly blended culture. Uniparental markers (mtDNA and NRY) coupled with HTLV-1 sequences (env and LTR) were studied to establish the genetic relationships linking them to African American and African populations. Results All genetic systems presented a high conservation of the African gene pool (African ancestry: mtDNA = 99.3%; NRY = 97.6%; HTLV-1 env = 20/23; HTLV-1 LTR = 6/8). Neither founder effect nor genetic drift was detected and the genetic diversity is within a range commonly observed in Africa. Higher genetic similarities were observed with the populations inhabiting the Bight of Benin (from Ivory Coast to Benin). Other ancestries were identified but they presented an interesting sex-bias. Whilst male origins spread throughout the north of the bight (from Benin to Senegal), female origins were spread throughout the south (from the Ivory Coast to Angola). Conclusions The Noir Marron are unique in having conserved their African genetic ancestry, despite major cultural exchanges with Amerindians and Europeans through inhabiting the same region for four centuries. Their maroon identity and the important number of slaves deported in this region have maintained the original African diversity. All these characteristics permit to identify a major origin located in the former region of the Gold Coast and the Bight of Benin; regions highly impacted by slavery, from which goes a sex-biased longitudinal gradient of ancestry.
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Affiliation(s)
- Nicolas Brucato
- Laboratoire d'Anthropobiologie Moléculaire et Imagerie de Synthèse, CNRS and Université Paul Sabatier, FRE2960, Toulouse, France.
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5
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Allele frequencies of 11 X-chromosomal loci of two population samples from Africa. Int J Legal Med 2010; 125:307-14. [DOI: 10.1007/s00414-010-0451-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2009] [Accepted: 03/17/2010] [Indexed: 11/26/2022]
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Veeramah KR, Connell BA, Ansari Pour N, Powell A, Plaster CA, Zeitlyn D, Mendell NR, Weale ME, Bradman N, Thomas MG. Little genetic differentiation as assessed by uniparental markers in the presence of substantial language variation in peoples of the Cross River region of Nigeria. BMC Evol Biol 2010; 10:92. [PMID: 20356404 PMCID: PMC2867817 DOI: 10.1186/1471-2148-10-92] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2009] [Accepted: 03/31/2010] [Indexed: 11/21/2022] Open
Abstract
Background The Cross River region in Nigeria is an extremely diverse area linguistically with over 60 distinct languages still spoken today. It is also a region of great historical importance, being a) adjacent to the likely homeland from which Bantu-speaking people migrated across most of sub-Saharan Africa 3000-5000 years ago and b) the location of Calabar, one of the largest centres during the Atlantic slave trade. Over 1000 DNA samples from 24 clans representing speakers of the six most prominent languages in the region were collected and typed for Y-chromosome (SNPs and microsatellites) and mtDNA markers (Hypervariable Segment 1) in order to examine whether there has been substantial gene flow between groups speaking different languages in the region. In addition the Cross River region was analysed in the context of a larger geographical scale by comparison to bordering Igbo speaking groups as well as neighbouring Cameroon populations and more distant Ghanaian communities. Results The Cross River region was shown to be extremely homogenous for both Y-chromosome and mtDNA markers with language spoken having no noticeable effect on the genetic structure of the region, consistent with estimates of inter-language gene flow of 10% per generation based on sociological data. However the groups in the region could clearly be differentiated from others in Cameroon and Ghana (and to a lesser extent Igbo populations). Significant correlations between genetic distance and both geographic and linguistic distance were observed at this larger scale. Conclusions Previous studies have found significant correlations between genetic variation and language in Africa over large geographic distances, often across language families. However the broad sampling strategies of these datasets have limited their utility for understanding the relationship within language families. This is the first study to show that at very fine geographic/linguistic scales language differences can be maintained in the presence of substantial gene flow over an extended period of time and demonstrates the value of dense sampling strategies and having DNA of known and detailed provenance, a practice that is generally rare when investigating sub-Saharan African demographic processes using genetic data.
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Affiliation(s)
- Krishna R Veeramah
- Centre for Society and Genetics, University of California, Los Angeles, 90095-722, USA.
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A multi-perspective view of genetic variation in Cameroon. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2009; 140:454-64. [DOI: 10.1002/ajpa.21088] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Malhi RS, Gonzalez-Oliver A, Schroeder KB, Kemp BM, Greenberg JA, Dobrowski SZ, Smith DG, Resendez A, Karafet T, Hammer M, Zegura S, Brovko T. Distribution of Y chromosomes among native North Americans: a study of Athapaskan population history. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2009; 137:412-24. [PMID: 18618732 DOI: 10.1002/ajpa.20883] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
In this study, 231 Y chromosomes from 12 populations were typed for four diagnostic single nucleotide polymorphisms (SNPs) to determine haplogroup membership and 43 Y chromosomes from three of these populations were typed for eight short tandem repeats (STRs) to determine haplotypes. These data were combined with previously published data, amounting to 724 Y chromosomes from 26 populations in North America, and analyzed to investigate the geographic distribution of Y chromosomes among native North Americans and to test the Southern Athapaskan migration hypothesis. The results suggest that European admixture has significantly altered the distribution of Y chromosomes in North America and because of this caution should be taken when inferring prehistoric population events in North America using Y chromosome data alone. However, consistent with studies of other genetic systems, we are still able to identify close relationships among Y chromosomes in Athapaskans from the Subarctic and the Southwest, suggesting that a small number of proto-Apachean migrants from the Subarctic founded the Southwest Athapaskan populations.
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Affiliation(s)
- Ripan Singh Malhi
- Department of Anthropology, University of Illinois Urbana-Champaign, IL 61801, USA.
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Allele frequencies of 11 X-chromosomal loci in a population sample from Ghana. Int J Legal Med 2008; 123:81-3. [DOI: 10.1007/s00414-008-0251-5] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2008] [Accepted: 04/29/2008] [Indexed: 10/21/2022]
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Rębała K, Mikulich AI, Tsybovsky IS, Siváková D, Džupinková Z, Szczerkowska-Dobosz A, Szczerkowska Z. Y-STR variation among Slavs: evidence for the Slavic homeland in the middle Dnieper basin. J Hum Genet 2007; 52:406-414. [PMID: 17364156 DOI: 10.1007/s10038-007-0125-6] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2006] [Accepted: 02/07/2007] [Indexed: 10/23/2022]
Abstract
A set of 18 Y-chromosomal microsatellite loci was analysed in 568 males from Poland, Slovakia and three regions of Belarus. The results were compared to data available for 2,937 Y chromosome samples from 20 other Slavic populations. Lack of relationship between linguistic, geographic and historical relations between Slavic populations and Y-short tandem repeat (STR) haplotype distribution was observed. Two genetically distant groups of Slavic populations were revealed: one encompassing all Western-Slavic, Eastern-Slavic, and two Southern-Slavic populations, and one encompassing all remaining Southern Slavs. An analysis of molecular variance (AMOVA) based on Y-chromosomal STRs showed that the variation observed between the two population groups was 4.3%, and was higher than the level of genetic variance among populations within the groups (1.2%). Homogeneity of northern Slavic paternal lineages in Europe was shown to stretch from the Alps to the upper Volga and involve ethnicities speaking completely different branches of Slavic languages. The central position of the population of Ukraine in the network of insignificant AMOVA comparisons, and the lack of traces of significant contribution of ancient tribes inhabiting present-day Poland to the gene pool of Eastern and Southern Slavs, support hypothesis placing the earliest known homeland of Slavs in the middle Dnieper basin.
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Affiliation(s)
- Krzysztof Rębała
- Department of Forensic Medicine, Medical University of Gdansk, ul. Marii Skłodowskiej-Curie 3A, 80-210, Gdansk, Poland.
| | - Alexei I Mikulich
- Institute for the Study of Arts, Ethnography and Folklore, National Academy of Sciences, Minsk, Belarus
| | - Iosif S Tsybovsky
- Institute of Problems of Criminology, Criminalistics and Forensic Expertise, Minsk, Belarus
| | - Daniela Siváková
- Department of Anthropology, Comenius University, Bratislava, Slovakia
| | - Zuzana Džupinková
- Department of Experimental and Applied Genetics, Institute of Preventive and Clinical Medicine, Slovak Medical University, Bratislava, Slovakia
| | | | - Zofia Szczerkowska
- Department of Forensic Medicine, Medical University of Gdansk, ul. Marii Skłodowskiej-Curie 3A, 80-210, Gdansk, Poland
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Gomes I, Alves C, Maxzud K, Pereira R, Prata MJ, Sánchez-Diz P, Carracedo A, Amorim A, Gusmão L. Analysis of 10 X-STRs in three African populations. Forensic Sci Int Genet 2007; 1:208-11. [PMID: 19083759 DOI: 10.1016/j.fsigen.2007.01.001] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2007] [Accepted: 01/27/2007] [Indexed: 11/27/2022]
Abstract
Three African populations were genetically studied through a decaplex X chromosome short tandem repeat (STR) system, which includes the following loci: DXS8378, DXS9898, DXS8377, HPRTB, GATA172D05, DXS7423, DXS6809, DXS7132, DXS101 and DXS6789. A total of 237 unrelated male individuals from Angola, Mozambique and Uganda were typed. DXS8377 revealed to be the most polymorphic marker and in contrast, locus DXS7423 was the least informative in Angola and Mozambique and DXS8378 in Uganda. No significant associations between alleles of any pair of loci were found in these three population groups. The overall mean exclusion chances for the 10-plex in parentage testing, when both mother and daughter are investigated are above 1 in 4.2 million being the highest in Mozambique (1 in 5.3 million); in duos these values are approximately 1 in 60 thousand. Concerning the overall power of discrimination, this decaplex can discriminate 1 in nearly 41 million Ugandan men and 1 in around 30 million Angolan and Mozambican men; raising an order of magnitude of over 13 digits in all population groups for women. All these parameters demonstrate the potential of this decaplex for parentage testing as well as for identification purposes.
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Affiliation(s)
- Iva Gomes
- IPATIMUP, Institute of Pathology and Molecular Immunology of the University of Porto, Porto, Portugal.
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Destro-Bisol G, Donati F, Coia V, Boschi I, Verginelli F, Caglià A, Tofanelli S, Spedini G, Capelli C. Variation of female and male lineages in sub-Saharan populations: the importance of sociocultural factors. Mol Biol Evol 2004; 21:1673-82. [PMID: 15190128 DOI: 10.1093/molbev/msh186] [Citation(s) in RCA: 115] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
In this paper, we present a study of genetic variation in sub-Saharan Africa, which is based on published and unpublished data on fast-evolving (hypervariable region 1 of mitochondrial DNA and six microsatellites of Y chromosome) and slow-evolving (haplogroup frequencies) polymorphisms of mtDNA and Y chromosome. Our study reveals a striking difference in the genetic structure of food-producer (Bantu and Sudanic speakers) and hunter-gatherer populations (Pygmies, Kung, and Hadza). In fact, the ratio of mtDNA to Y-chromosome Nupsilon is substantially higher in food producers than in hunter-gatherers as determined by fast-evolving polymorphisms (1.76 versus 0.11). This finding indicates that the two population groups differ substantially in female and male migration rate and/or effective size. The difference also persists when linguistically homogeneous populations are used and outlier populations are eliminated (1.78 vs 0.19) or when the jacknife procedure is applied to a paired population data set (1.32 to 7.84 versus 0.14 to 0.66). The higher ratio of mtDNA to Y-chromosome Nnu in food producers than in hunter-gatherers is further confirmed by the use of slow-evolving polymorphisms (1.59 to 7.91 versus 0.12 to 0.35). To explain these results, we propose a model that integrates demographic and genetic aspects and incorporates ethnographic knowledge. In such a model, the asymmetric gene flow, polyginy, and patrilocality play an important role in differentiating the genetic structure of sub-Saharan populations. The existence of an asymmetric gene flow is supported by the phylogeographic features of mtDNA and Y-chromosome haplogroups found in the two population groups. The role of polyginy and patrilocality is sustained by the evidence of a differential pressure of genetic drift and gene flow on maternal and paternal lineages of food producers and hunter-gatherers that is revealed through the analysis of mitochondrial and Y-chromosomal intrapopulational variation.
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