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Ninety-six single nucleotide polymorphisms (SNPs) and seventeen short tandem repeat (STRs) were investigated on the Y-chromosome of 288 unrelated healthy individuals from populations in Benin (Bariba, Yoruba, and Fon) and the Ivory Coast (Ahizi and Yacouba). We performed a multidimensional scaling analysis based on FST and RST genetic distances using a large extensive database of sub-Saharan African populations. There is more genetic homogeneity in Ivory Coast populations compared with populations from Benin. Notably, the Beninese Yoruba are significantly differentiated from neighbouring groups, but also from the Yoruba from Nigeria (FST>0.05; P<0.01). The Y-chromosome dataset presented here provides new valuable data to understand the complex genetic diversity and human male demographic events in West Africa., (Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.)

Madagascar is located at the crossroads of the Asian and African worlds and is therefore of particular interest for studies on human population migration. Within the large human diversity of the Great Island, we focused our study on a particular ethnic group, the Antemoro. Their culture presents an important Arab-Islamic influence, but the question of an Arab biological inheritance remains unresolved. We analyzed paternal (n=129) and maternal (n=135) lineages of this ethnic group. Although the majority of Antemoro genetic ancestry comes from sub-Saharan African and Southeast Asian gene pools, we observed in their paternal lineages two specific haplogroups (J1 and T1) linked to Middle Eastern origins. This inheritance was restricted to some Antemoro sub-groups. Statistical analyses tended to confirm significant Middle Eastern genetic contribution. This study gives a new perspective to the large human genetic diversity in Madagascar.

Seventeen Y-chromosomal short tandem repeats (STRs) were analyzed in 347 healthy, unrelated, autochthonous males from the Andalusian provinces of Huelva (N=167) and Granada (N=180). AmpFlSTR Y-filer PCR Amplification kit (Applied Biosystems) was used to type the Y-STR markers. A total of 156 and 166 different haplotypes for the 17 Y-STR set were detected in Huelva, and Granada, respectively. The same haplotype diversity was found for both samples (0.998±0.001), and the overall discrimination capacity was 0.904. The most common minimal haplotype (DYS19, DYS389 I, DYS389 II, DYS390, DYS391, DYS392, DYS393) in both subpopulations was 14-13-16-24-11-13-13, which is also the most frequent haplotype among Atlantic European populations. Comparison analysis using pairwise R(ST) values and Analysis of Molecular Variance (AMOVA) revealed a significant genetic distance between our Andalusian samples and other ones from the northern Iberian fringe (including Basque and Pyrenean populations). However, results from the multi-dimensional scaling analysis (MDS) yielded a well-defined group of Iberian populations separated from the other Mediterranean clusters observed., (Copyright © 2011 Elsevier Ireland Ltd. All rights reserved.)

The Noir Marron communities are the direct descendants of African slaves brought to the Guianas during the four centuries (16th to 19th) of the Atlantic slave trade. Among them, three major ethnic groups have been studied: the Aluku, the Ndjuka and the Saramaka. Their history led them to share close relationships with Europeans and Amerindians, as largely documented in their cultural records. The study of Gm polymorphisms of immunoglobulins may help to estimate the amount of gene flow linked to these cultural exchanges. Surprisingly, very low levels of European contribution (2.6%) and Amerindian contribution (1.7%) are detected in the Noir Marron gene pool. On the other hand, an African contribution of 95.7% redraws their origin to West Africa (F(ST) < or = 0.15). This highly preserved African gene pool of the Noir Marron is unique in comparison to other African American populations of Latin America, who are notably more admixed.

DNA typing of 15 short tandem repeat (STR) loci included in the AmpFlSTR Identifiler PCR amplification kit (Applied Biosystems), was carried out in three Egyptian populations of different ethnic groups: the Berbers from the Siwa oasis (in the North-Western Egyptian desert), the Muslims and the Copts from Adaima (Upper Egypt). A total of 297 individuals were typed. After Bonferroni's correction, no deviations from the Hardy-Weinberg equilibrium were observed for all samples at the 15 STR loci. All loci are highly polymorphic and population differentiation tests showed that 7, 10 and 8 out of 15 loci have significant differences between the Berbers and the Muslim samples, between the Berbers and the Copts, and between the two samples from Adaima, respectively. Comparative analyses between our population data and other geographically related populations gathered from the literature were performed.

The allele frequency distribution of 15 short tandem repeats (STR) loci contained in the AmpFlSTR Identifiler PCR Amplification Kit (Applied Biosystems), was determined in two Berber populations from Asni and Bouhria, in Central and Eastern Morocco, respectively. A total of 209 individuals were typed. No deviations from the Hardy-Weinberg equilibrium were observed for Asni at the 15 STRs loci whereas for the Bouhria samples, two loci (D5S818 and TH01) showed significant departures from Hardy-Weinberg expectations (after Bonferroni's correction). All loci are highly polymorphic and population differentiation tests showed that the Moroccan samples from Asni and Bouhria have significant differences in 4 out of 15 loci (D21S11, D7S820, D16S539 and TPOX). The aim of the study was to obtain accurate allele frequencies relevant for forensic applications. Comparative analyses between our population data and other population samples gathered from the literature are also presented.

The GM immunoglobulin allotype polymorphism was investigated in four Moroccan populations: three Berber groups from Khenifra (Middle Atlas), Amizmiz (High Atlas), and Bouhria (Beni Snassen) and one Arabic-speaking sample from the Doukkala area (Abda, Chaouia, Doukkali, and Tadla districts in south-central Morocco). In order to characterize the genetic relationships between the populations, our results were compared with those obtained for other North African groups (from Morocco, Algeria, Tunisia, and Niger) and for Middle-East Africans, sub-Saharans, and Southwest Europeans. Based on GM haplotype frequencies, Factorial Correspondence Analyses, F(ST) significance testing, and hierarchical analyses of variance were performed. Our results reveal that Moroccan populations have heterogeneous GM profiles with high frequencies of GM haplotypes in Europeans (from 76% for Doukkala to 88% for Bouhria) and relatively high frequencies of GM haplotypes in sub-Saharans (from 11% for Bouhria to 23% for Amizmiz). The genetic diversity observed among Moroccans is not significantly correlated with either geographic or linguistic differentiation. In spite of their cultural and historical differentiation, we did not discover any significant genetic differences between Berbers and Arabic-speakers from Morocco. However, when large geographical areas are considered, our population samples are integrated in the North African GM variation, significantly distant from sub-Saharan groups but with a close relationship with Southwest European populations., (Am. J. Hum. Biol. 18:23-34, 2006. (c) 2005 Wiley-Liss, Inc.)

Microsatellite variation (CAG and GGC repeats) of the androgen receptor (AR) gene shows remarkable differences among African and non-African populations. In vitro studies have demonstrated an inverse relationship between the length of both microsatellites and AR activity. This fact may explain the observed association of the AR gene with prostate cancer and the strong ethnic differences in the incidence of this cancer. CAG and GGC genetic variation has been tested in a large set of populations from the Ivory Coast as well as 12 Mediterranean samples whose variation is described for the first time. The pattern of frequencies observed in the Ivory Coast agrees with data previously reported for other Sub-Saharan populations. Concerning the Mediterranean variation, Sardinian samples are characterised by low genetic diversities, and Egyptian Siwa Berbers by a particular pattern of GGC frequencies. High and Middle Atlas Moroccan Berbers are the most closely related to the Sub-Saharan variation. For both the CAG and GGC repeats, the Ivory Coast and some Moroccan samples exhibit high frequencies of low size alleles (CAG under 18 repeats, and GGC under 15 repeats) that have been associated with prostate cancer.

The Western Mediterranean Basin joins a set of ethnically different populations as Iberians and Basques in the North shore and Berbers and Arab-speakers in the South one. In spite of this differentiation, they have maintained historical contacts since ancient times. The existence of a possible common genetic background (specially for Berbers and Iberians) together with the genetic impact of the Islamic occupation of the Iberian Peninsula during 7 centuries are some of the intriguing anthropological questions that have been studied in this area using several classical and DNA markers. The aim of this work is to present the results on a survey of polymorphic Alu elements in 10 human populations of the Western Mediterranean. Recent Alu subfamilies include a significant number of polymorphic Alu insertions in humans. The polymorphic Alu elements are neutral genetic markers of identical descent with known ancestral states. This fact turns Alu insertions into useful markers for the study of human population genetics. A total number of 14 Alu insertions were analyzed in 5 Iberian populations, 3 Berber groups from North-Western Africa, an Arab-speaker population from Morocco and a sub-Saharan ethnic group from Ivory Coast. The results of this study allow the genetic characterization of Berber populations, which show a certain degree of differentiation from Arab-speaking groups of the same geographic area. Furthermore, a closer genetic distance between South Spain and Moroccan Berbers as compared with other Spanish samples supports a major genetic influx consistent with some (but not all) previous genetic studies on populations from the two shores of the Gibraltar Straits.

Ten population samples from different geographic origins were tested serologically for the AG polymorphism of human beta-lipoproteins. Their haplotype frequencies were used with previously published data to perform a wide analysis of AG genetic differentiations throughout the world. Coancestry coefficients were computed from weighted F(ST)s among populations by using a matrix of molecular distances among AG haplotypes, which is here determined on the basis of DNA studies. Coancestry coefficients derived from unweighted F(ST)s and more classical Prevosti distances were computed on the same data and used for a comparison. In all cases a highly significant correlation was found between genetics and geography on a worldwide scale, while the significance of the correlation with linguistics differed. A test of significance of the pairwise F(ST)s among populations also gave different results depending on whether the molecular distance matrix among AG haplotypes was included. Globally, this study shows that in spite of being highly significantly correlated to each other, different genetic distance measures can lead to different interpretations of the same data set. Moreover, the elucidation of the molecular models related to the presently known serological polymorphisms may represent an additional tool for analyzing such polymorphisms in human population genetics studies.

Sequences of exons 6 and 7 of the O allele of the ABO gene were studied in 317 individuals of the O phenotype from five different ethnic groups (Basques, Berbers, Akans from the Ivory Coast, and Amerindians: Cayapas from Ecuador and Aymaras from Bolivia). Twenty-one O alleles were characterized, among which 9 differed from all O alleles reported to date. The nine alleles differed from either the O01 allele (four out of nine) or O02 allele (five out of nine) by one to three point mutations. The number of different O alleles in population samples varied greatly: the highest number (13) was observed in Akans, and the lowest (5) in Amerindians. Some rare alleles previously reported by others at low frequencies were found with high frequencies in the Akans. The results also revealed a decreasing frequency of Ov7 alleles from south to north (Akans, Berbers, Basques). Berbers and Basques share two rare alleles, Ov6 and O03, which were not encountered in the other populations studied here.

GM and KM immunoglobulin (Ig) allotypes were tested in 118 autochthonous Basques from northern Navarre. The results are compared to those obtained for the same genetic markers in 6 other Basque subpopulations, 3 from Spain (Guipúzcoa, Vizcaya, and Alava) and 3 from France: Macaye, Saint-Jean Pied de Port, and Mauleon. The northern Navarrese appear genetically closer to the Alava and Saint-Jean Pied de Port subpopulations. The Basques present 3 GM haplotypes that are uncommon in Caucasian populations, suggesting that they have not been completely isolated either from Asian or African populations. The GM*1,17 23' 10,11,13,15,16 north Asian haplotype was probably the first to be introduced into the Basque area. The GM*1,17 23' 5* haplotype, considered an African genetic marker although also detected in Central Asia, would have reached the Iberian Peninsula through consecutive historic migrations from North Africa. The rare haplotype GM*1,17 23 21,28 results probably from a genetic recombination or crossing-over between the 2 common haplotypes GM*1, 17 23' 21,28 and GM*3 23 5*. It is also found with a low frequency in other neighboring regions and countries; but the possibility of its having been introduced through the main passage connecting western France and Spain during the Roman Empire and Middle Ages cannot be ruled out.

The eight short tandem repeat (STR) polymorphic systems mapping on the male-specific region of the human Y chromosome, DYS19, DYS388, DYS389I, DYS389II, DYS390, DYS391, DYS392 and DYS393, were typed in four populations from northwest (NW) Africa (Moroccan Arabs, southern Moroccan Berbers, Saharawis and Mozabites). Allele frequency distributions showed statistically significant differences for all loci among all the populations except for DYS19. Complete typing was obtained for 185 chromosomes, which showed 74 different haplotypes. The two most frequent haplotypes were found in 16.2% and 15.1% of the individuals, although the latter was almost exclusively found in the Mozabites. Locus and haplotype informativeness were measured by means of the gene diversity (D). The haplotype diversity ranged from 0.856 (Mozabites) to 0.967 (southern Moroccan Berbers). For some loci, allele frequencies in NW Africans were clearly different from those in Europeans. The most common NW African haplotype was found only in one individual out of a total of 494 Europeans typed for the whole STR set. Thus, NW African and European Y chromosomes are clearly differentiated.

Four hundred and thirteen unrelated individuals (202 autochthonous and 211 non-autochthonous) of Val d'Aran (Catalan Pyrenees) have been analysed for the GM and KM immunoglobulin genetic system using the inhibition haemagglutination method. This population was defined by eight GM haplotypes (GM*3 23 5*, GM*3 5*, GM*1,17 21,28, GM*1,2,17 21,28, GM*1,17 5*, GM*1,17 5,6,11,24, GM*1,17 10,11,13,15 and GM*1,17 10,11,13,15,16) inferred from the 17 observed phenotypes. The Val d'Aran population frequencies conform to Hardy-Weinberg expectations. The frequencies of phenotypes and haplotypes show a definite homogeneity between the autochthonous and non-autochthonous people of Val d'Aran and 11 other Pyrenean populations (Mauléon, Macaye, St. Jean Pied de Port, Vallée de L'Ouzom, Gavarnie, Barèges, Luz St. Sauveur, Esparros, Camurac, Capcir and Pays de Sault) that have already been studied for the same allotypes. A factorial correspondence analysis was performed for the 12 autochthonous Pyrenean populations, showing a high frequency of the GM*3 23 5* haplotype in the three Pyrenean regions (Western, Central and Eastern), while the GM*1,17 21,28 haplotype is mainly found in the Central region, GM*3 5* in the Eastern and Western zones, and the GM*1,2,17 21,28 is mainly present in the Central and Eastern populations. The results show a relative regional homogeneity, so there is no evidence of a frequency gradient in the Pyrenean populations for the GM and KM genetic systems. It may, however, be noticed that the Central Pyrenean populations form a group, with one population (Vallée de l'Ouzom) isolated from the rest, probably because of its particular model of inheritance by which the heritage is passed to the first born without sex consideration. It has been possible to point out some differences in the genetic structure of the autochthonous and non-autochthonous Val d'Aran population and to place the autochthonous Aranese group among its Pyrenean neighbours.

GM and KM immunoglobulin (Ig) allotypes have been tested in 310 autochthonous Basques from the three subpopulations of Vizcaya, Guipúzcoa, and Alava, Spain. They are compared with allotypes occurring in autochthonous French Basques, some Pyrenean subpopulations in France, and European populations. The analysis suggests that the Basque subpopulations show noticeable genetic distances between them and with other European populations. The genetic similarity between Basques and European populations is greater in the Basques from France than in the Basques from Spain. The genetic distances between Basque subpopulations in Spain fit well with the different historical levels of the spatial implantation of the Basque language. Guipúzcoa, the Basque province with the highest number of Basque-speaking people, shows the most genetic distinctiveness. The main underlying cause of this spatial genetic pattern seems to be admixture with surrounding populations. Our results do not support the hypothesis that Basques are a relict population of ancient Europeans. They might be a consequence of the colonization of the Basque area by a long-distance migrating group, probably a small Neolithic North Caucasian population that introduced agriculture in the region. They experienced early, rapid demographic growth, and they did not breed with the few hunter-gatherers wandering throughout the area. The North Caucasian migrants could have admixed with North Asian groups dating from many centuries before. Furthermore, Basques present polymorphic frequencies of a common African haplotype, suggesting that they have not been completely isolated from populations of Africa. However, another focus of the African haplotype has been detected in Central Asia, and the Basque frequencies alternatively might be due to North Asian groups.

HLA class II alleles were identified in 181 healthy unrelated Ethiopian children of both sexes and in 350 European controls from the South of France. The Ethiopian individuals belonged to the two major ethnic groups of the country: Oromo (N=83) and Amhara (N=98). In both panels, genetic polymorphism of HLA class II alleles was analysed for the first time by molecular typing of DRB1, DQA1 and DQB1 loci. Allelic and phenotypic frequencies were compared with those of European controls and other African populations. Construction of HLA class II three-locus haplotypes was also performed. The study revealed some differences between the two groups. Characteristic features of Central and North African populations appeared on the Ethiopian HLA genotypes. Surprisingly, DRB1*11 presented one of the lowest gene frequencies in both Ethiopian ethnic groups in contrast to Europeans and West Africans. Furthermore, this decrease was more marked than those observed using serological techniques in other geographically close East African countries. Oromo and Amhara only showed minor differences in spite of their different origins and histories. One significant difference consisted of a lower DRB1*01 gene frequency in Oromo as reported in most West African people. Some new or rare haplotypes were also observed in the Oromo group. Our results underline the distinctive features of the Ethiopian populations among the few HLA genotyping data available for East African groups and emphasise the major interest of such investigations in this region of Africa.

GM haplotype frequencies were examined in 49 Amerindian tribes (from North, Central, and South America) to investigate the congruence of genetic variation with that observed in language and geography. We used two approaches: (1) the mobile site method, which allows a two-dimensional representation of genetic variation where the distances between reference points (i.e., the locations of the populations in the geographic map after displacements) are close to the genetic distances, and (2) a multivariate analysis (factorial correspondence analysis), which permits a visual interpretation of the geographic distribution of GM haplotypes on a map, completed by a cluster analysis. The results show a strong gradient from the Bering Strait to South America. The Eskimo and Na-Dene are genetically different from all other Amerindians, reflecting their more recent migrations. The orientation of most trajectories of the tribes from Central and South America can be interpreted as earlier migrations along the Pacific and Atlantic coasts. We conclude that geographic and linguistic factors played a part in the genetic diversity of Amerindian tribes.