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Human Y chromosomes belonging to the haplogroup R1b1-P25, although very common in Europe, are usually rare in Africa. However, recently published studies have reported high frequencies of this haplogroup in the central-western region of the African continent and proposed that this represents a 'back-to-Africa' migration during prehistoric times. To obtain a deeper insight into the history of these lineages, we characterised the paternal genetic background of a population in Equatorial Guinea, a Central-West African country located near the region in which the highest frequencies of the R1b1 haplogroup in Africa have been found to date. In our sample, the large majority (78.6%) of the sequences belong to subclades in haplogroup E, which are the most frequent in Bantu groups. However, the frequency of the R1b1 haplogroup in our sample (17.0%) was higher than that previously observed for the majority of the African continent. Of these R1b1 samples, nine are defined by the V88 marker, which was recently discovered in Africa. As high microsatellite variance was found inside this haplogroup in Central-West Africa and a decrease in this variance was observed towards Northeast Africa, our findings do not support the previously hypothesised movement of Chadic-speaking people from the North across the Sahara as the explanation for these R1b1 lineages in Central-West Africa. The present findings are also compatible with an origin of the V88-derived allele in the Central-West Africa, and its presence in North Africa may be better explained as the result of a migration from the south during the mid-Holocene. [ABSTRACT FROM AUTHOR]

The most significant and widely studied remodeling of the African genetic landscape is the Bantu expansion, which led to an almost total replacement of the previous populations from the sub-Saharan region. However, a poor knowledge exists about other population movements, namely, the Nilotic migration, which is a pastoralist dispersal that, contrary to the Bantu expansion, impacted only East African populations. Here, samples from a Ugandan Nilotic-speaking population were studied for 37 Y chromosome-specific SNPs, and the obtained data were compared with those already available for other sub-Saharan population groups. Although Uganda lies on the fringe of both Bantu and Nilotic expansions, a low admixture with Bantu populations was detected, with haplogroups carrying M13, M182 and M75 mutations prevailing in Nilotes together with a low frequency of the main Bantu haplogroups from clade E1b1a-M2. The results of a comparative analysis with data from other population groups allowed a deeper characterization of some lineages in our sample, clarifying some doubts about the origin of some particular Y-SNPs in different ethnic groups, such as M150, M112 and M75. Moreover, it was also possible to identify a new Y-SNP apparently specific to Nilotic groups, as well as the presence of particular haplogroups that characterize Nilotic populations. The detection of a new haplogroup B2a1b defined by G1, could be, therefore, important to differentiate Nilotes from other groups, helping to trace migration and admixture events that occurred in eastern Africa. [ABSTRACT FROM AUTHOR]

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. [Copyright &y& Elsevier]

Allele frequencies, together with some parameters of forensic interest, for 17 STRs included in the AmpF/STR Identifiler (CSF1PO, D2S1338, D3S1358, D5S818, D7S820, D8S1179, D13S317, D16S539, D18S51, D19S433, D21S11, FGA, TH01, TPO and VWA) and Powerplex 16 System (CSF1PO, D3S1358, D5S818, D7S820, D8S1179, D13S317, D16S539, D18S51, D21S11, FGA, Penta D, Penta E, TH01, TPO and VWA) were estimated from a sample of 135–144 unrelated individuals from Mozambique. No deviations from Hardy–Weinberg equilibrium were observed with the exception of the FGA locus (using the Bonferroni correction for the number of loci analysed, the departure observed at this locus was not significant).Comparative analyses between our population data and other African databases, namely Promega’s African–Americans, AB Applied Biosystems African–Americans and two other population samples from Mozambique and Guine´ Bissau, are presented and discussed.Genotype inconsistencies between both commercial kits (for D16S539 and D8S1179) and other genotypic variations (three-banded allele patterns for TPO) are also reported. [Copyright &y& Elsevier]

San Basilio de Palenque is an Afro-descendant community near Cartagena, Colombia, founded in the sixteenth century. The recognition of the historical and cultural importance of Palenque has promoted several studies, namely concerning the African roots of its first inhabitants. To deepen the knowledge of the origin and diversity of the Palenque parental lineages, we analysed a sample of 81 individuals for the entire mtDNA Control Region as well as 92 individuals for 27 Y-STRs and 95 for 51 Y-SNPs. The results confirmed the strong isolation of the Palenque, with some degree of influx of Native American maternal lineages, and a European admixture exclusively mediated by men. Due to the high genetic drift observed, a pairwise FST analysis with available data on African populations proved to be inadequate for determining population affinities. In contrast, when a phylogenetic approach was used, it was possible to infer the phylogeographic origin of some lineages in Palenque. Contradicting previous studies indicating a single African origin, our results evidence parental genetic contributions from widely different African regions. [ABSTRACT FROM AUTHOR]

In 1020 males out of 13 population samples from Argentina, Brazil, Costa Rica, Macao, Mozambique, Portugal and Spain, GATA allele 17 was found exclusively in Mozambique [Forensic Sci. Int. 135 (2003) 158]. In the present work, allele 17 was further observed in samples from Angola (9.33%), Mozambique (10.79%) and S. Tome´ e Prı´ncipe (3.53%). This allele differs by at least two repeat units from all reported alleles: no instance of allele 18 was ever found. Allele 17 frequency and distribution, together with the absence of one-step-derived alleles, is compatible with a very low mutation rate and so potentially a good marker for African ancestry and haplogroup identification. We verified this hypothesis in two ways: (a) the sequencing of nine alleles 17 showed that the small number of uninterrupted repeats can explain the low mutation rate and (b) the simultaneous GATA C4 and SNP typing in 75 individuals from Angola, 85 from S. Tome´ e Prı´ncipe and 417 from Mozambique proved that, out of 56 samples carrying allele 17, 55 belong to B* paragroup and one to A*, both said to be ancient African lineages. Therefore, GATA C4 allele 17 most probably was originated as a unique event and its extreme association with AB* is compatible with its use as a marker for the assignment to this paragroup. [Copyright &y& Elsevier]

Abstract: There is growing interest in the study of X-chromosome markers in population and forensic genetics. Since most of the studies focused on Short Tandem Repeats (STRs), data concerning Single Nucleotide Polymorphisms (SNPs) are still scarce. In the present work, male samples from Africa (Angola: n =46; Mozambique: n =42) and Asia (Taiwan: n =21; China: n =43; Bangladesh: n =58) were analysed for 25 SNPs located on the X chromosome to evaluate the diversity pattern in the populations from the two continents. Data were compared with previously published results from Somalia and Mediterranean populations. The results showed a clear genetic differentiation between Sub-Saharan populations and those from northern Africa and the Mediterranean. The differentiation between eastern and southern Africa was also recognizable, with Angola and Mozambique being statistically different from Somalia but not from each other. Likewise, the Asian samples formed a separate cluster with Bangladesh exhibiting a statistically significant difference from those of China and Taiwan. [Copyright &y& Elsevier]

Abstract: The Karimojong, an African group from the Karamoja region of Northeast Uganda, were genetically analysed using a decaplex system for X chromosome short tandem repeats (X-STRs). A total of 255 individuals (117 males and 138 females) were genotyped for the following loci: DXS8378, DXS9898, DXS7133, GATA31E08, GATA172D05, DXS7423, DXS6809, DXS7132, DXS9902 and DXS6789. Allele frequencies and parameters for forensic evaluation were calculated for each STR. No association was found between any pairs of loci studied. DXS6789 was the most polymorphic marker in this sample, followed by DXS6809, with gene diversities of 84.79% and 83.94%, respectively. The less discriminating locus observed was DXS7133, with a gene diversity of 39.79%. High overall values of power of discrimination were obtained for female (1 in 1.8×1010) and male samples (1 in 1.6×106), as well as high power of exclusion in father/mother/daughter trios (99.9997%), in father daughter duos (99.9862%) and in half sisters with same father (99.0331%). These results confirm the potential of this 10-plex in parentage testing and in human identification. [Copyright &y& Elsevier]

Abstract: Haplotype, allele frequencies and population data of 12 Y-chromosome STR loci DYS19, DYS385, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS437, DYS438 and DYS439 were determined from a sample of 150 unrelated male individuals from El Salvador, Central America. A total of 131 haplotypes were identified by the 12 Y-STR loci of which 118 were unique. The haplotype diversity (99.08%) and the proportion of different haplotypes (87.33%) were estimated. R ST genetic distances were calculated between El Salvador and other populations from Southern and Central America, Europe and Africa. The highest R ST genetic distances were found when comparing El Salvador with African populations (0.334⩽ R ST ⩽0.395). The lowest non-significant distance was found in the comparison with Honduras. The observed genetic distances between El Salvador and Southern and Central Native groups presented a wide range of values (from 0.024 to 0.210) that can be explained by the differences in the proportion of European versus Amerindian contributions in these population groups. The Multi Dimensional Scaling (MDS) plot analysis, based on pairwise R ST values, showed that the general population of El Salvador is closer to the European cluster (composed by European and South American general population samples from Brazil, Argentina, Colombia and Venezuela) than to the Southern/Central American cluster of Native and Mestizo populations. [Copyright &y& Elsevier]

There is little knowledge on the demographic impact of the western wave of the Bantu expansion. Only some predictions could be made based mainly on indirect archaeological, linguistic, and genetic evidences. Apart from the very limited available data on the mitochondrial DNA (mtDNA) side, there are not, however, Y-chromosome studies revealing-if any-the male contribution of western Bantu-farmers. To elucidate the still poorly characterized western Bantu expansion, we analyzed Y-chromosome (25 biallelic polymorphisms and 15 microsatellite markers) and mtDNA (hypervariable control regions I and II and selected coding region RFLPs) variation in a population of 110 individuals from southwest Africa, and compared it with a database of 2,708 Y-chromosome profiles and of 2,565 mtDNAs from all other regions of Africa. This study reveals (1) a dramatic displacement of male and female Khoisan-speaking groups in the southwest, since both the maternal and the paternal genetic pools were composed exclusively by types carried by Bantu-speakers; (2) a clear bias in the admixture process towards the mating of male Europeans with female Sub-Saharan Africans; (3) the assimilation of east African lineages by the southwest (mainly mtDNA-L3f and Y-chromosome-B2a lineages); and (4) signatures of recent male and female gene flow from the southeast into the southwest. The data also indicate that the western stream of the Bantu expansion was a more gradual process than the eastern counterpart, which likely involved multiple short dispersals.