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- Y-chromosomal diversity in the population of Guinea-Bissau: a multiethnic perspectivePublication . Rosa, Alexandra; Ornelas, Carolina; Jobling, Mark A.; Brehm, António; Villems, RichardThe geographic and ethnolinguistic differentiation of many African Y-chromosomal lineages provides an opportunity to evaluate human migration episodes and admixture processes, in a pan-continental context. The analysis of the paternal genetic structure of Equatorial West Africans carried out to date leaves their origins and relationships unclear, and raises questions about the existence of major demographic phenomena analogous to the large-scale Bantu expansions. To address this, we have analysed the variation of 31 binary and 11 microsatellite markers on the non-recombining portion of the Y chromosome in Guinea-Bissau samples of diverse ethnic affiliations, some not studied before.Results: The Guinea-Bissau Y chromosome pool is characterized by low haplogroup diversity (D = 0.470, sd 0.033), with the predominant haplogroup E3a*-M2 shared among the ethnic clusters and reaching a maximum of 82.2% in the Mandenka people. The Felupe-Djola and Papel groups exhibit the highest diversity of lineages and harbor the deep-rooting haplogroups A-M91, E2-M75 and E3*-PN2, typical of Sahel's more central and eastern areas. Their genetic distinction from other groups is statistically significant (P = 0.01) though not attributable to linguistic, geographic or religious criteria. Non sub-Saharan influences were associated with the presence of haplogroup R1b-P25 and particular lineages of E3b1-M78. Conclusion: The predominance and high diversity of haplogroup E3a*-M2 suggests a demographic expansion in the equatorial western fringe, possibly supported by a local agricultural center. The paternal pool of the Mandenka and Balanta displays evidence of a particularly marked population growth among the Guineans, possibly reflecting the demographic effects of the agriculturalist lifestyle and their putative relationship to the people that introduced early cultivation practices into West Africa. The paternal background of the Felupe-Djola and Papel ethnic groups suggests a better conserved ancestral pool deriving from East Africa, from where they have supposedly migrated in recent times. Despite the overall homogeneity in a multiethnic sample, which contrasts with their social structure, minor clusters suggest the imprints of multiple peoples at different timescales: traces of ancestral inhabitants in haplogroups AM91 and B-M60, today typical of hunter-gatherers; North African influence in E3b1-M78 Y chromosomes, probably due to trans-Saharan contacts; and R1b-P25 lineages reflecting European admixture via the North Atlantic slave trade.
- Y-chromosome lineages in Cabo Verde Islands witness the diverse geographic origin of its first male settlersPublication . Gonçalves, Rita; Rosa, Alexandra; Freitas, Ana; Fernandes, Ana; Kivisild, Toomas; Villems, Richard; Brehm, AntónioThe Y-chromosome haplogroup composition of the population of the Cabo Verde Archipelago was profiled by using 32 single-nucleotide polymorphism markers and compared with potential source populations from Iberia, west Africa, and the Middle East. According to the traditional view, the major proportion of the founding population of Cabo Verde was of west African ancestry with the addition of a minor fraction of male colonizers from Europe. Unexpectedly, more than half of the paternal lineages (53.5%) of Cabo Verdeans clustered in haplogroups I, J, K, and R1, which are characteristic of populations of Europe and the Middle East, while being absent in the probable west African source population of Guiné-Bissau. Moreover, a high frequency of J* lineages in Cabo Verdeans relates them more closely to populations of the Middle East and probably provides the first genetic evidence of the legacy of the Jews. In addition, the considerable proportion (20.5%) of E3b(xM81) lineages indicates a possible gene flow from the Middle East or northeast Africa, which, at least partly, could be ascribed to the Sephardic Jews. In contrast to the predominance of west African mitochondrial DNA haplotypes in their maternal gene pool, the major west African Y-chromosome lineage E3a was observed only at a frequency of 15.9%. Overall, these results indicate that gene flow from multiple sources and various sex-specific patterns have been important in the formation of the genomic diversity in the Cabo Verde islands.
- Phylogenetic relationships of Lygodactylus geckos from the Gulf of Guinea islands: rapid rates of mitochondrial DNA sequence evolution?Publication . Jesus, José; Brehm, António; Harris, D. JamesMitochondrial DNA (12S rRNA, 16S rRNA and cytochrome b) sequences and nuclear sequences (C-mos) were analysed within Lygodactylus thomensis from three volcanic islands in the Gulf of Guinea that have never been connected to the continent. Our aim was to assess interrelationships between the three subspecies to test a recent hypothesis suggesting high rates of mitochondrial DNA (mtDNA) sequence evolution in geckos. Our results indicate, based on mtDNA sequence data, that the three subspecies are genetically differentiated at a level more typically observed between species. However, the forms cannot be differentiated using the nuclear marker C-mos. These results further substantiate the hypothesis of rapid rates of mtDNA sequence evolution in geckos, although the alternative that C-mos is evolving more slowly cannot be discounted. They also suggest that present calibrations for molecular clocks are at the upper limit of divergence over time.
- Phylogeography of Y-chromosome haplogroup I reveals distinct domains of Prehistoric gene flow in EuropePublication . Rootsi, Siiri; Kivisild, Toomas; Benuzzi, Giorgia; Help, Hela; Bermisheva, Marina; Kutuev, Ildus; Barać, Lovorka; Peričić, Marijana; Balanovsky, Oleg; Pshenichnov, Andrey; Dion, Daniel; Grobei, Monica; Zhivotovsky, Lev A.; Battaglia, Vincenza; Achilli, Alessandro; Al-Zahery, Nadia; Parik, Jüri; King, Roy; Cinnioğlu, Cengiz; Khusnutdinova, Elsa; Rudan, Pavao; Balanovska, Elena; Scheffrahn, Wolfgang; Simonescu, Maya; Brehm, António; Gonçalves, Rita; Rosa, Alexandra; Moisan, Jean-Paul; Chaventre, Andre; Ferak, Vladimir; Füredi, Sandor; Oefner, Peter J.; Shen, Peidong; Beckman, Lars; Mikerezi, Ilia; Terzić, Rifet; Primorac, Dragan; Cambon-Thomsen, Anne; Krumina, Astrida; Torroni, Antonio; Underhill, Peter A.; Santachiara-Benerecetti, A. Silvana; Villems, Richard; Magri, Chiara; Semino, OrnellaTo investigate which aspects of contemporary human Y-chromosome variation in Europe are characteristic of primary colonization, late-glacial expansions from refuge areas, Neolithic dispersals, or more recent events of gene flow, we have analyzed, in detail, haplogroup I (Hg I), the only major clade of the Y phylogeny that is widespread over Europe but virtually absent elsewhere. The analysis of 1,104 Hg I Y chromosomes, which were identified in the survey of 7,574 males from 60 population samples, revealed several subclades with distinct geographic distributions. Subclade I1a accounts for most of Hg I in Scandinavia, with a rapidly decreasing frequency toward both the East European Plain and the Atlantic fringe, but microsatellite diversity reveals that France could be the source region of the early spread of both I1a and the less common I1c. Also, I1b*, which extends from the eastern Adriatic to eastern Europe and declines noticeably toward the southern Balkans and abruptly toward the periphery of northern Italy, probably diffused after the Last Glacial Maximum from a homeland in eastern Europe or the Balkans. In contrast, I1b2 most likely arose in southern France/Iberia. Similarly to the other subclades, it underwent a postglacial expansion and marked the human colonization of Sardinia approximately 9,000 years ago.
- MtDNA profile of West Africa Guineans: towards a better understanding of the Senegambia regionPublication . Rosa, Alexandra; Brehm, António; Kivisild, Toomas; Metspalu, Ene; Villems, RichardThe matrilineal genetic composition of 372 samples from the Republic of Guiné-Bissau (West African coast) was studied using RFLPs and partial sequencing of the mtDNA control and coding region. The majority of the mtDNA lineages of Guineans (94%) belong to West African specific sub-clusters of L0-L3 haplogroups. A new L3 sub-cluster (L3h) that is found in both eastern and western Africa is present at moderately low frequencies in Guinean populations. A non-random distribution of haplogroups U5 in the Fula group, the U6 among the "Brame" linguistic family and M1 in the Balanta-Djola group, suggests a correlation between the genetic and linguistic affiliation of Guinean populations. The presence of M1 in Balanta populations supports the earlier suggestion of their Sudanese origin. Haplogroups U5 and U6, on the other hand, were found to be restricted to populations that are thought to represent the descendants of a southern expansion of Berbers. Particular haplotypes, found almost exclusively in East-African populations, were found in some ethnic groups with an oral tradition claiming Sudanese origin.
- Ethiopian mitochondrial DNA heritage: tracking gene flow across and around the gate of tearsPublication . Kivisild, Toomas; Reidla, Maere; Metspalu, Ene; Rosa, Alexandra; Brehm, António; Pennarun, Erwan; Parik, Jüri; Geberhiwot, Tarekegn; Usanga, Esien; Villems, RichardApproximately 10 miles separate the Horn of Africa from the Arabian Peninsula at Bab-el-Mandeb (the Gate of Tears). Both historic and archaeological evidence indicate tight cultural connections, over millennia, between these two regions. High-resolution phylogenetic analysis of 270 Ethiopian and 115 Yemeni mitochondrial DNAs was performed in a worldwide context, to explore gene flow across the Red and Arabian Seas. Nine distinct subclades, including three newly defined ones, were found to characterize entirely the variation of Ethiopian and Yemeni L3 lineages. Both Ethiopians and Yemenis contain an almost-equal proportion of Eurasian-specific M and N and African-specific lineages and therefore cluster together in a multidimensional scaling plot between Near Eastern and sub-Saharan African populations. Phylogeographic identification of potential founder haplotypes revealed that approximately one-half of haplogroup L0-L5 lineages in Yemenis have close or matching counterparts in southeastern Africans, compared with a minor share in Ethiopians. Newly defined clade L6, the most frequent haplogroup in Yemenis, showed no close matches among 3,000 African samples. These results highlight the complexity of Ethiopian and Yemeni genetic heritage and are consistent with the introduction of maternal lineages into the South Arabian gene pool from different source populations of East Africa. A high proportion of Ethiopian lineages, significantly more abundant in the northeast of that country, trace their western Eurasian origin in haplogroup N through assorted gene flow at different times and involving different source populations.
- Evolution of the obscura group Drosophila species.: III. phylogenetic relationships in the subobscura cluster based on homologies of chromosome APublication . Brehm, A.; Krimbas, C. B.The Drosophila subobscura cluster comprises D. subobscura, D. madeirensis and D. guanche, species closely related to some interspecific crosses are possible. This paper clarifies definitively the homologies of the segments of the sex chromosome A (= X) among these species and thus permits a phylogenetic seriation of them. This seriation is identical to the one suggested by the study of chromosome O and concordant with similar data for the remaining three rod autosomes (J, U and E), which, however, do not provide qualitative evidence on this subject.
- Structure and evolution of the mitochondrial DNA complete control region in the Drosophila subobscura subgroupPublication . Brehm, A.; Harris, D. J.; Hernández, M.; Cabrera, V. M.; Larruga, J. M.; Pinto, F. M.; González, A. M.The complete A + T-rich region of mitochondrial DNA (mtDNA) has been cloned and sequenced in the species of the Drosophila subobscura subgroup D. subobscura, D. madeirensis and D. guanche. Comparative analysis of these sequences with others already published has identified new sequence motifs that are conserved in Drosophila and other insects. A putative bi-directional promoter and a stop signal are proposed to be involved in the primary mtDNA strand replication of Drosophila. This region strongly resolves relationships of the species included in a phylogenetic analysis, both for closely related species and also at deeper phylogenetic levels when only the left and central domains are taken into account.
- Relationships of Scincid Lizards (Mabuya spp; Reptilia: Scincidae) from the Cape Verde Islands based on mitochondrial and nuclear DNA sequencesPublication . Brehm, A.; Jesus, J.; Pinheiro, M.; Harris, D. J.Partial DNA sequences from two mitochondrial (mt) and one nuclear gene (cytochrome b, 12S rRNA, and C-mos) were used to estimate the phylogenetic relationships among the six extant species of skinks endemic to the Cape Verde Archipelago. The species form a monophyletic unit, indicating a single colonization of the islands, probably from West Africa. Mabuya vaillanti and M. delalandii are sister taxa, as indicated by morphological characters. Mabuya fogoensis and M. stangeri are closely related, but the former is probably paraphyletic. Mabuya spinalis and M. salensis are also probably paraphyletic. Within species, samples from separate islands always form monophyletic groups. Some colonization events can be hypothesized, which are in line with the age of the islands. C-mos variation is concordant with the topology derived from mtDNA.
- The phylogeny of nine species of the Drosophila obscura group inferred by the banding homologies of chromosomal regions: 11. Element EPublication . Brehm, António; Krimbas, Costas B.The phylogenetic relationships among nine species of Drosophila belonging to the obscura group were investigated by establishing (according to their banding similarities) the homologous chromosome segments of element E (equivalent to chromosome O of D. subobscura). The phylogenetic relationships were based on the existence of segments in different triads of species, which could only be produced by overlapping inversions. This permitted the ordering of the species belonging to each triad. Drosophila obscura, D. ambigua and D. tristis were found to be very closely related and thus forming a cluster in which D. ambigua occupies an intermediate position between the other two species. Drosophila obscura seems to be the species more directly linked to three other separate lineages, that of D. subsilvestris, the two African species (D. microlabis and D. kitumensis), and the subobscura cluster. The species from this last cluster may be ordered as follows: D. subobscura-D. madeirensis-D. guanche. It is not clear which species of this triad is the direct link to D. obscura. These results completely agree with those produced in an independent study, where element B was considered for the same nine species. Furthermore, the present study clarifies some ambiguities concerning the phylogenetic relationships which remained obscure due to the conservative nature of chromosome B.