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- 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.
- Review of the leaf-litter skinks (Scincidae: Panaspis) from the Gulf of Guinea Oceanic Islands, with the description of a new speciesPublication . Soares, Leonor B.; Ceríaco, Luis M. P.; Marques, Mariana P.; Bastos-Silveira, Cristiane; Scheinberg, Lauren A.; Harris, D. James; Brehm, António; Jesus, JoséLeaf-litter skinks of the genus Panaspis are currently represented in the oceanic islands of the Gulf of Guinea by two species, Panaspis africana and P. annobonensis. Here we describe a third species, Panaspis thomensis sp. nov., endemic to São Tomé Island. Data from previous studies and a new phylogenetic analysis using the mitochondrial 16S gene shows that the new species is genetically divergent and reciprocally monophyletic with respect to P. africana. Morphological data (scalation and morphometry) identify consistent, yet subtle, phenotypic differences between the two island populations. We also confirm that P. annobonensis represents a valid species, sister to the species pair P. africana + P. thomensis sp. nov., based on both molecular and morphological evidence. This description raises the number of known Panaspis species in the Gulf of Guinea oceanic islands to three, with consequences for the interpretation of local endemicity.
- Phylogenetic relationships of gadfly petrels Pterodroma spp. from the Northeastern Atlantic Ocean: molecular evidence for specific status of Bugio and Cape Verde petrels and implications for conservationPublication . Jesus, José; Menezes, Dília; Gomes, Sara; Oliveira, Paulo; Nogales, Manuel; Brehm, AntónioIt is widely accepted that the gadfly petrels of the Macaronesian islands comprise three closely related and morphologically similar taxa, Petrodroma madeira from Madeira island, P. deserta (also treated as P. feae deserta) from Bugio and P. feae (also treated as P. feae feae) from Cape Verde Islands. However, the taxonomic rank of each taxon is not well defined, and has been subject to a long debate. Partial sequences of cytochrome b (893 bp) from 39 individuals (five from Madeira, 18 from nearby Bugio, and 16 from Fogo) and morphometric data from five characters from 102 individuals (74 from Bugio and 28 from Fogo in Cape Verde), were used to compare and estimate phylogenetic relationships and the taxonomic status of these petrels. In the phylogenetic analysis and sequence divergence estimation, we also include 23 sequences of 19 Pterodroma species available from GenBank. Our results show that Macaronesian gadfly petrels form a monophyletic clade. Birds from Bugio and Cape Verde are the most closely related taxa followed by those from Madeira. The group formed by the three taxa studied is closely related to Bermuda Petrel P. cahow and Black-capped Petrel P. hasitata. A hypothesis for the colonization of the islands is presented. The level of sequence divergence is sufficient to consider the populations of Bugio and Cape Verde as separate species. Reproductive isolation is supported by exclusive haplotypes and fixed changes. Despite the presence of some significant differences in bill and tarsus measurements, the two species seem to be morphologically similar because the great overlap of variation intervals in the measurements hinders identification. It therefore appears suitable for consideration as a cryptic species. An important conservation implication is that the world population of both species is very small; if treated as a full species, deserta on Bugio may qualify for uplisting to ‘Vulnerable’ on the IUCN Red List.
- The Y-chromosome short tandem repeats variation within haplogroup E3b: evidence of recurrent mutation in SNPPublication . Fernandes, A. T.; Rosa, A.; Gonçalves, R.; Jesus, José; Brehm, A.Haplogroup E3b is defined by a single nucleotide mutation (SNP) in locus M35 and is found at high fre quency (more than 35%) in populations from North Africa with a heterogeneous distribution. On the basis of compilation of 553 Y-chromosomes from Europe and 633 from sub-Saharan Africa we selected 130 individuals belonging to haplogroup E3b and characterized subhaplogroups according to the Y-Chromosome Consortium nomenclature. Y-chromosome haplo types can be defined using short tandem repeats (STR). The use of STRs makes it possible to measure diversity and esti mate age coalescence. Significant differences on frequencies of Y-chromosome STR loci were found among the E3b sub haplogroups and the same was observed when haplotype frequencies were considered. Some mutations in SNPs were detected when comparing E3b subhaplogroups with the correspondent STR haplotypes. These results show that the mutation rate for some SNPs could be higher than previously thought and also that it is important to associate both haplo type and haplogroup in Y-chromosome studies
- Phylogenetic relationships of Hemidactylus geckos from the Gulf of Guinea islands: patterns of natural colonizations and anthropogenic introductions estimated from mitochondrial and nuclear DNA sequencesPublication . Jesus, José; Brehm, António; Harris, D. JamesMitochondrial DNA (12S rRNA, 16S rRNA, and cytochrome b) sequences and nuclear sequences (C-mos and alpha-Enolase) were analyzed within all known Hemidactylus species from all three volcanic islands in the Gulf of Guinea that have never been connected to the continent. These comprise both endemic and widespread species. Our aim was to determine if the widespread species was introduced anthropogenically, to determine the number of distinct genetic lineages within the islands, and to determine if the endemic forms constituted a monophyletic group. Our results suggest that a previously undescribed species on São Tomé is the sister taxon to Hemidactylus newtoni, endemic to Annobon. Genetic variation between populations of Hemidactylus greefii from São Tomé and Principe is very high based on mtDNA sequences, but the forms cannot be distinguished using the nuclear DNA sequences. Hemidactylus mabouia appears to have been anthropogenically introduced to all three islands. The island endemics do not form a monophyletic group, suggesting multiple independent colonizations of the islands.
- Lack of congruence between morphometric evolution and genetic differentiation suggests a recent dispersal and local habitat adaptation of the Madeiran lizard Lacerta dugesiiPublication . Brehm, António; Khadem, Mahnaz; Jesus, José; Andrade, Paula; Vicente, LuísGenetic differentiation among nine populations of the endemic lizard Lacerta dugesii Milne-Edwards 1829 (Lacertidae) from four groups of islands constituting the Archipelago of Madeira, was investigated by protein electrophoresis at 23 enzyme loci. Among twenty polymorphic loci, the total genetic diversity was due primarily to intra-population variation. The allele and genotypic frequencies among populations showed some heterogeneity, allowing the species to present a structuring pattern compatible with their geographical clustering. Some evidence suggests that selection acting on some loci in different ecological conditions may be responsible for the clustering of the populations studied. There was no apparent isolation effect expected under an "island" model of population divergence, and no correlation was found between genetic and geographic distances among populations. Morphological variation of the proposed three L. dugesii subspecies is not congruent with the allozyme analysis. This most probably suggests a rapid colonization of the islands followed by a strong effect of selection operating over the morphological characters used to define the subspecies.
- Distribution of HLA alleles in Portugal and Cabo Verde. Relationships with the slave trade routePublication . Spínola, Hélder; Brehm, A.; Williams, F.; Jesus, J.; Middleton, D.HLA-A,-B, and -DR frequencies were analysed in populations from Portugal and the Madeira and Cabo Verde Archipelagos, aiming to characterize their genetic composition. Portuguese settlers colonized both Archipelagos in the 15th and 16th centuries. Madeira received many sub-Saharan slaves to work in the sugar plantations, and Cabo Verde served as a pivotal market in the Atlantic slave trade and was populated by individuals coming from the Senegambia region of the West African coast. The population of Madeira shows the highest genetic diversity and the presence of alleles and haplotypes usually linked to sub-Saharan populations, the haplotypes accounting for 3±5% of the total. Cabo Verde presents typical markers acknowledged to be of European or IberoMediterranean origin, thus revealing the admixture of European settlers with Sub-Saharan slaves. Altogether the number of European haplotypes reaches 15% of the total. The Portuguese population shows a perceivable and significant heterogeneity both in allele and haplotype frequencies, unveiling a differential input of peoples from different origins. A PCA of the populations studied, plus other relevant ones, clearly shows gene heterogeneity in mainland Portugal as well as the differences and relationships between these populations and Madeira and Cabo Verde.
- Role of the lizard Teira dugesii as a potential host for Ixodes ricinus tick-borne pathogensPublication . Sousa, R. de; Carvalho, I. Lopes de; Santos, A. S.; Bernardes, C.; Milhano, N.; Jesus, J.; Menezes, D.; Núncio, M. S.PCR screening of ticks and tissue samples collected from 151 Teira dugesii lizards seems to indicate a potential role of this lizard species in the maintenance and transmission cycle of some Ixodes ricinus tick-borne agents, such as Rickettsia monacensis, Rick ettsia helvetica, and Borrelia lusitaniae, that are circulating on Madeira Island.
- Phylogenetic relationships of African green snakes (genera Philothamnus and Hapsidophrys) from São Tomé, Príncipe and Annobon islands based on mtDNA sequences, and comments on their colonization and taxonomyPublication . Jesus, José; Nágy, Zoltan T.; Branch, William R.; Wink, Michael; Brehm, António; Harris, D. JamesMitochondrial sequences (16S rRNA and cytochrome b) of the colubrine snake genera Philothamnus and Hapsidophrys were analysed. Samples were obtained from three volcanic islands in the Gulf of Guinea. The main objective was to infer phylogenetic relationships between the taxa and to trace back the colonization patterns of the group. Both insular species, Philothamnus girardi and Philothamnus thomensis, form a monophyletic unit indicating a single colonization event of one island (probably São Tomé) followed by dispersal to Annobon. Genetic divergence was found to be relatively low when compared with other Philothamnus species from the African mainland, but sufficient to consider the two taxa as distinct sister species. Here we also present evidence on the distinct phylogenetic position of Hapsidophrys sp. from the island of Príncipe, which should be considered as a distinct species, Hapsidophrys principis, a sister taxon of H. smaragdina.
- Phylogeography of the Madeiran endemic lizard Lacerta dugesii inferred from mtDNA sequencesPublication . Brehm, A.; Jesus, J.; Spínola, H.; Alves, C.; Vicente, L.; Harris, D. J.Partial sequences from two mitochondrial DNA genes, cytochrome b and 12S rRNA, were used to assess the phylogenetic relationships of populations of Lacerta dugesii from the volcanic Atlantic islands of Madeira, the Desertas, Porto Santo, and the Selvagens. All four-island groups are genetically distinguishable and populations within each contain similar degrees of genetic diversity. Molecular clock estimates suggest that the islands were colonized much later after their emergence compared to other Atlantic islands, possibly due to their greater geographical isolation. Mismatch analysis of all populations is consistent with exponential growth, as expected after colonization of empty niches. The Selvagens contain genetic substructuring between the islets
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