Sara Rocha

New primers for the amplification and sequencing of nuclear loci in a taxonomically wide set of reptiles and amphibians

We report new primers for the amplification and sequencing of 11 nuclear markers in squamate reptiles and anuran amphibians (five in squamates, six in anurans). Ten out of the 11 loci are introns (three of which are linked) that were amplified using an exon-primed, intron-crossing (EPIC) PCR strategy, whereas an eleventh locus spans part of a protein-coding gene. Squamate and anuran primers were initially developed for Lacerta schreiberi (Squamata: Lacertidae) and Pelodytes spp. (Anura: Pelodytidae), respectively. Cross-species amplification of the squamate markers was evaluated in four genera representing two additional families, whereas for anurans three genera corresponding to three additional families were tested. Three out of the five loci were successfully sequenced in all squamate taxa tested. Cross-amplification of the six anuran markers had lower, but still significant, success. We predict these markers will be of great utility for both population genetics and phylogenetic studies.

Genetic exchange across a hybrid zone within the Iberian endemic golden-striped salamander, Chioglossa lusitanica

The study of hybrid zones resulting from Pleistocene vicariance is central in examining the potential of genetically diverged evolutionary units either to introgress and merge or to proceed with further isolation. The hybrid zone between two mitochondrial lineages of Chioglossa lusitanica is located near the Mondego River in Central Portugal. We used mitochondrial and nuclear diagnostic markers to conduct a formal statistical analysis of the Chioglossa hybrid zone in the context of tension zone theory. Key results are: (i) cline centres are not coincident for all markers, with average widths of ca. 2–15 km; (ii) heterozygote deficit was not observed across loci near the transect centre; (iii) associations of parental allele combinations (‘linkage disequilibrium’R) were not detected either across loci or across the transect. These observations suggest that the Chioglossa hybrid zone is not a tension zone with strong selection against hybrids but instead one shaped mostly by neutral mixing. The patterns uncovered suggest a complex history of populations over a small scale that may be common in southern Pleistocene refugia.

Multigene phylogeny of Malagasy day geckos of the genus Phelsuma

CIBIO, Centro de Investigacao em Biodiversidade e Recursos Geneticos, Instituto de Ciencias Agrarias de Vairao, Rua Padre Armando Quintas, 4485-661 Vairao, Portugal Departamento de Zoologia e Antropologia, Faculdade de Ciencias, Universidade do Porto, Praca Gomes Teixeira 4099-002, Portugal Departamento de Bioquimica, Genetica e Inmunologia, Facultad de Biologia, Universidad de Vigo, Vigo 36310, Spain d Technical University of Braunschweig, Zoological Institute, Spielmannstr. 8, 38106 Braunschweig, Germany e Zoologische Staatssammlung Munchen, Munchhausenstr. 21, 81247 Munchen, Germany

A comparison of tools for the simulation of genomic next-generation sequencing data

Computer simulation of genomic data has become increasingly popular for assessing and validating biological models or for gaining an understanding of specific data sets. Several computational tools for the simulation of next-generation sequencing (NGS) data have been developed in recent years, which could be used to compare existing and new NGS analytical pipelines. Here we review 23 of these tools, highlighting their distinct functionality, requirements and potential applications. We also provide a decision tree for the informed selection of an appropriate NGS simulation tool for the specific question at hand.

Phylogeography and diversification history of the day-gecko genus Phelsuma in the Seychelles islands

BackgroundLying in a shallow continental shelf cyclically affected by oscillating sea levels since the Miocene, the Seychelles islands are particularly interesting for evolutionary studies. Recent molecular studies are generating an emerging picture of the origin of its biota, yet very little is known regarding their phylogeographic structure or on the factors promoting diversification within the archipelago. Here we aimed to obtain a detailed depiction of the genetic structure and evolution of one of the most widespread vertebrate groups in the archipelago: the day-geckos of the genus Phelsuma. In parallel, we aimed to infer divergence times between species and subspecies, testing a long-standing hypothesis that argues for different time since sympatry between species as the cause of their different morphological differentiation across the archipelago.ResultsMolecular data corroborated the existence of two main lineages, corresponding to the two currently recognized species. Divergences between species likely date back to the Mio-Pliocene, while more recent, Pleistocenic, divergences are suggested within each species. Populations from outer islands share mtDNA haplotypes with inner island populations, suggesting very recent dispersals (or introductions). We found no evidence of current gene flow between species, but results pointed to the possibility of gene flow between (now allopatric) subspecies. Time estimates suggest a synchronous divergence within each species (between island groups).ConclusionsThe geographic patterns of genetic variation agree with previous taxonomic subdivisions within each species and the origin of outer islands populations is clearly tracked. The similar intraspecific divergence time estimates obtained suggest that the differential body-size differentiation between species within each group of islands may be driven by factors other than character displacement proportional to time since sympatry, as previously suggested. These factors could include different habitats/resources available within each island group, niche differentiation and/or character displacement. We also bring again into consideration the hypothesis of body size being influenced by the distribution of native vegetation and social systems within this group, although it remains to be tested. Our results highlight not only the necessity of clarifying the role of ecology and interspecific interactions in this group’s morphological diversification and community assemblage, but also the importance of co-evolutionary mechanisms and their importance for appropriate conservation of island biodiversity. Further, we provide a detailed description of the phylogeographic structure of these taxa across these islands, which still remain poorly characterized in this respect.

Phylogenetic relationships of Trachylepis skink species from Madagascar and the Seychelles (Squamata: Scincidae).

Lizards of the genus Trachylepis are a species-rich group of skinks mainly inhabiting Africa, Madagascar, and several other islands in the western Indian Ocean. All except one probably introduced species of Madagascan Trachylepis are endemic. Two species groups have been distinguished on the basis of subocular scale shape but their phylogenetic relationships remained unclear. We inferred a multilocus phylogeny of the Madagascan Trachylepis species, based on a concatenated dataset of 3261 bp from 3 mitochondrial and 4 nuclear genes with a dense Madagascan taxon sampling and find high support for the monophyly of the endemic Madagascan Trachylepis. The two species groups in Madagascar are highly supported as clades. The highland species T. boettgeri is nested in the T. aureopunctata species group of mainly arid-adapted species, suggesting a colonization of highland swamps by ancestors inhabiting dry western Madagascar. The Seychellois species were sister to the T. maculilabris/T. comorensis clade, suggesting their origin directly out of Africa as with Seychellois chameleons. In Madagascar, a high intraspecific molecular variation was confirmed for T. gravenhorstii, T. elegans, and T. vato, indicating a need for taxonomic revision.

Genetic diversity and phylogenetic relationships of Mabuya spp. (Squamata: Scincidae) from western Indian Ocean islands

Western Indian Ocean islands (excluding Madagascar) are inhabited by at least five species of the lizard genus Mabuya, for which diversity and inter-island phylogenetic relationships are still unclear, particularly concerning island populations of M. maculilabris, M. comorensis and M. striata. With a comprehensive sampling across the Comoros archipelago and the islands of Zanzibar and Pemba (Tanzania) we use molecular data and previously published sequences of these species to describe genetic variation across their insular range and explore the possible distinction of insular populations of the different species, contributing to the clarification of their status and knowledge of their colonization patterns. We describe patterns of cryptic diversity within M. comorensis, revealing a West to East colonization of the Comoros archipelago and clarify the status of Malagasy populations of this species. Cryptic variation is also observed within M. maculilabris and M. striata, and the status of several continental and island populations discussed. M. sechellensis is shown to be paraphyletic relative to M. wrightii. Available data for all Afro-Malagasy Mabuya reveals additional possible instances of paraphyly within some species but does not allow for further resolution of basal relationships within this group, pointing to rapid and simultaneous divergences within this group and the need for multiple independent markers to recover the history of this group.

Assessment of mtDNA genetic diversity within the terrapins Pelusios subniger and Pelusios castanoides across the Seychelles islands

Two terrapin subspecies are currently considered Seychelles endemisms and Critically Endangered according to IUCN criteria, with several conservation measures having been proposed and actively initiated in the recent years. We use molecular data to examine their population diversity and structure across the archipelago and find a complete lack of variation at the mtDNA level. This can be explained by the strong founder effect associated with island colonisation, allied to the low evolution rate described for turtle mtDNA. However, a very recent arrival of Seychellois terrapins to the archipelago by human action cannot be discarded. The use of highly variable markers such as microsatellites and the clarification of their (native or not) status is therefore essential and should be implemented as an urgent priority in species management plans. Some differentiation between the Seychellois and Malagasy P. castanoides is observed but should be taken carefully until geographically broad level sampling across Madagascar is available.

Influence of the Drying Conditions of Sargassum sp. Alga on the Bioadsorption of Hexavalent Chromium

Industrial wastes containing synthetic organic compounds and heavy metals are among the most dangerous residues, whose growth has followed the increase in industrial activity. Heavy metals are readily assimilated into the food chain and therefore easily accumulated in the ecosystem. To remove heavy metals from aqueous solutions, marine algae may be used as adsorbents either in their natural form or after treatments by a cross-linking process to improve their mechanical resistance. Drying of biosorbents, such as marine algae, is mentioned in many previous works as a step preceding the adsorption/dessorption cycle. Concerning algae, drying of its fresh biomass allows for proper storage and enhances performance in the sorption of heavy metals. In this work, physical and morphological analyses of fresh and dried Sargassum sp. marine algae, harvested offshore São Sebastião, São Paulo state, Brazil, were performed in order to assess the influence of drying conditions on the biosorption process. Chromium concentrations were also determined in different parts of the algal structure before and after the biosorption process. The drying promoted structural changes in the algae, like shrinkage and porosity reduction. It was also observed that the chromium retention was dependent on the structural arrangement of the alga parts, in which the leaf was the major biosorbent.

Parthenogenesis through the ice ages: A biogeographic analysis of Caucasian rock lizards (genus Darevskia).

Darevskia rock lizards include both sexual and parthenogenetic species, mostly distributed in the heterogeneous and ecologically diverse Caucasus. The parthenogenetic species originated via directional hybridogenesis, with only some of the sexual species known to serve as parentals. However, it remains unclear when and where these events happened and how many parental lineages were involved. A multilocus phylogeographic analysis was performed on the parthenogens D. unisexualis, D. bendimahiensis and D. uzzeli, and their putative maternal species D. raddei. Results show the parthenogenetic species all have relatively recent origins, approximately 200-70kyr ago, and at least three hybridization events were involved in their formation. Ecological niche models identify the region where hybridization events leading to the formation of D. unisexualis took place, namely in the northeast of the current distribution. Models also suggest that the sexual D. raddei might have undergone a habitat shift between the Last Interglacial and the Last Glacial Maximum.