NCBI Mass Sequence Downloader–Large dataset downloading made easy

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Concatenator: sequence data matrices handling made easy

Concatenator is a simple and user-friendly software that implements two very useful functions for phylogenetics data analysis. It concatenates NEXUS files of several fragments in a single NEXUS file ready to be used in phylogenetics software, such as paup and mrbayes and it converts FASTA sequence data files to NEXUS and vice-versa. Additionally, concatenated files can be prepared for partition tests in paup. It is freely available in http://cobig2.fc.ul.pt.info:eu-repo/semantics/publishedVersio

Genetic variability on worldwide populations of the scale insect Pulvinariella mesembryanthemi

The South African scale insect Pulvinariella mesembryanthemi was introduced worldwide in several coastal areas with Mediterranean climate, probably through infested plants of Carpobrotus sp. Its high host specificity and its capacity to produce severe damages in the invasive Carpobrotus sp. plants makes this insect a potential biocontrol agent. To test the efficiency and host range of insects used for biocontrol, population genetic studies can help to unravel cryptic complexes and intraspecific diversity. In this study we performed a genetic analysis including native and exotic populations of P. mesembryanthemi, through Sanger sequencing of mitochondrial (cytochrome c oxidase I, COI) and ribosomal (D2–D3 expansion segments of the large subunit ribosomal RNA gene 28S) gene fragments. Accidentally, an endosymbiont was sequenced with one of the pair of primers used. The exotic populations of the insect did not show any variability among populations for both studied genes, which suggest a common origin of all studied introduced populations. Contrastingly, native populations showed high variability and seemed to be a cryptic species complex. Moreover, the Gauteng populations (from NE South Africa) were phylogenetically the closest to the exotic ones, suggesting that the exotic populations could be original from somewhere near this area. An endosymbiont of P. mesembryanthemi was detected, and the sequenced coxA gene was similar to that of the Rickettsiaceae family from the α-Proteobacteria, and close to other insect endosymbionts. To the best of our knowledge, this was the first mention of this endosymbiont in P. mesembryanthemi, although α-Proteobacteria endosymbionts have been reported for other sap-sucking insects.info:eu-repo/semantics/publishedVersio

Ancient divergence, a crisis of salt and another of ice shaped the evolution of the west Mediterranean butterfly Euchloe tagis

The Mediterranean region is an extremely complex hotspot where, since the Miocene, extensive geological, habitat and climate changes have taken place, alternating between warm and cold periods. These phenomena have taken a toll on the genetic composition of species, and surviving lineages have often adapted locally and diverged to the point of (complete) speciation. To study these phenomena, in this study we used one of the most enigmatic butterflies, the Portuguese dappled white, Euchloe tagis, a west Mediterranean endemic with fragmented, morphologically differentiated populations whose status have long been disputed. Even its affiliations with other Anthocharidini are largely unresolved. We used mitochondrial and nuclear markers under a phylogenetic and phylogeographical framework to evaluate its placement among relatives and population differentiation, reconstructing its evolutionary history. We found that this species had a Miocene origin ~15 Mya and was nearest to Euchloe s.s. and Elphinstonia. Its populations showed high genetic diversity but all coalesced to 5.3 Mya, when European and all but one African population diverged. Our multiple findings concerning the evolution of E. tagis through a changing, narrow habitable area might provide a more general perspective on how species survive within this hotspot of paramount importance.info:eu-repo/semantics/publishedVersio

New insights into adaptation and population structure of cork oak using genotyping by sequencing

Species respond to global climatic changes in a local context. Understanding this process, including its speed and intensity, is paramount due to the pace at which such changes are currently occurring. Tree species are particularly interesting to study in this regard due to their long generation times, sedentarism, and ecological and economic importance. Quercus suber L. is an evergreen forest tree species of the Fagaceae family with an essentially Western Mediterranean distribution. Despite frequent assessments of the species' evolutionary history, large-scale genetic studies have mostly relied on plastidial markers, whereas nuclear markers have been used on studies with locally focused sampling strategies. In this work, "Genotyping by sequencing" is used to derive 1,996 single nucleotide polymorphism markers to assess the species' evolutionary history from a nuclear DNA perspective, gain insights into how local adaptation is shaping the species' genetic background, and to forecast how Q. suber may respond to global climatic changes from a genetic perspective. Results reveal (a) an essentially unstructured species, where (b) a balance between gene flow and local adaptation keeps the species' gene pool somewhat homogeneous across its distribution, but still allowing (c) variation clines for the individuals to cope with local conditions. "Risk of Non-Adaptedness" (RONA) analyses suggest that for the considered variables and most sampled locations, (d) the cork oak should not require large shifts in allele frequencies to survive the predicted climatic changes. Future directions include integrating these results with ecological niche modeling perspectives, improving the RONA methodology, and expanding its use to other species. With the implementation presented in this work, the RONA can now also be easily assessed for other organisms.info:eu-repo/semantics/publishedVersio

Revision of the morphology, phylogenetic relationships, behaviour and diversity of the Iberian and Italian ant-like Tachydromia Meigen, 1803 (Diptera: Hybotidae)

Phylogenetic inference, based on five molecular markers (COI, 28S, AATS, 12S, PGD), corroborates the synonymy of the flightless genera Pieltainia Arias, 1919 and Ariasella Gil, 1923 with Tachydromia Meigen, 1803. The secondary structure of the 28S rRNA gene is used for the first time in this family to align the multiple sequences. Molecular and morphological data are largely congruent for all known species of flightless Tachydromia. This paper treats ten western Mediterranean species (nine Iberian and one Italian) in detail, including the description of four new species: T. ebejeri Gonçalves, Grootaert & Andrade sp. nov., T. stenoptera Gonçalves, Grootaert & Andrade sp. nov., T. cantabrica Gonçalves, Grootaert & Andrade sp. nov. and T. nigrohirta Gonçalves, Grootaert & Andrade sp. nov. The male of Tachydromia pieltaini (Gil Collado, 1936) and the female of Tachydromia apterygon Plant & Deeming, 2006 are described for the first time, while a lectotype is assigned to Tachydromia pandellei (Séguy, 1941). A key to all non-macropterous Tachydromia is supplied. Knowledge on the geographic distribution of most species is considerably enhanced. The mating behaviour of Tachydromia semiaptera (Gil Collado, 1923) and Tachydromia iberica (Arias, 1919) is documented for the first time, and we propose a change in the definition of terms apterous and micropterous to properly accommodate the diversity of wing states in this cluster of species.info:eu-repo/semantics/publishedVersio

Ovule transcriptome analysis discloses deregulation of genes and pathways in sexual and apomictic Limonium species (Plumbaginaceae)

The genus Limonium Mill. (sea lavenders) includes species with sexual and apomixis reproductive strategies, although the genes involved in these processes are unknown. To explore the mechanisms beyond these reproduction modes, transcriptome profiling of sexual, male sterile, and facultative apomictic species was carried out using ovules from different developmental stages. In total, 15,166 unigenes were found to be differentially expressed with apomictic vs. sexual reproduc- tion, of which 4275 were uniquely annotated using an Arabidopsis thaliana database, with different regulations according to each stage and/or species compared. Gene ontology (GO) enrichment analy- sis indicated that genes related to tubulin, actin, the ubiquitin degradation process, reactive oxygen species scavenging, hormone signaling such as the ethylene signaling pathway and gibberellic acid- dependent signal, and transcription factors were found among differentially expressed genes (DEGs) between apomictic and sexual plants. We found that 24% of uniquely annotated DEGs were likely to be implicated in flower development, male sterility, pollen formation, pollen-stigma interactions, and pollen tube formation. The present study identifies candidate genes that are highly associated with distinct reproductive modes and sheds light on the molecular mechanisms of apomixis expression in Limonium spinfo:eu-repo/semantics/publishedVersio

Highly regional population structure of Spondyliosoma cantharus depicted by nuclear and mitochondrial DNA data

Resolution of population structure represents an effective way to define biological stocks and inform efficient fisheries management. In the present study, the phylogeography of the protogynous sparid Spondyliosoma cantharus, in the East Atlantic and Mediterranean Sea, was investigated with nuclear (S7) and mitochondrial (cytochrome b) DNA markers. Significant divergence of four regional genetic groups was observed: North Eastern Atlantic, Mediterranean Sea, Western African Transition (Cape Verde) and Gulf of Guinea (Angola). The two southern populations (Cape Verde and Angola) each comprised reciprocally monophyletic mtDNA lineages, revealed low levels of diversity in Cape Verde and high diversity for Angola despite being represented by only 14 individuals. A complete divergence between North Atlantic and Mediterranean populations was depicted by the mitochondrial marker, but a highly shared nuclear haplotype revealed an incomplete lineage sorting between these regions. Bayesian skyline plots and associated statistics revealed different dynamics among the four regions. Cape Verde showed no expansion and the expansion time estimated for Angola was much older than for the other regions. Mediterranean region seems to have experienced an early population growth but has remained with a stable population size for the last 30000 years while the North Atlantic population has been steadily growing. The lack of genetic structuring within these regions should not be taken as evidence of demographic panmixia in light of potential resolution thresholds and previous evidence of intra-regional phenotypic heterogeneity.info:eu-repo/semantics/publishedVersio

Shortcomings of phylogenetic studies on recent radiated insular groups: a meta-analysis using Cabo Verde biodiversity

ReviewOver the previous decades, numerous studies focused on how oceanic islands have contributed to determine the phylogenetic relationships and times of origin and diversification of di erent endemic lineages. The Macaronesian Islands (i.e., Azores, Madeira, Selvagens, Canaries, and Cabo Verde), harbour biotas with exceptionally high levels of endemism. Within the region, the vascular plants and reptiles constitute two of the most important radiations. In this study we compare relevant published phylogenetic data and diversification rates retrieved within Cabo Verde endemic lineages and discuss the importance of choosing appropriate phylogeny-based methods to investigate diversification dynamics on islands. From this selective literature-based review, we summarize the software packages used in Macaronesian studies and discuss their adequacy considering the published data to obtain well-supported phylogenies in the target groups. We further debate the importance of Next Generation Sequencing (NGS), to investigate the evolutionary processes of diversification in the Macaronesian Islands. Analysis of genomic data provides phylogenetic resolution for rapidly evolving species radiations, suggesting a great potential to improve the phylogenetic signal and divergence time estimates in insular lineages. The most important Macaronesian reptile radiations provide good case-studies to compare classical phylogenetic methods with new tools, such as phylogenomics, revealing a high value for research on this hotspot areainfo:eu-repo/semantics/publishedVersio

Revisiting Vitis vinifera Subtilase Gene Family: A Possible Role in Grapevine Resistance against Plasmopara viticola

Subtilisin-like proteases, also known as subtilases, are a very diverse family of serine peptidases present in many organisms. In grapevine, there are hints of the involvement of subtilases in defense mechanisms, but their role is not yet understood. The first characterization of the subtilase gene family was performed in 2014. However, simultaneously, the grapevine genome was re-annotated and several sequences were re-annotated or retrieved. We have performed a re-characterization of this family in grapevine and identified 82 genes coding for 97 putative proteins, as result of alternative splicing. All the subtilases identified present the characteristic S8 peptidase domain and the majority of them also have a pro-domain I9 inhibitor, a protease-associated (PA) domain, and a signal peptide for targeting to the secretory pathway. Phylogenetic studies revealed six subtilase groups denominated VvSBT1 to VvSBT6. As several evidences have highlighted the participation of plant subtilases in response to biotic stimulus, we have investigated subtilase participation in grapevine resistance to Plasmopara viticola, the causative agent of downy mildew. Fourteen grapevine subtilases presenting either high homology to P69C from tomato, SBT3.3 from Arabidopsis thaliana or located near the Resistance to P. viticola (RPV) locus were selected. Expression studies were conducted in the grapevine-P. viticola pathosystem with resistant and susceptible cultivars. Our results may indicate that some of grapevine subtilisins are potentially participating in the defense response against this biotrophic oomycete.info:eu-repo/semantics/publishedVersio