Genomic basis of ecological niche divergence among cryptic sister species of non-biting midges

Background: There is a lack of understanding the evolutionary forces driving niche segregation of closely related organisms. In addition, pinpointing the genes driving ecological divergence is a key goal in molecular ecology. Here, larval transcriptome sequences obtained by next-generation-sequencing are used to address these issues in a morphologically cryptic sister species pair of non-biting midges (Chironomus riparius and C. piger). Results: More than eight thousand orthologous open reading frames were screened for interspecific divergence and intraspecific polymorphisms. Despite a small mean sequence divergence of 1.53% between the sister species, 25.1% of 18,115 observed amino acid substitutions were inferred by α statistics to be driven by positive selection. Applying McDonald-Kreitman tests to 715 alignments of gene orthologues identified eleven (1.5%) genes driven by positive selection. Conclusions: Three candidate genes were identified as potentially responsible for the observed niche segregation concerning nitrite concentration, habitat temperature and water conductivity. Additionally, signs of positive selection in the hydrogen sulfide detoxification pathway were detected, providing a new plausible hypothesis for the species’ ecological differentiation. Finally, a divergently selected, nuclear encoded mitochondrial ribosomal protein may contribute to reproductive isolation due to cytonuclear coevolution

Appeasement versus fighting: a new slavemaker employs alternative raiding strategies

Trabalho final de mestrado integrado em Medicina (Urologia), apresentado á Faculdade de Medicina da Universidade de CoimbraA disfunção miccional que sucede ao traumatismo vertebro-medular, frequentemente designada de bexiga neurogénica, é uma das consequências mais importantes e limitativas para o indivíduo, após este tipo de lesão. A reorganização das vias de inervação da bexiga altera o controlo voluntário da micção e causa a emergência de reflexos não fisiológicos, de onde advêm os diferentes sintomas. Ainda que a incidência dos traumatismos tenha vindo a diminuir, as sequelas devastadoras impostas ao indivíduo, quer imediatas quer futuras, que condicionam a sua qualidade de vida e dificultam uma recuperação funcional completa, fazem com que estes nunca deixem de representar uma importante causa de morbilidade. Décadas de investigação na área e os conhecimentos adquiridos acerca dos mecanismos moleculares, organizacionais e neuroquímicos permitiram desenvolver estratégias de tratamento cada vez mais eficazes, particularmente na área da farmacologia. Actualmente, os objectivos passam pelo desenvolvimento de agentes que se revelem seguros e com um adequado perfil de reacções adversas, contra novos alvos terapêuticos. Este artigo de revisão pretende, assim, analisar e resumir a anatomia e a fisiologia do tracto urinário inferior e do processo miccional, bem como a fisiopatologia da sua disfunção de etiologia neurogénica. Pretende ainda abordar as manifestações clínicas que subjazem a esta patologia, os meios de diagnóstico disponíveis ao seu estudo e as estratégias terapêuticas recomendadas actualmente. Para a sua realização, foi pesquisada a literatura científica relevante através da base de dados PubMed, dando preferência aos estudos mais recentes, quando possível. Foram ainda consultados livros e publicações da especialidade.Voiding dysfunction following spinal cord injury, often referred to as neurogenic bladder, is one of the most important and limiting consequences for the individual, after this kind of injury. The reorganization of bladder innervation pathways alters the voluntary control of micturiton and causes the emergence of non-physiological reflexes, from which the different symptoms arise. Even though the incidence of spinal cord injuries has been declining, the devastating sequelae imposed upon the individual, either immediate or upcoming, which affect his quality of life and hinder a full functional recovery, make that these never cease to represent a major morbidity cause. Decades of research in the field and the acquired knowledge about the molecular, organizational and neurochemical mechanisms allowed developing increasingly effective treatment strategies, particularly in the area of pharmacology. Currently, the objective is the development of agents found to be safe and with a proper adverse event profile, against new therapeutic targets. This review thus aims to analyze and summarize the anatomy and physiology of the lower urinary tract and voiding process, as well as the pathophysiology of its dysfunction of neurogenic etiology. It also intends to address the clinical manifestations that underlie this pathology, the diagnostic procedures available for its study and the treatment strategies currently recommended. For accomplishing this, relevant scientific literature was searched via PubMed database and preference was given to the more recent studies, whenever possible. Books and publications of the specialty were also consulted

Are autosomal sex-determining factors of the housefly (Musca domestica) spreading north?

Multiple sex-determining factors have been found in natural populations of the housefly, Musca domestica. Their distribution seems to follow a geographical cline. The 'standard' system, with a male-determining factor, M, located on the Y chromosome, prevails at higher latitudes and altitudes. At lower latitudes and altitudes M factors have also been found on any of the five autosomes. Such populations often also harbour a dominant autosomal factor, F(D), which induces female development even in the presence of several M factors. Autosomal M factors were first observed some 50 years ago. It has been hypothesized that following their initial appearance, they are spreading northwards, replacing the standard XY system, but this has never been systematically investigated. To scrutinize this hypothesis, we here compare the current distribution of autosomal M factors in continental Europe, on a transect running from Germany to southern Italy, with the distribution reported 25 years ago. Additionally, we analysed the frequencies of the F(D) factor, which has not been done before for European populations. In contrast to earlier predictions, we do not find a clear change in the distribution of sex-determining factors: as 25 years ago, only the standard XY system is present in the north, while autosomal M factors and the F(D) factor are prevalent in Italy. We discuss possible causes for this apparently stable polymorphism.</p

Short read Illumina data for the de novo assembly of a non-model snail species transcriptome (Radix balthica, Basommatophora, Pulmonata), and a comparison of assembler performance

Peer reviewe

An Annotated Draft Genome for Radix auricularia (Gastropoda, Mollusca)

Molluscs are the second most species-rich phylum in the animal kingdom, yet only 11 genomes of this group have been published so far. Here, we present the draft genome sequence of the pulmonate freshwater snail Radix auricularia. Six whole genome shotgun libraries with different layouts were sequenced. The resulting assembly comprises 4,823 scaffolds with a cumulative length of 910 Mb and an overall read coverage of 72×. The assembly contains 94.6% of a metazoan core gene collection, indicating an almost complete coverage of the coding fraction. The discrepancy of ∼690 Mb compared with the estimated genome size of R. auricularia (1.6 Gb) results from a high repeat content of 70% mainly comprising DNA transposons. The annotation of 17,338 protein coding genes was supported by the use of publicly available transcriptome data. This draft will serve as starting point for further genomic and population genetic research in this scientifically important phylum

Factors and processes shaping the population structure and distribution of genetic variation across the species range of the freshwater snail radix balthica (Pulmonata, Basommatophora)

Background: Factors and processes shaping the population structure and spatial distribution of genetic diversity across a species' distribution range are important in determining the range limits. We comprehensively analysed the influence of recurrent and historic factors and processes on the population genetic structure, mating system and the distribution of genetic variability of the pulmonate freshwater snail Radix balthica. This analysis was based on microsatellite variation and mitochondrial haplotypes using Generalised Linear Statistical Modelling in a Model Selection framework. Results: Populations of R. balthica were found throughout North-Western Europe with range margins marked either by dispersal barriers or the presence of other Radix taxa. Overall, the population structure was characterised by distance independent passive dispersal mainly along a Southwest-Northeast axis, the absence of isolation-by-distance together with rather isolated and genetically depauperated populations compared to the variation present in the entire species due to strong local drift. A recent, climate driven range expansion explained most of the variance in genetic variation, reducing at least temporarily the genetic variability in this area. Other factors such as geographic marginality and dispersal barriers play only a minor role. Conclusions: To our knowledge, such a population structure has rarely been reported before. It might nevertheless be typical for passively dispersed, patchily distributed taxa (e.g. freshwater invertebrates). The strong local drift implied in such a structure is expected to erode genetic variation at both neutral and coding loci and thus probably diminish evolutionary potential. This study shows that the analysis of multiple factors is crucial for the inference of the processes shaping the distribution of genetic variation throughout species ranges. Additional files Additional file 1: Distribution of Radix taxa. Spatial distribution of the Radix MOTU as defined in Pfenninger et al. 2006 plus an additional, newly discovered taxon. This map is the basis for the inference of the species range of R. balthica. Additional file 2: Sampling site table and spatial distribution of diversity indices, selfing estimates and inferred population bottlenecks for R. balthica. Table of sampling site code, geographical position in decimal degrees latitude and longitude, number of individuals analysed with microsatellites (Nnuc), expected heterozygosity (HE) and standard deviation across loci, mean rarefied number of alleles per microsatellite locus (A) and their standard deviation, number of individuals analysed for mitochondrial variation (Nmt), rarefied number of mitochondrial COI haplotypes (Hmt), number of individuals measured for body size (Nsize). Figures A1 - A3 show a graphical representation of the spatial distribution of He, Hmt and, s, respectively. Additional file 3: Assessment of environmental marginality. PCA (principle component analysis) on 35 climatic parameters for the period from 1960 - 2000 from publicly availableWorldClim data. Additional file 4: Inference of a recent climate driven range expansion in R. balthica. Analysis of the freshwater benthos long term monitoring data of the Swedish national monitoring databases at the Swedish University of Agricultural Sciences SLU with canonical correspondence analysis

The effect of temperature on sex determination

In most animals the genes dictate whether an individual develops into a male or a female. For example, in humans and other mammals maleness is determined by the Y chromosome. However, in many cold-blooded animals, such as reptiles and fish, the sex of an individual is determined by the temperature of its environment. Recent work on the molecular basis of sex determination challenges the classical dichotomy between genetic sex determination (GSD) and temperature dependent sex determination (TSD). Underlying gene networks are quite similar and small changes can convert a GSD system into TSD and vice versa. Moreover, several species have been discovered where both genes and temperature affect sexual development. In this thesis I develop evolutionary models based on these new insights, and I use the housefly as experimental model to study the interaction of temperature and genes leading to sexual development. My models show that mixtures of GSD and TSD can evolve easily and that rapid evolutionary transitions between GSD and TSD are expected, in agreement with observations. A detailed model based on field data from the snow skink, a live-bearing lizard where some populations have TSD and others GSD, correctly predicts the evolved sex determining system based on local temperature variation and demography of the lizards. In the housefly, different GSD systems coexist and are distributed along a north-south cline on the northern hemisphere. I discovered a very similar but opposite south-north cline on the southern hemisphere, and analysis of climatic conditions of the different housefly populations shows that temperature is an important but not the only climatic factor that can explain this.

Data from: Gene expression patterns associated with caste and reproductive status in ants: worker-specific genes are more derived than queen-specific ones

Variation in gene expression leads to phenotypic diversity and plays a central role in caste differentiation of eusocial insect species. In social Hymenoptera, females with the same genetic background can develop into queens or workers, which are characterized by divergent morphologies, behaviors and lifespan. Moreover, many social insects exhibit behaviorally distinct worker castes, such as brood-tenders and foragers. Researchers have just started to explore which genes are differentially expressed to achieve this remarkable phenotypic plasticity. Although the queen is normally the only reproductive individual in the nest, following her removal, young brood-tending workers often develop ovaries and start to reproduce. Here, we make use of this ability in the ant Temnothorax longispinosus and compare gene expression patterns in the queens and three worker castes along a reproductive gradient. We found the largest expression differences between the queen and the worker castes (~2,500 genes), and the smallest differences between infertile brood-tenders and foragers (~300 genes). The expression profile of fertile workers is more worker-like, but to a certain extent intermediate between the queen and the infertile worker castes. In contrast to the queen, a high number of differentially expressed genes in the worker castes are of unknown function, pointing to the derived status of Hymenopteran workers within insects