Alternative reproductive tactics and sex-biased gene expression : the study of the bulb mite transcriptome

The sexes experience different selective pressures, which can lead to highly divergent phenotypes that are achieved via sex-biased gene expression. The effect of sexual dimorphism on the degree of sex-bias in gene expression can be studied in species characterized by sexually selected alternative male phenotypes. We analyzed gene expression in the bulb mite Rhizoglyphus robini (Acari, Acaridae), in which more sexually dimorphic, aggressive fighter males, possessing thickened legs of the third pair which are used to kill rivals, coexist with unarmored scrambler males. We sequenced transcriptomes of adult females and both types of males and de-novo assembled 114,456 transcriptome-based gene models (TGMs). Significantly more TGMs had male-biased expression than female-biased expression. Among TGMs that were over expressed in one, but not both, male morphs (compared to expression in females), we found about four times more fighter-biased genes than scrambler-biased genes. This demonstrates that the degree of expression bias reflects the degree of sexually selected dimorphism. However, the number of sex-biased genes was much higher than the number of genes differentially expressed between male morphs, and most male-biased genes were shared between morphs, suggesting that selection pressures act similarly on males irrespective of their morph. Furthermore, we found that male-biased genes evolved at a faster rate than female-biased genes, as evidenced by a higher rate of both gene-turnover and amino acid substitution, indicating that sexual selection, acting more strongly on males, accelerates the rate of molecular evolution. Interestingly, gene turnover was relatively higher, but amino acid substitution rate relatively lower among fighter-biased genes, suggesting that different components of sexual selection may have different effects on the evolution of sex-biased genes

Molecular Inversion Probes for targeted resequencing in non-model organisms

Applications that require resequencing of hundreds or thousands of predefined genomic regions in numerous samples are common in studies of non-model organisms. However few approaches at the scale intermediate between multiplex PCR and sequence capture methods are available. Here we explored the utility of Molecular Inversion Probes (MIPs) for the medium-scale targeted resequencing in a non-model system. Markers targeting 112 bp of exonic sequence were designed from transcriptome of Lissotriton newts. We assessed performance of 248 MIP markers in a sample of 85 individuals. Among the 234 (94.4%) successfully amplified markers 80% had median coverage within one order of magnitude, indicating relatively uniform performance; coverage uniformity across individuals was also high. In the analysis of polymorphism and segregation within family, 77% of 248 tested MIPs were confirmed as single copy Mendelian markers. Genotyping concordance assessed using replicate samples exceeded 99%. MIP markers for targeted resequencing have a number of advantages: high specificity, high multiplexing level, low sample requirement, straightforward laboratory protocol, no need for preparation of genomic libraries and no ascertainment bias. We conclude that MIP markers provide an effective solution for resequencing targets of tens or hundreds of kb in any organism and in a large number of samples

Single nucleotide polymorphisms reveal genetic structuring of the Carpathian newt and provide evidence of interspecific gene flow in the nuclear genome

Genetic variation within species is commonly structured in a hierarchical manner which may result from superimposition of processes acting at different spatial and temporal scales. In organisms of limited dispersal ability, signatures of past subdivision are detectable for a long time. Studies of contemporary genetic structure in such taxa inform about the history of isolation, range changes and local admixture resulting from geographically restricted hybridization with related species. Here we use a set of 139 transcriptome-derived, unlinked nuclear single nucleotide polymorphisms (SNP) to assess the genetic structure of the Carpathian newt (Lissotriton montandoni, Lm) and introgression from its congener, the smooth newt (L. vulgaris, Lv). Two substantially differentiated groups of Lm populations likely originated from separate refugia, both located in the Eastern Carpathians. The colonization of the present range in north-western and south-western directions was accompanied by a modest loss of variation; admixture between the two groups has occurred in the middle of the Eastern Carpathians. Local, apparently recent introgression of Lv alleles into several Lm populations was detected, demonstrating increased power for admixture detection in comparison to a previous study based on a limited number of microsatellite markers. The level of introgression was higher in Lm populations classified as admixed than in syntopic populations. We discuss the possible causes and propose further tests to distinguish between alternatives. Several outlier loci were identified in tests of interspecific differentiation, suggesting genomic heterogeneity of gene flow between species

454 sequencing reveals extreme complexity of the class II Major Histocompatibility Complex in the collared flycatcher

<p>Abstract</p> <p>Background</p> <p>Because of their functional significance, the Major Histocompatibility Complex (MHC) class I and II genes have been the subject of continuous interest in the fields of ecology, evolution and conservation. In some vertebrate groups MHC consists of multiple loci with similar alleles; therefore, the multiple loci must be genotyped simultaneously. In such complex systems, understanding of the evolutionary patterns and their causes has been limited due to challenges posed by genotyping.</p> <p>Results</p> <p>Here we used 454 amplicon sequencing to characterize MHC class IIB exon 2 variation in the collared flycatcher, an important organism in evolutionary and immuno-ecological studies. On the basis of over 152,000 sequencing reads we identified 194 putative alleles in 237 individuals. We found an extreme complexity of the MHC class IIB in the collared flycatchers, with our estimates pointing to the presence of at least nine expressed loci and a large, though difficult to estimate precisely, number of pseudogene loci. Many similar alleles occurred in the pseudogenes indicating either a series of recent duplications or extensive concerted evolution. The expressed alleles showed unambiguous signals of historical selection and the occurrence of apparent interlocus exchange of alleles. Placing the collared flycatcher's MHC sequences in the context of passerine diversity revealed transspecific MHC class II evolution within the Muscicapidae family.</p> <p>Conclusions</p> <p>454 amplicon sequencing is an effective tool for advancing our understanding of the MHC class II structure and evolutionary patterns in Passeriformes. We found a highly dynamic pattern of evolution of MHC class IIB genes with strong signals of selection and pronounced sequence divergence in expressed genes, in contrast to the apparent sequence homogenization in pseudogenes. We show that next generation sequencing offers a universal, affordable method for the characterization and, in perspective, genotyping of MHC systems of virtually any complexity.</p

INNOVATION IN A PRODUCER GROUP FOCUSED ON MILK PRODUCTION OF THE SILESIAN PROVINCE

The aim of the work was to analyse the level of innovation in the group of milk producers and production efficiency. The work covered its scope with the producer group established in 2010, which brings together six producers of cow's milk. The farms are run based on a conventional production system. The source data used in the analysis covers the years 2010-2017. The analysis covered the number of implemented innovations, the type of innovation and the level of expenditures borne by producers for introducing the innovations. Based on the results obtained, the relative benefits achieved by the producer group resulting from the introduction of innovative solutions were determined

Characterization of power transistors as high dose dosimeters

A bipolar transistor, previously investigated as a possible radiation dosimeter and tested under industrial irradiation conditions in high-activity gamma and high-energy, high-power electron beam facilities has been subjected to stability test in order to understand its behaviour and help to improve its performances. Charge carrier lifetime was measured for several sets of transistors which were then irradiated with various doses (3-60 kGy): seven sets with Co-60 gamma rays and eight with a 10MeV electron beam. After irradiation all the transistors were measured and each set was divided into three groups: one group was left untreated, the second group was heated at 100 degrees C for 30 minutes and the third group was heated at 150 degrees C for 30 minutes, for testing the stability of the lifetime. Our data showed that heat treatment quite successfully eliminates post-irradiation changes in the response. Response measurements of the irradiated transistors, heat-treated and untreated, were carried out at room temperature over several weeks after irradiation to establish post-irradiation stability and assess if these transistors could be used for recording dose history. Calibration curves in the range 3-60 kGy for the thermally treated and untreated devices are presented. Dependence of the response of the transistors on the temperature of the measurements in the range 20-50 degrees C is reported

PRODUCTION POTENTIAL OF AN ENTERPRISE OPERATING AS A GROUP OF AGRICULTURAL PRODUCERS

The research study describes an analysis of the management efficiency of an enterprise focused on egg production. The enterprise runs market cooperation as a group of agricultural producers. The aim of the work was to analyse the functioning of agricultural producers groups in Poland in terms of formal, legal and production conditions. A detailed analysis included a group focused on the production of table eggs, based in the Malopolskie province

Constraint and adaptation in newt Toll-like receptor genes

Acute die-offs of amphibian populations worldwide have been linked to the emergence of viral and fungal diseases. Inter and intraspecific immunogenetic differences may influence the outcome of infection. Toll-like receptors (TLRs) are an essential component of innate immunity and also prime acquired defenses. We report the first comprehensive assessment of TLR gene variation for urodele amphibians. The Lissotriton newt TLR repertoire includes representatives of 13 families and is compositionally most similar to that of the anuran Xenopus. Both ancient and recent gene duplications have occurred in urodeles, bringing the total number of TLR genes to at least 21. Purifying selection has predominated the evolution of newt TLRs in both long (∼70 Ma) and medium (∼18 Ma) timescales. However, we find evidence for both purifying and positive selection acting on TLRs in two recently diverged (2–5 Ma) allopatric evolutionary lineages (Lissotriton montandoni and L. vulgaris graecus). Overall, both forms of selection have been stronger in L. v. graecus, while constraint on most TLR genes in L. montandoni appears relaxed. The differences in selection regimes are unlikely to be biased by demographic effects because these were controlled by means of a historical demographic model derived from an independent data set of 62 loci. We infer that TLR genes undergo distinct trajectories of adaptive evolution in closely related amphibian lineages, highlight the potential of TLRs to capture the signatures of different assemblages of pathogenic microorganisms, and suggest differences between lineages in the relative roles of innate and acquired immunity

Heart transcriptome of the bank vole (Myodes glareolus): towards understanding the evolutionary variation in metabolic rate

Longer reads and higher sequence yield per run provided by the 454 Titanium technology in comparison to earlier generations of pyrosequencing proved beneficial for the quality of assembly. An almost full representation of genes known to be expressed in the mouse heart was identified. Usage of the extensive genomic resources available for the house mouse, a moderately (20-40 mln years) divergent relative of the voles, enabled a comprehensive assessment of the transcript completeness. Transcript sequences generated in the present study allowed the identification of candidate SNPs associated with divergence of selection lines and constitute a valuable permanent resource forming a foundation for RNAseq experiments aiming at detection of adaptive changes both at the level of gene expression and sequence variants, that would facilitate studies of the genetic basis of evolutionary divergence