Anadromy,potamodromy and residency in brown trout Salmo trutta: the role of genes and the environment

Brown trout Salmo trutta is endemic to Europe, western Asia and north-western Africa; it is a prominent member of freshwater and coastal marine fish faunas. The species shows two resident (river-resident, lake-resident) and three main facultative migratory life histories (downstream–upstream within a river system, fluvial–adfluvial potamodromous; to and from a lake, lacustrine–adfluvial (inlet) or allacustrine (outlet) potamodromous; to and from the sea, anadromous). River-residency v. migration is a balance between enhanced feeding and thus growth advantages of migration to a particular habitat v. the costs of potentially greater mortality and energy expenditure. Fluvial–adfluvial migration usually has less feeding improvement, but less mortality risk, than lacustrine–adfluvial or allacustrine and anadromous, but the latter vary among catchments as to which is favoured. Indirect evidence suggests that around 50% of the variability in S. trutta migration v. residency, among individuals within a population, is due to genetic variance. This dichotomous decision can best be explained by the threshold-trait model of quantitative genetics. Thus, an individual's physiological condition (e.g., energy status) as regulated by environmental factors, genes and non-genetic parental effects, acts as the cue. The magnitude of this cue relative to a genetically predetermined individual threshold, governs whether it will migrate or sexually mature as a river-resident. This decision threshold occurs early in life and, if the choice is to migrate, a second threshold probably follows determining the age and timing of migration. Migration destination (mainstem river, lake, or sea) also appears to be genetically programmed. Decisions to migrate and ultimate destination result in a number of subsequent consequential changes such as parr–smolt transformation, sexual maturity and return migration. Strong associations with one or a few genes have been found for most aspects of the migratory syndrome and indirect evidence supports genetic involvement in all parts. Thus, migratory and resident life histories potentially evolve as a result of natural and anthropogenic environmental changes, which alter relative survival and reproduction. Knowledge of genetic determinants of the various components of migration in S. trutta lags substantially behind that of Oncorhynchus mykiss and other salmonines. Identification of genetic markers linked to migration components and especially to the migration–residency decision, is a prerequisite for facilitating detailed empirical studies. In order to predict effectively, through modelling, the effects of environmental changes, quantification of the relative fitness of different migratory traits and of their heritabilities, across a range of environmental conditions, is also urgently required in the face of the increasing pace of such changes.     

Phylogenetics and taxonomy of the New World leafy spurges,Euphorbia section Tithymalus (Euphorbiaceae)

The 480 species of leafy spurges, Euphorbia subgenus Esula, represent the main temperate radiation in the large genus Euphorbia. This group is distributed primarily in temperate Eurasia, but with smaller, disjunct centres of diversity in the mountains of the Old World tropics, in temperate southern Africa and in the New World. The majority of New World diversity (32 species) occurs in a single section, section Tithymalus. We analysed sequences of the nrITS and plastid ndhF, trnH‐psbA, trnS‐trnG and trnD‐trnT regions to reconstruct the phylogeny of section Tithymalus and to examine the origins and diversification of the species native to the New World. Our results indicate that the New World species of section Tithymalus form a clade that is sister to the widespread, weedy E. peplus. The New World species fall into two primary groups: a ‘northern annual clade’ from eastern North America and a diverse clade of both annual and perennial species that is divided into three subgroups. Within the second group, there is a small ‘southern annual clade’ from Texas and northern Mexico, a perennial ‘Brachycera clade’ from the western United States and northern Mexico, and a perennial ‘Esuliformis clade’ from montane areas of Mexico, Guatemala, Honduras and the Caribbean island of Hispaniola. Ancestral state reconstructions indicate that the annual habit probably evolved in the ancestor of E. peplus and the New World clade, with a subsequent reversal to the perennial habit. In conjunction with this phylogenetic framework, the New World species of section Tithymalus are comprehensively reviewed. © 2014 The Linnean Society of London, Botanical Journal of the Linnean Society, 2014, 175 , 191–228.     

Biostimulation and Bioaugmentation of Anaerobic Pentachlorophenol Degradation in Contaminated Soils

The effects of bioaugmentation with a pentachlorophenol (PCP)-adapted consortium and biostimulation with glucose as a carbon source on anaerobic bioremediation of PCP-contaminated soil were investigated in terms of the initial PCP removal rate and the extent of PCP dechlorination and mineralization. Samples from two PCP-contaminated sites were prepared, put into a series of Hungate tubes, inoculated, and fed under different conditions. Chlorophenols in the tubes were monitored over a 4-month period to measure PCP transformation in the soil. In less contaminated soil (10 mg PCP/kg soil), it was found that biostimulation with glucose at 1 g/kg soil or bioaugmentation at 0.14 g volatile suspended solids (VSS)/kg soil could greatly improve PCP degradation. The best PCP degradation was obtained when both bioaugmentation and biostimulation were applied, but higher levels of glucose (2 g/kg soil) or inoculum (0.56 g VSS/kg soil) had little additional effect. The highest initial PCP-removal rate reached 8.1 μmol/kg soil-d, which is almost 20 times greater than in the unamended controls. PCP was dechlorinated to lesser chlorinated phenols with 0.6 chlorine remaining on average, and the extent of mineralization approached 70% in 4 months. In highly PCP-contaminated soil (90 mg PCP/kg soil), PCP degradation was partially inhibited, but the relative effects of augmentation, stimulation, and combined treatments were the same as in the less contaminated soil.     

Distinctive Profile of IsomiR Expression and Novel MicroRNAs in Rat Heart Left Ventricle

MicroRNAs (miRNAs) are single-stranded non-coding RNAs that negatively regulate target gene expression through mRNA cleavage or translational repression. There is mounting evidence that they play critical roles in heart disease. The expression of known miRNAs in the heart has been studied at length by microarray and quantitative PCR but it is becoming evident that microRNA isoforms (isomiRs) are potentially physiologically important. It is well known that left ventricular (patho)physiology is influenced by transmural heterogeneity of cardiomyocyte phenotype, and this likely reflects underlying heterogeneity of gene expression. Given the significant role of miRNAs in regulating gene expression, knowledge of how the miRNA profile varies across the ventricular wall will be crucial to better understand the mechanisms governing transmural physiological heterogeneity. To determinine miRNA/isomiR expression profiles in the rat heart we investigated tissue from different locations across the left ventricular wall using deep sequencing. We detected significant quantities of 145 known rat miRNAs and 68 potential novel orthologs of known miRNAs, in mature, mature* and isomiR formation. Many isomiRs were detected at a higher frequency than their canonical sequence in miRBase and have different predicted targets. The most common miR-133a isomiR was more effective at targeting a construct containing a sequence from the gelsolin gene than was canonical miR-133a, as determined by dual-fluorescence assay. We identified a novel rat miR-1 homolog from a second miR-1 gene; and a novel rat miRNA similar to miR-676. We also cloned and sequenced the rat miR-486 gene which is not in miRBase (v18). Signalling pathways predicted to be targeted by the most highly detected miRNAs include Ubiquitin-mediated Proteolysis, Mitogen-Activated Protein Kinase, Regulation of Actin Cytoskeleton, Wnt signalling, Calcium Signalling, Gap junctions and Arrhythmogenic Right Ventricular Cardiomyopathy. Most miRNAs are not expressed in a gradient across the ventricular wall, with exceptions including miR-10b, miR-21, miR-99b and miR-486.