Influence of environmental and biological factors on the overwinter growth rate of Atlantic salmon Salmo salar parr in a UK chalk stream

Smolt lengths are increasingly recognised as an important determinant of salmonid marine survival rates. Overwintering growth rates could thus strongly influence adult return rates. In Atlantic salmon Salmo salar, most overwintering studies focus on rivers in harsh climates with minimal growth, yet in more southerly rivers, overwintering growth rates can be relatively high. Here, the factors influencing annual overwinter growth rates were tested for juvenile S. salar in a temperate chalk stream in southern England over 13 years, where over 10,000 salmon parr were tagged annually in autumn and a proportion recaptured the following spring during smolt emigration. Winters of higher and more variable water temperatures, with longer periods of high flows, showed increased overwintering growth rates. Faster growth rates were recorded from sites further upstream and that had lower parr densities; smaller individuals also grew more than expected for their initial size. These results suggest that a range of factors influences overwintering salmonid growth rates and can be used to inform management decisions to maximise the quality of emigrating smolts

Atlantic salmon return rate increases with smolt length

Recent declines in Atlantic salmon Salmo salar populations are generally attributed to factors in their marine life-phase. However, it is postulated that factors affecting their freshwater life-phase might impact their marine survival, such as the influence of body size. While larger smolts are widely hypothesized to have higher marine survival rates, empirical support remains scant, in part due to inadequate data and ambiguous statistical analyses. Here, we test the influence of smolt body size on marine return rates, a proxy for marine survival, using a 12-year dataset of 3688 smolts tagged with passive integrated transponders in the River Frome, Southern England. State-space models describe the probability of smolts surviving their marine phase to return as 1 sea-winter (1SW) or multi-sea-winter adults as a function of their length, while accounting for imperfect detection and missing data. Models predicted that larger smolts had higher return rates; the most parsimonious model included the effect of length on 1SW return rate. This prediction is concerning, as freshwater juvenile salmon are decreasing in size on the River Frome, and elsewhere. Thus, to maximize adult returns, restoration efforts should focus on freshwater life-stages, and maximize both the number and the size of emigrating smolts

Chemical Screening Method for the Rapid Identification of Microbial Sources of Marine Invertebrate-Associated Metabolites

Marine invertebrates have proven to be a rich source of secondary metabolites. The growing recognition that marine microorganisms associated with invertebrate hosts are involved in the biosynthesis of secondary metabolites offers new alternatives for the discovery and development of marine natural products. However, the discovery of microorganisms producing secondary metabolites previously attributed to an invertebrate host poses a significant challenge. This study describes an efficient chemical screening method utilizing a 96-well plate-based bacterial cultivation strategy to identify and isolate microbial producers of marine invertebrate-associated metabolites

Biological and environmental influences on the migration phenology of Atlantic salmon Salmo salar smolts in a chalk stream in southern England

1. Migration enables animals to access important resources throughout their lifetime but exists in a trade-off with elevated mortality risk. In spring, juvenile Atlantic salmon (smolts) migrate from their natal rivers for marine feeding grounds, with the timing of their marine entry a potentially important determinant of their long-term survival. However, there is relatively little known on how the interaction of biological and environmental factors affect smolt migration phenology at the individual level, and how these vary throughout the duration of the smolt seaward migration (run). 2. Using 15-year tag, recapture, and detection datasets of individual smolts (marked with passive integrated transponder tags) from a chalk stream in southern England, the influences of a range of biological and environmental variables were tested on the run timing of individual smolts, measured as the timing of their arrival in a lower river reach. 3. The probability of smolts arriving earlier in the lower river reach was elevated following winters that were relatively warm, and when there were larger positive daily changes in water temperature and discharge during the run. Early migrants tended to be larger individuals and from sites lower in the catchment, from where the smolts had to migrate relatively shorter distances. Later migrants were more likely to migrate in schools, but with schooling behaviour also more likely to occur during daylight than at night. 4. The relative influence of some of these variables altered throughout the run. Relative changes in daily water temperature were not important during the middle period of the smolt run but were important at the start and end of the run. Relative changes in daily discharge were most influential towards the end of the run, when even relatively small changes in discharge had a strong influence on migration. 5. These results reveal the importance of a wide range of biological and environmental variables on the phenology of smolt migrations, and how their influence can alter throughout the run. With predictions of annually increasing river temperatures, more frequent and intense discharge events, and associated shifts to earlier migration, these results emphasise that such changes in climate are likely to have substantial consequences on the future success of smolt migrations and thereby future numbers of returning adult spawners

Place recognition using batlike sonar

Echolocating bats have excellent spatial memory and are able to navigate to salient locations using bio-sonar. Navigating and route-following require animals to recognize places. Currently, it is mostly unknown how bats recognize places using echolocation. In this paper, we propose template based place recognition might underlie sonar-based navigation in bats. Under this hypothesis, bats recognize places by remembering their echo signature - rather than their 3D layout. Using a large body of ensonification data collected in three different habitats, we test the viability of this hypothesis assessing two critical properties of the proposed echo signatures: (1) they can be uniquely classified and (2) they vary continuously across space. Based on the results presented, we conclude that the proposed echo signatures satisfy both criteria. We discuss how these two properties of the echo signatures can support navigation and building a cognitive map. DOI: http://dx.doi.org/10.7554/eLife.14188.00

A two-stage genome-wide association study of sporadic amyotrophic lateral sclerosis

The cause of sporadic amyotrophic lateral sclerosis (ALS) is largely unknown, but genetic factors are thought to play a significant role in determining susceptibility to motor neuron degeneration. To identify genetic variants altering risk of ALS, we undertook a two-stage genome-wide association study (GWAS): we followed our initial GWAS of 545 066 SNPs in 553 individuals with ALS and 2338 controls by testing the 7600 most associated SNPs from the first stage in three independent cohorts consisting of 2160 cases and 3008 controls. None of the SNPs selected for replication exceeded the Bonferroni threshold for significance. The two most significantly associated SNPs, rs2708909 and rs2708851 [odds ratio (OR) = 1.17 and 1.18, and P-values = 6.98 x 10–7 and 1.16 x 10–6], were located on chromosome 7p13.3 within a 175 kb linkage disequilibrium block containing the SUNC1, HUS1 and C7orf57 genes. These associations did not achieve genome-wide significance in the original cohort and failed to replicate in an additional independent cohort of 989 US cases and 327 controls (OR = 1.18 and 1.19, P-values = 0.08 and 0.06, respectively). Thus, we chose to cautiously interpret our data as hypothesis-generating requiring additional confirmation, especially as all previously reported loci for ALS have failed to replicate successfully. Indeed, the three loci (FGGY, ITPR2 and DPP6) identified in previous GWAS of sporadic ALS were not significantly associated with disease in our study. Our findings suggest that ALS is more genetically and clinically heterogeneous than previously recognized. Genotype data from our study have been made available online to facilitate such future endeavors

Incorporating phylogenetic uncertainty on phylogeny-based palaeontological dating and the timing of turtle diversification

Methods improving the performance of molecular dating of divergence time of clades have improved dramatically in recent years. The calibration of molecular dating using the first appearance of a clade in the fossil record is a crucial step towards inferring the minimal diversification time of various groups and the choice of extinct taxa can strongly influence the molecular dates. Here, we evaluate the uncertainty on the phylogenetic position of extinct taxa through non-parametric bootstrapping. The recognition of phylogenetic uncertainty resulted in the definition of the Bootstrap Uncertainty Range (BUR) for the age of first appearance of a given clade. The BUR is calculated as the interval of geological time in which the diversification of a given clade can be inferred to have occurred, based on the temporal information of the fossil record and the topologies of the bootstrap trees. Divergence times based on BUR analyses were calculated for three clades of turtles: Testudines, Pleurodira and Cryptodira. This resulted in extensive uncertainty ranges of topology-dependent minimal divergence dates for these clades.Fil: Sterli, Juliana. Museo Paleontológico Egidio Feruglio; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Nacional Patagónico; ArgentinaFil: Pol, Diego. Museo Paleontológico Egidio Feruglio; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Nacional Patagónico; ArgentinaFil: Laurin, M.. Museum National d Histoire Naturelle. Batiment de Geologie; Franci

A novel SMC-like protein, SbcE (YhaN), is involved in DNA double-strand break repair and competence in Bacillus subtilis

Bacillus subtilis and most Gram positive bacteria possess four SMC like proteins: SMC, SbcC, RecN and the product of the yhaN gene, termed SbcE. SbcE is most similar to SbcC but contains a unique central domain. We show that SbcE plays a role during transformation in competent cells and in DNA double-strand break (DSB) repair. The phenotypes were strongly exacerbated by the additional deletion of recN or of sbcC, suggesting that all three proteins act upstream of RecA and provide distinct avenues for presynapsis. SbcE accumulated at the cell poles in competent cells, and localized as a discrete focus on the nucleoids in 10% of growing cells. This number moderately increased after treatment with DNA damaging agents and in the absence of RecN or of SbcC. Damage-induced foci of SbcE arose early after induction of DNA damage and rarely colocalized with the replication machinery. Our work shows that SMC-like proteins in B. subtilis play roles at different subcellular sites during DNA repair. SbcC operates at breaks occurring at the replication machinery, whereas RecN and SbcE function mainly, but not exclusively, at DSBs arising elsewhere on the chromosome. In agreement with this idea, we found that RecN-YFP damage-induced assemblies also arise in the absence of ongoing replication