Plaice (Pleuronectes platessa L.) nursery habitat on the Forth Estuary and the Firth of Forth

The nursery function of the Forth estuary and Firth of Forth for juvenile plaice was investigated using several methods. Growth rates of juvenile plaice in the estuary were compared with growth rates of juvenile plaice in the Firth of Forth. Growth was estimated for comparisons between sites because growth is expected to indicate the quality of a particular habitat as a nursery. Growth was estimated at four sites in 2005 using two methods and in 2006 using a single method: 1) Tracking changes in length - frequency distributions of newly - settled plaice over time was used in both years and 2) Plaice were aged to the day using otolith microstructure in 2005 only, and the ages were regressed against length to estimate growth rates as a 'ground - truthing' of method 1). The growth rates of plaice were found to be similar between estuarine and outer firth sites, but lower at all four sites in 2006 than 2005. A temperature - dependent model was used to compare maximum growth rates with estimated growth rates to determine if plaice were growing optimally, and growth was less than optimal at all four sites in both years, with some evidence of density - dependence. A push net was used to sample plaice for length measurements at each site on each sampling date, and efficiencies of the net were estimated to determine actual densities of plaice and whether the net was length selective. No length selectivities were found, however, the efficiency of the net was less than 100 % and lower on muddy sites than on sandy sites. The effect of salinity on growth of juvenile plaice was assessed in a laboratory experiment. Plaice were found to grow faster at salinity 25, next fastest at salinity 30 and lowest at salinity. Assessment of consumption rates showed that the differences were likely to be caused by the effects of salinity on physiological performance of fish. A new method of inferring contribution of juvenile plaice from each habitat to adult recruitment, using stable isotopic composition of plaice otoliths was assessed. Plaice from the estuary could not be distinguished from outer firth plaice on the basis of otolith isotopic composition on the small scale used here, however, the work provides a baseline for this area in larger scale studies. Sediment isotopic composition showed differences between the estuary and outer firth, with differences between sediment types and a detectable influence of marine photosynthesis.EThOS - Electronic Theses Online ServiceGBUnited Kingdo

Plaice(Pleuronectes platessa L.) nursery habitat on the Forth estuary and the Firth of Forth

The nursery function of the Forth estuary and Firth of Forth for juvenile plaice was investigated using several methods. Growth rates of juvenile plaice in the estuary were compared with growth rates of juvenile plaice in the Firth of Forth. Growth was estimated for comparisons between sites because growth is expected to indicate the quality of a particular habitat as a nursery. Growth was estimated at four sites in 2005 using two methods and in 2006 using a single method: 1) Tracking changes in length - frequency distributions of newly - settled plaice over time was used in both years and 2) Plaice were aged to the day using otolith microstructure in 2005 only, and the ages were regressed against length to estimate growth rates as a 'ground - truthing' of method 1). The growth rates of plaice were found to be similar between estuarine and outer firth sites, but lower at all four sites in 2006 than 2005. A temperature - dependent model was used to compare maximum growth rates with estimated growth rates to determine if plaice were growing optimally, and growth was less than optimal at all four sites in both years, with some evidence of density - dependence. A push net was used to sample plaice for length measurements at each site on each sampling date, and efficiencies of the net were estimated to determine actual densities of plaice and whether the net was length selective. No length selectivities were found, however, the efficiency of the net was less than 100 % and lower on muddy sites than on sandy sites. The effect of salinity on growth of juvenile plaice was assessed in a laboratory experiment. Plaice were found to grow faster at salinity 25, next fastest at salinity 30 and lowest at salinity. Assessment of consumption rates showed that the differences were likely to be caused by the effects of salinity on physiological performance of fish. A new method of inferring contribution of juvenile plaice from each habitat to adult recruitment, using stable isotopic composition of plaice otoliths was assessed.Plaice from the estuary could not be distinguished from outer firth plaice on the basis of otolith isotopic composition on the small scale used here, however, the work provides a baseline for this area in larger scale studies. Sediment isotopic composition showed differences between the estuary and outer firth, with differences between sediment types and a detectable influence of marine photosynthesis

Calling time on Oronsay: revising settlement models around the mesolithic–neolithic transition in Western Scotland, new evidence from Port Lobh, Colonsay

For over 120 years, the shell middens of western Scotland and the series of open-air sites on Oronsay have been the focus of debate in European Mesolithic studies. This paper challenges the significance of Oronsay in light of results from the geophysical survey and test-excavation of a new limpet and periwinkle shell midden dated to the late 5th or start of the 4th millennium cal BC at Port Lobh, Colonsay that offers fresh evidence to re-evaluate critically the role of Oronsay and coastal resources in island settlement models ahead of the Mesolithic–Neolithic transition. Test excavations recovered a marine molluscan assemblage dominated by limpet and periwinkle shells together with crab, sea urchin, a fishbone assemblage composed mainly of Gadidae, some identifiable bird and mammal bone, carbonised macroplant remains, and pumice as well as a bipolar lithic assemblage and coarse stone implements. Novel seasonality studies of saithe otolith thin-sections suggest wintertime tidal fishing practices. At least two activity events may be discerned, dating from the late 5th millennium cal BC. The midden could represent a small number of rapidly deposited assemblages or maybe the result of stocastic events within a more extended timeframe. We argue that alternative research questions are needed to advance long-standing debates about seasonal inter island mobility versus island sedentism that look beyond Oronsay to better understand later Mesolithic occupation patterns and the formation and date of Oronsay middens. We propose alternative methodological strategies to aid identification of contemporaneous sites using geophysical techniques and lithic technological signatures

Salt stress in the renal tubules is Linked to TAL specific expression of uromodulin and an upregulation of heat shock genes

Previously, our comprehensive cardiovascular characterisation study validated Uromodulin as a blood pressure gene. Uromodulin is a glycoprotein exclusively synthesised at the thick ascending limb of the loop of Henle and is encoded by the Umod gene. Umod(-/-) mice have significantly lower blood pressure than Umod(+/+) mice, are resistant to salt-induced changes in blood pressure, and show a leftward shift in pressure-natriuresis curves reflecting changes of sodium reabsorption. Salt stress triggers transcription factors and genes that alter renal sodium reabsorption. To date there are no studies on renal transcriptome responses to salt stress. Here we aimed to delineate salt stress pathways in tubules isolated from Umod(+/+) mice (a model of sodium retention) and Umod(-/-) mice (a model of sodium depletion) +/-300mOsmol sodium chloride (n=3 per group) performing RNA-Seq. In response to salt stress, the tubules of Umod(+/+) mice displayed an up regulation of heat shock transcripts. The greatest changes occurred in the expression of: Hspa1a (Log2 fold change 4.35, p=2.48e-12) and Hspa1b (Log2 fold change 4.05, p=2.48e-12). This response was absent in tubules of Umod(-/-) mice. Interestingly, 7 of the genes discordantly expressed in the Umod(-/-) tubules were electrolyte transporters. Our results are the first to show that salt stress in renal tubules alters the transcriptome, increasing the expression of heat shock genes. This direction of effect in Umod(+/+) tubules suggest the difference is due to the presence of Umod facilitating greater sodium entry into the tubule cell reflecting a specific response to salt stress

The effect of salinity on growth and weight loss of juvenile plaice (Pleuronectes platessa, L): An experimental test

Previous population estimates of the 0+ plaice (Pleuronectes platessa L.) in the Firth of Forth, east central Scotland, did not take account of the Forth estuary west of the Forth bridges. Previous work found plaice in the estuary grew as fast as, or faster than, the outer firth plaice. It was hypothesised that salinity may affect growth rates of early 0+ plaice. This hypothesis was tested in a laboratory experiment, by exposing juvenile plaice to three different, but naturally — experienced by the juveniles, salinities; 25, 30 and 35. Plaice fed a minimum ration did not grow in length. Mean weight decreased at all three salinities, however, the lowest weight loss was found at the lowest salinity (25) and the highest weight loss was found at the highest salinity (35). The minimum feeding ration was halted and plaice were then fed ad libitum. Consumption rates were not significantly different during the ad libitum feeding, while significant differences in mean weight change were found between the highest and lowest salinities

Carbon stable isotopes in estuarine sediments and their utility as migration markers for nursery studies in the Firth of Forth and Forth Estuary, Scotland

The stable carbon isotope ratios (?13C) of the organic fraction of intertidal sediments in the Forth Estuary and the Firth of Forth, Scotland, were measured to determine if terrestrially derived carbon was present in the estuarine sediments. It was hypothesised that differences in the inputs from marine vs. terrestrial sources to the organic carbon of estuarine and marine sediments, as well as differences in ambient seawater stable oxygen isotope (?18O) ratios between the estuary and the Outer Firth, would allow the use of these two stable isotopes as habitat markers for juvenile plaice (Pleuronectes platessa), to allow determination of nursery habitats. Muddy and sandy sediments from the estuary and sandy sediments from the Outer Firth were sampled and ?13C measured. Juvenile plaice were caught at two estuarine sites and at two Outer Firth sites and otoliths were removed for ?13C and ?18O analysis. The sandy sediments in the estuary showed a strong gradient of ?13C enrichment with distance down the estuary, while the muddy sediments showed a much shallower gradient. ?13C and ?18O measured in the carbonate of juvenile plaice otoliths showed no clear difference between otoliths of fish caught at one of the estuarine sites and at the two Outer Firth sites. However, the isotope ratios of both carbon and oxygen in plaice otoliths from the other estuarine site showed the expected trend of depletion in the heavier isotopes. While the measurements recorded here did not conclusively distinguish between otoliths from juveniles caught in the estuarine site and those caught in the other three sites, they show that stable isotopes have potential to distinguish between estuarine habitats with terrestrial carbon inputs, and coastal marine habitats with predominantly marine carbon inputs

Otolith chemistry reveals seamount fidelity in a deepwater fish

There are thousands of seamounts (underwater mountains) throughout the world's deep oceans, many of which support diverse faunal communities and valuable fish stocks. Although seamounts are often geographically and bathymetrically isolated from one another, it is not clear how biologically isolated they are from one another. We analysed the chemical signature of the otoliths of a deepwater fish, the roundnose grenadier (Coryphaenoides rupestris) to test the null hypothesis that there is random exchange between individuals from a seamount and other adjacent areas. The fish were sampled on the Scottish west coast, from the Rosemary Bank seamount and two adjacent locations of similar depth, in the same year at roughly the same time of year. We used flow-injection inductively coupled plasma mass spectrometry to measure trace element concentrations from micro-milled portions of the otolith corresponding to adult and juvenile life history stages. The elemental signatures of the fish from the seamount were distinguishable from the fish from the two other areas during both the juvenile and adult life-history phase. We infer that once juveniles settle on the seamount they remain there for the rest of their lives. Evidence for population structure should be factored into exploitation strategies to prevent local depletion and is an important consideration with respect to Rosemary bank being included in a network of Marine Protected Areas around Scotland

Correction to: De novo transcriptome assembly, annotation and comparison of four ecological and evolutionary model salmonid fish species

Following the publication of this article [1], the authors noticed found that they incorrectly reported the BUSCO completeness for the PhyloFish brown trout and European whitefish transcriptomes. This was due to an error in their TransDecoder pipeline and restricted to those two datasets and their interpretation. They apologise for this misreported result and thank the authors of the PhyloFish database for bringing it to their attention

De novo transcriptome assembly, annotation and comparison of four ecological and evolutionary model salmonid fish species

Background: Salmonid fishes exhibit high levels of phenotypic and ecological variation and are thus ideal model systems for studying evolutionary processes of adaptive divergence and speciation. Furthermore, salmonids are of major interest in fisheries, aquaculture, and conservation research. Improving understanding of the genetic mechanisms underlying traits in these species would significantly progress research in these fields. Here we generate high quality de novo transcriptomes for four salmonid species: Atlantic salmon (Salmo salar), brown trout (Salmo trutta), Arctic charr (Salvelinus alpinus), and European whitefish (Coregonus lavaretus). All species except Atlantic salmon have no reference genome publicly available and few if any genomic studies to date. Results: We used paired-end RNA-seq on Illumina to generate high coverage sequencing of multiple individuals, yielding between 180 and 210 M reads per species. After initial assembly, strict filtering was used to remove duplicated, redundant, and low confidence transcripts. The final assemblies consisted of 36,505 protein-coding transcripts for Atlantic salmon, 35,736 for brown trout, 33,126 for Arctic charr, and 33,697 for European whitefish and are made publicly available. Assembly completeness was assessed using three approaches, all of which supported high quality of the assemblies: 1) ~78% of Actinopterygian single-copy orthologs were successfully captured in our assemblies, 2) orthogroup inference identified high overlap in the protein sequences present across all four species (40% shared across all four and 84% shared by at least two), and 3) comparison with the published Atlantic salmon genome suggests that our assemblies represent well covered (~98%) protein-coding transcriptomes. Thorough comparison of the generated assemblies found that 84-90% of transcripts in each assembly were orthologous with at least one of the other three species. We also identified 34-37% of transcripts in each assembly as paralogs. We further compare completeness and annotation statistics of our new assemblies to available related species. Conclusion: New, high-confidence protein-coding transcriptomes were generated for four ecologically and economically important species of salmonids. This offers a high quality pipeline for such complex genomes, represents a valuable contribution to the existing genomic resources for these species and provides robust tools for future investigation of gene expression and sequence evolution in these and other salmonid species