Find research datasets worth reusing
Search datasets from major research repositories and use ShareScore to quickly assess how well each record supports discovery, access, and reuse.
730
datasets available to search
ShareScore release 0.9.0
Dataset results
730 results for “Trout”
FIGURE 1 in Body shape and robustness response to water flow during development of brown trout Salmo trutta parr
FIGURE 1 (a) Landmark positions () on Salmo trutta parr that were digitised twice and then averaged to minimize measurement error. (b) Shape changes associated with principal components (PCs) 1–3. PCs were derived from a between-group PC analysis of Procrustes superimposed landmarks., Consensus shape with numbered landmark positions;, Shape changes associated with each PC. Shape changes are scaled to observed PC scores: Left hand side shape changes (back outlines) are scaled to the minimum value observed across the sample on each respective PC (shown below the image) and right hand side shape changes (black outlines) are scaled to the maximum value observed across the sample on each respective PC. PC1 describes a change in head size, PC2 describes dorso-ventral arching of the body and PC3 describes changes in overall robustness and body depth
Caudal fin area: body length ratio (A:L 2; mean..) FIGURE 5 CF s S E measured from photographs of Salmo trutta parr at 20 and 32 weeks after exercise treatment initiation. A:L 2 values between the two CF s groups were significantly different (Welch's two sample t- test p <0.05) in Body shape and robustness response to water flow during development of brown trout Salmo trutta parr
Caudal fin area: body length ratio (A:L 2; mean..) FIGURE 5 CF s S E measured from photographs of Salmo trutta parr at 20 and 32 weeks after exercise treatment initiation. A:L 2 values between the two CF s groups were significantly different (Welch's two sample t- test p <0.05)
F I G U R E 3 A in A low-density single nucleotide polymorphism panel for brown trout (Salmo trutta L.) suitable for exploring genetic diversity at a range of spatial scales
F I G U R E 3 A priori discriminant analysis of principal components (DAPC) plot of Camel trout. Each point represents the genotype of an individual fish, with centroids for each site labelled. Discriminant function 1 (DF1) is represented by the x axis, and discriminant function 2 (DF2) by the y-axis
F I G U R E 1 in A low-density single nucleotide polymorphism panel for brown trout (Salmo trutta L.) suitable for exploring genetic diversity at a range of spatial scales
F I G U R E 1 Map showing the location of rivers sampled for brown trout within the UK, France and Ireland. The left panel shows the rivers used to assess the performance of the single nucleotide polymorphisms (SNP) panel at characterising genetic parameters within and outside the target region. The top right (blue) panel shows the locations of the four sampled rivers in Mount's Bay, Cornwall (Case Study 1). The bottom right (red) panel shows the location of the sample locations in the Camel catchment (Case Study 2). The red box within the bottom right panel gives the position of the impassable De Lank quarry site
FIGURE 3 in Habitat associations of rainbow trout Oncorhynchus mykiss and brown trout Salmo trutta fry
FIGURE 3 Salmo trutta fry abundances from the four sites in which three pass removals were conducted in July through October 2018 and associations with D50 and presence of wood. The trendline shows the relationship between S. trutta fry abundance and D50 in the three sites in which wood was absent () Wood () No Wood
FIGURE 5 in Habitat associations of rainbow trout Oncorhynchus mykiss and brown trout Salmo trutta fry
FIGURE 5 Oncorhynchus mykiss fry abundances from the four sites in which three pass removals were conducted in July through October 2018 and associations with (a) velocity and (b) depth. A trendline shows the relationship between each habitat variable and the fry abundance data for both the sites that were stocked (dotted line) and not stocked (solid line) () Not Stocked () Stocked
FIGURE 1 in Habitat associations of rainbow trout Oncorhynchus mykiss and brown trout Salmo trutta fry
FIGURE 1 Fry site locations used to obtain abundance estimates or single-pass counts for Salmo trutta and Oncorhynchus mykiss in the upper Colorado River study section in Grand County, Colorado, downstream of Windy Gap Reservoir. The 20 15.2 m sites, sampled five times from July through October 2018, included one abundance estimation and four single-pass sites at the Sheriff Ranch, four single-pass sites at Kinney Creek, two abundance estimation and five single-pass sites in the Red Barn area and one abundance estimation and three single-pass sites at Hitching Post
F I G U R E 2 A in A low-density single nucleotide polymorphism panel for brown trout (Salmo trutta L.) suitable for exploring genetic diversity at a range of spatial scales
F I G U R E 2 A priori discriminant analysis of principal components (DAPC) of trout genotypes from rivers flowing into Mount's Bay, Cornwall. Individuals are represented by individual points, with centroids for each river labelled. Discriminant function 1 (DF1) is represented by the x axis, and discriminant function 2 (DF2) by the y-axis
FIGURE 2 in Habitat associations of rainbow trout Oncorhynchus mykiss and brown trout Salmo trutta fry
FIGURE 2 Salmo trutta fry single-pass counts and associations with (a) D50, (b) depth and (c) velocity
FIGURE 2 in Body shape and robustness response to water flow during development of brown trout Salmo trutta parr
FIGURE 2 (a) Principal component (PC) () C00, () C04, () C10, () C20, () C32, () E04, () E10, () E20, and () E32 and (b) linear discriminant (LD) scores for Salmo trutta treatment groups (C, control; E, exercise) across experimental weeks (i.e., age 00 (control sample before treatment initiation) to 32 (32 weeks of treatment); n = 6 individuals per group). PC1 and PC3, derived from a between-group PC analysis of Procrustes superimposed landmarks corrected for the arching artefact (PC2). LD1 and LD2, derived from a LD analysis on the corrected principal component scores. Ellipses demarcate 95% confidence intervals; O, group centroids. N.B. The change of direction for head size on LD1 resulting from a negative association with PC1 (see Table 2)
FIGURE 4 in Body shape and robustness response to water flow during development of brown trout Salmo trutta parr
FIGURE 4 Box plots showing median (), 25th–75th percentiles () and range () of Salmo trutta condition at length (KÞ for exercised () and control () Salmo trutta cohorts across the experimental period (i.e., age) weeks 4–32 after treatment initiation (n = 6 per group). *, significant differences of pairwise least-squares means between exercised and control cohorts; different lower-case letters (black, exercise; grey, control) denote significant differences of pairwise least-squares means within treatments across the experimental period
F I G U R E 4 in A low-density single nucleotide polymorphism panel for brown trout (Salmo trutta L.) suitable for exploring genetic diversity at a range of spatial scales
F I G U R E 4 Correlation between geographic distance (km) against genetic distance (linear FST) for the trout samples from the River Camel. The red points represent those between the De Lank and all other sites, the black points for all pair-wise comparisons excluding the De Lank. Linear regression for all sites including the De Lank is given by the red line (r2 = 0.321, P = 0.231), and linear regression for all pair-wise sites excluding the De Lank is given by the black line (r2 = 0.658, P = 0.0671)
FIGURE 4 in Habitat associations of rainbow trout Oncorhynchus mykiss and brown trout Salmo trutta fry
FIGURE 4 Oncorhynchus mykiss fry counts from sites in which O. mykiss were or were not (i.e., natural reproduction) stocked and associations with (a) D50 and (b) velocity. A trendline shows the relationship between each habitat variable and the fry count data for both the sites that were stocked (dotted line) and not stocked (solid line) () Not Stocked () Stocked
F I G U R E 2 in Differences in growth between offspring of anadromous and freshwater brown trout Salmo trutta
F I G U R E 2 The experimental design: 12 anadromous (A) and 12 freshwater resident (R) Salmo trutta of each sex were crossed. Parallel groups of the fertilized eggs from each cross were incubated at two temperatures (±S.D.), either 4.4 ± 1.5 C or 7.1 ± 0.6 C. After hatching, parallel groups were reared at natural River Imsa temperature until the commencement of the growth experiment when parallels of the 16 reared groups were tested at two temperatures (±S.D.), either 14.9 ± 2.2 C or 18.3 ± 1.5 C 14.9. Ten S. trutta were used in each group tested, 320 fish altogether
FIGURE 2 in The thermal dependence of the protein-sparing effect in rainbow trout (Oncorhynchus mykiss, Walbaum 1792)
FIGURE 2 Ammonia quotient (AQ) of rainbow trout (Oncorhynchus mykiss) fed three isonitrogenous diets with different energy contents [high energy (HE) = 20.50 MJ kg 1, medium energy (ME) = 18.76 MJ kg 1, low energy (LE) = 17.35 MJ kg 1) at five temperatures (12 C, 14 C, 16 C, 18 C, 20 C). A quadratic dependency model was used to analyse the data. Parabolas describe the quadratic dependency of AQ values on temperature. Calculated lowest AQ values for each parabola are marked with a cross (). Each data point represents the measurement of one tank with rainbow trout at each respective diet and temperature. (n = 3)
FIGURE 1 in The thermal dependence of the protein-sparing effect in rainbow trout (Oncorhynchus mykiss, Walbaum 1792)
FIGURE 1 Percentage of retainable energy (RE) relative to gross energy intake (GEI) of rainbow trout (Oncorhynchus mykiss) fed three isonitrogenous diets with different energy contents [high energy (HE) = 20.50 MJ kg 1, medium energy (ME) = 18.76 MJ kg 1, low energy (LE) = 17.35 MJ kg 1) at five temperatures (12 C, 14 C, 16 C, 18 C, 20 C). Each data point represents measurement of one tank with rainbow trout at each respective diet and temperature (n = 3)
Phenotypes and genotypes of brown trout used for breeding experiments in 2014
<p><span>Adult brown trout were caught via electrofishing around the beginning of the spawning season from the River Aare and its tributaries Gürbe, Worble, Giesse, Kiese, and Rotache (Bern canton, Switzerland). They were kept in the <em>Fischereistützpunkt Reutigen</em> until </span><span>eggs could be stripped from females</span><span>. Adults were </span><span>narcoticised when ready to spawn and gametes were stripped for block-wise full-factorial in vitro fertilisations (e.g. Marques da Cunha et al. 2019). Photographs were taken from all fish, standard length and wet weight were determined, and fin clips were taken for molecular analyses. All fish were then released back into the streams of origin. Samples of 24 freshly fertilized eggs per experimentally produced full-sib family were used for various laboratory experiments (e.g. Marques da Cunha et al. 2019). The remaining embryos were raised </span><span>in the <em>Fischereistützpunkt Reutigen</em> and used for stocking the streams of parental origin and various nursery streamlets, following the routine of the stocking program of the Bern canton. These stocked fish were later sampled at various stages of their life cycle, and 13 microsatellite markers could be used to assign these fish to their parents.</span></p> <p><span>Marques da Cunha L., Uppal A., Seddon E., Nusbaumer D., Vermeirssen E.L.M., Wedekind C. 2019. </span>No additive genetic variance for tolerance to ethynylestradiol exposure in natural populations of brown trout (<em>Salmo trutta</em>). Evol. Appl. 12(5), 940-950. (doi:10.1111/eva.12767).</p>
Data from: Sex-specific life history affected by stocking in juvenile brown trout
<p>Salmonids are a socioeconomically and ecologically important group of fish that are often managed by stocking. Little is known about potential sex-specific effects of stocking, but recent studies found that the sexes differ in their stress tolerances already at late embryonic stage, i.e., before hatchery-born larvae are released into the wild and long before morphological gonad formation. It has also been speculated that sex-specific life histories can affect juvenile growth and mortality, and that a resulting sex-biassed demography can reduce population growth. Here we test whether juvenile brown trout (Salmo trutta) show sex-specific life histories and whether such sex effects differ in hatchery- and wild-born fish. We modified a genetic sexing protocol to reduce false assignment rates and used it to study the timing of sex differentiation in a laboratory setting, and in a large-scale field experiment to study growth and mortality of hatchery and wild-born fish in different environments. We found no sex-specific mortality in any of the environments we studied. However, females started sex differentiation earlier than males, and while growth rates were similar in the laboratory, they differed significantly in the field depending on location and origin of fish. Overall, hatchery-born males grew larger than hatchery-born females while wild-born fish showed the reverse pattern. Whether males or females grew larger was location-specific. We conclude that juvenile brown trout show sex-specific growth that is affected by stocking and by other environmental factors that remain to be identified.</p>
Development of a high-density 665 K SNP array for rainbow trout genome-wide genotyping. Supplemental VCF file
<p>Single nucleotide polymorphism (SNP) arrays, also named « SNP chips », enable very large numbers of individuals to be genotyped at a targeted set of thousands of genome-wide identified markers. We used preexisting variant datasets from USDA, a French commercial line and 30X-coverage whole genome sequencing of INRAE isogenic lines to develop an Affymetrix 665 K SNP array (HD chip) for rainbow trout. In total, we identified 32,372,492 SNPs that were polymorphic in the USDA or INRAE databases. A subset of identified SNPs were selected for inclusion on the chip, prioritizing SNPs whose flanking sequence uniquely aligned to the Swanson reference genome, with homogenous repartition over the genome and the highest Minimum Allele Frequency in both USDA and French databases. Of the 664,531 SNPs which passed the Affymetrix quality filters and were manufactured on the HD chip, 65.3% and 60.9% passed filtering metrics and were polymorphic in two other distinct French commercial populations in which, respectively, 288 and 175 sampled fish were genotyped. Only 576,118 SNPs mapped uniquely on both Swanson and Arlee reference genomes, and 12,071 SNPs did not map at all on the Arlee reference genome. Among those 576,118 SNPs, 38,948 SNPs were kept from the commercially available medium-density 57K SNP chip. We demonstrate the utility of the HD chip by describing the high rates of linkage disequilibrium at 2 kb to 10 kb in the rainbow trout genome in comparison to the linkage disequilibrium observed at 50 kb to 100 kb which are usual distances between markers of the medium-density chip.</p> <p> </p> <p>File submitted correspond to the supplementary data 1 of the publication (under submission) : INRAE_USDA_MAF1.vcf.gz</p>
FIGURE 8 in A new perspective on the molecular dating of the brown trout complex with an extended phylogeographic information on the species in Serbia
FIGURE 8 Simplified palinspastic map for the Pliocene (compiled and modified after Popov et al., 2004, 2006; Neubauer et al., 2015) with the indication of hypothetic BT colonization routes (arrows). Interrupted lines mark migration routes that are, in our opinion, less likely. Green areas represent brackish environments, light blue freshwater lakes or marshes and rivers, dark blue seas, dark gray mountain ranges, and light gray land mass; all geographic features are tentatively positioned. 1 – Ancestral trout originated in the Ponto-Caspian system and crossed from the paleo-Danube into the Western Mediterranean basin via stream capture of Alpine rivers in Pliocene; 2 – Ancestral trout originated in the Balkans basin and colonized other parts of the Mediterranean Basin from here; 3 – Colonization of the Central Alps took place in the Pliocene after the paleo-Rhône separated from the paleo-Danube and reached the Mediterranean; 4 – Atlantic basin was colonized when the Rhine captured Central Alpine rivers; 5 – Atlantic basin was colonized along the Mediterranean coastline and via Gibraltar; 6 – Ponto-Caspian basin was colonized from the Mediterranean basin following a presumed sea corridor in the upper Euphrates valley or using the paleo-Euphrates, which might have been connected with the Mediterranean until the Middle Pliocene; 7 – Ponto-Caspian basin was colonized via a possible Pliocene gateway that connected the Dacic basin and the Aegean Sea; 8 – Ponto-Caspian basin was colonized through the Bosphorus gateway.
ScienceDex guides
Understand access before you commit
These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.