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221 results for “rainbow trout”
Underlying data - Digital Twin for Rainbow Trout (Oncorhynchus mykiss) land-based aquaculture
<p>Datasets for replicating Figures 5, 6, 7 and 8 of the article "Digital twins for land-based aquaculture: a case study for rainbow trout (<em>Oncorhynchus mykiss</em>)", by Adriano C. Lima, Edouard Royer, Matteo Bolzonella, and Roberto Pastres.</p>
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
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 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
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)
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>
Fig. 1 in Survival Of Embryos And Larvae Of The Rainbow Trout (Oncorhynchus Mykiss, Walbaum, 1792) Under Influence Of Optical Radiation At Various Temperature Regimes
Fig. 1. Linear dependencies of the probit (logit) effect of the death of rainbow trout larvae in vitro from the logarithm of days of fasting for various types of optical radiation at a temperature of 12 (a), 11 (b), 10 (c), 9 (d), 8(e) ° C.
Рис. 1. Места отΛовов микижи в Хабаровском крае: 1 — о. БоΛьшой Шантар (попуΛяция рек СреΑняя и ОΛенья); 2 — мыс Δжаоре; 3 — р. Чоме; 4 — устье р. Тумнин; 5 — р. Матвеевка in Kamchatka Rainbow Trout (Salmonidae) At The Boundaries Of The Botchinsky Nature Reserve: Invasion Or New Area Data?
Рис. 1. Места отΛовов микижи в Хабаровском крае: 1 — о. БоΛьшой Шантар (попуΛяция рек СреΑняя и ОΛенья); 2 — мыс Δжаоре; 3 — р. Чоме; 4 — устье р. Тумнин; 5 — р. Матвеевка
Fig. 3 in Call survey indicates rainbow trout farming alters glassfrog community composition in the Andes of Ecuador
Fig. 3. Map of the study area. Inset: Pichincha Province, Ecuador. Main: Blue points indicate non-trout farm sites whereas red points indicate trout farm sites. Yellow line represents the equator (latitude 0).
Fig. 2 in Call survey indicates rainbow trout farming alters glassfrog community composition in the Andes of Ecuador
Fig. 2. Glassfrog species found during surveys. (A) Centrolene heloderma, (B) Centrolene ballux, (C) Esparana prosoblepon, (D) Nymphargus lasgralarias, (E) Centrolene peristictum, (F) Nymphargus grandisonae, (G) Centrolene lynchi, (H) Egg mass from C. ballux. Nymphargus griffithsi was not encountered during the 2017 survey but has been documented at Kathy's creek in 2012 and 2013 (by Jane A. Lyons). Photographs by Dana G. Wessels (A–F) and Timothy J. Krynak (G–H).
Fig. 1 in Call survey indicates rainbow trout farming alters glassfrog community composition in the Andes of Ecuador
Fig. 1. Trout farming in the Mindo region of Ecuador utilizes a flow-through aquaculture technique. Stream water is diverted into tandem raceways/holding reservoirs and then flows through these reservoirs back into the natural stream system. This figure displays a panoramic view of Finca de Jaime's (FJ) set-up. Photograph by Katherine L. Krynak.
Fig. 4 in Call survey indicates rainbow trout farming alters glassfrog community composition in the Andes of Ecuador
Fig. 4. Two-dimensional NMDS ordination of survey sites and glassfrog species based upon presence of frogs audibly documented in 2017 survey conducted in the Mindo region of Ecuador (Stress = 3%). Red points and labels represent glassfrog species; grey points represent trout farms; and black points represent non-trout farms. RSR = Río Santa Rosa, LC = Lucy's Creek, Bcrk = Ballux Creek, KC = Kathy's Creek, M = Michelle's, C = tributary of the Chalguayacu Grande River, 5F = Five Frog Creek, LRSR = Lower Río Santa Rosa, ST = Santa Teresita, FJ = Finca de Jaime, LS = La Sierra, VC = Verdecocha, EP = El Paraíso del Pescador. Trout farms EP, LS, and VC are not included in the analysis because glassfrogs were not observed at these sites. A significant difference in glassfrog community composition between trout farm and non-trout farm sites was indicated by MRPP (delta = 0.59, A = 0.11, P = 0.03). NMDS1 correlated with elevation; NMDS2 correlated with: percent canopy openness, dissolved oxygen (mg/L), total dissolved solids (mg/L), and conductivity (µS).
Trout of Hokkaido data (Rainbow, Brown, Brook, and Sockeye)
<p>This is a data set of 928 presents points (and 3 NA locations) for invasive trout species across Hokkaido for the masters thesis "<strong>Perception of fishermen towards invasive salmonids in Hokkaido and the contribution of citizen science to their long-term monitoring</strong>". It is comprised of Scientific studies, gray literature, YouTube videos, social media sites, blogs, word of mouth, email, and iNaturalist data. Please feel free to use this data for research on these species.</p> <p>Columns are broken up into 10 parts.</p> <p>-------------------------------Columns are--------------------------------</p> <p><strong>Hits</strong>: Hits on the map one per site.</p> <p><strong>Paper/source</strong>: where the study or citizen data came from. (Please feel free to check out the blogs as they update with new data often) The key as follows</p> <p> FLK = Fliker / IG = Instagram / TW = Twitter / WEB = website / YTV = youtube</p> <p><strong>Contributor</strong>: then Name of the citizen sciences contributor. Blogs, Twitter names, Instagram names, Youtube channel names, etc... </p> <p><strong>Xcoord</strong>: the X coordinate</p> <p><strong>Ycoord</strong>: the y coordinate</p> <p><strong>Specie</strong>: one of 4 species denoted as its scientific name</p> <p><strong>Start Date</strong>: When the study or post started collecting data</p> <p><strong>End Date</strong>: When the study or post ended collecting data</p> <p><strong>Science / Citizen</strong>: denotes where the data came from.</p> <p> Broken up into a few groups,</p> <p> <strong>Science</strong>: from scientific source and grey litterture</p> <p> *Science (old) : data was used as a base line for the study</p> <p> <strong>Active</strong>: Citizen data that has been reported during the study period of the study</p> <p> Please go the the iNaturalist link to get that data. </p> <p> <strong> Passive</strong>: Citizen data that came from lots of different places.</p> <p> *Passive(site) : places that are mapped as fishing spots per speceis by fishing shops and tours</p> <p><strong>Number per hit</strong>: reported or counted species per hit point on the map (accuracy is not 100% ensured) </p> <p>Notes-----------------------------------------------------------------------------------------------</p> <p>River points should be close to actual points caught but lake points should not be used for precise data as much of it was not precisely listed and so guess work on location took place.</p> <p> </p>
Dataset for "Diets supplemented with Saccharina latissima influence the expression of genes related to lipid metabolism and oxidative stress modulating rainbow trout (Oncorhynchus mykiss) fillet composition" (doi.org/10.1016/j.fct.2020.111332)
<p>Dataset corresponding to the following article:</p> <p>Ferreira, M., Larsen, B.K., Granby, K., Cunha, S.C., Monteiro, C., Fernandes, J.O., Nunes, M.L., Marques, A., Dias, J., Cunha, I., Castro, L.F.C., Valente, L.M.P., 2020. Diets supplemented with <em>Saccharina latissima </em>influence the expression of genes related to lipid metabolism and oxidative stress modulating rainbow trout (<em>Oncorhynchus mykiss</em>) fillet composition. Food Chem. Toxicol. 140, 111332. <a href="https://doi.org/10.1016/j.fct.2020.111332">https://doi.org/10.1016/j.fct.2020.111332</a></p>
Growth genes are implicated in the evolutionary divergence of sympatric piscivorous and insectivorous rainbow trout (Oncorhynchus mykiss)
<p>Identifying ecologically significant phenotypic traits and the genomic mechanisms that underly them are crucial steps in understanding the traits associated with population divergence. We used genome-wide data to identify genomic regions associated with a key trait that distinguishes two ecotypes of rainbow trout (Oncorhynchus mykiss) – insectivores and piscivores – that coexist in Kootenay Lake, southeastern British Columbia, for the non-breeding portion of the year. "Gerrards" are large-bodied (breeding maturity at >60cm) piscivores that spawn 50km north of Kootenay Lake in the Lardeau River, in contrast to the insectivorous populations that are on average smaller in body size, mainly forage on aquatic insects, and spawn in tributaries immediately surrounding Kootenay Lake. We used pool-seq data covering 60 percent of the genome to assess the level of genomic divergence between ecotypes, test for genotype-phenotype associations, and identify loci that may play functional or selective roles in their divergence. Analysis of nearly seven million SNPs provided a genome-wide mean FST estimate of 0.18, indicating a high level of reproductive isolation between populations. The window-based FST analysis did not reveal "islands" of genomic differentiation; however, the window with highest FST estimate did include a gene associated with insulin secretion. Although we explored the use of the "Local score" approach to identify genomic outlier regions, this method was ultimately not used because simulations revealed a high false discovery rate (20 percent). Gene Ontology (GO) analysis identified several growth processes as enriched in genes occurring in the 200 most divergent genomic windows, indicating the importance of genetically-based growth and growth-related metabolic functions in the divergence of these ecotypes. In spite of their sympatric coexistence, a high degree of genomic differentiation separates the populations of piscivores and insectivores, indicating little to no contemporary genetic exchange between ecotypes. Our results further indicate that the large body piscivorous 27 phenotype is likely not due to one or a few loci of large effect, rather it may be controlled by several loci of small effect, thus highlighting the power of whole-genome low-coverage sequencing in phenotypic association studies.</p>
Plasma NMR metabolomic of rainbow trout fed diets with different levels of marine and plant ingredients.
<p>The NMR and biochemical datasets used in the manuscript draft entiteld "Intestinal microbiota in rainbow trout, <em>Oncorhynchus mykiss</em>, fed diets with different levels of marine and plant ingredients: A correlative approach with some plasma metabolites."</p> <p>François-Joël Gatesoupe1*, Benoît Fauconneau1, Catherine Deborde2,3**, Blandine Madji Hounoum1,2, Daniel Jacob2,3,Annick Moing2,3, Geneviève Corraze1, Françoise Médale1. 1 UMR 1419 NuMeA, INRA, Université de Pau et des Pays de l’Adour, Saint Pée sur Nivelle, France 2 Bordeaux Metabolome Facility, CGFB, MetaboHUB, Centre INRA Nouvelle -Aquitaine-Bordeaux, Villenave d'Ornon, France 3 UMR1332 Biologie du Fruit et Pathologie, Centre INRA Nouvelle -Aquitaine-Bordeaux, Villenave d'Ornon, France<br> *Corresponding author Joel.Gatesoupe@partenaire-exterieur.ifremer.fr</p> <p>**NMR dataset Corresponding author catherine.deborde@inra.fr</p> <p> </p> <p> </p> <p> </p>
Data from: Personality determines population-level effects of microplastics consumption in a modelled population of stream-dwelling rainbow trout (Oncorhynchus mykiss)
<p>Microplastics in freshwater habitats are consumed by fish, including stream-dwelling salmonids, which can alter food consumption or negatively affect swimming and foraging behaviour. As population-level effects are largely unknown, a simulated population of stream-dwelling rainbow trout (<em>Oncorhynchus mykiss</em>) was created using the agent-based model 'inSTREAM 7' to model population-level effects (biomass) of behavioural changes caused by microplastics consumption. Individual fish were assigned all possible combinations of two personality traits (dominance, boldness/shyness), and consumed microplastics while foraging, while their abundance, body size, and microplastics consumption were tracked for three different life stages (fry, juvenile, adult) for a 10-year simulation period. Three additive scenarios were explored: a low-impact scenario with decreased food consumption, a medium-impact scenario with added lower swimming speed, and a high-impact scenario with added reductions in prey capture efficiency. Each was tested with microplastics concentrations of 0%, 1% (i.e., current levels), and 3% (i.e., future levels) of drift food. Overall, microplastics consumption did not strongly affect trout population abundance. Dominant adult trout consumed disproportionally more microplastics than all other fish, especially with higher microplastics concentrations. Different personality types were affected differently in the three scenarios: dominant and bold adults were smaller when food consumption was reduced, shy and subordinate adults were smaller when swimming speed was lowered, and all dominant adults, regardless of boldness, were smaller when foraging efficiency was impeded, with dominant and bold fry also less abundant in this scenario. However, effects on fish body size were only found with microplastic concentrations of 3%, indicating these outcomes can be prevented, as current levels of microplastics pollution are unlikely to affect salmonid body size. Nevertheless, microplastics ingestion represents an additional stressor that may potentially interact with a myriad of anthropogenic impacts that already affect wild salmonid populations.</p>
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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)
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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.