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1,025 results for “salmon”
Compiled datasets and R codes for enzymatic activities in Atlantic salmon tissues
<p>Folder with two datasets of enzyme activities (CS and LDH) with associated details of fish, incuding genotypes, body size, and metabolic rates, and R codes for linear mixed models as described in the manuscript Prokkola et al (submitted 2023). See README file for more information.</p>
Data: Methods for tagging an ectoparasite, the salmon louse Lepeophtheirus salmonis
<p>Monitoring individuals within populations is a cornerstone in evolutionary ecology, yet<span> </span>individual tracking of invertebrates and particularly parasitic organisms remains rare. To address this gap, we describe here a method for attaching radio frequency identification<span> </span>(RFID) tags to individual adult females of a marine ectoparasite, the salmon louse<span> </span><em><span>Lepeophtheirus salmonis</span></em>. Comparing two alternative types of glue, we found that one of them<span> </span>(2-octyl cyanoacrylate, <em><span>2oc</span></em>) gave a significantly higher tag retention rate than the other (ethyl<span> </span>2-cyanoacrylate, <em><span>e2c</span></em>). This glue comparison test also resulted in a higher loss rate of adult ectoparasites from the population where tagging was done using <em><span>2oc</span></em>, but this included males<span> </span>not tagged and thus could also suggest a mere tank effect. Corroborating this, a more extensive analysis using data collected over two years showed no significant difference in<span> </span>mortality after repeated exposure to the <em><span>2oc </span></em>glue, nor did it show any significant effect of the<span> </span>tagging procedure on the reproduction of female salmon lice. The proportion of RFID-tagged<span> </span>individuals followed a negative exponential decline, with tag retention among the living<span> </span>female population generally high. The projected retention was found to be about 88% after<span> </span>30 days or 80% after 60 days, although one of the four batches of glue used, purchased from<span> </span>a different supplier, appeared to give significantly lower tag retention and with greater initial<span> </span>loss (74% and 60% respectively). Overall, we find that RFID tagging is a simple and effective technology that enables documenting individual life histories for invertebrates of a suitable size, including marine and parasitic species, and that it can be used over long periods of study.</p>
Pacific salmon population time-series dataset to support Appendix S1: Data and additional information on declines of Pacific Salmon
<p>Dataset used to support the main paper 'Protecting our coast for everyone’s future: Indigenous and scientific knowledge support marine spatial protections proposed by Central Coast First Nations in Pacific Canada' by Reid et al. 2022. Dataset cited in Appendix S1 regarding trends in adult salmon abundances in the Central Coast. The data were as compiled by Will Atlas from the <a href="https://wildsalmoncenter.org/">Wild Salmon Center</a> to describe trends in the abundance of adult salmon returning to the Central Coast, which is the sum of escapement and harvest, as derived from the following sources:</p> <ol> <li>Escapement data from DFO: <a href="https://open.canada.ca/data/en/dataset/c48669a3-045b-400d-b730-48aafe8c5ee6">NuSEDS-New Salmon Escapement Database System - Open Government Portal (canada.ca)</a></li> <li>Harvest rates estimated by Karl English and colleagues and available at: <a href="https://data.salmonwatersheds.ca/data-library/">Salmon Watersheds Program - Data Library</a>.</li> <li>Information on total harvest that is reported in the DFO post season review (DFO 2020).</li> </ol>
Data from randomized control trials released hatchery salmon treated with anti-parasitic treatment
<p>Data used in the article "<strong>Parasite spillback from fish farms reduce return rate of wild salmon"</strong></p> <p> </p> <p>Each release group has been used as a randomized control trials (RCT) of hatchery reared salmon smolts where half of the fish has been treated with an antiparasitic drug. Description of this method has been given in various other publications (Vollset et al. 2014, Vollset et al 2016, Skilbrei et al. 2013). The method involves rearing salmon eggs originating from the national Gene Bank to smolt size in hatchery facilities during one year, and then treating the salmon smolts with fish feed pellets coated with emamectin benzoate (SLICE®). These fish are then released into the river or transported in tanks or mobile net pens further out in the fjord before release. The fish are tagged with either coded-wire-tags (CWT; years 2000-2017) or Passive Integrated Transponders (PIT; 2015-2019) so that it is possible to identify them as they are recaptured or registered on an antenna upon their return as adults. In a few trials, another antiparasitic treatment (Substance EX) has been used, but in most cases the EB has been the only available treatment. Releases of hatchery reared salmon in freshwater have not been successful in this system, i.e. very few fish have returned from any group released in the river, lakes or estuary of Vosso. Since the release groups are also a part of a restoration effort of the Vosso salmon, some years fish have only been released in the fjord. There has been some variation in the release sites in the fjords, but for the purpose of this study we group the release groups in either group that has been released in the outer fjord (70-105 km from the river mouth) and the inner fjord (15-70 km from the river mouth), and freshwater (approx -10 to 15 km from the river mouth). The two most prevalent locations are at Manger (WGS84; 60.63918, 4.92149) and Arna (WGS84; 60.50812, 5.37777).</p> <p> </p> <p><em>Sea lice surveillance</em></p> <p> </p> <p>Sea lice surveillance on sea trout has been conducted at Herdla, the northern peninsula of the island Askøy (WGS84; 60.568972, 4.963010) since 2009. Here, trout have been caught using a trap net that has been developed specifically to capture and treat trout while minimizing sea lice loss during handling (Barlup et al. 2013). From an earlier study by Vollset et al. (2018), it has been shown that the lice numbers on sea trout on this site correlate with the infestation pressure of fish farms in the outer region of the fjord. This area is also one of the largest fish farm zones with coordinated production and fallowing in the outer fjord system where all the released salmon smolts must migrate (see Vollset et al. 2018). This is also the area where surface salinity layers permit salmon lice to overlap with out-migrating salmon smolts (Vollset et al. 2016).</p> <p> </p> <p>The number of trout caught during the monitoring season has varied with weather conditions, sampling intensity, and number of traps operated. The way that trout are handled is described in more detail in Vollset et al. (2018), but in brief, the trap chambers are checked daily, and individual trout are transferred from the trap using a hand held dip net and are either euthanized and placed in zip-lock bag or transported in a large bucket with aerated water to land. Euthanized samples are kept cold and frozen when at land, and later thawed and counted in the lab, while live samples are counted after being sedated with half dose (0.05 g/L) of MS222 and then assessed for salmon lice in a high-contrast bucket using a headlamp by trained personnel. Since 2015 the sea lice surveillance at Herdla is also operated as a part of the Norwegian national sea lice monitoring program.</p> <p>We aimed to use a standardized time period from which to assess sea lice numbers on sea trout that can be representative of the lice infestation pressure from when the tagged hatchery salmon smolts are released. When counting sea lice on sea trout, the most observable lice are large chalimus and mobile stages, while recently attached copepods are more likely to be missed. Therefore, we use total lice counts on sea trout from Julian day 135 to 165 as an assessment of the infestation pressure the salmon smolts must experience. This corresponds to approximately 15 May to 15 of June, and is based on a study on progression rate of salmon smolts from hatchery smolt in this area (Vollset et al. 2016). To account for the fact that larger fish will attract more parasites, we use parasites per gram fish per individual and average data to get one index per year. This method is expected to provide a fair index of interannual variation of the infestation pressure.</p> <p> </p> <p>Table 1 Description of column names in csv file</p> <table> <tbody> <tr> <td>Name</td> <td>Description</td> </tr> <tr> <td>release_year</td> <td>Year of release as smolts</td> </tr> <tr> <td>release_place</td> <td>Name of release place location</td> </tr> <tr> <td>release_date</td> <td>Date of release as smolts</td> </tr> <tr> <td>Released</td> <td>Number of hatchery smolt released</td> </tr> <tr> <td>Recaptured</td> <td>Number of hatchery smolt recaptured as adults</td> </tr> <tr> <td>treat</td> <td>Treatment (either treatment or control)</td> </tr> <tr> <td>tag</td> <td>Tag type (either CWT or PIT)</td> </tr> <tr> <td>release_category</td> <td>Release place (either river, outer fjord or inner fjord)</td> </tr> <tr> <td>lpg</td> <td>Lice per gram fish on trout during surveillance from 15 of May to 15 of June the year of release</td> </tr> <tr> <td>pr</td> <td>Percent (%) recaptures as adults</td> </tr> </tbody> </table> <p> </p>
Modelled hydrodynamic profiles and salmon louse larval densities at Norwegian salmon farms
<p>Data compiled for use by the PreventLice web app, a decision support tool intended to help Norwegian salmon farmers avoid salmon louse infestations: <a href="https://havforskningsinstituttet.shinyapps.io/preventlice">https://havforskningsinstituttet.shinyapps.io/preventlice</a></p> <p>Each file contains the relevant data for a registered salmonid farm in Norway, identified by its locality number according to the Norwegian <a href="https://sikker.fiskeridir.no/akvakulturregisteret/web/sites">Aquaculture Registry</a>. A total of 1023 localities are included in version 1.0.0.</p> <p>The data are in long rectangular format, with each row corresponding to a single depth interval on a single date. Each row provides variables for locality number ("loc"), date ("date"), depth (m, "depth"), daily mean temperature (°C, "meanTemp"), daily mean salinity (ppt, "meanSal"), daily mean current speed (ms<sup>-1</sup>, "meanCurrSpd"), daily 95th percentile current speed (ms<sup>-1</sup>, "95PercCurrSpd"), daily salmon louse infestation pressure (copepodids m<sup>-3</sup>, "meanCopDensity"), and daily mean significant wave height (m, "SignWaveHeight").</p> <p>Temperature, salinity and current speeds are taken from the NorFjords-160 model (<a href="https://doi.org/10.1016/j.ecss.2020.107028">Dalsøren et al. 2020</a>), a finer-scale update of the NorKyst-800 model (<a href="https://doi.org/10.1007/s10236-020-01378-0">Asplin et al. 2020</a>). Wave height data are taken from the MyWaveWAM800m Norwegian coastal wave forecasting system (<a href="https://thredds.met.no/thredds/fou-hi/mywavewam800.html">Norwegian Meteorological Institute</a>). Salmon louse copepodid densities are estimated by coupling louse biology and behaviour parameters with hydrodynamic predictions from NorKyst-800 (<a href="https://doi.org/10.1371/journal.pone.0201338">Myksvoll et al. 2018</a>).</p>
High-resolution surface wind observations over complex terrain: Big Southern Butte, Salmon River Canyon, Birch Creek
<p>This dataset contains high-resolution wind observations from three field campaigns that took place during 2010-2014 at Big Southern Butte, Salmon River Canyon, and Birch Creek, Idaho. There are three SQLite databases containing 30-s averaged 3-m wind speed, wind direction, and wind gust data from 30-90 cup-and-vane anemometers over a period of 2-4 months at each field site.</p>
Pink salmon smolt survey in Iceland in 2022
<p>This dataset was created during the PinkSIES project. It consists of data collected during a fishing survey of pink salmon juveniles in Iceland in mid-May 2022 with measurements of fork length and wet mass of a subsample of fish captured. The juveniles were kept frozen in plastic bags before measurements. At the lab, the thawed fish were measured in length (to the nearest mm below) and weight to 1 mg.</p> <p>The data have been already published in a paper in the <em>Journal of Fish Biology</em> with open access (<strong>Evidence of successful recruitment of non-native pink salmon <em>Oncorhynchus gorbuscha</em> in Iceland</strong>; https://onlinelibrary.wiley.com/doi/10.1111/jfb.15556).<br> <br> The authors kindly request to cite the above paper, if you want to reuse the data. <br> <br> This project has received funding from the European Union’s Horizon 2020 Research and Innovation Programme under the Marie Skłodowska-Curie grant agreement No 101026030</p>
Salmon Creek radon data
Open the record for dataset details and reuse information.
Illuminating the planktonic stages of salmon lice: a unique fluorescence signal for rapid identification of a rare copepod in zooplankton assemblages.
<p>The Excitation Emission Matrix (EEM) measurements were taken with Shimadzu's proprietary software ‘LabSolutions RF’. All files are in the exported csv format with columns representing the excitation wavelengths and rows the emission wavelengths. Wavelengths range from 200-600 nm with a 2 nm increment. Fluorescence intensity was influenced by the fluctuating number of animals in the path of the excitation beam during the 5 minute measurement. We compensated for this artefact by repeating measurements of each sample five times, calculating the mean, and applying a smoothing function which found the median value within 10 nm. The fluorescence intensity was further normalized on a 0 to 1 scale by dividing intensity by the maximum fluorescence within each EEM measurement.</p> <p>Supplemental Table 1. The metadata of EEM measurements. The measurements were used for the spectrum section analysis and correspond to those depicted in Figures 2, 3, 4, & 5. See sections 3.1, 3.1.1, & 3.1.2. The Sample column indicates which lab culture cohort the sea lice came from (BGO*), which wild caught fish sample they came from (WC*), or the sampling date of non-target copepods (DDMMYY). The filename of each mean measurement is listed and indicates the first of 5 repeated measurements. Corresponding files can be found in the deposited.csv files at Zendo. In those files, data columns represent the excitation wavelengths, 200nm to 600nm increasing in 2 nm increments. Likewise, the rows represent the emission wavelengths. NaN’s are present where scattering layers were removed. All fluorescence intensity values are normalized to the maximum within each EEM.</p>
Differentiation of human monocytes into macrophages (RNA-seq, Salmon 1.4.0, GENCODE 36)
<p>RNA-seq of differentiation of human monocytes into macrophages as described in:</p> <p>Phanstiel et al "Static and Dynamic DNA Loops form AP-1-Bound Activation Hubs during Macrophage Development" Molecular Cell, Volume 67, Issue 6, 2017, Pages 1037-1048.e6.</p> <p>https://doi.org/10.1016/j.molcel.2017.08.006</p> <p>See publication for full author list.</p> <p>Data from publication was reprocessed by Michael Love. Paired end reads were quantified with Salmon 1.4.0 and GENCODE 36 human transcripts.</p>
Time spent in distinct life-history stages has sex-specific effects on reproductive fitness in wild Atlantic salmon
<p><span>In species with complex life cycles, life history theory predicts that fitness is affected by conditions encountered in previous life history stages. Here, we use a four-year pedigree to investigate if time spent in two distinct life history stages has sex-specific reproductive fitness consequences in anadromous Atlantic salmon (<i>Salmo salar</i>). We determined the amount of years spent in fresh water as juveniles (freshwater age, FW, measured in years), and years spent in the marine environment as adults (sea age, SW, measured in sea winters) on 264 sexually mature adults collected on a river spawning ground. We then estimated reproductive fitness as the number of offspring (reproductive success) and the number of mates (mating success) using genetic parentage analysis (>5000 offspring). Sea age is significantly and positively correlated with reproductive and mating success of both sexes whereby older and larger individuals gained the highest reproductive fitness benefits (females: 62.2% increase in offspring/SW and 34.8% increase in mate number/SW; males: 201.9% offspring/SW and 60.3% mates/SW). Younger freshwater age was significantly related to older sea age and thus increased reproductive fitness, but only among females (females: -33.9% offspring/FW and -32.4% mates/FW). This result implies that females can obtain higher reproductive fitness by transitioning to the marine environment earlier. In contrast, male mating and reproductive success was unaffected by freshwater age and more males returned at a younger age than females despite the reproductive fitness advantage of later sea age maturation. Our results show that the timing of transitions between juvenile and adult phases has a sex-specific consequence on female reproductive fitness, demonstrating a life-history trade-off between maturation and reproduction in wild Atlantic salmon.</span></p>
Autopolyploidy Genome Duplication Preserves Other Ancient Genome Duplications in Atlantic Salmon (Salmo salar) Supplementary Datasets
<p>For various species, alignments were found between a protein database (produced from Zebrafish) and the sequenced genome of that species. Using Perl scripts and the alignments, gene models were identified in the various species based on the protein sequences. </p> <ul> <li>The gene models, for the various species, can be found in the .gff3 files. Some of the .gff3 files have had ribosomal proteins removed. </li> <li>Homeologous regions were then identified using Perl scripts and can be found in .gff3 files as well. They have Homeologous_Regions.gff3 in their title. </li> <li>Homeologous genes in these regions were counted (named XX_XX_Homeologous_Regions.txt), and compared to all of the genes (not just homeologous genes) in these regions (named Gene_Count_Homeolgous_XX_XX_XX.txt) to find the density. </li> <li>Homeologous gene sequences were compared to each other to identify the Ps values between them using a program called SNAP (Files with _Homeologous_region_analysis_version_1.2.txt at the end). </li> <li>The analyses of these files are summarized in "Pn_Ps_Values_Vertebrate_Homeologous_Regions.ods." </li> <li>The synteny between species can be found in the files with .seg extensions (These can be opened in IGV). </li> <li>A comparison between the gene density and Ps value for each homeologous region can be found in the file, "Gene_Density_Compared_to_Ps_Values.ods."</li> </ul> <p>Included is an extended readme file and Perl scripts (.pl extension) in a compressed file (Final_Scripts.tar.gz).</p>
Empirical data on growth and residency of juvenile Pacific salmon in North America estuaries
<p>Dataset compiling empirical data on estuarine growth and residency of Pacific salmon in North America. We conducted a systematic literature review to create this database, starting with a literature search in <i>Web of Science Core Collection</i> through Simon Fraser University's library proxy on April 24th, 2018, using the search parameters (salmon, Oncorhynchus) AND (estuary*) AND (residen* OR growth OR survival OR mortality), which returned 681 results (these results were presented in Arbeider 2018). We updated the search on March 29th, 2020, which produced 24 additional papers published after April 2018, and again on July 7th, 2022 which yielded another 31 papers published since March 2020. From these results, we extracted papers that research Pacific salmonids and whose study estuary was in North America. From this reduced list of papers, we extracted growth and residency parameters, as well as other relevant data. For complete methods please refer to:</p><p>Arbeider, M. et al. (In press). The estuarine growth and residency of juvenile Pacific salmon in North America: a compilation of empirical data. <i>Canadian Journal of Fisheries and Aquatic Sciences.</i></p>
Reproductive success of hatchery- and natural-spawning sockeye salmon, Auke Creek, Alaska
<p>Evaluating salmon hatchery supplementation programs requires assessing not only program objectives but identifying potential risks to wild populations as well. Such evaluations can be hampered by difficulty in distinguishing between hatchery- and wild-born returning adults. Here, we conducted three years (2011–2013) of experimental hatchery supplementation of sockeye salmon in Auke Lake, Juneau, Alaska where a permanent weir allows sampling and genotyping of every returning adult (2008–2019). We identified both hatchery- and wild-born returning adults with parentage assignment, quantified the productivity (adult offspring/spawner) of hatchery spawners relative to that of wild spawners, and compared run timing, age, and size at age between hatchery- and wild-born adults. Hatchery-spawning females produced approximately six to 50 times more returning adults than did naturally spawning females. Supplementation had no discernable effect on run timing and limited consequences for size at age, but we observed a distinct shift to younger age at maturity in the hatchery-born individuals in all three brood years. The shift appeared to be driven by hatchery-born fish being more likely to emigrate after one, rather than two, years in the lake but the cause is unknown. In cases when spawning or incubation habitat is limiting sockeye salmon production, hatchery supplementation can be effective for enhancing the number of returning adult fish but not without the risk of phenotypic change in the recipient population, which can be an undesired outcome of hatchery supplementation. This study adds to a growing body of evidence suggesting that phenotypic change within a single generation of captive spawning might be widespread in salmon hatchery programs.</p>
F I G U R E 6 in Variation in the post-smolt growth pattern of wild one sea-winter salmon (Salmo salar L.), and its linkage to surface warming in the eastern North Atlantic Ocean
F I G U R E 6 Back-calculated mean body length (±95% confidence interval) of Salmo salar at the midpoint of the winter annulus, following the conclusion of the post-smolt growth period
F I G U R E 1 in Variation in the post-smolt growth pattern of wild one sea-winter salmon (Salmo salar L.), and its linkage to surface warming in the eastern North Atlantic Ocean
F I G U R E 1 Hierarchical cluster analysis of intercirculus spacing for scales of Salmo salar. (a) The dendrogram for k = 20 using Euclidean distance and Ward linkage for z-scored and interpolated data. The five major sub-branches (A–E) and the 20 clusters are ordered sequentially from the left. (b) The standardized intercirculus spacing plots for the 20 clusters. Clusters are colour-coded and ordered as in (a). The LOESS fits for each cluster are shown as a black line and the number of fish per cluster (n) is also shown
F I G U R E 2 in Variation in the post-smolt growth pattern of wild one sea-winter salmon (Salmo salar L.), and its linkage to surface warming in the eastern North Atlantic Ocean
F I G U R E 2 Tabulation of significant under- and over-representation of the 10 most frequent growth pattern categories (and "Others") for Salmo salar scales amongst the 20 dendrogram clusters. Proportions of growth pattern frequency were compared to the overall population proportion of scales for k = 20 with Ward linkage, and clustering of the z-scored and interpolated data. Light shading (−) indicates significant under-representation and dark shading (+) indicates over-representation. Sample sizes (n) for each growth pattern across the time-series are shown
FIGURE 8 in Effects of repeated anaesthesia on gill and general health of Atlantic salmon, Salmo salar
FIGURE 8 Seven Box plot of median (), 25th and 75th percentiles (), range () and outlier () leukocytes counts of whole blood smears from Salmo salar given single (n = 10) or repeated (n = 30) exposure to the anaesthetics MS-222 (80 mg l−1), metomidate (12.5 mg l−1) and AQUI-S (17 mg l−1). (a) lymphocytes; (b) thrombocytes; (c) neutrophils, (d) monocytes. *, P <0.05
FIGURE 7 in Effects of repeated anaesthesia on gill and general health of Atlantic salmon, Salmo salar
FIGURE 7 Box plot of median (), 25th and 75th percentiles (), range () and outlier () glucose concentrations of plasma from Salmo salar after single (n = 10) or repeat exposure (n = 30) to the anaesthetics MS-222 (80 mg l−1), metomidate (12.5 mg l−1) and AQUI-S (17 mg l−1). No significant differences were found using a Van der Waerden test
FIGURE 4 in Effects of repeated anaesthesia on gill and general health of Atlantic salmon, Salmo salar
FIGURE 4 Mean (+SE) accumulation of anaesthetics MS-222, metomidate and AQUI-S in muscle tissue of Salmo salar, as detected by liquid chromatography mass spectrometry. Repeated exposure groups were anaesthetized to Stage III Plane 1 at seven timepoints every four days (Figure 1), followed by a lethal dose of anaesthetic at day 28. Single exposure groups were left undisturbed throughout the experiment, until day 28 and then treated with a lethal dose of anaesthetic. No significant differences were found between single and repeated doses of respective anaesthetics () Single, and () Repeated
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Allen Brain Atlas
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DANDI Archive for NWB datasets
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International Brain Laboratory public data
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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.