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176 results for “Chinook salmon”
SNP amplicons results of 50 hybrid Chinook-Coho salmon
<p>These SNP panel results confirm the hybrid origin in 50 Chinook-Coho Salmon individuals. The SNP panel is composed of two amplicons and five diagnostic SNPs. DNA amplicons OkiOts_120255 and Oki_RAD41030 have SNP sites fixed for alternate base pairs in Chinook and Coho salmon (Beacham and Wallace 2019). The panel examined genotypes at one diagnostic position in OkiOts_120255 SNP: 113 (Reference=A, Variant=C) and four positions in Oki_RAD41030: 45 (TC), 51(CG), 195 (GA), and 198 (TG) called via Proton software Variant Caller®. The hybrid salmon were heterozygous for a Chinook and Coho haplotype at both SNP loci, confirming these as the parental species involved in the hybridization and consistent with all being F1 or higher order (F2 or back-cross) hybrid individuals. </p> <p>Beacham, T. D. & Wallace, C. G. (2019). Salmon species identification via direct DNA sequencing of single amplicons. <i>Conservation Genetics Resources,</i> 1-7<i>. </i><a href="https://doi.org/10.1007/s12686-o19-01102-1">https://doi.org/10.1007/s12686-o19-01102-1</a>.</p>
Harvest estimates of Chinook and other salmon taken in the non-spawning tributaries of the Johnson, Kialik, Gweek, and Paillek Slough, 2021.
<p>This dataset contains reported and estimated harvests of Chinook salmon taken in 2021 from tributaries of the Kuskokwim River designated as 'Non-spawning'. Information include estimates of households, estimates of salmon harvest, residence of harvest, location of harvest above or below the 100-yard marker indicating the end of legal Kuskokwim river main stem waters.</p>
Single parentage dataset for Chinook salmon
<p>Objective<br>Parentage analysis is a routine methodology in fisheries research, but study systems exist where it is impractical to sample both parents. The ability to reliably assign offspring to a single parent is beneficial in these situations. We apply single-parentage assignments to a naturally spawning population of Chinook Salmon <em>Oncorhynchus tshawytscha</em> to quantify production of anadromous returns by unsampled precocial males.</p> <p>Methods</p> <p>We use an approach that addresses two important aspects of parentage analyses: 1.) addressing the presence of family structure within the sampled parents and 2.) controlling for false-positive and false-negative assignments.</p> <p>Result</p> <p>Results indicate that 30% of reproductively successful males were precocials which produced 20% of the returning anadromous offspring.</p> <p>Conclusion</p> <p>This study provides a framework for applying single-parent assignments in a salmonid study system while explicitly addressing sources of assignment errors.</p>
Supplementary data for: Outmigrating central valley Chinook Salmon
<p>Intraspecific diversity plays a critical role in the resilience of Chinook salmon populations. California's Central Valley historically hosted one of the most diverse population complexes of Chinook salmon in the world. However, anthropogenic factors have dramatically decreased this diversity, with severe consequences for population resilience. Here we use next generation sequencing and an archive of thousands of tissue samples collected across two decades during the juvenile outmigration to evaluate phenotypic diversity between and within populations of Central Valley Chinook salmon. To account for highly heterogeneous sample qualities in the archive dataset, we develop and test an approach for population and subpopulation assignments of Central Valley Chinook salmon that allows inclusion of relatively low-quality samples while controlling error rates. We find significantly distinct outmigration timing and body size distributions for each population and subpopulation. Within the archive dataset, spring run individuals that assigned to the Mill and Deer Creeks subpopulation exhibited an earlier and broader outmigration distribution as well as larger body sizes than individuals that assigned to the Butte Creek subpopulation. Within the fall run population, individuals that assigned to the late-fall run subpopulation also exhibited an earlier and broader outmigration distribution and larger body sizes than other fall run fish in our dataset. These results highlight the importance of distinct subpopulations for maintaining remaining diversity in Central Valley Chinook salmon, and demonstrates the power of genomics-based population assignments to aid the study and management of intraspecific diversity.</p>
Building Habitat Resiliency for Chinook Salmon in Alaska's Deshka River Watershed - thermal imagery shape files
<p>Cook Inletkeeper contracted NV5 Geospatial (formerly, Quantum Spatial Incorporated) to collect thermal infrared (TIR) during the summer of 2020 for the main channel of Deshka River in the Matanuska-Susitna Borough in Alaska. This section of Deshka River was contracted to be flown at the beginning of the summer and during the afternoon hours in order to maximize the thermal contrast between the river’s water and the banks. The survey extends for 52 km / 32 miles of the Deshka River starting from the confluence of Moose and Kroto Creeks upstream and ending at the confluence with the Susitna River. The data were collected to aid the Cook Inletkeeper team to identify the spatial variability in surface temperatures as well as thermal influence of point sources, tributaries, and surface springs. The data will also be used to identify high-value habitats for the Deshka River chinook salmon population.</p> <p>Note: These data and related items of information have not been formally disseminated by NOAA and do not represent any agency determination, view, or policy.</p> <p>Funding for this project came, in part, from the Alaska Sustainable Salmon Fund (AKSSF Project #53004).</p>
Mitochondrial DNA assay of 63 Chinook-Coho salmon hybrids
<p>Mitochondrial DNA sequences can identify the maternal species involved in hybridization events and provide behavioural clues of the matings. In this study, Mitochondrial DNA indicated hybrids were the offspring of female Coho salmon spawning with Chinook salmon males (all but two individuals from a reciprocal cross). This finding suggested two possible scenarios: accidental fertilization in crowded spawning grounds or heterospecific choice of mate when conspecifics were not available (e.g. differential abundance).</p>
Alaska Sustainable Salmon Fund Project #52002: Climate warming effects on Chinook Salmon foraging conditions and growth
<p>The Chena River hosts one of the largest populations of Chinook Salmon in the Alaska portion of the Yukon River drainage, which has recently experienced poor Chinook returns throughout. Past work suggests that these fish do poorly when they grow slowly due to cold, high-flow conditions during their first summer in the river as juveniles, and the population does well when juveniles experience warm, low-flow years and grow larger. Because high flow drives low water temperatures and vice versa, it was previously unclear to what extent each factor—flow and temperature—affects the fish population.</p> <p>We collected data to run foraging and bioenergetics models that simulate how flow and temperature affect growth. We invented two sampling devices, a suction pump to sample drifting prey and a computer vision system to measure the inedible debris that occupy most of a fish's feeding effort. We combined our data with USGS and NOAA records to predict temperature, turbidity, prey, and debris on a daily basis throughout our study years (2019-2020) and others.</p> <p>This dataset contains the data we collected and compiled from other sources on fish growth, temperature, invertebrate drift, and drifting debris.</p>
Data from: A correlation between seasonally changing photoperiod, whole body lipid, and condition factor in juvenile spring Chinook Salmon (Oncorhynchus tshawytscha)
<p><span></span></p> <p>The regulation of lipid stores is a central process for the physiology and ecology of fishes. Seasonal variation in lipid stores has been directly linked to survival of fishes across periods of food deprivation. We assessed whether a seasonally changing photoperiod was correlated to seasonal changes in energetic status to help better understand these important processes. Groups of first-feeding Chinook salmon fry were introduced to a seasonal photoperiod cycle, but the point of entrance into the seasonal cycle varied from near the winter solstice (December), to either side of the spring equinox (February & May). Temperature and feeding rate were similar for all treatments. Subsequently, condition factor and whole-body lipid content were assessed through a seasonal progression. Throughout most of the experiment, length and weight did not differ between the different photoperiod treatments, however whole body lipid and Fulton's condition factor did. Furthermore, changes in both whole body lipid and Fulton's condition factor in all treatment groups followed a similar seasonal pattern that was inversely related to day length (highest K and lipid levels found during days with the least light). These results suggest that regardless of age or size, there is a correlation between seasonal changes in photoperiod and changes in body composition in juvenile Chinook salmonids.</p>
Data from: Contemporary distribution of non-native Chinook salmon (Oncorhynchus tshawytscha) in South America
<p class="MsoNormal"><span>The dataset incorporates information on Chinook salmon occurrences by basin in South America, which was obtained from the literature and from unpublished information obtained from research monitoring efforts conducted in Chile, Argentina, and Uruguay. The information was divided into two periods: historical (prior to 2006) and contemporary information (2006 onwards). Year or range of years in which the observation was taken was also included. This dataset was used to construct Fig. 1 of the manuscript "<span class="fontstyle0">Contemporary distribution of non-native Chinook salmon (</span><em><span class="fontstyle2">Oncorhynchus tshawytscha</span></em><span class="fontstyle0">) in South America</span>".</span></p>
Associated model data for: Size-selective predation effects on juvenile Chinook salmon cohort survival off Central California evaluated with an individual-based model
<p><span>T</span>his dataset corresponds to the paper "Size-selective predation effects on juvenile Chinook salmon cohort survival off Central California evaluated with an individual-based model" which is in press at Fisheries Oceanography. The abstract for this paper is as follows: </p> <p>Variation in the recruitment of salmon is often found to be correlated with marine climate indices, but mechanisms behind environment-recruitment relationships remain unclear and correlations often break down over time. We used an ecosystem modeling approach to explore bottom-up and top-down mechanisms linking a variable environment to salmon recruitment variations. Our ecosystem model incorporates a regional ocean circulation sub-model for hydrodynamics, a nutrient-phytoplankton-zooplankton sub-model for producing planktonic prey fields, and an individual-based model (IBM) representing juvenile Chinook salmon (<em>Oncorhynchus</em> <em>tshawytscha</em>), combined with observations of foraging distributions and diet of a seabird predator. The salmon IBM consists of modules, including a juvenile salmon growth module based on temperature and salmon-prey availability, a behavior-based movement module, and a juvenile salmon predation mortality module based on juvenile salmon size distribution and predator-prey interaction probability. Seabird-salmon interactions depend on spatial overlap and juvenile salmon size, whereby salmon that grow past the size range of the prey distribution of the predator will escape predation. We used a 21-year historical simulation to explore interannual variability in juvenile Chinook salmon growth and predation-mediated survival under a range of ocean conditions for sized-based mortality scenarios. We based a series of increasingly complex predation scenarios on seabird observational data to explore variability in predation mortality on juvenile Chinook salmon. We initially included information about the predator spatial distribution, then added population size, and finally, the predator's diet percentage made up of juvenile salmon. Model agreement improves with added predator complexity, especially during periods when predator abundance is high. Overall, our model found that when the fraction of juvenile salmon in seabird diet increased relative to alternate prey (e.g., Northern anchovy <em>Engraulis</em> <em>mordax</em>, and juvenile rockfish <em>Sebastes</em> spp.), there was a concomitant decrease in salmon cohort survival during their first year at sea.</p>
Intraspecific variation among Chinook salmon populations indicates physiological adaptation to local environmental conditions
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Population variability in thermal performance of pre-spawning adult Chinook salmon
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Heritability and genomic basis of age-at-maturity in Chinook Salmon
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Rearing environment affects the genetic architecture and plasticity of DNA methylation in Chinook salmon
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Single parentage dataset for Chinook salmon
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Alaska Sustainable Salmon Fund Project #52002: Climate warming effects on Chinook Salmon foraging conditions and growth
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Supplementary data for: Outmigrating central valley Chinook Salmon
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Exposure to exogenous egg cortisol does not rescue juvenile Chinook salmon body size, condition, or survival from the effects of elevated water temperatures
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Inter-method differences (SIMS vs. IRMS) in oxygen isotope fractionation: Insights from Chinook salmon otoliths
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Data from: Evaluation of a single nucleotide polymorphism baseline for genetic stock identification of Chinook Salmon (Oncorhynchus tshawytscha) in the California Current Large Marine Ecosystem
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