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176 results for “Chinook salmon”
Copper River, Alaska, Chinook Salmon Inriver Abundance Estimate 2018-2021 DATA ARCHIVE
<p>Long-term monitoring of returning adult Chinook salmon (<em>Oncorhynchus tshawytscha</em>) abundance on the Copper River, AK, has been conducted using fishwheels and two-sample mark-recapture methods since 2003. This data archive is from from the 2018-2021 field seasons. The annual objective was to estimate the inriver abundance of Copper River Chinook salmon such that the estimate was within 25% of the true abundance 95% of the time. This data represents annual catch, bycatch, tagging site data, recapture site data, session data, QC check tables, CPUE, mark-recapture matrix, mark-recapture stratification tables, effort, and daily catch matrix. </p> <p>See annual report for methodology, analyses and results @ http://akssf.org/default.aspx?id=3477 or contact the Alaska Sustainable Salmon Fund or U.S. Fish and Wildlife Service Office of Subsistence Management Fisheries Resource Monitoring Program or Native Village of Eyak DENR. </p> <p> </p>
Tagging and tracking information for radiotagged Chinook Salmon in the Copper River, Alaska 2021
<p>The first worksheet (2021 Raw Data) consists of each radiotagged fish and its relevant information including date of capture, the frequency and code of the transmitter, length (MEF) and age. Subsequent columns are Julian dates when they passed fixed tracking stations. The final 4 columns are fate columns. The last column is a general description of the general fate of each fish.</p> <p> </p> <p>The final worksheet (2021 summary) summarizes fates of all fish by tagging date. This is the primary input file for the Program R which has a code written to do the data analyses for this study.</p>
A large dataset of detection and submeter-accurate 3-D trajectories of juvenile Chinook salmon
<p>Acoustic telemetry has been used extensively to study the behavior of aquatic animals. The Juvenile Salmon Acoustic Telemetry System (JSATS) is one such system; it was developed for studying juvenile salmonids but has been used to study numerous species. A recent innovation of the JSATS system is an injectable acoustic transmitter that is small enough to be implanted through injection instead of surgery. Use of the JSATS system involves deploying cabled acoustic receivers at hydroelectric dams and autonomous acoustic receivers in free-flowing sections of a river. The raw detections from acoustic-tagged fish are processed to remove potential false positives. The clean detections (5,147,996 total) are used to generate detection events and to compute 3-D trajectories (403,900 total), which are used to assign fish to a passage route through a dam. Controlled field testing involving a high-accuracy Global Positioning System receiver is done to validate the submeter accuracy of the trajectories. The JSATS dataset could be reused for expanding the understanding of near-dam fish behavior.</p>
Tagging and tracking information for radiotagged Chinook Salmon in the Copper River, Alaska, 2019 and 2020.
<p>This is a 2 year data set that summarizes the information collected for a study funded by the Alaska Sustainable Salmon Fund (AKSSF), project number 52004. Data was collected on Chinook Salmon in the Copper River by the Alaska Department of Fish and Game, Sport Fish Division and the Native Village of Eyak. The data set includes the following information on Chinook Salmon: tagging date, radio tag frequency and code, length of fish, age of fish and then the date each fish passed a series of fixed tracking stations along the Copper River, expressed as Julian dates. Below is the citation for the study plan which details the methodology including tagging location and placement of the fixed-tracking stations.</p> <p>Schwanke, C. J. 2019. Run timing and spawning distribution of Copper River Chinook salmon. Alaska Department<br> of Fish and Game, Regional Operational Plan ROP.SF.3F.2019.04, Fairbanks.</p> <p>http://www.adfg.alaska.gov/FedAidPDFs/ROP.SF.3F.2019.04.pdf</p>
Data from: Patterns of sperm swimming behaviour depend on male mating tactic and spawning environment in chinook salmon
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Juvenile life history, migration, and habitat use of natural- versus hatchery-origin Chinook salmon
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Identification of infectious agents in early marine Chinook and Coho salmon associated with cohort survival
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Body size and early marine conditions drive changes in Chinook salmon productivity across northern latitude ecosystems
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Subyearling Chinook salmon diets in Lower Columbia River estuarine habitats
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A large dataset of detection and submeter-accurate 3-D trajectories of juvenile Chinook salmon
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Redwood Creek Chinook salmon life cycle model code and data
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Data from: A synthesis of the coast-wide decline in survival of west coast Chinook salmon (Oncorhynchus tshawytscha, Salmonidae)
<p>We collated smolt-to-adult return rate (SAR) data for Chinook salmon from all available regions of the Pacific coast of North America to examine the large-scale patterns of salmon survival. For consistency, our analyses primarily used coded wire tag-based (CWT) SAR estimates. Survival collapsed over the past half century by roughly a factor of three to ca. 1% for many regions. Within the Columbia River, the SARs of Snake River populations, often singled out as exemplars of poor survival, are unexceptional and in fact higher than estimates reported from many other regions of the west coast lacking dams. Given the seemingly congruent decline in SARs to similar levels, the notion that contemporary survival is driven primarily by broader oceanic factors rather than local factors should be considered. Ambitious Columbia River rebuilding targets may be unachievable because other regions with nearly pristine freshwater conditions, such as SE Alaska and northern BC, also largely fail to reach these levels. Passive integrated transponder (PIT) tag-based SAR estimates available for Columbia River basin populations are generally consistent with CWT findings; however, PIT tag-based SARs are not adjusted for harvest which compromises their intended use because harvest rates are large and variable. More attention is needed on how SARs should be quantified and how rebuilding targets are defined. We call for a systematic review by funding agencies to assess consistency and comparability of the SAR data generated and to further assess the implications of survival falling to similar levels in most regions of the west coast.</p>
Data from: Overlap of spatial and temporal spawning distributions of spring and summer Chinook Salmon results in hybridization in the upper Columbia River
<p>The upper Columbia River in Washington State (main-stem and tributary habitat between McNary and Chief Joseph dams) is inhabited by two major lineages of Chinook Salmon (<i>Oncorhynchus tshawytscha</i>); endangered spring Chinook Salmon and summer Chinook Salmon which are not ESA listed. The lineages are highly genetically divergent from one another and historically spatial and temporal isolating mechanisms maintained these genetic differences. Both lineages occur in the Entiat River, a system where anthropogenic activity has changed habitat, flows, species composition, and the distribution of the two lineages over the past century. We examined the spatial and temporal overlap in spawning distributions between Entiat River spring and summer Chinook Salmon and we used genetic markers to assess the level of introgression between lineages. Redd surveys were conducted from 2003 to 2017 to describe spatial and temporal spawning patterns of both lineages. We genotyped sub-yearling juvenile Chinook Salmon captured in the Entiat River from 2009–2014 at 90 SNP loci to determine lineage and hybridization status. There was temporal overlap in spawning between lineages in several years and considerable spatial overlap in redd locations annually. Genetic analysis revealed hybridization between lineages does occur, albeit at relatively low rates (2.6% of sub-yearling juveniles genotyped). We detected hybrids each year samples were collected and they were distributed throughout the Entiat River basin. Hybridization between lineages of Chinook Salmon could result in introgression and a loss of genetic diversity between the lineages, and/or, a loss of production by ESA-listed spring Chinook Salmon. The presence of hybrids warrants concern for ESA-listed spring Chinook Salmon in both the Entiat River system and throughout the upper Columbia River basin.</p>
Rearing environment affects the genetic architecture and plasticity of DNA methylation in Chinook salmon
<p>Genetic architecture and phenotypic plasticity are important considerations when studying trait variation within and among populations. Since environmental change can induce shifts in the genetic architecture and plasticity of traits, it is important to consider both genetic and environmental sources of phenotypic variation. While there is overwhelming evidence for environmental effects on phenotype, the underlying mechanisms are less clear. Variation in DNA methylation is a potential mechanism mediating environmental effects on phenotype due to its sensitivity to environmental stimuli, transgenerational inheritance, and influences on transcription. To characterize the effect of environment on methylation, we created two 6x6 (North Carolina II) Chinook salmon breeding crosses and reared the offspring in two environments: uniform hatchery tanks and semi-natural stream channels. We sampled the fish twice during development, at the alevin (larval) and fry (juvenile) stages. We measured DNA methylation at 13 genes using a PCR-based bisulfite sequencing protocol. The genetic architecture of DNA methylation differed between rearing environments, with greater additive and non-additive genetic variance in hatchery fish and greater maternal effects in semi-natural channel fish, though gene-specific variation was evident. We observed plasticity in methylation across all assayed genes, as well as gene-specific effects at two genes in alevin and six genes in fry, indicating developmental stage-specific effects of rearing environment on methylation. Characterizing genetic and environmental influences on methylation is critical for future studies on DNA methylation as a potential mechanism for acclimation and adaptation.</p>
Quantifying thermal exposure for migratory riverine species: phenology of Chinook salmon populations predicts thermal stress
<p>Migratory species are particularly vulnerable to climate change because habitat throughout their entire migration cycle must be suitable for the species to persist. For migratory species in rivers, predicting climate change impacts is especially difficult because there is a lack of spatially-continuous and seasonally-varying stream temperature data, habitat conditions can vary for an individual throughout its life cycle, and vulnerability can vary by life stage and season. To predict thermal impacts on migratory riverine populations, we first expanded a spatial stream network model to predict mean monthly temperature for 465,775 river km in the western U.S., and then applied simple yet plausible future stream-temperature change scenarios. We then joined stream temperature predictions to 44,396 spatial observations and life stage-specific phenology (timing) for 26 ecotypes (i.e. geographically distinct population groups expressing one of four distinct seasonal migration patterns) of Chinook salmon (<i>Oncorhynchus tshawytscha</i>), a phenotypically diverse anadromous salmonid that is ecologically and economically important but declining throughout its range. Thermal stress, assessed for each life stage and ecotype based on federal criteria, was influenced by migration timing rather than latitude, elevation, or migration distance, such that sympatric ecotypes often showed differential thermal exposure. Early-migration phenotypes were especially vulnerable due to prolonged residency in inland streams during the summer. We evaluated the thermal suitability of 31,699 stream km which are currently blocked by dams to explore reintroduction above dams as an option to mitigate the negative effects of our warmer stream temperature scenarios. Our results showed that negative impacts of stream temperature warming can be offset for almost all ecotypes if formerly occupied habitat above dams is made available. Our approach of combining spatial distribution and phenology data with spatially- and temporally-explicit temperature predictions enables researchers to examine thermal exposure of migrating populations that use seasonally-varying habitats.</p>
Exposure to exogenous egg cortisol does not rescue juvenile Chinook salmon body size, condition, or survival from the effects of elevated water temperatures
<p class="NormalThesis">Climate change is leading to altered temperature regimes which are impacting aquatic life, particularly for ectothermic fish. The impacts of environmental stress can be translated across generations through maternally-derived glucocorticoids, leading to altered offspring phenotypes. Although these maternal stress effects are often considered negative, recent studies suggest this maternal stress signal may prepare offspring for a similarly stressful environment (environmental match). We applied the environmental match hypothesis to examine whether a prenatal stress signal can dampen the effects of elevated water temperatures on body size, condition, and survival during early development in Chinook salmon <i>Oncorhynchus tshawytscha</i> from Lake Ontario, Canada. We exposed fertilized eggs to prenatal exogenous egg cortisol (1000ng*mL<sup>-1</sup> cortisol or 0ng*mL<sup>-1</sup> control) and then reared these dosed groups at temperatures indicative of current (+0°C) and future (+3°C) temperature conditions. Offspring reared in elevated temperatures were smaller and had a lower survival at the hatchling developmental stage. Overall, we found that our exogenous cortisol dose did not dampen effects of elevated rearing temperatures (environmental match) on body size or early survival. Instead, our eyed stage survival indicates that our prenatal cortisol dose may be detrimental, as cortisol-dosed offspring raised in elevated temperatures had lower survival than cortisol-dosed and control reared in current temperatures. Our results suggest that a maternal stress signal may not be able to ameliorate the effects of thermal stress during early development. However, we highlight the importance of interpreting the fitness impacts of maternal stress within an environmentally relevant context.</p>
Data from: Discovery and characterization of single nucleotide polymorphisms in Chinook salmon, Oncorhynchus tshawytscha
Molecular population genetics of non-model organisms has been dominated by the use of microsatellite loci over the last two decades. The availability of extensive genomic resources for many species is contributing to a transition to the use of single nucleotide polymorphisms (SNPs) for the study of many natural populations. Here we describe the discovery of a large number of SNPs in Chinook salmon, one of the world's most important fishery species, through large-scale Sanger sequencing of expressed sequence tag (EST) regions. More than 3MB of sequence was collected in a survey of variation in more than 131KB of unique genic regions, from more than 225 separate ESTs, in a diverse ascertainment panel of 24 salmon. This survey yielded 117 TaqMan (5' nuclease) assays, almost all from separate EST regions, which were validated in population samples from 5 major stocks of salmon from the three largest basins on the Pacific coast of the coterminous United States: the Sacramento, Klamath and Columbia Rivers. The proportion of these loci that was variable in each of these stocks ranged from 86.3 to 90.6% and the mean minor allele frequency ranged from 0.194 to 0.236. There was substantial differentiation between populations with these markers, with a mean FST estimate of 0.107, and values for individual loci ranging from 0 to 0.592. This substantial polymorphism and population-specific differentiation indicates that these markers will be broadly useful, including for both pedigree reconstruction and genetic stock identification applications.
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
Chinook Salmon is an economically and ecologically important species, and populations from the west coast of North America are a major component of fisheries in the North Pacific Ocean. The anadromous life history strategy of this species generates populations (or stocks) that typically are differentiated from neighboring populations. In many cases, it is desirable to discern the stock of origin of an individual fish or the stock composition of a mixed sample to monitor the stock-specific effects of anthropogenic impacts and alter management strategies accordingly. Genetic stock identification (GSI) provides such discrimination, and we describe here a novel GSI baseline composed of genotypes from more than 8000 individual fish from 69 distinct populations at 96 single nucleotide polymorphism (SNP) loci. The populations included in this baseline represent the likely sources for more than 99% of the salmon encountered in ocean fisheries of California and Oregon. This new genetic baseline permits GSI with the use of rapid and cost-effective SNP genotyping, and power analyses indicate that it provides very accurate identification of important stocks of Chinook Salmon. In an ocean fishery sample, GSI assignments of more than 1000 fish, with our baseline, were highly concordant (98.95%) at the reporting unit level with information from the physical tags recovered from the same fish. This SNP baseline represents an important advance in the technologies available to managers and researchers of this species.
Evaluating Effects of Climate Change, Restoration Scenarios, and Hatchery Effects on Chinook Salmon in the Stillaguamish River Basin with the HARP Model
<p>Model code (R) to accompany the 2023 NOAA report "<strong>Evaluating Effects of Climate Change, Restoration Scenarios, and Hatchery Effects on Chinook Salmon in the Stillaguamish River Basin with the HARP Model</strong>"</p>
Data from: Changes to climate patterns significantly alter the growth of juvenile Chinook and steelhead in the Salmon River, Idaho
<p>dataset used for: Changes to climate patterns significantly alter the growth of juvenile Chinook and steelhead in the Salmon River, Idaho</p>
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