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61 results for “Pacific Salmon”
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>
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>
Data for: Performance of a high-frequency (180 kHz) acoustic array for tracking juvenile Pacific salmon in the coastal ocean
<p><b>Background</b></p> <p>Acoustic telemetry is now a key research tool used to quantify juvenile salmon survival, but transmitter size has limited past studies to larger smolts (>130 mm fork length). New, smaller, higher-frequency transmitters ("tags") allow studies on a larger fraction of the smolt size spectrum (>95 mm); however, detection range and study duration are also reduced, introducing new challenges. The potential cost implications are not trivial. With these new transmitters in mind, we designed, deployed, and tested the performance of a dual-frequency receiver array design in the Discovery Islands region of British Columbia, Canada. We double-tagged 50 juvenile steelhead (<i>Oncorhynchus mykiss</i>) with large 69 kHz tags (VEMCO model V9-1H) and small 180 kHz tags (model V4-1H). The more powerful 69 kHz tags were used to determine fish presence in order to estimate the detection efficiency (DE) of the 180 kHz tags. We then compared the standard error of the survival estimate produced from the tracking data using the two tag types which has important implications for array performance and hypothesis testing in the sea.</p> <p><b>Results</b></p> <p>Perfect detection of the 69 kHz tags allowed us to determine the DE of the 180 kHz tags. Although the 180 kHz tags began to expire during the study, the estimated DE was acceptable at 76% (SE = 9%) when we include single detections. However, confidence intervals on steelhead survival (64%) were 1.5x larger for the 180 kHz tags (47-85% vs. 51-77% for 69 kHz) because of the reduced DE.</p> <p><b>Conclusions</b></p> <p>The array design performed well; however, single detections of the 180 kHz tags indicates that under slightly different circumstances the DE could have been compromised, emphasizing the need to carefully consider the interaction of animal migration characteristics, study design, and tag programming when designing telemetry arrays. To increase DE and improve the precision of 180 kHz-based survival estimates presented here requires either an increase in receiver density, an increase in tag sample size (and modified transmitter programming), or both. The optimal solution depends on transmitter costs, array infrastructure costs, annual maintenance costs, and array use (i.e., contributors). Importantly, the use of smaller tags reduces potential tag burden effects and allows early marine migration studies to be extended to Pacific salmon populations that have been previously impossible to study.</p>
Data from: Forestry impacts on stream flows and temperatures: A quantitative synthesis of paired catchment studies across the Pacific salmon range
<p>Forestry is pervasive across temperate North America and may influence aquatic environmental conditions such as flows and temperatures, as well as important species such as Pacific salmon (<em>Oncorhynchus</em> spp.). While there have been many large-scale forestry experiments using paired catchment designs, these studies have yet to be quantitatively synthesized. Thus, it remains unclear whether forestry impacts are consistent, context-dependent, or unpredictable. This study aims to quantitatively synthesize forestry impacts on streamflow and temperature, through a systematic review and synthesis of paired catchment studies across the range of Pacific salmon. Specifically, we investigated whether generalizable relationships exist between forestry intensity (percent watershed harvested) and impacts to streamflow and temperature. We also examined whether watershed features (climate, hydrology, lithology) and harvest method mediated forestry impacts. We extracted information from 35 unique paired-catchments from California to Alaska. Forestry had strong impacts on peak and low flows and maximum summer water temperatures, but responses were quite variable. Across all catchments, forestry elevated peak flows ~20% (n = 31 catchments), reduced low flows ~25% (n = 13 catchments), and increased maximum summer temperatures ~15% (n = 35 catchments) on average. However, these impacts were variable and were not predictable based on forestry intensity, thus broader stressor-response relationships were not supported. Forestry impacts on peak flows and maximum summer temperatures varied spatially. Peak flow impacts increased with increased northward latitude and temperature impacts decreased with eastward longitude. However, the magnitude of impacts were unrelated to other watershed attributes, which included climate (precipitation and aridity), rain vs. snow hydrology, elevation, and bedrock lithology. Harvest method and riparian buffer presence also had no detected effects on forestry impacts across studies and statistical models explained a low proportion of variation overall. Collectively, our results indicate that forestry can have substantial impacts on key environmental conditions; however, the magnitude of impact was variable and could not be clearly linked to easily-measured watershed characteristics. This implies that forestry impacts are not broadly predictable. Probabilistic risk models based on distributions of potential impacts may therefore be more useful for watershed management in data-poor situations.</p>
Pacific salmon in the Canadian Arctic highlight a range-expansion pathway for sub-Arctic fishes
<p>The R code and data to support the manuscript "Pacific salmon in the Canadian Arctic highlight a range-expansion pathway for sub-Arctic fishes" published by Dunmall & Langan et al. 2024 in Global Change Biology. Briefly, this study investigated the mechanisms behind variable, rising catches of Pacific salmon by subsistence fishers in the Canadian Arctic. Detailed descritptions of the data and the performed analyses are provided in the associated manuscript.</p>
Coronary Circulation Enhances the Aerobic Performance of Pacific Salmon, Particularly for Females
<p>Female Pacific salmon often experience higher mortality than males during their once-in-a-lifetime up-river spawning migration, particularly when exposed to secondary stressors (e.g. high temperatures). However, the underlying mechanisms remain unknown. One hypothesis is that female Pacific salmon hearts are more oxygen-limited than males and are less able to supply oxygen to the body's tissues during this demanding migration. Such oxygen limitations can develop from naturally occurring coronary blockages (<em>i.e.</em>, coronary arteriosclerosis) found in mature salmon hearts. To test this hypothesis, we measured resting (RMR) and maximum metabolic rate (MMR), aerobic scope (AS) and acute upper thermal tolerance in coho salmon (<em>Oncorhynchus kisutch</em>) with an intact or artificially blocked coronary oxygen supply. We also assessed venous blood oxygen and chemistry (cortisol, ions, and metabolite concentrations) at different time intervals during recovery from exhaustive exercise. We found that coronary blockage impaired MMR, but to a greater extent in females than males. Thus, coronary oxygen supply is more important in females than males to support peak metabolism, which is essential during upriver swimming. Furthermore, the coronary blockage reduced AS and PvO<sub>2</sub> during exercise recovery but did not differ between sexes. Coronary ligation lowered acute upper thermal tolerance by 1.1°C. Our findings highlight the importance of coronary blood supply for mature salmon and show evidence that elevated female mortality may be linked to cardiac limitation, particularly during warm water conditions.</p>
Data from: Surfing the tidal wave: use of transiently-aquatic habitat by juvenile Pacific salmon and other fishes in estuaries
<p>Tide and species count data used in the note "Surfing the tidal wave: use of transiently-aquatic habitat by juvenile Pacific salmon and other fishes in estuaries."</p>
Phenological shifts in out-migrating juvenile Pacific salmon
<p><span>This dataset contains the rates of change in juvenile migration timing of 66 Pacific salmon populations ranging from Oregon to Alaska, the rates of change in timing of the initiation of spring phytoplankton bloom in nearby coastal regions, and covariates. Species represented in this dataset include coho salmon (<em>Oncorhynchus kisutch</em>), sockeye salmon (<em>O. nerka</em>), Chinook salmon (<em>O. tshawytscha</em>), pink salmon (<em>O. gorbuscha</em>), chum salmon (<em>O. keta</em>), and steelhead trout</span> (<span><em>O. mykiss</em>). Rates of change in salmon phenology includes rate of change in peak date, and rate of change in range (number of days between 25<sup>th</sup> and 75<sup>th</sup> quantile of migration).</span></p>
Allele surfing causes maladaptation in a Pacific salmon of conservation concern
<p>How different factors including demography, recombination or genome duplication may impact selection efficacy and the burden of deleterious mutations in different populations is a central question of evolutionary biology and genetics. Here we show that key evolutionary processes, including variation in effective population size through postglacial change in demography and recombination rates have affected the efficacy of selection and impacted the genetic load in Coho salmon (<em>Oncorhynchus kisutch</em>), a widely distributed salmonid species on the west coast of North America. Using whole genome resequencing data from 14 populations at different travelled migratory distances from their southern glacial refugium, we found support for postglacial gene surfing, with reduced <em>N</em><sub><em>e</em></sub> at the range recolonization front, thus inducing both a reduction in the efficacy of selection and a surf of deleterious alleles in populations evolving at low <em>N</em><sub><em>e</em></sub>. This inference was robust to various proxies of the load. In addition, comparing residual tetrasomic and re-diploidizing regions of the salmon genome, we found support for a prime role of recombination rates in shaping the within-genome variation of the load. Overall, our empirical results are remarkably consistent with expectations under the nearly neutral theory of molecular evolution. We discuss the fundamental and applied implications of these findings for evolutionary and conservation genomics.</p> <p> </p>
Coronary Circulation Enhances the Aerobic Performance of Wild Pacific Salmon
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Data for: Performance of a high-frequency (180 kHz) acoustic array for tracking juvenile Pacific salmon in the coastal ocean
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Dataset: Spatiotemporal patterns of salmon winter habitat usage in the Northeast Pacific uncovered by environmental DNA
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Pacific salmon in the Canadian Arctic highlight a range-expansion pathway for sub-Arctic fishes
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Phenological shifts in out-migrating juvenile Pacific salmon
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Pacific Rim Chinook salmon genetic stock identification baseline of SNP genotypes
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Direction and magnitude of natural selection on body size differs among age classes of seaward migrating Pacific salmon
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Freshwater life-cycle timing of Pacific salmon and steelhead (Oncorhynchus spp.) in Canada
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Data from: Forestry impacts on stream flows and temperatures: A quantitative synthesis of paired catchment studies across the Pacific salmon range
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Data from: Landscape heterogeneity and local adaptation define the spatial genetic structure of Pacific salmon in a pristine environment
Identifying the spatial distribution of genetic variation across the landscape is an essential step in informing species conservation. Comparison of closely related and geographically overlapping species can be particularly useful in cases where landscape may similarly influence genetic structure. Congruent patterns among species highlight the importance that landscape heterogeneity plays in determining genetic structure whereas contrasting patterns emphasize differences in species-specific ecology and life-history or the importance of species-specific adaptation to local environments. We examined the interacting roles of demography and adaptation in determining spatial genetic structure in two closely related and geographically overlapping species in a pristine environment. Using single nucleotide polymorphism (SNP) loci exhibiting both neutral and putative adaptive variation, we evaluated the genetic structure of sockeye salmon in the Copper River, Alaska; these data were compared to existing data for Chinook salmon from the same region. Overall, both species exhibited patterns of isolation by distance; the spatial distribution of populations largely determined the distribution of genetic variation across the landscape. Further, both species exhibited largely congruent patterns of within- and among-population genetic diversity, highlighting the role that landscape heterogeneity and historical processes play in determining spatial genetic structure. Potential adaptive differences among geographically proximate sockeye salmon populations were observed when high FST outlier SNPs were evaluated in a landscape genetics context. Results were evaluated in the context of conservation efforts with an emphasis on reproductive isolation, historical processes, and local adaptation.
Data from: Environmental DNA for the enumeration and management of Pacific salmon
Pacific salmon are a keystone resource in Alaska, generating annual revenues of well over ~US$500 million/yr. Due to their anadromous life history, adult spawners distribute amongst thousands of streams, posing a huge management challenge. Currently, spawners are enumerated at just a few streams because of reliance on human counters and, rarely, sonar. The ability to detect organisms by shed tissue (environmental DNA, eDNA) promises a more efficient counting method. However, although eDNA correlates generally with local fish abundances, we do not know if eDNA can accurately enumerate salmon. Here we show that daily, and near-daily, flow-corrected eDNA rate closely tracks daily numbers of returning sockeye and coho spawners and outmigrating sockeye smolts. eDNA thus promises accurate and efficient enumeration, but to deliver the most robust numbers will need higher-resolution stream-flow data, at-least-daily sampling, and a focus on species with simple life histories, since shedding rate varies amongst jacks, juveniles, and adults.
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Allen Brain Atlas
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Annotated Behaviour and Observability Dataset (ABODe)
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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.