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Dataset results
22 results for “Oncorhynchus nerka”
Data for: Dynamic coastal pelagic habitat drives rapid changes in growth and condition of juvenile sockeye salmon (Oncorhynchus nerka) during early marine migration
<p>Migrating marine taxa encounter diverse habitats that differ environmentally and in foraging conditions over a range of spatial scales. We examined body (RNA/DNA, length-weight residuals) and nutritional (fatty acid composition) condition of juvenile sockeye salmon (<em>Oncorhynchus</em> nerka) in British Columbia while migrating through oceanographically variable waters. Fish were sampled in the stratified northern Strait of Georgia (NSoG); the highly mixed Johnstone Strait (JS); and the transitional zone of Queen Charlotte Strait (QCS). In 2015, body and nutritional condition were high in the NSoG but rapidly declined to reach the lowest levels in JS where prey availability was low, before showing signs of compensatory growth in QCS. In 2016, juvenile salmon had a significantly lower condition in the NSoG than in 2015, although zooplankton biomass was similar, condition remained low in JS, and no compensatory growth was observed in QCS. We provide evidence that differences in juvenile salmon condition between the two years were due to changes in the food quality available to juvenile fish. We propose that existing hypotheses about fish survival need to be extended to incorporate food quality in addition to quantity to understand changes in fish condition and survival between years.</p>
Data for: Dynamic coastal pelagic habitat drives rapid changes in growth and condition of juvenile sockeye salmon (Oncorhynchus nerka) during early marine migration
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Data from: Patterns of selection and allele diversity of class I and class II major histocompatibility loci across the species range of sockeye salmon (Oncorhynchus nerka)
The major histocompatibility complex (MHC), an important component of the vertebrate immune system, provides an important suite of genes to examine the role of genetic diversity at non-neutral loci for population persistence. We contrasted patterns of diversity at the two classical MHC loci in sockeye salmon (Oncorhynchus nerka), MHC class I (UBA) and MHC class II (DAB), and neutral microsatellite loci across 70 populations spanning the species range from Washington State to Japan. There was no correlation in allelic richness or heterozygosity between MHC loci or between MHC loci and microsatellites. The two unlinked MHC loci may be responding to different selective pressures; the distribution of FST values for the two loci was uncorrelated, and evidence for both balancing and directional selection on alleles and lineages of DAB and UBA was observed in populations throughout the species range but rarely on both loci within a population. These results suggest that fluctuating selection has resulted in the divergence of MHC loci in contemporary populations.
Data from: An empirical comparison of SNPs and microsatellites for parentage and kinship assignment in a wild sockeye salmon (Oncorhynchus nerka) population
Because of their high variability, microsatellites are still considered the marker of choice for studies on parentage and kinship in wild populations. Nevertheless, single nucleotide polymorphisms (SNPs) are becoming increasing popular in many areas of molecular ecology, owing to their high-throughput, easy transferability between laboratories and low genotyping error. An ongoing discussion concerns the relative power of SNPs compared to microsatellites – that is, how many SNP loci are needed to replace a panel of microsatellites? Here, we evaluate the assignment power of 80 SNPs (HE=0.30, 80 independent alleles) and 11 microsatellites (HE =0.85, 194 independent alleles) in a wild population of about 400 sockeye salmon with two commonly used software packages (Cervus3, Colony2) and, for SNPs only, a newly developed software (SNPPIT). Assignment success was higher for SNPs than for microsatellites, especially for parent pairs, irrespective of the method used. Colony2 assigned a larger proportion of offspring to at least one parent than the other methods, though Cervus and SNPPIT detected more parent pairs. Identification of full sib groups without parental information from relatedness measures was possible using both marker systems, though explicit reconstruction of such groups in Colony2 was impossible for SNPs because of computation time. Our results confirm the applicability of SNPs for parentage analyses and refute the predictability of assignment success from the number of independent alleles.
Data from: Genotyping-in-Thousands by sequencing panel development and application to inform kokanee salmon (Oncorhynchus nerka) fisheries management at multiple scales
<p>The ability to differentiate life history variants is vital for estimating fisheries management parameters, yet traditional survey methods can be inaccurate in mixed-stock fisheries. Such is the case for kokanee, the resident freshwater form of sockeye salmon (<i>Oncorhynchus nerka</i>), which exhibits various reproductive ecotypes (stream-, shore-, deep-spawning) that co-occur with each other and/or anadromous <i>O. nerka</i> in some systems across their pan-Pacific distribution. Here, we developed a multi-purpose Genotyping-in-Thousands by sequencing (GT-seq) panel of 288 targeted single nucleotide polymorphisms (SNPs) to enable accurate kokanee stock identification by geographic basin, migratory form, and reproductive ecotype across British Columbia, Canada. The GT-seq panel exhibited high self-assignment accuracy (93.3%) and perfect assignment of individuals not included in the baseline to their geographic basin, migratory form, and reproductive ecotype of origin. The GT-seq panel was subsequently applied to Wood Lake, a valuable mixed-stock fishery, revealing high concordance (>98%) with previous assignments to ecotype using microsatellites and TaqMan<span> </span>SNP genotyping assays, while improving resolution, extending a long-term time-series, and demonstrating the scalability of this approach for this system and others.</p>
Data from: Genome-wide analysis reveals demographic and life history patterns associated with habitat modification in land-locked, deep-spawning sockeye salmon (Oncorhynchus nerka)
<p>Human-mediated habitat fragmentation in freshwater ecosystems can negatively impact genetic diversity, demography and life history of native biota, while disrupting the behaviour of species that are dependent on spatial connectivity to complete their life cycles. In the Alouette River system (British Columbia, Canada), dam construction in 1928 impacted passage of anadromous sockeye salmon (<i>Oncorhynchus nerka</i>), with the last records of migrants occurring in the 1930's. Since that time, <i>O. nerka</i> persisted as a resident population in Alouette Reservoir until experimental water releases beginning in 2005 created conditions for migration; two years later, returning migrants were observed for the first time in ~70 years, raising important basic and applied questions regarding life history variation and population structure in this system. Here, we investigated the genetic distinctiveness and population history of Alouette Reservoir <i>O. nerka</i> using genome-wide SNP data (n=7,709 loci) collected for resident and migrant individuals, as well as for neighbouring anadromous sockeye salmon and resident kokanee populations within the Fraser River drainage (n=312 individuals). Bayesian clustering and principal components analyses based on neutral loci revealed five distinct clusters, largely associated with geography, and clearly demonstrated that Alouette Reservoir resident and migrant individuals are genetically distinct from other <i>O. nerka</i> populations in the Fraser River drainage. At a finer-level, there was no clear evidence for differentiation between Alouette Reservoir residents and migrants; although we detected eight high-confidence outlier loci, they all mapped to sex chromosomes suggesting that differences were likely due to uneven sex ratios rather than life history. Taken together, these data suggest that contemporary Alouette Reservoir <i>O. nerka</i> represents a landlocked sockeye salmon population, constituting the first reported instance of deep-water spawning behaviour associated with this life history form. This finding punctuates the need for re-assessment of conservation status and supports on-going fisheries management activities in Alouette Reservoir. </p>
Data from: Genome-wide investigation of the multiple origins hypothesis for deep-spawning kokanee salmon (Oncorhynchus nerka) across its pan-Pacific distribution
<p>Salmonids have emerged as important study systems for investigating molecular processes underlying parallel evolution given their tremendous life history variation. Kokanee, the resident form of anadromous sockeye salmon (<i>Oncorhynchus nerka</i>), have evolved multiple times across the species' pan-Pacific distribution, exhibiting multiple reproductive ecotypes including those that spawn in streams, on lake-shores, and at lake depths >50 meters. The latter has only been detected in five locations in Japan and British Columbia, Canada. Here, we investigated the multiple origins hypothesis for deep-spawning kokanee, using 9,721 SNPs distributed across the genome analyzed for the vast majority of known populations in Japan (Saiko Lake) and Canada (Anderson, Seton, East Barrière Lakes) relative to stream-spawning populations in both regions. We detected 397 outlier loci, none of which were robustly identified in paired-ecotype comparisons in Japan and Canada independently. Bayesian clustering and principal components analyses based on neutral loci revealed six distinct clusters, largely associated with geography or translocation history, rather than ecotype. Moreover, a high level of divergence between Canadian and Japanese populations, and between deep- and stream-spawning populations regionally, suggest the deep-spawning ecotype independently evolved on the two continents. On a finer level, Japanese kokanee populations exhibited low estimates of heterozygosity, significant levels of inbreeding, and reduced effective population sizes relative to Canadian populations, likely associated with transplantation history. Along with preliminary evidence for hybridization between deep-spawning and stream-spawning ecotypes in Saiko Lake, these findings should be considered within the context of on-going kokanee fisheries management in Japan.</p>
Data from: Patterns of selection and allele diversity of class I and class II major histocompatibility loci across the species range of sockeye salmon (Oncorhynchus nerka)
Open the record for dataset details and reuse information.
Data from: An empirical comparison of SNPs and microsatellites for parentage and kinship assignment in a wild sockeye salmon (Oncorhynchus nerka) population
Open the record for dataset details and reuse information.
Data from: Genotyping-in-Thousands by sequencing panel development and application to inform kokanee salmon (Oncorhynchus nerka) fisheries management at multiple scales
Open the record for dataset details and reuse information.
Data from: Genome-wide analysis reveals demographic and life history patterns associated with habitat modification in land-locked, deep-spawning sockeye salmon (Oncorhynchus nerka)
Open the record for dataset details and reuse information.
Data from: Genome-wide investigation of the multiple origins hypothesis for deep-spawning kokanee salmon (Oncorhynchus nerka) across its pan-Pacific distribution
Open the record for dataset details and reuse information.
Data from: Identification of multiple QTL hotspots in sockeye salmon (Oncorhynchus nerka) using genotyping-by-sequencing and a dense linkage map
Understanding the genetic architecture of phenotypic traits can provide important information about the mechanisms and genomic regions involved in local adaptation and speciation. Here, we used genotyping-by-sequencing and a combination of previously published and newly generated data to construct sex-specific linkage maps for sockeye salmon (Oncorhynchus nerka). We then used the denser female linkage map to conduct quantitative trait locus (QTL) analysis for 4 phenotypic traits in 3 families. The female linkage map consisted of 6322 loci distributed across 29 linkage groups and was 4082 cM long, and the male map contained 2179 loci found on 28 linkage groups and was 2291 cM long. We found 26 QTL: 6 for thermotolerance, 5 for length, 9 for weight, and 6 for condition factor. QTL were distributed nonrandomly across the genome and were often found in hotspots containing multiple QTL for a variety of phenotypic traits. These hotspots may represent adaptively important regions and are excellent candidates for future research. Comparing our results with studies in other salmonids revealed several regions with overlapping QTL for the same phenotypic trait, indicating these regions may be adaptively important across multiple species. Altogether, our study demonstrates the utility of genomic data for investigating the genetic basis of important phenotypic traits. Additionally, the linkage map created here will enable future research on the genetic basis of phenotypic traits in salmon.
Pasagshak River sockeye Salmon (Oncorhynchus nerka) escapement monitoring data 2022–2024
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Data from: Identification of multiple QTL hotspots in sockeye salmon (Oncorhynchus nerka) using genotyping-by-sequencing and a dense linkage map
Open the record for dataset details and reuse information.
Consequences of high temperatures and premature mortality on the transcriptome and blood physiology of wild adult sockeye salmon (Oncorhynchus nerka)
GEO Series GSE33586. Oncorhynchus mykiss; Oncorhynchus nerka; Salmo salar; Oncorhynchus tshawytscha; Osmerus mordax; Coregonus clupeaformis. 40 samples. Type: Expression profiling by array.
Ecological transcriptomics of lake-type and riverine sockeye salmon (Oncorhynchus nerka) muscle tissue
GEO Series GSE31214. Oncorhynchus nerka; Salmo salar. 30 samples. Type: Expression profiling by array.
Sockeye salmon (Oncorhynchus nerka) from Aniakchak National Monument and Preserve muscle transcriptome
GEO Series GSE42985. Oncorhynchus nerka; Salmo salar. 49 samples. Type: Expression profiling by array.
Transcriptomics of environmental adaptation and survival in wild adult Pacific Sockeye Salmon (Oncorhynchus nerka) during spawning migration
GEO Series GSE22346. Oncorhynchus mykiss; Oncorhynchus nerka; Salmo salar. 121 samples. Type: Expression profiling by array.
Pasagshak River Sockeye Salmon (Oncorhynchus nerka) Escapement Monitoring 2019–2021
<p>Since 2011, sockeye salmon (<em>Oncorhynchus nerka)</em> escapement through the Pasagshak River into Lake Rose Teed on the Kodiak Island road system has been estimated with a weir. A continuation of funding from the Alaska Sustainable Salmon Fund (AKSSF, Project #52009) allowed the Alaska Department of Fish and Game (ADF&G), Division of Commercial Fisheries to operate a PVC floating weir near the mouth of Lake Rose Teed during the 2019 through 2021 seasons. This data set includes the number and species of fish counted through the weir, and the age, sex, and length (ASL) information gathered from sockeye salmon captured and sampled at the weir.</p>
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