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65 results for “sockeye salmon”
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>
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>
Reproductive success of hatchery- and natural-spawning sockeye salmon, Auke Creek, Alaska
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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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Physiological condition and salinity preference in freshwater migrating juvenile sockeye salmon
<p>The amount of time that juvenile salmon remain in an estuary varies among and within populations, with some individuals passing through their estuary in hours while others remain in the estuary for several months. Underlying differences in individual physiological condition, such as body size, stored energy, and osmoregulatory function, could drive individual variation in the selection of estuary habitat. Here we investigated the role of variation in physiological condition on the selection of estuarine and ocean habitat by sockeye salmon (<em>Oncorhynchus nerka</em>) smolts intercepted at the initiation of their 650 km downstream migration from Chilko Lake, Fraser River, British Columbia (B.C.). Behavioural salinity preference experiments were conducted on unfed smolts held in fresh water at three time intervals during their downstream migration period, representing the stage of migration at lake exit, and the expected timing for estuary entry, and ocean entry (0, 1, and 3 weeks after lake exit, respectively).</p>
Commercial Harvest of Klawock Lake Sockeye Salmon in the District 103 and 104 Purse Seine Fisheries, Southeast Alaska, 2018–2021
<p>The Klawock Lake sockeye salmon (<em>Oncorhynchus nerka</em>) run supports one of the most heavily used subsistence fisheries in Southeast Alaska and is the primary sockeye salmon subsistence resource for the communities of Klawock and Craig. During the period 2011–2017, the average spawning population declined by 63% and the average reported subsistence harvest declined by 50% compared to the previous decade. A major source of uncertainty regarding the decline in Klawock Lake sockeye salmon abundance is the lack of information regarding harvest in commercial fisheries. This project will provided estimates of the harvest and run timing of Klawock Lake sockeye in nearby commercial purse seine fisheries for four years (2018–2021) through genetic mixed stock analysis of sampled harvests. The commercial fisheries in management Districts 103 and 104 were targeted because they are terminal to Klawock Lake and most of the commercial harvest of Klawock Lake sockeye salmon likely occurs in those districts. We further split District 103 into two spatial strata: Northern District 103 (subdistricts 50-90) and Southern District 103 (subdistricts 11-40). The commercial harvest of Klawock Lake sockeye salmon was highest in Northern District 103 in three of four years (2018–2020), and highest in District 104 in one year (2021). Klawock Lake sockeye were virtually absent in the commercial harvest in Southern District 103 in all four years (2018-2021). The total commercial harvest (Districts 103 and 104) of Klawock Lake sockeye salmon was 2,619 fish in 2018, 5,523 fish in 2019, 3,352 fish in 2020, and 6,677 fish in 2021. These data, combined with escapement and subsistence harvests, were used to produce the first estimates of total run size for Klawock Lake sockeye salmon. The total run size varied from year to year, with 13,147 fish in 2018, 14,953 fish in 2019, 19,702 fish in 2020, and 13,600 fish in 2021. Similarly, overall harvest rates varied from 43.9% in 2018 to 59.9% in 2021 (average = 50.9%). Commercial harvest rates averaged lower than the historical averages from nearby sockeye salmon stocks at Hugh Smith and McDonald Lakes. Commercial harvest rates were higher in odd-years than even-years, presumably due to increased fishing pressure on more abundant odd-year pink salmon. The subsistence harvest rates averaged higher (20.1%) than the subsistence harvest rates on McDonald and Hugh Smith Lakes (average < 2%).</p>
Afognak Lake Sockeye Salmon Monitoring Project (2020–2022)
<p>The Afognak River (Litnik) has historically supported one of the largest sockeye salmon subsistence fisheries for Kodiak Archipelago residents. In the 2000s, the number of sockeye salmon returning to Afognak River had diminished substantially resulting in closures to commercial, sport, and subsistence fishing in Afognak Bay. Local subsistence users, represented by the Kodiak-Aleutians Regional Advisory Council, Kodiak Fish and Game Advisory Committee, and Kodiak Tribal Council, stressed the importance of the Afognak River system to local subsistence users and contended that continued closures would make it more difficult for local residents to meet their sockeye salmon needs and shift fishing efforts to small nearby sockeye salmon runs. The Afognak Lake Sockeye Salmon Stock Monitoring Project enumerates adult sockeye salmon into Afognak Lake through a weir located on the Afognak River, describes run-timing, or proportional daily passage, of sockeye salmon through the weir, estimates the age and sex composition of adult sockeye salmon returns, and estimates the average length (mm) by age and sex of sockeye salmon passing through the weir. Data collected from this project provide salmon management biologists the ability to make in-season decisions to execute commercial and sport fisheries. In addition, the information that is gathered from these projects refines the escapement goals and improves preseason run forecasts to allow for maximum sustainable yield and prevent unnecessary restrictions of federal and state subsistence fisheries.</p>
Behavior of brown bears foraging on sockeye salmon in Lake Aleknagik, Alaska (foraging tactics and success)
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Afognak Lake Sockeye Salmon Monitoring Project (2020–2022)
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Physiological condition and salinity preference in freshwater migrating juvenile sockeye salmon
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Data from: Kokanee–sockeye salmon hybridization leads to intermediate morphology and resident life history: implications for fisheries management
Stocking programs designed to return extirpated species to their historical range have become increasingly prevalent, punctuating the need to better understand the risks posed to recipient ecosystems. Here, we investigated the genetic and biological consequences of an anadromous sockeye salmon (Oncorhynchus nerka) stocking program in Skaha Lake, British Columbia, where substantial levels of hybridization/introgression with the native freshwater resident ecotype (kokanee) have been detected. We genetically-assigned 543 individuals (adult spawners, age-0 juveniles) to estimate stock proportions (pure-stock sockeye/kokanee or hybrid) between 2010 and 2017, with a subset undergoing otolith microchemistry analysis to determine migratory life history and maternal ancestry. Proportion of hybrid spawners varied from 5-20% across sampling years, while hybrid age-0 juveniles remained relatively constant (~11%). Hybrid spawners exhibited intermediate size relative to pure-stocks, with the vast majority being non-anadromous (92%) and of resident maternal ancestry (76%). Our results provide empirical support for previously hypothesized mechanisms of hybridization between O. nerka life-history forms, and underscore the importance of continued monitoring of stocking programs to quantify long-term fitness impacts of introgression and refine management strategies.
Data from: Using time series analysis to characterize evolutionary and plastic responses to environmental change: a case study of a shift toward earlier migration date in sockeye salmon
Environmental change can shift the phenotype of an organism through either evolutionary or nongenetic processes. Despite abundant evidence of phenotypic change in response to recent climate change, we typically lack sufficient genetic data to identify the role of evolution. We present a method of using phenotypic data to characterize the hypothesized role of natural selection and environmentally driven phenotypic shifts (plasticity). We modeled historical selection and environmental predictors of interannual variation in mean population phenotype using a multivariate state-space model framework. Through model comparisons, we assessed the extent to which an estimated selection differential explained observed variation better than environmental factors alone. We applied the method to a 60-year trend toward earlier migration in Columbia River sockeye salmon Oncorhynchus nerka, producing estimates of annual selection differentials, average realized heritability, and relative cumulative effects of selection and plasticity. We found that an evolutionary response to thermal selection was capable of explaining up to two-thirds of the phenotypic trend. Adaptive plastic responses to June river flow explain most of the remainder. This method is applicable to other populations with time series data if selection differentials are available or can be reconstructed. This method thus augments our toolbox for predicting responses to environmental change.
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: Identification and characterization of sex-associated loci in sockeye salmon using genotyping-by-sequencing and comparison with a sex-determining assay based on the sdY gene
Loci that can be used to screen for sex in salmon can provide important information for study of both wild and cultured populations. Here, we tested for associations between sex and genotypes at thousands of loci available from a genotyping-by-sequencing (GBS) dataset to discover sex-associated loci in sockeye salmon (Oncorhynchus nerka). We discovered seven sex-associated loci, developed high-throughput assays for two loci, and tested the utility of these two assays in eight collections of sockeye salmon sampled throughout North America. We also screened an existing assay based on the master sex-determining gene in salmon (sdY) in these collections. The ability of GBS-derived loci to assign fish to their phenotypic sex varied substantially among collections suggesting that recombination between the loci that we discovered and the sex-determining gene has occurred. Assignment accuracy to phenotypic sex was much higher with the sdY assay but was still less than 100%. Alignment of sequences from GBS-derived loci to draft genomes for two salmonids provided strong evidence that many of these loci are found on the chromosome orthologous to the known sex chromosome in sockeye salmon. Our study is the first to describe the approximate location of the sex-determining region in sockeye salmon and indicates that sdY is also the master sex-determining gene in this species. However, discordances between sdY genotypes and phenotypic sex and the variable performance of GBS-derived loci warrant more research.
Data from: Sockeye salmon repatriation leads to population re-establishment and rapid introgression with native kokanee
Re-establishing salmonid populations to areas historically occupied has substantial potential for conservation gains, however, such interventions also risk negatively impacting native resident stocks. Here, we assessed the success of the hatchery-assisted reintroduction of anadromous sockeye salmon (Oncorhynchus nerka) into Skaha Lake, British Columbia, Canada, and evaluated the genetic consequences for native kokanee, a freshwater-obligate ecotype, using single nucleotide polymorphism genotypic data collected from reference samples of spawning Okanagan River sockeye and Skaha Lake kokanee pre-sockeye reintroduction, along with annual trawl survey and angler-caught samples obtained over an eight-year period. Significant differentiation was detected between sockeye and kokanee reference samples, with >99% stock assignment. Low proportions of sockeye and hybrids were detected within 2008 and 2010 age-0 trawl samples, however, by 2012, 28% were sockeye, rising to 41% in 2014. The number of hybrids detected rose proportionally with the increase in sockeye, and exhibited an intermediate phenotype. Our results indicate that reintroduction of anadromous sockeye to Skaha Lake is succeeding, with large numbers returning to spawn. However, hybridization with native kokanee is of concern due to the potential for demographic or genetic swamping, with on-going genetic monitoring necessary to assess the long-term effects of introgression and to support interactive fisheries management.
Data from: Parallel signatures of selection at genomic islands of divergence and the major histocompatibility complex in ecotypes of sockeye salmon across Alaska
Understanding the genetic mechanisms that facilitate adaptive radiation is an important component of evolutionary biology. Here, we genotyped 82 neutral SNPs, seven SNPs in islands of divergence identified in a previous study (island SNPs), and a region of the major histocompatibility complex (MHC) in 32 populations of sockeye salmon to investigate whether conserved genes and genomic regions are involved in adaptive radiation. Populations representing three ecotypes were sampled from seven drainages with differing habitats and colonization histories spanning a range of 2,000 km. We found strong signatures of parallel selection across drainages at the island SNPs and MHC, suggesting that the same loci undergo divergent selection during adaptive radiation. However, patterns of differentiation at most island SNPs and the MHC were not associated with ecotypes, suggesting that these loci are responding differently to a mosaic of selective pressures. Our study provides some of the first evidence that conserved genomic islands may be involved in adaptive divergence of salmon populations. Additionally, our data provide further support for the hypothesis that sockeye salmon inhabiting rivers unconnected to lakes harbor similar genetic diversity across large distances, are likely the ancestral form of the species, and have repeatedly recolonized lake systems as they have become available after glacial recession. Finally, our results highlight the value and importance of validating outlier loci by screening additional populations and regions, a practice that will hopefully become more common in the future.
Afognak Lake sockeye salmon stock monitoring project (2017–2019)
<p>The Afognak River (Litnik) has historically supported one of the largest sockeye salmon subsistence fisheries for Kodiak Archipelago residents. In the 2000s, the number of sockeye salmon returning to Afognak River had diminished substantially resulting in closures to commercial, sport, and subsistence fishing in Afognak Bay. Local subsistence users, represented by the Kodiak-Aleutians Regional Advisory Council, Kodiak Fish and Game Advisory Committee, and Kodiak Tribal Council, stressed the importance of the Afognak River system to local subsistence users and contended that continued closures would make it more difficult for local residents to meet their sockeye salmon needs and shift fishing efforts to small nearby sockeye salmon runs. The Afognak Lake Sockeye Salmon Stock Monitoring Project enumerates adult sockeye salmon into Afognak Lake through a weir located on the Afognak River, describes run-timing, or proportional daily passage, of sockeye salmon through the weir, estimates the age and sex composition of adult sockeye salmon returns, and estimates the average length (mm) by age and sex of sockeye salmon passing through the weir. Data collected from this project provide salmon management biologists the ability to make in-season decisions to execute commercial and sport fisheries. In addition, the information that is gathered from these projects refine the escapement goals and improve preseason run forecasts to allow for maximum sustainable yield and prevent unnecessary restrictions of federal and state subsistence fisheries.</p>
Data from: Population structure of sea-type and lake-type sockeye salmon and kokanee in the Fraser River and Columbia River drainages
Population structure of three ecotypes of Oncorhynchus nerka (sea-type Sockeye Salmon, lake-type Sockeye Salmon, and Kokanee) in the Fraser River and Columbia River drainages was examined with microsatellite variation, with the main focus as to whether Kokanee population structure within the Fraser River drainage suggested either a monophyletic or polyphyletic origin of the ecotype within the drainage. Variation at 14 microsatellite loci was surveyed for sea-type and lake-type Sockeye Salmon and Kokanee sampled from 121 populations in the two river drainages. An index of genetic differentiation, FST, over all populations and loci was 0.087, with individual locus values ranging from 0.031 to 0.172. Standardized to an ecotype sample size of 275 individuals, the least genetically diverse ecotype was sea-type Sockeye Salmon with 203 alleles, whereas Kokanee displayed the greatest number of alleles (260 alleles), with lake-type Sockeye Salmon intermediate (241 alleles). Kokanee populations from the Columbia River drainage (Okanagan Lake, Kootenay Lake), the South Thompson River (a major Fraser River tributary) drainage populations, and the mid-Fraser River populations all clustered together in a neighbor-joining analysis, indicative of a monophyletic origin of the Kokanee ecotype in these regions, likely reflecting the origin of salmon radiating from a refuge after the last glaciation period. However, upstream of the mid-Fraser River populations, there were closer relationships between the lake-type Sockeye Salmon ecotype and the Kokanee ecotype, indicative of the Kokanee ecotype evolving independently from the lake-type Sockeye Salmon ecotype in parallel radiation. Kokanee population structure within the entire Fraser River drainage suggested a polyphyletic origin of the ecotype within the drainage. Studies employing geographically restricted population sampling may not outline accurately the phylogenetic history of salmonid ecotypes.
Data from: Linkage mapping reveals strong chiasma interference in sockeye salmon: implications for interpreting genomic data
Meiotic recombination is fundamental for generating new genetic variation and for securing proper disjunction. Further, recombination plays an essential role during the rediploidization process of polyploid-origin genomes because crossovers between pairs of homeologous chromosomes retain duplicated regions. A better understanding of how recombination affects genome evolution is crucial for interpreting genomic data; unfortunately, current knowledge mainly originates from a few model species. Salmonid fishes provide a valuable system for studying the effects of recombination in nonmodel species. Salmonid females generally produce thousands of embryos, providing large families for conducting inheritance studies. Further, salmonid genomes are currently rediploidizing after a whole genome duplication and can serve as models for studying the role of homeologous crossovers on genome evolution. Here, we present a detailed interrogation of recombination patterns in sockeye salmon (Oncorhynchus nerka). First, we use RAD sequencing of haploid and diploid gynogenetic families to construct a dense linkage map that includes paralogous loci and location of centromeres. We find a nonrandom distribution of paralogs that mainly cluster in extended regions distally located on 11 different chromosomes, consistent with ongoing homeologous recombination in these regions. We also estimate the strength of interference across each chromosome; results reveal strong interference and crossovers are mostly limited to one per arm. Interference was further shown to continue across centromeres, but metacentric chromosomes generally had at least one crossover on each arm. We discuss the relevance of these findings for both mapping and population genomic studies.
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