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19 results for “salmon abundance”
F I G U R E 3 in Estimating multiple years, tributary-specific, and overall Atlantic salmon smolt abundance in a large Canadian catchment using capture-mark-recapture experiments
F I G U R E 3 (a) Posterior distribution of the difference between the true value and posterior distribution estimates (in percentage of the true value) of annual total smolt abundance obtained from DM (Dirichlet-multinomial) model M5 (simulation exercise). Each line is a year, and the 10 (one for each replicate) distributions are overlaid. The overall average difference is indicated in the left corner of the panel and represented by a red dashed vertical line. (b) C.V. of the posterior distributions of total abundance obtained from DM model M5. Each blue dot corresponds to the C.V. of a unique year/replicate, and each dashed blue horizontal line corresponds to the average C.V. of a replicate across years. The average C.V. across years and replicates (red dashed line) is also indicated in the top-right corner of the panel.
F I G U R E 4 in Estimating multiple years, tributary-specific, and overall Atlantic salmon smolt abundance in a large Canadian catchment using capture-mark-recapture experiments
F I G U R E 4 (a–c) Posterior distribution of the relative contribution of the smolt abundance associated with each upstream rotary screw trap (RST) and (d) posterior distribution of the relative contribution of the "rest" of the smolt abundance in relation to the total abundance for the DM (Dirichletmultinomial) model M5 (simulation exercise). The red dots correspond to the true values in the simulated dataset.
F I G U R E 1 in Estimating multiple years, tributary-specific, and overall Atlantic salmon smolt abundance in a large Canadian catchment using capture-mark-recapture experiments
F I G U R E 1 Restigouche River catchment map with main streams and lakes. Red dots indicate the location of the rotary screw traps (RST). Black polygons indicate subcatchments draining into upstream RSTs. Top-right panels: zoom on the location of the two downstream RSTs and example of a smolt with a streamer tag. Photo credit: Marie-Camille St-Amour.
F I G U R E 5 in Estimating multiple years, tributary-specific, and overall Atlantic salmon smolt abundance in a large Canadian catchment using capture-mark-recapture experiments
F I G U R E 5 (left panels, a–e) Posterior distributions of the estimated annual catchability θt,k at each rotary screw trap (RST), (middle panels, f– h) posterior distributions of the annual smolt abundance estimates associated with each upstream RST (Nmt,i), (i) the total smolt abundance for the Restigouche catchment (Nmtot), and (right panels, j–m) posterior distributions of the annual relative proportions of the total smolt abundance t of the Restigouche catchment estimated for each upstream RST and for the unsampled areas (rest, bottom-right panel) using the Restigouche dataset. In the catchability panels (a–e), the dashed gray line is the median, and the light and dark gray areas indicate the 2.5th–97.5th and 25th– 75th interquantile ranges, respectively, of the hyperparameter μθ, that is, the average catchability of each RST of the time series. In the relative k proportions panels (f–i) the thick dashed colored line in the top three panels indicates the average proportion of the total catchment abundance estimated at the upstream RST. The thick dashed gray lines indicate the proportions of the Restigouche catchment wetted areas of the subbasins sampled at the upstream RST(j–l) and the wetted area for the remainder of the Restigouche catchment not sampled by any upstream RST (m); the proportions for the rest of the catchment area change over years based on the specific upstream RSTs that operated in a given year. For all panels, the colored dot is the median, and the thin and thick vertical segments indicate the 2.5th–97.5th and 25th–75th interquantile ranges, respectively.
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>
Salmon on the lam: Drivers of escaped farmed fish abundance in rivers
<p>Abstract:</p> <ol> <li>The production of Atlantic salmon in aquaculture has grown substantially over the last 40 years. The unintentional release of domesticated salmon poses a significant risk to the long-term persistence of wild Atlantic salmon populations through ecological interactions and genetic introgression. Our ability to link aquaculture production to farmed escaped salmon in rivers is still limited and hinders identifying the appropriate production capacity of salmon aquaculture to reduce unwanted interactions between wild and escaped Atlantic salmon. </li> <li>Here, we use a 14-year dataset of farmed escapee abundance in rivers to model how the a priori selected covariables of wild salmon abundance, aquaculture intensity, river discharge, hydropower, and fjord placement of the river affects escapee abundance across 54 rivers in western Norway. Then, we evaluate the predictive strength of the model to provide context for its use to minimize escapees. </li> <li>We found that the abundance of farmed escaped Atlantic salmon in rivers is correlated to aquaculture intensity. Furthermore, the abundance of wild Atlantic salmon, mean yearly discharge, and the interaction between fjord placement and wild salmon abundance were important predictors of escapee abundance in rivers. </li> <li>The model was 40% accurate when predicting the abundance of farmed escaped salmon in rivers. However, the accuracy improved to 75% when using risk categories derived from modeled intrusion rates that induced long-term genetic changes to the wild population (low < 4%, medium 4 – 10%, and high > 10% escaped farmed salmon).</li> <li><em>Synthesis and applications: </em>This study links aquaculture production, at relevant spatiotemporal scales (75 km from rivers), to the abundance of escaped farmed Atlantic salmon in rivers, and provides governmental agencies with a tool to help regulate domesticated salmon production based on the carrying capacity of the system to buffer against introgression between conspecifics. Furthermore, understanding this relationship will be beneficial when establishing new aquaculture sites in pristine ecosystems where they would overlap with wild Atlantic salmon. Finally, future mitigation efforts should continue to focus on new technologies (e.g., triploid females) that can eliminate the risk of introgression without limiting aquaculture production.</li> </ol> <p> </p> <p> </p> <p> </p>
How riparian and floodplain restoration modify the effects of increasing temperature on adult salmon spawner abundance in the Chehalis, River, WA
<p>Model code (R) to accompany the manuscript "How riparian and floodplain restoration modify the effects of increasing temperature on adult salmon spawner abundance in the Chehalis River, WA", PLOS ONE.</p>
Considering sampling bias in close-kin mark-recapture (CKMR) abundance estimates of Atlantic salmon
<p>Genetic methods for the estimation of population size can be powerful alternatives to conventional methods. Close-kin mark-recapture (CKMR) is based on the principles of conventional mark-recapture, but instead of being physically marked, individuals are marked through their close kin. The aim of this study was to evaluate the potential of CKMR for the estimation of spawner abundance in Atlantic salmon and how age, sex, spatial, and temporal sampling bias may affect CKMR estimates. Spawner abundance in a wild population was estimated from genetic samples of adults returning in 2018 and of their potential offspring collected in 2019. Adult samples were obtained in two ways. First, adults were sampled and released alive in the breeding habitat during spawning surveys. Second, genetic samples were collected from out-migrating smolts PIT tagged in 2017 and registered when returning as adults in 2018. CKMR estimates based on adult samples collected during spawning surveys were somewhat higher than conventional counts. Uncertainty was small (CV<0.15), due to the detection of a high number of parent-offspring-pairs. Sampling of adults was age- and size-biased and correction for those biases resulted in moderate changes in the CKMR estimate. Juvenile dispersal was limited, but spatially balanced sampling of adults rendered CKMR estimates robust to spatially biased sampling of juveniles. CKMR estimates based on returning PIT tagged adults were approximately twice as high as estimates based on samples collected during spawning surveys. We suggest that estimates based on PIT tagged fish reflect the total abundance of adults entering the river, while estimates based on samples collected during spawning surveys reflect the abundance of adults present in the breeding habitat at the time of spawning. Our study showed that CKMR can be used to estimate spawner abundance in Atlantic salmon, with a moderate sampling effort, but a carefully designed sampling regime is required.</p>
Atlantic salmon (Salmo salar) transfer to seawater by gradual salinity changes exhibited an increase in the intestinal microbial abundance and richness data
<p>The host's physiological history and environment determine the microbiome structure. In that sense, the strategy used for the salmon transfer to seawater after parr-smolt transformation may influence the Atlantic salmon’s intestinal microbiota. Therefore, this study aimed to explore the diversity and abundance of the Atlantic salmon intestinal microbiota and metagenome functional prediction during seawater transfer under three treatments. One group was exposed to gradual salinity change (GSC), the other to salinity shock (SS), and the third was fed with a functional diet (FD) before the seawater (SW) transfer. The microbial profile was assessed through full-16S rRNA gene sequencing using the Nanopore platform. In addition, metagenome functional prediction was performed using PICRUSt2. The results showed an influence of salinity changes on Atlantic salmon gut microbiota richness, diversity, and taxonomic composition. The findings reveal that GSC and the FD increased the Atlantic salmon smolt microbiota diversity, suggesting a positive association between the intestinal microbial community and fish health during seawater transfer. The reported knowledge can be applied to surveil the microbiome in smolt fish production, improving the performance of Atlantic salmon to seawater transfer.</p>
Including environmental covariates clarifies the relationship between endangered Atlantic salmon (Salmo salar) abundance and environmental DNA
<p><span>Collecting environmental DNA (eDNA) as a nonlethal sampling approach has been valuable in detecting the presence/absence of many imperiled taxa; however, its application to indicate species abundance poses many challenges. A deeper understanding of eDNA dynamics in aquatic systems is required to better interpret the substantial variability often associated with eDNA samples. Our sampling design took advantage of natural variation in juvenile Atlantic salmon (</span><span><em>Salmo</em> <em>salar</em></span><span>) distribution and abundance along 9 km of a single river in the Province of New Brunswick (Canada), covering different spatial and temporal scales to address the unknown seasonal impacts of environmental variables on the quantitative relationship between eDNA concentration and species abundance. First, we asked whether accounting for environmental variables strengthened the relationship between eDNA and salmon abundance by sampling eDNA during their spring seaward migration. Second, we asked how environmental variables affected eDNA dynamics during the summer as the parr abundance remained relatively constant. Spring eDNA samples were collected over a 6‐week period (12 times) near a rotary screw trap that captured approximately 18.6% of migrating smolts, whereas summer sampling occurred (i) at three distinct salmon habitats (9 times) and (ii) along the full 9 km (3 times). We modeled eDNA concentration as a product of fish abundance and environmental variables, demonstrating that (1) with inclusion of abundance and environmental covariates, eDNA was highly correlated with spring smolt abundance and (2) the relationships among environmental covariates and eDNA were affected by seasonal variation with relatively constant parr abundance in summer. Our findings underscore that with appropriate study design that accounts for seasonal environmental variation and life history phenology, eDNA salmon population assessments may have the potential to evaluate abundance fluctuations in spring and summer.</span></p>
Considering sampling bias in close-kin mark-recapture (CKMR) abundance estimates of Atlantic salmon
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Including environmental covariates clarifies the relationship between endangered Atlantic salmon (Salmo salar) abundance and environmental DNA
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Data from: Stock composition of juvenile salmon taken by an abundant, pursuit-diving seabird in the coastal waters of British
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McMurdo Sound, Antarctica: Benthic macrofaunal abundances in Explorers Cove in 1970s and 2010 and in Salmon Bay in 1988-89 and 2010
In 2010 we had the opportunity to revisit historical transects and experiments set up by Dayton et al. in the 1960s, 70s, and 80s. Using the SCINI ROV we were able to revisit sites we had dived previously, including some deeper sites that are no longer diveable by current United States Antarctic Program policies. Revisitng these sites enabled us to study and document long-term changes in benthic biota at McMurdo Sound, Antarctica. These are data on benthic macrofaunal abundance collected in the 1970s, late 1980s, and 2010. We are making these data available to researchers for future observations of community change in the nearly pristine environment of the Ross Sea, Antarctica.
Data from: Supportive breeding boosts natural population abundance with minimal negative impacts on fitness of a wild population of Chinook salmon
While supportive breeding programs strive to minimize negative genetic impacts to populations, case studies have found evidence for reduced fitness of artificially produced individuals when they reproduce in the wild. Pedigrees of two complete generations were tracked with molecular markers to investigate differences in reproductive success (RS) of wild and hatchery-reared Chinook salmon spawning in the natural environment to address questions regarding the demographic and genetic impacts of supplementation to a natural population. Results show a demographic boost to the population from supplementation. On average, fish taken into the hatchery produced 4.7 times more adult offspring, and 1.3 times more adult grand-offspring than naturally reproducing fish. Of the wild and hatchery fish that successfully reproduced, we found no significant differences in RS between any comparisons but hatchery-reared males typically had lower RS values than wild males. Mean relative reproductive success (RRS) for hatchery F1 females and males was 1.11 (p = 0.84) and 0.89 (p = 0.56), respectively. RRS of hatchery-reared fish (H) that mated in the wild with either hatchery or wild origin (W) fish were generally equivalent to WxW matings. Mean RRS of HxW and HxH matings was 1.07 (p = 0.92) and 0.94 (p = 0.95), respectively. We conclude that fish chosen for hatchery rearing did not have a detectable negative impact on the fitness of wild fish by mating with them for a single generation. Results suggest that supplementation following similar management practices (e.g., 100% local, wild-origin brood stock) can successfully boost population size with minimal impacts on the fitness of salmon in the wild.
Data from: Supportive breeding boosts natural population abundance with minimal negative impacts on fitness of a wild population of Chinook salmon
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F I G U R E 2 in Estimating multiple years, tributary-specific, and overall Atlantic salmon smolt abundance in a large Canadian catchment using capture-mark-recapture experiments
F I G U R E 2 Schematic representation of the different capture–mark–recapture (CMR) events occurring in the Restigouche catchment in a given year. The letters C, M, and R correspond to the captured, marked, and recaptured fish, respectively. The total nonmarked smolt population Nmtot comprises four components: Kedgwick, Upsaquitch, and Matapedia abundance Nm, and the smolt abundance originating from the rest t 1:3,t of the catchment Nmrest. Note that the "rest" component can vary between years because not all rotary screw traps (RST) are operated annually. t Each year, each operating upstream RST is associated with a CMR experiment. Marked smolts in the upstream RSTs (Mt,1:3) can also be recaptured at the downstream RSTs (Rt,1:5). Each downstream RST samples an unknown fraction of the total population of smolts migrating out of the catchment. Due to the low number of recaptures at the downstream RSTs, it is not possible to estimate this fraction, and it is confounded with the catchabilities at the downstream RSTs. Variables in square boxes are known, and variables in round boxes are unknown.
Data from: High summer macrophyte cover increases abundance, growth and feeding of juvenile Atlantic salmon
<p>Aquatic habitats are severely threatened by human activities. For anadromous species, managing freshwater habitats to maximise production of more, larger juveniles could improve resilience to threats in marine habitats and enhance population viability. In some juvenile salmonid habitats, complexity created by large substrates provides resources and reduces competitive interactions, thereby promoting juvenile production. In lowland rivers, which lack large substrates, aquatic plants might provide similar complexity and enhance fish productivity. To test the influence of aquatic plants on juvenile Atlantic salmon and sympatric brown trout in a lowland river, we directly manipulated cover of the dominant macrophyte, <i>Ranunculus</i>, in nine sites during summer and autumn for two years. We quantified the abundance, site retention and growth of salmon and trout under high, medium and low <i>Ranunculus</i> cover. To investigate the effects of <i>Ranunculus </i>cover on feeding opportunities and interspecific competition, we quantified available prey biomass and body size, fish diet composition, and compared dietary niche overlap. Experimentally increased <i>Ranunculus</i> cover supported higher salmon abundance in summer and autumn, and higher site retention and growth of salmon in summer. Trout abundance and growth were not influenced by <i>Ranunculus</i> cover, but trout site retention doubled in high relative to low cover sites. Despite weak effects of <i>Ranunculus </i>cover on prey availability, salmon and trout inhabiting high cover sites consumed larger prey and a higher biomass of prey. Furthermore, dietary niche overlap was lower in high relative to low cover sites, suggesting that abundant <i>Ranunculus </i>reduced interspecific competition. This field experiment shows that high <i>Ranunculus </i>cover can support more and better growing juvenile salmon, and facilitate foraging and co-existence of sympatric salmonid species. Maintaining or enhancing natural macrophyte<i> </i>cover can be achieved through sympathetic in-river and riparian vegetation management and mitigating pressures on them, such as sediment inputs and low flows, or through planting. Further research should test whether<i> </i>macrophyte cover benefits propagate to subsequent life-stages, particularly juvenile overwintering associated with high mortality. This knowledge, in combination with our findings, would further clarify whether beneficial juvenile habitat can improve the viability of at-risk salmonid populations. Overall, our findings suggest that the aims of river restoration might be achieved through promotion of instream aquatic vegetation.</p>
Data from: High summer macrophyte cover increases abundance, growth and feeding of juvenile Atlantic salmon
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