Showing papers in "Canadian Journal of Fisheries and Aquatic Sciences in 2017"
TL;DR: Many physical, chemical, and biological processes in freshwater ecosystems mobilize the nutrient phosphorus (P) from sediments, which in turn may contribute to the formation of harmful algal blooms as mentioned in this paper.
Abstract: Many physical, chemical, and biological processes in freshwater ecosystems mobilize the nutrient phosphorus (P) from sediments, which in turn may contribute to the formation of harmful algal blooms...
155 citations
TL;DR: The objective was to determine how spatial distribution of samples and “bioinformatic stringency” affected eDNA-metabarcoding estimates of species richness compared with capture-based estimates in a 2.2 ha reservoir.
Abstract: Species richness is a metric of biodiversity that represents the number of species present in a community. Traditional fisheries assessments that rely on capture of organisms often underestimate true species richness. Environmental DNA (eDNA) metabarcoding is an alternative tool that infers species richness by collecting and sequencing DNA present in the ecosystem. Our objective was to determine how spatial distribution of samples and “bioinformatic stringency” affected eDNA-metabarcoding estimates of species richness compared with capture-based estimates in a 2.2 ha reservoir. When bioinformatic criteria required species to be detected only in a single sample, eDNA metabarcoding detected all species captured with traditional methods plus an additional 11 noncaptured species. However, when we required species to be detected with multiple markers and in multiple samples, eDNA metabarcoding detected only seven of the captured species. Our analysis of the spatial patterns of species detection indicated that ...
146 citations
TL;DR: The historical context of spatial models in fisheries science is overviewed, recent advances in spatial modeling are highlighted, and how spatial models have been incorporated into the management process are discussed.
Abstract: Fishery management decisions are commonly guided by stock assessment models that aggregate outputs across the spatial domain of the species. With refined understanding of spatial population structures, scientists have begun to address how spatiotemporal mismatches among the scale of ecological processes, data collection programs, and stock assessment methods (or assumptions) influence the reliability, and ultimately, appropriateness of regional fishery management (e.g., assigning regional quotas). Development and evaluation of spatial modeling techniques to improve fisheries assessment and management have increased rapidly in recent years. We overview the historical context of spatial models in fisheries science, highlight recent advances in spatial modeling, and discuss how spatial models have been incorporated into the management process. Despite limited examples where spatial assessment models are used as the basis for management advice, continued investment in fine-scale data collection and associated...
78 citations
TL;DR: Data from two methods of scat analysis were combined to quantify the species and life stages of salmon consumed by harbour seals in the Strait of Georgia, Canada, where juvenile Chinook and coho salmon survival is poor.
Abstract: Knowing the species and life stages of prey that predators consume is important for understanding the impacts that predation may have on prey populations, but traditional methods for determining di...
69 citations
TL;DR: In this paper, a spatial dynamic factor analysis (SDFA) model was developed to decompose covariation in multispecies catch rates into components representing spatial variation and fishing behavior.
Abstract: Estimating trends in abundance from fishery catch rates is one of the oldest endeavors in fisheries science. However, many jurisdictions do not analyze fishery catch rates due to concerns that these data confound changes in fishing behavior (adjustments in fishing location or gear operation) with trends in abundance. In response, we developed a spatial dynamic factor analysis (SDFA) model that decomposes covariation in multispecies catch rates into components representing spatial variation and fishing behavior. SDFA estimates spatiotemporal variation in fish density for multiple species and accounts for fisher behavior at large spatial scales (i.e., choice of fishing location) while controlling for fisher behavior at fine spatial scales (e.g., daily timing of fishing activity). We first use a multispecies simulation experiment to show that SDFA decreases bias in abundance indices relative to ignoring spatial adjustments and fishing tactics. We then present results for a case study involving petrale sole (...
62 citations
TL;DR: While the presence of shelter decreased stress hormone levels following human disturbance, it also decreased growth and smolt migration success, an effect particularly pronounced at high densities, and it is suggested that this type of structural enrichment should be avoided for Atlantic salmon smolts held at high density.
Abstract: Hatchery-reared salmonids released into the wild generally have poor survivability compared with wild conspecifics. To assess potential hatchery rearing improvements, behavioral and physiological effects of reducing animal density and adding in-tank shelter were investigated. Atlantic salmon (Salmo salar) parr were placed in barren or shelter-enriched tanks at high or low density up until release as smolts. Lowered density rendered positive effects on growth and intestinal barrier function, and both lowered density and shelter decreased conspecific aggression, as inferred by fin damage. Furthermore, while the presence of shelter decreased stress hormone levels following human disturbance, it also decreased growth and smolt migration success, an effect particularly pronounced at high densities. Therefore, we suggest that this type of structural enrichment should be avoided for Atlantic salmon smolts held at high densities and conclude that a lowered animal density with or without shelter has the highest po...
57 citations
TL;DR: Converting juvenile Chinook salmon into adult equivalents, it is found that by 2015, pinnipeds consumed double that of resident killer whales and six times greater than the combined commercial and recreational catches.
Abstract: Conflicts can arise when the recovery of one protected species limits the recovery of another through competition or predation. The recovery of many marine mammal populations on the west coast of t...
57 citations
TL;DR: The results highlight the importance of urea and lipid extraction and demonstrate the confounding effects of these compounds, making it impossible to use C:N of non-urea-extracted samples as a basis for adjustment of δ13C.
Abstract: Stable isotope analysis (SIA) is becoming a commonly used tool to study the ecology of elasmobranchs. However, the retention of urea by elasmobranchs for osmoregulatory purposes may bias the analysis and interpretation of SIA data. We examined the effects of removing urea and lipid on the stable isotope composition of 14 species of sharks, skates, and rays from the eastern North Pacific Ocean. While effects were variable across taxa, removal of urea generally increased δ15N and C:N. Urea removal had less influence on δ13C, whereas extracting urea and lipid generally increased δ15N, C:N, and δ13C. Because C:N values of nonextracted tissues are often used to infer lipid content and adjust δ13C, shifts in C:N following urea extraction will change the inferred lipid content and bias any mathematical adjustment of δ13C. These results highlight the importance of urea and lipid extraction and demonstrate the confounding effects of these compounds, making it impossible to use C:N of non-urea-extracted samples as ...
55 citations
TL;DR: Evaluating the utility of multi-SNP haplotyping for mixture analysis in western Alaska Chinook salmon found it increased the accuracy of mixture analysis for closely related populations by up to seven percentage points relative to single- SNP genotype data for a set of 500 loci.
Abstract: A common challenge for fisheries management is resolving the relative contribution of closely related populations where accuracy of genetic assignment may be limited. An overlooked method for increasing assignment accuracy is the use of multi-SNP (single nucleotide polymorphism) haplotypes rather than single-SNP genotypes. Haplotypes increase power for detecting population structure, and loci derived from next-generation sequencing methods often contain multiple SNPs. We evaluated the utility of multi-SNP haplotyping for mixture analysis in western Alaska Chinook salmon (Oncorhynchus tshawytscha). Multi-SNP haplotype data increased the accuracy of mixture analysis for closely related populations by up to seven percentage points relative to single-SNP genotype data for a set of 500 loci; 90% accuracy was achievable with as few as 150 loci with multi-SNP haplotypes but required at least 300 loci with single-SNP genotypes. Individual assignment to reporting groups showed an even greater increase in accuracy ...
52 citations
TL;DR: Steelhead trout adult abundance time series along with smolt-to-adult return (smolt survival) time series from 48 populations from Washington, Oregon, and the Keogh River in British Columbia are analyzed.
Abstract: Examination of population abundance and survival trends over space and time can guide management and conservation actions with information about the spatial and temporal scale of factors affecting ...
50 citations
TL;DR: The abundance of domesticated fishes now dwarfs related wild fishes in some coastal seas, changing the dynamics of their infectious diseases, causing an increasing shortfall in wild seafood supply and an expansion of aquaculture.
Abstract: Global fisheries landings ceased increasing decades ago, causing an increasing shortfall in wild seafood supply and an expansion of aquaculture. The abundance of domesticated fishes now dwarfs rela...
TL;DR: It is concluded that CO2 altered silver and bighead carp movement in outdoor ponds and recommend further research to determine barrier effec...
Abstract: Resource managers need effective methods to prevent the movement of silver carp (Hypophthalmichthys molitrix) and bighead carp (Hypophthalmichthys nobilis) from the Mississippi River basin into the...
TL;DR: Across lakes, eDNA concentrations were greater and more homogeneous in the water column during mixis; however, when stratified, e DNA concentrations were great in the hypolimnion; overall, the findings demonstrate that eDNA techn...
Abstract: Environmental DNA (eDNA) sampling has proven to be a valuable tool for detecting species in aquatic ecosystems. Within this rapidly evolving field, a promising application is the ability to obtain ...
TL;DR: The distribution of native brook trout in eastern North America is often limited by temperature and introduced brown trout, the relative importance of which is not well understood.
Abstract: The distribution of native brook trout (Salvelinus fontinalis) in eastern North America is often limited by temperature and introduced brown trout (Salmo trutta), the relative importance of which i...
TL;DR: In this article, the authors proposed a method to estimate trends in relative stock abundance in fish stock assessments, which is a primary input to fish stock assessment and is essential for successful conservation and management.
Abstract: Estimated trends in relative stock abundance are a primary input to fish stock assessments. Accurate and precise estimates are essential for successful conservation and management. Scientifically d...
TL;DR: Attempt rate is used to assess motivation of 447 brook trout entering three culverts under a range of hydraulic, environmental, and biological conditions and shows a positive correlation between elevated motivation and successful passage.
Abstract: Culverts can restrict movement of stream-dwelling fish. Motivation to enter and ascend these structures is an essential precursor for successful passage. However, motivation is challenging to quantify. Here, we use attempt rate to assess motivation of 447 brook trout (Salvelinus fontinalis) entering three culverts under a range of hydraulic, environmental, and biological conditions. A passive integrated transponder system allowed for the identification of passage attempts and success of individual fish. Attempt rate was quantified using time-to-event analysis allowing for time-varying covariates and recurrent events. Attempt rate was greatest during the spawning period, at elevated discharge, at dusk, and for longer fish. It decreased during the day and with increasing number of conspecifics downstream of the culvert. Results also show a positive correlation between elevated motivation and successful passage. This study enhances understanding of factors influencing brook trout motivation to ascend culvert...
TL;DR: The bodies of anguillid leptocephali are filled with transparent gelatinous material, possibly reducing predation rates and providing an energy reserve for swimming and metamorphosis, and first-feeding success linked to primary producers contributing to marine snow production.
Abstract: Recruitment declines of anguillid eels are difficult to understand because both anthropogenic impacts on juveniles and adults and oceanic changes affecting larval survival or dispersal may be contr...
TL;DR: A logistic regression revealed that data sharing was positively related to researchers with collaborative tendencies, who belong to a telemetry network, who are prolific publishers, and who express altruistic motives for their research.
Abstract: The potential for telemetry data to answer complex questions about aquatic animals and their interactions with the environment is limited by the capacity to store, manage, and access data across th...
TL;DR: Parentage-based tagging and genetic stock identification were used to identify individual coho salmon to specific populations and brood years and the overall accuracy of assignment was 100%, and to correct brood year within population was also 100%.
Abstract: Parentage-based tagging (PBT) and genetic stock identification (GSI) were used to identify individual coho salmon (Oncorhynchus kisutch) to specific populations and brood years. In total, 20 242 in...
TL;DR: An assessment of factors affecting the stock identification accuracy indicated that the identification success is largely defined by the interaction of genetic divergence and the baseline sample sizes.
Abstract: Addressing biocomplexity in fisheries management is a challenge requiring an ability to differentiate among distinct populations contributing to fisheries. We produced extensive genetic baseline data involving 36 sampling locations and 33 microsatellite markers, which allowed characterization of the genetic structure and diversity in a large Atlantic salmon (Salmo salar) population complex of the River Teno system, northernmost Europe. Altogether, we identified 28 hierarchically structured and genetically distinct population segments (global FST = 0.065) corresponding exceptionally well with their geographical locations. An assessment of factors affecting the stock identification accuracy indicated that the identification success is largely defined by the interaction of genetic divergence and the baseline sample sizes. The choice between the two statistical methods tested for performance in genetic stock identification, ONCOR and cBAYES, was not critical, albeit the latter demonstrated slightly higher ide...
TL;DR: A study of PIT-tagged sea lamprey ascending four fishways comprising three designs at two dams on the Connecticut River, USA suggested that although some lampreys were able to pass fishways, they did so with difficulty, and delays incur.
Abstract: This article describes a study of PIT-tagged sea lamprey (Petromyzon marinus) ascending four fishways comprising three designs at two dams on the Connecticut River, USA. Migration between dams was rapid (median migration rate = 23 km·day−1). Movement through the fishways was much slower, however (median = 0.02–0.33 km·day−1). Overall delay at dams was substantial (median = 13.6–14.6 days); many fish failed to pass (percent passage ranged from 29% to 55%, depending on fishway), and repeated passage attempts compounded delay for both passers and failers. Cox regression revealed that fishway entry rates were influenced by flow, temperature, and diel cycle, with most lampreys entering at night and at elevated flows, but with no apparent effect of sex or length. Overall delay was influenced by slow movement through the fishways, but repeated failures were the primary factor determining delay. These data suggest that although some lamprey were able to pass fishways, they did so with difficulty, and delays incur...
TL;DR: This article analyzed monitoring data from small Boreal Shield lakes to understand how variations in air temperature and precipitation affect the phenology and amount of habitat for lake trout (Salvelinus namaycush).
Abstract: We analyzed monitoring data (1970–2013) from small Boreal Shield lakes to understand how variations in air temperature and precipitation affect the phenology and amount of habitat for lake trout (Salvelinus namaycush). Annual air temperatures increased by ∼2 °C (significant in fall and winter). In response, ice cover was reduced by ∼19 days. Despite earlier ice-offs, springs became longer, allowing lake trout longer access to littoral regions when water temperatures were cool. Although summer surface water temperatures increased, the summer did not lengthen. Instead, later spring-warming and fall-cooling of lakes caused summer to shift later in the year, potentially delaying fall spawning. Complete loss of optimal oxythermal habitat volume occurred in all lakes and became more prevalent over time, more so in the darkest lakes. Although air temperatures did not become more variable, several habitat measures did, including mean summer surface water temperatures, duration of ice cover, timing of ice-off, and...
TL;DR: A spatially explicit simulation model was developed to determine how biological reference points differ among common population structures and to investigate the performance of management quantities that were calculated assuming incorrect spatial population dynamics.
Abstract: Misidentifying spatial population structure may result in harvest levels that are unable to achieve management goals. We developed a spatially explicit simulation model to determine how biological reference points differ among common population structures and to investigate the performance of management quantities that were calculated assuming incorrect spatial population dynamics. Simulated reference points were compared across a range of population structures and connectivity scenarios demonstrating the influence of spatial assumptions on management benchmarks. Simulations also illustrated that applying a harvest level based on misdiagnosed spatial structure leads to biased stock status indicators, overharvesting, or foregone yield. Across the scenarios examined, incorrectly specifying the connectivity dynamics (particularly misdiagnosing source–sink dynamics) was often more detrimental than ignoring spatial structure altogether. However, when the true dynamics exhibited spatial structure, incorrectly a...
TL;DR: In this paper, the state of knowledge and status of wild salmon in Canada have indeed improved after its adoption in 2005, using two indices of improvement: (i) monitoring effort and (ii) abundance of spawning adults.
Abstract: Canada’s Policy for Conservation of Wild Pacific Salmon has been heralded as a transformative approach to the management of wild salmon whereby conservation is the highest priority. Given that changes to the Policy are under consideration, it is timely that we understand whether our state of knowledge and the status of wild salmon in Canada have indeed improved after its adoption in 2005. To answer these questions, we used two indices of improvement: (i) monitoring effort and (ii) abundance of spawning adults. Our results, based on data for all species from British Columbia’s north and central coasts, show that monitoring effort has continued to erode, abundance of spawning adults has significantly declined for several species, the status of many salmon Conservation Units are in zones of concern, and 42% of the Conservation Units that we assessed as Red (threatened) would have improved in status had the Canadian fishery been reduced. We conclude with recommendations to help improve our knowledge of the st...
TL;DR: In this paper, the authors proposed a spatial-stream-network (SSN) model to estimate the population size of stream fishes using density surveys for trout species from 108 sites in a 735 km river network, and used block kriging to summarize discrete map areas and make population estimates at stream, river, and network scales.
Abstract: Population size estimates for stream fishes are important for conservation and management, but sampling costs limit the extent of most estimates to small portions of river networks that encompass 100s–10 000s of linear kilometres. However, the advent of large fish density data sets, spatial-stream-network (SSN) models that benefit from nonindependence among samples, and national geospatial database frameworks for streams provide the components to create a broadly scalable approach to population estimation. We demonstrate such an approach with density surveys for trout species from 108 sites in a 735 km river network. Universal kriging was used to predict a continuous map of densities among survey locations, and block kriging (BK) was used to summarize discrete map areas and make population estimates at stream, river, and network scales. The SSN models also accommodate covariates, which facilitates hypothesis testing and provides insights about factors affecting patterns of abundance. The SSN–BK population...
TL;DR: Results suggest that blacktip sharks exhibited intense bouts of fighting behaviour at the onset of hooking, while nurse and tiger sharks displayed more subdued acceleration values during capture.
Abstract: The response to capture is important in fisheries because it can reveal potential threats to species beyond fishing mortalities resulting from direct harvest. To date, the vast majority of studies ...
TL;DR: It is estimated that the maximum sustainable yield (MSY) of wild spawning fish in PWS has increased slightly, while in regions of Alaska without pink salmon hatchery programs the MSY has trip...
Abstract: Hatchery production of juvenile fish for release into the wild has been practiced for well over a century in an effort to increase the number of salmon available to harvest. In this study, we evaluate the net impact of the largest such program in North America, the hatchery program for pink salmon (Oncorhynchus gorbuscha) in Prince William Sound (PWS), Alaska. At the same time the hatchery program was increasing in output, there was a major change in productivity in the North Pacific so that throughout Alaska pink salmon increased dramatically in abundance between the 1970s and the 2000s. Using other regions of Alaska as reference sites, we estimate that the PWS hatchery program has increased the total catch by an average of 17 million fish, of which 8 million have been allocated to pay hatchery operating expenses. We estimate that the maximum sustainable yield (MSY) of wild spawning fish in PWS has increased slightly (28%), while in regions of Alaska without pink salmon hatchery programs the MSY has trip...
TL;DR: The spatial footprint of individual run-of-river (RoR) hydropower facilities is smaller than reservoir-storage hydroelectric projects and their impacts to aquatic ecosystems are often assumed to be...
Abstract: The spatial footprint of individual run-of-river (RoR) hydropower facilities is smaller than reservoir-storage hydroelectric projects and their impacts to aquatic ecosystems are often assumed to be...
TL;DR: In this article, the authors focus on understanding rates and drivers of changing temperature regimes in southcentral Alaska streams and their implications for the future of Alaska's water supply and water management.
Abstract: Climate is changing fastest in high-latitude regions, focusing our research on understanding rates and drivers of changing temperature regimes in southcentral Alaska streams and implications for sa...
TL;DR: A classic case of rapid change in body size of five species of Pacific salmon caught in Canadian waters, with a six-decade analysis (1951–2012), is revisited.
Abstract: Body size can sometimes change rapidly as an evolutionary response to selection or as a phenotypic response to changes in environmental conditions. Here, we revisit a classic case of rapid change in body size of five species of Pacific salmon (Oncorhynchus spp.) caught in Canadian waters, with a six-decade analysis (1951–2012). Declines in size at maturity of up to 3 kg in Chinook (Oncorhynchus tshawytscha) and 1 kg in coho salmon (Oncorhynchus kisutch) during the 1950s and 1960s were later reversed to match or exceed earlier sizes. In contrast, there has been little change in sockeye salmon (Oncorhynchus nerka) sizes and initial declines in pink (Oncorhynchus gorbuscha) and chum salmon (Oncorhynchus keta) sizes have halted. Biomass of competing salmon species contributed to changes in size of all five species, and ocean conditions, as reflected by the North Pacific Gyre Oscillation and the Multivariate ENSO (El Nino – Southern Oscillation) indices, explained variation in four of the species. While we hav...