Sustainable aquaculture and aquatic resources management

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Table of Contents for Canadian Journal of Fisheries and Aquatic Sciences. List of articles from both the latest and ahead of print issues.

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When does hypoxia affect management performance of a fishery? A management strategy evaluation of Dungeness crab (Metacarcinus magister) fisheries in Hood Canal, Washington, USA

Published on 21/3/2017
Canadian Journal of Fisheries and Aquatic Sciences, e-First Articles. <br/> Management strategies for fisheries typically do not account for environmental stressors, such as hypoxia (dissolved oxygen < 2 mg·L−1). Hypoxia can lead to shoaling of organisms into normoxic habitats, enhancing catchability, which could reduce the performance of fishery management strategies. Here, we conducted a management strategy evaluation of Dungeness crab (Metacarcinus magister) fisheries in Hood Canal, Washington, a seasonally hypoxic fjord in Puget Sound. Specifically, we asked whether the current management strategy was robust to hypoxia-induced catchability changes under alternative scenarios of illegal take, incidental capture mortality, and reproductive limitation. We find that the management strategy performed well to changes in catchability when illegal and incidental fishing mortality was low and fishing did not lead to reproductive limitation. However, the performance eroded markedly (reduced long-term catch and (or) population and higher catch variation) under the alternative scenarios. These findings underscore the benefit of applying an ecosystem approach to fisheries management because it identifies potential risks to management strategies in systems subject to environmental change.

Managing mixed-stock fisheries: genotyping multi-SNP haplotypes increases power for genetic stock identification

Published on 23/1/2017
Canadian Journal of Fisheries and Aquatic Sciences, Volume 74, Issue 4, Page 429-434, April 2017. <br/> 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 of up to 17 percentage points when multi-SNP haplotypes were used. Haplotyping multiple SNPs shows promise to improve the accuracy of assigning unknown fish to population of origin whenever haplotype data are available.

Is motivation important to brook trout passage through culverts?

Published on 22/1/2017
Canadian Journal of Fisheries and Aquatic Sciences, e-First Articles. <br/> 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 culverts and shows that attempt rate is a dynamic phenomenon, variable over time and among individuals. It also presents methods that could be used to investigate other species’ motivation to pass natural or anthropogenic barriers.

Population biology of infectious diseases shared by wild and farmed fish

Published on 17/1/2017
Canadian Journal of Fisheries and Aquatic Sciences, Volume 74, Issue 4, Page 620-628, April 2017. <br/> 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 related wild fishes in some coastal seas, changing the dynamics of their infectious diseases. Transport and trade of seafood, feed, eggs, and broodstock bring pathogens into new regions and into contact with naïve hosts. Density-dependent transmission creates threshold effects where disease can abruptly switch from endemic to epizootic dynamics. Hydrodynamics allow pathogens to disperse broadly, interconnecting farms into metapopulations of domesticated host fish in regions that also support related species of wild fish. Spillover and spillback dynamics of pathogen transmission between wild and farmed fish can create novel transmission pathways or bioamplify pathogen abundance, potentially depressing or endangering wild fish. Mortality from natural predator–prey interactions may be synergistic or compensatory with these increased infections. Domestic environments may favour the evolution of undesirable pathogen traits, such as virulence and drug resistance, leading to the emergence of strains that cause high mortality and (or) evade treatment. Overall, these changes to the dynamics of infectious disease in coastal seas impose new constraints on the sustainability of both wild and farmed fish.

Development and evaluation of a habitat suitability model for young lake sturgeon (Acipenser fulvescens) in the North Channel of the St. Clair River, Michigan

Published on 1/12/2016
Canadian Journal of Fisheries and Aquatic Sciences, e-First Articles. <br/> We evaluated the quantity, quality, and spatial distribution of riverine nursery habitat for larval, young-of-year (YOY), and juvenile (<500 mm) lake sturgeon (Acipenser fulvescens) in the North Channel of the St. Clair River (SCR), Michigan, using habitat suitability modeling (HSM) and fish collections. This HSM was developed using georeferenced habitat information on substrates, invertebrate densities, benthic flow velocities, and water depth. High-quality habitat comprised 29.1% of the study area, primarily in river bends and other areas where water velocities were highly varied. In all, 283 larval lake sturgeon were collected, with the majority found in high-quality habitat (81%) and heavily clustered in three locations (91.2% of total catch). Substrate composition and benthic flow velocity were the best indicators of observed larval catch-per-unit-effort (CPUE) patterns. Available data on captured YOY and juveniles were used to corroborate modeled habitat output and revealed strong associations between modeled habitat conditions and young lake sturgeon presence. An abundance of suitable habitat for young lake sturgeon within the North Channel of the SCR suggests that lack of suitable spawning habitat or high mortality early in life limits recruitment success in this system.

Cause or consequence? Exploring the role of phenotypic plasticity and genetic polymorphism in the emergence of phenotypic spatial patterns of the European eel

Published on 30/11/2016
Canadian Journal of Fisheries and Aquatic Sciences, e-First Articles. <br/> The European eel (Anguilla anguilla), and generally, temperate eels, are relevant species for studying adaptive mechanisms to environmental variability because of their large distribution areas and their limited capacity of local adaptation. In this context, GenEveel, an individual-based optimization model, was developed to explore the role of adaptive phenotypic plasticity and genetic-dependent habitat selection, in the emergence of observed spatial life-history traits patterns for eels. Results suggest that an interaction of genetically and environmentally controlled growth may be the basis for genotype-dependent habitat selection, whereas plasticity plays a role in changes in life-history traits and demographic attributes. Therefore, this suggests that those mechanisms are responses to address environmental heterogeneity. Moreover, this brings new elements to explain the different life strategies of males and females. A sensitivity analysis showed that the parameters associated with the optimization of fitness and growth genotype were crucial in reproducing the spatial life-history patterns. Finally, it raises the question of the impact of anthropogenic pressures that can cause direct mortalities but also modify demographic traits and act as a selection pressure.

Mercury bioaccumulation increases with latitude in a coastal marine fish (Atlantic silverside, Menidia menidia)

Published on 30/11/2016
Canadian Journal of Fisheries and Aquatic Sciences, e-First Articles. <br/> Human exposure to the neurotoxic methylmercury (MeHg) occurs primarily via the consumption of marine fish, but the processes underlying large-scale spatial variations in fish MeHg concentrations [MeHg], which influence human exposure, are not sufficiently understood. We used the Atlantic silverside (Menidia menidia), an extensively studied model species and important forage fish, to examine latitudinal patterns in total mercury (Hg) [Hg] and [MeHg]. Both [Hg] and [MeHg] significantly increased with latitude (0.014 and 0.048 μg MeHg·g dry weight−1 per degree of latitude in juveniles and adults, respectively). Four known latitudinal trends in silverside traits help explain these patterns: latitudinal increase in MeHg assimilation efficiency, latitudinal decrease in MeHg efflux, latitudinal increase in weight loss due to longer and more severe winters, and latitudinal increase in food consumption as an adaptation to decreasing length of the growing season. Given the absence of a latitudinal pattern in particulate MeHg, a diet proxy for zooplanktivorous fish, we conclude that large-scale spatial variation in growth is the primary control of Hg bioaccumulation in this and potentially other fish species.

The effects of riparian disturbance on the condition and summer diets of age-0 brook trout (Salvelinus fontinalis) in three central Appalachian streams

Published on 28/11/2016
Canadian Journal of Fisheries and Aquatic Sciences, e-First Articles. <br/> Forested headwater streams are dependent on their riparian zones for many critical goods and services. It is assumed that riparian disturbance affects stream food webs, but for some ecologically and economically important taxa like brook trout (Salvelinus fontinalis), little research has been performed. This study found that intense but spatially limited riparian disturbance resulted in significant but context-dependent changes in the diets and condition of age-0 brook trout in three central Appalachian streams. Dietary shifts in two of the streams appeared to enable age-0 brook trout to maintain or increase condition following riparian tree removal. A significant relationship between fish condition and the importance of Ephemeroptera as prey was observed. The lack of dietary shift to energetically important ephemeropterans coincided with decreased fish condition within one stream previously identified to be mildly impacted by acid precipitation. The context within which riparian disturbance occurs plays an important role in determining the overall impact to age-0 brook trout and should be an important consideration in future regulatory and management decisions.

Omic-style statistical clustering reveals old and new patterns in the Gulf of Maine ecosystem

Published on 28/11/2016
Canadian Journal of Fisheries and Aquatic Sciences, e-First Articles. <br/> The burgeoning of omic technology has spawned a new subfield of statistics aimed at interpreting the complex information contained in omic data. Some of these statistical methods can be applied to any data set with taxonomic counts, and they have the potential to provide additional insights over traditional approaches. We test this potential by reanalyzing a well-studied zooplankton data set — the Gulf of Maine continuous plankton recorder series — using a modified Dirichlet-multinomial mixture (DMM) model. The data set has ∼50 years of approximately monthly samples along a transect from Boston, USA, to Yarmouth, Canada. The results from the DMM analysis were largely consistent with previous analyses but also provided new insights. Notably, the Calanus-dominated communities that returned following a reduction in the 1990s showed a loss of background diversity, suggesting a shift in sources and possibly higher vulnerability of these communities. The DMM analysis also revealed a breakdown of seasonal ecological succession in the 1990s. These changes could be a precursor to similar changes in other Calanus-dominated systems. The approach demonstrates a path toward linking traditional analyses with recent omic-style analyses.

Empirical evidence of plasticity in life-history characteristics across climatic and fish density gradients

Published on 24/11/2016
Canadian Journal of Fisheries and Aquatic Sciences, Volume 74, Issue 4, Page 464-474, April 2017. <br/> Understanding how environmental productivity and resource competition influence somatic growth rates and plasticity in life-history traits is a critical component of population ecology. However, evolutionary effects often confound the relationship between plasticity in life-history characteristics and environmental productivity. We used a unique set of experimentally stocked populations of rainbow trout (Oncorhynchus mykiss) to empirically test predictions from life-history theory relating to patterns in immature growth rates, age- and size-at-maturity, and the energy allocated into reproduction across climatic and fish density gradients. Our results support theoretical predictions that plasticity in life-history characteristics is a function of environmental variables. In particular, we demonstrate that immature growth rates are best explained by climatic and density-dependent competition effects and that age-at-maturity and the energy allocated to reproduction depends on juvenile growth conditions. Empirical evidence of these relationships helps to improve our understanding of optimal life-history strategies of fish populations.

Modelling the impact of poaching on metapopulation viability for data-limited species

Published on 7/11/2016
Canadian Journal of Fisheries and Aquatic Sciences, e-First Articles. <br/> We developed a spatially explicit simulation model of poaching behaviour to quantify the relative influence of the intensity, frequency, and spatial distribution of poaching on metapopulation viability. We integrated our model of poaching with a stochastic, habitat-based, spatially explicit population model, applied it to examine the impact of poaching on northern abalone (Haliotis kamtschatkana) metapopulation dynamics in Barkley Sound, British Columbia, Canada, and quantified model sensitivity to input parameters. While demographic parameters remained important in predicting extinction probabilities for northern abalone, our simulations indicate that the odds of extinction are twice as high when populations are subjected to poaching. Viability was influenced by poaching variables that affect the total number of individuals removed. Of these, poaching mortality was the most influential in predicting metapopulation viability, with each 0.1 increase in mortality rate resulting in 22.6% increase in the odds of extinction. By contrast, the location and spatial correlation of events were less important predictors of viability. When data are limited, simulation models of poaching combined with sensitivity analyses can be useful in informing management strategies and future research directions.

Climate change alters the quantity and phenology of habitat for lake trout (Salvelinus namaycush) in small Boreal Shield lakes

Published on 3/11/2016
Canadian Journal of Fisheries and Aquatic Sciences, e-First Articles. <br/> 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 minimum volumes of optimal oxythermal habitat. Our results suggest that future warming will impose greater thermal stress on lake trout, but may be tempered by longer springs.

Effects of multispecies and density-dependent factors on MSY reference points: example of the Baltic Sea sprat

Published on 3/11/2016
Canadian Journal of Fisheries and Aquatic Sciences, e-First Articles. <br/> In this paper, maximum sustainable yield (MSY) parameters for the Baltic Sea sprat (Sprattus sprattus) are estimated in relation to pressure from cod (Gadus morhua) predation and the influence of density dependence on sprat growth. This study is based on long-term deterministic and stochastic simulations in which sprat density-dependent growth and predation mortality are considered. The resultant model is a relatively simple tool that allows for streamlined analyses of problems typically approached using complex multispecies models. The analysis indicates that estimates of the MSY parameters (i.e., MSY and FMSY) and equilibrium biomass differ significantly between approaches that hold growth and natural mortality constant and those that allow for density-dependent growth and natural mortality. Based on the cod biomass observed in the 1980s, the MSY parameters estimated by a model that accounts for density-dependent growth and by a model assuming constant growth may differ by a factor of 2. As such, the MSY parameters decline (approximately linearly) with the size of the cod stock.

Modeling the implications of stock mixing and life history uncertainty of Atlantic bluefin tuna

Published on 2/11/2016
Canadian Journal of Fisheries and Aquatic Sciences, e-First Articles. <br/> Atlantic bluefin tuna (Thunnus thynnus) is currently managed as two separate eastern and western stocks, despite information indicating considerable stock mixing. Using a simulation model, we explored how scenarios of population-specific migration and uncertainty in aspects of bluefin tuna biology affect the magnitude, distribution, and mixed stock nature of the resource and catch of its associated fisheries. The analytical framework was a stochastic, age-structured, stock-overlap model that was seasonally and spatially explicit with movement of eastern- and western-origin tuna informed by tagging and otolith chemistry data. Alternate estimates of movement and assumptions regarding maturity and recruitment regime for western-origin fish were considered. Simulation of the operating model indicated considerable stock mixing in the western and central Atlantic, which resulted in differences between the stock and population view of western bluefin tuna. The relative biomass of the western population and its spatial and temporal distribution in the Atlantic was sensitive to model assumptions and configurations. Simulation modeling can provide a means to ascertain the potential consequences of stock mixing on the assessment and management of fishery resources.

Flow and water temperature affect reproduction and recruitment of a Great Plains cyprinid

Published on 1/11/2016
Canadian Journal of Fisheries and Aquatic Sciences, e-First Articles. <br/> Conservation of stream fishes requires an understanding of how their reproduction and recruitment are affected by environmental conditions. Flow regulation and habitat loss in North American Great Plains streams threaten many native fishes, including pelagic-broadcast spawning cyprinids. Pelagic-broadcast spawning by flathead chub (Platygobio gracilis), a species declining throughout much of its extensive range, began after temperatures exceeded 15 °C in Fountain Creek, Colorado (USA), despite different annual flows. Alternatively, streamflow patterns controlled recruitment of juveniles because high-magnitude summer flows (spikes) reduced abundance of larvae hatched just prior to or during such events. Juvenile recruitment was highest for larvae hatched just after summer flow spikes occurred or during stable base flow periods. Understanding environmental conditions suitable for reproduction as well as subsequent recruitment should inform conservation actions, especially in flow-altered streams, and improve prospects for persistence of imperiled Great Plains cyprinids, including flathead chub.

Quantifying predation on Baltic cod early life stages

Published on 27/10/2016
Canadian Journal of Fisheries and Aquatic Sciences, e-First Articles. <br/> Predation on cod (Gadus morhua) eggs by sprat (Sprattus sprattus) and herring (Clupea harengus) is known to be one of the processes influencing reproductive success of the eastern Baltic cod and has been reported to have contributed to lack of recovery of the stock in the 1990s. This study quantifies the predation on cod eggs in the Bornholm Basin, the major spawning area of cod in the central Baltic Sea, in the 1990s in comparison with the second half of the 2000s. The analyses involve estimating daily consumption rates of predator populations, which are then compared with corresponding daily egg production rates. As a methodological advancement compared with earlier studies, spatially resolved information on predator distribution and abundance is utilized in quantifying predator stock size. This resulted in more realistic consumption estimates in relation to overall egg production compared with earlier studies that consistently overestimated predation pressure by clupeids. Our results suggest a generally lower predation pressure on cod eggs in the mid- to late 2000s, due to a combination of reduced predator abundance and lower daily rations by individual predators.

Estimation of occupancy, density, and abundance of larval lampreys in tributary river mouths upstream of dams on the Columbia River, Washington and Oregon

Published on 27/10/2016
Canadian Journal of Fisheries and Aquatic Sciences, e-First Articles. <br/> We estimated occupancy, density, and abundance of larval Pacific lamprey (Entosphenus tridentatus) and Lampetra spp. in tributary river mouths to impounded portions of the Columbia River, Washington and Oregon, using count data from deepwater electrofishing. Count data were analyzed by Bayesian methods using zero-inflated N-mixture models modified to include our experimentally derived estimate of capture probability of 0.70 (95% CI: 0.63–0.77). Lampetra spp. were only collected in river mouths in Bonneville Reservoir, while Pacific lamprey were also captured from river mouths in The Dalles and John Day reservoirs. In occupied river mouths, mean densities were commonly 0.2–0.3·m−2, but ranged from 0.18 to 1.72·m−2 for Pacific lamprey and 0.24 to 1.72·m−2 for Lampetra spp. Although there was spatial overlap, estimated density peaked in the Klickitat River mouth (556 600 larvae) for Pacific lamprey and in the Wind River mouth (544 800 larvae) for Lampetra spp. Our study demonstrates considerable larval rearing in river mouths to impounded portions of the Columbia River; however, information on survival is needed to evaluate the contribution of this production to population growth and conservation.

The North American invasive zooplanktivore Bythotrephes longimanus is less hypoxia-tolerant than the native Leptodora kindtii

Published on 20/10/2016
Canadian Journal of Fisheries and Aquatic Sciences, e-First Articles. <br/> The predatory cladoceran Bythotrephes longimanus (spiny water flea) has been invading lakes and damaging food webs across the central part of North America since the early 1980s. To understand its niche and that of the taxonomically related and native predatory cladoceran Leptodora kindtii, we investigated species survival after 12 h exposures to low dissolved oxygen (DO) concentrations in the laboratory. Bythotrephes longimanus (n = 690) exhibited a hypoxia tolerance limit (LC50) of 1.65 mg·L−1 DO (95% confidence interval: 1.59, 1.72 mg·L−1) and was significantly less tolerant of hypoxia than L. kindtii (n = 380), which exhibited an LC50 of 0.58 mg·L−1 DO (0.51, 0.65 mg·L−1). These lab-based physiological results are consistent with landscape-scale observations that B. longimanus successfully invades primarily mesotrophic and oligotrophic lakes, while L. kindtii inhabits a wider range of lakes that includes eutrophic ones. Climate change throughout the 21st century may increase the occurrence and severity of hypoxia in the hypolimnia of lakes and may provide a growing barrier to B. longimanus invasion.

Harbour seals target juvenile salmon of conservation concern

Published on 18/10/2016
Canadian Journal of Fisheries and Aquatic Sciences, e-First Articles. <br/> 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 diets often cannot provide sufficient detail. We combined data from two methods of scat analysis (DNA metabarcoding and morphological prey ID) to quantify the species and life stages of salmon (Oncorhynchus spp.) consumed by harbour seals (Phoca vitulina) in the Strait of Georgia, Canada, where juvenile Chinook (Oncorhynchus tshawytscha) and coho (Oncorhynchus kisutch) salmon survival is poor. Harbour seals primarily consumed adult salmon of lesser conservation concern in the fall (August–November): chum (Oncorhynchus keta: 18.4%), pink (Oncorhynchus gorbuscha: 12.6%), sockeye (Oncorhynchus nerka: 7.4%), Chinook (7.1%), and coho (1.8%). However, the opposite species trend occurred during the spring when seals preferred juvenile salmon of greater conservation concern (April–July): coho (2.9%), Chinook (2.9%), sockeye (2.5%), pink (1.4%), and chum (0.8%) — percentages that can equate to many individuals consumed. Our data suggest that harbour seals select juveniles of salmon species that out-migrate at ages >1 year and provide evidence of a potential causal relationship between harbour seal predation and juvenile salmon survival trends.

Dynamics of growth-based survival mechanisms in Japanese anchovy (Engraulis japonicus) larvae

Published on 13/10/2016
Canadian Journal of Fisheries and Aquatic Sciences, e-First Articles. <br/> Three growth-based survival mechanisms were tested for multiple cohorts of Japanese anchovy (Engraulis japonicus) larvae in Sagami Bay. Through otolith microstructure analysis, growth trajectories and histories of samples of the survivors were compared with those of the original populations to examine size- and growth-selective mortality to test the “bigger is better” and “growth-selective predation” mechanisms, respectively. The effects of growth rates on the timing of metamorphosis were examined to test the “stage duration” mechanism. The bigger is better and growth-selective predation mechanisms were detected to be effective in two and six of eight seasonal cohorts, respectively. Results contrary to the bigger is better and growth-selective predation mechanisms were obtained from three and two of eight cohorts, respectively. The stage duration mechanism was evaluated to be effective for both of two cohorts that were testable. Overall, none of the three mechanisms were universally appropriate for all of the cohorts. The relative contributions of the three mechanisms were dynamic, although the growth-selective predation mechanism was identified to be the major one in anchovy larvae in the study site.

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