Canadian Journal of Fisheries and Aquatic Sciences

Lake size effects on food webs have been most clearly demonstrated for predator fish across large gradients in ecosystem size and species richness. We isolated the influence of lake size to assess food web metrics in six fish species with diverse ecologies across five lakes with similar lake characteristics in Algonquin Provincial Park (Ontario, Canada) using d13C, d15N, and d34S. Lake volume was a significant factor influencing food web metrics across most fish species. However, relationships between lake volume and food web metrics (trophic position, littoral carbon use, d34S, and niche area) were weak. For most species, trophic position decreased with lake volume, opposite from previous studies that included a wider range of lake sizes and biodiversity. Littoral carbon use and d34S showed negative and positive relationships with lake volume, respectively, suggesting a shift to pelagic offshore energy in larger lakes. Albeit weak, our results highlight that multiple co-occurring fish species within a community can have similar responses in littoral carbon use, trophic position, d34S, and niche area across a small range of lake sizes.

Most of the fishing ground research focuses on real-time predictions and lacks continuous forecasting for future changes over a certain period. Traditional models characterized by large, single temporal scales lack effectiveness in accounting for the autocorrelation of environmental factors. Deep learning has demonstrated superior performance and promising development prospects due to its accurate and efficient ability to mine nonlinear information in the era of big data. Therefore, we take Ommastrephes bartramii as an example and constructed 28 different temporal scales and lead periods cases based on U-Net and compared them with GAM, NN and ConvLSTM model results. The input factors of this model are sea surface temperature (SST) and the output factors are the center fishing ground data (1998-2019). The results reveal that the optimal temporal scale and lead period for this model is 15 days and 4 on U-Net. The SST fluctuation information between different lead periods of environmental field and the coupling degree in fishing grounds may be essential factors affecting the model performance differences. It enhances marine fisheries understanding from artificial intelligence.

Floodplain habitat restoration has become a common component of river restoration throughout the Pacific Northwest and is critical to the recovery of Pacific salmon (Oncorhynchus spp.) and steelhead (O. mykiss), yet little information exists on the physical or biological response to these habitat restoration efforts. Using an extensive post-treatment design and a combination of remote sensing and field surveys, we sampled 17 floodplain projects designed to benefit anadromous fish in the Columbia River Basin. We detected significant increases in side channel metrics (area, length, and the ratio of bankfull side-channel to main channel length), sinuosity, pool frequency, large wood, and the Morphological Quality Index (MQI). On average, juvenile Chinook (O. tshawytsch), coho (O. kisutch), steelhead, and salmonid combined abundance was 1.17, 4.62, 1.62, and 1.65 times higher, respectively, in treatment reaches compared to control reaches, though these increases were only significant for steelhead and all salmonids combined. Our study demonstrated that a combination of remote sensing and field data can be used to monitor floodplain and instream habitat and detect fish response to floodplain restoration projects.

Bioenergetic modelling is valuable for addressing many questions in animal ecology. However, applying these models to wild animals is limited by challenges with collecting in situ energetics data. Accelerometers have emerged as a popular tool to estimate field metabolic rates. We conducted laboratory experiments using a swim tunnel respirometer on wild (n=28) and hatchery-origin (n=19) walleye (Sander vitreus) to calibrate acoustic accelerometer transmitters (InnovaSea V13A and V16AT) for estimating metabolic rate (ṀO2). Walleye (0.36-3.06 kg) underwent ramp-Ucrit swim trials (n=70) amongst temperatures (5-21°C). Using mixed-effects models, we analyzed critical swimming speed (Ucrit), swimming speed, tailbeat frequency, and ṀO2 as functions of body mass, acceleration, sex, and water temperature. ṀO2 decreased with body mass and increased with higher swimming speeds, acceleration values, and water temperatures. Notably, ṀO2 increased more rapidly with acceleration at higher temperatures. No mass-specific sex differences were observed across measured parameters, and there were no differences in Ucrit or ṀO2 between control and tagged fish. These findings support the use of accelerometers to generate field estimates of energy expenditure in wild walleye.

Climate change is poised to reshape ecological communities globally by driving species into new environments and altering interactions between species. Conservation efforts should not only address current pressures but also plan for future pressures, such as sensitive species moving into degraded environments or arising problematic trophic interactions. This study sought to assess how climate change may affect the end-of-century distributions of New Zealand’s native and non-native freshwater fish, including consequences for the overlap between trout (a non-native sports fish) and native species vulnerable to trout predation. Random forest modelling was used to predict end-of-century distributions for New Zealand’s freshwater fish based on six hydrologically downscaled global climate models across four representative concentration pathways. Severe climate change impacts could drive nine native fish species to extinction or near-extinction and cause substantial declines in another eight native species. Seven non-natives are also predicted to decline substantially, including a 30-40% reduction in the extent of trout. To avert these potential extinctions, it is crucial to mitigate climate change severity and improve land use impacting freshwater ecosystems.

How are fish prices determined in the largest formal market in the Solomon Islands? The Honiara Central Market is the country’s primary fresh produce market, serving as an important conduit between rural food producers and urban consumers. One distinctive characteristic of this market is that despite a diverse range of reef fish species being available, all reef fish are traded nominally as homogeneous goods with no price differentiation. Using transaction-level data collected from the market, we show the prevalence of informal pricing, wherein the unit price of fish is implicitly differentiated based on fish species groups, quality, and buyers’ attributes. This result aligns with our expectation that diverse species groups and qualities are traded in a competitive environment with many vendors and buyers, where reef fish are indeed traded as heterogeneous products. Although fish provide a vital source of food and income for Pacific Island countries, the pricing of this vital natural resource is poorly understood. Our study provides new insights into how fish prices are determined in a formal market within the context of small island developing states.

Hatchery-reared salmon often have lower fitness in the wild than wild fish, a difference that appears to result from rapid adaptation to the hatchery environment. Size at release is heritable and positively correlated with survival at sea. Therefore, selection should favor traits that promote fast growth in the hatchery even if those traits are maladaptive in the wild. Modifying hatchery conditions to reduce the variation in size among families should decrease the opportunity for selection. Using a mix of 15 full-sibling families of winter run steelhead (Oncorhynchus mykiss) we tested two modifications designed to benefit the normally slower-growing fish: (1) the addition of structure to rearing tanks and (2) increased water flow. Neither treatment substantially changed the variance in size at release relative to controls. Furthermore, there was a very high correlation among family mean size across all environments. We conclude that simple changes to the hatchery environment such as those tested here cannot overcome the large family effects and are unlikely to substantially reduce the opportunity for selection on size at release.

In Québec, Canada, brook charr (Salvelinus fontinalis) is the most sought-after species for recreational fisheries, which makes it economically important. To improve population monitoring and better anticipate climate change impacts on brook charr, bioenergetics models can be useful. The objective of this research was to evaluate the performance of a resident brook charr Wisconsin Energy Budget (WEB) model applied to an anadromous strain under two salinity treatments. Growth and food consumption were predicted by the model and compared to the observed values obtained after a 60-day experiment in the laboratory on fish reared in fresh or brackish water. Predictions for fish reared in fresh water better estimated growth rate and consumption than for fish reared in brackish water, for which growth was overestimated and consumption was underestimated. Overall, these results suggest that there is a difference for the WEB model’s predictions depending on the salinity and that observed food consumption is predicted more accurately than growth.

In the Bay of Fundy, American lobster (Homarus americanus) abundance has soared since the early 1990s, and predators have declined, either of which could have caused juvenile lobster populations in preferred hard-bottom habitat to expand onto less-protective mud bottom. To investigate whether juvenile lobsters have increased use of mud bottom, we used SCUBA surveys (1989-2021) in Maces Bay and Seal Cove, in the Bay of Fundy. Whereas the 1990s surveys found no juveniles on mud at either site (though they were present on hard bottom), in subsequent decades, juveniles inhabited mud burrows at densities of 0.00039 m-2 to 0.0081 m-2. In Maces Bay, mud occupancy occurred after juvenile density increases on hard bottom, but evidence was mixed as to whether increased competition within hard-bottom habitat drove this change. Concurrent cod, haddock, hake, and wolffish declines suggest reduced predation also increased occupancy and survival on mud. Although it supports low juvenile densities, mud habitat may contribute to recruitment given its prevalence, particularly as warming seas allow lobster recruitment into cooler, deeper water over mud bottom.

Identification of ecologically significant units at different spatial scales is essential for management of biodiversity attributes. This case study illustrates a coupled methodological approach to delineate benthic habitats and associated assemblages at different spatial scales. Two complementary analyses were employed based on the occurrences of 99 epibenthic invertebrate species in Atlantic Canada, sampled during depth-stratified random trawl sets. To identify epibenthic assemblage types, isometric feature mapping and partitioning around medoids (ISOPAM) was used in combination with a joint species distribution model (JSDM), which also produced continuous distribution surfaces across the spatial domain. ISOPAM identified nine significantly spatially coherent assemblages (biotopes) at spatial scales of hundreds of meters to hundreds of kilometers, with associated diagnostic species. Those assemblages were closely matched by eight regions of common profile using the JSDM, indicating strong environmental influences on their distributions. These smaller-scale assemblages were grouped into three biophysical units. The results from the JSDM were validated with independent data showing good congruence. This indicates that the spatial units ascribed to identified assemblages are robust and suitable for marine spatial planning and monitoring.

Growth during early life stages is critical to fish population persistence. Few studies explore how river discharge and thermal regimes impact growth dynamics of young-of-the-year (YOY) fishes. We used otolith biochronologies and generalised additive mixed models to partition the effects of age, individual, river, temperature, discharge, and variance in discharge on daily growth rates of YOY fishes with an opportunistic life-history strategy: Galaxias vulgaris and Gobiomorphus breviceps. Growth of both species increased with temperature. Galaxias growth decreased with discharge, while Gobiomorphus growth increased with lowered discharge but only to a point (ca. 1/3 of median discharge), after which growth plateaued. Floods had a strong negative effect on YOY growth. Our study systems and species had different characteristics to those that formed the basis of the Riverscape Recruitment Synthesis Model (RRSM) and may explain why our results were only partially consistent with flow predictions for opportunistic species of the RRSM. Further, Galaxias growth was a negative function of high-frequency, daily variation in flow, and we present testable hypotheses to explain this result.

Sedentary benthic species such as Alcyonacea corals form critical habitat for fishes and invertebrates. Assessing anthropogenic risks to these organisms requires unbiased, species distribution models (SDMs) that attempt to map probabilities of coral presence in relation to bio-physical ocean characteristics; however, in deep-water settings, the accuracy of SDMs is highly variable and dependent on spatial and taxonomic resolution. Here we investigated how data and model types affect SDM predictions of Alcyonacea probability of presence. We compared predictions from generalized additive models (GAMs) fitted to presence-absence observations over a stratified-random survey design with predictions from maximum entropy models (Maxent) fitted to presence-only bycatch records from commercial fisheries. We use a simulation analysis to show that both model types (i.e., GAM or Maxent) using presence-only bycatch data produced biased estimates of species distribution. Additionally, the maxent model fit using presence-only bycatch data produced biased estimates of performance metrics (AUC, TSS) that were overly optimistic. This study demonstrates a need for presence-absence data collected using a robust survey sampling design to fit SDMs that will better inform marine protected area placement while minimizing unnecessary economic losses, such as forgone fishing yield, due to sub-optimal placement.

Most studies of brown trout (Salmo trutta) populations in headwater streams have focused on the year-to-year variability in recruitment and survival, but only few analyzed long-term trends in trout densities, under both control and regulated flow conditions. Here, we conducted trend analyses of brown trout age class densities on 36 stream reaches over the 1990-2020 period, including reaches located in a bypassed section. We also investigated long-term trends in a panel of key environmental variables (water temperature, stream flow, current velocity and habitat suitability). We found that annual water temperatures significantly increased by a median of +0.21 °C per decade. Analyses of stream flow revealed only a few significant trends, including a general increase in median values in spring and a general decrease in fall. A significant general decline in adult trout densities was observed, although disparities between geographic areas were highlighted. This decline is likely due to multifactorial effects, including possible interacting factors. Our results highlight the need to maintain and extend long-term monitoring of trout populations, which should be combined with extensive environmental monitoring.

Adult Pacific salmon (Oncorhynchus spp.) in the Fraser River, British Columbia, can die trying to retrace and ascend the river network to their natal spawning grounds due to hydraulic barriers, where encounter velocities exceed swim speeds of adult salmon. We evaluated river hydraulics, river morphology, and swimming ability to better understand these potential hydraulic barriers. A 375 km centerline velocity survey of the Fraser Canyon identified 22 high velocity locations where the distribution of velocity within the reach could produce a hydraulic barrier. We identified and studied three flow types associated with these 22 high velocity locations: 1) plunging flows, 2) rapids, and 3) overfalls, using drone footage at various discharges to examine flow structure and compare surface velocities with swimming modes. Complex flow within the major hydraulic features highlight the spatial locations requiring anaerobic swimming and areas of potential recovery that change with discharge. This approach can be used to improve the understanding of fish migration limits in a natural river system and aid in future mitigation.

Many studies have investigated the loss of adaptive potential in endangered or exploited species experiencing recent population declines. Less research has studied adaptive genomic variation in small populations known to have persisted for long periods, despite the unique contribution that such populations provide for determining mechanisms underlying population persistence in evolutionary and conservation modeling. Small populations of Brook trout (Salvelinus fontinalis) have persisted in Cape Race, Newfoundland for >12,000 years. We used genotyping-by-sequencing data to investigate the demographic history and adaptive genomic variation of 26 populations with effective population sizes (Ne) ranging from 11 to 442, and to explore mechanisms underlying long-term persistence. We show that all populations experienced demographic declines following postglacial colonization but have remained in their current, small Ne state for thousands of years. We also reveal greater homozygosity in adaptive alleles within the smallest populations and found signatures of adaptive divergence in small populations relating to several abiotic and biotic factors. Our study illustrates how the demographic history of a species can influence the adaptive dynamics of small populations persisting over long time periods.

Sponges have been identified as ecosystem engineers, providing habitat structure for many other benthic organisms, but are vulnerable to the impacts of bottom contact fishing. The Sambro Bank Sponge Conservation Area (SBSCA) protects a globally unique aggregation of the glass sponge (Vazella pourtalesii) off the east coast of Canada. Here, we present the first comprehensive, high-resolution mapping study of this site. Multispectral multibeam echosounder (MBES) mapping at three operating frequencies and benthic drop camera surveys were conducted at the SBSCA in 2022. Video data were analysed to quantify the abundance and location of V. pourtalesii and all associated benthic fauna and sediment characteristics. Using the MBES data as predictor variables, the study created a generalized linear mixed model of V. pourtalesii presence in the SBSCA, with 90.1% accuracy. Four seafloor benthoscape classes were identified from the video imagery, with statistically distinct benthic macrofaunal communities associated with each class. The study creates a baseline assessment of the current community composition and habitat characteristics of the site, which can be used for future ecological monitoring and management.

Fixed-gear commercial fisheries are unique due to their occupancy nature, claiming areas of the ocean for discrete periods. As space conflicts arise from competing ocean uses, there is an increased need to understand and categorize fixed-gear fisheries to incorporate into marine spatial planning (MSP) efforts. We used fishery-dependent data and input from stakeholders to discern fleet dynamics of all gillnet and trap/pot fisheries in U.S. waters of the Northwest Atlantic Ocean. A Fixed-Gear Fishery Layer (FGFL) was developed combining fishery subgroups that were categorized around gear type, gear configuration, and species landed. Fishing effort from each subgroup was spatially allocated onto a 1 nm^2 (1.9 km^2) grid using methods that relied on the level of detail available from trip reporting and monitoring, each with differing degrees of spatial resolution. This stepwise process allowed trips reported with minimal spatial detail to be included while not compromising trips where greater spatial precision existed. We demonstrate how the FGFL has been used for two MSP projects focused on protected species conservation and wind energy development.

Conservation aquaculture has prevented extirpation of Upper Columbia River white sturgeon Acipenser transmontanus, but uncertainty remains on how hatchery-origin fish move between habitats located within Canada and the United States. We describe how core and home ranges of sturgeon varied by environmental (country, season) and biological (age, sex, size) factors and determined residence at important habitats. Core range represented areas where individuals spent the majority of their time while home range represented most areas occupied. Fidelity to specific habitats was high, with home ranges averaging 10 km2 and 50% of individuals occupied the same core range across their entire detection period. Only 12% of individuals had home ranges encompassing both countries. Core and home ranges were larger during the summer compared to winter and larger within the United States compared to Canada. Larger (>120 cm) sturgeon had increased core and home ranges. We documented spawning capable hatchery-origin males and confirmed their residence at spawning sites when spawning was detected. Results improve our understanding of species biology and directly inform adaptive management of population recovery.

Growth processes mediate survival and fecundity within fish populations, which are fundamental in regulating population dynamics. Therefore, accurate estimates of population scale and sustainable exploitation levels in contemporary fishery stock assessment models rely heavily on understanding and accurately characterizing growth processes. However, empirical studies that relate population-level changes in growth patterns to observable ecosystem and population conditions remain scarce. In particular, few studies directly consider the influence of intra-specific competition (i.e., cohort effects) on growth variability, and its associated implications for stock assessment estimates. Focusing on Alaska sablefish as a case study, we illustrate how multiple unprecedented large recruitment events since 2014 resulted in density-dependent declines in growth on the population-level scale, using a state-space growth model. Furthermore, we demonstrate how incorporating cohort-specific growth variability within the Alaska sablefish stock assessment model resulted in substantial differences in estimates of spawning biomass and recommended harvest levels. Overall, results from this study underscore the significance of cohort effects on growth processes and their implications for stock assessment models and associated harvest recommendations.

Hatchery production is common in salmonid management for harvest and conservation. Many hatcheries employ integrated broodstock programs, where wild-origin fish are included as broodstock and uni- or bi-directional gene flow between wild and hatchery components of the population is encouraged. Such approaches often assume that opportunistically obtained wild fish meet the genetic goals of minimizing hatchery–wild differentiation and maintaining genetic diversity. This may be incorrect if fine-scale spatial genetic structure exists. Here we investigate the population genetic consequences of such hatchery operations in coho salmon (Oncorhynchus kisutch) in a small river system featuring a large integrated broodstock program. We do so using 11 082 SNPs scored in wild-origin and hatchery-origin fish collected throughout the system. We found no evidence for genetic differentiation between hatchery-origin and wild-origin fish, no evidence of lowered genetic diversity in hatchery-origin fish, and no evidence for genetic differentiation among fish sampled throughout the river system. In addition, we did not detect inbreeding. Collectively, these results are consistent with current practices meeting integrated hatchery program goals of adequately sampling the genetic diversity present in wild-origin fish, although they may slightly reduce the effective population size of the combined population.

Sympatric populations of Atlantic cod with distinct spawning times in winter and spring have been identified within the Gulf of Maine. A new western Gulf of Maine stock assessment unit in U.S. waters lumps winter and spring spawning populations into a single stock unit and future monitoring and assessment of their abundance will require mixed stock analysis. The goal of this study was to evaluate the utility of otolith-based stock identification techniques to discriminate spawning populations. Significant differences in otolith structure and microchemistry were identified between winter and spring spawners with the highest degree of classification accuracy based on both features. Mixed stock analysis applied to fishery samples of unknown origin indicated the contemporary (2015-2016) commercial fishery is dominated by winter spawners. Exploratory classification of historical fishery samples suggested a change over time with spring and winter spawners present in near equal proportion in the early 1990s and winter spawners dominating in the early 1980s. Otolith-based stock composition analysis has the potential to support monitoring and assessment of cod populations in the Gulf of Maine.

Understanding spatial variation of aquatic food web structure and how ecosystem boundaries should be delineated is important. Here, we investigated the spatial variation in food web structure within Lake Erie across its three basins using δ13C and δ15N. Fish and lower trophic level composition were similar but differences in food web structure were observed between basins. The food web in the central basin had the smallest δ13C and δ15N range and total area based on stable isotope values by the aquatic community, likely due to chronic epibenthic hypoxia in the summer that affects fish habitat and resources. The largest δ15N range was in the east, driven by the high trophic position of lake trout present in this deepest basin. The western basin had the largest mean distance to the centroid (CD) of all three basins, indicating a large trophic diversity, probably due to high nutrient loadings and productivity. This research revealed spatial variability of food web structure in large lake ecosystems and the importance of considering smaller sub-units, such as basin, in large lakes.

For the live-bearing and egg-laying class of chondrichthyan fishes a three parameter logistic ‘maternity’ function with a variable upper asymptote, PMax, can be used to predict the average probability of a female giving birth or laying eggs in a season. Although fundamental to calculating the reproductive capacity of a population, few studies report maternity functions, with maturity functions often used as a proxy. Applying logistic models to simulated and empirical data showed that it was feasible to estimate PMax from maternal data and that accuracy, bias, and confidence interval coverage often improved compared to when a fixed value was used. However, sample sizes of 100–200 maternal females were typically required for accurate estimation of PMax. While maturity parameters could be estimated with greater accuracy, substituting them for maternity parameters overestimated lifetime reproductive output. Greater use of maternity functions has the potential to improve calculation of reproductive output in quantitative populations models. In addition to improvements in parameter estimation, this method involves fewer assumptions and enables statistical inferences to be made on frequency of reproduction.

Due to rapid ocean warming at higher latitudes, northward habitat shifts of the dominant anadromous fish in the Northern Hemisphere, chum salmon (Oncorhynchus keta), have recently been reported. Physiological development is considered to be a trigger for habitat shifts during early life. However, the possibility of physiological adaptations to future ocean warming is not fully understood, because data on the physiological traits of juveniles, such as metabolic rate and swimming performance, are limited. Using swim tunnel respirometers, we identified the metabolic traits of different-sized chum salmon juveniles originating from the Sanriku coastal river, Japan, which is far from the northern feeding grounds. The weight gain of >2 g steeply increased the prolonged swimming performance, and the metabolic cost of swimming against the southward current in the Sanriku coast decreased with weight gain under the sea water temperature range of 8–12 °C. These findings indicate weight gain and inhabiting areas with temperatures < 13 °C might provide potential benefits for northward migration. These results will be valuable when assessing the increased costs associated with changing ocean conditions.

Quantifying recruitment at the sibling group offers a powerful methodology for understanding density-dependent and environmental drivers of recruitment. We propose a modeling framework that combines sibship and abundance estimation datasets to estimate mean sibling group size, sibling group size process error, environmental and density-dependent effects on sibling group size, dispersal, and mortality rate. Geographic states in the model consist of discrete habitat patches connected via dispersal. Simulations were used to investigate the influence of sampling processes and sibling group size on parameter estimation within our modeling framework. Mean sibling-group size, environmental effects on recruitment, and dispersal rate among habitat patches were estimated with high accuracy under a wide range of sampling conditions, including imprecise out-of-model estimates of capture probability and subsampling both within and among habitat patches. Density-dependent effects on recruitment and process error tended to be estimated with lower accuracy, though accuracy improved as sibling group size or sampling intensity increased. The main contribution of this research is a flexible quantitative modeling framework for parameterizing mechanistic models of recruitment dynamics with empirical sibship data.