The diversity and adaptability that make small-scale fisheries socially resilient also make them statistically elusive and difficult for sample-based monitoring programs. The classical design-based approach, although conceptually elegant, has limited practical success as it depends on idealized conditions that small-scale fisheries rarely meet. By contrast, in a Bayesian model-based approach, the sampling design can become ignorable for inference, provided exchangeability and ignorability are acceptable properties. We devise a generalizable Bayesian survey sampling framework suited to respect the structural and logistical characteristics and limitations of small-scale fisheries and propose Polya-posterior-based estimates as official statistics. Their frequentist performance at a sampling fraction of only 5.5% in a two-stage sampling plan showed good performance when estimating, simultaneously, the landings of multiple species along with the total fishing effort. Measured accuracies were compatible with recommendations by FAO for sample-based fishery monitoring programs. We conclude that the Bayesian Polya urn is a promising fisheries sampling monitoring approach that can improve sustainable fisheries in the long run, worldwide.
The early life stage of animals shapes later survival and reproductive success, yet this period remains poorly understood for many fish species. We examined how early juvenile Round Goby Neogobius melanostomus, a highly invasive benthic fish, use habitat and food resources during development. We quantified spatial and temporal distribution patterns of early juveniles (<25 mm standard length, SL) through field sampling and then analysed diet composition and feeding-related morphology across size classes in the laboratory. We documented a developmental progression involving shifts in habitat use, foraging behaviour, and functional morphology with smaller juveniles (10.79 ± 0.32 mm SL) using pelagic zones and surface waters at night and consuming a broad array of zooplankton prey. Larger juveniles (23.62 ± 0.23 mm SL) increasingly moved to benthic habitats and a more specialized diet comprised in part by benthic macroinvertebrates. Morphological shifts in mouth and eye position aligned with this transition toward benthic foraging. Together, these results reveal integrated behavioural, morphological, and trophic changes during early development that likely reduce intraspecific competition and enhance establishment success in novel environments.
Twenty years after its adoption, Canada’s Wild Salmon Policy remains a globally significant framework intended to conserve Pacific salmon biodiversity, yet implementation has lagged behind its ambition. Drawing on ten papers in this Special Collection and discussions at a 2026 workshop of researchers and policy practitioners from Indigenous and federal governments, academia, and the non-profit sector, we synthesize five major themes that define the current state of Policy implementation. These themes highlight the need to invest in monitoring and assessment capacity, modernize decision frameworks for a changing climate, strengthen governance and accountability, integrate ecosystem processes, and advance rights-based co-governance with Indigenous Peoples. Building on these themes, we present 20 consensus recommendations intended to strengthen implementation of the Wild Salmon Policy and improve the long-term conservation and recovery of wild Pacific salmon.
In Saginaw Bay, a large productive embayment of Lake Huron, yellow perch (Perca flavescens) experienced a multi-decadal decline in adult abundance despite increasing fall age-0 abundance, suggesting a shift in recruitment dynamics. To assess the relative influence of ecosystem changes in altering yellow perch stock-recruit relationships, we compared candidate models, assuming either stationary or nonstationary dynamics, to evaluate potential shifts in the age at which year-class strength is set and the importance of environmental and biotic factors in explaining yellow perch age-0 and age-1 relative abundance (1970-2022). Results indicate that the age when year-class strength is established may have shifted from age-0 to age-1 in the early-2000s. Models incorporating nonstationarity best explained annual variation in yellow perch age-0 (~83%) and age-1 (~65%) relative abundance. High age-0 production was attributed to reduced competition and predation following the 2003-2004 collapse of alewife (Alosa pseudoharengus). However, increasing walleye (Sander vitreus) abundance, coincident with alewife declines, may have increased predation on age-1 yellow perch, leading to declines in age-1 relative abundance.
Information on the density and distribution of wide-ranging cetaceans is difficult to obtain but essential for assessing population status, evaluating risk from anthropogenic threats, and informing spatial management. In Canadian Pacific waters, several cetacean populations are recovering from historical depletion, yet recent patterns of habitat use and range expansion remain poorly documented, particularly in offshore areas. In summer 2018, we conducted systematic ship-based surveys throughout the coastal and offshore waters of British Columbia. Density surface modelling was applied to four commonly encountered species: humpback whale, fin whale, Dall's porpoise, and Pacific harbour porpoise. Our results provide the first systematic coverage and spatially-explicit density estimation for cetaceans in Canada’s entire Pacific Exclusive Economic Zone, and highlight areas of apparent reoccupation by recovering populations. Densities of fin whales and Dall’s porpoises were high in offshore waters west of the continental shelf break, whereas humpback whales and harbour porpoises primarily occurred in shelf and nearshore habitats. We discuss patterns of spatial separation and overlap among ecologically similar species in relation to habitat preferences and potential niche partitioning.
Seaward migration of diadromous fish is frequently impeded by anthropogenic barriers, yet the effects of consecutive obstacles on migration success remain poorly understood. We used acoustic telemetry to quantify passage success, barrier delay, and determinants of barrier passage for European Eel (Anguilla anguilla) at a pumping station and subsequent tidal sluice which are separated by a lake. Of 40 tagged individuals, 35 passed the pumping station and 27 successfully migrated seaward via the tidal sluice, with a mean cumulative barrier delay of 34 days. At the pumping station, eels in better body condition accumulated more passage opportunities before passing, while those with higher migration speeds required fewer. Eels that encountered more passage opportunities at the pumping station missed fewer at the tidal sluice. Passage at the pumping station increased with longer discharge events and higher wind speeds; lower moon illumination increased passage at the tidal sluice. Management must account for barrier-specific passage drivers and cumulative delays along source-to-sea migration routes.
Phenological changes are occurring around the world as climate change alters the timing of life history processes, such as animal migrations. This study demonstrates linkages between environmental change and Atlantic Salmon ( Salmo salar) migration dynamics. From 1983 to 2019, adult Atlantic Salmon returned earlier from the ocean to the Penobscot River, Maine. Median return dates advanced 12 days per decade for one sea-winter (1SW) salmon and 7 days per decade for multi-sea-winter (MSW) salmon. The strongest advances occurred late in the run, with the 95th percentile of adults returning 19 (1SW) and 23 (MSW) days earlier per decade. Late-stage advancement contracted run duration by 12 (1SW) and 17 (MSW) days per decade. Ocean seasonality—particularly the length of winter and summer based on sea surface temperatures—was most strongly associated with earlier returns. For some run segments, the timing of freshwater flows and the start of summer riverine temperatures influenced return dates. Findings reveal changes in Northwest Atlantic Ocean temperature phenology, link shifting environmental phenology to migration phenology, and identify concerns about Atlantic Salmon adaptiveness.
Riverine fishes are vulnerable to habitat fragmentation caused by interrupted access to vital habitats. Fragmentation using artificial structures can be used to limit the spread of invasive fishes by inhibiting movement between critical habitats. Thus, tradeoffs exist between maintaining connectivity for native species and restricting movement of invasive fishes. A nonphysical deterrent has been proposed to prevent invasive Grass Carp ( Ctenopharyngodon idella) from reaching spawning habitats in the Sandusky River, a tributary to Lake Erie, during late spring–summer. However, this timing overlaps with spawning periods of a suite of native fishes. We used acoustic telemetry and ichthyoplankton surveys to examine movement and spawning activity of multiple native species and to assess potential impacts of deterrent operation on reproduction. All species used the proposed deterrent location during the Grass Carp spawning period, and their movements corresponded with larval fish collections, indicating upstream spawning. These findings suggest the deterrent could unintentionally restrict native species’ access to essential habitats. Balancing habitat connectivity and invasive species control will likely depend on species-specific responses and careful timing of deterrent operation.
Declining water clarity driven primarily by increases in dissolved organic carbon (DOC; i.e. ‘brownification’) has been broadly reported across the Northern Hemisphere. In Ontario, Canada, increasing lake DOC concentrations have been reported regionally, however no broad spatial and temporal water clarity trends for Ontario lakes currently exist. Here, we use data from two provincial monitoring programs to analyze historical (1962–1984), contemporary (2008–2023), and long-term (1962–2023) changes in water clarity, measured as DOC concentration and Secchi depth, across 684 Ontario lakes that were sampled two to six times over the study period. Our findings suggest that water clarity in Ontario lakes has declined since 1962, with the greatest declines in water clarity occurring in the contemporary time period. Water clarity declines were greatest in oligotrophic lakes, where DOC concentrations were also shown to have increased over time. Our findings highlight the importance of regional, temporal, and trophic contexts when considering the magnitude and direction of water clarity changes in Ontario lakes.
Invasive carp, including Silver Carp (Hypophthalmichthys molitrix) and Grass Carp (Ctenopharyngodon idella), are increasing their range within the Mississippi River Basin, threatening native fishes and ecosystem function. We conducted a 3-year field test of a multi-modal deterrent that uses sound, bubbles, and light to test its ability to impede upstream passage by invasive carp. The test was performed at a lock and dam on the Cumberland River, Kentucky, USA, using acoustic telemetry to track the movements of Silver Carp, Grass Carp, and several native fish species. When the deterrent was operating, the estimated probability of upstream lock passage was 53% lower (95% CI: 41%–63%) for Silver Carp but 74% higher (95% CI: 3%–190%) for Grass Carp compared to times when the deterrent was not operating. Paddlefish (Polyodon spathula) passage was reduced by 43% (95% CI: 71% reduction to 9% increase), although this was not statistically significant. We detected no significant effects on Freshwater Drum (Aplodinotus grunniens) or Smallmouth Buffalo (Ictiobus bubalus). However, sample sizes were small for these native species, limiting our ability to identify effects. Water temperature, tailwater elevation, and vessel lockages affected passage rates, although this varied among species.
Although zebra mussels (Dreissena polymorpha) have been established in the Great Lakes-St. Lawrence River system for over 30 years, recent detections in Quebec’s inland lakes signal a concerning acceleration in secondary spread. In 2022, the species was detected in Lake Témiscouata, then the easternmost confirmed occurrence in North America. Within 3 years, mean lake-wide densities increased from <30 mussels m−2 to >5500 mussels m−2, exceeding 30 000 mussels m−2 at one site. A coordinated response was initiated to monitor expansion across eastern Canada. By 2024 they had spread into New Brunswick, with an established population in Edmundston and presence in Mactaquac. In Quebec, surveys detected mussels in four additional lakes, with suspected presence in six others. Detection proved difficult despite multiple sampling methods (i.e., eDNA, veligers, visual surveys). Boater surveys indicated that overland transport of recreational watercraft may facilitate secondary spread, an important concern given the high suitability of many eastern Canadian waterbodies for colonization. Newly infested sites may act as stepping stones for further expansion, highlighting the need for effective prevention strategies.
Acoustic telemetry is a powerful tool for aquatic animal movement studies, and to enhance its potential to inform management and conservation, sound data management and quality control structures are crucial. The Ocean Tracking Network (OTN) has been a leader in the coordination of acoustic telemetry researchers globally, connecting tracking programs through standardized data formats and processes. The OTN Data Centre (OTNDC) provides reliable, transparent, and internationally certified data management structures which support researchers as they embark on their animal tracking programs. This article details OTNDC’s data pipelines and processes, governance, and “network of networks” data model (implemented via database nodes) and how this system influences the acoustic telemetry research landscape. The OTNDC is continually adapting to meet the needs of the research community, and its partner networks, to remain relevant and reliable. Researchers supported by OTNDC’s structures are addressing key questions about the movements of ecologically, culturally, and economically important species across the globe.
Increased aquatic turbidity often co-occurs with other environmental stressors, such as warming waters and low oxygen (hypoxia), which may impact the behaviour and physiology of aquatic organisms. Using three experiments, we examined whether chronic turbidity exposure affects the standard metabolic rate, hypoxia tolerance, and growth of the Endangered Lake Chubsucker ( Erimyzon sucetta) and whether acute exposure to turbidity impacts the behaviour and thermal tolerance of this species. Our results suggest that chronic exposure to turbidity decreases growth and decreases critical oxygen tension ( P crit ) in Lake Chubsucker relative to the chronic exposure to clear water. Across turbidity treatments, the mean P crit and oxygen level at loss of equilibrium were 26.3% air saturation and 4.7% air saturation, respectively. When Lake Chubsucker were acutely exposed to medium turbidity, they exhibited fewer calm behaviours compared to when fish were exposed to the control or low turbidity. However, turbidity exposure did not impact thermal tolerance in both the lab and field experiments. As this is the first study to house and test environmental tolerances of Lake Chubsucker to turbidity in Canada, our research provides unique insights into this Endangered species that may inform conservation efforts.
Freshwater fish provide direct economic benefit through commercial and recreational fisheries, and as a local Indigenous food source. A diverse freshwater fish fauna also provides important ecological benefits through ecosystem services. In February 2024, a symposium on applying genetic tools to freshwater fisheries titled “Genes, genetics and genomics in fish conservation and fisheries” hosted by the Society of Canadian Aquatic Sciences was held in Fredericton, New Brunswick, Canada. This special issue presents a collection of studies that applied genetic tools, including environmental DNA, genomics, and transcriptomics (e.g., transcriptional profiling), to address pressing management and conservation issues in freshwater aquatic environments. These contributions demonstrate how molecular approaches can improve understanding of biodiversity, population structure, species distributions, and physiological responses to environmental stressors. Molecular genetic tools have provided incredible opportunities to address fundamental questions related to fisheries management and conservation, and, when integrated with conventional approaches, offer a more effective framework for managing critical resources.
The zooplankton Mysis diluviana is a major component of the Laurentian Great Lakes food web and has recently declined in abundance in both lakes Michigan and Huron. Drivers of these declines are not well understood. Here, we explore the hypothesis that recent increases in water clarity have contributed to the decline of M. diluviana (mysids) by limiting the availability of daytime dark refuge from visual predators. Using Secchi depth data from 1996 to 2021, we estimate that dark refuge has decreased substantially in lakes Michigan and Huron where mysids have declined, but dark refuge has remained more stable in lakes Ontario and Superior where mysid populations did not decline. Results from a 2021 uncrewed surface vessel hydroacoustic survey and lake-wide, net-based sampling in lakes Michigan and Huron revealed significantly more mysids in areas with dark refuge, such as Lake Michigan's northern basin. Conversely, Lake Huron contains sparse dark refuge consistent with low mysid densities in that lake. Higher water clarity leading to increased predation may be a primary driver of mysid declines in the Great Lakes.
Fisheries management relies on catch level projections developed from stock assessment models. Assumptions about future recruitment are highly influential when forecasting the catch levels that lead fisheries towards management objectives. Yet, there are not precise guidelines for configuring forward projections, and scientists around the world use different methods and assumptions. In this article, we review various assumptions made in fishery stock assessments to set up catch level projections. In addition, we identify an approach that matches recent stock dynamics with the projection period while maintaining the link between spawners and recruits. We recommend adjusting the equilibrium stock-recruitment relationship using the average recruitment deviations estimated during the last years of the assessment period. First applied to Indian Ocean Yellowfin Tuna in 2024, this approach was designed to handle recruitment trends and possible model misspecification. We consider this approach best suited for developing catch level projections from integrated stock assessments and conducting simulations in management strategy evaluation.
Marine fishes often suffer from parasitism, which can affect life-history traits such as maturity and mortality. Rockfishes (Sebastes spp.) in the northeast Pacific are commonly parasitized by Sarcotaces spp. copepods that form large cysts in muscle or body cavities. Baseline data on Sarcotaces prevalence and effects are limited. We analyzed Sarcotaces sp. prevalence in 23 rockfish species (including two thornyhead species Sebastolobus spp.), using over 37 000 individuals sampled during Fisheries and Oceans Canada groundfish surveys in British Columbia. Parasitism occurred throughout surveyed areas and depths. Prevalence reached up to 10% in some species, and was highest in Pacific Ocean Perch, Silvergray, Rougheye/Blackspotted complex, Yellowmouth, and Yelloweye rockfishes. Parasitism was linked to delayed maturation, particularly in males, which matured at lengths 22.3 mm larger (95% credible interval: 5.5–39.8 mm). Immature fish were more likely to be parasitized than mature ones. Speculatively, Sarcotaces sp. parasitism may act as a co-morbidity reducing survival. Body condition showed little association with parasite prevalence, except from a slight (≈5%) increase in condition with infection for some species. To our knowledge, this study provides the first large-scale assessment of Sarcotaces sp. prevalence and its effects on rockfish life-history.
Fish otolith elemental composition is used to infer natal origins and early life histories, but the relative roles of environmental exposure versus maternal influences remain uncertain for many species. We examined otolith elemental fingerprints of larval Lake Whitefish (Coregonus clupeaformis) in Green Bay, Lake Michigan, finding two distinct geochemical groupings among wild-caught larvae. To identify mechanisms generating this variation, we conducted a reciprocal transplant experiment testing whether incubation environment drives larval otolith signatures. Larval signatures differed primarily by maternal spawning origin, while incubation environment contributed minimally. Classification analyses showed high assignment success to maternal source, with most misclassification among groups sharing maternal origin. These results indicate that maternally associated chemical signatures dominate larval otolith fingerprints through early development, complicating interpretation of larval otolith chemistry as a “natal environment” signal. Our findings clarify when larval signatures likely reflect maternal provenance versus environmental exposure and highlight the need for additional reference collections and temporal validation to strengthen natal assignment frameworks in the Great Lakes.
Treatment of natural mortality is a major consideration in assessment models and state-space approaches allow estimation of temporal variation in this mortality rate as well as effects of specific covariates. However, there has been no investigation of the reliability of inferences made from state-space assessment models when there is process error or covariate effects on natural mortality. We conducted a large-scale simulation study with operating models simulating data assuming alternative levels of observation error, types and magnitude of process error, and magnitude of covariate effects on natural mortality. We fit estimating models to the simulated data with alternative assumptions regarding the inclusion of covariate effects, estimation of the median natural mortality rate, and type of process error. We found estimating covariate effects on natural mortality required ideal scenarios with lower observation uncertainty, contrast in fishing pressure, and higher covariate variability, but the source of process error could be mis-specified. Estimating annual natural mortality rates as random effects was also challenging, but spawning stock biomass and fishing mortality were reliable in a wide range of scenarios.
Hydroelectric developments can impact connectivity of migratory fishes in rivers. To assess population structure and to inform an upstream fish passage program designed to mitigate impacts of Site C, a new hydroelectric dam on the Peace River, northeastern British Columbia (Canada), we collected single nucleotide polymorphism (SNP) data for six freshwater fish species from the river and seven of its tributaries. Bull Trout, Arctic Grayling, and Rainbow Trout (Salmonidae) showed strong differentiation between spawning populations upstream and downstream of the dam. Slimy Sculpin (Cottidae), Redside Shiner, and Longnose Dace (Leuciscidae) showed variable differentiation between an upstream tributary and Peace River sites, but little differentiation among Peace River sites. Applying SNP assays (6–11 loci) to the salmonids sampled in the Peace River from 2016 to 2024 assigned most Bull Trout and Arctic Grayling to tributaries upstream of the dam (93.8% and 92.2%, respectively). Rainbow Trout assignments were more evenly distributed between upstream (53.5%) and downstream tributaries (29.0%). Our results highlight the value of a multispecies approach to understand habitat use and connectivity across species, and suggest that upstream fish passage is vital to maintain connectivity between habitats upstream and downstream of the dam.
