Canadian Journal of Fisheries and Aquatic Sciences

Understanding population structure is critical for effective fisheries management in species with complex life histories and variable recruitment. Southern flounder (Paralichthys lethostigma) is a valuable flatfish species with declining populations in the Southeast United States. Improved management may depend on a better understanding of fine-scale and temporal population genetic structure in this region; however, such structure remains poorly characterized. To address our lack of understanding of the spatial and temporal population structure of this important species, we used double digest reduced-representation genome sequencing (ddRADSeq) on juveniles from estuaries in North Carolina and Texas between 2014 and 2023. We found significant genetic differentiation between the Gulf of Mexico and Atlantic populations, supporting the management of these regions as distinct stocks. By contrast, we detected significant variance in genetic structure within Texas and North Carolina populations that was not consistent across sampling years between estuaries in close proximity. The population genetic structure of southern flounder suggests significant, temporally variable genetic differences within estuarine locations that may result from variation in larval dispersal and recruitment patterns. Our findings highlight the value of integrating fine-scale, multi-year genetic data to capture temporal dynamics and avoid misleading conclusions based on single-year or broad-scale sampling.

Fledging is a critical period of a seabird life cycle. Using satellite telemetry, we compared movements and survival proxies (transmission duration) of chinstrap penguin fledglings tracked in 2017 (n=8) and 2025 (n=17) relative to krill fishing vessel activity. In 2017, fishing vessels operated intensively near colonies during summer, resulting in early, frequent encounters (median 1.3 days post-fledging) and short transmission durations (median 9.2 days). In 2025, reduced fishing delayed encounters (median 10.0 days) and tripled tracking duration (median 24.0 days). Hidden Markov Models revealed that vessel encounters reduced the probability of transitioning from foraging to transit behavior ({beta} = -0.76), an effect stronger than the productivity ({beta} = -0.11). While 87.5% of 2017 fledglings ceased transmission prematurely within weeks (half of those right after entering areas intensively used by fishing vessels), 65% of 2025 fledglings survived beyond March, with half of those five transmitting until May after dispersing eastward to the South Orkney Islands. These findings suggest that spatiotemporal overlap with krill fisheries during the critical post-fledging window affected foraging behavior and was associated with shorter transmission durations. Our results support further research of post-fledging penguin ecology to better understand the potential impact of fishery, and, following the precautionary principle, support fishing seasonal protection of important areas during critical periods of krill predators life cycle.

Global climate change has increased the frequency and severity of stressful temperatures that freshwater fishes experience, necessitating rapid and sensitive methods to monitor wild populations. Tissues used to measure transcriptional responses traditionally involved invasive or lethal sampling, which may be undesirable for imperilled species. Epidermal mucus offers a non-lethal and minimally invasive alternative, but whether thermal thresholds can be detected in mucus to identify fish experiencing thermal stress is unclear. Bull trout (Salvelinus confluentus) are a legally protected salmonid and cold-water specialist, generally occupying waters 12 {degrees}C and below, with higher temperatures resulting in cellular stress. Therefore, we measured a suite of 56 genes using high-throughput qPCR to compare machine learning classifiers developed with transcriptional profiles of epidermal mucus, gill, liver, and muscle to classify laboratory reared juvenile bull trout as below (9 {degrees}C, 12 {degrees}C) or above (15 {degrees}C, 18 {degrees}C) cellular thermal thresholds. Mucus profiles most resembled gills but represented an intermediate transcriptional response to all tissues. A reduced biomarker panel of 10 genes in mucus assigned fish to stress categories with 94.1% (95% CI = 71.3-99.9%) accuracy, which was comparable to gill (100.0%, CI = 82.4- 100%), liver (95.0%, CI = 75.1-99.9%), and muscle (100.0%, CI = 80.5-100.0%). Sex-specific temperature effects were evident in all tissues, but less pronounced in mucus and gill than in liver and muscle. Our findings demonstrate that transcriptional profiling of mucus can reliably identify individuals experiencing thermal stress, highlighting the promise of this non-lethal approach for monitoring at-risk species.

SO_SCPLOWUMMARYC_SCPLOWAge is a fundamental life-history parameter in animal ecology and wildlife management. Age informs key ecological characteristics including population age structure, recruitment strength, extinction risk, reproductive maturity, and mortality rates. This importance has necessitated the development of chronological age estimation methods for wild animals. However, estimating chronological age is challenging for wild species, with noisy and potentially biased measures typically gathered from morphometrics, physical characteristics or, more recently, molecular methods like DNA methylation. These measures of age require at least some initial validation set of known-age individuals, or known time intervals, which is difficult to obtain for many species. Here, we present a solution to inferring the relationship between chronological age and error-prone observed age that does not require known-age individuals. The model couples the formulae for occurrence rates of half-sibling pairs, which decrease as a function of the birth-year gap between two sampled individuals, with time of capture. A pseudo-likelihood framework is developed for parameter estimation that can resolve linear and non-linear relationships and provide variance parameter estimates. We explore the methods efficacy for estimating chronological age using forward-in-time simulation and validate prior estimates of the relationship between vertebral band counts and chronological age for 3,000 school shark (Galeorhinus galeus) from an Australian fishery.

Littoral mysids facilitate benthic-pelagic coupling through horizontal migration, yet quantitative monitoring in structurally complex habitats remains methodologically challenged where traditional active gears fail. We evaluated the efficacy of standardized light traps for monitoring littoral mysids (Neomysis integer, Praunus flexuosus) and mesopredatory three-spined sticklebacks (Gasterosteus aculeatus) in the northern Baltic proper, Baltic Sea. Using a paired experimental design with predator-exclusion and unmodified traps, alongside concurrent passive benthic trapping, we assessed abiotic drivers affecting catchability, biotic interactions, and statistical power to monitor changes in population size over time. Results indicated significant biotic interference: unmodified traps attracted high densities of sticklebacks, which reduced mysid catches by approximately 85% through predation or behavioural avoidance. Consequently, physical predator exclusion is mandatory for accurate mysid sampling. Generalized Linear Mixed Models (GLMMs) confirmed that catch rates for all taxa were primarily driven by night duration rather than water temperature. While passive benthic trap catches tracked metabolic activity (peaking in warm summer months), light trap efficiency peaked in spring and collapsed during summer, confirming that sampling efficiency was strictly limited by the short duration of the night. Simulation-based power analysis revealed a stark contrast in monitoring utility based on spatial aggregation. For highly aggregated mysids, the method demonstrated low precision (Power < 0.25 to detect a 50% decline), rendering it suitable primarily for detecting substantial population collapses (>90%). In contrast, for less aggregated sticklebacks, the method achieved a more robust statistical power (>0.80 for a 60% decline), validating light traps as a precise tool for monitoring these abundant mesopredators. We conclude that light traps fill a critical methodological gap for winter and early spring monitoring when traditional passive gears underperform. Appropriate abundance indices should be based on statistical models accounting for night duration and strictly employ physical exclusion barriers when targeting mysids.

Absorption of CO2 by global oceans is decreasing pH resulting in ocean acidification (OA). Impacts on shellfish have been documented in ecologically and commercially important species. We examined the influence of diet and OA between two populations of red abalone (Haliotis rufescens) a species of aquaculture importance and declining wild populations. Populations experience different exposure histories: strong upwelling (Van Damme, California [VD]) historically exposed to low-pH conditions and weak-intermittent upwelling (Santa Barbara, California [SB]). Abalone were cultured under control-pH or OA-conditions and fed crustose coralline algae (CCA) or diatoms used in aquaculture. We tested treatment effects of population, settlement diet, and OA-exposure on survival as influenced by larval-energy stores. Survival in both populations was enhanced by CCA when cultured under both treatment conditions; however, by later stages, this effect remained only for SB. SB had reduced post-settlement survival when cultured under OA-conditions, whereas post-settlement survival of VD was not. Diet affected the relationship between larval-energy and post-settlement survival; a positive relationship when fed diatoms and a negative relationship with CCA. The relationship between larval energy and post-settlement survival was stronger in VD. CCA enhanced juvenile growth in SB cultured abalone at both three-months and one-year post-settlement. Settlement diets can reduce the impacts of OA on early-life stages of abalone, but population differences driven by underlying energetics affect the consistency of this outcome. These findings illuminate the impacts from OA, suggesting populations may be at risk, and inform strategies for developing and sustaining shellfish aquaculture in the face of changing ocean conditions.

Downstream migration and sea entry are periods of high mortality for sea trout smolts and migration timing is a critical aspect of survival. We aimed to investigate migration timing of PIT-tagged sea trout smolts across a latitudinal gradient in five freshwater systems across Europe: Norway, Sweden, Denmark, France and Portugal. In two systems, smolt migration was further examined to assess a) differences in sex, body size and condition between autumn and spring migrants; b) the influence of spatial origin within the stream; and c) relationships between individual body size and migration date. Tagged smolts were not detected migrating in the Portuguese watershed. Spring migration timing differed significantly between watersheds in Norway, Sweden, Denmark and France. Generally, there was a trend of earlier migration at lower latitudes. Autumn vs spring migration was examined in Gudso-Denmark. Autumn migrants were larger in both length and mass, with no differences in sex ratios or body condition. Fish originating from an upstream site were more likely to migrate in the autumn compared to the spring and vice versa. Size dependent migration was found in the Swedish system, Haga [a]-Sweden, with larger individuals migrating earlier in the spring than smaller individuals. Outward-migrating smolts were also more likely to originate from a downstream site than an upstream site. Overall, these results show both large-scale geographic and fine-scale individual influences on migration timing. Given that climate change may have large impacts on migration patterns in sea trout, understanding variability in migratory patterns across a latitudinal gradient is an important tool for predicting responses to environmental changes.

Capelin (Mallotus villosus), a key forage fish in the Northwest Atlantic, links zooplankton to predators including commercial fishes, seabirds, and marine mammals, yet its life-cycle movements in the Gulf of St. Lawrence (GSL) remain poorly understood. Between 2022 and 2024, otoliths from 927 individuals collected during and after spawning were analysed by Laser Ablation Inductively Coupled Plasma Mass Spectrometry (LA-ICP-MS). Building on previous work on regional structuring, seven trace elements (Li, B, Mg, K, Zn, Sr, Ba) were used to discriminate three regions. Early-life regional signatures were inferred through an edge-to-core approach, assigning otolith core chemistry to one of these regions using quadratic discriminant analysis. The core was treated as an integrated early-life signal (late-larval to early juvenile period) rather than a strictly natal signature. Spatial variation in core chemistry was consistent across cohorts, mirroring the stability documented on the otolith edge. Results revealed widespread dispersal alongside partial regional residency: individuals with northeastern early-life signatures showed the strongest correspondence between early-life and capture regions, whereas other regions were more connected. Fish sampled during spawning were more often reassigned to their inferred early-life region than post-spawning fish, a regional-scale homing-like pattern consistent with regional spawning fidelity. This coexistence of dispersive and resident strategies likely generates a portfolio effect buffering the population against environmental variability and localised reproductive failures.

The queen conch (Aliger gigas) is a key native species of the Caribbean Sea and a primary source of income for thousands of fishers. Historically, it has been a highly valuable resource for the fishing sectors of countries such as the Bahamas, Turks and Caicos, Honduras, and Nicaragua. However, due to its high economic value, the species has been extensively overfished across the region. Overfishing, combined with limited larval dispersal, low recruitment, and poor population connectivity, has led to a drastic decline in population numbers of the species, resulting in its current classification as Threatened. Despite this status, likely impacts of climate change on its populations remain poorly understood, posing significant challenges to conservation efforts. To address this gap, we integrated occurrence records, climate data, and satellite-derived marine habitat data to develop ecological niche models estimating the current and future distribution of the queen conch under different climate change scenarios. We found substantial losses of suitable areas for queen conch along the northern Atlantic coast of South America and Central America, part of the Greater Antilles and the Lesser Antilles. The entire Caribbean region is projected to lose suitability entirely within 20-30 years under the moderate and most extreme climate scenarios. Conversely, our models estimate some suitable areas to persist or expand along the southeastern coast of the United States at least until sometime between 2040 and 2060. Overall, our results suggest a northward shift in the range of this species, with the magnitude of this shift closely tied to the severity of climate change impacts. This work aims to build upon and enhance existing knowledge about survival of queen conch populations in the Caribbean over time. Anticipating future habitat availability will be key to protecting this economically and ecologically important species.

Quagga mussels (Dreissena rostriformis bugensis) are ecosystem engineers that can alter nutrient cycling, benthic-pelagic coupling, and food-web structure in deep lakes. Although their invasion trajectories are well documented in the Laurentian Great Lakes in North America, depth-specific population dynamics remain poorly resolved in recently invaded European perialpine lakes. We analyzed five annual lake-wide surveys (2021-2025) from 54 stations spanning 2.4-253 m depth in Lake Constance to quantify changes in quagga mussel density, biomass, and shell-length distribution. Contrary to expectations of lake-wide exponential growth, shallow-water populations (< 20 m) showed no significant increase during the study period and appear to have reached carrying capacity before monitoring began. In contrast, densities increased monotonically at intermediate depths (40-125 m), indicating ongoing expansion into deeper strata. Mean shell length declined with depth, and size distributions in shallow waters shifted toward larger individuals, consistent with a transition from active recruitment to somatic growth of established mussels. Compared with the Laurentian Great Lakes, Lake Constance already has substantially higher shallow-water biomass, whereas deeper invasion trajectories are broadly similar. These results show that quagga mussel invasion in deep European lakes can combine rapid littoral saturation with slower profundal expansion, complicating direct transfer of predictions from the Great Lakes. Continued depth-stratified monitoring will be essential for anticipating future ecosystem effects in perialpine lakes.

Non-compliance with regulations threatens the sustainability of fisheries worldwide. Understanding the interconnected feedbacks of this complex social-ecological problem is key for sustainability but rarely integrated into fisheries management. We provide an adaptive stochastic modelling framework that integrates economic, social behavior, and ecological aspects of the Chilean kelp fishery, which plays a critical economic and ecological role in coastal social-ecological ecosystem. High levels of non-compliance is threatening sustainability, fishers well-being, and ecosystem health. Our model considers inherent environmental uncertainties and enables the assessment of different harvesting and compliance scenarios and the role of market-based economic incentives in reducing non-compliance. Results show that, unlike the sustainability obtained under an idealized full-compliance scenario, under dynamic compliance the social, economic, and ecological feedbacks leads to system collapse. Importantly, price premiums can promote compliance and sustainability, but the probability of collapse, albeit small, still exist. Our generalizable stochastic modeling framework evidenced that accounting for inherent uncertainty in natural resource management is key to designing interventions for sustainability.

Here, we report the first genetic confirmation of golden mussels (Limnoperna fortunei) in North America, and the subsequent development, optimization, and deployment of golden mussel eDNA monitoring procedures. Aquatic species invasions are economically costly, disrupt ecosystem functionality, and impact native aquatic communities. Early detection of new invasive species enables rapid response via implementation of effective eradication or control measures and is key for reducing harmful outcomes. Initial species detection and taxonomic identification can be aided by genetic methods that have high detection sensitivity and accuracy. Genetic methods such as environmental DNA (eDNA) sampling can be used to detect invasive species before they become established in new systems, providing an early alert system to inform resource managers. Golden mussels were first detected in North America in October 2024 near the Port of Stockton in the San Francisco Estuary (SFE). The SFE is particularly vulnerable to invasion due to the access and connectivity provided by the presence of engineering infrastructure and shipping lanes. Collaborative efforts between public agencies and academic institutions are underway to develop a coordinated detection and response plan. Early detection followed by a rapid response is the best defense against prolific invasive species, such as the golden mussel.

Coastal wetlands of the Laurentian Great Lakes support abundant populations of fish, invertebrates, and vegetation, though the trophic linkages connecting primary production and lower consumers is not well understood in these systems. We implemented a multiple-tracer approach to evaluate trophic pathways, pairing traditional food web isotope tracers like carbon ({delta}13C) and nitrogen ({delta}15N) with total mercury concentrations (THg). We predicted that filamentous algae would be the dominant energy resource in the diet of lower trophic-level invertebrates in the Grand River Estuary, a network of riverine coastal wetlands adjacent to Lake Michigan. In addition, we predicted that adding THg as a tracer would improve the resolution of our food web models by clarifying trophic levels and relationships between wetland species. Four basal energy sources were sampled, including filamentous algae, emergent macrophytes, submersed macrophytes, and phytoplankton, along with organic detritus. Aquatic invertebrates were sampled across multiple functional guilds to represent primary and secondary consumers and included amphipods and odonates. Our findings suggest that organic detritus is the dominant resource responsible for energetically supporting these lower trophic levels in the Grand River estuary, although submersed macrophytes were important alternative energy sources for secondary consumers. THg concentrations enhanced the resolution of dietary contribution estimates in MixSIAR models applied to consumer and source data. Isotope biplots revealed that THg concentrations were a more reliable predictor of trophic position than {delta}15N in Grand River Estuary (GRE) sites. This methodology has important implications for future food web studies in complex ecosystems such as coastal wetlands and demonstrates the novel use of mercury as an ecological tracer in a Bayesian mixing model approach.

Seafood nutrients from global fisheries are of increasing importance for research and policy in food security and nutrition. As the chemical composition of fish is determined by what they eat, their energetic demands, and the environment in which they live, nutrient content reflects aspects of physiology and life history, ecological and environmental traits, as well as evolutionary history. Here we present data from Bayesian model estimates of 12 key nutrients (calcium, iron, phosphorus, magnesium, selenium, zinc, vitamin A, vitamin B9, vitamin B12, vitamin D, omega-3 fatty acids, and protein) in wild fish, using a database of reported nutrient content for freshwater and marine species. We then predict the nutrient content of 5588 fish species with traits available from FishBase. We compare our previous model using traits alone with a new model of both traits and phylogeny, and present the data, code, and predictions for models coded in PyMC. These models and predictions, made freely available through FishBase, can be used to explore the historical, current, and future nutrient content of fisheries catch.

Fall-run Atlantic Sturgeon occupy riverine habitat for extensive periods of up to several months during periods of spawning. It is generally not feasible to eliminate potential anthropogenic stressors during the entire time Atlantic Sturgeon are on spawning habitat. If data were available to accurately predict when eggs and larvae are in the water column, potential impacts could be minimized for this relatively short timeframe, compared to the entire season of freshwater residency by adults. This research used acoustic telemetry data for adult female sturgeon, along with water temperature and discharge, to predict when females were likely releasing eggs versus merely staging in spawning habitat waiting to spawn. The descriptive and Bayesian model results predict that egg release is associated with water temperatures ranging from 20-26{degrees}C and pulses in river discharge, often confining egg release to a few days or weeks. By using weather data that predict relatively short periods of when egg release occurs versus longer periods that includes staging, resource managers can more feasibly collaborate with water usage groups to ameliorate egg/larvae survival.

High concentrations of steroidal hormone compounds are a growing source of concern for environmental pollution in aquatic ecosystems. In this study, we examine the effects of two estrogenic compounds (estriol and 17-ethinylestradiol) on fitness traits in the aquatic microcrustacean, Daphnia magna, a key bioindicator species for toxicology studies. The impacts were compared of two forms representing a natural and synthetic estrogenic compound. Growth and reproduction traits were assayed by exposing Daphnia to each estrogen type at four concentrations reflecting potential environmental exposure conditions up to acute toxicity levels (ranging from 0.1 - 50 {micro}g/L). Assaying the effects at a variety of concentrations is important given that it is known that hormone exposures can often result in non-monotonic responses. Both forms of estrogen impact a subset of the traits assessed, in some cases leading to beneficial changes and others causing harm. Estriol, the naturally-occurring estrogen, and EE2, the synthetic version, at high doses shift fitness traits in opposite directions such as adult growth rate as do at low doses for fecundity. In conclusion, our results support the need to assay a wide array of traits using multiple forms of steroidal hormones at a range of doses in order to assess non-monotonic patterns and their impact on an organismal fitness. In particular, assays that extend beyond the conventional measurements of lethality during acute exposure windows will be essential for understanding the impact of increased levels of hormone pollution on aquatic organisms and ecosystem health.

Thiamine Deficiency Complex (TDC) is a reproductive disorder that affects recruitment of diverse salmonine populations globally. Typical symptoms include behavioral and neurological abnormalities and high offspring mortality. TDC is common in hatcheries that rear salmonines obtained from wild populations, and symptoms are mitigated by thiamine treatment. However, no studies have quantified thiamine concentrations in wild embryos. Here, we evaluated whether fertilized eggs and/or embryos may acquire thiamine from natural sources (e.g., biotic breakdown products and diet) during development. Lake trout (Salvelinus namaycush) gametes were obtained from feral adults in Lake Champlain and fertilized eggs were grouped by family with paired rearing under natural (Lake Champlain) and artificial (controlled laboratory) conditions. Average thiamine concentrations were similar between lake-reared and laboratory-reared fish prior to hatch; however, lake-reared fish experienced significant increases in thiamine concentrations at and after hatching compared to previous stages and compared to laboratory-reared fish; laboratory-reared fish experienced no increases in thiamine concentrations. Water samples revealed an abundance of thiamine precursors and byproducts in the natural environment, which may serve as sources of thiamine for developing embryos. These results demonstrate that salmonine embryos can acquire thiamine from natural sources during development, which may mitigate effects of TDC.

Knowledge regarding variation in habitat use among individuals is crucial for understanding population dynamics and for management and conservation measures. This is especially important for diadromous fishes that shift between habitats, being affected by external pressures and environmental change in different habitats over ontogeny. Herer, we assessed individual variation in habitat use of European eel along a salinity gradient, ranging from fully marine to freshwater in northern Europe, using otolith microchemistry data from >3600 eel together with established time-series segmentation and clustering methods. We show that eel display high degree of individual variation in habitat use. Assigned life-histories included coastal resident, freshwater resident, and coastal and freshwater habitat shifting individuals. Coastal resident eels were observed in a large range of salinities. Given the widespread occurrence of migration barriers in freshwater, it is unknown whether the coastal resident eel preferred that habitat, or if it was the only available habitat for them. Our findings nonetheless highlight the need to include coastal habitats when assessing population development and silver eel production of the critically endangered European eel.

Environmental DNA (eDNA) has emerged as a promising tool for estimating fish abundance, yet linking eDNA concentration to true density remains a significant challenge in seasonal systems, where the signal is strongly influenced by temperature. We investigated whether eDNA can serve as an abundance index for three-spined stickleback (Gasterosteus aculeatus) in four coastal bays of the Baltic Sea (5.7-20.5{degrees}C, April-July 2023), by pairing eDNA sampling with two trap types of contrasting catchability. Light traps capture fish by phototactic attraction during darkness, so their catchability is driven primarily by night duration rather than temperature, while benthic traps respond to temperature through the same activity-driven mechanism as eDNA production. The temperature sensitivity of eDNA estimated from field data was far higher than physiological expectation (Q10 = 12.4, against a maximum metabolic rate benchmark of Q10 = 3.5), indicating that the field temperature signal reflects ecological change in addition to metabolism. We then compared how well three eDNA predictors tracked a combined trap-based abundance index: uncorrected eDNA, eDNA corrected with the temperature response constrained to the laboratory metabolic rate (a first-principles correction), and eDNA corrected with the response estimated from the field data. Uncorrected and first-principles-corrected eDNA were both strong predictors of abundance (standardised slopes of 0.45 and 0.43), whereas the field-corrected predictor was not (0.08). Uncorrected and first-principles-corrected eDNA performed comparably because temperature and abundance increased together over the season; the first-principles correction is nonetheless preferable, as it remains reliable when this covariation is unknown a priori. We conclude that estimating a temperature correction from field data should be avoided in seasonal eDNA monitoring, because it removes the abundance signal together with the temperature effect and assumes a stability in abundance that cannot be verified without independent reference data.

Habitat degradation and biodiversity loss in the Black and Azov Seas necessitate improved tools for spatially explicit conservation planning. We employed stacked species distribution modelling (SSDM) to assess habitat quality for the three resident cetacean species, the common dolphin (Delphinus delphis ponticus), the bottlenose dolphin (Tursiops truncatus ponticus), and the harbour porpoise (Phocoena phocoena relicta), which serve as apex predators and indicators of ecosystem health. Occurrence data were compiled from the Global Biodiversity Information Facility (GBIF), and ensemble species distribution models (ESDMs) were constructed using nine algorithms within the SSDM framework, with eight environmental predictors extracted from Bio-ORACLE v3.0. Individual ESDMs demonstrated excellent predictive performance (AUC: from 0.82 to 0.83; TSS: from 0.65 to 0.67; prop.correct: from 0.82 to 0.83). However, the initial continuous stacking method (pSSDM) yielded low community-level prediction success (0.36), prompting evaluation of three correction approaches. The Probability Ranking Rule (PRR) substantially improved performance (prediction.success = 0.459, sensitivity = 0.704, Jaccard = 0.465), effectively mitigating the overprediction bias inherent in stacked models. Species richness mapping identified multi-species hotspots along the southwestern Black Sea shelf, the Crimean coast, the Kerch Strait, and parts of the eastern coast, while the deep central basin exhibited the lowest richness. Variable importance ranking revealed bathymetry as the primary community-level driver (41.2%), followed by dissolved oxygen (13.8%), sea surface temperature (11.9%), and salinity (10.4%). Species-specific importance patterns confirmed ecological niche segregation, with common dolphins favouring deeper offshore waters and bottlenose dolphins and harbour porpoises associated with shallower shelf environments. The moderate richness observed in the highly productive northwestern shelf, despite high nutrient inputs, may reflect a combination of natural factors (elevated turbidity, reduced salinity) and anthropogenic pressures (fisheries bycatch, shipping, coastal development, and military activity) that limit species co-occurrence. Our findings demonstrate that PRR-corrected SSDM provides a robust framework for mapping cetacean habitat quality and identifying conservation priorities in the Black and Azov Seas, offering an evidence-based tool to inform ecosystem-based management in this ecologically unique and increasingly pressured marine region.