Cichlid fishes of the genus Rubricatochromis are widely distributed across western, central, and northern Africa, yet their taxonomy has long remained unstable because of overlapping morphological characters, variable coloration, and inconsistent use of species names. We present an integrative taxonomic revision of the genus based on mitochondrial DNA sequence data, molecular species delimitation analyses, morphometric and meristic analyses, qualitative assessment of live coloration, and a previously published multilocus phylogeny. Phylogenetic analyses recovered several deeply divergent lineages, some of which had already been informally recognized in the aquarium trade. Although morphological overlap among species was substantial, several taxa could be diagnosed by combinations of morphometric traits and coloration patterns. We describe four new species, Rubricatochromis gabonensis sp. nov., R. jebeli sp. nov., R. stephenthorntoni sp. nov., and R. vanheusdeni sp. nov.; validate R. fugax; and synonymize R. exsul, R. letourneuxi, R. paynei, and R. saharae with R. guttatus, as well as R. lifalili with R. stellifer. Several newly recognized taxa appear to have highly restricted distributions and may qualify as threatened, emphasizing the conservation importance of West and Central African river systems and the urgent need for biodiversity assessments and habitat protection in these understudied regions.
This study examined the effects of dietary carbohydrate levels on growth performance, immune response, and antioxidant capacity of male giant freshwater prawn Macrobrachium rosenbergii. Prawns with an initial body weight of 15.04 ± 0.08 g were fed for 9 weeks on five isonitrogenous, isolipidic diets formulated to contain 10%, 15%, 20%, 25%, and 30% carbohydrate (designated CHO10–CHO30). Weight gain rate and specific growth rate rose from CHO10 to CHO20 and then declined (peak in CHO20); broken-line regression of weight gain rate estimated the optimal dietary carbohydrate level at approximately 19.36% under the present experimental conditions. Moderate carbohydrate inclusion (15–20%) enhanced hepatopancreatic total antioxidant capacity (T-AOC), superoxide dismutase (SOD) and catalase (CAT) activities together with the transcription of cu/znsod, cat and glutathione peroxidase (gsh-px), whereas levels ≥ 25% lowered these defenses and raised hepatopancreatic malondialdehyde (MDA). High-carbohydrate diets also increased hemolymph glucose, triglyceride, total cholesterol and low-density lipoprotein cholesterol, progressively altered the mRNA expression of genes involved in the Toll-like receptor (TLR)/myeloid differentiation primary response 88 (MyD88) signaling pathway (upregulated tlr, myd88, relish and tumor necrosis factor; downregulated inhibitor of NF-κB alpha (IκB-α)), and altered the expression of apoptosis-related genes (downregulated B-cell lymphoma 2 (bcl-2), upregulated caspase-3). These results suggest that M. rosenbergii has an estimated optimal dietary carbohydrate level of approximately 19.36% under the present experimental conditions; intakes at or above 25% are associated with compromised hepatopancreatic health and growth, likely through the induction of oxidative stress, altered transcription of TLR/MyD88 pathway-related genes, and changes in apoptosis-related gene expression.
Substrate availability is a key environmental factor for burrowing bivalves, yet its physiological importance in adult clams remains poorly understood. This study evaluated the effects of short-term substrate manipulation on growth performance, intermediary metabolism, and fatty acid (FA) composition of adult Ruditapes decussatus. Clams were reared for 15 months either with or without sediment and subsequently exposed for 40 days to the opposite substrate condition. Growth performance, metabolic parameters (glucose, glycogen, lactate, triglycerides, and cholesterol), and tissue FA composition were determined. No mortality was recorded, and substrate manipulation had no relevant effects on growth performance. In contrast, substrate removal induced significant decreases in glucose, triglyceride, and cholesterol concentrations, together with increased lactate levels, while glycogen remained unchanged. Conversely, substrate addition did not modify metabolic parameters but promoted selective tissue FA remodeling, characterized by reduced saturated FAs and increased unsaturated, particularly long-chain polyunsaturated FAs. These findings demonstrate that adult R. decussatus exhibits considerable physiological plasticity, with metabolic and membrane lipid responses differing according to the type of substrate manipulation and the previous acclimation history. The results also highlight the value of integrating metabolic and lipid biomarkers with conventional growth indicators to improve the assessment of the physiological status of cultured clams.
Lauric acid (LA), a medium-chain fatty acid abundant in coconut oil and Hermetia illucens larvae, has been reported to promote growth performance and exhibit antimicrobial and immunostimulatory properties. This review examines current studies on its effects on growth performance, intestinal health, microbiota modulation, and immune responses in aquatic species. Studies in finfish and crustaceans were evaluated according to the LA source, distinguishing purified LA, LA derivatives such as monoglycerides, and LA rich ingredients, when considering LA rich ingredients. Overall, LA was associated with changes in growth performance, feed efficiency, survival, intestinal morphology, gut microbiota, and immune and antioxidant responses, although effects varied with source, dose, species, and experimental conditions. Reported effects include increased villus height and goblet cell density, modulation of gut microbiota, altered cytokine expression, increased antioxidant enzyme activity, and reduced lipid peroxidation. Overall, LA appears to be a promising functional component in aquafeeds for finfish and crustacean species. Nevertheless, inconsistent experimental designs, differences in LA sources, and species-specific responses make direct comparisons among studies difficult. Further studies that use standardized experimental protocols, including consistent LA sources, dietary inclusion levels, trial durations and evaluation criteria, are needed to define optimal inclusion levels in different aquatic species.
Trace element contamination in Amazonian freshwater ecosystems threatens riverine food security. This study evaluated two post-harvest treatments—ethylenediaminetetraacetic acid (EDTA) and Lactobacillus fermentum—to assess cadmium (Cd) and lead (Pb) variations in edible muscle of four Amazonian fish species (Cichla monoculus, Pimelodus jivaro, Platynematichthys notatus, and Serrasalmus rhombeus). Concentrations were determined using ICP-OES. Platynematichthys notatus exhibited the highest baseline bioaccumulation, whereas C. monoculus showed the lowest. Although main treatment effects should be considered exploratory, distinct species-dependent trends emerged. EDTA achieved the highest Cd reduction in P. notatus (49.78%), while L. fermentum demonstrated notable Cd and Pb reductions in C. monoculus, P. notatus, and S. rhombeus. Conversely, relative concentration increases occurred in P. jivaro under both treatments, reflecting matrix-related effects. These findings suggest that post-harvest efficiency depends on fish species and metal type. Probiotic post-harvest processing represents a promising strategy for reducing dietary exposure to Cd and Pb in Amazonian fisheries, though optimizing operational parameters for community-level applications remains necessary.
The rapid intensification of global aquaculture, particularly the widespread application of recirculating aquaculture systems (RAS), has substantially improved aquatic product yield [...]
Global inland fisheries depend on large reservoirs, yet many assessments assume spatial homogeneity despite complex embayed morphometry. We tested whether khor-scale structure within Lake Nasser, Egypt, explains variation in two commercially important catfishes. Six distinct khors spanning the north–south axis (Ghazal, Sheniara, Garf Hussein, Amada, Toshka, and Hamedo) were sampled with standardized effort (72 net-nights; 12 per khor, 3 representative areas ≥ 500 m apart × 4 campaigns, March–June 2021), yielding 398 fish (268 Chrysichthysauratus, 130 C. rueppelli). Abundance was expressed as standardized CPUE (fish·net-night−1). C. auratus CPUE ranged from 2.83 (Ghazal) to 5.92 (Garf Hussein), while C. rueppelli CPUE was relatively uniform (1.50–1.92). C. auratus attained the largest TL in Ghazal (25.51 ± 2.9 cm) and the highest condition K in Garf Hussein (1.46 ± 0.18). C. rueppelli attained the greatest TL and weight in southern khors, especially Hamedo (23.3 ± 2.33 cm, 146.7 ± 30.5 g), while its highest condition was in Toshka (1.30 ± 0.15). Sex ratio was significantly female-biased for C. auratus (92 M:176 F, 1:1.91, p < 0.001) but not for C. rueppelli (55 M:75 F, 1:1.36, p = 0.079). Results show embayment-scale CPUE and condition, not whole-lake means, capture key population patterns, improving precision of mega-reservoir fisheries management.
This study compared conventional aquaponics (AP), biofloc-based aquaponics (FLOCponics, FP), and hydroponics (HP) in terms of juvenile eel (Anguilla japonica) growth, ‘Caipira’ lettuce (Lactuca sativa) productivity, and water-quality characteristics. The AP and FP treatments each comprised three replicate fish tank–plant cultivation systems stocked with 119 eels per tank, whereas HP was included as a control for plant production. Eels reared in FP exhibited a higher estimated final biomass and specific growth rate and a lower feed conversion ratio than those reared in AP. The total and shoot biomass of lettuce were higher in FP than in AP and were comparable to those obtained in HP.
This study investigates the length–weight relationship, growth patterns, and population structure of Prochilodus nigricans in a tropical river environment, providing biometric information relevant to ecological studies, fisheries assessment, and conservation planning. A total of 139 individuals were sampled across rainy and dry seasons, and biometric variables (BD—Body Depth, TL—Total Length, SL—Standard Length, TW—Total Weight, and GW—Gonad Weight) were compared using descriptive statistics and regression analyses. Significant differences in biometric parameters were observed between seasons and sexes. Among the sampled individuals, body depth, standard length, total length, and total weight were significantly higher during the rainy season for both sexes; however, these differences should be interpreted with caution because different gill-net mesh sizes were used between hydrological periods. Gonad weight and gonadosomatic index (GSI) differed significantly between males and females in both seasons. A significant overall effect of season was detected for gonad weight, although pairwise seasonal differences were observed only in males, whereas no significant seasonal effect was detected for GSI. Length–weight relationships indicated isometric growth in both sexes. These results provide baseline biometric information useful for future ecological studies and complementary fisheries assessments of P. nigricans in the Tocantins–Araguaia Basin.
Understanding niche differentiation and interspecific coexistence patterns of macrobenthos provides critical references for ecological assessment of bivalve aquaculture. Seasonal field surveys (Autumn 2023–Summer 2024) across 12 sampling sites were conducted in an intensive Meretrix meretrix tidal flat farm in Rudong, Jiangsu. Synchronous water depth, sediment grain size and total organic carbon (TOC), and salinity were measured at each station to characterize habitat gradients; no unfarmed reference tidal flats were included, so all community patterns only reflect within-farm variation. The study area has sustained 10-year continuous bottom culture with baseline juvenile stocking density of 250 ind./m2 and twice-yearly manual harvesting. A total of 58 macrobenthic taxa were identified, and 13 dominant species were screened with a dominance index threshold Y > 0.02. All abundance data were fourth-root-transformed before Bray–Curtis community analysis to reduce bias of hyper-abundant taxa. Standardized Shannon niche breadth (0–1 normalized, r = 48 site–season composite units) and permutation-tested (999 replicates) Pianka niche overlap/similarity coefficients were calculated to quantify resource utilization similarity. Niche breadth ranged from 0.018 to 0.971, with farmed M. meretrix showing the maximum value, indicating broader seasonal resource adaptation. High niche overlap (>0.50) was detected between M. meretrix and four wild dominant species (Nephtys californiensis, Moerella iridescens, Lingula anatina, Umbonium thomasi). Notably, niche metrics derived solely from spatial abundance data cannot directly confirm interspecific competition or trophic segregation; the stable coexistence observed in our assemblage is tentatively hypothesized to be driven by vertical sediment partitioning and divergent feeding guilds based on published functional studies, without direct in situ trophic or stratified sediment evidence from this work. Hierarchical UPGMA clustering (0.35 Bray–Curtis distance threshold) and corrected NMDS ordination (48 site–season units, dominant-species fitted vectors) illustrated distinct functional groups. Based on the observed niche convergence among filter-feeding bivalves under local farming conditions, the range of 230–280 ind./m2 is presented as an observational reference. Controlled manipulative experiments with gradient stocking densities are needed to test whether this range can balance aquaculture yield and benthic biodiversity.
To evaluate the economic and ecological potential of black soldier fly larvae (BSFL) slurry as a fishmeal alternative, 270 juvenile Pangasius (initial body weight: 7.20 ± 0.07 g) were acclimated for two weeks and randomly allocated to three dietary treatments (T0, T1, T2), with three biological replicates per treatment. The feeding trial lasted six weeks (42 days). Fish in T0 were fed the basal diet, while T1 and T2 diets replaced 50% and 100% of fishmeal with BSFL on an isonitrogenous basis, respectively. At trial termination, whole-body proximate composition, muscle texture, and intestinal microbiota were analyzed. BSFL inclusion at 50–100% fishmeal replacement did not compromise growth performance. Moisture and ash content did not differ among treatments (p > 0.05), whereas BSFL supplementation significantly altered muscle texture, reducing hardness and resilience while increasing springiness, chewiness, cohesiveness, and adhesiveness. Both 50% and 100% BSFL replacement enhanced hepatic antioxidant capacity, evidenced by significantly higher superoxide dismutase (SOD) activity (p < 0.05). BSFL also modulated intestinal microbiota and enhanced community evenness, though without significant intergroup differences in bacterial abundance (p > 0.05). This study demonstrated that BSFL could replace 50–100% of fishmeal in diets for juvenile Pangasius, maintaining growth performance while modifying nutritional profiles, muscle texture, hepatic antioxidant status, and intestinal microbiota. Nevertheless, 100% fishmeal replacement triggered distinct shifts in intestinal microbial composition despite satisfactory growth, and the 50% substitution level was, therefore, recommended as a safe proportion for practical aquafeeds.
Catch-and-release (C&R) fishing has become a common practice. Anatomical hooking location (AHL) can be crucial to fish survival. The length of the slack line connecting the hook to the rest of the rig (leader) can affect both the anatomical hooking location and catch efficiency. In this study, we set out to determine whether such a scenario would occur. A total of 2826 fish representing nine species were captured during the study. The shorter leader (15 cm) yielded 1462 fish (51.7%), whereas 1364 fish (48.3%) were captured using the 40 cm leader. Mean catch per unit effort (CPUE) was higher for the shorter leader (44.3 fish h−1) than for the longer leader (41.3 fish h−1). Fish were most frequently hooked in superficial, non-critical anatomical hooking locations within the mouth (upper and lower jaw and mouth corners). Safe hook placements accounted for 88.0% of captures with the 15 cm leader and 78.7% with the 40 cm leader. The research supported our hypothesis and predictions: a shorter leader is safer for fish and less likely to cause deep hooking in critical anatomical locations. On the other hand, shallower hooking was associated with higher catch efficiency. Our findings can help anglers design terminal tackle appropriately.
This study investigated the effects of glycerol monolaurate (GML) on the growth performance, physiological efficacy, intestinal structure, and microbiota of hybrid juvenile ♀ Epinephelus fuscoguttatus × ♂ E. lanceolatus. A total of 594 groupers were administered diets supplemented with 0, 2, 4, 6, 8, or 10 g/kg of GML over an 80-day period. The findings indicated that the group receiving 4 g/kg GML supplementation demonstrated significantly enhanced growth performance, as evidenced by increased weight gain, specific growth rate, and a reduced feed conversion ratio compared with the control and other experimental groups. This growth enhancement was associated with elevated catalase and glutathione levels, suggesting improved antioxidant capacity that may contribute to enhanced immune function. Furthermore, fish in the 4 g/kg group exhibited increased digestive enzyme activity and significantly improved intestinal morphology, characterized by thicker muscular layers and a greater fold width and height. Furthermore, compared with the control group, GML supplementation elevated the relative abundance of Proteobacteria while reducing that of Firmicutes at the phylum level. At the genus level, GML markedly suppressed the relative abundance of Mycoplasma and Vibrio. These compositional alterations are potentially linked to improved energy acquisition and a decreased risk of pathogenic infections. Collectively, these results reveal that GML acts as a promising functional feed additive to boost growth performance, optimize digestive capacity, and sustain intestinal structural integrity in hybrid grouper. Based on these results, the optimal GML supplementation dose was determined to be 4 g/kg, providing valuable insights into the role of GML in aquaculture practices for hybrid grouper.
The yellow clam, Amarilladesma mactroides, is an abundant component of the intertidal infauna of the southwestern Atlantic Ocean and an important source of food and income for local communities. In recent years, this species has been increasingly affected by anthropogenic and environmental pressures, contributing to the decline and collapse of several populations. In this study, we characterized the reproductive cycle of A. mactroides in the southernmost region of Brazil using standard approaches, including gonadal histology and biometric parameters, complemented by analyses of proximal composition and fatty acid profiles. Monthly samples of ≥100 clams were collected from October 2021 to September 2022. The results revealed two distinct reproductive peaks: a major peak from October to December (austral spring–summer) and a less pronounced peak from May to July (autumn–winter). Although gonadal histology, particularly oocyte diameter, provided the primary evidence for defining these reproductive peaks, the condition index and concentrations of total lipids and n-3 polyunsaturated fatty acids (n-3 PUFA) also proved useful indicators of reproductive activity. These findings provide new insights into the reproductive dynamics of A. mactroides in southern Brazil and may contribute to the development of strategies for the sustainable management, conservation and aquaculture of this ecologically and socioeconomically important bivalve.
The development of first-feeding protocols is a critical step in the domestication of native fish species for aquaculture. This study aimed to evaluate the first-feeding management of Pseudopimelodus atricaudus, a Neotropical catfish with aquaculture potential, using four prey types: Artemia nauplii (AN), decapsulated Artemia cysts (DC), wild zooplankton smaller than 400 µm (WZ < 400), and larger than 400 µm (WZ > 400). Larvae of P. atricaudus begin exogenous feeding at 30 h post-hatch (1.5 ± 0.02 mg and 5.2 ± 0.01 mm) and have a maximum mouth width of 611.4 ± 11.7 µm. Larvae fed WZ > 400 µm showed significantly higher growth (13.7 ± 0.2 mm, 94.6 ± 1.8 mg) and final survival (91.2 ± 2.2%) compared to the other treatments (p < 0.05), as well as a greater intestinal fold height (129.8 ± 8.4 µm, p < 0.05). No significant differences in hypoxia stress resistance were detected among treatments (p > 0.05). This study demonstrated that WZ > 400 µm is an appropriate prey for managing the first feeding of P. atricaudus.
Large yellow croaker (Larimichthys crocea) is an economically important marine fish, yet rapid and non-destructive discrimination between sea-caught and farmed collection-source groups remains challenging. This study developed a fish-level analytical workflow integrating YOLO11n-seg instance segmentation with visible–near-infrared hyperspectral imaging to extract relative reflectance ratios from six anatomical regions. The analytical cohort comprised 258 unique fish, including 171 sea-caught and 87 farmed individuals. Source categories were assigned according to the original capture or cage-culture collection channels. Fish identity was used as the grouping unit in five-fold internal cross-validation, and classification performance was evaluated based on out-of-fold fish-level predictions. Logistic-regression models achieved AUC values ranging from 0.985 to 1.000 across the six individual anatomical regions. The combined six-region model achieved an accuracy of 0.996 (95% CI, 0.988–1.000) and an AUC of 1.000 (95% CI, 1.000–1.000) within the present cohort. For anatomical-region segmentation, the 20-image validation set contained 140 annotated instances. Bounding-box precision, recall, mAP@0.5, and mAP@0.5–0.95 were 0.976, 0.983, 0.981, and 0.700, respectively, while the corresponding mask metrics were 0.969, 0.976, 0.972, and 0.669. These results indicate that region-specific hyperspectral information can support highly accurate internal discrimination between the two collection-source groups and provide an interpretable basis for characterizing source-associated spectral differences. However, the source labels were not independently verified, potentially influential covariates were incompletely recorded, and no independent external cohort was available. Therefore, the present findings should be interpreted as internally validated collection-source discrimination rather than verified provenance authentication or evidence of external generalizability.
Photobacterium damselae subsp. damselae (PDD), a marine fish pathogen, has an unclear contribution of tonB genes to iron acquisition and pathogenicity. ΔtonB1-PDD and ΔtonB2-PDD mutants as well as their complemented strains were generated via homologous recombination from the virulent strain PDD1605. Growth was evaluated by monitoring OD600 with viable-count calibration, intracellular iron was measured using a colorimetric assay, biofilm was detected by crystal violet staining, transcription was analyzed through qRT-PCR, and pathogenicity was assessed via an 8-day intramuscular challenge in black rockfish (Sebastes schlegelii). Under iron limitation induced by 100 μM 2,2′-dipyridyl, the maximum density decreased from 4.51 × 108 CFU/mL in wild-type (WT-PDD) to 4.00 × 108 and 3.64 × 108 CFU/mL in ΔtonB1-PDD and ΔtonB2-PDD respectively, and was largely restored after complementation. The intracellular iron content declined from 3.75 × 10−4 ± 4.00 × 10−6 nmol/106 cells in WT-PDD to 3.13 × 10−4 ± 1.05 × 10−5 nmol/106 cells in ΔtonB1-PDD and 2.55 × 10−4 ± 2.00 × 10−5 nmol/106 cells in ΔtonB2-PDD. Compared with WT-PDD, biofilm formation was reduced by 22.1% in ΔtonB1-PDD and by 24.8% in ΔtonB2-PDD. Deletion of tonB2 induced mild yet statistically significant transcriptional alterations in multiple iron acquisition and virulence-related genes, while colony morphology, swarming motility, hemolysis, phospholipase activity, biochemical traits, and antimicrobial susceptibility remained unchanged. In the high-dose challenge assay, WT-PDD caused 100% mortality within 2 days, whereas ΔtonB1-PDD and ΔtonB2-PDD caused 17/20 and 18/20 deaths respectively; all infected groups reached 100% mortality by day 3. In the low-dose challenge assay, WT-PDD, ΔtonB1-PDD, and ΔtonB2-PDD caused 12/20, 12/20, and 13/20 deaths by day 2, with cumulative mortalities reaching 80%, 70%, and 80% by day 8, respectively. Kaplan–Meier analysis detected no significant differences among the survival curves at either challenge dose. These findings suggest that tonB1 and tonB2 play roles in iron acquisition, low-iron adaptation, and biofilm formation, with tonB2 deletion exerting greater effects on growth and intracellular iron accumulation under iron-limited conditions.
Culvert construction at stream crossing sites can lead to zones of high-velocity water flow which can disrupt the dispersal and connectivity of species of greatest conservation need (SGCN) in Texas. To help inform effective culvert design, the swimming performance of the following seven fish species has been measured, the first three of which are SGCN themselves, and the last four serve as hosts for glochidia of SGCN mussels (mussel genera indicated in parentheses): Colorado Roundnose Minnow, Texas Shiner, Headwater Catfish, Largemouth Bass (host for Lampsilis spp.), Green Sunfish (host for Lampsilis spp.), Channel Catfish (host for Cyclonaias spp.) and Blacktail Shiner (host for Fusconaia spp.). The primary objective was to measure the critical swimming speeds (Ucrit) under a range of relevant temperatures (15, 22.5, and 30 °C) to be used in site-specific calculations of culvert water velocities (Vf). A secondary objective was to collect additional physiological endpoints of relevance to overall swimming performance, including maximum burst swimming speed (Umax), metabolic rate measurements (i.e., standard (SMR), maximum (MMR) and aerobic scope (AS)) and calculations of cost of transport (COT) and optimal swimming speed (Uopt). As expected, Ucrit tended to increase with increasing temperature for several species with metabolic rate measurements following congruent trends, whereas Umax exhibited thermal independence for all species.
Using a three-factor orthogonal design, we investigated the transcriptomic and histological responses of triploid rainbow trout (Oncorhynchus mykiss) gills across three salinities (10, 20, and 30 ppt) over 60 days, with temperature and body size as background conditions. Results showed that 20 ppt was associated with extensive transcriptional reprogramming, with 3333 differentially expressed transcripts (DETs), whereas 30 ppt induced only 120 DETs; WGCNA further identified salinity-correlated modules involved in ion transport and ribosome biogenesis. Histological alterations remained within physiological ranges with no salinity-dependent severity gradient, as confirmed by semi-quantitative scoring. These findings demonstrate that triploid rainbow trout gills employ distinct molecular strategies at medium versus high salinity. Within the 10–30 ppt range examined, 20 ppt was the salinity at which transcriptional reprogramming was most active, suggesting that this intermediate salinity warrants further investigation as a potential acclimation stage.
Rainbow trout (Oncorhynchus mykiss) is an important cold-water aquaculture species and a tractable salmonid model for functional genomics. Rapid advances in chromosome-level genome assemblies, genetic variation resources, regulatory annotations, tissue and cell models, controlled challenge systems, and genome-editing technologies have established an increasingly integrated framework for linking genomic variation with measurable phenotypes. Evidence from studies of mucosal immunity, disease-resistance genetics, and environmental stress responses indicates that these resources can improve candidate-gene prioritization and mechanistic interpretation across molecular, cellular, tissue, and whole-fish levels. However, differential gene expression, quantitative trait locus and genome-wide association signals, genomic predictions, and cell-type localization remain largely associative and rarely provide direct evidence of causality. Interpretation is further complicated by salmonid-specific whole-genome duplication, because retained paralogues may exhibit tissue-specific divergence, functional redundancy, and compensatory responses. Further progress will require the integration of pangenomics, regulatory annotation, single-cell and spatial analyses, and paralogue-aware functional perturbation in both cell-based and whole-fish systems. Such integration will strengthen causal inference, clarify genotype–phenotype relationships, and support disease-resistant breeding, healthy aquaculture, and environmental risk assessment.
