Fishes

18 pages, 888 KB

Open AccessArticle

Life-History Traits and Reproductive Potential of a Female-Biassed Population of River-Resident Japanese Eels (Anguilla japonica): A Three-Year Baseline Study

by Takaomi Arai and Shogo Kimura

Fishes 2026, 11(7), 429; https://doi.org/10.3390/fishes11070429 - 21 Jul 2026

Abstract

The reproductive contribution of river-resident (freshwater) Japanese eels (Anguilla japonica) remains poorly understood, particularly following recent paradigm shifts that emphasise the predominance of ocean-resident “sea eels.” To elucidate the riverine life history and maturation strategies of freshwater residents, we investigated the [...] Read more.

The reproductive contribution of river-resident (freshwater) Japanese eels (Anguilla japonica) remains poorly understood, particularly following recent paradigm shifts that emphasise the predominance of ocean-resident “sea eels.” To elucidate the riverine life history and maturation strategies of freshwater residents, we investigated the age structure, morphological traits, and gonadal development of 100 river-resident Japanese eels captured over a three-year period (2007–2009: n = 33, 40, and 27, respectively) in the middle reaches (25–50 km upstream) of the Oi River, Shizuoka Prefecture, Japan. Age determination using sagittal otoliths revealed a broad age distribution from 4 to 15 years. Among the female population (n = 85), highly significant positive correlations were observed between age and growth parameters (Total Length, R² = 0.771; Body Weight, R² = 0.709; p < 0.001). Highly mature silver eels with markedly elevated gonadosomatic indices (GSI) were captured at the uppermost sampling site, immediately downstream of an impassable dam barrier. This spatial concentration of mature females suggests an energetic and temporal life-history strategy in which river-resident eels initiate precocious maturation in the upper reaches to compensate for the prolonged downstream migration to the river mouth. Notably, the calculated female growth rate of approximately 3.6 cm/year was significantly slower than that reported for coastal and estuarine conspecifics in Japan, indicating a distinct slow-growth history unique to river-resident cohorts. Although historical baselines exhibit significant annual variation (ANOVA, p < 0.05), they provide an invaluable benchmark for river-resident cohorts prior to the severe depletion of wild stocks. Our findings underscore that large freshwater-resident females may serve as vital somatic and reproductive reserves, and provide key recommendations for rigorous habitat conservation within river systems to sustain the species. Full article

(This article belongs to the Special Issue Studies on Age, Growth and Reproduction of Fishes)

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14 pages, 1255 KB

Open AccessArticle

Effect of Stocking Rate on Growth of Pacific Calico Scallop (Argopecten ventricosus) Spat in Land-Based Downweller and Upweller Nursery Systems

by Yuanzi Huo, Jordan Pritzl and Mark Drawbridge

Fishes 2026, 11(7), 428; https://doi.org/10.3390/fishes11070428 - 21 Jul 2026

Abstract

To optimize spat stocking rates for Pacific calico scallop (PCS, Argopecten ventricosus) during nursery culture, two consecutive 8-week trials were conducted to evaluate growth in land-based downweller and upweller systems. Four stocking rates (60%, 70%, 80%, and 90% of silo bottom coverage) [...] Read more.

To optimize spat stocking rates for Pacific calico scallop (PCS, Argopecten ventricosus) during nursery culture, two consecutive 8-week trials were conducted to evaluate growth in land-based downweller and upweller systems. Four stocking rates (60%, 70%, 80%, and 90% of silo bottom coverage) of spat at 3.83 ± 0.10 mm in shell height were tested in the downweller system, whereas three stocking rates (50%, 70%, and 90% of silo bottom coverage) of spat at 0.56 ± 0.029 mm in shell height were evaluated in the upweller system. In the downweller system, spat stocked at 60% generally exhibited the best growth performance, with significantly higher relative growth rate (RGR, mm/day) in shell height compared with higher stocking rates. In the upweller system, spat stocked at 50% and 70% showed similar growth performance and both outperformed the 90% stocking rate treatment in shell height, dry weight, RGR, specific growth rate (SGR, %/day), and condition index (CI). These results suggest that moderate stocking rates, approximately 60% in downweller systems and 50–70% in upweller systems, provide favorable conditions for PCS spat growth while maintaining practical space-use efficiency under the present culture conditions. The present study demonstrates the feasibility of PCS spat nursery culture in land-based systems and provides practical information for hatchery production and nursery management of this emerging aquaculture species. Full article

(This article belongs to the Special Issue Advances in Shellfish Aquaculture)

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29 pages, 10227 KB

Open AccessArticle

To Initiate or to Terminate: Effects of Endurance Status and Hydraulic Factors on Fish Upstream Attempt Behavior Under High-Flow Conditions

by Kaixiao Chen, Xiaogang Wang, Yun Li, Jingjuan Li, Lijian Wu, Jianzhang Lv, Yongzeng Huang, Biao Wang and Guoxiu Shang

Fishes 2026, 11(7), 427; https://doi.org/10.3390/fishes11070427 - 20 Jul 2026

Abstract

Understanding the upstream-attempt behavior of fish in high-flow environments is important for refining behavioral simulations, optimizing fish-passage design, and protecting aquatic ecosystems. This study investigates Schizothorax oconnori, an endemic fish in the Yarlung Tsangpo River on the Qinghai–Tibet Plateau, using a multi-model [...] Read more.

Understanding the upstream-attempt behavior of fish in high-flow environments is important for refining behavioral simulations, optimizing fish-passage design, and protecting aquatic ecosystems. This study investigates Schizothorax oconnori, an endemic fish in the Yarlung Tsangpo River on the Qinghai–Tibet Plateau, using a multi-model analytical framework integrating a generalized linear mixed-effects model, Random Forest, SHapley Additive exPlanations, and GeoDetector. Results showed that remaining endurance and nominal flow velocity were positively associated with fish upstream-attempt initiation. Attempt termination reflected endurance depletion, initial endurance, and hydraulic variability. Model-predicted termination probability increased markedly when (i) cumulative endurance consumption during the current attempt exceeded ~11% or (ii) fish began an attempt with an initial endurance status below ~95%. These model-derived change points represent within-attempt endurance depletion and reduced endurance available at attempt initiation, respectively. Across attempt sequences, the dominant explanatory factors showed an apparent shift from physiological condition during the first attempt to hydraulic variability during subsequent attempts. This sequence-related pattern is consistent with behavioral adjustment based on repeated experience in the flow environment, although cumulative fatigue, stress, individual differences, and experimental procedures may also contribute. Hydraulic-variability metrics along the trajectory showed greater explanatory importance than several instantaneous hydraulic variables, and physiological condition and hydraulic variability together enhanced explanatory power. This study provides a quantitative multi-model framework for analyzing upstream-attempt behavior and offers a scientific basis for refining behavioral simulations and optimizing fish-passage facilities. Full article

(This article belongs to the Special Issue New Conservation Strategies for Freshwater and Marine Fishes: Habitat Is the Key)

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18 pages, 16626 KB

Open AccessArticle

Hydrodynamics and Wake Dynamics of Three Fish in an Oblique Tandem Arrangement

by Jiewei Liao, Yuhai Chen, Zhenchao Ding, Jin Yan, Bo Hu and Ji Huang

Fishes 2026, 11(7), 426; https://doi.org/10.3390/fishes11070426 - 18 Jul 2026

Abstract

Fish schooling is a common phenomenon in nature, and offers valuable inspiration for the design of underwater biomimetic propulsors. To investigate the fluid interaction mechanisms among individuals in an oblique tandem arrangement, this study conducts two-dimensional numerical simulations of three airfoil-based biomimetic fish [...] Read more.

Fish schooling is a common phenomenon in nature, and offers valuable inspiration for the design of underwater biomimetic propulsors. To investigate the fluid interaction mechanisms among individuals in an oblique tandem arrangement, this study conducts two-dimensional numerical simulations of three airfoil-based biomimetic fish models. Using Computational Fluid Dynamics, the effects of streamwise spacing (

L_{x} = 0.8

–

1.2

) and orientation angle (

θ = 10

–

30 °

) on the hydrodynamic performance and wake characteristics of each fish are examined for a selected set of five representative cases. The results show that, within the present parameter range, the overall time-averaged thrust coefficient of the three-fish school in an oblique tandem arrangement is higher than that of a single fish, with an increase ranging from 16% to 22%. As the streamwise spacing increases, the mutual interference among individuals weakens, and the overall thrust gain gradually decreases. With increasing orientation angle, the thrust gain of the leading and middle fish decreases, whereas that of the trailing fish transitions from negative to positive. At a small orientation angle (

θ = 10 °

), the leading and middle fish show a substantial thrust increase. This preliminary study indicates that, within the examined parameter space, appropriately adjusting the streamwise spacing and orientation angle can effectively enhance the overall thrust of a fish school in an oblique tandem arrangement and enable the trailing fish to achieve a thrust gain. Full article

(This article belongs to the Special Issue Engineering Solutions for Sustainable Offshore Aquaculture and Fisheries)

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23 pages, 4688 KB

Open AccessArticle

FinSight-Net: A Prior-Guided Degradation-Aware Network for Underwater Fish Detection in Smart Aquaculture

by Jinsong Yang, Hongxi Tao, Zeyuan Hu, Yue Wang and Hong Yu

Fishes 2026, 11(7), 425; https://doi.org/10.3390/fishes11070425 - 17 Jul 2026

Abstract

Underwater fish detection (UFD) is pivotal for smart aquaculture and marine ecological monitoring. While recent detectors improve accuracy using stacked feature extractors or heavy attention modules, they often incur substantial computational overhead and, more importantly, neglect the underwater optical degradation that fundamentally limits [...] Read more.

Underwater fish detection (UFD) is pivotal for smart aquaculture and marine ecological monitoring. While recent detectors improve accuracy using stacked feature extractors or heavy attention modules, they often incur substantial computational overhead and, more importantly, neglect the underwater optical degradation that fundamentally limits UFD: wavelength-dependent absorption and turbidity-induced scattering significantly degrade contrast, blur fine structures, and introduce back-scattering noise, leading to unreliable localization and recognition. To address these challenges, we propose FinSight-Net, an efficient and prior-guided detection framework tailored to complex aquaculture environments. FinSight-Net introduces a Prior-guided Optical Decoupling (PIOD) bottleneck for degradation-aware underwater feature representation. PIOD decomposes features into four degradation-aware branches—forward-scattering blur, back-scattering veil, spectral attenuation, and high-frequency structural decay—and supervises their degradation response maps using image-derived pseudo priors. We further design a Sparsity-constrained High-frequency Adaptive Routing Pyramid (SHARP-FPN), which uses gradient-based salience responses and sparse cross-scale fusion to preserve boundary-sensitive cues and reduce redundant skip contributions, improving fish localization under severe blur and turbidity. Extensive experiments on DeepFish, AquaFishSet, and our challenging UW-BlurredFish benchmark demonstrate that FinSight-Net achieves state-of-the-art performance. In particular, on UW-BlurredFish, FinSight-Net achieves a state-of-the-art 92.8% mAP₅₀, outperforming YOLOv11s, YOLOv12s, and YOLO26s by 4.8%, 2.0%, and 1.8%, respectively, while reducing the parameter count by 28.7%, 28.0%, and 29.5%, providing a strong and lightweight solution for real-time automated monitoring in smart aquaculture. Full article

(This article belongs to the Section Fishery Facilities, Equipment, and Information Technology)

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38 pages, 13935 KB

Open AccessArticle

Machine Learning-Based Prediction of Hydrodynamic Coefficients and Structural Responses in Tuna Longline Gear

by Abdulai Jalloh, Thierry Bruno Nyatchouba Nsangue, Liming Song, Nkansah Antwiwaa Esther, Jordan Cabrel Njitack Ngnipiep and Tchogom Manga Josué

Fishes 2026, 11(7), 424; https://doi.org/10.3390/fishes11070424 - 17 Jul 2026

Abstract

The accurate prediction of hydrodynamic characteristics and structural responses in underwater fishing gear is critical for optimizing design, ensuring operational safety, and minimizing environmental impact. To overcome the computational costs and scalability limitations of traditional physical modeling, this study evaluates three machine learning [...] Read more.

The accurate prediction of hydrodynamic characteristics and structural responses in underwater fishing gear is critical for optimizing design, ensuring operational safety, and minimizing environmental impact. To overcome the computational costs and scalability limitations of traditional physical modeling, this study evaluates three machine learning algorithms such as Random Forest (RF), Light Gradient Boosting Machine (LightGBM), and Support Vector Machine with a Radial Basis Function kernel (SVM-RBF) to predict the hydrodynamic coefficients and structural responses of tuna longline components, including mainlines and branch lines. Models were trained and validated using a comprehensive flume tank dataset encompassing six gear configurations tested across varying flow velocities and lead-line weights. Results demonstrate that optimal model selection is inherently task dependent. For hydrodynamic coefficients, LightGBM achieved superior predictive accuracy for branch-line drag (whole-dataset R² = 0.8315), while both LightGBM and SVM-RBF excelled in lift prediction. Conversely, structural responses (sinking depth and x-displacement) proved inherently more difficult to model deterministically due to high-frequency transient dynamics and stochastic variability. While LightGBM provided balanced generalization for sinking depth, SVM-RBF exhibited severe overfitting for x-displacement. In contrast, RF maintained the most conservative and consistent performance across structural targets, effectively mitigating the memorization of dynamic noise observed in the more complex algorithms. Beyond predictive modeling, feature importance analysis identified flow velocity, lead-line weight, material stiffness, and geometric parameters as dominant physical drivers, validating the physical plausibility of the models. Crucially, the integration of experimental and ML analyses revealed that a polylactic acid (PLA)-integrated midsection configuration consistently yielded the lowest and most stable drag force (0.004–0.13 N at 0.49 m/s), representing a 30–60% reduction compared to conventional nylon lines. Furthermore, the study uncovered novel physical phenomena, including velocity-independent deformation stability, progressive transient sinking kinetics, and tension-induced load redistribution. These findings establish machine learning as a reliable, scalable surrogate for longline gear design, advocating for thin-diameter, biodegradable PLA-integrated lines to enhance hydrodynamic efficiency and mitigate marine plastic pollution, while underscoring the necessity of task-specific algorithm selection for robust engineering applications. Full article

(This article belongs to the Section Fishery Facilities, Equipment, and Information Technology)

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25 pages, 3015 KB

Open AccessArticle

Seasonal Dynamics of Gonadal Antioxidant Biomarkers Associated with Reproductive Indices in Capoeta umbla and Capoeta trutta

by Nurgül Şen Özdemir, Muammer Kırıcı, Fatma Caf, Muharrem Güneş, Teoman Özgür Sökmen, Cebrahil Türk and Nurullah Demir

Fishes 2026, 11(7), 423; https://doi.org/10.3390/fishes11070423 - 17 Jul 2026

Abstract

Seasonal variability and reproductive investment influence oxidative metabolism in fish; however, the relationship between reproductive dynamics and antioxidant responses in freshwater cyprinids remains insufficiently understood. This study investigated seasonal and biological factors affecting antioxidant biomarkers in the gonads of Capoeta umbla and Capoeta [...] Read more.

Seasonal variability and reproductive investment influence oxidative metabolism in fish; however, the relationship between reproductive dynamics and antioxidant responses in freshwater cyprinids remains insufficiently understood. This study investigated seasonal and biological factors affecting antioxidant biomarkers in the gonads of Capoeta umbla and Capoeta trutta inhabiting the Karasu River (Türkiye). A total of 152 individuals were examined between April 2023 and March 2024, and reproductive indices (total body weight, gonad weight, and gonadosomatic index) were evaluated together with oxidative stress biomarkers, including malondialdehyde (MDA), superoxide dismutase (SOD), catalase (CAT), glutathione reductase (GR), and glutathione peroxidase (GPx). Multivariate analyses (PERMANOVA, SIMPER, and principal coordinate analysis) were used to determine the factors shaping oxidative responses. Females exhibited higher reproductive investment, while reproductive activity increased during spring and summer, accompanied by elevated MDA levels and antioxidant enzyme activities. PERMANOVA identified season as the primary factor explaining variation in oxidative biomarkers (p = 0.001), followed by reproductive parameters, and PCO revealed clear seasonal separation among groups. These findings indicate that oxidative balance in gonadal tissues is strongly associated with seasonal reproductive cycles and environmental variability in wild freshwater cyprinids. Full article

(This article belongs to the Special Issue Reproductive Physiology of Fishes)

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12 pages, 372 KB

Open AccessCommunication

Effect of Dietary Supplementation with Omega-3 Fatty Acids on Seminal Plasma Arginase Activity and Semen Quality Parameters in Rainbow Trout (Oncorhynchus mykiss Walbaum, 1792)

by Seyma Ozer Kaya, Sinan Ozcan, Emre Kaya, Seyfettin Gur, Kenan Koprucu, Mustafa Sonmez, Gaffari Turk and Mine Erisir

Fishes 2026, 11(7), 422; https://doi.org/10.3390/fishes11070422 - 17 Jul 2026

Abstract

Background: This study was conducted to determine the effect of various fatty acid ratios added to diets of rainbow trout (Oncorhynchus mykiss, Walbaum) on some sperm parameters and parameters related to arginase activity. Methods: A total of 99 male rainbow trout [...] Read more.

Background: This study was conducted to determine the effect of various fatty acid ratios added to diets of rainbow trout (Oncorhynchus mykiss, Walbaum) on some sperm parameters and parameters related to arginase activity. Methods: A total of 99 male rainbow trout were used in this study, with the fish averaging 3 years old. Semen was collected by abdominal massage. Four different experimental groups were created in the study: a control group without n-3 series fatty acids added to their diets, and groups with n-3 series fatty acids added at ratios of 1% (D1), 2% (D2), and 3% (D3), respectively. Results: While no significant difference in semen volume was observed between the D1 and D3 groups and the control group, semen volume was significantly higher in the D2 group. Compared with the control group, the time required for sperm motility to decline to both 50% and 0% was significantly prolonged in the D1 and D3 groups. Seminal plasma arginase activity did not differ significantly in the D2 and D3 groups compared with the control group but was significantly higher in the D1 group. Conclusions: Consequently, considering the doses used in the study, fatty acid supplementation was found to lead to changes in sperm quality parameters, specifically volume (only 2%) and arginase activity (only 1%). Given that the rate of decrease in sperm motility was later in groups D1 and D2, it was concluded that the added fatty acids may be beneficial. Full article

(This article belongs to the Section Nutrition and Feeding)

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20 pages, 4028 KB

Open AccessArticle

Evidence of Growth Overfishing of Striped Mullet (Mugil cephalus) and White Mullet (Mugil curema) at the Mouth of the Soto La Marina River, Within the Laguna Madre Protected Area in the Gulf of Mexico: A Data-Limited Diagnosis in a High-Priority Conservation Zone

by Jorge Homero Rodríguez-Castro, Sandra Edith Olmeda-de la Fuente, Jorge Alejandro Rodríguez-Olmeda, Uriel Jeshua Sánchez-Reyes, Gonzalo Hernández-Ibarra, Luis Gerardo Yáñez-Chávez and Mayela Rodríguez-González

Fishes 2026, 11(7), 421; https://doi.org/10.3390/fishes11070421 - 16 Jul 2026

Abstract

The striped mullet (Mugil cephalus) and white mullet (Mugil curema) support artisanal fishing at the mouth of the Soto La Marina River, Gulf of Mexico, an area of great ecological value within the Laguna Madre and Rio Bravo Delta [...] Read more.

The striped mullet (Mugil cephalus) and white mullet (Mugil curema) support artisanal fishing at the mouth of the Soto La Marina River, Gulf of Mexico, an area of great ecological value within the Laguna Madre and Rio Bravo Delta Protected Natural Area, the Terrestrial Priority Region RTP-83, and the Marine Priority Region RMP-44. Given the absence of historical catch and effort time series—a typical constraint of data-limited fisheries—a length-based frequency approach was used to estimate growth parameters, mortality rates, and the exploitation rate (E = F/Z). During 2018–2019, 1134 specimens of M. cephalus and 339 of M. curema were sampled. Due to sexual dimorphism in M. cephalus, analyses were performed separately for females, males, and combined sexes, while M. curema was analyzed with sexes combined. Growth (L∞, k) and mortality (Z, M, F) parameters for combined sexes were: M. cephalus (562 mm, 0.14 year⁻¹; 3.72, 0.21, 3.51 year⁻¹) and M. curema (329 mm, 0.15 year⁻¹; 1.46, 0.25, 1.21 year⁻¹). Exploitation rates (E) substantially exceeded Gulland (E = 0.5) and Patterson (E = 0.4) reference points: M. cephalus females (0.891), males (0.915), combined sexes (0.944), and M. curema (0.828). It is concluded that both stocks show strong evidence of growth overfishing, with exploitation rates well above established reference points, revealing a disconnect between the area’s conservation designations and the actual condition of the resource. Full article

(This article belongs to the Special Issue Ecology of Fish: Age, Growth, Reproduction and Feeding Habits)

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15 pages, 2419 KB

Open AccessArticle

Disruption of Osmotic Balance and Metabolic Shifting in Oncorhynchus kisutch Under Hypoxic Stress: Implications for Salmon Aquaculture Climate Resilience

by Luis Vargas-Chacoff, Ricardo Oyarzún-Salazar, Oscar de Lázaro, Pedro Cortés, Kurk Paschke and José Luis P. Muñoz

Fishes 2026, 11(7), 420; https://doi.org/10.3390/fishes11070420 - 16 Jul 2026

Abstract

As climate changes worldwide, aquaculture is increasingly exposed to stressors such as warming, altered ocean chemistry, increased CO₂ “ocean acidification”, and reduced dissolved oxygen (DO) (i.e., hypoxia). Hypoxic events may also occur naturally during upwelling, when nutrient-rich but low-oxygen deep waters reach [...] Read more.

As climate changes worldwide, aquaculture is increasingly exposed to stressors such as warming, altered ocean chemistry, increased CO₂ “ocean acidification”, and reduced dissolved oxygen (DO) (i.e., hypoxia). Hypoxic events may also occur naturally during upwelling, when nutrient-rich but low-oxygen deep waters reach the surface, a process that may intensify with climate change along coastal areas such as the U.S. West Coast and Chile. The aim of this study was to determine the effects of hypoxia on several osmoregulatory organs and tissues of Oncorhynchus kisutch, including gills, kidney, intestine (foregut, midgut, and hindgut), muscle, red blood cells, and brain. Fish were exposed for 28 days to four hypoxic conditions (60, 50, 35, and 25% DO) and a normoxic control. Plasma chloride increased significantly at 25% DO, while plasma pH decreased significantly only under this condition. Plasma osmolality and calcium showed only non-significant tendencies. NKA activity decreased significantly in gills at 50, 35, and 25% DO and in kidney under all hypoxic conditions; however, kidney H⁺-ATPase remained unchanged. Gill H⁺-ATPase decreased significantly only at 35 and 25% DO. Intestinal responses varied among segments, whereas muscle and red blood cells showed higher NKA activity at 35% DO, with no significant changes in H⁺-ATPase activity. Overall, prolonged hypoxia affected osmotic regulation in a tissue-specific way, with reduced NKA activity in key osmoregulatory organs and compensatory NKA responses in peripheral tissues, which may indicate a shift in energy use toward oxygen transport under severe hypoxia. Full article

(This article belongs to the Special Issue Salmon Aquaculture)

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20 pages, 7925 KB

Open AccessArticle

Fish Community Composition and Seasonal Variation in the Coastal Waters of Sanya (Hainan, China) Based on eDNA Metabarcoding

by Chuanzheng Dong, Yaojie Guo and Zhi Chen

Fishes 2026, 11(7), 419; https://doi.org/10.3390/fishes11070419 - 16 Jul 2026

Abstract

To characterize the fish community composition and seasonal variation in the coastal waters of Sanya, a tropical coastal region on Hainan Island in the northern South China Sea, and to evaluate the applicability of environmental DNA (eDNA) metabarcoding for biodiversity monitoring, water samples [...] Read more.

To characterize the fish community composition and seasonal variation in the coastal waters of Sanya, a tropical coastal region on Hainan Island in the northern South China Sea, and to evaluate the applicability of environmental DNA (eDNA) metabarcoding for biodiversity monitoring, water samples were collected from 16 nearshore sampling sites in June 2024 and January 2025. Fish community structure was analyzed using eDNA metabarcoding, combined with diversity indices and multivariate statistical analyses. A total of 488 marine fish species were detected, including 426 species in summer and 205 species in winter, with higher species richness observed in summer. Perciformes was the dominant order in both seasons. Dominant species composition varied seasonally, with a relatively dispersed pattern in summer and a dominance concentration structure in winter. The Chao1 and Shannon indices were significantly higher in summer than in winter, whereas evenness showed no significant seasonal difference. NMDS and ANOSIM analyses revealed significant seasonal differences in community structure, and low Sørensen similarity coefficients indicated substantial species variation between seasons. These results indicate that fish communities in the coastal waters of Sanya exhibit clear seasonal variation. eDNA metabarcoding provides an effective complementary approach for monitoring fish diversity in complex coastal habitats, although its results may be influenced by eDNA transport, degradation, and reference database limitations. Full article

(This article belongs to the Section Biology and Ecology)

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17 pages, 1660 KB

Open AccessArticle

Effects of Small Shelter-like Structure Types on Tank Behavioral Responses of Juvenile Black Seabream (Acanthopagrus schlegelii)

by Qiang Cao, Yuange Chen, Ruiliang Fan, Longling Ouyang, Nannan Li, Wei Jiang and Weimin Quan

Fishes 2026, 11(7), 418; https://doi.org/10.3390/fishes11070418 - 16 Jul 2026

Abstract

Small shelter structures may affect the spatial use, locomotor state, and group spatial relationships of juvenile black seabream (Acanthopagrus schlegelii), but behavioral responses induced by different structure types remain insufficiently examined using multiple behavioral metrics. In this study, we conducted a [...] Read more.

Small shelter structures may affect the spatial use, locomotor state, and group spatial relationships of juvenile black seabream (Acanthopagrus schlegelii), but behavioral responses induced by different structure types remain insufficiently examined using multiple behavioral metrics. In this study, we conducted a tank experiment to test three hypotheses: compared with a structure-free control, cuboid and cylindrical structures would increase juvenile use of the central structure-placement zone, alter locomotor state, and affect inter-individual distance. Three treatments were established, including cuboid structure, cylindrical structure, and structure-free control, and fish behavior was observed under daytime and nighttime conditions. Video tracking and image analysis were used to quantify area-standardized average occurrence rate, average swimming speed, percentage of active time, and inter-individual distance. Both structures increased juvenile use of S1, namely the central structure-placement zone within a radius of 0–20 cm from the shelter-structure center. During the daytime, the average occurrence rates in S1 were 54.1% ± 6.33% and 46.7% ± 2.32% in the cuboid and cylindrical structure groups, respectively, which were higher than those in the structure-free control group (15.2% ± 3.08%). At night, the corresponding values were 50.2% ± 0.55%, 42.8% ± 3.77%, and 13.3% ± 1.57%, respectively. Locomotor behavior and inter-individual distance also varied with structure type, observation period, and diel condition. Under tank conditions, small shelter-like structures altered the short-term spatial use, locomotor state, and group spatial relationships of juvenile black seabream. These findings provide experimental evidence for how juvenile black seabream respond to simple shelter-like structures under controlled tank conditions and may help researchers, hatchery managers, and stock-enhancement practitioners select small structures for short-term behavioral assessment and shelter enrichment. Full article

(This article belongs to the Section Biology and Ecology)

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18 pages, 5997 KB

Open AccessArticle

Non-Equilibrium Recovery of Plankton Communities in the Yangtze River Estuary: Three Years After the Fishing Ban

by Bangping Deng, Wei Liu, Qiliang Song, Yuchen Guo, Chenxing Yang, Lin Zhu, Jun Li, Lijia Liu, Yin Yang and Xiucheng Yu

Fishes 2026, 11(7), 417; https://doi.org/10.3390/fishes11070417 - 16 Jul 2026

Abstract

Large-scale fishing bans are increasingly implemented to restore aquatic ecosystems, yet their effects on lower trophic levels remain poorly understood. As one of the world’s largest estuarine systems, the Yangtze River Estuary has been subjected to a ten-year fishing ban since 2021, providing [...] Read more.

Large-scale fishing bans are increasingly implemented to restore aquatic ecosystems, yet their effects on lower trophic levels remain poorly understood. As one of the world’s largest estuarine systems, the Yangtze River Estuary has been subjected to a ten-year fishing ban since 2021, providing a unique opportunity to potentially examine the response of plankton community to reduced fishing pressure along a steep salinity–nutrient gradient. This study relies on one-off environmental and plankton field surveys conducted in autumn 2024 (a sampling instead of multi-year time-series monitoring), we applied redundancy analysis, Mantel tests, and threshold indicator taxa analysis to tentatively clarify the roles of nutrients and salinity in structuring post-ban plankton communities. Species richness may have increased substantially compared with pre-ban levels, but community evenness declined and the dominance of Skeletonema costatum could have intensified, revealing a possible non-equilibrium recovery pattern. Zooplankton density increased substantially, which may not be fully consistent with the expectation under a simple top-down release scenario. Threshold analysis showed that S. costatum exhibited bidirectional responses to dissolved inorganic nitrogen and phosphate, with its positive response thresholds matching ambient nutrient concentrations in the inner estuary; this discrepancy is only a plausible inference since we lack direct measurements of fish predation and zooplankton grazing rates to verify causal trophic interactions. Our findings suggest that bottom-up forces driven by persistent eutrophication remain the dominant control on plankton community structure three years after the ban. From a watershed management perspective, our observational results provide a tentative implication that substantial reductions in nutrient loading might be required to mitigate unbalanced plankton community recovery; otherwise, the structural integrity of plankton assemblages could lag far behind the recovery of species richness under the current eutrophic background. Full article

(This article belongs to the Special Issue Sustainable Fisheries Dynamics)

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20 pages, 3423 KB

Open AccessArticle

Body Length, Tow Conditions, and Guide-Net Angle as Joint Predictive Contributors to Catch Loss in a Marine Mammal Bycatch Reduction Device: An Interpretable Machine Learning Analysis

by Kyu-Suk Choi, Jung-Mo Jung and Hyun-Young Kim

Fishes 2026, 11(7), 416; https://doi.org/10.3390/fishes11070416 - 16 Jul 2026

Abstract

Guide-net marine mammal bycatch reduction devices (BRDs) are intended to reduce protected species interactions in trawl fisheries, but their use may also cause catch loss of commercial fish and cephalopods. We restructured June and September 2024 sea trial records into a final six-taxon [...] Read more.

Guide-net marine mammal bycatch reduction devices (BRDs) are intended to reduce protected species interactions in trawl fisheries, but their use may also cause catch loss of commercial fish and cephalopods. We restructured June and September 2024 sea trial records into a final six-taxon BRD/COD modeling dataset containing 5641 individual records from 24 unique haul clusters. Logistic GLM, random forest, and XGBoost models were evaluated using haul-grouped cross-validation, and random forest SHAP and permutation analyses were used as exploratory variable contribution diagnostics. Model discrimination was modest and split-sensitive, but Brier score and accuracy were interpreted cautiously because the catch loss prevalence was 0.163 and trivial baselines were strong. Body length and headline height were the leading non-species contributors, while nominal guide-net angle remained a relevant design variable but ranked below several biological, tow condition, and realized gear geometry variables. Additional haul-clustered GEE sensitivity analyses treated nominal guide-net angle as a two-level categorical factor (30°/45°). Across four GEE specifications, the 45° angle term was consistently positive, but confidence intervals were wide, p-values were not significant, and the full species-adjusted model showed suspected quasi-separation in the hairtail term. These results indicate that nominal angle contribution cannot be cleanly isolated from species composition and realized gear geometry in this field dataset. We therefore interpret guide-net angle as an exploratory predictive contributor rather than as a causal factor of catch loss. Full article

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13 pages, 1308 KB

Open AccessArticle

Linking Ontogenetic, Seasonal, and Spatial Variability in the Trophic Biology of Citharichthys spilopterus to Environmental Conditions in a Tropical Estuary

by Castillo-Rivera Manuel and Hernández-Ruiz Hortencia

Fishes 2026, 11(7), 415; https://doi.org/10.3390/fishes11070415 - 16 Jul 2026

Abstract

The flatfish Citharichthys spilopterus is a common predatory species in the estuaries of the southwestern Gulf of Mexico. In general, factors controlling the foraging behavior of fish can be extrinsic (environmental conditions) or intrinsic (size-related differences). The main objective of this study was [...] Read more.

The flatfish Citharichthys spilopterus is a common predatory species in the estuaries of the southwestern Gulf of Mexico. In general, factors controlling the foraging behavior of fish can be extrinsic (environmental conditions) or intrinsic (size-related differences). The main objective of this study was to analyze spatiotemporal and body size-related variations in the diet of this species and their coupling with main environmental conditions. Every two months, 24 h sampling cycles were conducted in two habitats, one with submerged vegetation and the other without vegetation. Fish were collected every 2 h during each cycle. Canonical correspondence analysis revealed that submerged vegetation and body size were the main factors influencing diet composition, while diurnal variation was not significant. Decapod larvae and copepods were consumed more frequently in the unvegetated habitat during the dry season and by smaller fish, while peracarids, shrimp, and fish were consumed more frequently in the vegetated habitat during the rainy season and by larger fish. PERMANOVA analysis detected significant differences in diet between size groups, habitats, and months. Similarly, the fullness index showed significant differences between size groups and months. These spatiotemporal and ontogenetic trophic changes reflect the adaptation processes of the species to the seasonal and spatial environmental variability of the system. Full article

(This article belongs to the Section Biology and Ecology)

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9 pages, 6754 KB

Open AccessOpinion

Loop Lines (Traplines): A New Emerging Terminal Device in Pelagic Longline Swordfish Fisheries

by José Carlos Báez and Andrés Domingo

Fishes 2026, 11(7), 414; https://doi.org/10.3390/fishes11070414 - 16 Jul 2026

Abstract

Loop lines (also known as traplines) represent a recent innovation in pelagic longline fisheries, particularly targeting swordfish (Xiphias gladius). Originating in Japanese fisheries during the mid-2000s, their use has expanded across the Pacific, Atlantic, and Mediterranean, yet remains poorly documented in [...] Read more.

Loop lines (also known as traplines) represent a recent innovation in pelagic longline fisheries, particularly targeting swordfish (Xiphias gladius). Originating in Japanese fisheries during the mid-2000s, their use has expanded across the Pacific, Atlantic, and Mediterranean, yet remains poorly documented in fishing gear classifications and scientific literature. Loop lines consist of concentric monofilament loops attached to the branch line, replacing the conventional hook-and-bait terminal component. Available evidence suggests that this device may enhance swordfish catch rates while exhibiting high selectivity and reduced bycatch of non-target species such as seabirds and turtles. Preliminary observations also indicate size selectivity towards medium-sized individuals. Despite these potential advantages, concerns remain regarding fish welfare, meat quality, operational efficiency, and the risk of increased plastic pollution through gear loss. Given their growing adoption and possible implications for stock assessment, ecosystem impacts, and fisheries management, systematic data collection and observer-based studies are urgently needed to properly characterize their performance and environmental effects. Full article

(This article belongs to the Section Fishery Economics, Policy, and Management)

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21 pages, 14810 KB

Open AccessArticle

Nutriphysiological Effects of Hermetia illucens Meal Low Inclusion in Common Carp as an Omnivorous Fish Model Species

by Jan Mazurkiewicz, Zaynab Mashood, Mateusz Rawski, Paula Skrzypczak, Agata Dankowiakowska, Patrycja Reszka and Magdalena Stanek

Fishes 2026, 11(7), 413; https://doi.org/10.3390/fishes11070413 - 14 Jul 2026

Abstract

Common carp (Cyprinus carpio) fry were fed diets containing defatted Hermetia illucens (HI) larvae meal at three inclusion levels to investigate its effects on the nutriphysiological status, focusing on protein and fat digestibility (in vitro and in vivo), growth performance parameters, [...] Read more.

Common carp (Cyprinus carpio) fry were fed diets containing defatted Hermetia illucens (HI) larvae meal at three inclusion levels to investigate its effects on the nutriphysiological status, focusing on protein and fat digestibility (in vitro and in vivo), growth performance parameters, diet utilization, somatic indices, and GIT histomorphology. The HI meal was included at 0%, 2%, 4%, and 6%. A total of 240 carp fry were randomly divided into four groups, six replicates each (10 fish/tank), and the growth trials lasted 60 days. The dietary inclusion of HI meal up to 6% in carp feed did not significantly affect growth performance, feed utilization, or homeostasis. In vitro protein digestibility exceeded 97% across all treatments with pepsin, indicating efficient hydrolysis. However, the highest crude protein digestibility coefficients were recorded in all treatment groups, which differed significantly from the control group (90.5%). Also, villus width and crypt depth did not differ significantly; however, other parameters, such as villus height and area, showed some significant variations across the treatment groups. No adverse effects were observed on liver condition, structure, or function, reinforcing the safety of HI up to 6% in carp diets. In conclusion, this study demonstrates that HI can be incorporated as a functional, health-promoting ingredient in the diets of common carp fry. Full article

(This article belongs to the Special Issue Nutritional Physiology and Environmental Toxicology of Aquatic Animals)

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16 pages, 1792 KB

Open AccessArticle

Effects of Incorporating Validated Juvenile Otolith Microincrements on Growth Estimation and Stock Assessment of the Southern Brazilian Stock of Mugil liza

by Vladmyr Mello Schlosser, Eidi Kikuchi, Rodrigo Sant’Ana, Bruno Leite Mourato, Thaís Garbin, Ricardo Vieira Rodrigues, Jorge Pablo Castello and Luís Gustavo Cardoso

Fishes 2026, 11(7), 412; https://doi.org/10.3390/fishes11070412 - 13 Jul 2026

Abstract

Understanding individual growth is essential for assessing exploitation status and supporting sustainable fishery management. For the southern Brazilian stock of the mullet Mugil liza, previous growth estimates were based on whole otolith readings and included few young individuals, potentially influencing growth parameter [...] Read more.

Understanding individual growth is essential for assessing exploitation status and supporting sustainable fishery management. For the southern Brazilian stock of the mullet Mugil liza, previous growth estimates were based on whole otolith readings and included few young individuals, potentially influencing growth parameter estimation and stock assessment outputs. In this study, daily otolith microincrements of juveniles were validated using oxytetracycline (OTC) marking and combined with age–length data from a previous study to evaluate the effect of incorporating validated juvenile ages into von Bertalanffy growth function estimates. The updated model yielded a 15% smaller asymptotic length (564 mm), a 47% higher growth coefficient (0.28 yr⁻¹), and a theoretical age at zero length closer to biologically plausible values (t0 = −0.11). Revised growth parameters were incorporated into an age-structured production model (ASPM). Although temporal trends in spawning biomass and fishing mortality remained similar, substantial differences were observed in biomass scale and biological reference points. These findings highlight the sensitivity of stock assessment outputs to growth parameterization and the importance of adequately representing early life stages in growth models. Full article

(This article belongs to the Special Issue Modeling Approach for Fish Stock Assessment)

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22 pages, 6638 KB

Open AccessArticle

Integrated Application of Iso-Seq and RNA-Seq Analyses to Uncover Genes Involved in Ovarian Development in Platypharodon extremus

by Zhuoyu Yang, Yanping Zhang, Wei Ka, Wenjing He, Yujie Yang, Wenlong Jiao and Jianlin Wang

Fishes 2026, 11(7), 411; https://doi.org/10.3390/fishes11070411 - 12 Jul 2026

Abstract

This study focused on Platypharodon extremus, a species endemic to the Qinghai–Tibet Plateau, and systematically analyzed its reproductive biology, sex steroid hormones, ovarian histology, and transcriptomic characteristics throughout its complete reproductive cycle (August 2020 to June 2021). The results demonstrated that the [...] Read more.

This study focused on Platypharodon extremus, a species endemic to the Qinghai–Tibet Plateau, and systematically analyzed its reproductive biology, sex steroid hormones, ovarian histology, and transcriptomic characteristics throughout its complete reproductive cycle (August 2020 to June 2021). The results demonstrated that the body length, height, body weight, and gonadal weight of female individuals continuously increased with age, while the Gonadosomatic index (GSI) was lowest during the breeding season (June–August) and gradually rose during the non-breeding period. Serum estradiol (E2) and progesterone (P4) exhibited rhythmic fluctuations corresponding to ovarian development: E2 rose from 25.77 ng/L in stage-I to 146.00 ng/L in stage-V, then declined post-ovulation; P4 increased from 59.88 pmol/L in stage-I to 239.03 pmol/L in stage-V, showing a significant decrease after ovulation. Histological observations classified ovarian development into stages I–VI, clearly delineating the complete process from oogonium proliferation, cortical vesicle formation, yolk accumulation, maturation to postpartum regression. To explore molecular changes during the transition from vitellogenesis to oocyte maturation, we built a reference transcriptome with 30,060 non-redundant transcripts (average length = 1975 bp) using PacBio and Illumina data, and 91.87% of these transcripts received functional annotation hits against public databases. A comparative differential expression analysis was performed between ovarian stage III (active yolk accumulation) and stage V (oocyte fully matured). A total of 11,324 differentially expressed genes were identified (5249 upregulated and 6175 downregulated) between these two stages. GO enrichment analysis revealed predominant involvement in cellular processes, cellular components, and catalytic activities, while KEGG analysis demonstrated significant enrichment in metabolic pathways, PI3K-Akt, MAPK, and calcium signaling pathways. Quantitative PCR (qPCR) validation confirmed that candidate genes, including pik3a, calm, mapk1 map2k ddx49, and igf2 were significantly upregulated at stage V. These differentially expressed genes (DEGs) may represent potential molecular signatures linked to the transition from vitellogenesis to oocyte maturation. Our integrated transcriptomic and qPCR data identify potential gene candidates involved in ovarian maturation; however, these findings reveal correlation rather than direct regulatory causality. This study offers fundamental data and theoretical insights for understanding the reproductive regulatory mechanisms and aquaculture management of this endemic species. Full article

(This article belongs to the Special Issue Physiological and Behavioral Studies in Aquaculture)

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