Fish Species Research Articles

Genomic analysis and phylogenetic characterization of Himalayan snow trout, Schizothorax esocinus based on mitochondrial protein-coding genes.

Mitochondrial DNA (mtDNA) has become a significant tool for exploring genetic diversity and delineating evolutionary links across diverse taxa. Within the group of cold-water fish species that are native to the Indian Himalayan region, Schizothorax esocinus holds particular importance due to its ecological significance and is potentially vulnerable to environmental changes. This research aims to clarify the phylogenetic relationships within the Schizothorax genus by utilizing mitochondrial protein-coding genes. Standard protocols were followed for the isolation of DNA from S. esocinus. For the amplification of mtDNA, overlapping primers were used, and then subsequent sequencing was performed. The genetic features were investigated by the application of bioinformatic approaches. These approaches covered the evaluation of nucleotide composition, codon usage, selective pressure using nonsynonymous substitution /synonymous substitution (Ka/Ks) ratios, and phylogenetic analysis. The study specifically examined the 13 protein-coding genes of Schizothorax species which belongs to the Schizothoracinae subfamily. Nucleotide composition analysis showed a bias towards A + T content, consistent with other cyprinid fish species, suggesting evolutionary conservation. Relative Synonymous Codon Usage highlighted leucine as the most frequent (5.18%) and cysteine as the least frequent (0.78%) codon. The positive AT-skew and the predominantly negative GC-skew indicated the abundance of A and C. Comparative analysis revealed significant conservation of amino acids in multiple genes. The majority of amino acids were hydrophobic rather than polar. The purifying selection was revealed by the genetic distance and Ka/Ks ratios. Phylogenetic study revealed a significant genetic divergence between S. esocinus and other Schizothorax species with interspecific K2P distances ranging from 0.00 to 8.87%, with an average of 5.76%. The present study provides significant contributions to the understanding of mitochondrial genome diversity and genetic evolution mechanisms in Schizothoracinae, hence offering vital insights for the development of conservation initiatives aimed at protecting freshwater fish species.

Composition of Large Prey Species of Irrawaddy Dolphins (Orcaella brevirostris) in the Mekong River: Implications for Conservation of the Prey Resources

Information on the feeding habits of the critically endangered Irrawaddy dolphin (Orcaella brevirostris) in the Mekong River and how their diet overlaps with that of the species targeted by fisheries is limited. The information provided herein will be helpful for evaluating and protecting important dolphin food resources. The composition of large prey species of Irrawaddy dolphins and the extent of fish resources were surveyed in the Mekong River, Cambodia, using local ecological knowledge. The results showed that Irrawaddy dolphins fed on 13 species of large fish, with Pangasius conchophilus, Cyclocheilichthys enoplos, and Hemibagrus wyckii the most frequently consumed prey. Twelve of the 13 reported prey species were usually caught by fishers. The results also revealed that the average weight of fish caught daily by fishers was significantly lower in 2019 than about five years before that, regardless of the season. A significant decline in fish resources and a high overlap of dolphin diets with fishery target species indicate that Irrawaddy dolphins may also be threatened by prey depletion, especially during the dry season when dolphins are concentrated in deep pools.

Evaluation of the Ecological Environment of the Fuhe River Based on the Diversity of Fish

This article takes the Fuhe River, which has water flowing into Baiyangdian all year round, as the research object. Through actual investigation and measurement of planktonic flora and fauna, benthic organisms, fish, and large vascular plants in the river, and based on fish diversity, the comprehensive evaluation index method is used to scientifically evaluate the ecological environment quality of the Fuhe River. The results showed that a total of 28 species of phytoplankton, 30 species of zooplankton, 11 species of benthic animals, 8 species of submerged plants, and 11 species of fish were detected in the survey area; From a diversity perspective, the diversity of the upstream and downstream river sections is higher than that of the downstream. Overall, the ecological environment quality of the Fuhe River in Baoding City ranges from medium to good, with good water quality in the upstream section and moderate water quality in the middle and downstream sections. This study provides a case study for the scientific evaluation of the ecological environment quality of the upper reaches of Baiyangdian.

Assessing the response of marine fish communities to climate change and fishing.

Globally, marine fish communities are being altered by climate change and human disturbances. We examined data on global marine fish communities to assess changes in community-weighted mean temperature affinity (i.e., mean temperatures within geographic ranges), maximum length, and trophic levels, which, respectively, represent the physiological, morphological, and trophic characteristics of marine fish communities. Then, we explored the influence of climate change and fishing on these characteristics because of their long-term role in shaping fish communities, especially their interactive effects. We employed spatial linear mixed models to investigate their impacts on community-weighted mean trait values and on abundance of different fish lengths and trophic groups. Globally, we observed an initial increasing trend in the temperature affinity of marine fish communities, whereas the weighted mean length and trophic levels of fish communities showed a declining trend. However, these shift trends were not significant, likely due to the large variation in midlatitude communities. Fishing pressure increased fish communities' temperature affinity in regions experiencing climate warming. Furthermore, climate warming was associated with an increase in weighted mean length and trophic levels of fish communities. Low climate baseline temperature appeared to mitigate the effect of climate warming on temperature affinity and trophic levels. The effect of climate warming on the relative abundance of different trophic classes and size classes both exhibited a nonlinear pattern. The small and relatively large fish species may benefit from climate warming, whereas the medium and largest size groups may be disadvantaged. Our results highlight the urgency of establishing stepping-stone marine protected areas to facilitate the migration of fishes to habitats in a warming ocean. Moreover, reducing human disturbance is crucial to mitigate rapid tropicalization, particularly in vulnerable temperate regions.

Sea anemone-anemonefish symbiosis: Behavior and mucous protein profiling.

Fish species of the genus Amphiprion (Perciformes: Pomacentridae) seek protection from predators among the tentacles of sea anemones as their natural habitat, where they live essentially unharmed from stinging by the host's nematocysts. The skin mucus of these anemonefish has been suggested as a protective mechanism that prevents the discharge of the nematocysts upon contact. Whereas some anemonefish species seem to produce their own protective mucous coating, others may acquire mucus (or biomolecules within) from the sea anemone during an acclimation period. In controlled experiments, we show that Amphiprion ocellaris acclimated successfully to their natural host anemone species Stichodactyla gigantea, and also to Stichodactyla haddoni, and in some cases Heteractis crispa, neither of which are natural host species. No symbiosis was observed for three other anemone species tested, Entacmaea quadricolor, Macrodactyla doreensis, and Heteractis malu. We explored the skin mucous protein profile from naive and experienced A. ocellaris during their acclimation to natural and unnatural host anemones. We confidently report the presence of metabolic and structural proteins in the skin mucus of all samples, likely involved in immunological defense, molecular transport, stress response, and signal transduction. For those anemonefish that established symbiosis, there was a clear increase in ribosomal-type proteins. We additionally provide evidence for the presence of anemone proteins only in the skin mucus of individuals that established symbiosis. Our results support previous speculation of the role of skin mucous-associated proteins in anemonefish-anemone symbiosis. Further exploration of these mucosal proteins could reveal the mechanism of anemonefish acclimation to host anemones.

Comparing Transcriptomic Points of Departure to Apical Effect Concentrations For Larval Fathead Minnow Exposed to Chemicals with Four Different Modes Of Action.

It is postulated that below a transcriptomic-based point of departure, adverse effects are unlikely to occur, thereby providing a chemical concentration to use in screening level hazard assessment. The present study extends previous work describing a high-throughput fathead minnow assay that can provide full transcriptomic data after exposure to a test chemical. One-day post-hatch fathead minnows were exposed to ten concentrations of three representatives of four chemical modes of action: organophosphates, ecdysone receptor agonists, plant photosystem II inhibitors, and estrogen receptor agonists for 24 h. Concentration response modeling was performed on whole body gene expression data from each exposure, using measured chemical concentrations when available. Transcriptomic points of departure in larval fathead minnow were lower than apical effect concentrations across fish species but not always lower than toxic effect concentrations in other aquatic taxa like crustaceans and insects. The point of departure was highly dependent on measured chemical concentration which were often lower than the nominal concentration. Differentially expressed genes between chemicals within modes of action were compared and often showed statistically significant overlap. In addition, reproducibility between identical exposures using a positive control chemical (CuSO4) and variability associated with the transcriptomic point of departure using in silico sampling were considered. Results extend a transcriptomic-compatible fathead minnow high-throughput assay for possible use in ecological hazard screening.

A non-native fish species reaches the south-western European waters: the Atlantic croaker, Micropogonias undulatus (Acanthuriformes, Sciaenidae) and its invasion history in Europe

A non-native fish species reaches the south-western European waters: the Atlantic croaker, Micropogonias undulatus (Acanthuriformes, Sciaenidae) and its invasion history in Europe

Exploring the prevalence and impact of Ligula intestinalis infection across fish species in Sistan region, Iran

Exploring the prevalence and impact of Ligula intestinalis infection across fish species in Sistan region, Iran

DETERMINANTS OF THE MORTALITY OF PATIN FISH IN TEMERLOH, PAHANG, MALAYSIA

This study explores the factors influencing Patin fish mortality in Malaysia's expanding aquaculture industry, which is crucial for meeting the rising global demand for fish and seafood. Analysing data from 135 fish farmers through SPSS Software, it finds significant correlations between mortality rates and variables like fish species, time until sale, and fish quantity per cage. At the same time, factors such as partnership numbers and feeding frequency have minimal impact. These results highlight the critical role of water quality management in fish health and production costs. The findings are vital for developing strategies to improve fish farming and water quality control in Malaysia, addressing the need to consider various factors to reduce fish mortality. Despite the significance of certain variables, the low adjusted R-squared value points to other yet unidentified factors affecting fish deaths, suggesting ongoing data collection and model refinement for stakeholders. This research contributes to understanding aquaculture costs and fish health, informing theories such as Interactive Governance Theory, Stress Response Theory, and Disease Ecology Theory and underscoring the importance of comprehensive strategies for sustainable aquaculture practices.

The gills and skin microbiota of five pelagic fish species from the Atlantic Ocean.

The gills and skin microbiota and microbiome of wild fish remain far more under-investigated compared to that of farmed fish species, despite that these animal-microbe interactions hold the same ecophysiological roles in both cases. In this study, the gills and skin bacterial microbiota profiles and their presumptive bacterial metabolisms were investigated in five open-sea fishes: bullet tuna (Auxis sp.), common dolphinfish (Coryphaena hippurus), Atlantic little tunny (Euthynnus alletteratus), Atlantic bonito (Sarda sarda) and Atlantic white marlin (Kajikia albida). Gills and skin tissues were collected from two to three individuals per species, from specimens caught by recreational trolling during summer of 2019, and their bacterial 16S rRNA gene diversity was analysed by high-throughput sequencing. The gills bacterial communities among the five species were clearly different but not the skin bacterial microbiota. The dominant operational taxonomic units belonged to the Moraxellaceae, Pseudomonadaceae, Rhodobacteraceae, Staphylococcaceae and Vibrionaceae families. Despite the differences in taxonomic composition, the presumptive bacterialmetabolisms between the gills and skin of the five fishes investigated here were ≥ 94% similarand were dominated by basic metabolism, most likely reflecting the continuous exposure of these tissues in the surrounding seawater.

Fish oil replacement with different vegetable oils in Onychostoma macrolepis: Effects on fatty acid metabolism based on whole-body fatty acid balance method and genes expression.

To evaluate the fatty acid (FA) metabolism status and possibility as a DHA source of farmed Onychostoma macrolepis, a total of 168 fish (2.03 ± 0.23 g) were fed four diets supplemented with fish oil (FO), linseed oil (LO), soybean oil (SO), and a mixture of LO and SO oil (MO), respectively, for 70 days. Body FA compositions were modified reflecting dietary FAs. Comparing liver and intestine fatty acids with fish fed four diets, the content of ARA in fish fed SO was significantly higher than others (P < 0.05), but showed no difference in muscle. The tissue FA profile showed that the FO-fed group successfully deposited DHA, while the LO-fed group converted ALA to DHA effectively, as well as the liver and intestine EPA was notably highest in the FO group, whereas no difference between the FO and LO group in the muscle. The FA results showed that the DHA contents in the muscle of Onychostoma macrolepis are at a medium-high level compared with several other fish species with the highest aquaculture yield. Correspondingly, in the fish fed diet with LO, SO, and MO, the genes of most FA biosynthesis, transportation, and transcriptional regulation factors were increased in the liver and muscle, but no significant difference was observed in the gene expression of Elovl4b, FATP1, and FABP10 in the muscle. In addition, the enzyme activity involved in PUFA metabolism was higher in fish fed vegetable oil-based diets, corroborating the results of the gene expression. Increased in vivo elongase and desaturase (Δ5, Δ6, and Δ9) activities were recorded in fish fed fish oil-devoid diets, which resulted in the appearance of products associated with elongase and desaturase activities in fish. Besides, as the specific n-3 PUFA synthesis substrate, the dietary supplementation of ALA not only retains most of the nutrition value but also ensures the muscular texture, such as fiber diameter and density. It is concluded that farmed O. macrolepis owns strong n-3 LC-PUFA biosynthetic capacity and high DHA contents so it can be a good DHA source for the population.

Estuary: A Natural Filter Emphasis on A Mathematical Model of Pollution in Mandovi River

An estuary is a partially enclosed coastal body of brackish water with one or more rivers or streams flowing into it and with a free connection to the open sea. These freshwater estuaries also provide many of the ecosystem services and functions that brackish estuaries do, such as serving as natural filters for runoff and providing nursery grounds for many species of birds, fish, and other animals. Estuaries are among the most productive ecosystems in the world. Mandovi River in Goa is one such important Estuary. A mathematical model is presented to protect the Ecosystem

Assessing Colouration in Ichthyology: Insights from the Melanophore Index Perspective

Fish colouration significantly influences various aspects of their biology, including communication, camouflage, and mate selection. Among the pigment cells responsible for generating colours, melanophores are particularly significant due to their ability to produce dark pigments called melanin. The Melanophore Index (MI) quantitatively evaluates melanophore density and distribution across different fish species. This comprehensive review delves into the significance of fish colouration, the biology of melanophores, methods for assessing MI, factors influencing MI variations, and the ecological and evolutionary implications of MI in fish populations. By synthesizing current research and highlighting gaps in knowledge, this review aims to provide a foundational understanding of assessing fish colouration through the lens of the Melanophore Index.

Myxobolus acanthogobii Hoshina, 1952 and Myxobolus selari n. sp. (Myxosporea: Myxobolidae) infecting brain of commercial fishes in Terengganu, Malaysia.

Myxosporean infection in marine water fishes has drawn less attention than in freshwater fishes, which resulted in a higher taxonomic variety in freshwater in Malaysia. This study aimed to address the gap by conducting a myxosporean survey on two commercially significant marine fish species, Nemipterus furcosus (Valenciennes) (Eupercaria incertae sedis: Nemipteridae) and Selar crumenophthalmus (Bloch) (Carangiformes: Carangidae), collected from the northeastern part of peninsular Malaysia. During the examination of the organs, two distinct Myxobolus Bütschli, 1882 species were discovered in the brain tissue of these fishes, despite the absence of any observable pathological signs. The two Myxobolus species were characterized through morphometry, morphology, and analysis of partial small subunit ribosomal RNA (18S rDNA) gene. As a result, Myxobolus acanthogobii Hoshina, 1952, which infects 2.3% of N. furcosus, is synonymous with a myxobolid species commonly found in Japanese waters, based on its morphological traits, tissue tropism, and molecular diagnostics. Furthermore, a novel species, Myxobolus selari n. sp., was described, infecting the brain of one (11%) individual S. crumenophthalmus. This unique species displayed distinctive features, placing it within a well-supported subclade primarily comprising brain-infecting myxobolids. Maximum likelihood analysis further revealed the close relationships among these brain-infecting myxobolids, underscoring the significance of tissue tropism and host taxonomy for myxobolids. This study represents the initial documentation of Myxobolus species within the southern South China Sea, shedding light on the potential diversity of marine myxosporean in this region. This article was registered in the Official Register of Zoological Nomenclature (ZooBank) as urn:lsid:zoobank.org:pub:7C400E35-7CB8-4DEE-92B7-F75FF3926441.

Assessing Diet &amp; Trophic Position of Fish in Chenderoh Reservoir, Malaysia: SCA &amp; SIA Approach

The present study assessed and compared the diet and trophic positions (TP) of two carnivorous fish H. macrolepidota and C. ocellaris from Chenderoh Reservoir, Malaysia. The focal goal of the study was to understand the effects of invasive non-indigenous species (NIS), C. ocellaris, on the native indigenous (IS) fish species, H. macrolepidota. Data were acquired from September 2014 to February 2015 within the study area. The assessment was grounded in stomach content analysis (SCA) and stable isotope analysis (SIA), which collectively clarified the feeding habits and trophic positions (TP) of these selected fish. In total, 184 fish samples (comprising 64 individuals of H. macrolepidota and 120 individuals of C. ocellaris) underwent stomach content analysis (SCA). Additionally, 24 individuals (12 of H. macrolepidota and 12 of C. ocellaris), sampled from December 2014 to February 2015, were selected for stable isotope analysis (SIA). The mean RGL values for H. macrolepidota and C ocellaris were 0.98 ± 0.18 and 1.10 ± 0.15 (Mean ± SD), respectively, aligning with known ranges for carnivorous fish. These values also clarified that both species occupy higher TP in the food web as tertiary or quaternary consumers. SCA findings also revealed that fish and crustaceans were the predominant food categories for H. macrolepidota, while C. ocellaris predominantly fed on fish. The mean stomach fullness index (MSF) and the gastrosomatic index (GSI) corroborated the differences in the foraging performance of the fishes, with C. ocellaris having a higher MSF (2.03) compared to H. macrolepidota (0.65). These implied that C. ocellaris had plentiful of food and encountered fewer diet-related challenges in the ecosystem. From SIA, δ13C values indicated that the primary carbon sources for both species are C3 plants, particularly aquatic vegetation. Further, δ15N values further ensured that both H. macrolepidota and C. ocellaris are carnivorous in nature and occupy higher TP in the ecosystem.

How to improve fishery eco-efficiency by building marine ranch in China

Based on the panel data of the province and municipality in 2010–2021, this paper measures the fishery eco-efficiency by using the SBM-DEA model and empirically analyses how China’s marine ranch construction improves the fishery eco-efficiency by using the double-difference fixed-effect model. The results show that, firstly, China’s marine ranch construction can improve the fishery eco-efficiency. Secondly, China’s marine ranch construction promotes fisheries eco-efficiency by improving the input efficiency of labor, fish species, fishing vessel, fishery technology extension, aquaculture area and by reducing pollutant outputs. Thirdly, the fishery eco-efficiency of the marine ranch construction region has increased annually since 2015, and technological changes, scale efficiency changes and technical efficiency changes can all contribute to the fishery eco-efficiency improvement, and increase in order. Based on the results of the empirical analyses, this paper proposes policy recommendations to improve the fishery eco-efficiency in the conjunction with the construction of marine ranch in China.

Leveraging relationships between species abundances to improve predictions and inform conservation

Abstract Many management and conservation contexts can benefit from understanding relationships between species abundances, which can be used to improve predictions of species occurrence and abundance. We present conditional prediction as a tool to capture information about species abundances via residual covariance between species. From a fitted joint species distribution model, this framework produces a species coefficient matrix that contains relationships between species abundances. The species coefficients allow co‐observed species to be treated as a second set of predictors supplementing covariates in the model to improve prediction. We use simulations to demonstrate the potential benefits and limitations of conditional prediction across data types and species covariance before applying conditional prediction to two management contexts with real data. Simulations demonstrate that conditional prediction provides the largest benefits to continuous data and when there is residual covariance between many species. In our first application, we show that conditioning on other species improves in‐sample and out‐of‐sample predictions of fish and invertebrate species, including Atlantic cod. In our second application, we show that the species coefficient matrix can be used to identify bird species at risk of nest parasitism by Brown‐headed Cowbirds. Synthesis and applications. We present guidelines for using conditional prediction, which can help understand relationships between species abundances, improve predictions and inform conservation in a variety of contexts.

Spatial and Temporal Changes in the Fish Fauna of a Low-Inflow Estuary following a Mass Mortality Event and Natural and Artificial Bar Breaches

Estuaries that become closed from the ocean through the formation of a sand bar are particularly susceptible to degradation and often experience poor water quality and fish kills. Sampling was conducted seasonally for two years in the deeper waters of the Vasse–Wonnerup (southwestern Australia) after a large fish mortality event to identify the fish species present and determine if richness, abundance, diversity and faunal composition differed among regions and over time. Species richness, abundance and diversity were far greater in the downstream regions than in the upstream regions, reflecting patterns in salinity. Catch rates of two marine estuarine-opportunist mugilids (Mugil cephalus and Aldrichetta forsteri) and an estuarine-resident sparid (Acanthopagrus butcheri), which were the species most affected by the mortality event, were relatively stable. It is suggested that before sampling commenced, mugilids had entered the estuary following an artificial sand bar breach, while the loss of 0+ (new recruits) A. butcheri in the mortality event and subsequent recruitment failure prevented stocks from increasing. Temporal shifts in fish composition were driven by less abundant species, which utilized the estuary more opportunistically. Increases in the occurrences and abundances of these species coincided with an open bar and salinities close to those of seawater. The data also show how the estuary responds to differing hydrodynamic phases and artificial breaches.

Development and validation of a TaqMan-based qPCR assay for reliable detection of invasive sailfin catfishes (Pterygoplichthys spp.) through measurements of environmental DNA

Sailfin catfishes (Pterygoplichthys spp.) are a group of fishes introduced to several freshwater habitats across the globe. Sailfin catfishes are a hard-armoured fish with no economic importance as a food species. These catfishes have been reported to be affecting the growth of several economically valuable species that are native to different freshwater ecosystems. In this manuscript, we developed a TaqMan-based assay targeting the mitochondrial cytochrome c oxidase subunit 1 (COX1) gene, to specifically detect the presence of catfishes by environmental DNA (eDNA) measurements. The developed assay was screened against 16 species of fish and mussel that co-occur in the habitats along with sailfin catfishes, and the qPCR reaction did not have any non-target amplifications. The assay was further validated under laboratory conditions by measuring eDNA from tanks having different biomass of catfishes (1 and 0.5 g L−1), and the copy number of the amplified product was directly proportional to the biomass maintained in the tanks. Overall, the study provides a robust molecular tool based on eDNA measurements to facilitate detection of invasive sailfin catfishes and, in turn, contributes towards the management of the invaded habitats.

Challenges in downstream dam passage and the effect of dam removal on Atlantic salmon (Salmo salar) smolt migrations.

Migration is critical for life-cycle completion in diadromous fish species. River connectivity is vital in facilitating these large-scale movement events, but the extent of present-day river fragmentation can interfere with these migrations. Fish passage solutions (FPSs) are commonly implemented with the aim of improving river connectivity. In our study, we investigated the performance of two types of FPSs, spill regimes and complete dam removal, on Atlantic salmon (Salmo salar) smolt migrations. We used acoustic telemetry to monitor migration behavior and passage success of 120 wild smolts released in three different groups/sites: one group with two dams to pass to reach the river mouth, a second group with one dam to pass, and a control group without any barriers to pass (upstream of a recently removed hydroelectric dam). Smolt passage probabilities were similar for the two studied dams (87% and 86%) but showed variation in path choice, delay times, and loss rates. Passage success was influenced by several factors, such as body size, diel period, and water temperature, but not flow. Cumulative passage success to the river mouth was 61%, with most individuals being lost within lentic river stretches, either in the forebays of hydroelectric power stations or in naturally wide river stretches. Within the recently rehabilitated river sections (post dam removal), passage speeds were significantly faster than all other sections of the river (post-rehabilitation x¯ = 56.1 km/day) with significantly faster speeds compared to pre-rehabilitation (pre-x¯ = 28.0 km/day). Our findings provide valuable information on the benefits of dam removal and highlight the need for further rehabilitation measures in upriver reaches where barriers still affect downstream passage.