Detecting population structure in a high gene-flow species, Atlantic herring (Clupea harengus): direct, simultaneous evaluation of neutral vs putatively selected loci

In many marine fish species, genetic population structure is typically weak because populations are large, evolutionarily young and have a high potential for gene flow. We tested whether genetic markers influenced by natural selection are more efficient than the presumed neutral genetic markers to detect population structure in Atlantic herring (Clupea harengus), a migratory pelagic species with large effective population sizes. We compared the spatial and temporal patterns of divergence and statistical power of three traditional genetic marker types, microsatellites, allozymes and mitochondrial DNA, with one microsatellite locus, Cpa112, previously shown to be influenced by divergent selection associated with salinity, and one locus located in the major histocompatibility complex class IIA (MHC-IIA) gene, using the same individuals across analyses. Samples were collected in 2002 and 2003 at two locations in the North Sea, one location in the Skagerrak and one location in the low-saline Baltic Sea. Levels of divergence for putatively neutral markers were generally low, with the exception of single outlier locus/sample combinations; microsatellites were the most statistically powerful markers under neutral expectations. We found no evidence of selection acting on the MHC locus. Cpa112, however, was highly divergent in the Baltic samples. Simulations addressing the statistical power for detecting population divergence showed that when using Cpa112 alone, compared with using eight presumed neutral microsatellite loci, sample sizes could be reduced by up to a tenth while still retaining high statistical power. Our results show that the loci influenced by selection can serve as powerful markers for detecting population structure in high gene-flow marine fish species.

Mercury levels of marine fish commonly consumed in Peninsular Malaysia

This study was conducted to determine the concentration of total mercury in the edible portion of 46 species of marine fish (n = 297) collected from selected major fish landing ports and wholesale markets throughout Peninsular Malaysia. Samples were collected in June to December 2009. Prior to analysis, the fish samples were processed which consisted of drying at 65 °C until a constant weight was attained; then, it was grounded and digested by a microwave digestion system. The analytical determination was carried out by using a mercury analysis system. Total mercury concentration among fish species was examined. The results showed that mercury concentrations were found significantly higher (p < 0.001) in demersal fish (the range was from 0.173 to 2.537 mg/kg in dried weight) compared to pelagic fish (which ranged from 0.055 to 2.137 mg/kg in dried weight). The mercury concentrations were also higher in carnivorous fish especially in the species with more predatory feeding habits. Besides, the family group of Latidae (0.537 ± 0.267 mg/kg in dried weight), Dasyatidae (0.492 ± 0.740 mg/kg in dried weight), and Lutjanidae (0.465 ± 0.566 mg/kg in dried weight) showed significantly (p < 0.001) higher mercury levels compared to other groups. Fish collected from Port Klang (0.563 ± 0.509 mg/kg in dry weight), Kuala Besar (0.521 ± 0.415 mg/kg in dry weight), and Pandan (0.380 ± 0.481 mg/kg in dry weight) were significantly higher (p = 0.014) in mercury concentrations when compared to fish from other sampling locations. Total mercury levels were significantly higher (p < 0.002) in bigger fish (body length >20 cm) and were positively related with fish size (length and weight) in all fish samples. Despite the results, the level of mercury in marine fish did not exceed the permitted levels of Malaysian and JECFA guideline values at 0.5 mg/kg methylmercury in fish.

Warming shelf seas drive the subtropicalization of European pelagic fish communities

Pelagic fishes are among the most ecologically and economically important fish species in European seas. In principle, these pelagic fishes have potential to demonstrate rapid abundance and distribution shifts in response to climatic variability due to their high adult motility, planktonic larval stages, and low dependence on benthic habitat for food or shelter during their life histories. Here, we provide evidence of substantial climate-driven changes to the structure of pelagic fish communities in European shelf seas. We investigated the patterns of species-level change using catch records from 57,870 fisheries-independent survey trawls from across European continental shelf region between 1965 and 2012. We analysed changes in the distribution and rate of occurrence of the six most common species, and observed a strong subtropicalization of the North Sea and Baltic Sea assemblages. These areas have shifted away from cold-water assemblages typically characterized by Atlantic herring and European sprat from the 1960s to 1980s, to warmer-water assemblages including Atlantic mackerel, Atlantic horse mackerel, European pilchard and European anchovy from the 1990s onwards. We next investigated if warming sea temperatures have forced these changes using temporally comprehensive data from the North Sea region. Our models indicated the primary driver of change in these species has been sea surface temperatures in all cases. Together, these analyses highlight how individual species responses have combined to result in a dramatic subtropicalization of the pelagic fish assemblage of the European continental shelf.

School density affects the strength of collective avoidance responses in wild-caught Atlantic herring Clupea harengus: a simulated predator encounter experiment

An experimental study in a semi-controlled environment was conducted to examine whether school density in wild-caught Atlantic herring Clupea harengus affects the strength of their collective escape behaviours. Using acoustics, the anti-predator diving responses of C. harengus in two schools that differed in density were quantified by exposing them to a simulated threat. Due to logistical restrictions, the first fish was tested in a low-density school condition (four trials; packing density = 1.5 fish m(-3); c. 6000 fish) followed by fish in a high-density school condition (five trials; packing density = 16 fish m(-3); c. 60 000 fish). The C. harengus in a high-density school exhibited stronger collective diving avoidance responses to the simulated predators than fish in the lower-density school. The findings suggest that the density (and thus the internal organization) of a fish school affects the strength of collective anti-predatory responses, and the extent to which information about predation risk is transferred through the C. harengus school. Therefore, the results challenge the common notion that information transfer within animal groups may not depend on group size and density.

Otolith shape: a population marker for Atlantic herring Clupea harengus

Otolith shape variation of seven Atlantic herring Clupea harengus populations from Canada, the Faroe Islands, Iceland, Ireland, Norway and Scotland, U.K., covering a large area of the species' distribution, was studied in order to see if otolith shape can be used to discriminate between populations. The otolith shape was obtained using quantitative shape analysis, transformed with Wavelet and analysed with multivariate methods. Significant differences were detected among the seven populations, which could be traced to three morphological structures in the otoliths. The differentiation in otolith shape between populations was not only correlated with their spawning time, indicating a strong environmental effect, but could also be due to differing life-history strategies. A model based on the shape differences discriminates with 94% accuracy between Icelandic summer spawners and Norwegian spring spawners, which are known to mix at feeding grounds. This study shows that otolith shape could become an accurate marker for C. harengus population discrimination.

Swimming performance of a pelagic species in the Yangtze River under different exposure modes of the total dissolved gas supersaturation

During flood discharges of upstream dams in the Yangtze River, the pelagic fish have a stress risk from total dissolved gas (TDG) supersaturation in the river water. This study took the silver carp as the object and systematically evaluated the effects of TDG supersaturation levels and exposure time on their critical swimming speed (Ucrit) at different temperatures. The external symptoms of gas bubble disease were found when TDG levels exceeded 130%. Both exposure time and TDG level did not significantly impact the Ucrit of fish under 6 days of non-lethal exposure (110%, 120%, 130% TDG) with lower or higher water temperature. Significant differences in Ucrit were found among different exposure times at 11.0 ± 1.0°C under 10 hours of lethal exposure (135%, 140%, 150% TDG) and the Ucrit reduced by 59.88%, 83.32%, and 92.40%, respectively. TDG level had a significant impact on the Ucrit at 21.0 ± 1.0°C when exposure time exceeded 8 hours. Ucrit at 21.0 ± 1.0°C water were significantly greater than those at 11.0 ± 1.0°C water where conditions had the same TDG supersaturation and exposure time. Differences in Ucrit between temperatures ranged from 3.24 to 6.12 BL/s under non-lethal exposure and from 6.38 to 13.88 BL/s under lethal exposure. The results of this study can provide a reference for fish conservation during flood discharge.

Dietary Exposure of the Taiwan Population to Mercury Content in Various Seafood Assessed by a Total Diet Study

This paper examines the health risks of exposure to methylmercury (MeHg) through the consumption of mercury-contaminated seafood in Taiwan, based on the total diet study (TDS) method. Samples of seafood (n = 140) were purchased at fishing harbors or supermarkets and classified into seven categories (pelagic fish, inshore fish, farmed fish, shellfish, cephalopods, crustaceans, and algae). For each sample, we analyzed raw and cooked versions and compared the concentration difference. Total mercury (THg) was detected at the highest rate and in the highest concentrations in pelagic fish, followed by inshore fish and other farmed fish. The average concentration of THg was higher after cooking. In a 75th percentile scenario, the hazard indices for children aged 1 to 3 years and children aged 4 to 6 years were higher than 100% of the provisional tolerable weekly intake. Taking into consideration the risk assessment results, MeHg concentrations, and the nutritional composition of fish, we have provided weekly consumption advisories for children aged 1 to 3 years, children aged 4 to 6 years, and childbearing women aged 19 to 49 years. The weekly consumption advisories for childbearing women are 35 g/week of pelagic fish and 245 g/week of inshore fish based on the risk results from MeHg and the potential benefits from eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA) intake.

The complete mitochondrial genome of the longfin dragonfish Tactostoma macropus (Stomiiformes: Stomiidae)

The complete mitochondrial genome (mitogenome) was determined for the longfin dragonfish Tactostoma macropus, which is the first for the genus and the third within the family Stomiidae. The mitogenome sequence is 17,690 bp in length containing 2 ribosomal RNA genes, 22 transfer RNA genes, 13 protein-coding genes, and a control region, as in most fishes. The gene order of T. macropus showed an unreported deviation from the typical vertebrate one. Phylogenetic reconstruction using the maximum likelihood method placed T. macropus in the monophyletic Stomiiformes. Three stomiid species were recovered as a moderately supported clade in the phylogenetic tree.

Genetic diversity and structure of circumtropical almaco jack, Seriola rivoliana: tool for conservation and management

The almaco jack, Seriola rivoliana, is a circumtropical pelagic fish of importance both in commercial fisheries and in aquaculture. To understand levels of genetic diversity within and among populations in the wild, population genetic structure and the relative magnitude of migration were assessed using mtDNA sequence data and single nucleotide polymorphisms (SNPs) from individuals sampled from locations in the Pacific and Atlantic Oceans. A total of 25 variable sites of cytochrome c oxidase subunit 1 and 3678 neutral SNPs were recovered. Three genetic groups were identified, with both marker types distributed in different oceanic regions: Pacific-1 in central Pacific, Pacific-2 in eastern Pacific and Atlantic in western Atlantic. Nonetheless, the analysis of SNP identified a fourth population in the Pacific coast of Baja California Sur, Mexico (Pacific-3), whereas that of mtDNA did not. This mito-nuclear discordance is likely explained by a recently diverged Pacific-3 population. In addition, two mtDNA haplogroups were found within the western Atlantic, likely indicating that the species came into the Atlantic from the Indian Ocean with historical gene flow from the eastern Pacific. Relative gene flow among ocean basins was low with _r m < 0.2, whereas in the eastern Pacific it was asymmetric and higher from south to north (_r m > 0.79). The results reflect the importance of assessing genetic structure and gene flow of natural populations for the purposes of sustainable management.

Multiple Assays on Non-Target Organisms to Determine the Risk of Acute Environmental Toxicity in Tebuconazole-Based Fungicides Widely Used in the Black Sea Coastal Area

The widespread use of Tebuconazole-based fungicides in phytosanitary treatments on a wide range of crops, on the one hand, and the lack of official reports on the amount of fungicide residues in nearby water basins, on the other hand, may lead to uncontrolled and hazardous contamination of water sources used by the resident population, and to serious effects on the environment and public health. Our study explores the acute toxicological risk of this fungicide on various organisms, from bacteria and yeast to fish, using a battery of tests (standardized Toxkit microbiotests and acute semi-static tests). By investigating the interaction between Tebuconazole and bacteria and yeast organisms, we observed that Gram-negative bacteria displayed a strong tolerance for Tebuconazole, while Gram-positive bacteria and yeasts proved to be very sensitive. The fish experiment was conducted on Chelon auratus juveniles exposed to five concentrations of the fungicide Tebustar EW (Tebuconazole, 250 g/L as active substance). After 96 h of exposure, the LC₅₀ for C. auratus was 1.13 mg/L. In the case of the Toxkit microbiotests' application, the following results were recorded: Spirodela polyrhiza EC₅₀ = 2.204 mg/L (after 72 h exposure), Thamnocephalus platyurus EC₅₀ = 0.115 mg/L (after 24 h), and Daphnia magna EC₅₀ = 2.37 mg/L (after 24-48 h). With the exception of bacteria and yeast, the same response pattern was observed for all non-target species tested; the response range expressed by concentrations causing growth inhibition or mortality was small, ranging between very close values that are quite low, thereby demonstrating the high toxicity of Tebuconazole-based fungicides to the environment.

One fish, two fish, three fish, more: novel resighting method produces precise and cost-effective estimates of abundance

Estimates of abundance are essential to manage and conserve marine species. Numerous methods are available to determine population size, but the suitability of methods for schooling fishes and the associated precision can vary depending on the species and system. Here, we developed and compared three mark-recapture/resight methods to assess the most robust method to estimate the abundance of silver trevally (Pseudocaranx georgianus). While the recapture rate was similar across the methods, the swim pass method (resighting) recorded the largest number of individuals (mean ± standard error 211 ± 14.9) and had the lowest coefficient of variation (CV; 4.5%-12%) compared to 360-video (resighting, 45 ± 2.1 individuals surveyed, 14.8%-22.2% CV) and large-scale capture methods (recapture, 30 ± 3.8 individuals surveyed, 17.3%-26.5% CV). The inclusion of individual identification into the abundance estimator models for large-scale capture did not change the abundance estimates and showed similar resolution between the models (CV 18.2%-26.7%). We showed that the swim pass method is logistically easy to implement and generates precise estimates of silver trevally abundance. This new method provides a low-cost, time-efficient resighting method that can be adapted to suit similar aggregating pelagic species interacting with wildlife tourism operations, enabling researchers to rapidly estimate the abundance of species that have been previously difficult to count.

Maximizing Use of Pelagic Capture Fisheries for Global Protein Supply: Potential and Caveats Associated with Fish and Co-Product Conversion into Value-Add Ingredients

Globally, capture fisheries contribute significantly to protein supply and the food security of a third of the world's population. Although capture fisheries production has not significantly increased in tonnes landed per annum during the last two decades (since 1990), it still produced a greater tonnage of protein than aquaculture in 2018. Policy in the European Union and other locations favors production of fish through aquaculture to preserve existing fish stocks and prevent extinction of species from overfishing. However, aquaculture production of fish in order to feed the growing global population would need to increase from 82 087 kT in 2018 to 129 000 kT by 2050. The Food and Agriculture Organization states that global production of aquatic animals was 178 million tonnes in 2020. Capture fisheries contributed 90 million tonnes (51%) of this. For capture fisheries to be a sustainable practice in alignment with UN sustainability goals, ocean conservation measures must be followed and processing of capture fisheries may need to adapt food-processing strategies already used extensively in the processing of dairy, meat, and soy. These are required to add value to reduced fish landings and sustain profitability.

Temporal declines in fecundity: A study of southern Gulf of St. Lawrence Atlantic herring (Clupea harengus) and implications for potential reproductive output

Individuals must reproduce to survive and thrive from generation to generation. In fish, the fecundity of individuals and estimates of total reproductive output are critical for evaluating reproductive success and understanding population dynamics. Estimating fecundity is an onerous task; therefore, many populations lack contemporary estimates of fecundity and size-fecundity relationships. However, reproductive dynamics are not static in time; therefore, it is important to develop contemporary fecundity estimates to better inform conservation and management action. To highlight the importance of contemporary fecundity estimates, we examined the fecundity of southern Gulf of St. Lawrence (sGSL) spring and fall spawning Atlantic herring in 2022, developed size-fecundity models, and compared these to historical fecundity estimates and models. Our results suggest that the average fecundity of sGSL spring and fall herring has undergone a substantial temporal decline of approximately 47% and 58%, respectively, since the 1970s and 1980s. The size-fecundity relationships for fall spawning herring have shifted, with fish of a given size exhibiting lower fecundity in 2022 compared to the 1970s. Alternatively, the size-fecundity relationships for spring spawning herring have remained relatively static. Furthermore, simulations highlighted a substantial reduction in potential reproductive output in 2022 compared to 1970 of approximately 32% and 68% for spring and fall spawners, respectively, based on a fixed number of mature females, which may have negative implications for stock rebuilding. Overall, our study provides support for periodic estimates of fecundity in fish populations to better understand temporal changes in reproductive and population dynamics.

Fatty Acids of European Sardine (Sardina pilchardus) White Muscle Can Discriminate Geographic Origin Along the Iberian Atlantic Coast

The European sardine (Sardina pilchardus) ranks among the most valuable species of Iberian fisheries, and the accurate tracing of its geographic origin, once landed, is paramount to securing sustainable management of fishing stocks and discouraging fraudulent practices of illegal, unreported, and unregulated (IUU) fishing. The present study investigated the potential use of S. pilchardus white muscle fatty acids (FAs) to successfully discriminate the geographic origin of samples obtained in seven commercially important fishing harbors along the Iberian Atlantic Coast. While 35 FAs were identified using gas chromatography-mass spectrometry in the white muscle of S. pilchardus, the following, as determined by the Boruta algorithm, were key for sample discrimination: 14:0, 22:6n-3, 22:5n-3, 18:0, 20:5n-3, 16:1n-7, 16:0, and 18:1n-7 (in increasing order of relevance). An average 83% correct allocation of landed specimens was achieved, with some landing locations presenting 100% correct allocation (e.g., Ría de Pontevedra in northern Spain and Peniche in central Portugal). Linear discriminant analysis revealed a separation of samples from northern Spain and Peniche, and a partial overlap of all other locations. The present results highlight the potential of using FAs of S. pilchardus white muscle to reliably discriminate the geographic origin of landed individuals along the Iberian Atlantic coast.

Estimation of life history traits and stock status for Scomber japonicus based on data-limited method

The age-structure data is usually unavailable for most traditional fishery species in the East China Sea. The data-limited method is thus particularly important to understand life history and population dynamics of commercial fishes. At the offshore waters of southern Zhejiang, Chub mackerel (Scomber japonicus) is one of the dominant economic species. Based on fork length data from 2016 to 2020, we estimated its life history traits with the data-limited method, including the growth parameters and mortality coefficients. We further evaluated the status of Chub mackerel by the yield per recruitment (YPR) model. The results showed that the relationship between fork length (L) and body weight (W) based on 1606 samples was estimated to be W=4.18×10-3L3.28(R2=0.96). The asymptotic fork length L∞ of Chub mackerel was 28.34 cm, the growth rate was 0.36 a-1, and the initial theoretical age was -0.40 a. The total mortality was estimated as 1.67 a-1, and the estimated natural mortality (M) was 0.85 a-1. The fishing mortality (F) was 0.82 a-1, and the development rate was 0.49. The current capture age was estimated to be 1.78 a, while the capture fork length was 15.44 cm. The YPR model results showed YPR value showed a trend of increasing and then decreasing with the increases of F. The values of biological reference points F0.1 and Fmax were 0.97 a-1 and 4.55 a-1, respectively, which were higher than the value of current F. The sensitivity analysis showed that the uncertainty of M greatly influenced the estimation results of YPR and biological reference points. A decrease in M significantly increased the YPR value, but F0.1 and Fmax decreased. The status of Chub mackerel stock at the offshore waters of southern Zhejiang is in good condition. However, the miniaturization of catch is intensifying. It is recommended to extend the capture fork length to 20 cm (the impact point age) to improve the quality of the catch, which would sustainably use the Chub mackerel resources.

Five new records of Luvarus imperialis (Acanthuroidei: Luvaridae) in the south-west Atlantic Ocean

Five new records of louvars Luvarus imperialis are documented for the south-west Atlantic Ocean, extending its distribution range in this ocean. The presence of one ripe specimen, associated with the previous records of larvae and juveniles, suggests that L. imperialis spawn in this region. The possible association of juveniles with shoals of skipjack tuna Katsuwonus pelamis is discussed.

Exploring Photoreceptor Gene Expression and Seasonal Physiology in Mediterranean Swordfish (Xiphias gladius)

Mature and immature female swordfish show different gonadal expression patterns of melatonin synthesis-related and opsin genes, indicating that seasonality affects gonadal circadian genes, especially through opsin modulation. The high energy demands of reproduction may cause mature female swordfish to become more susceptible to environmental stressors/changes, potentially affecting their health post-reproduction. The modulation of melatonin and opsin expression may also influence swordfish biology, impacting basal metabolism and stress responses. This study aimed to investigate the hepatic expression patterns of genes involved in melatonin and opsins activity after the reproductive period, comparing mature and immature females. Liver samples of swordfish females, collected from the Central Adriatic Sea, were analyzed to evaluate the expression of a melatonin receptor (mel1b), acetylserotonin O-methyltransferase (asmt), opsins (sws, VA opsin and opsin4), and stress response (sod1, sod2 and hsp4b) genes, while histological analysis focused on hepatic melanomacrophages, melanomacrophage centers, and lipid content. The expression of all genes analyzed did not differ between mature and immature females except for sws, which was significantly downregulated in mature females. The overall health conditions of mature and immature females appeared comparable, as suggested by the histological analysis and the absence of significant differences in the expression of stress response genes. Although the study used a limited number of samples and lacked a comparison between the reproductive and non-reproductive periods, the preliminary results suggest that opsins may play a role in modulating physiological processes beyond reproduction.

The History of the Brazilian Sardine (Sardinella brasiliensis) Between Two Fishery Collapses: An Ecosystem Modeling Approach to Study Its Life Cycle

The inter-annual fluctuations of abundance of the Brazilian sardine (Sardinella brasiliensis) during the last decades have deeply modified the purse seine fishery dynamics. This study evaluates the trophic relationships of the main species exploited by this fishery and the importance of its biomass for the southeast-south Brazil marine ecosystem (22° S-34° S). Data were analyzed using a mass balance model (ECOPATH) between the two fishery collapses: 2000 and 2017. From 2000 onwards, the sardine fishery adopted a multi-species character. The mean trophic level of the catches (MTL) showed a decreasing trend until 2008, when more modern vessels with greater autonomy entered the fishery, and expanded the traditional fishing area to exploit northern fishing grounds. The MTL in the expanded fishing area suddenly increased and was characterized by high biomass of the Brazilian sardine and other species with a high biomass and high ecotrophic impact, falling again to the lowest level in 2016. The model evidenced high estimates for fishing mortality, natural mortality, and flow to detritus between 2008 and 2016, when sardine fishing collapsed. During this period, a sharp drop in the primary production required to sustain the catches from 2012 onwards accompanied a significant fall in the biomass accumulation rate. This pattern was coincidental with the increasing mean temperature of the catches, which was probably acting as a limiting factor for the primary production, resulting in a higher natural mortality and flow to detritus. Furthermore, the higher fishing mortality may have led the stock to collapse.

Considering the influence of land use/land cover on estuarine biotic richness with Bayesian hierarchical models

The composition of land use/land cover (LULC) in coastal watersheds has many implications for estuarine system ecological function. Land use/land cover can influence allochthonous inputs and can enhance or degrade the physical characteristics of estuaries, which in turn affects estuaries' ability to support local biota. However, these implications for estuaries are often poorly considered when assessing the value of lands for conservation. The focus of research regarding terrestrial and estuarine interfaces often evaluates how LULC may stress estuarine ecosystems, but in this study we sought to understand how LULC may both positively and negatively affect estuaries using measures of observed biotic richness as proxies for estuarine function. We investigated the influence of LULC on estuarine biotic richness with Bayesian hierarchical models using multiple geospatial data sets from 33 estuaries and their associated watersheds along the Gulf of Mexico coastal region of the United States. We designed the hierarchical models with observed species richness of three functional groups (FGs) (i.e., pelagic fishes, forage fishes, and shrimp) from fishery-independent trawl surveys as response variables. We then set salinity and water temperature as trawl-specific covariates and measures of influence from six LULC classes as estuary-specific covariates and allowed the models to vary by estuary, trawl program, salinity, and temperature. The model results indicated that the observed richness of each FG was both positively and negatively associated with different LULC classes, with estuarine wetlands and forested lands demonstrating the strongest positive influences on each FG. The results are generally consistent with past studies, and the modeling framework provides a promising way to systematically quantify LULC linkages with the biotic health of estuaries for the purposes of potentially valuing the estuarine implications of land conservation.