To investigate the response of the fish community structure to a natural disturbance in their habitat, fish abundance, biomass and species composition were analysed in relation to temporal variability of environmental conditions in a seagrass Zostera marina bed. A total of 3024 fishes belonging to 46 taxa (22 families) were collected by quantitative sampling for 10 years from 2007 to 2016 in the Seto Inland Sea, south-western Japan. Seagrass shoot density decreased to less than 1/20 of its original density after disappearance of vegetation caused by heavy rain in the autumn of 2011 and the area did not recover for the next five years. In order to analyse temporal changes of fish community, the fishes were divided into three groups depending on their habitats or lifestyles: pelagic or migratory species (PM), sand or mud bottom-associated species (SM) and seagrass (Z. marina) – or substrate (rocky bottom including macrophytes) – associated species (ZS). Multiple regression analysis showed seagrass shoot density had the most significant effect on biomass of ZS among the three groups, with higher fish biomass under higher seagrass shoot density. Fish community composition changed after the disappearance of the seagrass vegetation coverage with an increase in abundance of SM during the five years of the post-disturbance period. Seagrass vegetation was concluded to affect temporal change of fish community structure through a stronger influence on fish species that are more dependent on seagrass beds as habitat.

Despite the prevalence of catch per unit effort (CPUE) as a key metric in fisheries assessments it can be fraught with inherent problems that often cause its use as an index of abundance to become contentious. This is particularly the case with abalone, a sedentary shellfish targeted by commercial dive fishers around the globe. It is common practice to standardize CPUE to at least partly address issues about how well it reflects the actual abundance of a stock. Differences between standardized and unstandardized trends may lead to controversy between scientists and stakeholders when standardized trends provide a less optimistic picture of stock status. It is within this context that we applied Linear Mixed Model (LMM) and Generalized Linear Mixed Model (GLMM) methods to standardize CPUE for the Western Zone blacklip abalone fishery in Victoria, Australia. This fishery was chosen for our evaluation because it included substantial population losses from a disease shock during the middle of the time series. The effects of diver, reef location, month and their interactions with year were included as random effects in these models and the results compared with nominal geometric means. The two standardization methods provided similar standardized CPUE trends and clearly demonstrated that a large proportion of the variance could be attributed to diver and spatial effects. The GLMM seemed to explain more variability in the data and produced better precision for standardized CPUEs than LMM. The temporal trend in variability attributed to divers and spatial scales reveals the impact of disease as well as any homo/heterogeneity effect. The CPUE trends responded to the impact of disease against a backdrop of declining stock, however when compared with the inter-annual pattern in nominal CPUE, the standardized trends showed that the decline immediately following the onset of disease was less precipitous. In contrast to what appeared to be an increase in the nominal series during the more recent post-disease period, there was only a slight non-significant increase observable in the standardized trends.

Thermoregulation has been suggested to influence mitochondrial DNA (mtDNA) evolution. Previous studies revealed that the mitochondrial protein-coding genes of fish living in temperate climates have smaller dN/dS (Non-synonymous substitution rate/Synonymous substitution rate) than tropical species. However, it is unknown whether different geographic populations of one fish species experience stronger selective pressures between cold and warm climates. The biological characteristics of the Japanese sand lance, Ammodytes personatus in the North-western Pacific is well-suited for assessing the performance of mtDNA evolution among separate geographic populations. In this study, we focused on the mitochondrial ATP6 gene of A. personatus using 174 individuals from eight different sea temperature populations. Two distinct haplotype lineages and a significant population structure (P = 0.016) were found in this species. The frequencies of the two lineages varied with the changes of annual sea temperature. The southern lineage (lineage A, dN/dS = 0.0384) showed a larger dN/dS value than the northern lineage (lineage B, dN/dS = 0.0167), suggesting that sea temperature greatly influences the evolution of the two lineages. The result provides robust evidence of local adaptation between populations in A. personatus.

Sexual differences in behaviours are often affected by the difference in individual interests between the sexes: growth in males and egg production in females. Some hermit crabs show sexual differences in shell use patterns during the reproductive season. In the non-reproductive season, however, when both sexes are focused on increasing growth, this sexual difference is expected to be reduced. In this study, we compared the pattern of shell use in the hermit crab Pagurus minutus between seasons, while focusing on the effects of shell shape on growth or egg production. As we predicted, sexual differences in shell use in P. minutus showed seasonal change. In the non-reproductive season, both sexes appeared to use shells well suited for growth. In the reproductive season, sexual differences became more evident, especially in larger solitary crabs and guarding pairs; males monopolized round-type shells such as those of Umbonium moniliferum, whereas more than 80% of females relied on high-spired Batillaria-type shells such as those of Batillaria zonalis. A lack of advantage for egg number in females using Batillaria-type shells suggests that female shell use is explained by factors other than maximizing clutch size. Both sexes can moult during the reproductive season, and larger body size is advantageous for reproduction. Given that Batillaria-type shells resulted in a lower growth increment and males have an advantage in shell fights in congeneric crabs, our findings suggest the importance of intersexual competition for shells and female compromise in determining the seasonal change of shell use patterns in P. minutus.

The phyllosoma larva of spiny and slipper lobsters (Palinuridae and Scyllaridae respectively) can disperse during several months before metamorphosing into a decapodid stage, which is the key phase for a successful settlement. The largest Scyllarus decapodid known to date was recently collected near the Canary Islands and identified by DNA analysis as Scyllarus subarctus. This species had never been previously reported from the area, and the decapodid stage is described here for the first time. The examination of further museum specimens has now significantly expanded the current distribution of S. subarctus, including much of the NW African coast, St Helena and Canary Islands. These results highlight the importance of combining molecular analysis of recently collected specimens with historical collections.

Peroxisomes are cytoplasmic organelles involved in fatty acid oxidation, ether-phospholipids biosynthesis, glyoxylate metabolism and purine catabolism among other metabolic pathways. However, these organelles are still poorly studied in molluscs. During a light and electron microscopy study of the digestive glands of cephalaspidean sea slugs unusually large peroxisomes reaching about 5 µm in diameter were found in basophilic cells of Philinopsis depicta (Aglajidae), being among the biggest ever reported in metazoan cells. These round or oval peroxisomes were clearly visible with the light microscope, and their diamond shaped core was strongly stained by the tetrazonium coupling reaction for protein detection. However, in the basophilic cells of Aglaja tricolorata, another aglajid cephalaspidean, peroxisomes were more variable in shape and no bigger than 1 µm in length. Round peroxisomes with a diameter of about 0.5 µm were common in basophilic cells of Philine quadripartita (Philinidae) and Haminoea navicula (Haminoidae), whereas in Bulla striata (Bullidae) these organelles frequently had a diameter of between 1.0 and 1.5 µm. Peroxisomes were larger in basophilic cells than in digestive ones. In all these species, the electron-dense peroxisomal cores were diamond-shaped, and in H. navicula two cores could be seen in each peroxisome. The abundance and large size of peroxisomes in the digestive gland points out the importance of these organelles in the metabolism of this organ.

Atlantic bonito, Sarda sarda, is one of the representatives of the Scombridae family in the Adriatic Sea. Larvae and juveniles have been found and described in the area, but no information has been published regarding adults spawning in the Adriatic Sea. To explore the strong possibility that Atlantic bonito are reproducing in the Adriatic Sea, 122 specimens of adult Atlantic bonito were collected from a purse seine net ‘palamidara’ over four seasons in 2017. The fork length of the analysed specimens varied from 37.5 to 60.8 cm, with a mean of 48.83 ± 5.59 cm, while total body weight varied between 742.68 and 3102.59 g, with a mean value of 1700.49 ± 543.82 g. Gonadosomatic index values showed an increasing trend from autumn (0.123 for males, 0.897 for females) until spring, while in the summer, they reached their maximum values (3.609 for males, 5.604 for females). This trend was also confirmed by histological and macroscopic analyses of gonads, which suggested that the Atlantic bonito spawning season is in the spring-summer in the Adriatic Sea. Hence, this confirms that this species is spawning in the Adriatic Sea.

Crustacean decapod assemblages were surveyed in Zostera marina beds adjacent to tidal flats (ET) and rocky shore (ER), and in unvegetated habitats (UV). Decapod samples were collected monthly throughout 2002 using a small beam trawl from northern Jinhae Bay, Korea. Water temperature, salinity, eelgrass biomass, sediment composition and organic matter were also monitored to assess any correlation between environmental variables and decapod fauna. A total of 31 decapod species belonging to five taxa (three prawns, 13 caridean shrimps, one hermit crab, one mud shrimp and 13 crabs) were collected at three different habitats. To assess variations in decapod assemblages in relation to habitat type and season, various multivariate analyses were used. The dominant caridean shrimps were Palaemon macrodactylus, Alpheus digitalis and Crangon uritai, and the dominant crabs were Charybdis japonica, Hemigrapsus penicillatus and Charybdis bimaculata. The number, abundance and diversity of decapod species varied greatly with habitat type and season, peaking in eelgrass beds and during spring, and showing the lowest catch rate in unvegetated habitat and during winter months. The nMDS ordination and multivariate analyses revealed that habitat type and season were determinant factors affecting the structure of decapod assemblages. Seasonal shifts in the abundance of decapods corresponded with changes in eelgrass biomass and loss on ignition (LOI), but not with water temperature or salinity.

In this study, we examine how the Guri catfish Genidens genidens uses estuarine and freshwater habitats along the largest South American coastal lagoon, through the chemical analysis of otoliths and microscopic analysis of gonads. Chemical composition (Sr:Ca) of otolith edges allowed distinguishing between individuals who used the estuarine or freshwater compartments of the lagoon. The analysis of core-to-edge chemical profiles of each individual otolith revealed that the population may present two different patterns of habitat use along the lagoon. The ‘type 1’ pattern (89.5%) includes fish who appear to have been born in estuarine waters, whereas ‘type 2’ (9.5%) includes those fish born in fresh water. Nevertheless, juveniles from both patterns appear to migrate to estuarine waters. The gonad analysis shows G. genidens may reproduce in fresh water, as nearly 57% of all sampled fish were found to spawn in the freshwater portion of the lagoon. Also, the otolith core of many adult fish presented freshwater signatures, thus suggesting consistent fresh water use during early life. Our findings based on otolith and gonadal analyses challenge the previous classification of G. genidens as an estuarine resident. Rather, our results allow the suggestion that this species should be placed in the ‘estuarine and fresh water’ guild, which includes both fish completing their life cycles within the estuary and fish who consistently use freshwater habitats.

Although the red striped mullet is one of the main target fish of the Hellenic demersal fisheries, information about its biology is limited. The aim of this study was to describe the reproductive biology and growth of the species in the south Aegean Sea based on 1032 individuals sampled under the Data Collection Framework Program in 2016. According to the monthly variation of the maturity stages and the gonadosomatic index, spawning activity took place from March to July, although it appeared to occur throughout the year. Length at 50% maturity (L50) was 153.3 and 139.2 mm in females and males, respectively. Individual ages were determined by counting the annuli of otoliths macroscopically. Marginal increment analysis (MIA) combined with complementary information derived from otolith edge analysis, the assessment of the reproductive period and the length–frequency distribution modes of the population showed that annulus formation occurs between February and April. The length–weight relationship revealed a significant sex effect and was described by the parameters α = 0.0155 and b = 2.915 in females, and α = 0.0032 and b = 2.976 in males. The von Bertalanffy growth function (VBGF) parameters for sexes combined were Linf = 346.1 mm, k = 0.299 year−1 and t0 = −0.984 years. Longevity (tmax) was estimated at 11.75 years. This study provides valuable data for the stock assessment of M. surmuletus in one of the major Hellenic fishing grounds located in the south Aegean Sea.

The objective of this study was to identify potential recruitment sources of Prochilodus lineatus from freshwater areas (Paraná and Uruguay rivers) to estuarine population of the Río de la Plata Estuary (La Plata Basin, South America), considering young (age-1) and adult (age-7) fish. LA-ICP-MS chemical analysis of the otolith core (nine element:Ca ratios) of an unknown mixed sample from Río de la Plata Estuary (2011 and 2017) was compared with a young-of-year baseline data set (same cohort) and classified into freshwater nurseries (Paraná or Uruguay river) by using maximum classification-likelihood models (MLE and MCL) and quadratic discriminant analysis (QDA). Considering the three models used, the Uruguay River was the most important contributor for both young and adult populations. The young population (2011) was highly mixed with contributions between 31.7 to 68.3%, while the degree of mixing was found to decrease in 2017 (adult fish) from 97.1 to 100% contributions. The three employed methods showed comparable estimates, however, the QDA showed a high similarity with the MCL model, suggesting sensitivity to evaluate small contributions, unlike the MLE method. Our results show the potential application of maximum likelihood mixture models and QDA for determining the relative importance of recruitment sources of fish in estuarine waters of the La Plata Basin.

This study investigated the diet of longnose stingray Hypanus guttatus in the tropical waters of north-eastern Brazil. Samples were obtained from monthly sampling of artisanal fisheries from August 2007 to July 2008. A total of 258 specimens were examined, 127 females and 131 males, and stomach contents analysis suggested H. guttatus to be a generalist and opportunistic predator feeding on the most available prey in the environment. There was no significant difference in the diet composition of males and females, or between seasons. However, an ontogenetic dietary shift was observed with larger individuals having an increased proportion of molluscs in the diet, whilst smaller individuals predated primarily on small crustaceans.

The aim of this study was to test the effective separation of shape indices of otoliths of three species belonging to the family Sciaenidae before and after in vitro digestion. We measured 328 sagittal otoliths and applied six shape indices. Before the experiment, the aspect ratio (otolith height/otolith length%), circularity, ellipticity and relative surface of the sulcus acusticus were suitable for differentiating the species of genera Paralonchurus and Stellifer. Among the species of Stellifer, the aspect ratio and rectangularity were suitable. Otoliths exposed to in vitro digestion showed no significant differences in their morphometry before and after the experiment. After in vitro digestion, the aspect ratio and circularity were effective in separating Paralonchurus and Stellifer. However, none of the indices used in the present study were efficient to separate otoliths of congeneric species after in vitro digestion.

Recent studies have shown that anguillid eel populations in habitats spanning the marine–freshwater ecotone can display extreme plasticity in the range of catadromy expressed by individual fish. The apparent use of marine and freshwater habitats by the European eel Anguilla anguilla was examined by analysing the strontium (Sr) and calcium (Ca) concentrations in otoliths of eels collected from a tidal Atlantic lake system in Ireland. Variations of the Sr:Ca ratio in the otoliths indicated that a variety of environmental salinities had been experienced in the habitats that were occupied during the growth phase of these individuals in the tidal Atlantic lake system. The otolith microchemistry of these eels indicated that most of the eels had entered each salinity environment (freshwater (FW); brackish water (BW); marine-dominated water (MW) and full seawater (SW)) from fresh water to full seawater just after recruitment and had stayed in each environment until maturation without movement to other salinity environments. Only 2 of 93 (2%) eels had shifted their habitat once in their lives. This result suggests that each individual might have an environmental habitat preference, although each individual could move along a short (<2 km) salinity gradient.

Differences between sexes may arise either during development or at the adult stage only. In both cases growth rate during development and level of allometry may influence sexual dimorphism and ontogenetic trajectories. To analyse the period in which sexual dimorphism appears during ontogeny and assess allometric ontogeny in Sesarmidae crabs, we evaluated: (1) sexual dimorphism in shape and size of the carapace and cheliped propodus of juveniles and adult Aratus pisonii and Armases rubripes, and (2) their ontogenetic trajectory, using geometric morphometric (GM) techniques. We tested the hypothesis that sexual dimorphism in sesarmid crab shape takes place before the puberty moult. In Aratus pisonii there was sexual dimorphism in the shape of the carapace in juveniles (before puberty moult) and variation between juveniles and adults was size-dependent, especially in the frontal region of the carapace. For Armases rubripes this shape sexual dimorphism was detected only after the puberty moult (adult phase). For males, carapace variation between juveniles and adults was also size-dependent, especially in the carapace frontal region, but for females, there was a change in shape with different trajectories. Our results also indicated that shape variation is a common pattern during growth for Sesarmidae species. This ontogenetic shape variation may be associated with spatial partitioning between juveniles and adults.

Three new species of snapping shrimps of the genus Alpheus are described from the Persian Gulf. These belong to the Alpheus edwardsii species-group, which is mainly characterized by unarmed orbital hoods and the presence of dorsal and ventral notches on the palm of the major chela. Alphus ankeri sp. nov. shows a close affinity to A. pacificus Dana, 1852 and A. heronicus Banner & Banner, 1982 bearing no balaeniceps crests in both sexes on the dactylus of the minor chela, and the merus of the major chela of both sexes are unarmed. This species differs from the closely related species by the absence of an overhanging proximal shoulder in the major chela. The other rock crevice inhabiting species, A. mohammadpouri sp. nov. is diagnosed by exhibiting sexual dimorphism in its balaeniceps crests and the armed merus of the major chela. These two characters are similar to those recorded for three sandy/rubble dwelling species: A. inopinatus Holthuis & Gottlieb, 1958, A. lobidens De Haan, 1849 and A. australiensis Banner & Banner, 1982. This new species is distinguishable from these latter species by the shape of the minor chela and colour pattern. A coral inhabiting species A. abumusa sp. nov. appears to be closely related to A. maindroni Coutière, 1898, showing an armed merus of the major chela and the absence of spine-like seta on the ischia of the third legs. This last new species is easily discriminated from A. maindroni by longer antennular segments, a markedly concave frontal margin between the rostrum and orbital hood, and a different colour pattern.

The bigfin reef squid Sepioteuthis lessoniana is a neritic species widely distributed in coastal waters of the Indo-Pacific region and is of interest to fisheries for its high commercial value. Squid samples were collected from Keelung (KL) and Penghu (PH), around northern Taiwan from October 2012 to September 2013. A total of 949 squid were examined, and 620 squid were aged using statoliths. The age range of the squid in KL (55–183 days) was similar to that in PH (77–186 days). The squid hatched almost year-round, except in January and December in KL. Two seasonal cohorts were identified: a spring cohort (hatched in March to May) and an autumn cohort (July to October). Concentrations of nine trace elements in statoliths were analysed using solution-based inductively coupled plasma mass spectrometry (ICP-MS). Significant differences in Fe/Ca, Cu/Ca and Sr/Ca were found between the two locations, while significant differences in concentration ratios of Sr/Ca and Ba/Ca were noted between the two seasonal cohorts. Results of a principal component analysis and cluster analysis varied in life-history traits between the two geographic stocks and in elemental concentrations between the two seasonal cohorts. Squid in KL and PH might undertake different migration routes, while seasonal variability in oceanographic conditions was apparent in the two locations.

The blue shark Prionace glauca is the most abundant species in the artisanal driftnet fishery off the coastal waters of Ivory Coast. The reproductive parameters were investigated with the aim of providing basic information on the reproductive biology for fisheries management. A total of 424 specimens (256 males and 168 females) ranging from 170–330 cm in total length (TL) were sampled between August 2014 and November 2016. Sample for embryonic sex ratio was obtained from 18 litters of 503 individuals (255 males and 248 females). The embryonic sex ratio was not significantly different from 1:1 (χ2 = 0.10, P > 0.05, N = 503). The size at 50% maturity (L50) was 218.1 cm TL for males and 223.3 cm TL for females. The litter size based on the number of embryos varied from 6 to 62, with an average of 30 embryos. Mating started in July whereas ovulation, fertilization and uterine eggs occurred in late October–November. Smallest embryos of 3–5 cm in stretch total length (STL) appeared in uterus from November to January. The embryo size varied widely among months, and well-pigmented embryos were already present in April–May samples, although most of them occurred in August–September, suggesting a gestation period of around 11 months. The absence of neonates in catches, as well as parturition females, does not support a hypothesis that parturition takes place in the Gulf of Guinea.

We propose three calibration scenarios of to date contemporary divergence of Anoplopomatidae (skilfish Erilepis zonifer and sablefish Anoplopoma fimbria) for a data set of two mtDNA loci (СOI and Control Region). The first scenario is based upon a fossil record and the second and third ones upon major palaeogeological events 3.5 and 15 Mya. Estimated evolution speeds indicate that COI evolves faster in the skilfish mitochondrial genome. There is also evidence of skilfish going through a bottleneck event limiting its genetic diversity in the relatively recent past near Japan. Sablefish had two refugia on both sides of the Pacific Ocean. The contemporary haplotype divergence was formed ~450 thousand years ago during an ice age in the Pleistocene and contemporary populations display no apparent geographic differentiation.

Fibropapillomatosis (FP) can be an important conservation threat to green sea turtles (Chelonia mydas) due to its widespread distribution and complex aetiology. Thus, understanding the impacts of FP in sea turtle populations is a research priority towards conservation efforts. The body condition index (BCI), based on straight carapace length (SCL) and body mass (BM), is an accurate indicator of body-nutritional condition that can be used in routine green turtle health evaluations. This study aimed to compare BCI in FP-free (N = 369) and FP-affected (N = 518) green turtles from Brazilian feeding areas. Body condition indices were evaluated in terms of the South-west Atlantic Fibropapillomatosis Score – FPSSWA (mild, moderate and severe), study sites (five Brazilian states), origin (intentional capture, fishery, stranding and afloat) and sex (when known). Curved and straight carapace lengths, and body mass were recorded in order to calculate BCI. Statistical analysis revealed significant differences in BCI among green turtles from different study areas (P = 0.02), and lower BCI values in FP-free than in FP-positive individuals (P < 0.0001). With regards to origin, the highest BCI was found in the intentional capture group (N = 245; 1.47 ± 0.16), followed by fishery (N = 180; 1.46 ± 0.20). Analysis according to sex revealed a higher mean BCI among females than males (P < 0.017). This study provides relevant data on the health and nutritional status of green turtles along the Brazilian coast, in important feeding areas for this species.