Elasmobranchs, with their slow growth, long lifespans and low reproductive output, are particularly sensitive to fluctuations in nutritional status and energy availability throughout ontogeny. Fatty acids serve as valuable biomarkers for studying trophic ecology, ontogenetic dietary shifts and energy allocation during key life periods such as growth and reproduction. This study examined fatty acid profiles in Raja undulata by analysing muscle and liver tissues to investigate ontogenetic dietary shifts, assess niche breadth and overlap between juveniles and adults, and explore how reproductive development influences fatty acid allocation after sexual maturity. The muscle fatty acid profiles of R. undulata varied across life stages, with adults showing a reduced trophic niche and a diet composed of higher-trophic-level prey compared to juveniles. This pattern suggested a dietary shift from a diverse, invertebrate-based diet in juveniles to more specialized predation on fish and larger crustaceans in adults. The liver fatty acid profiles varied across reproductive stages, with an increasing proportion of omega-3 (C22:6n-3, docosahexaenoic acid [DHA]; 22:5n-3, docosapentaenoic acid) and omega-6 polyunsaturated (C20:4n-6, arachidonic acid [ARA]) fatty acids, alongside a marked decline in eicosapentaenoic acid (C20:5n-3), likely reflecting its direct allocation to the ovaries. Additionally, the elevated monounsaturated fatty acids levels in adults and their decline during gametogenesis highlighted their key role as energy sources for oocyte development, supporting previous findings on reproductive energy mobilization in elasmobranchs. While DHA and ARA proportions increased, their stable absolute values suggested a different allocation pattern compared to viviparous species, potentially due to R. undulata's oviparous strategy. Our findings, in line with previous studies, showed that analysing different tissues is key to understanding how diet and energy use are linked in elasmobranchs.

Abstract At the inception of the ICES Journal of Marine Science, first published in 1926, elasmobranchs were largely peripheral to fisheries science. Beyond a few commercially valuable species such as basking shark and spurdog, knowledge of occurrence, life history, population structure, and trends of the ∼105 elasmobranch species occurring across the ICES area was limited. This is reflected in the fact that the first elasmobranch-focused paper in the Journal was published by Holden and Meadows in 1964. However, as commercial fisheries expanded and population declines and local extirpations were documented in the late 20th century, elasmobranchs gained increasing attention from both commercial and conservation perspectives. The ICES Working Group for Elasmobranch Fishes, established in 2003, pioneered methods for estimating removals and stock status despite significant data limitations. From issuing the first advice sheets for six “stocks” in 2005, the group now provides assessments for 56 stocks—more than any other ICES assessment group. This review traces the evolution of elasmobranch science within ICES, examining advances in data quality, assessment methodologies, and the shifting priorities that have transformed this taxon from a marginal concern to a central focus of marine conservation and fisheries management. Past and present Working Group Chairs provide perspectives on key developments, persistent challenges, and future directions for elasmobranch research and advice.

There is increasing interest in using eDNA for deriving abundance indices for biodiversity monitoring and in support of fisheries management. However, eDNA concentrations are affected by animal behavior, such as diel vertical migration, which has repercussions for designing eDNA sampling strategies for deriving unbiased abundance indices. In this study, we investigated the potential impact of diel vertical migration or other diel activity variations on measured eDNA concentrations for European hake (Merluccius merluccius), European seabass (Dicentrarchus labrax) and blackspot seabream (Pagellus bogaraveo). For hake, in situ eDNA concentrations near the sea floor differed systematically between samples taken before sunrise and after sunset, with the average concentration in morning samples being 24% of the average evening samples. For the two other species, only a weak diel signal in eDNA concentrations was found. Modeling the dispersal and decay of eDNA particles through a Lagrangian approach revealed that eDNA concentrations might decrease to 21%-41% of their initial value during the absence of a species moving entirely up from the sea floor during the night. For M. merluccius, the coherence between observed diel variations in eDNA concentrations near the sea floor and modeling results indicates that diel vertical migration behavior needs to be accounted for when devising eDNA sampling plans. The necessity is less clear for D. labrax and P. bogaraveo.

The biodiversity crisis driven by anthropogenic pressures significantly threatens marine ecosystems. The rate of climate change and anthropogenic impacts outpace our traditional observation tools' capabilities, underscoring the urgency for new assessment methods. Environmental DNA (eDNA; DNA traces released by organisms) metabarcoding, a non-invasive method widely developed over the last decade, represents a promising biomonitoring tool thanks to a large spatio-temporal coverage, high detection of rare species and its time and cost-effectiveness. However, capturing fish diversity using eDNA requires genetic reference databases, currently lacking. Improving reference databases relies on opportunistic sampling enabling the reporting of sequences for new species. The data provided here consists of barcoding 86 species of fishes over the 12S mitochondrial DNA gene. We generated 156 sequences of the mitochondrial 12S gene adapted to the "Teleo" barcodes from fishes sampled in the Bay of Biscay (BoB; Northeast Atlantic, France) between 2017 and 2019. In addition, we provided each individual the barcode details (Genbank accession number, chromatograms), a photograph, 5 ecomorphological measures and 11 life-history traits documenting ecological functions (e.g., dispersion, habitat use, diet). Furthermore, we provided the sampling metadata (e.g., date, time, gear, coordinates, depth) and environmental variables measured in situ (e.g., conductivity, water/air temperature). This data set is valuable to improve the Northeast Atlantic eDNA genetic database, thus helping to better understand the effects of environmental forcing in the BoB, a transition zone housing mixed assemblages of boreal, temperate, and subtropical fish species susceptible to display variability in functional traits to adapt to changing conditions. The detailed Metadata for this abstract published in the Data Article section of the journal is available in MetaCat in JaLTER at https://jalter.diasjp.net/data/ERDP-2024-09.

Stock collapse has profound impacts on ecosystems and fisheries, while the economic impacts have been less studied. The blackspot seabream stock collapsed in the early 1980s and has remain depleted since. The relationship between landings and prices was strongly negative during the decades spanning the collapse (1973–1990) and less during the low stock period with management measures (2003–2020). For other selected species, a significant negative relationship was only found for two species (out of 14) during the earlier period. In contrast, since 2003 prices decreased with landings for most species (10/17) irrespective of their characteristics and their management by a TAC or not. Short-term variations in blackspot seabream prices and landings were also negatively related during the collapse period, indicating rapid market adjustment to decreasing availability. In contrast, in recent years, short-term price variations were not linked to availability change, neither for blackspot seabream nor for most other species (10/17). The study reveals the strong unique effect the blackspot seabream collapse had on price. In the recent period, blackspot became the highest priced fish species in France, making the TAC management essential to limiting catches at sustainable level

The International Council for the Exploration of the Sea (ICES) typically provides advice on fishing opportunities on a stock-by-stock basis. Nevertheless, levels of total allowable catch (TAC) are sometimes set for a collection of stocks and species (i.e. a common TAC). An explicit expectation of these is that landings will scale with ICES advice, especially when ICES advice is used to calculate the common TAC. This expectation is tested for skates and rays in the Northeast Atlantic, spanning 26 stocks, 8 species, and 3 ecoregions. Using ICES landings and ICES advice data from 2016 to 2022, we show that landings of several stocks and species have overshot their respective ICES advice, whereas others have undershot. Specifically, some stocks of blonde ray (Raja brachyura) in North Sea and Celtic Seas ecoregions are being landed at a rate that often exceeds double its ICES advice. By collating species based on their ICES assessment category and life-history traits, we find that those considered data-poor and potentially most vulnerable to fishing are consistently landed at higher-than-expected rates in the Celtic Seas. This study questions the appropriateness of a common TAC for skates and rays and calls for shifts towards the use of single-stock catch allocations and the application of advanced stock assessment methodologies.

Environmental DNA (eDNA) metabarcoding is a method to detect taxa from environmental samples. It is increasingly used for marine biodiversity surveys. As it only requires water collection, eDNA metabarcoding is less invasive than scientific trawling and might be more cost effective. Here, we analysed data from both sampling methods applied in the same scientific survey targeting Northeast Atlantic fish in the Bay of Biscay. We compared the methods regarding the distribution of taxonomic, phylogenetic, and functional diversity. We found that eDNA captured more taxonomic and phylogenetic richness than bottom trawling and more functional richness at the local scale. eDNA was less selective than trawling and detected species in local communities spanning larger phylogenetic and functional breadths, especially as it detected large pelagic species that escaped the trawl, even though trawling detected more flat fish. eDNA indicated differences in fish community composition that were comparable to those based on trawling. However, consistency between abundance estimates provided by eDNA metabarcoding and trawl catches was low, even after accounting for allometric scaling in eDNA production. We conclude that eDNA metabarcoding is a promising method that can complement scientific trawling for multi-component biodiversity monitoring based on presence/absence, but not yet for abundance.

Species distribution models (SDM) are commonly used to identify potential habitats. When fitting them to heterogeneous, opportunistically collated presence/absence data, imbalance in the number of presence and absence observations often occurs, which could influence results. To robustly identify potential habitats for blackspot seabream (Pagellus bogaraveo) throughout its distribution area in the Northeast Atlantic and the western Mediterranean Sea, we used an ensemble species distribution modelling (eSDM) approach, modelling gridded presence–absence data with environmental predictors for two types of occurrence data sets. The first data set displayed the observed unbalanced spatially heterogeneous presence/absence ratio and the second a balanced presence/absence ratio. The data covered the full distribution area, including the European Atlantic shelf, the Azorean region and the Western Mediterranean Sea. Across these regions, populations display variable status. The main environmental predictors for potential habitats were bathymetry and annual maximum SST. The fitted ensemble compromise (eSDM) was projected over the whole grid to create a habitat suitability map. This map exhibited higher probabilities of presence for the balanced-ratio data set. A binary presence–absence map was then generated using optimized presence probability thresholds for four validation indices. Using the true skill statistic to optimize the threshold, the surface areas of the binary presence–absence map was 53% smaller for the balanced data set than for the observed unbalanced data set. However, the choice of validation index had an even greater impact (up to 15 000%). This indicates that studies using opportunistic data for SDM fitting need to pay attention to the effects of presence/absence data imbalance and the choice of validation index to fully evaluate uncertainty.

The spatio-temporal dynamics of the black scabbardfish ( Aphanopus carbo Lowe, 1839) abundance in the northeast Atlantic was modeled using two linked Bayesian state-space models fitted to fishery-dependent data from trawlers operating to the west and north off the British Isles and longliners off the west coast of Portugal. The stage-structured life cycle models included species vital processes and fishing, and are linked by the migration flow between the two areas. Although data on spawner abundance and recruitment are missing, the hierarchical nature of state-space models allows a convenient representation of black scabbardfish dynamics using reliable data from the two studied areas, which correspond to two of the three main fishing grounds for the species. The approach presented is comparable to the few models developed for other species, such as European eel, where spawning and recruitment occur at restricted and distant regions. This approach is likely to remain the only option for black scabbardfish stock assessment and fisheries monitoring, as it is unlikely that data about the unobserved spawning and early life stages will become available in the near future.

We present practical lessons learned from applying the recent close-kin mark-recapture (CKMR) abundance estimation method to thornback ray (Raja clavata). For CKMR, related individuals are identified from their genotypes and their number and pattern is used for abundance estimation. We genotyped over 7000 individuals collected in the Bay of Biscay using Single Nucleotide Polymorphism (SNP) markers finding 99 parent-offspring pairs. The estimated number of adult thornback rays in the central Bay of Biscay was around 135000 (CV 0.19) in 2013. In total, four lessons were drawn: (i) CKMR helps identifying metapopulation structure, which if ignored might affect abundance estimates and/or time trends. There was strong evidence for two distinct local populations of thornback ray with no demographic connectivity. (ii) Demographic sample composition can affect precision and needs to include a range of birth years, which turned out to be difficult for thornback ray. (iii) Reasonable age information for potential offspring is essential. (iv) The sex of potential parents is needed and might be identified from sex-related SNPs. Reliable abundance estimation by CKMR appears feasible for a wide range of species provided that: sampling adequately covers potential local population structure, has appropriate demographic composition, and the age of potential offspring is reasonably well-known.

AbstractThe global biodiversity crisis from anthropogenic activities significantly weakens the functioning of marine ecosystems and jeopardizes their ecosystem services. Increasing monitoring of marine ecosystems is crucial to understand the breadth of the changes in biodiversity, ecosystem functioning and propose more effective conservation strategies. Such strategies should not only focus on maximizing the number of species (i.e., taxonomic diversity) but also the diversity of phylogenetic histories and ecological functions within communities. To support future conservation decisions, multicomponent biodiversity monitoring can be combined with high‐throughput species assemblage detection methods such as environmental DNA (eDNA) metabarcoding. Here, we used eDNA to assess fish biodiversity along the coast of southern Brittany (France, Iroise Sea). We filtered surface marine water from 17 sampling stations and applied an eDNA metabarcoding approach targeting Actinopterygii and Elasmobranchii taxa. We documented three complementary biodiversity components—taxonomic, phylogenetic, and functional diversity—and three diversity facets—richness, divergence and regularity. We identified a north/south contrast with higher diversity for the three facets of the biodiversity components in the northern part of the study area. The northern communities showed higher species richness, stronger phylogenetic overdispersion and lower functional clustering compared to the ones in the southern part, due to the higher diversity of habitats (reefs, rocky shores) and restricted access for fishing. Moreover, we also detected a higher level of taxonomic, phylogenetic, and functional uniqueness in many offshore stations compared to more coastal ones, with the presence of species typically living at greater depths (> 300 m), which suggests an influence of hydrodynamic structures and currents on eDNA dispersion and hence sample composition. eDNA metabarcoding can, therefore, be used as an efficient sampling method to reveal fine‐scale community compositions and in combination with functional and phylogenetic information to document multicomponent biodiversity gradients in coastal marine systems.

Sex-determining modes remain unknown in numerous species, notably in fishes, in which a variety of modalities have been reported. Additionally, noninvasive individual sexing is problematic for species without external sex attributes or for early life stages, requiring cytogenetic or molecular analyses when sex chromosomes or sex-linked markers have been characterized. Genomics now provide a means to achieve this. Here, we review common sex-determination systems and corresponding statistical methods for identifying sex-linked genetic markers and their use for sex assignment, focusing on single nucleotide polymorphism (SNP) markers derived from reduced representation sequencing methods. We demonstrate the dependence of expected sex assignment error on the number of sex-linked SNPs and minor allele frequency. The application of three methods was made here: (a) identification of heterozygote excess in one sex, (b) FST outlier analysis between the two sexes and (c) neuronal net modelling. These methods were applied to a large SNP data set (4604 SNPs) for 1680 thornback rays (Raja clavata). Using method (a), nineteen putative sex-linked SNPs were identified. Comparison with the reference genome of a related species (Amblyraja radiata) indicated that all 19 SNPs are probably located on the same chromosome. These results suggest that thornback ray has a XX/XY sex-determination system. Method (b) identified eight SNPs probably located on different chromosomes. Method (a) led to the lowest sex assignment error among the three methods (4.2% error for females and 3.7% for males).

Uncommon records of fishes may evidence local or global changes in fish composition resulting from environmental change or anthropogenic activities. Significant records of uncommon marine fishes, including migrant, non-native, cryptic, rare and threatened species, collected in French waters or by French vessels in European waters, observed by scuba divers or beachgoers, are reported for the year 2018. They include first, new, rare and unusual records for the following 52 species: Hexanchus griseus, Squatina squatina, Gymnura altavela, Acipenser sturio, A. gueldenstaedtii, Dalophis imberbis, Nemichthys curvirostris, Eurypharynx pelecanoides, Maulisia mauli, M. microlepis, Sagamichthys schnakenbecki, Melanostomias bartonbeani, Astronesthes niger* , Leptostomias gladiator*, Chlorophthalmus agassizi, Magnisudis atlantica, Evermannella balbo, Regalecus glesne, Luvarus imperialis, Raniceps raninus, Fistularia cf. petimba* , Trigla lyra, Lepidotrigla dieuzeidei, Micrenophrys lilljeborgii, Howella atlantica*, Pomatomus saltatrix, Serranus cabrilla, Caranx crysos, Seriola rivoliana, Trachinotus ovatus, Lobotes surinamensis, Sarpa salpa, Chelon ramada, Pseudoscopelus altipinnis* , Trachinus draco, Parablennius pilicornis, P. ruber, Buenia affinis, B. jeffreysii, Chromogobius zebratus, Didogobius splechtnai, Gammogobius steinitzi, Gobius couchi, G. kolombatovici, Lebetus sp., Speleogobius trigloides , Thorogobius macrolepis, Vanneaugobius dollfusi, Siganus rivulatus* , Lepidocybiumflavobrunneum, Hyperoglyphe sp. et Pegusa cf. nasuta, among which six, marked with an asterisk (*), represent additions to the Checklist of the marine fishes from metropolitan France and one, N. curvirostris, is a first record for the Mediterranean.

Abstract Effective population size (Ne) is a key parameter of population genetics. However, N e remains challenging to estimate for natural populations as several factors are likely to bias estimates. These factors include sampling design, sequencing method, and data filtering. One issue inherent to the restriction site‐associated DNA sequencing (RADseq) protocol is missing data and SNP selection criteria (e.g., minimum minor allele frequency, number of SNPs). To evaluate the potential impact of SNP selection criteria on Ne estimates (Linkage Disequilibrium method) we used RADseq data for a nonmodel species, the thornback ray. In this data set, the inbreeding coefficient F IS was positively correlated with the amount of missing data, implying data were missing nonrandomly. The precision of Neestimates decreased with the number of SNPs. Mean Ne estimates (averaged across 50 random data sets with2000 SNPs) ranged between 237 and 1784. Increasing the percentage of missing data from 25% to 50% increased Ne estimates between 82% and 120%, while increasing the minor allele frequency (MAF) threshold from 0.01 to 0.1 decreased estimates between 71% and 75%. Considering these effects is important when interpreting RADseq data‐derived estimates of effective population size in empirical studies.

The negative impacts that scientific monitoring may have on marine ecosystems has been a neglected topic, mainly on the basis that its magnitude is minor compared to commercial fisheries, even though this raises ethical and, in certain cases, conservation issues. We argue that ethical principles should lead us to reconsider marine wildlife resource monitoring such as the fish and shellfish trawl surveys providing the science-based evidence needed for fisheries management and assessment of how environmental change affects marine shelf communities worldwide. Recent scientific and technological progress has provided methods and tools which might now be harnessed to reduce the impact of marine monitoring. We review these alternative methods, consider modifications to current practices and identify areas requiring further research.

Sustainable fisheries management requires assessment of exploited populations and communities. Traditional fisheries stock assessment methods need species-specific input data, which for skates have only recently become available in Europe. To overcome this limitation, a Bayesian multispecies biomass production model was developed. In addition to aggregated landings, input data are short time series with species-specific information (landings and biomass indices). Applying the approach to four main skate species and a group of two skate species, all managed together in the Bay of Biscay (Northeast Atlantic), long-term changes in the skate assemblage composition were identified. Since the 1990s, Leucoraja naevus became increasingly dominant, while the contributions of the other three species (Raja brachyura, Raja clavata and Raja montagui) declined. The abundance of the grouped Leucoraja fullonica and L. circularis has also strongly decreased, suggesting long-term overexploitation. All species except this species group are expected to increase over the next decade under current harvest rates. Currently, the species considered here are managed under a single fishing quota making it unlikely that the group of the two most depleted species will recover soon. The multispecies modelling approach bears promise for other harvested assemblages for which only grouped harvest information is available for certain periods.

Studying demographic and genetic connectivity can help assess marine metapopulation structure. Rays and skates have no larval phase; hence, population connectivity can only result from active movement of individuals. Using thornback ray (Raja clavata) in European waters as a case study, demographic and genetic connectivity were studied for 11 putative populations with unequal population abundances and two hypotheses of dispersal rates. Genetic simulation results highlighted three large metapopulations: in the Mediterranean, around the Azores, and on the Northeast Atlantic shelf. Demographic results highlighted a finer population structure indicating that several pairs of putative populations might be demographically linked. Results were highly sensitive to dispersal assumptions and relative population abundances, which provided insights into the potential magnitude of genetic and demographic connectivity differences. Accounting for demographic connectivity appears to be crucial for managing and conserving rays and skates, while genetic connectivity provides a longer-term perspective and less subtle spatial structures. Moreover, accounting for heterogeneity in population abundances is a key factor for determining or interpreting metapopulation connectivity.

Sustainable exploitation of marine populations is a challenging task relying on information about their current and past abundance. Fisheries-related data can be scarce and unreliable making them unsuitable for quantitative modelling. One fishery independent method that has attracted attention in this context consists in estimating the effective population size (N-e), a concept founded in population genetics. We reviewed recent empirical studies on N-e and carried out a simulation study to evaluate the feasibility of estimating N-e in large fish populations with the currently available methods. The detailed review of 26 studies found that published empirical N-e values were very similar despite differences in species and total population sizes (N). Genetic simulations for an age-structured fish population were carried out for a range of population and samples sizes, and N-e was estimated using the Linkage Disequilibrium method. The results showed that already for medium-sized populations (1 million individuals) and common sample sizes (50 individuals), negative estimates were likely to occur which for real applications is commonly interpreted as indicating very large (infinite) N-e. Moreover, on average, N-e estimates were negatively biased. The simulations further indicated that around 1% of the total number of individuals might have to be sampled to ensure sufficiently precise estimates of N-e. For large marine populations, this implies rather large samples (several thousands to millions of individuals). If however such large samples were to be collected, many more population parameters than only N-e could be estimated.

Trace metal concentrations in muscle and liver tissues from two offshore species of skate were examined. Concentrations of mercury in muscle of Leucoraja circularis (n = 20; 23-110.5 cm total length, 157-490 m water depth) and L. fullonica (n = 24; 28.5-100 cm total length, 130-426 m water depth) were 0.02-1.8 and 0.04-0.61 mg kg(-1), respectively. Concentrations of both As and Hg increased with total length. Only the largest specimen had a concentration of Hg in muscle > 1.0 mg kg(-1). Data were limited for specimens > 90 cm long, and further studies on contaminants in larger-bodied skates could usefully be undertaken.

Nature Ecology & Evolution 1, 0170 (2017); published 26 May 2017; corrected 12 June 2017. In the original version of this Article, the European Commission was mistakenly included as an affiliation for Christos D. Maravelias. His contribution to this work was exclusively completed while at the Hellenic Centre for Marine Research.