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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. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

The transitory and long-term elasticities of the Bay of Biscay ecosystem to densityindependent and density-dependent influences were estimated within a state space model that accounted for both process and observation uncertainties. A functional group based model for the Bay of Biscay fish ecosystem was fit to time series obtained from scientific survey and commercial catch and effort data. The observation model parameters correspond to the unknown catchabilities and observation error variances that vary across the commercial fisheries and fishery-independent scientific surveys. The process model used a Gompertz form of density dependence, which is commonly used for the analysis of multivariate ecological time series, with unknown time-varying fishing mortalities. Elasticity analysis showed that the process model parameters are directly interpretable in terms of one-year look-ahead prediction elasticities, which measure the proportional response of a functional group in the next year given a proportional change to a variable or parameter in the current year. The density dependent parameters were also shown to define the elasticities of the long term means or quantiles of the functional groups to changes in fishing pressure. Evidence for the importance of indirect effects, mediated by density dependence, in determining the ecosystem response of the Bay of Biscay to changes in fishing pressure is presented. The state space model performed favourably in an assessment of model adequacy that compared observations of catch per unit effort against cross-validation predictive densities blocked by year. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

The thornback ray (Raja clavata) in the Bay of Biscay is presumed to have declined during the 20th Century. To evaluate this decline and estimate biomass trajectories, a hypothetical catch time series was created for the period 1903-2013. A Bayesian state-space biomass production model with a Schaefer production function was fitted to the hypothetical catch time series and to a shorter research vessel Catch Per Unit Eeffort (CPUE) time series (1973-2013, with missing years). A censored likelihood made it possible to obtain biomass estimates without a CPUE time series or only with an estimate of biomass depletion. A simulation-estimation approach showed a high sensitivity of results to the prior for the intrinsic growth rate. The model provided biomass trajectories which corroborated and quantified the decline of the Bay of Biscay population. The estimated biomass corresponding to the maximum sustainable yield, BMSY, was 32 000 tonnes, which is 17 times higher than the estimated biomass in 2014. The biomass estimates obtained without a CPUE time series were highly uncertain. Adding a current biomass depletion observation improved precision, though the biomass time trend was sensitive to this value. Results should be interpreted carefully as several assumptions were necessary to create the long catch time series and to define informative priors, notably for the intrinsic growth rate. Despite this, the results confirm the depleted state of the thornback ray in the Bay of Biscay with the estimated biomass in 2014 being around 3% of carrying capacity. [ABSTRACT FROM AUTHOR]

Highlights: [•] GAMs were built for variable and fixed fishing cost categories and gross-added value. [•] Explanatory variables were days-at-sea, total revenue, fuel price, gear, vessel power or length. [•] Some models fitted to the Bay of Biscay also performed well for the English Channel. [•] Precise model-based cost estimates provide input for bio-economic analyses. [•] Data sampling programs can be optimised. [Copyright &y& Elsevier]

Copyright of Canadian Journal of Fisheries & Aquatic Sciences is the property of Canadian Science Publishing and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Mahévas, S., Trenkel, V. M., Doray, M., and Peyronnet, A. 2011. Hake catchability by the French trawler fleet in the Bay of Biscay: estimating technical and biological components. – ICES Journal of Marine Science, 68: 107–118. Several factors affect trawl catchability: (i) gear and vessel technical characteristics, (ii) anthropogenic factors, and (iii) biological factors. The objectives of this study were to assess the relative contribution of each factor to variations in hake (Merluccius merluccius) landings by the French trawler fleet operating on the shelf of the northern Bay of Biscay (ICES Subdivision VIIIa). Using generalized linear models, the impact of technical and anthropogenic factors was evaluated using landings per unit effort (lpue) obtained from logbooks. Variations in hake lpue were explained primarily by anthropogenic factors. For studying the biological components of catchability, the results of a scientific trawl survey in July 2006 involving three similar trawlers of the French trawler fleet were used. Daytime accessibility to large hake was lower than at night, and about zero for small hake (<19 cm). Estimates of spatial variation made using generalized linear mixed models showed a patchy fine-scale spatial distribution, but a random larger-scale distribution of hake over the area surveyed. [ABSTRACT FROM PUBLISHER]

Copyright of Aquatic Living Resources is the property of EDP Sciences and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Copyright of Aquatic Living Resources is the property of EDP Sciences and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

According to the Ideal Free Distribution theory, individual fish are distributed where environmental conditions are optimal, and the occupied area may vary with population abundance. Thus, observed distributions are a combination of habitat suitability and density-dependent effects. Data from an annual bottom trawl survey taking place in autumn were used to assess associations between the distributions of eight demersal fish species, separately for juveniles and adults, and habitat characteristics (depth, temperature and salinity) in the Bay of Biscay and Celtic Sea. Cumulative distribution functions were used to describe the general frequency distributions of environmental variables and their relationships with fish density. During the period 1992–2006, observed bottom temperatures fluctuated with no time trend (ΔT = 8°C in the first 80 m) and population abundances varied significantly. Juvenile hake, poor cod, blue whiting, adult red gurnard, adult megrim, and lesser-spotted dogfish were found to be significantly associated with specific depth ranges. Associations with bottom temperature and salinity were weaker. For some species, preferred environmental conditions changed over time, independently of variations in environmental conditions. In general, most species seemed to be able to cope with the experienced range of conditions. Habitat associations were not influenced by abundance variations. Fluctuating abundances had an impact on spatial occupation only for red gurnard adults, lesser-spotted dogfish and blue whiting juveniles, independent of absolute densities. [ABSTRACT FROM AUTHOR]

Trenkel, V. M., Mazauric, V., and Berger, L. 2008. The new fisheries multibeam echosounder ME70: description and expected contribution to fisheries research. – ICES Journal of Marine Science, 65: 645–655. Recently, Simrad in collaboration with Ifremer developed a calibrated, multibeam, vertical echosounder (ME70) for fisheries research. We describe its capabilities and technical limitations. The ME70 has up to 45 beams with distinct frequencies in the range 70–120 kHz, spanning at most 150°. All beams are stabilized in vessel roll and pitch. It has reduced side-lobe levels, up to −70 dB (two-way) instead of the −25 dB (one-way) of conventional systems. We outline research areas for which the ME70 might provide new types of information and hence lead to novel insights. We illustrate the potential contributions with datasets collected in the English Channel and on the continental-shelf break of the Bay of Biscay. Finally, future research and developments using the new system are outlined. [ABSTRACT FROM PUBLISHER]

Survey indices play an important role in stock assessments as they provide information on stock trends. In certain cases, large interannual variations have been observed that are unlikely to reflect true underlying stock changes but are rather outliers. When survey indices for several species appear to be outliers for the same year, the suspicion is raised that something happened during the survey of that year. This is called a year effect in survey catches. To study the potential year effect in survey catches for the French autumn groundfish survey taking place in the Bay of Biscay, several indicators for survey design and wind conditions were derived as explanatory variables, and principal component analysis was used to study the relationship between these variables. Using multiple linear regression models, we found that, on average, 20% of interannual variation in abundance indices could be explained by survey conditions for benthic species, 11% for demersal, and none for pelagic species. In contrast, survey conditions explained a smaller and decreasing part of the interannual variability in the coefficients of variations of these abundance indices and in species mean weight for benthic, demersal, and pelagic species. Thus survey indices of benthic species seemed most affected by survey design and wind conditions. [ABSTRACT FROM AUTHOR]

Trenkel, V. M., Rochet, M-J., and Mesnil, B. 2007. From model-based prescriptive advice to indicator-based interactive advice. – ICES Journal of Marine Science, 64: 768–774. Traditional advice for fisheries management, especially in the ICES world, focuses on short-term stock projections relative to reference points. Primarily, two numbers, spawning-stock biomass and fishing mortality rate, are considered in the advice, although a range of biological processes are included in the stock assessment models. We propose an alternative form of final advice that would not rely on stock predictions and only two numbers, but on a suite of indicators that are combined to provide stock assessment and management advice. For a single stock, the approach consists of monitoring a set of indicators of population state and fishing pressure. Stock reference status at some time in the past is assessed, based on these indicators and/or other available information. Changes in indicator values after this reference time are then estimated, interpreted, and finally combined into a diagnostic that highlights possible causes of the changes observed. After considering management objectives, appropriate management actions can then be proposed. The proposed approach is illustrated for anglerfish stocks in the Celtic Sea and the Bay of Biscay. [ABSTRACT FROM PUBLISHER]

Abstract: The behaviour of eight large benthopelagic fish taxa was analysed using video records collected with an ROV on the mid-slope of the Bay of Biscay. The studied species were roundnose grenadier (Coryphaenoides rupestris), orange roughy (Hoplostethus atlanticus), deep-sea scorpionfish (Trachyscorpia cristulata echinata), and black scabbardfish (Aphanopus carbo), as well as individuals belonging to the families Alepocephalidae, Chimaeridae, and Scyliorhinidae, and to the order Squaliformes. Some of the observed fish were grouped at the family taxonomical level due to visual identification to species being unreliable. Assumed natural (undisturbed) behaviour was categorised in terms of (i) body position with respect to the bottom sea floor, (ii) locomotion and (iii) activity type. Reaction (disturbed) behaviour to the approaching ROV was categorised in terms of reaction type and distance. Environmental conditions (depth, temperature, current speed and direction) and observation conditions (ROV speed and altitude) were recorded simultaneously with fish observations in order to explain the variability in the observed reaction behaviour. A multivariate analysis identified three groups corresponding to a behaviour pattern of a sit and wait strategist (one species), an active bottom hunter (three taxa), and a group of species displaying little activity in their bottom habitat (three taxa). At species level the environmental and observation conditions had some explanatory power for individual behaviour variability. It is hypothesised that the varied behaviour of mid-slope benthopelagic fish contributes to maintain a high species diversity of large predators in an energy poor environment. [Copyright &y& Elsevier]

During the VITAL cruise in the Bay of Biscay in summer 2002, two devices for measuring the length of swimming fish were tested: 1) a mechanical crown that emitted a pair of parallel laser beams and that was mounted on the main camera and 2) an underwater auto-focus video camera. The precision and accuracy of these devices were compared and the various sources of measurement errors were estimated by repeatedly measuring fixed and mobile objects and live fish. It was found that fish mobility is the main source of error for these devices because they require that the objects to be measured are perpendicular to the field of vision. The best performance was obtained with the laser method where a video-replay of laser spots (projected on fish bodies) carrying real-time size information was used. The auto-focus system performed poorly because of a delay in obtaining focus and because of some technical problems. [ABSTRACT FROM AUTHOR]

[Display omitted] • The spatiotemporal dynamics of demersal fish communities were investigated in the Bay of Biscay (BoB) and Celtic Sea (CS). • Two decades of changes in temperature, trophic resources, habitat and fishing pressure on community were assessed. • Diversity patterns showed greater variability in space than in time and species richness and abundance weakly changed. • Communities are becoming more spatially similar (homogeneous) in the CS and differentiated in the BoB. • Such patterns are best explained by the dynamics of trophic resources mediated by small pelagic species. Climate change and resource exploitation represent strong selection pressure affecting the spatio-temporal dynamics of marine assemblages that ensure food provision for humans. However, such dynamics remain poorly documented, and their drivers unclear. Here, we investigate changes in fish assemblages of two key European fishing areas, the Bay of Biscay (BoB) and the Celtic Sea (CS), during the last two decades. We quantify the relative contribution of change in energy (i.e. temperature and trophic resources), habitat (depth, substrate, oxygen) and fishing pressure to explaining observed spatial and temporal variations in fish diversity. We used long-term scientific surveys to evaluate the spatio-temporal changes in species richness (SR), abundance and composition of demersal fish (Actinopterygii) assemblages at different spatial scales combined with a range of regression models and variance partitioning. Diversity patterns showed greater variability in space than in time: SR weakly changed over time, while compositional dissimilarity showed local patterns of taxonomic homogenization in the CS and differentiation in the southern BoB, where local assemblages were becoming more similar and dissimilar over time, respectively. Energy funnelled through small pelagic species as a potential trophic link affecting the dynamics of demersal assemblages was the most important driver, while habitat and fishing pressure had limited importance. Our study revealed contrasted dynamics of demersal fish assemblages at a regional scale that were best explained by the dynamics of small pelagic species. Direct effects of environmental forcing and fishing pressure were limited in both regions which have a long history of fishing and still remain relatively buffered from global warming effects. This research paved the way to combine methods inspired by biogeography with scientific monitoring surveys to detect spatio-temporal dynamics of fish assemblages and their drivers in marine ecosystems under multiple pressures. [ABSTRACT FROM AUTHOR]

Highlights: [•] The study provides an evaluation of the potential impact of fishing in the Bay of Biscay. [•] It compares simulated and contemporary mean weights for 18 fish populations. [•] Contemporary mean weights were 88% to 30% smaller. [Copyright &y& Elsevier]

• We analysed the temporal dynamics of 12 juvenile marine fishes in the Bay of Biscay. • Time-series of annual fish abundance were derived from beam trawl survey data. • Dynamic factor analysis detected synchronous changes in abundance among species. • Interspecific synchrony was explained by climate and environmental factors. • Potential drivers were sea bottom temperature and the East Atlantic Pattern. The existence of synchronous fluctuations among sympatric species is an important property of a community, potentially reducing temporal stability of ecosystem services. Yet, community synchrony and its potential drivers have rarely been studied in marine ecosystems. Here, we analyzed a 14-year time-series (2007–2020) of fish abundance data collected by a scientific beam trawl survey in the Bay of Biscay, a temperate marine ecosystem located in the North-east Atlantic. We used dynamic factor analysis to reveal common trends in abundance among juvenile demersal marine fishes, and to identify potential environmental drivers. Our results revealed synchronous changes in juvenile fish abundance among the 12 marine species examined in the study. This strong temporal coherence was likely related to the influence of climate and environmental factors, notably sea bottom temperature and the East Atlantic Pattern. We also found some support for alternative drivers of early-life fish dynamics, namely the North Atlantic Oscillation and sea surface chlorophyll-a concentration, the later suggesting bottom-up trophic control. In the context of ongoing environmental changes, our findings raise questions about the future stability of the demersal marine fish community in the Bay of Biscay. [ABSTRACT FROM AUTHOR]