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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]

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). [ABSTRACT FROM AUTHOR]

Long-term ecological surveys (LTES) often exhibit strong variability among sampling dates. The use and interpretation of such interannual variability is challenging due to the combination of multiple processes involved and sampling uncertainty. Here, we analysed the interannual variability in ∼30 years of 150 species density (fish and invertebrate) and environmental observation time series in four aquatic systems (stream, river, estuary, and marine continental shelf) with different sampling efforts to identify the information provided by this variability. We tested, using two empirical methods, whether we could observe simultaneous fluctuation between detrended time series corresponding to widely acknowledged assumptions about aquatic population dynamics: spatial effects, cohort effects, and environmental effects. We found a low number of significant results (36%, 9%, and 0% for spatial, cohort, and environmental effects, respectively), suggesting that sampling uncertainty overrode the effects of biological processes. Our study does not question the relevance of LTES for detecting important trends, but clearly indicates that the statistical power to interpret interannual variations in aquatic species densities is low, especially in large systems where the degree of sampling effort is always limited. [ABSTRACT FROM AUTHOR]

In this paper, I argue that we have at hand what is needed to provide scientific advice for ecosystem-based management of small pelagics and other species groups now. The ingredients for this advice are (i) large marine ecosystems as spatial management units; (ii) maintaining ecosystem productivity and exploiting at multispecies maximum yield as overarching management objectives; (iii) assessment of ecosystems by evaluating changes in primary productivity; (iv) an operational management procedure in which single-species catch proposals are adjusted to ecosystem productivity using a set of control rules. Inspection of historic landings for small pelagics and other small species in the Northeast Atlantic (ICES area) reveals that most likely fisheries exploitation does not, and never did, exceed system productivity in most LMEs and is therefore overall sustainable, although not necessarily for individual stocks. [ABSTRACT FROM AUTHOR]

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. • Ensemble species distribution modelling to identify potential habitat of rare fish. • Comparison of two occurrence data sets: imbalanced and balanced presence–absence. • Main predictors: bathymetry and sea surface temperature. • Higher presence probabilities for the balanced data set. • Effect of validation index on habitat map larger than data imbalance effect. [ABSTRACT FROM AUTHOR]

Zebrafish were exposed through diet to two environmentally relevant polycyclic aromatic hydrocarbons (PAHs) mixtures of contrasted compositions, one of pyrolytic (PY) origin and one from light crude oil (LO). Monoamine concentrations were quantified in the brains of the fish after six month of exposure. A significant decrease in noradrenaline (NA) was observed in fish exposed to both mixtures, while a decrease in serotonin (5HT) and dopamine (DA) was observed only in LO-exposed fish. A decrease in metabolites of 5HT and DA was observed in fish exposed to both mixtures. Several behavioural disruptions were observed that depended on mixtures, and parallels were made with changes in monoamine concentrations. Indeed, we observed an increase in anxiety in fish exposed to both mixtures, which could be related to the decrease in 5HT and/or NA, while disruptions of daily activity rhythms were observed in LO fish, which could be related to the decrease in DA. Taken together, these results showed that (i) chronic exposures to PAHs mixtures disrupted brain monoamine contents, which could underlie behavioural disruptions, and that (ii) the biological responses depended on mixture compositions. [ABSTRACT FROM AUTHOR]

Active- and passive-acoustic methods are widely used tools for observing, monitoring, and understanding marine ecosystems. From 25 to 28 May 2015, 214 scientists from 31 nations gathered for an ICES symposium on Marine Ecosystem Acoustics (SoME Acoustics) to discuss three major themes related to acoustic observations of marine ecosystems: (i) recent developments in acoustic and platform technologies; (ii) acoustic characterisation of aquatic organisms, ecosystem structure, and ecosystem processes; and (iii) contribution of acoustics to integrated ecosystem assessments and management. The development of, and access to new instruments, such as broad bandwidth systems, enables insightful ecological studies and innovative management approaches. Unresolved ecological questions and the increasing move towards ecosystem based management pose further challenges to scientists and instrument developers. Considering the SoME Acoustics presentations in the context of three previous ICES symposia on fisheries acoustics, topics increasingly emphasize ecosystem studies and management. The continued expansion of work and progress in marine ecosystem acoustics is due to the cross-disciplinary work of fisheries acousticians, engineers, ecologists, modellers, and others. An analysis of the symposium co-authorship network reveals a highly connected acoustic science community collaborating around the globe. [ABSTRACT FROM AUTHOR]

We present a framework for evaluating fisheries management plans comprehensively, both rebuilding plans and others. The framework includes a first rapid appraisal of the likelihood that the plan will result in management meeting its objectives, and guides subsequent quantitative analyses of potential weaknesses in the proposed plan. The framework includes four steps: (i) evaluating if a set of management objectives, if achieved, would result in a sustainable fishery, (ii) using qualitative analysis of a bio-economic model to evaluate whether the set of stock management tactics might be capable of achieving the specified fisheries objectives, (iii) using empirical criteria derived from the literature to evaluate if other management measures in the plan related to the ecological, social or economic context of the fishery actually contribute to sustainability, and (iv) carrying out quantitative simulations to compare alternative implementation options. Generally, several management measures have to be combined to increase stock size without sacrificing the economic benefits to the fishers remaining in the fishery. We demonstrate application of the framework for evaluating the stock rebuilding plan for plaice ( Pleuronectes platessa) and sole ( Solea solea) in the North Sea and, the management measures currently in place for the roundnose grenadier ( Coryphaenoides rupestris) stock exploited to the west of the British Isles. [ABSTRACT FROM AUTHOR]

To implement an ecosystem approach to fisheries management, there is a need to characterize the total pressure exerted by fisheries at the community level. French onboard observer data were used to derive catch metrics and compare fishing distribution across community components between two sites in the Southern Bay of Biscay. Sample-based rarefaction curves were used to standardize metrics across different active and passive gears, and correct for sample size differences. Six metrics for species, length and functional catch composition were tested. Length and functional metrics were found the most relevant metrics to highlight differences in catches between gears, sites, and gear-site interactions. Significant differences were found between gears, mainly in mean length and proportion of piscivores. None of the gears had the most diverse catch across all metrics. Small differences were found between sites, mainly in length range and species richness. [ABSTRACT FROM AUTHOR]

The status of an exploited population is ideally determined by monitoring changes in abundance and distributional range and pattern over time. Area of occupancy is a measure of the current distribution. Unfortunately, for many populations, scientific abundance and distribution information is not readily available. To evaluate the reliability of commercial fishing data for deriving occupancy indicators that could serve as proxies for stock abundance, we investigated four questions: 1) Occupancy changes with stock biomass, but is this change strong enough to make occupancy a sensitive indicator of population biomass? 2) Fishing boats follow fish, but when does such activity alter the positive macroecological relationship between occupancy and abundance? 3) When does the activity of pursuing fish adversely affect occupancy estimates derived from catch and effort data? 4) How does uncertainty in fishing effort data affect occupancy estimates? Spatial simulations mimicking the dynamics of four deep-water fish species showed that biomass-occupancy relationships can be weak. Fishers following fish can modify the spatial distribution of target species, even reversing the sign of the biomass-occupancy relationship in certain cases, and can affect the reliability of occupancy indicators, which can also be impaired by error in effort data. Using commercial catch and effort data and abundance indices for deep-sea fish populations to the west of the British Isles it was found that only for roundnose grenadier might occupancy provide insights into biomass changes. In conclusion, care should be taken when using occupancy for evaluating range changes in cases where fishing might have modified spatial distributions, uncertain commercial data are used or when the abundance-occupancy relationship is too flat. [ABSTRACT FROM AUTHOR]

Abstract: Long-term time series of sardine and anchovy landings often suggest negative dependence between these species, and an array of mechanisms have been proposed as explanations. We reduce these propositions to four basic hypotheses of (1) independence, (2) correlated process noise, (3) interspecific interactions, and (4) correlated observational error. We use a Bayesian approach to develop priors for parsimonious state space models with both process noise and observation error that represent each of these hypotheses, and apply this approach to five long-term time series of landings collected from the Pacific and Atlantic Oceans. Model comparison criteria suggest that the hypothesis of correlated process noise has the broadest support, where the temporal dependence of anchovy and sardines may be caused in part by either direct environmental influence on their physiology, or indirect bottom-up effects on their prey. However, all hypotheses find some degree of support within the five time series, and in general, the sardine and anchovy landings suggest weak intraspecific density dependence and susceptibility to both environmental and anthropogenic perturbation. Results additionally suggest that the best fitting hypothesis depends on the choice of geographic scale, temporal scale, and stock definition of the recorded landings. [Copyright &y& Elsevier]

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]

Abstract: Fisheries acoustic instruments provide information on four major groups in aquatic ecosystems: fish with and without swim bladder (tertiary and quaternary consumers), fluidlike zooplankton (secondary consumers) and small gas bearing organisms such as larval fish and phytoplankton (predominantly primary producers). We entertain that this information is useable to describe the spatial structure of organism groups in pelagic ecosystems. The proposal we make is based on a multi-frequency indicator that synthesises in a single metric the shape of the acoustic frequency response of different organism groups, i.e. the dependence of received acoustic backscattered energy on emitting echosounder frequency. We demonstrate the development and interpretation of the multi-frequency indicator using simulated data. We then calculate the indicator for acoustic water-column survey data from the Bay of Biscay and use it to create reference maps for the spatial structure of the four scattering groups as well as their small scale spatial variability. These maps provide baselines for monitoring future changes in the structure of the pelagic ecosystem. [Copyright &y& Elsevier]

According to portfolio theory applied to fisheries management, economic returns are stabilised by harvesting in a portfolio stocks of species whose returns are negatively correlated and for which the portfolio economic return variance is smaller than the sum of stock specific return variances. Also, variability is expected to decrease with portfolio width. Using a range of indicators, these predictions were tested for the French fishing fleets in the Bay of Biscay (Northeast Atlantic) during the period 2001–2009. For this, vessels were grouped into eight fishing fleets based on the gears used and exploited species were grouped into five functional groups. The portfolio width of fleets ranged from 1–3 functional groups, or 4–19 species. Economic fleet returns (sale revenues minus fishing costs) varied strongly between years; the interannual variability was independent of portfolio width (species or functional groups). Energy ratio expressed by the ratio between fuel energy used for fishing and energy contained in landings varied from 0.3 for purse seines to 9.7 for trawlers using bottom trawls alone or in combination with pelagic trawls independent of portfolio width. Interannual variability in total sale revenues was larger than the sum of species specific sales revenue variability, except for fleets using hooks and pelagic trawlers; it increased with the number of species exploited. In conclusion, the interannual variability of economic returns or energy ratios of French fisheries in the Bay of Biscay did not decrease with the number of species or functional groups exploited, though it varied between fleets. [ABSTRACT FROM AUTHOR]

Catch curves are widely used to estimate total mortality for exploited marine populations. The usual population dynamics model assumes constant recruitment across years and constant total mortality. We extend this to include annual recruitment and annual total mortality. Recruitment is treated as an uncorrelated random effect, while total mortality is modelled by a random walk. Data requirements are minimal as only proportions-at-age and total catches are needed. We obtain the effective sample size for aggregated proportion-at-age data based on fitting Dirichlet-multinomial distributions to the raw sampling data. Parameter estimation is carried out by approximate likelihood. We use simulations to study parameter estimability and estimation bias of four model versions, including models treating mortality as fixed effects and misspecified models. All model versions were, in general, estimable, though for certain parameter values or replicate runs they were not. Relative estimation bias of final year total mortalities and depletion rates were lower for the proposed random effects model compared with the fixed effects version for total mortality. The model is demonstrated for the case of blue ling ( Molva dypterygia) to the west of the British Isles for the period 1988 to 2011. [ABSTRACT FROM AUTHOR]

Abstract: Kaup''s arrowtooth eel Synaphobranchus kaupii is a small-bodied fish and an abundant inhabitant of the European continental slope. To estimate its local density video information using the remotely operated vehicle (ROV) Victor 6000 were collected at three locations in the Bay of Biscay slope. Two methods for estimating local densities were tested: strip transect counts and bait experiments. For bait experiments three behaviour types were observed in about equal proportions for individuals arriving near the seafloor: moving up the current towards the ROV, moving across the current and drifting with the current. Visible attraction towards the bait was the highest for individuals swimming against the current (80%) and about equally low for the other two types (around 30%); it did not depend on current speed nor temperature. Three main innovations were introduced for estimating population densities from bait experiments: (i) inclusion of an additional behaviour category—that of passively drifting individuals, (ii) inclusion of reaction behaviour for actively swimming individuals and (iii) a hierarchical Bayesian estimation framework. The results indicated that about half of individuals were foraging actively of which less than one third reacted on encountering the bait plume and the other half were drifting with the current. Taking account of drifting individuals and the reaction probability made density estimates from bait experiments and strip transects more similar. [Copyright &y& Elsevier]

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]

1. Metrics have become a standard way for summarizing environmental monitoring results. Different metrics react differently to natural variations and human-induced stressors. We suggest that combined analysis of time trends in selected biological metrics allows identification of biological processes (e.g. individual growth, mortality or recruitment) that have changed (increased or decreased) persistently. Alternatively, time trends in the abundance of sensitive species could indicate changes in environmental stressors. 2. We calculate the joint likelihood of time trends in three metrics and use it to evaluate the evidence in the data for different combinations of metric time trends. A simulation study provides guidelines for interpreting log-likelihood differences. 3. We illustrate the approach for identifying biological process changes for three North Sea fish stocks (cod Gadus morhua, lesser-spotted dogfish Scyliorhinus canicula and whiting Merlangius merlangius) using metrics derived from international bottom-trawl survey data for the period 1997–2008. Over the period, a decrease in recruitment and several simultaneous process changes were most likely for cod, while a recruitment increase, mortality decrease and several process changes were most likely for lesser-spotted dogfish. No significant persistent process changes were found for whiting. 4. Synthesis and applications. The likelihood approach offers a way of combining monotonic time trends in multiple metrics for identifying persistent changes in exploited populations or environmental stressors, given suitable metric time series and tables for interpreting joint time trends. For data rich fish populations, the proposed method can supplement analytical stock assessments. For many other populations with no fisheries-dependent data, it offers a way to identify population changes, which will be crucial for implementing the ecosystem approach to fisheries management and the European marine strategy framework directive. [ABSTRACT FROM AUTHOR]

1. The development of ecosystem approaches to environmental management implies the need to account for multiple pressures on ecosystems. Trends in multiple metrics that respond differently to changes in major environmental pressures need to be combined to evaluate the impacts of fishing and environmental changes on fish communities. 2. An exploited fish community is viewed as a three-level food chain in which the two upper levels, or functional groups, are targeted by fishing fleets, while the lowest level is subject to environmental variation. Qualitative modelling is used to predict changes at the two upper levels, that is, top-down vs. bottom-up perturbations. Abundance and length metrics are calculated from survey data for 14 Mediterranean and East-Atlantic groundfish shelf communities at both population and functional group levels. The joint likelihood of time trends in metrics is used to evaluate the evidence for different causes of changes. 3. A wide diversity of impacts is found to have equal evidence at the population level within each community. Consistency between the impacts identified and changes in pressures known from independent information is found at the functional group and community level. The results suggest that there is some compensation between species within functional groups. 4. Synthesis and applications. The method can be used to conduct an integrated assessment of community dynamics subject to multiple pressures. Joint trends in metrics provide evidence of which known pressures are having an impact on the community, and thus, which management actions should be taken to mitigate these changes. [ABSTRACT FROM AUTHOR]

This paper provides an overview of the progress Ifremer has made recently in fisheries acoustics and the study of small pelagic fish by: i) pushing observation frontiers using a range of platforms including an autonomous underwater vehicle, AUV, ii) developing measuring instruments and methods and iii) studying fish distributions. Presently, information from several frequencies of single-beam echosounders is routinely collected together with data from the ME70 multibeam echosounder. For onboard data acquisition control the HERMES software was developed. The new MOVIES 3D software includes modules for simultaneous realistic 3D visualisation and post-processing such as bottom detection, school extraction and calculation of descriptors and integration of all acoustic data. Several data analysis methods are being developed and some initial results are presented. Finally, results on the spatial distribution of small pelagic fish schools in the Bay of Biscay illustrate the role that acoustics can play, and are already playing, in the implementation of an ecosystem approach to fisheries. [ABSTRACT FROM AUTHOR]

Abstract: Using indicator time series for assessment and management requires methods for characterising recent time trends. We propose an approach where first the indicator time series is smoothed using a generalised additive model with optimal selection of the degree of smoothness. Second an intersection–union test is carried out using two test statistics which are the occurrence of the global maximum (or minimum) within the most recent years and the signs of the estimated annual first derivatives of the smoothed indicator times series during the same period, including years with missing data. The proposed test is applied to fish abundance indices for the North Sea, for which it is they are able to pick up changes happening during the last 3–5 years in contrast to linear regression and the Mann–Kendall test which find much fewer significant recent trends. An additional test for changes in trends using the second derivatives of the smoothed indicator time series provide early warnings for subsequent trends for certain species. [Copyright &y& Elsevier]

Ecosystem assessments of fisheries based only on survey data will often have to use surveys that were designed historically for special purposes, e.g. for assessing abundances of two or three target species, or for tuning VPAs. An important question then is whether the previously collected data can provide informative time series of abundance indices and other state indicators for a wider range of target and non-target species. Some potential shortcomings of existing data series are treated in this paper leading to four questions which can guide the user to determine the suitability of an existing time series: did the survey cover the stock of each species adequately? Did survey catchability vary significantly between length or age classes? Did survey catchabilities vary significantly in space or time? Was the sampling effort sufficient? Simple methods for investigating these questions are proposed and illustrated with examples. [ABSTRACT FROM AUTHOR]

A simple two-stage biomass random effects population dynamics model is presented for carrying out fish stock assessments based on survey indices using no commercial catch information. Recruitment and biomass growth are modelled as random effects, reducing the number of model parameters while maintaining model flexibility. No assumptions regarding natural mortality rates are required. The performance of the method was evaluated using simulated data with emphasis on identifying parameter redundancy, which showed that the variance of the biomass growth random effect might only be estimable if large (>0.2). The full and two nested models were fitted to European anchovy (Engraulis encrasicolus) in the Bay of Biscay using two survey series. The best-fitting model had fixed biomass growth and random recruitment following a lognormal distribution. [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]

In the summer of 2004, a video survey was carried out in the northern part of the central mud bank (Grande Vasière) of the Bay of Biscay to study the small scale relationship between the dominant crustacean megafauna Nephrops norvegicus, Munida rugosa and Goneplax rhomboides and juvenile hake ( Merluccius merluccius). Using a towed body, high-resolution videos were recorded in six sampling sites. Statistical modelling using generalised additive models (GAM) revealed variations in activity patterns for two species. More N. norvegicus were observed outside their burrows at dawn and somewhat at dusk (no observations during night) while G. rhomboides was less observed in the morning. In addition, reduced spatial overlap between G. rhomboides and N. norvegicus suggested reduced competition for food but also space as both are burrowing species. The observed temporal and spatial activity patterns may contribute to regulating assemblage structure as competing species may be actively foraging at different times and locations thus reducing direct competition. [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]

The end effect in trawl catches is defined as the proportion of the fish catch taken during shooting and hauling of the net, a period excluded from that nominally referred to as haul duration. If important, this effect will lead to biased abundance estimates, because the swept area will be underestimated. An experimental survey was carried out to compare catch numbers obtained in standard research 30-min hauls with those from 0-min hauls, the latter referring to the trawl being hauled as soon as the trawl geometry stabilized on the seabed. Average catch ratios (0-min/30-min hauls) ranged from 0.05 (s.d. 0.06) for sole to 0.34 (s.d. 0.64) for hake, indicating that the end effect might be more important and more variable for highly mobile species. As a consequence, the bias in abundance indices derived from swept area estimates that ignore end effects will be species-dependent. [Copyright &y& Elsevier]

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]

We propose a random effects model for disentangling population abundance and capture efficiency effects on bottom-trawl catches. The spatial distribution of individual fish is assumed random leading to a Poisson distribution for the number of individuals in the trawl path (no schooling). Capture efficiency, i.e. the proportion of individuals in the trawl path being retained by the gear, is modelled as a random variable. We propose model extensions that include the effects of body size on haul efficiency. We applied the models to several species from the Celtic Sea groundfish community based on small-scale repetitive hauls. The resulting abundance estimates allowed us to study population abundance ratios; the estimated capture efficiencies were comparable between species and showed that generally gear efficiency increases for larger species with the exception of haddock (Melanogrammus aeglefinus), which had low estimated gear efficiency despite its large body size. Model identifiability was studied using simulations and an independent trawl data set from the same area. [Copyright &y& Elsevier]

Discarding is an issue of increasing concern and there is a growing number of studies aiming at estimating discard amounts and characteristics. However, the sampling design and methods used in these studies generally rely on implicit assumptions. In this perspective, we examine the available evidence in favour of or refuting these assumptions. We find that (i) the assumptions most commonly used for estimating discards, namely that discards are proportional to catch or to effort, are generally not supported by the available evidence, (ii) both environmental conditions and fishing methods influence the amounts and composition of discards, but because of the huge variability, sampling stratification according to these factors might not result in any improvement of the precision of discard estimates, and (iii) many intricate factors can play a role in determining discards in a particular fishery. We conclude that assumptions should be more carefully checked prior to being taken for granted in discard studies and that more studies designed to improve knowledge of the discarding processes are needed. [ABSTRACT FROM AUTHOR]

Choice of sampling method and survey period can have an important impact on the perception of the structure and dynamics of an ecological community. For the Celtic Sea fish assemblage we compared data obtained by three different trawl surveys: an autumn groundfish survey with a GOV trawl, and a spring and an autumn groundfish survey, both carried out with a Portuguese high-headline trawl. Time-series of abundance estimates were not consistent among surveys for all species and were generally very noisy. An analysis of variance components showed that the sampling method contributed more to the variance in abundance estimates compared to survey period, interannual variability, or even sampling variance. Overall community assessments based on indicators such as proportions of non-commercial and piscivorous species, and the proportion of benthic species showed similar trends for all data series. The shape of the size spectrum based on abundances per length class summed over all fish species, although stable over time, was highly sensitive to the sampling method. With the exception of size spectra, community indicators for marine fish assemblages monitored by surveys seem to be robust to survey period and trawling gear, but species abundance trends are method dependent. [Copyright &y& Elsevier]

Examines the performance of population and community indicators derived from abundance estimates for detecting the impact of fishing on the Celtic Sea groundfish community. Change in fishing mortality required to reverse population growth rate; Biodiversity index; Proportion of noncommercial species; Distribution of mean population length.

Examines the population and community descriptors that might be used as indicators of the impact of fishing. Total mortality rates; Mean length of catch; Indicators for assemblages; Food web models.

For prudent wildlife management based on population dynamics models, it is important to incorporate parameter uncertainty into the management advice. Much parameter uncertainty originates when it is not possible to parameterize the population management model for a population of interest using data from that population alone. Instead, information about parameter values obtained from other populations of the same species, or even from similar species, must be used. In addition, the age structure of wildlife populations is generally unknown. We show how sequential importance sampling can be used for combining information on demographic processes, obtained from closely studied populations, with aggregated count and cull information from the population to be managed. We resample parameter sets using kernel smoothing, which has the effect of perturbing parameter values. We show how the fitted model can be used to explore alternative culling strategies for red deer in Scotland. [ABSTRACT FROM AUTHOR]

Ecosystem-based approaches are increasingly used in fisheries management to account for the direct trophic impacts of fish population harvesting. However, fisheries can also indirectly alter ecosystem structure and functioning, for instance via the provision of new feeding opportunities to marine predators. For instance, marine depredation, where predators feed on fishery catches on fishing gear, is a behaviour developed by many marine species globally. This behaviour can modify both the ecological role of predators and fisheries performance. Yet, these ecosystem-wide effects of depredation are rarely considered holistically. In this study, we explored different ways of incorporating depredation into an Ecopath trophic model. We assessed, through a subantarctic case study, how three alternative model structures can account for depredation effects on fishery catches, predator and non-commercial prey populations, as well as target fish stocks. While none adequately addresses all facets of depredation, the alternative models can to some extent capture how depredation can lead to increased fishing pressure on stocks. As structural specificities of Ecopath prevented us from representing other depredation effects such as provisioning effects for predator populations, we conclude this study with a set of guidance to effectively capture the complex effects of depredation in marine ecosystems and fisheries models. [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]

• We developed a generic qualitative model to capture depredation impacts on fisheries. • We assessed responses of depredation-impacted fisheries to long-term perturbations. • Responses of depredation-impacted systems can be classified into 4 categories. • We illustrate the 4 types of depredation-impacted fisheries with documented examples • We identify several conditions for the viability of depredation-impacted fisheries. Depredation can broadly affect marine socio-ecological systems, yet it has been little studied via modelling approaches. Here we used qualitative mathematical modelling of system feedback (Puccia and Levins' loop analysis) and a system of ordinary differential equations to represent major interactions between a fishery, an exploited stock and a depredating species. We then assess response of depredation-impacted fisheries to three scenarios of sustained changes: i) increased fishing effort, ii) increased abundance of depredating species and iii) increased abundance of the exploited stock. Persistence of depredation-impacted fisheries depends on (1) the fishers' success in retrieving fish onboard being relatively greater than the ability of depredating species to remove the catch from the gear and (2) sustainable management of the exploited and depredated stock. Moreover, predicted responses of depredation-impacted systems can be summarised according to four broad categories, which partially depend on (1) the population dynamics of the stock and its exploitation status, and (2) the ecology of the depredating species and the magnitude of its competition with fishers. In all categories, an increase in the rate of growth of the depredating species reduces fishery yield, which is likely to intensify fishing effort as fishers try and compensate for losses. However, such an increase in effort is only sustainable for well-managed stocks harvested by a fishery that is sufficiently profitable to support extra costs. We identify several processes that determine the co-existence of fishers, exploited stocks and depredating species and propose a suite of recommendations to better represent depredation in marine ecosystem and fisheries models. [ABSTRACT FROM AUTHOR]

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]

Temporal changes in occupancy of the Georges Bank (NE USA) fish and invertebrate community were examined and interpreted in the context of systems ecological theory of extinction debt (EDT). EDT posits that in a closed system with a mix of competitor and colonizer species and experiencing habitat fragmentation and loss, the competitor species will show a gradual decline in fitness (occupancy) eventually leading to their extinction (extirpation) over multiple generations. A corollary of this is a colonizer credit, where colonizer species occupancy may increase with fragmentation because the disturbance gives that life history a transient relative competitive advantage. We found that competitor species occupancy decreased in time concomitant with an increase in occupancy of colonizer species and this may be related to habitat fragmentation or loss owing to industrialized bottom trawl fishing. Mean species richness increased over time which suggests less specialization (decreased dominance) of the assemblage that may result from habitat homogenization. These analyses also showed that when abundance of species was decreased by fishing but eventually returned to previous levels, on average it had a lower occupancy than earlier in the series which could increase their vulnerability to depletion by fishing. Changing occupancy and diversity patterns of the community over time is consistent with EDT which can be exacerbated by direct impacts of fishery removals as well as climate change impacts on the fish community assemblage. [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]

Depredation has become a major concern worldwide as it jeopardises both socio-economic activities and species conservation. While modelling can help to inform the management of these conflicts, effectiveness may be hampered by the complexity of interactions that depredation generates within socio-ecological systems. Based on a systematic literature review, we summarised current practices and identified major gaps and research priorities for depredation modelling. We found that 74% of reviewed studies used statistical models to quantify depredation levels, identify environmental or anthropogenic factors influencing these levels or assess the effectiveness of specific mitigation measures. Only 8% of studies used models incorporating elements related to the three main entities involved in depredation: human activity, depredating species and depredated resource. Such integrated modelling approaches are however crucial to comprehensively assess management trade-offs. We highlighted future research priorities to comprehensively model depredation and inform the management of human-wildlife conflicts. • We carried out a systematic review to identify relevant approaches to study specific aspects of depredation through modelling. • We found statistical models to be predominantly used. • We identified the main factors driving depredation modelling efforts. • We provided recommendations for effective depredation modelling. • We highlighted research priorities to comprehensively model depredation. [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]

The use of modelling approaches in marine science, and in particular fisheries science, is explored. We highlight that the choice of model used for an analysis should account for the question being posed or the context of the management problem. We examine a model-classification scheme based on Richard Levins' 1966 work suggesting that models can only achieve two of three desirable model attributes: realism, precision, and generality. Model creation, therefore, requires trading-off of one of these attributes in favour of the other two: however, this is often in conflict with the desires of end-users (i.e. mangers or policy developers). The combination of attributes leads to models that are considered to have empirical, mechanistic, or analytical characteristics, but not a combination of them. In fisheries science, many examples can be found of models with these characteristics. However, we suggest that models or techniques are often employed without consideration of their limitations, such as projecting into unknown space without generalism, or fitting empirical models and inferring causality. We suggest that the idea of trade-offs and limitations in modelling be considered as an essential first step in assessing the utility of a model in the context of knowledge for decision-making in management. [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]

The benefits of physiological biomarkers, knowledge and concepts are well-established in fish and wildlife management as they confer the ability to understand mechanistic processes, identify cause-and-effect relationships, and develop predictive models. Although this approach is gaining momentum in the context of species conservation, the use of physiological biomarkers in exploited marine fish stock management and recovery plans remains relatively rare. Here, we present five essential issues to consider to implement physiological biomarkers in fisheries management: (i) choice of relevant biomarkers that have a well-known mechanistic basis, (ii) identification of species-specific biomarkers reflecting a meaningful timespan for management, (iii) selection of biomarkers compatible with data collection during routine scientific fisheries surveys, (iv) use of biomarkers as early-warning signals and complementary indicators of population-level changes in life history traits and (v) how physiological biomarkers may help to refine long-term population dynamic projections under climate change and management scenarios. Overall, if based on well-established mechanisms linked to individuals' fitness, a focus on physiological biomarkers should help to better understand the mechanisms behind stock declines, changes in stock characteristics, and thus more efficiently manage marine fisheries and conserve populations. As this approach is transferable among species, locations, and times, the integration of physiological biomarkers in fisheries science has the potential to more broadly enhance assessments and management of fish stocks. [ABSTRACT FROM AUTHOR]

Competition and predation can play different roles in mediating the influence of external pressures, such as fishing or environmental variations, on marine communities. Pressure effects propagate through food webs along predation links. These predator-prey interactions may result in trophic cascades, but they can be buffered by competitive interactions. We investigated these mechanisms by taking a functional-group approach. Are functional groups affected by external pressures in a predictable way? Within functional groups, do all species respond in the same way, or does competitive release allow for compensation among species? We constructed a simple community model, with functional groups connected by predation links. Loop analysis was used to make qualitative predictions of the changes in functional groups that might result through either direct or indirect effects from changes in pressures. Actual changes in biomass and average weight in functional groups were then tracked from fish trawl-survey data; compensation within groups was examined with dynamic factor analysis. This approach was applied to the Georges Bank, Bay of Biscay, and North Sea fish communities, which have been subject to different fishing regimes and have undergone environmental changes over the last decades. All three communities changed substantially. Compensation did not prevent impacts from propagating through the three food webs; rather, antagonistic pressures did. Community responses to perturbation were mostly determined by community structure and by fisheries selectivity with respect to both functional groups and species. [ABSTRACT FROM AUTHOR]

This paper introduces a semiqualitative approach to analyse the joint dynamics of fleets and stocks in a multispecies, multifleet fishery. We ask whether changes in fleets affect resource dynamics and whether trends in resource influence fleet dynamics more than external drivers do. External drivers include vessel buyback, fuel price, and fish prices, as well as environmental fluctuations. Resource status is measured by abundance and length metrics; fleet capacity is measured by total horse power, and economic metrics such as profitability and earnings are examined as well. A maximum likelihood approach is used to identify the combined metric trends with the largest support in the data. The approach is applied to the French Bay of Biscay fisheries in 2000-2007. Combined-metric time trends suggest that decreases in fleet capacity did not result in decreasing fishing impacts; trends in stocks and fish prices were not the major drivers of changes in fleets either. Rather, the vessel buyback program might have been the main factor determining fleet dynamics over that period. [ABSTRACT FROM AUTHOR]