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Effective population size (Ne) is a key parameter of population genetics. However, Ne 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 FIS 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. SNP‐based estimates of effective population size were found to be sensitive to SNP filtering threshold values. 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 by around 70%. Sample size had a small effect beyond a minimum number.

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. Environmental DNA concentrations are affected by animal behavior, such as diel vertical migration (DVM), which has repercussions for designing eDNA sampling strategies. The effect of DVM was identified for hake using samples from the Bay of Biscay and corroborated using theoretical Lagrangian particle‐tracking modeling.

The 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. By filtering surface marine water and using eDNA we assessed fish biodiversity along the coast of southern Brittany (Iroise Sea). For 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 gradient with a higher diversity for the three facets of the biodiversity components in the northern part of the study area.

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.

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.

In contrast to generally sparse biological communities in open-ocean settings, seamounts and ridges are perceived as areas of elevated productivity and biodiversity capable of supporting commercial fisheries. We investigated the origin of this apparent biological enhancement over a segment of the North Mid-Atlantic Ridge (MAR) using sonar, corers, trawls, traps, and a remotely operated vehicle to survey habitat, biomass, and biodiversity. Satellite remote sensing provided information on flow patterns, thermal fronts, and primary production, while sediment traps measured export flux during 2007-2010. The MAR, 3,704,404 km(2) in area, accounts for 44.7% lower bathyal habitat (800-3500 m depth) in the North Atlantic and is dominated by fine soft sediment substrate (95% of area) on a series of flat terraces with intervening slopes either side of the ridge axis contributing to habitat heterogeneity. The MAR fauna comprises mainly species known from continental margins with no evidence of greater biodiversity. Primary production and export flux over the MAR were not enhanced compared with a nearby reference station over the Porcupine Abyssal Plain. Biomasses of benthic macrofauna and megafauna were similar to global averages at the same depths totalling an estimated 258.9 kt C over the entire lower bathyal north MAR. A hypothetical flat plain at 3500 m depth in place of the MAR would contain 85.6 kt C, implying an increase of 173.3 kt C attributable to the presence of the Ridge. This is approximately equal to 167 kt C of estimated pelagic biomass displaced by the volume of the MAR. There is no enhancement of biological productivity over the MAR; oceanic bathypelagic species are replaced by benthic fauna otherwise unable to survive in the mid ocean. We propose that globally sea floor elevation has no effect on deep sea biomass; pelagic plus benthic biomass is constant within a given surface productivity regime.

Europe has a long tradition of exploiting marine fishes and is promoting marine economic activity through its Blue Growth strategy. This increase in anthropogenic pressure, along with climate change, threatens the biodiversity of fishes and food security. Here, we examine the conservation status of 1,020 species of European marine fishes and identify factors that contribute to their extinction risk. Large fish species (greater than 1.5 m total length) are most at risk; half of these are threatened with extinction, predominantly sharks, rays and sturgeons. This analysis was based on the latest International Union for Conservation of Nature (IUCN) European regional Red List of marine fishes, which was coherent with assessments of the status of fish stocks carried out independently by fisheries management agencies: no species classified by IUCN as threatened were considered sustainable by these agencies. A remarkable geographic divergence in stock status was also evident: in northern Europe, most stocks were not overfished, whereas in the Mediterranean Sea, almost all stocks were overfished. As Europe proceeds with its sustainable Blue Growth agenda, two main issues stand out as needing priority actions in relation to its marine fishes: the conservation of marine fish megafauna and the sustainability of Mediterranean fish stocks. Assessing the conservation status of 1,020 European marine fishes reveals half of large (>1.5 m) fishes are threatened with extinction and stock status diverges geographically: almost all Mediterranean stock is overfished, most northern European stock is not.

The red pandora, Pagellus bellottii , is a tropical and subtropical demersal porgy (Sparidae) distributed in the eastern Atlantic, mostly along African coast. Several recent records in the Gulf of Cádiz suggests a northward migration of the species. Two specimens of the red pandora were caught in the southeast Bay of Biscay during the 2014 French fishery survey programme. They represent the first records of the species for the Bay of Biscay and for French waters. In Europe the species has been previously recorded only in the Gulf of Cádiz in the Atlantic and in Spanish Mediterranean waters. The hypothesis that global climate change is a factor for this almost 7° northward species range extension, commonly distributed in the tropical and subtropical eastern Atlantic along the African coast, is analysed using temperature data from the World Ocean Atlas 2013. The northern extension of the distribution range of Pagellus bellottii most probably is a consequence of the warming waters of the Bay of Biscay over the past decades.

Much is known in very broad terms about the distribution of deep-sea fishes, but information on fine-scale habitat selection and behaviour in the largest living space on earth is still rare. Based on video sequences from 4 dives performed with the manned submersible ‘Nautile’ at depths between 400 and 2000 m in the Bay of Biscay, NE Atlantic, we studied the behaviour of co-occurring slope-dwelling deep-sea fishes. Five different habitats were identified according to depth range or topographical and hydrological characteristics. For each fish species or genus that could be identified, estimates of absolute abundance were provided. The most frequently occurring species, roundnose grenadierCoryphaenoides rupestris, blackmouth catsharkGaleus melastomus, bluemouthHelicolenus dactylopterus dactylopterus, orange roughyHoplostethus atlanticus, North Atlantic codlingLepidion eques, greater forkbeardPhycis blennoides, and northern cutthroat eelSynaphobranchus kaupiwere quantitatively compared with respect to the relative frequencies of disturbance responses to the submersible, locomotion behaviour, and vertical positioning above the bottom. Clear variations in behaviour and abundance among species and habitats were found, reflecting both species-specific and flexible adjustment to small-scale spatial and temporal variability on the Bay of Biscay continental slope. These results have important implications for the development of sustainable deep-water fisheries management.

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.