Survival was recorded at the endpoint for all batches of each group (2n-control, 2n-wild, 2n-commercial, 2nR, 3nR and 3n-commercial). Similarly, initial and final yield were recorded, corresponding to the total weight of the live oysters at deployment and at the endpoint. Finally, shell length and total weight for individually recorded at reception and at the endpoint.

The Delmoges project aims to generate new ecological and fisheries knowledge to reduce dolphin bycatch in the Bay of Biscay (GoG). This dataset presents maps produced by a hierarchical model of the seasonal and interannual distribution of dolphins' main prey, small pelagic fish. The model integrates 3 types of data: presence-absence and biomass of fish from scientific campaigns and presence of fish from fishing data. For the first time, the model has provided a quantitative description of the seasonal spatial dynamics of sardines and associated fisheries. The main sardine distribution areas were coastal, from the mouth of the Gironde to south-west Brittany. On average, sardines were distributed over a wider area in small aggregations in spring. They seemed to concentrate in their main distribution areas in summer, and to disperse offshore in autumn, but to a lesser extent than in spring. Fishing was concentrated in the sardine's main coastal distribution areas, and was more intense in summer, then autumn, and less intense in spring.

The Mytilobs network, carried out by IFREMER (French Research Institute for Exploitation of the Sea), is a national network dedicated to building long-term physiological variations time series of blue mussels (Mytilus edulis), across a large spatial scale. This observation network, initially designed to survey production yields, also provides valuable data to track environmental variations of coastal ecosystems. Mussels exhibit high phenotypic plasticity in response to environmental variations. Collection of data describing phenotypic variations, over an extended period, reveals small-scale climate and habitat variations. With its broad deployment across time and space, the data produced under Mytilobs will be useful for the establishment of a baseline condition when studying the effect of a perturbation affecting an ecosystem’s functioning. Finally, the monitoring of mussel biometric traits and mortality was coupled with high-frequency measurements of salinity, temperature, and sea level, complementing this multi-layer observational framework.

Data were collected from the regional program LOUPE (Observation of the habitat and associated communities in the context of the fisheries of the Capbreton Canyon). It consisted in the observations of two métiers practiced around the canyon. The observations were carried out between July 2011 and April 2013 on coastal boats. Observations and interviews were made on board commercial vessels. The longlines used in the hake fishery are semi-pelagic and are deployed on the edge of the Capbreton Canyon. It is an emblematic and major métier benefiting from a particular regulation as they take advantage of a prohibition of net and trawl fishing on their fishing grounds. Between 8 and 14 costal boats practice this métier during the year and the fleet characteristics are homogeneous. Boats lay between 1,200 and 1,800 hooks per day, baited with frozen pilchard (Sardina pilchardus). Two or three men are on board these vessels. Fishing is mostly practiced in spring and summer but a small number of vessels work all year. Generally, trips last between ten and twelve hours; longline is set before sunrise and retrieved three or four hours later. Hake is the main targeted species; other targets are pollack (Pollachius pollachius), red sea bream (Pagellus bogaraveo) and conger (Conger conger). Netting is a major métier in terms of vessels involved and the number of trips. Crew composition varies and depends on boat length (from one to four men on average). This métier is practiced by 30 to 35 boats all year round, but fleet characteristics are less homogeneous than in the case of longliners . The strategy of these netters operating in the coastal area is based on the use of several types of nets (gillnets and trammel nets) targeting several species, often sold directly to consumers on the docks. Gillnets, consisting of a single mesh, target hake, sea bass and sea bream species (Diplodus spp, Sparus aurata, Litognathus mormyrus), while the trammel nets (three meshes) are used to capture benthic fish, such as common sole, monkfish (Lophius spp), turbot and brill (Scophthalmus rhombus). Generally, trips last less than twelve hours for coastal netters (less than 15 m), which predominate in the sector, and a few days for large netters. On average, the coastal vessels set 6000 to 8000 m. nets daily.

The data come from organisms and pictures collected during the MEDITS annual bottom trawl surveys conducted between 2011 and 2013 (Bertrand et al. 2002). MEDITS surveys cover the continental shelf (10 m to 200 m depth) and the upper part of the continental slope (200 m to 800 m) on the Mediterranean. A total of 1511 individuals from 85 fish species were collected from seven Mediterranean areas (South Adriatic Sea, Sardinia, Gulf of Lions, around Cyprus, Mallorca, Tyrrhenian Sea, and North West Ionian Sea). A set of 14 morphological traits related to the habitat and the diet of the species were measured in the field and on pictures using the ImageJ software (version 1.47, http://imagej.nih.gov/ij/) (see Granger et al. 2015 and Brind'Amour et al. submitted for details) (Figure 1). Replicats of measures vary between 1 (e.g. Scorpaena loppei) to 53 (e.g. Serranus hepatus) according to fish species. Twelve of the chosen traits consist in continuous biological characteristics measured on each individual (measured in cm). The two remaining traits are categorical and determined at the species level.

Long-term time series of coliform bacteria concentration (fecal coliform or Escherichia coli) in shellfish in four submarine areas (North Sea/Channel, Britany, Atlantic, Mediterranean).

In 2003 two experiments were carried out in the Bay of Biscay to compare catch numbers obtained in standard research 30-min hauls with those from 0-min hauls to determine the so called end effect. 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 what is nominally referred to as haul duration. In 0-hauls the trawl was hauled as soon as the trawl geometry stabilized on the seabed. The trawl used was a beam trawl rigged as twin trawl. Overall 24 hauls were carried out, six 30-min and 18 0-min hauls. 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.

Ifremer conducts numerous fisheries surveys dedicated to benthic and demersal populations (commercial / non-commercial fishes and invertebrates). For several years, in application of the ecosystem approach, all benthic invertebrate fauna collected in fishing gear has been systematically monitored: megabenthic invertebrates captured have been sorted, identified, counted and weighted. All these surveys are based on fixed or random stratified sampling strategy with varying intensity depending on the covered survey area. These data are stored, in historical access-based databases or for the most recent years in the centralised “Harmonie” database held in the Ifremer Fishery Information Systeme (SIH). The species nomenclature used was standardized using WoRMS database. Taxa caught at least once a year are listed for each monitoring area on the basis of already available data series. In order to facilitate the identification of individuals sampled on board vessels and to improve the training of onboard scientists, the present work aims to define the minimum level of identification for each of them. The analysis identifies taxa that appears recurrently on available historical series or gathers them on less precise taxonomic levels if this is not the case, which may indicate potential identification difficulties. The following procedure was used: all taxa expressed at the species level were first aggregated at genus level if they occurred less 90% of the years over the available time series. For MEDITS, EPIBENGOL and ORHAGO, the occurrence threshold was set to 70% and to only 50% for NOURMONT because the datasets were less than 10 years long. Then to be kept at that taxonomic level, a given genus had to be observed over 90% of the time (for example over at least 9 years if the dataset contains 10 years). Otherwise it was iteratively regrouped into a higher taxonomic level (family, order, class, division) following the same criteria (Foveau et al, 2017). For instance, for the NOURSEINE survey, this resulted into the aggregation of the 103 origin taxa into 35 taxonomic groups. The name of the final taxon after data processing represents the minimum level of identification defined by the analysis. However, these results are very theoretical. This is why they were sent to scientists who embark regularly in order to refine the level of taxonomic identification with field experience. The first dataset is composed of 8 tables relevant to the different vessel surveys. The first column of each table represents the permanent code of the taxon in the Ifremer taxonomic referential, the second the systematic number and the third the species abbreviated code. The other columns are the different taxonomic levels of the taxon. The minimum level of identification at sea defined by the data processing appears in blue. The level determined by feedback of scientist’s field experience, which is the one to use at sea, appears in green. The second dataset summaries the results detailed in the first table and indicates directly for each taxon identified to far, the minimum level of identification required for the benthic invertebrates by-catch of each fisheries surveys studied.

Input data, TMB (C++) and R code for close-kin mark recapture (CKMR) abundance estimation for two subpopulations of thornback ray (Raja clavata) in the central Bay of Biscay (offshore and Gironde estuary, see figure). Samples were taken between 2015 to 2020. Parent-offspring pairs were identified using SNP genotype information. Birth years of individuals were estimated using length information and growth curves by sex.

This dataset comprises stomach contents of small pelagic fish species on the french shelf of the Bay of Bisacy, in spring, autumn and winter, from 2004 to 2024. The spring data were acquired in May on the pelagic survey series PELGAS from 2004 to 2024, the autumn data in October/Novermber on the demersal survey series EVHOE from 2020 to 2024 and the winter data were acquired on chartered fishing vessels in February 2023 and 2024. The dataset concerns anchovy (Engraulis encrasicolus) and sardine (Sardina pilchardus) in the 3 seasons and also mackerel (Scomber scombrus), sprat (Sprattus, sprattus) and horse mackerel (Trachurus trachurus) in spring for some years. The dataset represents a unique long-term monitoring of stomach contents characterized with a low taxonomic resolution and semi-quantitative abundance quotation.  The pelagic ecosystem survey PELGAS (Doray et al., 2018) is run in each year in May since 2000, to monitor the Bay of Biscay pelagic ecosystem at springtime and assess the biomass of its small pelagic fish species. During the survey, pelagic trawl hauls are undertaken to identify echotraces to species and to measure individual fish traits. All hauls are performed during day time. In 2010, some hauls were undertaken at night to sample stomach contents over the day/night cycle. The fish stomachs are sampled from the haul catch. For a given species, twenty individuals are selected at random from the catch, their stomachs dissected and preserved. This is repeated at three hauls in each of the ten spatial strata defined to cover the entire Biscay shelf. In some years, fish length categories (lower and greater than 14 cm for anchovy and 18 cm for sardine) were also considered when sampling the stomachs. Stomach sampling by species depended on the trawl haul catch and all species were not systematically sampled jointly at the same trawl haul. Also, the number of stations with stomach sampling varied between species and years. The stomachs were preserved in formaline until 2018 and in ethanol since. Anchovy and sardine stomach sampling on the demersal survey EVHOE (Mahe and Poulard, 2005) followed the same protocole as for PELGAS but with fewer stations, depending on the catch of anchovy and sardine in the bottom trawl. In 2020 due to the Covid pandemic, the PELGAS survey was canceled and to compensate, a pair-trawler was chartered in autumn to perform some pelagic trawl hauls during the EVHOE 2020 survey. In winter 2023 and 2024 a pair-trawler was also chartered, for identifying echotraces observed previously on the survey DRIX (Doray et al., 2024) in the area delimited by the Gironde and Loire estuaries, the coast and the 100 m isobath. On the fishing vessels the fish were frozen onboard, the stomachs were dissected on land in the laboratory and preserved in ethanol.  The taxonomic analysis of the stomach contents was performed in the laboratory under a binocular magnifyer by the company LAPHY. A simplified taxonomic resolution was used, which considered five ichtyoplankton groups, two copepod groups, euphausids or mysids, amphipods, two decapod groups, other crustacea, other zooplankton, phytoplankton and pulp. Taxon abundance was defined by a quotation : 0 (absence), 1 (presence : <10 individuals), 2 (abundant : between 10 and 100), 3 (very abundant : > 100). The dataset comprises trawl haul information, information on the quality of the stomach contents and abundance quotes for the list of plankton taxons. A preliminary analysis of the data (Petitgas, 2024) showed a large overlap in stomach contents between species, the importance of small copepods in the diets, and how different drivers such as habitat and length influence the diets.