Cupped oysters (Ostreidae, genus Crassostrea) occupy nearshore marine and estuarine habitats worldwide, providing many ecosystem goods and services as well as being a commercially important group of bivalves. In this study, the species identification of an “adulterant” oyster with small body size, which is often misidentified as a “young individual” of other sympatric species, including C. sikamea and C. hongkongensis, was determined for the first time, based on molecular markers (partial mitochondrial cox1 and rrnL genes), phylogenetic analysis, and morphometric approaches. This novel species, C. zhanjiangensis, commonly known as the “cat ear oyster” in Guandu (a famous estuarine oyster farming region of Zhanjiang, Guangdong Province, China), appears to potentially influence the efficiency of C. hongkongensis spat collection due to niche competition on spat collection devices. Phylogenetic analyses confirm its status as the most basal taxon of the Indo-Pacific Crassostrea. A comparative study of the shell characteristics of C. zhanjiangensis, and other Crassostrea species revealed several distinctive morphological traits, including a generally smaller body size, a deeply cupped left valve, and a right valve that is convex in adults but flat in young individuals. Other distinctive features of the new species include life cycle traits that are unique compared with the sympatric C. hongkongensis and C. sikamea species, such as a higher growth rate in the fast growth phase after settlement, followed by a significantly slower growth rate and mass mortality during subsequent life stages. This study provides the basic information necessary for further ecological and population genetic studies on this new species.

Conservation of threatened large sharks and management of shark-human interactions requires an understanding of shark occurrence and movement patterns. Here, we present the first catch, movement and behaviour data of adult bull sharks, Carcharhinus leucas, in New Caledonia. Amongst six adult C. leucas tagged with passive acoustic tags, four females were caught in coastal waters while males were only found at an isolated oceanic barrier coral reef over 100 km from the nearest river mouth. Two females were monitored in the southern New Caledonia lagoon for 707 and 208 days respectively and displayed classical transient behaviour and sporadic short-term residency around a coastal reef bay, with movements in and out a river detected prior to spring. Adult C. leucas in New Caledonia may develop a sex-based spatial segregation with an atypical presence of adult males in oceanic environments, probably influenced by the unique estuarine-marine continuum of the New Caledonian great lagoon.

Beaked redfish inhabits North Atlantic waters in the depth range 100–950 m, over thecontinental shelf, slope and the open ocean. Individuals can live demersal or pelagic, atvarious stages of their life cycle. The geographical distribution of the species extendsto most of the Atlantic waters from Newfoundland and the Labrador basin in the west to theBarents Sea in the east. Monitoring beaked redfish is challenging because of the specieswide geographical distribution and large scale migrations; deep distribution, whichcomplicates trawling and hydroacoustic surveys; difficulties with tagging; and persistentdifficulties in taxonomic identification. These challenges make it a particularlyproblematic species to observe with conventional research methods. We review these keychallenges and provide recommendations for the coordinated observation of Sebastesmentella in the North Atlantic that would best contribute to the assessment andecological research on this species.

With slow growth rates, late maturity and a high maximum age of 100 years or more, orange roughy can be classified as a vulnerable deepwater fish species that can only sustain low rates of exploitation. Historical patterns of exploitation associated with this species suggest that it is currently not possible to manage its fisheries in the Northeast Atlantic sustainably, and the total allowable catch for orange roughy has been gradually reduced to zero for European fisheries since 2010. Orange roughy to the west of Ireland and Britain occurs on distinct bathymetric features (seamounts, hills and canyons) as well as on flat ground along the continental slope. Productivity-susceptibility analysis (PSA) was performed to evaluate the biological vulnerability of orange roughy in relation to other deepwater species and the risk that recent and current fisheries pose to its populations in the study area. Time-dependant PSA, based on the spatial overlap between orange roughy distribution and recent and current deepwater fisheries demonstrated a strong reduction in risk over time when fisheries stopped directed targeting practices and continued with mixed deepwater trawl fisheries. Some spatial overlap between the species and current fisheries remains, and while the method can show relative risk reduction, it cannot provide information on whether the risk is low enough to allow the recovery of depleted populations.

The status of an exploited population is ideally determined by monitoring changes inabundance and distributional range and pattern over time. Area of occupancy is a measureof the current distribution. Unfortunately, for many populations, scientific abundance anddistribution information is not readily available. To evaluate the reliability ofcommercial fishing data for deriving occupancy indicators that could serve as proxies forstock abundance, we investigated four questions: 1) Occupancy changes with stock biomass,but is this change strong enough to make occupancy a sensitive indicator of populationbiomass? 2) Fishing boats follow fish, but when does such activity alter the positivemacroecological relationship between occupancy and abundance? 3) When does the activity ofpursuing fish adversely affect occupancy estimates derived from catch and effort data? 4)How does uncertainty in fishing effort data affect occupancy estimates? Spatialsimulations mimicking the dynamics of four deep-water fish species showed thatbiomass-occupancy relationships can be weak. Fishers following fish can modify the spatialdistribution of target species, even reversing the sign of the biomass-occupancyrelationship 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 dataand abundance indices for deep-sea fish populations to the west of the British Isles itwas found that only for roundnose grenadier might occupancy provide insights into biomasschanges. In conclusion, care should be taken when using occupancy for evaluating rangechanges in cases where fishing might have modified spatial distributions, uncertaincommercial data are used or when the abundance-occupancy relationship is too flat.

The biology, ecology, and dynamics of the deep-sea teleost black scabbardfish in thenortheast Atlantic are reviewed. The black scabbardfish is a commercial bathypelagicspecies found in the NE Atlantic mostly from Iceland to the Canary Islands and WesternSahara, at depths from 800 to 1300 m. The spatial structure of its population is stilluncertain, although the existence of one single stock that migrates around the NE Atlanticdriven by feeding and reproduction is the most likely hypothesis consistent with availabledata. This review is based on data from commercial fisheries off the Faroe Islands, HattonBank, the west of the British Isles, and Portugal (mainland, Azores, and Madeira) and fromIcelandic and Scottish scientific surveys collected between 1988 and 2012. Spawning ofblack scabbardfish occurs around Madeira and the Canary Archipelagos during the lastquarter of the year. According to the migratory hypothesis, eggs, larvae, and possiblyjuveniles move north to areas from south of Icelandic and Faroe Islands to the west of theBritish Isles where they remain for some years to feed and grow. Then, they move south tothe area off mainland Portugal, where they reach the size of first maturity but do notreproduce, and later move further south to the spawning grounds. Further studies areneeded to understand which of the environmental conditions prevailing around Madeira andthe Canaries, but not elsewhere, allow this species to mature and subsequently reproduce.This review suggests that a multidisciplinary approach is required to confirm thespatiotemporal migration and habitats used by black scabbardfish populations in the NEAtlantic at different life stages. Otolith contour shape and microchemistry, fatty acids,carbon and nitrogen stable isotopes, as well as steroid hormones are proposed as promisingalternative tools for responding to this challenge.

Information about the spatial distribution of bycatch species and their spatial overlap with the target species is essential for fisheries management. The present study used fishery-dependent data (vessel monitoring systems, logbooks and official daily landings) to study the spatial distribution and overlap between black scabbardfish Aphanopus carbo and leafscale gulper shark Centrophorus squamosus taken by the longline fishery operating off mainland Portugal. The geostatistical method kriging was applied to estimate the distribution of the leafscale gulper shark in relation to black scabbardfish and thus assess the impact of the fishery on the leafscale gulper shark. Results indicate that in fishing grounds where the black scabbardfish is more abundant, the relative occurrence of deepwater sharks is reduced. These findings have implications for alternative management measures to be adopted in this particular fishery, particularly where it concerns the minimization of deepwater shark bycatch.

A statistical approach to evaluate the temporal trends in the abundance of female Centroscymnus coelolepis in Portuguese waters of ICES division IXa is presented. A state space model is used, which integrates all the available information of the species’ life history as well as knowledge of its biological dynamics. The model involves two processes that run in parallel: a non-observed process (the state process) that describes the annual female population abundance and an observational process of annual fisheries catches in numbers, assumed to be measured with error. Estimation is done within the Bayesian paradigm using sequential importance sampling with resampling. To evaluate the sensitivity of the model to the prior distributions chosen for the parameters, three scenarios with different levels of prior information were considered. Trends in population abundance level and the abundance levels themselves are quite similar in the two scenarios using biological information, but the model that incorporated all the available biological information in the priors provided the best fit to the observed data. The results indicate that taking into account the main biological drivers and the fishing information in the same state space model provides a coherent picture of the population abundance trends, further suggesting that the fishing impact on the population inhabiting Portuguese mainland waters was low.

Deepwater fish are characterized by long lifespans, late maturity and low productivity. This implies slow recovery from low biomass levels and it is, therefore, important to manage these stocks correctly to avoid overfishing. However, these stocks are generally data poor, which it makes difficult to apply quantitative assessment models on which to base their management. The management strategy evaluation (MSE) approach consists in evaluating the performance of management strategies by simulation before their implementation. In the evaluation, the main sources of uncertainty in a fishery system and its management process should be taken into account in order to find robust management strategies. Thus, the MSE approach is relevant to the management of data-poor stocks. We used the FLBEIA software, an FLR library coded in the R statistical language, to conduct a bio-economic impact assessment of fisheries management strategies. We evaluated the performance of several management strategies in three different deepwater case studies using the MSE approach: beaked redfish (Sebastes mentella) in the Norwegian Sea, blackspot seabream (Pagellus bogaraveo) in the Strait of Gibraltar, and French mixed deepwater fisheries in the North East Atlantic. In conclusion, we found that the S. mentella stock is very sensitive to the stock recruitment relationship chosen. For P. bogaraveo, simulations showed that the present constant catch management is as good as more sophisticated strategies. Finally, in mixed fisheries, case study fleet dynamics were key for the success of management strategies

Data from the MEDITS bottom trawl surveys in the Eastern Ionian Sea, covering a depth range of 28 to 845 m were analysed for the period 1998–2008. For each trawling location, environmental and geographical parameters were recorded, while biomass, abundance, biodiversity and size-based metrics were estimated for the total megafaunal community, as well as for four taxonomic sub-communities (Osteichthyes, Chondrichthyes, Crustacea and Cephalopoda) which were expected to respond differently to environmental changes and fishing. In addition, biomass and abundance of ten species selected based on commercial interest, depth range and life history traits were explored, with particular emphasis on deep-sea species. Fishing effort data collected during the study period were analysed and showed a decreasing trend, mainly due to a decrease in the activity of static nets. The relation between the estimated parameters and environmental and spatial factors, as well as temporal (interannual) effects and the effect of fishing effort were explored using generalized additive models (GAMs). Results of GAMs showed that depth and location explained much of the variation in community metrics, probably reflecting mesoscale spatial features and species/communities requirements. Even though the different communities and species exhibited variant patterns in bathymetric and spatial distribution, some common aggregation patterns in productive areas were identified. Despite the relatively short time series, GAMs were effective in detecting increasing trends for several metrics; taking into account spatial factors further contributed to attributing the remaining deviance to temporal effects. These trends were partly explained by the observed decline of fishing effort, which is further supported by the fact that negative relations between several metrics and fishing effort were identified, for some of the selected communities and populations. Abundance, species richness and maximum length proved the most informative metrics concerning the effect of fishing. The current decline in fishing effort in the area seems to be a move in the right direction and should be complemented by additional measures aiming to prevent allocation of effort towards the deep sea.

This paper aims to investigate the potential interest of using a Vessel Monitoring System (VMS) based on GPRS/GSM (Global System for Mobile Communications) technology to obtain a better estimation of fishing activity and distribution of a small-scale artisanal fleet, for which the European satellite-based system is not available. Since the early 1980s, the artisanal fishery targeting blackspot seabream (Pagellus bogaraveo), commonly known as “voraz”, has been developing along the Strait of Gibraltar area. Up to now the fishing effort was estimated using the number of sales, a proxy for the number of fishing days. This measure does not, however, capture the “missing effort”, i.e., fishing days resulting in no catch or not enough catch to be sold at public auction. The European satellite-based VMS provides information about the dynamics of different fishing fleets, but is not installed on small vessels (<15 m), such as those used by the artisanal “voracera” fleet targeting blackspot seabream in the Strait of Gibraltar. The Andalucía Regional Government installed its own vessel monitoring system on several artisanal fleets using GPRS/GSM cellular network technology that sends data on vessel positions and speed every three minutes. Data collected from 2009 to 2011 using this system were filtered and analysed to estimate fishing effort, catch rates and the spatial distribution of the blackspot seabream fishery. The estimates obtained seem to provide a good representation of fishery reality. As expected, the missing effort increases as the resource levels decrease. Additionally, expert knowledge of the fishery allowed application of an algorithm for splitting these daily trips into estimated fishing hauls. Afterwards the spatial distribution of catches and Catch per Unit Effort (CPUE) could be obtained linking VMS locations with landings information. This study provides a considerably finer spatial scale view of the fishery than data available in the past.