Quantitative analysis of the spatial patterns in age-structured fish populations provides a useful complement to stock assessment methods. The spatial distribution of an age-structured population is characterized by indicators for location, dispersion and aggregation, which are estimated from survey data. The times series of spatial indicators are organised in a 3D data structure with dimensions along indicators, age classes and years. Multi factor analysis (MFA) is applied to quantify the reproducibility in time of the multivariate structure between age classes and indicators. MFA computes the mean annual pattern over the age classes. The deviation around that pattern in each year is also quantified. A multivariate indicator that characterise the spatial pattern over all age classes is developed. Its variation in time is evaluated with quality control methods. The multivariate indicator is shown to be $\chi ^{2}$ distributed and a CUSUM control chart is used to detect any significant changes in time. Software for implementing the method is presented and described. To illustrate this new method, North Sea cod data are analysed, and changes in the spatial patterns of the age-structured population are detected and interpreted.

The reproductive dynamics of swordfish (Xiphias gladius) was investigated from catches of the Reunion Island-based longline swordfish fishery between 19–25 °S and 48–54 °E. Thus, 1727 swordfish (size range 75–289 cm, lower jaw-to-fork length, LJFL) were sampled on board commercial fishing vessels during the period of May 1998 to January 2001. Reproductive activity was assessed using macroscopic gonad characteristics, trends of gonadal indexes for both sexes, oocyte size-frequency distributions and microscopic investigation of oocyte development stages. Size at first maturity (L50) for female and male swordfish was estimated in Indian Ocean for the first time. L50 was estimated at 170 cm and 120 cm (LJFL) for females and males, respectively. Spawning occurred from October to April in the vicinity of Reunion Island where sex ratio of caught populations fluctuated seasonally. The seasonal changes in sex ratio and the incidence of larger individuals at the beginning of the spawning season provide some preliminary indications of synchronized movements of swordfish between spawning grounds and neighboring regions. Our results add significantly to knowledge about the reproductive biology of swordfish in the southwestern Indian Ocean. An overview of the available information on reproductive biology and dynamics of swordfish in Indian Ocean and eastern Pacific indicated that spawning activity is localized in discrete areas, and showed that there is incomplete information on spawning grounds in this extended area.

This review aims at comparing the fisheries management systems existing in New Zealand and in the European Union. The involvement of stakeholders at all stages of the management process is generally more transparent and better established in New Zealand than in the EU. Both systems aim at achieving an adequate balance between sustainability and utilisation and consider the precautionary approach as a founding principle. The socialobjectives are probably more explicit in the EU management system. In New Zealand, B MSY is a legal management target for all stocks in the quota management system (QMS), but management strategies were poorly explicituntil most recently. In the EU, there have not been any legal management targets or strategies until 1999. Since 1999, a number of multi-annual recovery and management plans have been established, including bothmanagement targets and strategies. Both management systems include conservation and access regulation measures. The EU management measures aim at regulating fisheries outputs and inputs, and discarding is tolerated. New Zealand management is almost exclusively output-based, and discarding practices are banned. In the EU, while individual quotas (IQs) are implicit in several countries, there is no consistent pattern across Member States for allocating TACs. In New Zealand, individual transferable quotas (ITQs) are implemented, and some flexibility in catch-quota balancing is provided by a carry-over allowance and the payment of a landing tax, the deemed value, for every fish landed above quota. If rights-based management were introduced in the EU based on, e.g., the New Zealand model, we suggest that concentration rules be set in accordance with the social objectives of the Common Fisheries Policy, and also that the deemed value should be set based on science and economics.

The queen conch, Strombus gigas, is an important fisheries resource in the Western Tropical Atlantic. In order to maintain harvesting success, improve fisheries management and contribute to mariculture pursuits, a detailed understanding of the life history traits of this species is required. Traditionally, this has been achieved by tedious and time-consuming long-term field observations. This study presents a highly versatile and rapid technique to estimate the timing and rate of shell growth based on sclerochronology. The Belizean S. gigas specimens (N = 2) from the offshore atoll, Glovers Reef, reached their final shell size (maximum shell height: 22.7 and 23.5 cm, respectively; completed formation of the flared lip) after only two years. However, seasonal growth rates varied considerably. Shells grew up to 6 mm d−1 during spring (April-June) and fall (September-November) but only 1 to 2 mm d−1d uring July and August. Furthermore, shell growth ceased between December and March. Fastest shell growth occurred nearly contemporaneously with times of maximum precipitation which probably resulted in increased food availability. Slowest shell growth however, occurred during times of reduced rainfall and reduced riverine runoff, i.e. during times of reduced food supply. Sea-water temperature apparently did not exert a major control on shell growth. Notably, the slow winter growth was marked by a distinct purple-colored growth line in the cross-sectioned flared lip. Formation of a second major growth line (brown) fell together with the main reproduction period (late October/early November). Shell microgrowth patterns potentially represent daily or semidiurnal periods but cannot be used to assign exact calendar dates to each shell portion, because they were not visible across the entire cross-section of the whorl. Also, the protruding spines developed on the outer shell surface do not function as time gauges. The time represented by the shell portion between consecutive spines varies greatly from 1 to 72 days. Sclerochronology can potentially facilitate maricultural strategies and aid in site pre-testing and selection to grow S. gigas.

The proliferation of the voluntarily-introduced cupped oyster, Crassostrea gigas, has attained the proportions of species invasion in many intertidal habitats in Europe, presumably resulting from successful reproduction of farmed individuals. It is thus imperative to better understand the reproductive characteristics of farmed oysters, since they are directly under human control. We quantified the dry tissue mass (DTM), gametosomatic index (GSI), and reproductive cycle of farmed oysters at two sites in Bourgneuf Bay, France, in relation to environmental parameters using continuously-recording probes in 2005 and 2006. The GSI was developed for this study, based on the actual area occupied by gametes, rather than the area of the gonad previously used for quantitative histological estimation of reproductive effort. The two sites, intermediate – (IT) and high-turbidity (HT), differed markedly in the amount and quality of particulate suspended matter, and also in fine-scale temperature variations. Oysters at both sites presented two spawning periods in both 2005 and 2006; Bourgneuf Bay is thus near the northernmost European limit for a 2-spawning cycle in Crassostrea gigas. Gonad maturation was initiated when spring water temperature reached 8–10 °C, and gamete atresia occurred when water temperatures transiently dipped to 15–18 °C. Spawns, which occurred above 18 °C, were timed by fine-scale water temperature variations. Particulate organic matter quality peaks, coinciding with gonad maturation, were related to DTM variations before spawning periods, for the IT oysters in both years, and for the HT oysters in 2006. The reproductive effort (GSI) of oysters was similar at both sites; however, the fates of the gametes differed according to site. At the first spawning, the IT oyster gamete emissions were +1 month delayed, as were peak water temperatures greater than 18 °C, and more pronounced, compared to the HT site. Although the second spawning showed high proportions of atretic oocytes at both sites in both years, the IT oysters evacuated twice as many gametes as the HT oysters in 2005. The IT conditions therefore appear more suited to Crassostrea gigas gamete evacuation than the HT conditions.

Batch fecundity and relative fecundity of swordfish (Xiphias gladius) in the southwestern Indian Ocean were estimated from seven gravid swordfish females (size range 127–225 cm lower jaw-to-fork length, LJFL) with unovulated, hydrated oocytes collected onboard Reunion-based (France) longline swordfish fishing vessels between December 1999 to January 2001. To investigate the spawning pattern of swordfish, we used data collected through a combination of two at sea sampling regimes. A total of 17 007 geo-located size data of swordfish were recorded during 8 years (1993-2001) and a total of 1727 (size range 75–289 cm, LJFL) swordfish gonads (1107 females and 620 males) were sampled from May 1998 to January 2001. The estimated batch fecundity ranged from 995 000 hydrated oocytes for the smallest ripe female to 4.3 millions for the largest female sampled measuring respectively 127 to 225 cm in curved length (LJFL). The relative fecundity ranged from 25 to 72 hydrated oocytes per gram of body weight. We found that batch fecundity was positively correlated with fish length and that the older/larger females have earlier and longer spawning seasons than younger/ smaller females. These findings suggested that older/larger females which are seasonally migrating in this spawning ground seem to play a major role in reproductive success of the species in producing significantly more offspring than younger females during an extended spawning season. Examination of the length-frequency date from the fishery indicated that the young fish are resident around Reunion and around the seamounts off Reunion Island. Our results highlight the important role of the older/larger females in the reproductive capacity of southwestern Indian Ocean stock. We discuss the potential implications of fishing the older/larger females for this stock in terms of reproduction and recruitment.

A selection of ten uni- and multivariate, nonparametric statistical methods thought to be useful for assessing trends in indicators estimated from trawl surveys is described. Nonparametric methods make minimal assumptions about the data and can therefore be suitable when parametric modelling methods, as typically preferred by fisheries scientists, are not suitable. The various methods described are sensitive to a variety of specific features of a trend thereby allowing many different forms of variation over time to be identified, e.g. changes in level, sloping straight or curved lines, and differing cyclicities. In contrast, model-based investigations can be constrained in this regard if the single model which is adopted and fitted to the trend is a simplification of its form.

Managing adequately the exploitation of commercial species subject to technical interactions is a key step towards the ecosystem approach to fisheries. We evaluate here, using a bio-economic modelling approach building on the ISIS-Fish simulation platform, the relative impact of total allowable commercial catches (TACC) and of taxes applicable to over-quota landings (deemed value) on the sustainability of a selection of species exploited by the New Zealand hoki (Macruronus novaezelandiae) fishery. We investigate some aspects of the hoki mixed fisheries, consisting of four fleets and nineteen métiers, by considering the technical interactions between hoki and Southern hake (Merluccius australis). The dynamics of effort allocation were modelled using gravity model, using value per unit of effort (VPUE) as attractivity coefficient. Several management scenarios, based on different levels of TACC, effort limits and deemed value have been defined. The impact of these strategies on spawning biomass and catches has been investigated. The results confirm that the deemed value may, in combination with TACC, be an efficient management tool. By increasing the hoki deemed value, we could somehow limit the decrease in the hoki TACC needed to harvest Western hoki sustainably. Constraining hoki fishing also restricts Southern hake fishing in the Chatham Rise and in the West Coast South Island, but leads to increased targeting of this species in the Sub-Antarctic area. The relative costs of renting/buying quota or paying the deemed value are most constraining when the hoki TACC is at relatively low level and when the hoki deemed value is more than 1.5 times the current value.

The eastern English Channel, the narrow channel of water separating northern France and southeast England is an area of intense human use of the array of resources concentrated into its relative small area. The vulnerability of living resources and their habitats brought together French and British maritime experts within a common project (called CHARM): to create an atlas of marine resource habitats in the eastern English Channel so as to provide planners and decision-makers with the necessary information to help managing the use of its living and non-living resources. This multidisciplinary and richly illustrated atlas provides abundant information on the legal framework and physical environment; benthic invertebrates, fish and their habitats; fishing activities; and a first attempt at developing a trophic network model (using ECOPATH software) and a marine conservation planning exercise (using MARXAN software, at a spatial resolution of 25 km$^{2})$. Although most of the data used were collected elsewhere, some were collected especially for the project. Similarly, most of the analyses performed on the data where entirely original for this geographical area. The CHARM atlas has significantly improved the knowledge about the eastern Channel while contributing to the recognition that such holistic or multidisciplinary approaches to exploited marine systems are necessary to efficiently and durably manage their resources use.

To make a preliminary exploration of the possibilities and limits of magnetic resonance imaging (MRI) for assessing body growth and gonad development of the Pacific oyster, Crassostrea gigas, individual monitoring was conducted on diploid and triploid oysters in their second year, maintained from February to October in a pond on the French Atlantic coast. Magnetic resonance imaging was done on each oyster on five dates during the study period. From these images, variations in the volumes of the flesh, digestive gland–gonad and adductor muscle, and the surface of the gills were measured over time. Apart from the well known differences between diploids and triploids related to maturation of gametes, other original observations of assessing growth were made from these MRI measurements using a non-invasive technique. The standard error of mean dry flesh variation was lower than that found by other commonly used measurement methods. A negative correlation was established between the volume of the gametes spawned and the increase in dry flesh volume after spawning. Moreover, these variations were correlated with the chemical composition of the adductor muscle. All these observations and conclusions need to be confirmed by further observations on oysters of different sizes or grown in different environments.

Statistical Process Control (SPC) methods are extensively used in manufacturing contexts to monitor production processes. This article illustrates their potential utility for monitoring the state of marine ecosystems, using survey indicators. We exemplify the use of one SPC tool, the cumulative sum (CUSUM) control chart, to detect persistent changes in the state of a system as new observations are collected, using simulated and real data. Practical guidelines are given on how the chart parameters can be tuned to achieve an acceptable compromise between the ability to detect anomalies quickly and keeping the risk of false alarms low. The common performance measures associated with control charts depend on some key assumptions being met, and the potential impact of their violation is indicated.

Day and night acoustic surveys were used to compare fish stock estimates at eight European reservoirs and one flooded mining pit. During both photoperiods of summer, higher fish biomass was observed in the uppermost 4 m of the water column by horizontal beaming than in deeper water by vertical beaming. Comparisons of volume backscattering coefficient (sv), fish biomass (kg ha−1), abundance (ind. ha−1) and average fish weight (g) did not show a common pattern among the reservoirs but were found to vary significantly across photoperiods. At most reservoirs, the night surveys had higher estimates than day surveys. However, at several reservoirs the opposite pattern was observed. These patterns could not be explained by the species composition of the fish stocks. Fish size distributions were found to be different between day and night. A higher proportion of 1+ and older fish were found during the night at two of three studied waterbodies. In general, it was not possible to decide whether day or night acoustic surveys gave more reliable fish stock assessments. We advise performing both day and night transects on a given water body before deciding when to conduct the full survey. For a complete fish assessment it is very desirable to combine acoustic mobile surveys with active sampling gear.

Fisheries research monitoring surveys provide an ensemble of measurements on fish stocks and their environment. Because the interannual variability in such survey-based indicators is high and because diagnostics on fish stocks cannot be based on noise, our concern is to make use of what is continuous in time to obtain a reliable diagnostic. In this paper, we show how min/max autocorrelation factors (MAFs) can be useful for assessing the status of a fish stock. Indeed, MAFs will allow us to (i) summarize the multivariate indicator signals into orthogonal factors that are continuous in time, (ii) select those indicators that carry the major signal in time, and (iii) forecast stock status by modelling the time continuity of the MAFs. These different potential uses of MAFs in an indicator-based approach to assessment were illustrated with North Sea cod, for which a suite of biological and spatial indicators are available over a 21-year survey series.

To better understand the effects of perturbations (e.g. global change) or habitat restorations on fish population dynamics, it is crucial to improve the knowledge about strategies of habitat use (especially in terms of velocity use) by fish. Many recent studies accurately describe kinematics or energetic budgets of swimming activities, which are often species-specific and hardly transferable to other species. The main goal of the present study was to revive more general ecomorphological relationships between body shape and strategies of velocity use by highlighting a functional aspect of fish morphology: the hydrodynamic potential. For this purpose, potential relationships between minimum drag coefficients (Cdmin, constant at high Reynolds numbers), velocity use, fish morphology and drag in given flow conditions were investigated. To assess these relationships, dead drag values (i.e. drag values measured on dead, straight individuals) of 27 riverine species (108 individuals in total) common in France were experimentally measured under various flow conditions. These values served to estimate the Cdmin of fish. For pelagic species, Cdmin values were related to both preferred and near-maximum flow velocity used by the fish in nature. Explaining 61% of its variability, Cdmin was described using six morphological variables, which demonstrates the functional link between fish morphology and velocity use. For all studied species, a model explained 94% of drag variability using the Reynolds number of fish and three morphological variables. The link between morphology and drag force at given velocity conditions provides simple elements for modelling fish energetics in the context of physical habitat use. Moreover, the relationships between fish velocity use and their Cdmin open many applied perspectives, such as assessing the species abilities to withstand discharge modulations.

Within the framework of the Chilean molluscan shellfish safety program, blooms of Alexandrium were detected in several aquaculture sites in northern Chile. An outbreak of Alexandrium was detected in May 2006 in Mejillones Bay. Wild and cultured phytoplankton and shellfish samples from this bloom were analyzed by high performance liquid chromatography with fluorescent detection (HPLC-FD). Neither phytoplankton net tows samples nor an Alexandrium culture started from the bloom were found to contain PSP toxins at detectable levels. The shellfish, however, showed the presence of C2, GTX2, GTX3 and dcGTX2. Two new PSP episodes were recorded in June 2006 in Guanaqueros and Tongoy Bays. In these instances, shellfish samples from the two bays were analyzed by mouse bioassay and HPLC-FD, showing PSP toxicities that ranged from 27 to 34 $\mu $g STX eq 100 g−1 and a toxin profile mainly characterized by the presence of STX, GTX2 and GTX3. Differences between toxin profiles in Mejillones Bay and the two other locations suggest that, in the area, this kind of toxicity is probably produced by different regional populations or strains of the genus Alexandrium other than Alexandrium catenella, since the toxin profile and optimal environmental conditions for this species are noticeably different from those recorded in the proliferations from northern Chile. This paper therefore presents the first report of this kind of toxicity from an area between parallels 13°55'S and 33°5'S, comprising the subtropical zone of the southeastern Pacific Ocean. Results suggest that, as in the northern Pacific coastal area of America, PSP toxicity may be widely distributed on the southern Pacific coast.

The European eel (Anguilla anguilla) is drastically declining in all its distribution area and listed in the red list of the IUCN (International Union for Conservation of Nature). A rebuilding plan was adopted at European level in 2007, Regulation R(CE) 100/2007, to restore eel abundance to the level observed during the seventies. Its implementation started on the 1st of January 2009. This species is heavily threatened by numerous activities including fishing, and its management can only be effective through a systemic approach minimizing the whole range of human-induced impacts on the resource and its habitat. In the framework of the European interregional programme INTERREG IIIB-Atlantic Area– the INDICANG project aimed at elaborating abundance indicators of the European eel in the central part of its distribution area (http://www.ifremer/fr/indicang/). A methodological guide was elaborated by this project to define the indicators needed for this resource assessment. In this framework, Ifremer (Institut Français pour l'Exploitation de la Mer) and the UPPA University (Université de Pau et des Pays de l'Adour) have developed a method to estimate the daily and seasonal biomass of glass eels with the view to evaluate the fishery's impact on the estuarine eel recruitment to the Adour catchment. The estimation method uses observations from nightly scientific surveys to estimate glass eels' densities in the water column during various flood tides characterized by different hydrodynamic conditions. Information on these conditions allows the estimation of the glass eels biomass migrating during the night. From these estimates and reported catches made by the fishery during the same night, the exploitation rate applied by the fishery on the flow of glass eels progressing upstream during night flood tides is estimated. The relationship between the exploitation rate, fishery catches and hydrodynamic conditions allowed the estimation of the exploitation rate and nocturnal biomass fluctuations during the fishing season, from November 1st to March 31st of the following year. Finally, from the chronological series of biomass migrating at night, the total biomass migrating every day and the total recruitment into the estuary, during the main glass eel migration period, are estimated. Estimations made between 1998 and 2005 indicate that the overall rate of exploitation of the marine and continental fisheries, on average, is of 15.7%, ranging between 8 and 25% according to fishing seasons.

One method to assess fish stocks using a suite of indicators is the traffic light approach. In this approach, the time series of the different indicators are mapped on a common colour scale to highlight alerts that occur when indicators cross reference limit values. Until now, however, the procedure has lacked a statistical framework. Here, we propose the cumulative sum (CUSUM) monitoring scheme as a suitable statistical framework. CUSUM is a statistical process control method that detects deviations from a reference mean, according to defined performance criteria. With the CUSUM monitoring scheme, alarm signals can be triggered when indicators cross defined in-control limits that correspond to defined probabilities of false alarm and non-alarm (i.e., precision and power of the CUSUM monitoring scheme). A table of CUSUM out-of-control deviations is constructed to serve as a diagnostics table. In this table, the deviations in the different indicators are quantitative and given in similar units of variance, which facilitates their integrated assessment. The CUSUM out-of-control table also shows how deviations accumulate over time and thus provides a view of the stock history. The procedure was applied to the North Sea cod stock to illustrate how a fishery-independent integrated assessment can be achieved using a suite of indicators derived from research survey data. The indicators used were related to the spatial distribution, abundance, length structure, length at maturity and apparent mortality. The stock was found to be outside its reference limits from 2001 and has shown a continued degradation in status since this time.

In the context of the European Water Framework Directive, the in- and outflow water quality from 13 German trout farms, rearing mainly rainbow trout (Oncorhynchus mykiss) and using inflow rates between 0.03–0.80 m3 s−1, were monitored for point-source pollution. The farms had a significant effect on the effluent quality and macro-invertebrate fauna in adjacent streams (saprobic index based on species assemblage and abundance was 1.56–2.10 upstream of the farms but increased to 2.06–2.37 downstream of the farms). Inflow water quality, type of rearing unit, feeding intensity (amount of feed input in relation to water resources) and effluent treatment method could be used to predict effluent quality by 50 to 88% for most water characteristics. Based on these results, different effluent treatment options were monitored for their treatment performance. Concrete sedimentation basins 11 m × 7 m × 1.2 m and 5.5 m ×  3.3 m × 1.5 m (L × W × H), respectively, used for total farm effluent had little or no treatment effects. The micro-screen examined was relatively effective on particulate water components, measured as total phosphorous (TP), biochemical oxygen demand (BOD5), chemical oxygen demand (COD) and total suspended solids (TSS), resulting in treatment efficiencies of 29–53%, which is less than expected from data in the literature. The constructed wetland examined showed the highest treatment efficiency: more than 35% for TP, COD, BOD5, TSS and total ammonia nitrogen (TAN). From these results and data from the literature, treatment strategies for trout farm effluents can be developed, depending on the rearing system and production intensity.

The studies carried out on the Adour estuary on the migration of glass eels lead to the characterisation of their swimming behavior. Individuals migrate passively with the flood tide current behind the dynamic tide front, and their movements into the water column are linked to the surrounding luminosity and water turbidity. A numerical model was built from observations gathered on glass eel densities during scientific surveys. It uses the outputs of a hydrodynamic model accounting for the variations in the river flow and tide coefficient. It allows the simulation of the displacement of a particle in the longitudinal axis of the estuary. The variation of the vertical movements through the water column takes into account the cloud cover, the moon phases, the alternation of days and nights and the water turbidity. The results allow displaying the migration speed of groups of glass eels entering the Adour estuary. These simulations are validated by the comparison with in situ observations and the outputs of the behavioral model make possible, on the one hand, to simulate the migration speed of glass eels according to hydrological data and, on the other hand, to define the environmental conditions that stop or slow down their displacement into the estuary.

This paper presents a non invasive, rapid and reliable way to quantitatively assess fin erosion in sea bass (Dicentrarchuslabrax). The method is based on a visual assessment of fin profile and area loss of all fins except the anterior dorsal, on a scale from 0 to 4 in comparison with a perfect fin. The effects of stocking density (SD) and temperature on fin damage were investigated under experimental conditions (100–250 g fish). Over a 4-month period, mean erosion index (mean erosion level of all fins) was 10 times higher at 120 than at 20 kg m−3, where most fins were undamaged. Damage was also dependent on time and oxygen concentration (35% lower at 53% O2 saturation than at 105%). Fin condition was also affected by temperature: mean erosion index was 0.22–0.25 at 13–16 °C, but five times higher at 25  °C. Caudal and dorsal fins were always the most eroded. Fin damage was then monitored in a large land-based farm using high SD, and in a small sea cage farm operating at low SD. At the first site, 6 batches of two market size groups were examined: L (850–930 g, 50–80 kg m−3) and S (375–400 g, 42–60 kg m−3). Fin condition was good in all batches (mean erosion index, 1.1–1.3) and lowest at the highest SD. At the second site, four batches of large fish (350–890 g, 26–24 kg m−3) and four other groups below market size (100–270 g, 8–16 kg m−3) were examined. Fin erosion was the highest in large fish (mean erosion index, 1.1–1.2) and in the sea cages most exposed to climatic disturbances. In both sites, the most eroded fins were the caudal and dorsal. Differences in other external injuries were also observed between the two sites (less necrosis and more scale injuries in sea cages). The causes of fin damage are discussed in relation to metabolic and/or behavioral adaptations to rearing conditions and the main actions that could be taken to improve fin condition are discussed.