Little is known about the feeding habits of large free ranging fish, due in large part to lack of an appropriate technique for quantifying feeding variables. A previous study demonstrated that changes in gastric pH can be used as a proxy for feeding events in free-ranging sharks. Here we describe the development of a new acoustic pH transmitter to remotely measure gastric pH in sharks in the field. The transmitter consists of a dual sensor (pH and temperature) continuous pinger, and was tested in captive adult blacktip reef sharks (Carcharhinus melanopterus). The transmitter was retained in the shark's stomach for between 5–12 days. The empty stomach had a low pH (1.6 ± 0.2) and feeding induced a rapid increase in gastric pH, which was clearly distinguishable from baseline levels. Meal size showed a significant linear relationship with the magnitude of the pH changes. Measurement accuracy of the pH transmitter ranged from 0.05–0.9, although resolution of the VR100 receiver that decoded the transmitter signal was 0.1 units. The pH transmitter can be used to determine when free-ranging sharks in the field are feeding and hence quantify feeding chronology, frequency and daily ration.

Catch rates (kg hour−1) of horse mackerel (Trachurus trachurus), blue whiting (Micromesistius poutassou) and hake (Merluccius merluccius) from a series of 22 groundfish surveys conducted off Portugal between 1989 and 1999 were analysed using integrated logistic and gamma Generalized Linear Models (GLM). This methodology deals with the large amount of zeros in survey data matrices by modelling the probability of catch and the amount of positive catch separately, and then integrating the two sub-models into a single catch rate model of abundance. Among the explanatory variables included in the models, the geographic areas occupied by fish assemblages, i.e., groups of persistent co-occurring species, explained most of the variability observed for horse mackerel and blue whiting, while depth was the most important factor for hake. Because of hake's ubiquity on the Portuguese margin, models for this species were less parsimonious and explained a lower proportion of total variability compared with the other species. The abundance of horse mackerel is much higher in the winter and reduces with depth. Blue whiting and horse mackerel exhibited opposite trends in abundance from 1991 to 1994, with the latter species presenting a higher abundance throughout this period. No clear temporal trends of abundance were detected for hake. The effect of trawling hour in models suggested that horse mackerel and blue whiting exhibit vertical migrations, staying close to the bottom by day, when abundance is higher. The current approach proved to cope well with sparse catch data matrices and brought out novel information on the ecology of fish species in the Portuguese continental margin by successfully integrating environmental information into the analysis of fish abundance.

Milling behaviour is problematic when using hydroacoustics to estimate the number of migrating fish in rivers. Milling behaviour was observed for adult sockeye salmon migrating upstream in the Wannock River, to their spawning grounds in the tributaries of Owikeno Lake in the central coast area of British Columbia, Canada. We classified the acoustic salmon tracks to separate the milling fish from the actively migrating fish in an attempt to obtain an estimate of sockeye salmon flux as they migrate to their spawning grounds. We used discriminant function analysis and found that three variables measured on each track were sufficient for the classification of the acoustic tracks into milling and non-milling categories with an approximate classification accuracy of 98%. The method we present can also be used to separate tracks of targets of interest from noise or debris tracks that occur in the acoustic data, if discrete track characteristics are ascertained.

The aggregate backscattering cross-section, σag is the sum of backscattering cross-sections of all fish in a shoal. It is a basic acoustical parameter used for shoal description and biomass estimation. Simulations were undertaken for evaluating the impact of horizontal dimension, density, depth and beam width on measurements of σag for shoals with constant abundance. The important factor determining measurement bias is the ratio of shoal size expressed as along cross-section length relative to along ship beam width at mean shoal depth. The results show that 10 log10(σag) is underestimated by about 8 dB for a 5 m long shoal located at 200 m depth if detected by a 7° beam. A formula for correcting σag estimates for shoal sizes bigger than 1.3 times the beam width is proposed. The negative measurement bias can also be reduced by using transducers with narrower beam widths.

A year-long study in the Bay of Banyuls-sur-Mer (France) assessed the inputsfrom the local intermittent Baillaury River and the stimulationof nearshore phytoplankton blooms.During flash-floods, dissolved inorganic nitrogen, phosphateand dissolved organic carbon concentrations in the river were neither correlated to the river discharge nor to the season.Silicate was correlated to the river discharge.The particulate organic matter load was diluted in a mineral matrix (3–4%)but had a high nutritional quality at the beginning of the flash-flood. The offshore response to the single major flow event (October 2005) was monitored dailyduring two weeks at 350 m (8 m water depth) and 1.4 km from the river mouth (long-term monitoring station, 27 m water depth).The flash-flood signal was partly hidden at the shallowest site by swell resuspension of bottom sediments. At the deepest station, three phases were identified: (1) at the beginning of flow, river dissolved inputs dilute conservatively leading to increased dissolved inorganic nitrogen and silicate concentrations and decreased seawater salinity, (2) during the main turbid pulse, phosphateis released and (3) after the water column cleared,diatom photosynthesis occurred at 3 m below the water surface, leading seven days after the flow peak discharge to a high of 2 µgL−1 of chlorophyll a, which vanished three days later.The nutrients and salinity recovered their pre-flow values at that time.This dynamics of nutrients and chlorophyll during a flash-flood event is consistent with long-term monitoring data.

Tidal embayments in the Bay of Biscay (France) host nursery grounds where common sole, Solea solea, is the most abundant flatfish species. This study aimed to appraise the way those habitats function as nurseries through juvenile sole's responses in somatic growth and condition (Fulton's K) during their first year of occupancy. Field data, two yearly trawling series, taken monthly, were compared with a 6-month-long mesocosm experiment involving reared fish of the same wild origin. Growth rates were compared with predicted maximum growth according to an experimentally established model in relation to temperature. In the field, 0-group sole total length (TL) averaged 130 mm from September onwards in 1999 and 2000. Mean growth rates were 0.7–0.9 mm day−1 in summer and ≤ 0.1 mm day−1 in autumn, when the model predicted 1.4 and 0.9 mm day−1, respectively. In the mesocosm, the growth rates were 0.9 and 0.4 mm day−1 for the same seasons and for stocking densities (300 fish 1000 m−2) about 10 times higher than usually recorded in the field. Wild sole remained in medium condition (K ca. 1 g cm−3) during the entire growing season, whereas they attained a higher K after being released into the mesocosm (1.2–1.3 g cm−3). During the mesocosm experiment, growth was shown to be primarily temperature-controlled: fish reached 150–160 mm (TL) in November. From this investigation, it can be concluded that sole's responses in condition and growth are altered over the whole growing season on nursery grounds. The situation is exacerbated in autumn when the sum of abiotic constraints increases as the competitive biomass does. This indicates impairment of the nursery functioning which, in the context of fish habitat conservation, emphasises the particular vulnerability of embayments to the addition of any further constraint.

Gaps in our knowledge of basic fish ecology have provided impetus for development of novel “ecology tags” to detect and quantify hard to observe behaviors such as spawning, schooling and feeding. The acoustic environment is one source of potentially useful information about these behaviors. We implanted an acoustic recording tag (Bioacoustic Probe) into the gut cavity of a blacktip reef shark to determine whether an implanted tag could successfully record external and internal sounds. The tag successfully recorded reef fish vocalizations, boat engine noise, the sound of the shark feeding and unidentified rhythmic sounds that may derive from shark tail beats. Technical challenges remain, but sound recording tags have the potential to provide novel insights into shark and fish ecology.

We investigated the impact of an invasive species, Crepidula fornicataon the hydrodynamics and transport properties of the benthic boundary layer. We present results obtainedby three different approaches: 1) in-situ measurements of near-bottom current and suspended sediment concentration on two sites in the Bay of Brest (Brittany, France), 2) velocity measurements in controlled laboratory experiments of flows over a bed of artificial Crepidula shells, and 3) numerical simulations of the flow over two-dimensional shell-like bed forms.Numerical and laboratory experiments showed that both the bed erosion and the exchange velocitybetween the canopy and the outer flow decrease as the roughness density increases. These results suggest a sheltering effect by the Crepidula shells increasing with the surface density of shells. This trend was also found in field measurements: during spring tides, higher particle resuspension was observed on the muddy sand bottom with few chains of slipper limpets compared with the high-density area. However, other processes may explain these data; their importance is thus discussed in this study.

Traditional telemetry methods have been used to quantify the horizontal and vertical displacement of marine species, but are unable to identify specific physical activities such as swimming or gliding, resting, foraging, or spawning. We tested the utility of an acceleration data logger to quantify activity patterns of three captive whitetip reef sharks (Triaenodon obesus) in an enclosed lagoon using internal and external attachment methods. Data obtained using both attachment methods allowed swimming and resting behavior to be differentiated. All sharks showed constant swimming for 5–14 hours post-tagging before adopting a pattern of daytime rest and nocturnal activity throughout the 6–16 day deployments. Sharks showed a diel activity pattern, spending 10–24% of their time swimming during the day, and 42–67% swimming at night. Overall, sharks spent an average of 35 ± 11% (mean ± SD) of their time swimming. Mean tailbeat frequency was found to be 0.89 ± 0.03 beats s−1 in one shark for which it was measured. Respirometry experiments that measured the metabolic rate of two neonate whitetips showed significantly higher metabolic rates at night compared to the day. When taken in conjunction with the acceleration data, these results suggest that whitetips are nocturnally active and show diel circadian rhythms shortly after birth. Our study demonstrates that acceleration data loggers can be used to quantify activity patterns and offer promise for quantifying energy budgets of various reef sharks both in captivity and in the field.

Patterns of spatial and temporal variability of coastal fish assemblages were compared between areas subjected to different levels of protection at two different depths using a visual census technique. A no take reserve was compared with recreational fishing areas around a small Mediterranean island at 5 m and 20 m depth. Univariate and multivariate statistical techniques were used to test the hypothesis that protection could have different effects at different depths. A total of 56 species were identified during the survey. The most represented families were Sparidae and Labridae. Results showed an interaction between depth and levels of protection that was not persistent across the study period. This result was consistent for the whole fish assemblage and for the target species; most species showed higher abundance in protected areas at 20 m depth.

GAMEFISTO simulation model is presented as a tool to improve the small scale fisheries bioeconomic simulation techniques. The main novelty of the current model is the implementation of game theoretic techniques for forecasting the fishing effort trends and consequently, the fish population levels and the economic outcome, including landings, income and net profits. The model assigns individual fishing strategies to individual vessels according to their technical characteristics. The fishermen within a fishing fleet exploiting a single stock are assumed to be the decision agents, who share not only a fish population (modelled through stock externality) but also a market, through an offer-demand function (market externality). Mediterranean fisheries need to be analysed at vessel level due to the heterogeneity of its fishing fleets. A ten year simulation on red shrimp, Aristeus antennatus, is presented as an application of the presented GAMEFISTO model.

Automated acoustic receivers are now widely used by biologists to study the behavior of fish. However, currently available acoustic receivers require physical recovery of the units to download stored data. Such operation is often difficult in remote study areas like in the open ocean. We present a new satellite-linked acoustic receiver (Vemco VR3-Argos) that allows downloading data through a satellite uplink (Argos). The VR3-Argos can last up to one year, sending GPS positions and tag data at regular time intervals. We illustrate the advantages of this new technology with tagging data from 121 fish of seven species (yellowfin tuna, bigeye tuna, skipjack tuna, wahoo, dolphinfish, silky shark and oceanic triggerfish) caught and released around drifting fish aggregating devices (FADs) in the Western Indian Ocean, far from any land. In opposition with the classic acoustic receivers (Vemco VR2), the use of VR3-Argos allowed to collect data for several weeks after leaving the drifting FADs. Maximum residence times of 3 days for bigeye tuna, 7 days for skipjack, 8 days for wahoo, 10 days for silky shark and 15 days for yellowfin tuna, dolphinfish and oceanic triggerfish could be recorded. VR2 and VR3-Argos are equivalent in terms of quality of residence times data, however depth data obtained through satellites are aggregated in 8 classes for compression purposes, which leads to a loss of precision available with raw data. Future directions of this technology are discussed.

Decommissioning programmes have been used in many countries in an attempt to reduce the level of overexploitation in fisheries. The extent to which human capital enhancement may offset capacity reductions, however, has not been previously examined. The study uses a stochastic production frontier model to estimate the impact of differing skipper, vessel and technology characteristics on the productivity of a set of UK trawlers operating in the English Channel. The results suggest that productivity improvements resulting from increased education and training could exceed those from increased technological adoption. Increased investment in human capital enhancement could potentially offset, at least to some degree, the effects of decommissioning in the fishery. The study highlights an apparent oversight in fisheries policy analysis. Considerable attention is paid to the potential problem of technological creep and input substitution. However, enhancing human capital may have a greater impact on stocks than technological adoption in established fisheries.

We explored the relationships between diet and morphology in 30 fish species from forested tropical streams of the Bolivian Amazon. These species were first assigned to eight broad trophic guilds based on stomach contents analysis. The relationships between diet and morphology were then examined using Redundancy Analysis, after having checked for potential phylogenetical effects. Results show that, independently of any phylogenetic constraints, some of the trophic guilds could be grossly predicted from few relevant morphological attributes (i.e. relative intestinal length, standard length and mouth orientation) and thus suggest a significant link between diet and morphology. In other words, species having similar diet tend to converge to some extent on some morphological attributes. This link was nevertheless rather weak, suggesting that even if morphology may set limits to patterns of resource use, these limits are broad enough to allow fishes changing their choice of prey resources to respond to local biotic and/or abiotic conditions.

Among the potential biotic factors affecting population dynamics, parasitism has received relatively little attention. The purpose of this study was to inventory marine bivalve parasites and to investigate relations between different parasite communities. Five intertidal stations along the French Atlantic shore were studied between Brittany and Arcachon Bay. Two bivalves (the edible cockle, Cerastoderma edule, and the Manila clam, Ruditapes philippinarum) were sampled and examined. The parasites included a bacterium (Vibrio tapetis), a protozoan (Perkinsus sp.), and digenetic trematode metacercariae (10 species). Perkinsus sp. prevalence and density in clams were higher than those measured in cockles (30 250 vs. 36 cells g−1 of gill wet weight, respectively) while digeneans were more common in cockles (46 metacercariae per cockle host vs. 1 per clam host). Distributions of digeneans and Perkinsus sp. were similar along the Atlantic shore. However, at each sampling station and at the individual scale, no correlation between Perkinsus sp. and digenean abundance was detected. These results suggest different ecological niches used by these two parasites within a community of bivalves but a similar response to environmental factors such as temperature and salinity. Vibrio tapetis was found at relatively high prevalence in all stations for both bivalve species (from 17% to 43% in cockles and from 23% to 50% in clams), but was associated with a low prevalence of Brown Ring Disease (BRD), a shell disease caused by this pathogen. No statistically significant relationship of these parasitic bacteria with trematodes and Perkinsus sp. was evidenced in the present study.

The Cyprinidae is the largest freshwater fish family in Vietnam, with over 220 recognised species, many of which play an important role in aquaculture or are harvested from the wild. Despite numerous studies on the taxonomy of this family based on traditional morphological data, the relationships between major cyprinid groups is poorly understood and the taxonomic validity of a number of these groups is under debate. While an increasing number of molecular studies on cyprinid relationships have been conducted many have used restricted sampling and none have incorporated Vietnamese species. In this study, mitochondrial 16S rRNA, D-loop and cytochrome b gene sequences from 25 species of cyprinids collected from Vietnam were obtained and combined with sequences of cyprinids available in GenBank, in order to investigate the taxonomic validity of subfamilies within Cyprinidae and their phylogenetic relationships. The molecular data supported traditional division of the Cyprinidae into two major lineages: Cyprinines and Leuciscines. The placement of the Danioninae as the sister lineage to this grouping was not supported. Many of the subfamily boundaries were questioned and doubt was raised on some of the generic level classifications. The validity of species designation in Cyprinus, Tor and Cyclocheilichthys was also questioned. This study will need to be extended with greater taxon and gene sampling to further consolidate our understanding of cyprinid relationships and classification.

Among benthic organisms, bivalves are often used as bioindicators of environmental pollution because of their high bioaccumulation capacities for heavy metals leading to metallothioneins (MT) induction. MT are small cytosolic metal-binding proteins involved in metal homeostasis and detoxification in living organisms. These proteins can also be induced by a wide range of factors, such as hormones, physical stress, parasitism. MT quantification in relation to parasitism is rarely reported in literature, while parasites are omnipresent and have deleterious impacts on bivalves. Moreover, only a few number of MT genes have been characterized in molluscs. This study describes the partial sequence of the MT gene (Cemt1) in the edible cockle Cerastoderma edule. The cockle's MT cDNA was sequenced and showed over 80% homology to several other bivalve MT sequences. This sequence was then used to determine MT specific primers which can be used in quantitative real time PCR. MT protein and gene expression levels were quantified for individuals selected under different conditions: free from or infected by the digenean trematode Himasthla elongata, and under cadmium exposure at 15 µg Cd L−1. Results evidenced that MT concentrations were significantly increased by both treatments; parasite infection and Cd exposure. Moreover, congruent results between MT protein and gene expression levels were obtained.

We conducted displacement experiments using acoustic tags to study the orientation abilities of dolphinfish (Coryphaena hippurus) around FADs. Eleven fish were passively monitored using coded transmitters and acoustic receivers attached to FADs, while seven others were actively tracked with a vessel using continuous acoustic tags equipped with pressure sensors. All these 18 dolphinfish were captured close to a FAD and released between 70 and 1720 m from it. Five fish out of the 14 that were displaced at more than 360 m from a FAD (estimated detection range of our acoustic receivers, defining the target area during our experiment) returned to the target area. With one individual successfully returning to the target area after having been released at 1600 m from the FAD, the rate of return of fish released up to this distance was significantly higher than expected if they were moving at random, but many fish released at intermediate distances moved in other directions. Based on detailed statistical analysis of the return score, we estimated that dolphinfish are able to orientate towards a FAD area from at least 820 m. The connection between our definition of the target area and the association area of dolphinfish around a FAD is discussed, as well as the impact of stress and motivation in the rates of return observed. More experiments should be conducted to improve this first estimate. Specific experiments should also be designed to more accurately determine the association range of fish around FADs and their motivation to orientate towards FADs.

The development and application of genomics has been facilitated in a number of fields by the availability of new methodologies and tools, such as high throughput DNA sequencing and complementary DNA (cDNA) microarrays. Genomic tools are already used in research on commercially important fish and shellfish species. Thousands of expressed sequence tags (EST) are now available for some of these species, and the sequencing of complete genomes of tilapia, cod, salmonids, flatfishes, sea bass and Pacific oyster has been proposed. Microarray technology through simultaneous analysis of the expression of thousands of genes allows the identification of candidate genes involved in the function of multiple physiological, morphological and behavioural traits of interests in organisms and populations from different environments. This paper reviews the current development of genomic technologies, and pinpoints their potential beneficial applications as well as implications for fisheries management and aquaculture.