Despite the importance of the dredge fishery in Portugal, few studies have focused on bycatch and discard mortality. Catches from three types of dredge: north dredge (ND); grid dredge (GD); and traditional dredge (TD), currently used in the Spisula solida (Bivalvia: Mactridae) fishery, were compared in order to characterize bycatch and to estimate discard mortality. In TD and ND, the catch was retained in a net bag, whereas in the GD a metallic grid cage was used. Tows were carried out on sandy bottoms at depths ranging from 5 to 10 m. Bycatch differed significantly between dredges. The ratio of bycatch abundance to S. solida was 0.22:1 for ND, 0.10:1 for GD and 0.33:1 for TD. The weight ratio was 0.15:1, 0.14:1 and 0.32:1 for ND, GD and TD, respectively. Although a lower bycatch was observed for GD, higher mortality (ND: 10%; TD: 20%; GD: 36%) was estimated for this dredge. However, taking into consideration the fishing yields obtained for each dredge combined with the fact that this fishery is managed by daily quota per vessel, our results showed that, at daily quota level, discard mortality was lower when GD was used. Our study suggests that in output-controlled fisheries, there are obvious advantages in developing dredges with rigid retention structures, such as metallic grids, because these are more selective and efficient than dredges that use net bags. At species level, the bycatch mortality to attain quota varied among dredges. A “selective” and persisting significant removal of bycatch species from biota may change benthic community structure. Therefore, clam fisheries should apply exploitation strategies that are goal-oriented and adaptive to the evolution of the macrofauna communities, which might include the use of different dredge types, thereby diversifying the bycatch and consequently avoiding the cumulative removal of specific macrofauna taxa.

Wobbegongs are benthic sharks that are commercially targeted in New South Wales (NSW), Australia. Given a dramatic reduction of more than 50% in landed catch in a decade, there is a clear need to ensure that basic ecological data such as distribution and abundance are available for management use. Opportunistic sightings of wobbegongs collected by recreational scuba-divers were used to assess the distribution and relative abundance of wobbegongs in NSW. From July 2003 until January 2005, 304 dives were undertaken by recreational divers and 454 wobbegongs were reported. Larger numbers of wobbegongs were sighted in northern compared to southern NSW. Spotted and ornate wobbegongs were sighted in similar numbers, but species composition was highly variable across locations. Only a few juvenile and newborn spotted wobbegongs were sighted, whereas small ornate wobbegongs were mostly sighted north of central NSW. The latter were possibly the third, cryptic species, the dwarf ornate wobbegong. The paucity of sightings of small wobbegongs suggests that juveniles and newborns are inconspicuous to divers or that small wobbegongs are found in areas not visited by divers. Potential species and size segregation suggest that closing areas to fishing may enable populations to sustain current levels of commercial exploitation. The cost-effectiveness of using recreational scuba-divers to opportunistically collect distribution and relative abundance data was apparent from this study. However, the lack of spatial and temporal homogeneity in diving effort suggests that future studies should consider incorporating organized surveys and a facilitator, rather than using opportunistic records of sightings.

Implementing the Ecosystem Approach to Fisheries is a demanding exercise even though a more or less sophisticated approach might be adopted depending on the fishery or problem concerned and on the capacity available to deal with it. In France, DEMOSTEM, a programme of Ifremer was established to try to practically apply the EAF principles across the high diversity of situations existing in the country. The article summarizes very briefly the lessons learned through this programme implementation and some of the key findings and outcomes. In conclusion, it offers some perspectives on the whole process.

An empirical approach was used to determine the sample size of transects in acoustic surveys to estimate the abundance of three pelagic species in northern Chile. Relationships between the coefficient of variation of fish density and modified degree of coverage were established, where the modified degree of coverage is proportional to the distance sailed and the surface occupation index (Co) of the species and inversely related to the square root of the study area. From this relationship, an equation was obtained to estimate the number of transects required in order to obtain a predefined level of precision, given a known level of occupation. The surface occupation index corrects the degree of coverage and explains to a large degree the differences in the estimated coefficients of variation among the different species. Results showed that sample size declined with an increase in the surface occupation index of the species, and the magnitude of that reduction was appreciably greater for higher levels of precision. The number of transects must be limited to sample sizes with a minimum transect separation in order to assure independence between transect densities. The empirical procedure used for the estimation of the number of transects can be applied to other species situations if the information is available from previous surveys, since the approach only requires repeated echo integrator surveys.

A population of the invasive slipper limpet (Crepidula fornicata) has been spreading in the Bay of Mont-Saint-Michel (Western English Channel) for 40 years. Sidescan sonar, underwater video and quantitative sampling were conducted in 1996 and 2004 to document the widening geographic spread of the species over the bay. The limpet population grew by 50% during this period, to reach a fresh biomass of about 150 000 t. This local study analyses causes and effects of the spread and provides a typical example of the limpet spreading process. This population increase has significant effects on the environment in the most densely colonized area (modification to the sediment and biodiversity), leading to the emergence of a new benthic community. Anthropic dredging activities are among the causative factors of the spread but are also adversely affected by the invasion.

The use of genetic, biochemical and electronic markers in population biology and ecology has been growing tremendously during the last two decades. The first part of this paper aims at reviewing the main principles and advances of these individual markers through a few key applications on exploited marine fish populations. The second part is more prospective and investigates some possibilities that could arise in the near future through: (i) the development of new markers, (ii) the combination of different markers and (iii) the combination of quantitative approaches -whether classical or new- with individual markers. It is finally stressed how crucial individual markers will be to unravel the biocomplexity of wild fish populations and the key role they should play in the implementation of the ecosystem approach to fisheries.

Ecosystem assessments of fisheries based only on survey data will often have to use surveys that were designed historically for special purposes, e.g. for assessing abundances of two or three target species, or for tuning VPAs. An important question then is whether the previously collected data can provide informative time series of abundance indices and other state indicators for a wider range of target and non-target species. Some potential shortcomings of existing data series are treated in this paper leading to four questions which can guide the user to determine the suitability of an existing time series: did the survey cover the stock of each species adequately? Did survey catchability vary significantly between length or age classes? Did survey catchabilities vary significantly in space or time? Was the sampling effort sufficient? Simple methods for investigating these questions are proposed and illustrated with examples.

The mean or average value of a measure or indicator variable used to monitor a fish population can be defined in various ways, each with a correspondingly different statistical estimator for use in the context of a trawl survey. When, as is typical for many species, fish are heterogeneously clustered over space, then scooped in clusters from restricted localities using a trawl, these different estimators can produce different sample mean values with contrasting variations over time, possibly leading to different inferences about the fish population. Two mean parameters and their intuitive estimators, the mean “over fish”, and the mean “over stations”, are discussed and found to present contrasting statistical properties. A third estimator based on fitting a mixed model is proposed which has intermediate properties based on the within-haul correlation. The three estimators are applied illustratively to length data for cod caught in the North Sea by the English groundfish survey from 1992 to 2007. The time series of the mean over stations was smoothest, that for the mean over fish much more variable, and the mixed mean fell between in all years. Variance estimators derived from the fitted mixed model are also put forward. Estimates made from the example suggested that the mixed mean is most efficient. The type of estimator used for the mean should always be considered carefully and mentioned when reporting indicator studies.

The diel vertical migration of fish and larvae of the phantom midge Chaoborus flavicans was studied using a combined 38 and 200 kHz echo sounder. Multi-mesh gill net was used to sample fish, and a Schindler-Patalas trap to sample Chaoborus. Oxygen and temperature profiles were also recorded. At 38 kHz, only fish were detected, without considerable interference from Chaoborus echoes. At 200 kHz, both fish and Chaoborus were detected and echoes from Chaoborus almost completely masked all fish echoes at night. During the day, Chaoborus remained hidden in an oxygen-poor refuge near the bottom. Tracks of fish diving into the Chaoborus refuge were observed on several occasions. At the onset of dusk, Chaoborus started to rise and by the time it was dark they were occupying the whole water column. Fish were found in patches in midwater during the day. In the dark, the fish were dispersed throughout the water column. Results suggest that a dual-frequency approach can be used to discriminate between fish and Chaoborus and to provide a rapid method for their selective monitoring.

Strategies for biomass control are actively sought in response to proliferation of the introduced, suspension-feeding gastropod Crepidula fornicata along European coasts. Among these, dredging, crushing and on-site rejection may only be envisaged if the risk of further dissemination through the release of gametes and of excapsulated embryos/larvae is found to be nil or extremely low. This study evaluates such risk using three approaches: (1) determination of the periods of brood presence/absence, (2) external fertilizations of gametes obtained by gonad stripping, (3) cultures of mechanically-excapsulated embryos and larvae. A period of near- or total brood absence was observed between September 2006 and January 2007. The few zygotes (1.5% to 7.5%) obtained from external fertilizations did not proceed beyond the 4-cell stage. Excapsulated young embryos and mid-stages died in less than 4 days of culture. Despite their ability to swim, grow and feed, excapsulated veligers all died before metamorphosis. No juveniles were obtained from external fertilizations and excapsulated cultures, indicating that the release of crushed catches directly at sea could not present a dissemination risk from the standpoint of gamete or prematurely-excapsulated larval dispersal. Furthermore, by carrying out the crushing operations during the period of brood absence, the dissemination risk becomes nil. Negative ecological impact of such operations could be offset by attraction of motile predators, as yet unaccustomed to this introduced species, and their subsequent generalization to live slipper limpets and invasive feral Crassostrea gigas. At the very least, this biomass reduction approach would concentrate bottom habitat unavailability to restricted zones, freeing up the rest of the subtidal for other, formerly displaced species, as well as reducing the pressure on the trophic carrying capacity of affected habitats.

The ecosystem-based approach to fisheries management and, more specifically, the European Marine Strategy Framework Directive require the assessment of the state and dynamics of an ecosystem in order to determine suitable management strategies. This paper takes an analytical approach to assess the state of the Bay of Biscay ecosystem in the early 1990s, chosen as a period of reference because key monitoring data series have been collected since then. To assess the state of the ecosystem, the pressures exerted by six broad categories of human activities were examined. A literature review of the ecosystem components was made and a component tree was tailored according to data availability. Data rich components were subdivided into subcomponents for their assessment while data poor components were assessed at an aggregated level. The component tree of the ecosystem comprised six main branches, four of which further divided into sub-components. In total, assessments were carried out at the level of 19 components. For four of these (fished species, sensitive fish species, marine mammals and turtles) the overall assessments were made combining the status of individual species. Impact from human activities were categorised as (i) “widespread” over the whole Bay of Biscay or “local” and (ii) “possible” when they could be logically expected or “documented” when they were reported in the literature. Fishing appeared to be the only activity exerting widespread documented impacts on several ecosystem components. Terrestrial activities had some possible and documented widespread impacts. With the exception of marine transport impacting seabirds at the regional scale through oil pollution, other activities had only local impacts, mostly nearshore. The reference state in the early 1990s, suggests that continuation of monitoring of vertebrates as well as estuarine and coastal habitats must be central to the monitoring programme and management strategies to be set in the context of the Marine Strategy Framework Directive. Additional monitoring is also required for benthos, substrate and micro-organisms.

This paper reviews a selection of nine indicators for assessing the biological state of a fish population monitored only by using trawl surveys in which catchability is assumed constant from time to time and place to place. The intention is to inform or remind of the range of possibilities and of associated practical and statistical issues. The indicators, grouped according to relationships with abundance, length, age, weight, and reproduction, are documented in a standard format covering estimation, interpretability, sensitivity, considerations for reference points where possible, and an example of their application. Lastly, selected indicators together with year-class curves fitted to abundance indices-at-age are applied to the North Sea cod to demonstrate the feasibility of an assessment based on only one trawl survey. Results support findings of the International Council for the Exploration of the Sea (ICES) working group on the assessment of demersal stocks in the North Sea and Skagerrak.

This paper provides an overview of the progress Ifremer has made recently in fisheries acoustics and the study of small pelagic fish by: i) pushing observation frontiers using a range of platforms including an autonomous underwater vehicle, AUV, ii) developing measuring instruments and methods and iii) studying fish distributions. Presently, information from several frequencies of single-beam echosounders is routinely collected together with data from the ME70 multibeam echosounder. For onboard data acquisition control the HERMES software was developed. The new MOVIES 3D software includes modules for simultaneous realistic 3D visualisation and post-processing such as bottom detection, school extraction and calculation of descriptors and integration of all acoustic data. Several data analysis methods are being developed and some initial results are presented. Finally, results on the spatial distribution of small pelagic fish schools in the Bay of Biscay illustrate the role that acoustics can play, and are already playing, in the implementation of an ecosystem approach to fisheries.

A reliable anaesthesia and sampling protocol for Pacific oysters will enable experiments to be conducted without sacrificing animals and will facilitate successive sampling of individuals for gametogenesis studies. As no such techniques were available for Crassostrea gigas, the present study aimed to define suitable anaesthetic conditions for use with this species. Three groups of ten oysters (mean weight ± SD, 32.1 ± 9.0 g) were anaesthetised in 5 L containers. Among different chemicals: benzocaine, eugenol and three different types of magnesium chloride (a laboratory one – Flucka® – and two designed for agriculture – DEUSA International® and Dead Sea Works®) and concentrations tested, one laboratory (concentration: 72 g L−1) and one agricultural (Dead Sea Works® 50 g L−1) type of magnesium chloride were the most effective, respectively inducing anaesthesia in 73 ± 3% and 80 ± 3$% after three hours. Lower oyster weight and a two day period of starving prior to treatment significantly increased the number of anaesthetised animals. Using this protocol, losses of 0 to 10% of oysters were observed one week after anaesthesia. Increasing anaesthesia duration from 3 to 16 h resulted in a significant increase in the number of anaesthetised oysters (from 50 ± 10 to 97 ± 7%) but no increase in mortality (7 ± 11%). On the other hand, reducing water temperature from 19.5 °C to 15.3 °C, resulted in a significant decrease in anaesthesia efficacy. A reliable anaesthesia protocol was developed: 100% of Pacific oysters are anaesthetised using 50 g L−1MgCl2 Dead Sea Work®for a 16 h duration. This long duration facilitates tissue sampling and does not increase the working time needed. This protocol was validated by monthly anaesthesia and gonad sampling during a three month period with the loss of only a single oyster. It can thus be used for routine applications.

In many atolls of the South Pacific, a shift has occurred in the past couple of decades from traditional to more intensive fishing practices. Increasing fishing pressure on coral reefs raises the need for long-term studies to understand how fish communities react to fishing practice changes. The objective of this study was to analyse the variations of reef fish communities (in terms of species richness, diversity, density and structure) during a long time lapse at Tikehau atoll (Tuamotu archipelago, French Polynesia). The same eight lagoon pinnacles were sampled in 1987 and 2003 at 6 and 12 m depth. Quantitative data were collected by visual census techniques (UVC) on 50 m × 5 m belt transects. Analyses were conducted using a multiple spatial scale (depth, pinnacle and whole lagoon) approach with a particular attention on commercial species such as Scaridae (parrotfish), Acanthuridae (surgeonfish), Lutjanidae (snapper), Lethrinidae (emperor), Serranidae (grouper). Despite an increased sampling effort between 1987 and 2003, the mean species richness per transect decreased significantly from 26.2 ± 6.2 to 21.6 ± 9.6. The mean diversity varied similarly. A stronger decrease happened at pinnacles close to the village, where fish density also decreased. Conversely, fish density, species richness and diversity increased at pinnacles less visited by inhabitants. The community structure shifted from commercial species to small site-attached species e.g. Pomacentridae (damselfish), Ptereleotridae (dartfish) as fishing reduced the abundance (and biomass) of targeted stocks. We argue that these spatiotemporal variations resulted from a drastic change in fishing practices over the 16 years period, that shifted a sustainable fishery using traditional fish traps to an unbalanced, species-threatening, selective fishery. This study underlines the need for management and for the implementation of marine protected areas (including no-take zones) in order to protect the coral reef ecosystem and favor sustainable fisheries at Tikehau atoll.

This paper presents the spatial indicators used in the European project FISBOAT. These are statistics intended to capture spatial patterns of fish populations, using fish density data collected during scientific surveys. To handle diffuse population limits, indicators are designed not to depend on arbitrary delineation of the domain. They characterize the location (centre of gravity and spatial patches), occupation of space (inertia, isotropy, positive area, spreading area and equivalent area) and microstructure. Collocation between different populations is summarized by a global index of collocation. These spatial indicators have the potential to be used in a monitoring system to detect changes in spatial distribution. They could be helpful for relating the spatial distribution properties of fish stocks to their dynamics, their habitats, or to climate change.

The temperature evolution over the past 40 years in the Bay of Biscay (North-East Atlantic) is investigated from an in situ data analysis, completed with a satellite SST (Sea Surface Temperature) analysis over the last 20 years. The in situ dataset is an interannual version of the BoByClim climatology, covering the Bay of Biscay area with a 10-km horizontal resolution and a 5-m vertical step. The satellite dataset is the European COastral Sea Operational Observing and Forcast System Program (ECOOP) daily analysis, covering the IBIROOS (Iberian-Biscay-Irish Sea) area with a 4-km resolution. The study area (43°N-50°N/12°W-1°W) extends over the intersection of the domains covered by these two analyses. In the 0–200 m layer of this domain, a heat budget has been computed from an ocean circulation model over the period 1965-2004. Heat is essentially imported from the west by the North Atlantic Drift, then exported southward and northward, or transferred downward into deeper layers. The annual average of air-sea flux is weak, with a zero isoline crossing the domain from the northwest to the southeast. Ocean and atmosphere, forming a coupled system, have comparable contributions and may both result in a heat sink or source. At the interannual scale, variability is mainly controlled by the air-sea flux, with a secondary contribution from oceanic transport. A strong warming of $\sim $0.2 °C/decade for the period 1965-2004 is apparent from the surface down to the 200-m depth. The decadal evolution is consistent with several analyses over the North Atlantic. Meanwhile, warming is approximately twice faster than in the whole basin. This trend is not steady, as a cooling period occurred until the early 1970's, and the temperature increase has been significantly stronger during the last 20 years ($\sim $0.3 °C/decade between 0 and 100 m, from 1986 to 2005). The trend and the interannual variability are maximal over the northern part of the shelf. The typical duration of interannual anomalies is two years and their penetration depth is ~100 m, although they occasionally exceed 200 m. The interseasonal anomalies are also stronger within the mixed layer (root-mean-square, RMS = 0.6 °C at the surface) than below (RMS = 0.3 °C at 100 m). Their geographic distribution is radically different between the surface and the deep levels. A seasonal dependence of the warming rate is evident in the upper layer, as the temperature trend is stronger in summer than in winter (by a factor of 2 at the surface). Some of the potential implications for the ecosystem are discussed, particularly in terms of species distribution and dynamics of species exploited by fisheries.

A study of the reproductive biology of the loliginid squid, Alloteuthis subulata in the North Sea, Irish Sea and Portuguese waters was carried out. A predominance of small squid (<50 mm ML) during autumn was observed in all three areas. Multi-modal size-frequency distributions were apparent in both sexes. The greatest complexity was observed in Portuguese waters, with males exhibiting possibly four or more modal size classes. Sexually mature squid were found throughout the year, with generally more mature squid in spring-summer and fewer in autumn-winter. In Portuguese waters, maturity in both sexes peaked in spring, whereas maturity in the other areas peaked in summer. Similar sizes-at-maturity were observed, with male squid maturing over a greater size range (40–125 mm ML) than females (30–50 mm ML). An apparent secondary peak in male maturity at 65 mm ML suggests two different size-maturation patterns in Portuguese waters. Estimates of potential fecundity in the Irish Sea ranged from $\sim $2200–13 500 eggs per female. Mean egg diameters of 0.45 mm and 1.55 mm were recorded for developing oocytes and mature ova, respectively. Three to four modal size classes of oocytes were apparent in each ovary. There was some indication of latitudinal effects on growth, maturation and reproduction of A. subulata across its geographic range. The greater complexity of size-structure in warmer waters suggests that water temperature may be the main factor involved, possibly through shorter incubation times, faster growth and maturation rates and extended spawning periods.

In order to protect and sustainably manage fishery resource species, it is essential to understand their movements and habitat use. To detect the hypothesised migration of maturing veined squid Loligo forbesi from the west coast of Scotland (UK) to the North Sea and identify possible inshore-offshore movements, we analysed seasonal, spatial and environmental patterns in abundance and size distribution, based on commercial fishery landings data and trawl survey data from Scottish coastal waters (International Council for the Exploration of the Sea, ICES areas IVa, IVb and VIa). A geographic information system (GIS) was used to build monthly contour maps of abundance. Generalised additive mixed models (GAMM) were used to quantify patterns in size distribution and abundance. In most years, there was no evidence of movement from the West to the East coast of Scotland. Evidence of inshore-offshore movements during the life-cycle of the cohort that recruits in autumn (winter breeders) was found instead. The winter breeding cohort appears to spawn in inshore waters and some evidence suggests that the spawning grounds of the summer breeders are also inshore. Across seasons, higher abundance of L. forbesi can generally be found in the north of Scotland at intermediate water depths and in warmer waters.