The diversity of reef ecosystems, the multiplicity of reef resource uses and the breadth of the range of the island socio-cultural contexts concerned make coral reef fisheries (CRF) management in the South Pacific a complex task. The health and state of the targeted resources depend both on ecosystem characteristics (as determined by ecological and biological factors) and on fishing pressure, whose effects are only partly known. Increasing harvests from commercial and recreational fishing increasingly overlap with traditional subsistence activity, creating an important CRF management challenge. This paper presents a new approach to CRF assessment and monitoring by providing a set of multidisciplinary indicators. The fisheries system is assessed from three different viewpoints: ecology of targeted populations, exploitation and the broader socio-economic fishery context. The use of complementary indicators chosen from each of these fields could balance the chronic lack of human and financial resources for the management of these fisheries. We suggest the use of these indicators through an assessment grid or an indicator dashboard specifically adapted to given situations and management objectives determined through a participatory approach. The operational efficiency of this dashboard depends on i) dialogue between users, ii) the objectivity of the proposed monitoring, iii) the visual transcription of divergent/convergent interests amongst stakeholders, and iv) stakeholder involvement in the decision-making process. The use and constraints of such a tool are described with reference to Ouvea atoll (New-Caledonia, South Pacific) for which an analysis of available indicators for assessing fisheries status is presented.

The Korean fishing industry is currently subject to overexploited resources arising from excessive levels of fishing effort. Measures to reduce effort in the industry have been instigated. However, for the mixed gear, multi-species inshore fleet, determining the appropriate level of effort is problematic. This is made more difficult through limited catch and effort data. In this paper, a simple surplus production bioeconomic model for the flounder fishery is developed based on different effort standardisation approaches to estimate the optimal level of effort in the fishery. The model is based on a subset of catch and effort data, and implications of this for the assessment of global effort levels are considered. The results indicate that even with poor information, relatively robust estimates of necessary reductions in fishing effort can be derived.

A simulation model is developed to analyse the variability of production functions in an exploited virtual ecosystem. We assume that a complex food web can be represented by a set of trophic components interacting through predation. Each component has a set of recruitment, growth, and survival models, a catch level and trophic preference function. Prey are consumed according to their abundance and predators' trophic preference functions are estimated in a pristine system. A parameter for the food consumption per unit biomass describes foraging for each trophic component. The FishBase database is used to parameterise some of the major processes in a generic model. A commercial fishery targets mostly high trophic levels through a set selectivity function. Some key ecosystem features are assessed in simulations: the intensity of top-down and of bottom-up controls, and the degree of trophic opportunism. Top-down control is the regulation of lower food-web components by one or several upper-levels predators. Bottom-up control is the regulation of trophic components by their prey. Results show that biological production functions are highly dependent on predation parameters and vary differently according to trophic level. Fishing activity modifies the biomass distribution between components and strongly affects higher trophic levels more sensitive to exploitation. Trophic dynamics within the system are altered through the rates of predation mortality. In systems where predation mortality is high, top-down control dominates and fishing affects all food web components. These “fishing-controlled” systems display compensatory mechanisms through a released predation control. We also show that systems where productivity is dependent on prey abundance are more “environment-controlled” and seem more sensitive to overexploitation, particularly the higher trophic levels. Trophic opportunism tends to dampen the propagation of top-down or bottom-up controls through the food web and thus stabilizes the ecosystem. Trophic relationships are therefore essential ecosystems characteristics that determine production and response to exploitation. Their routine analysis is a key part of the ecosystem approach.

This article aims to review 1) the major and most frequent human-induced physical disturbances and their consequences on coral reef habitats using a multi-scale approach, and 2) the scale-related indicators and conceptual aspects used to detect and measure the effects of these physical impacts. By physical disturbances, we mean direct perturbations that lead to the destruction/erosion of the carbonate framework. Human-induced direct physical disturbances are numerous from coastal development, tourism, harvesting, accidents and nuclear/weapon testing. Since methods for monitoring and measuring indicators are generally scale-implicit, coral reefs are first presented according to different ecological-spatial scales of organization, from colony to region (colony, reefscape, reef zone, whole reef, island and region). In this way, it is easier to link a couple {habitat, disturbance} to their potential indicators and to the descriptors they target. Three classes of descriptors, related to the response of the living component of coral reef ecosystem, are considered here: stony coral, reef fishes and the human uses. A synthesis of the different options for coral habitat assessments is proposed. We sort them according to their objectives (monitor, initial status or improvement of knowledge), their specificities (identification or not of a specific disturbances) and their scale of investigation (small, meso- or large scales). Usually, the majority of the indicators of human-induced disturbances are non-specific. They reveal that something is happening but not the actual causality and can only detect differences across time or space. A major weakness lies in the difficulty in deconvoluting the signals from a conjunction of stressors occurring at different scales. As such, a hierarchical concept of disturbances in coral reefs would be the next logical step to enhance our capabilities in monitoring and forecasting coral reefs status.

The present paper aims at identifying and assessing indicators of the effects of Marine Protected Areas (MPAs) in coral reef regions, based on a bibliography review in ecology, economics and social sciences. First the various effects studied within each of these domains and the variables used to measure them were censused. Potential ecological indicators were assessed through their link with the question used (here termed “relevance”) and their “effectiveness” which encompasses the issues of precision, accuracy and statistical power. Relevance and effectiveness were respectively measured by the frequency of use of each indicator and the proportion of significant results in the reviewed articles. For social and economic effects, the approach was not possible due to the low number of references; we thus discussed the issue of finding appropriate indicators for those fields. Results indicate: 1- the unbalance in literature between disciplines; 2- the need for protocols and methodologies which include controls in order to assess MPA effects; 3- an important proportion of ecological indicators with low effectiveness; 4- the large number of ecological effects still not studied or not demonstrated at present.

The loliginid squid Loligo forbesi has a flexible life-cycle, involving variable size and age at maturity, presence of summer and winter breeding populations, and extended periods of breeding and recruitment. This paper reviews life history data collected since 1983 from the commercial fishery in Scottish (UK) waters, alongside fishery data collected since 1970, and examines (a) the relationship between body size and timing of maturation, (b) evidence for shifts in the relative abundance of the summer and winter breeding populations, and (c) the possible role of environmental signals in determining the timing of breeding. Evidence from fishery data suggests that, since the 1970s, the summer breeding population has declined while the winter breeding population now dominates and breeds later than was previously the case. Length-weight relationships and size at maturity showed significant inter-annual and seasonal variation during the period 1983-2001. Males are shown to decline in relative weight as they mature while females increase in relative weight; possible interpretations are discussed. High autumn/winter temperatures (high winter NAO values) were associated with high squid abundance and precocious maturation and tended to favour high abundance in the following year, along with increased body weight at length and a decrease in the proportion of animals breeding in December. High abundance in summer, conversely, leads to a fall of body weight at length in the following year. Thus there may be alternation of precocious and slow maturation, and/or summer and winter breeding, driven by a combination of environmental conditions and intraspecific competition.

Face to the increasing anthropogenic disturbances that affect coral reef ecosystems, it becomes urgent to define appropriate ecological indicators for monitoring purposes. One useful approach is to search for a simplified description of the structure of biological communities that are highly diverse and complex on coral reefs. To this end, we propose to represent the trophic structure of coral reef fish assemblages by using fractional trophic levels assigned to each fish species. Fish abundance trophic spectra (i.e., the distributions of fish abundance per trophic level) were established for the fringing reefs of two bays located in the city of Nouméa (New Caledonia). The comparison of these trophic spectra revealed a similar trophic structure in the two bays, in spite of contrasted levels of fish abundance due to habitat damages. The embayment degree was characterized by changes in the fish trophic structure, reflecting a decreasing influence of urban and industrial wastes discharged in the bottom of the bays. This case of study shows the interest of using fractional trophic levels for the description of highly diverse biological communities. The trophic level-based approach offers new prospects in the search for ecological indicators, by characterizing the structure of biological communities by trophic signatures which testify to the disturbance level affecting their environment.

A total of 212 carnivorous coastal fish species from New Caledonia, represented by 7335 individuals, were analysed for their diet. Fifty two prey items were identified and later grouped into broader taxonomic categories refered as “prey types”. For each fish species 6 biological traits were defined: maximum adult size, major biotope, schooling behaviour, home range, nycthemeral behaviour, degree of crypticity. A general linear model was fit to the diet data taking into account these traits, and depth of capture and fish family. This model was applied to the average number of prey types/stomach and to the volume of 5 prey types: nekton, crustaceans, molluscs, echinoderms, worms. A second analysis was performed on the effect of observed size on diet composition, taking into account these traits and taxonomy. This analysis was restricted to species with at least five individuals, representing 113 species from 33 families. More detailed information is given for the three major families, Serranidae, Lutjanidae and Lethrinidae and intra-family variations are illustrated for Lethrinidae. All the factors tested had significant effects on diet, fish size and taxonomy being the two major factors. The five prey types analysed in detail displayed marked differences according to the factors studied. In particular nekton increased in importance with fish size, whereas crustaceans decreased and molluscs presented a dome shaped relationship. Nekton and crustaceans made the bulk of the diet of most species, with molluscs being at times important. Echinoderms and worms were never a major food item and were eaten only by a restricted range of species.

Despite many previous studies on the life history of the squid Loligo forbesi, the roles of internal and external factors in growth and maturation have not previously been investigated in detail. The present study takes advantage of the availability of statistical techniques, namely generalised additive models, which permit simultaneous evaluation of the effects of multiple explanatory variables while avoiding the need to assume linear relationships. This has the further advantage that the size of body parts can be entered directly into the models rather than expressed as indices (e.g., gonado-somatic index). The present analysis is based on measurements taken from monthly market samples during 1989-1991 and aims to infer patterns of reproductive and somatic investment though comparison of large numbers of individuals at different (post recruit) life-cycle stages. Results indicate that, once the effect of body size is removed, gonad weight in both sexes is affected by month and digestive gland weight, consistent with seasonal triggering of maturation, and with energy for gonad growth being derived from food. There is also evidence of a negative relationship between somatic and ovary growth in females, possibly indicating remobilisation of somatic tissue to grow the ovary. In males, relationships between variables tended to have more complex forms, probably related to the existence of two or more growth patterns leading to different sizes at maturity. As found in previous work, maturation begins around 1-2 months earlier in males, suggesting that sensitivity to external triggers is controlled by a sex-dependent internal factor.

Coral reefs in French Polynesia, just like many others throughout the world, have been subjected to several natural disturbances including 15 cyclones, seven major bleaching events, and several Acanthaster planci outbreaks since the 1980s. In order to document the effects of these perturbations on coral assemblages, we initiated a long-term monitoring program that extended over both local and regional scales. Coral cover was quantified at 20 sites situated on the outer reef slope of 13 islands. The results from the first decade (1992-2002) are analyzed and the adequacy of our approach is discussed in the context of identifying potential indicators of coral reef health. Among 13 islands in French Polynesia, only two were unaffected by natural disturbances. We found important local and regional variation in the impacts of coral bleaching and cyclones, and three major temporal trends were distinguished: 1) 10 sites where coral cover decreased in relation to the occurrence of major disturbances; 2) nine sites where coral cover increased, despite the occurrence of disturbances affecting seven of them; and 3) a site where no significant variation in coral cover was found. The responses to perturbations were different among coral genera: Acropora species were particularly susceptible to bleaching events, whereas physical damages induced by cyclones concerned mainly branching species of Acropora and Pocillopora. Thus, monitoring surveys could be improved by selecting different and complementary indicators (one on the variation in diversity, one estimating changes in the abundance/cover, and one estimating the potential for recovery), by integrating several spatial scales, and by including at least the most informative species. High frequency recordings of environmental parameters (e.g. sea surface temperature) may be also a complementary tools for identifying causal relationships between changes in coral reef community structure and the factors causing the changes.

The effect of providing algal food to female Crassostrea gigas broodstock sampled at a favourable time of year was investigated using pre-defined indices of oocyte quality and subsequent larval and post-larval performances. Broodstock were collected in the Aber Benoît estuary (Brittany, France) at the end of April 2002 and were divided into two groups, a starved control (S, 1 µm – filtered seawater) and a fed group (F, ad libidum algal mixture of Isochrysisgalbana clone T-Iso and Chaetoceros calcitrans), maintained under these conditions for six weeks prior to fertilizations. For each conditioning type, two batches of larvae and post-larvae were reared from two identified females. Quality criteria were defined in terms of predictors (oocyte lipid contents, mature oocyte diameters, ovarian maturity and presence/absence of atresia) and validators (larval growth, algal consumption and time to settlement, and post-larval growth). Each female was considered as a treatment, and parametric and non-parametric ANOVAs were performed, where appropriate, on predictors and validators between each treatment. In both conditions, a surplus of oocytes was produced, in relation to expected market conditions. No effect of the conditioning treatment was detected either on oocyte quality predictors or on subsequent validators. It is likely that winter reserve accumulation is more important than trophic conditioning for successful gametogenesis in the productive Aber Benoît environment. Given the considerable cost of abundant feeding during the conditioning of broodstock collected at the end of winter and destined for gamete stripping (the prevalent practice in France), we suggest that feeding be minimal or suppressed altogether when the condition index is favourable.

Field studies describe echinoplutei not only as grazers but also as prey of naturally occurring fish and shellfish larvae. This finding suggests their potential as live feed in aquaculture. This paper reports on consistent spawnings of the captive sea urchin Paracentrotus lividus (Lamarck 1816) (Echinodermata: Echinoidea) throughout the year using diets of plant origin (yellow maize and/or dried seaweed) with fixed environmental conditions equivalent to field conditions during late spring (14 h of daily illumination and 18 °C of temperature). Broodstock maturation without unwanted spontaneous spawnings was achieved in two ways: extending the natural season of reproduction and inducing out-of-season wild specimens to mature. Controlled spawnings of captive sea urchins were induced every month of the year by KCl 0.5 M injections. The diet maize/seaweed combination gave the best results (79% of the tested urchins) in terms of consistent large spawnings throughout the year, followed by the pure maize diet (50%) and the pure seaweed diet (36%). When out-of-season wild sea urchins were induced to maturation, the majority (72%) of tested individuals required at least 60 days to spawn under KCl injection when fed the combination diet. The results demonstrate the feasibility of producing larval P. lividus in that high numbers of fertilized eggs (up to 5 million per female) can be obtained year round. The main limitation of exploiting P. lividus as planktonic feed seems to be the mortality of broodstock after injection with 1 ml KCl 0.5 M, which prevents reutilization. The 1-month post-injection survival rate was 30 ± 8% (mean ± SE). All surviving sea urchins spawned again after re-injection 1 month later, with a 1-month survival rate of 29%.

This review presents environmental and biological indicators of the impact of three major categories of inputs in coral reef lagoons i.e. particles, nutrients and metals. Information was synthesized to extract well established indicators together with some interesting new concepts currently under development, and to provide the reader with an assessment of their respective advantages and drawbacks. The paper has been organized according to the capacity of three categories of indicators to respond either in a specific or a non specific way to a given source of input. The first section focuses on abiotic indicators which main interest is to respond instantaneously and in a truly specific way to a given source of input. The second and third sections present informations on bioindicators either at the sub-individual level or at the individual to community level, indicator specificity generally decreasing as a direct function of biological or ecological complexity. This review showed that even though significant work has already been done on coral reef ecosystems, much more scientific studies are still needed to answer the growing local demands for simple and truly validated tools to be used in environmental surveys. It is further stressed that, due to the biological and environmental diversity of coral reef lagoons, a preliminary step of on-site validation must be considered as an absolute prerequisite when indicators are planned to be used in the frame of a local environmental monitoring programme.

Recruitment variability is commonly attributed to variation in spawning stock size and environmental variability. Here, the abundance of Loligo forbesi in the English Channel was estimated using cohort analysis. Environmental and adult biomass effects on recruitment variation were then tested. A stochastic length-age key was included in the cohort analysis, considering inter-individual variability in age at length. The number of recruits and parental stock biomass per monthly age-class were computed for a series of 13 fishing seasons (1989-2002). Recruitment was examined in relation to adult biomass and environmental parameters (sea surface temperature, SST, and the North Atlantic Oscillation, NAO) at the time of hatching. Recruits were approximately 7 months old and recruitment for each annual cohort occurred between April and August. Squid bigger than the length at maturity were assumed to be spawners. In the spawning season (September December), spawners were 11–13 months old. Parametric stock-recruitment curves (Ricker, Beverton and Holt, Shepherd, etc.) fitted poorly, while SST was negatively correlated with recruitment in a simple linear model. Recruitment was unrelated to NAO. A model combining SST and adult biomass showed that recruitment is probably density-dependent when stock size is high, and negatively correlated with temperature. The study did not indicate obvious recruitment overfishing in the English Channel L. forbesi population.

Because of natural complexity, field studies are often inconclusive with regards to the ultimate cause of a given change observed in wild animal populations. As a consequence, there is scope to develop an Experimental Ecology Approach (EEA). In this paper, we favour the use of experimental ecology studies to evaluate the effects of environmental factors on fish biology. We identify the advantages of EEA: disentangling the effects of several factors and identifying their respective roles, generating artificial scenarios and increasing our capability to collect and analyse data. This study emphasises the constraints of this approach: fish biological performances may be altered by rearing conditions, by domestication and by the prevention of some behaviours. It also considers the extrapolation of experimental results with regard to the sea including the realism of experimental design and the constraints of scaling or extending the results to larger scales. We also propose some experimental ecosystems which are well adapted to the requirements of EEA and a careful selection of fish species which fit this approach very well. Atlantic Cod (Gadus morhua) is identified as a good candidate for experimental studies and we present examples of the contribution of EEA to the description and quantification of the effects of environmental factors in this species. We conclude by highlighting the respective contribution of field studies (describing a situation in the wild and suggesting some possible causes) and EEA (allowing an active investigation of phenomena and identifying their final causes).

Habitat utilisation by juveniles of 13 commercially important fish species was studied in five habitats located in Chwaka Bay, Zanzibar: mangrove creeks, mangrove channel, sand/mud flats, a seagrass area close to mangroves, and a seagrass area far from mangroves. Fish samples were collected from each habitat using a seine net, and fish abundance and size were measured to determine habitat utilisation. The seagrass beds near to mangroves showed the most diverse fish assemblage of all habitats, possibly because it functions as a corridor between the mangroves and deeper parts of the embayment. Juveniles of Cheilio inermis, Hipposcarus harid,Leptoscarus vaigiensis, and Scolopsis ghanam inhabited seagrass beds only. Juveniles of Gerres filamentosus and Monodactylus argenteus were mainly found in the mangrove habitats. Lethrinus variegatus, Pelates quadrilineatus and Siganus sutor were found in more than two habitats, with highest abundances in seagrass beds. Juveniles of Gerres oyena, Lethrinus lentjan, Lutjanus fulviflamma and Sphyraena barracuda were the most generalist species and were found in all studied embayment habitats. Visual census surveys supported the seine net data showing that most fishes in the embayment habitats were juveniles or sub-adults. In terms of habitat utilisation by different size classes, five of the 13 species (Lethrinus lentjan, L. variegatus, P. quadrilineatus, Siganus sutor and Sphyraena barracuda) were found as small-sized individuals in shallow and turbid mangrove areas, whereas large-sized individuals were observed in deeper and less turbid seagrass beds. A possible explanation for this pattern could be an ontogenetic shift in habitat utilisation, although this could not be proven. The patterns observed in the present study show a high similarity to those observed in marine embayments in the Caribbean, indicating that similar mechanisms are at work which make these systems attractive juvenile habitats.

The terms ‘ecosystem-based fisheries management’, ‘ecosystem-based management’ and ‘ecosystem approach to fisheries’ have recently entered the vernacular of fisheries management. Examination of contemporary guidelines and proposals for such an approach illustrates that ecosystem-based fisheries management is, for all intents and purposes, a re-expression of the objectives and processes associated with ecologically sustainable development (and associated international instruments). Since the early 1990's, all levels of government in Australia have committed themselves to the concept of ecologically sustainable development, and a complex network of policies and laws exist to support this, particularly in natural resource management. One significant outcome of these instruments is the application of environmental impact assessment to the management of fisheries. This has forced extensive deliberation of the ecological impact of fisheries and stimulated the development and application of new research tools. Application of environmental impact assessment to the management of fisheries has been a crucial step for the implementation of ecosystem-based fisheries management in Australia. These assessments are embedded within a range of legal and policy instruments that capture the ecological, economic and social dimensions of fisheries. The scientific challenges associated with many aspects of ecosystem-based fisheries management are very significant, but it is likely that the value-based nature of the underlying environmental issues will continue to dominate the managerial agenda.

The Argentine shortfin squid (Illex argentinus) is a common neritic species occurring in waters off Brazil, Uruguay, Argentina, and the Falkland/Malvinas Islands in the southwest Atlantic. Illex argentinus is the most important fished cephalopod species in the area and plays a significant role in the ecosystem. It is object of major fisheries using both trawlers (mostly from European countries) and jigging vessels (mainly from Asian countries) and estimated total annual average catch for the last 15 years (1988-2003) is about 700 000 tons. The present paper aims to develop predictive models of squid abundance in relation to physical and environmental conditions, models that could ultimately be applied to fishery forecasting. Fishery and biological data collected by scientific observers aboard commercial trawlers between 1988 and 2003 were analysed in relation to physical and environmental factors to establish the spatio-temporal pattern of the species' distribution and quantify the influence of environmental variables (e.g. SST, depth) on local abundance. The data included 26 168 fishing haul records, of which 11 103 were positive for Illex. CPUE (Catch Per Unit Effort, kg h−1) was used as abundance index. The analyses were based on time-series maps created using Geographical Information Systems (GIS). GIS maps showed that highest CPUE values were recorded during the first four months of the year (the Austral summer-autumn), with peak values higher than 5000 kg h−1 mainly located within 42° S, 46° S and MN (North part of Malvinas/Falkland) areas. Generalised additive models (GAMs) were used to describe variation in Illex argentinus abundance in relation to geographical and environmental variables. The presence/absence (PA) of Illex and its abundance (CPUE) in areas of presence were modelled separately. Predictors retained in the optimal models included SST, latitude, longitude, month, average fishing depth and year. Both models suggest a clear seasonal effect: maximum catchability was found during March (PA model) and the maximum abundances were found during the first quarter of the year (CPUE model). GAM models also demonstrated that higher catches and maturity of squid were related, in general terms, to warmer and deeper water.

Allozyme and Random Amplified Polymorphic DNA (RAPD) variation was surveyed in the freshwater crayfish Cherax destructor Clark, an ecologically and commercially important species that is widespread throughout the freshwater systems of central Australia. At the intra-population level, allozymes revealed a similar level of variation to that found in other freshwater crayfish; RAPDs showed less diversity than allozymes, which was unexpected. At the inter-population level, both techniques revealed significant population structure, both within and between drainages. RAPD results were consistent with phylogeographic patterns previously identified using mtDNA. Although allozyme data showed little geographic pattern in relation to genetic variation based on multidimensional-scaling (MDS) plots on matrices of genetic distance, results of AMOVA and Mantel tests indicated significant population structuring. Each of the mtDNA lineages proposed in a previous study also showed significant genetic structure at similar levels as revealed by RAPDs but different levels by allozymes. These results reject hypotheses previously put forward on genetic homogenisation within the species due to wide-scale translocation. The implications of the findings for conservation and aquaculture of C. destructor are also discussed.