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.

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.

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.

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).

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 functioning of estuaries relies on a natural dynamism imposed on these systems by riverine and marine influences. The increasing abstraction of fresh water from both large and small river catchments in southern Africa has had the effect of forcing some estuaries into artificial cycles, i.e. natural successions now have human imposed trajectories that are changing estuarine variability and forcing some systems into extreme states. The ichthyofauna has responded to these changes in a variety of ways. Where river flow has declined considerably, or ceased altogether for extended periods, fish recruitment has shown a considerable decrease. This can be related to the collapse in planktonic productivity which negatively affects zooplanktivorous fishes, as well as decreased amounts of olfactory cues entering the sea for the attraction of larval and juvenile marine fishes into these estuaries. Hypersaline conditions can result in both a reduced species diversity and abundance. However, where estuaries lose their normal estuarine salinity gradient and become “arms” of the sea, there is often an increase in fish species diversity due to stenohaline marine taxa entering the estuary. Unfortunately the gain in small numbers of marine stragglers is insufficient to compensate for the decline in estuarine dependent fishes that usually dominate these systems. Conversely, major river flooding often causes temporary decreases in both species diversity and abundance due to a rapid decline in salinity, increased suspended sediments, reduced dissolved oxygen levels, and a collapse in the availability of pelagic and benthic food resources. However, the “resetting” of estuaries by episodic events is part of the essential cycle that maintains and enhances estuarine productivity and habitat diversity. Recovery by estuary associated fishes from such events is usually rapid and linked to a variety of factors, especially estuary morphometry which has a direct influence on the flushing or retention of estuarine biota. Freshwater flows interact directly and indirectly with the fishes that inhabit estuaries, e.g. river floods directly influence estuarine morphometry, water temperature, salinity, pH, turbidity, nutrient status, organic inputs, dissolved oxygen concentrations and olfactory cues; and indirectly affect mouth status, tidal prism, habitat diversity, primary and secondary productivity, fish recruitment, food availability and competition. Depletion or removal of components of river flow to an estuary have major short and long-term negative impacts on the ichthyofauna, some of which can be ameliorated by the provision of an environmental freshwater allocation that is appropriate to that particular system.

Determining the timing or frequency of movement of fish and the relative importance of different habitats is difficult. Advances in otolith chemical techniques and interpretations (including elemental ratios and stable isotopes) suggest that this is a powerful method for determining movement of fish. To date, the majority of applications have involved marine fish, however, otolith chemistry has the potential to determine movements of diadromous and freshwater fish; I therefore review freshwater applications of otolith chemistry in this paper. Despite some limitations regarding strontium:calcium (Sr:Ca) ratios (e.g. Sr concentration of the water is not always measured, Sr:Ca ratios in freshwater can exceed marine waters, and mixed results for the relationship between otolith Sr and salinity), they have been widely used for a variety of applications involving diadromous species and more recently freshwater fish. In addition, barium:calcium (Ba:Ca) ratios have recently been used to determine movements of diadromous and estuarine species, as ambient ratios are possibly linked to environmental flows. Several studies have also investigated the use of multielemental otolith composition to discriminate between groups of fish collected from different lake or river systems, but a wider range of applications are possible. Several applications of Sr isotopes have also been investigated, most of which is focused on salmonids (e.g. distinguishing fish from different river systems, determining movement history of individual fish). Relatively few studies have investigated the use of other isotopes (e.g. oxygen, sulphur) for determining movements. Otolith elemental ratios and stable isotopes have great potential to determine movements of freshwater species, with possible applications likely to increase as analytical technology improves.

Marine fisheries and the ecosystems that sustain them are increasingly beset by environmental deterioration, and the problem is particularly acute in coastal zones where human populations are increasing. In the best of circumstances, fishery managers are faced with the multiple, often conflicting, demands of resource users, politicians, and scientists when considering strategies for resource management. A further challenge is that management decisions must be made against a backdrop of a deteriorating environment and the shifting status of coastal ecosystem integrity. Traditional tools for single-species management may be inadequate in these settings. Furthermore, the necessary empirical data to appropriately parameterize models with vital rates representative of an altered environment are often lacking. Thus, we need approaches that better approximate the complicated dynamics between environmental conditions, fishery impacts, and multi-species interactions. Spatially-explicit, individual-based simulation modeling potentially permits this kind of integration, but it has seen limited use in marine resource management, especially with respect to benthic resources. My colleagues and I have used this approach, combined with targeted experimental work, to explore the impacts of nursery habitat deterioration, coastal freshwater management, and fishery activities on Caribbean spiny lobster populations and sponge community structure in the Florida Keys, Florida (USA). Although not applicable for all resource management situations, our experiences provide an example of the potential use of spatially-explicit, individual-based modeling and targeted empirical science in predicting resource conditions in a dynamic environment.

This research investigates a status assessment approach for remnant lake salmonin populations, using the lake charr (Salvelinus namaycush Walbaum) of Crean Lake (105 km2) as an example. A mark-recapture program was implemented employing small-mesh gill nets to ensnare charr by the teeth at spawning. Prior to sampling, potential spawning sites were designated primary or secondary based on habitat. Most charr were caught on three primary reefs, with some spawners moving between reefs. The spawning period peaked at day 2, enhancing spawning synchrony, and lasted up to 10 days. Results produced very low sampling mortality (5.7%), consistent estimates of the number of spawning charr ( $\sim $ 60 y−1) and a very low (<2000) estimate of the total number of mature charr in Crean Lake. The approach offers an effective means of assessing remnant salmonins with minimal impact on their populations.

The Australian freshwater crayfish, Cherax destructor is cultured commercially and has been translocated throughout much of Australia. Previous investigation on C. destructor using 16S rRNA sequences of samples collected from natural environments has revealed a significant phylogeographic structure in this species with three well supported geographically non-overlapping clades, namely ‘northern’ C. d. destructor, ‘southern’ C. d. destructor and C. d. albidus. Movement of individuals beyond their natural range of distribution may have adverse effects on genetic integrity of the species. In the present study, aspects of translocations of the species were genetically investigated. Sequences of the 16S rRNA gene region of the mitochondrial DNA (mtDNA) were obtained from samples collected in nine quasi-natural waterbodies, supplemented with sequences of samples obtained from 31 natural waterbodies examined in a previous study. Results of phylogeographic analysis provide evidence that certain haplotypes from major clades of C. destructor have been translocated. The findings of this study have important implications for the conservation and management of genetic diversity within C. destructor.