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© 2016 Macmillan Publishers Limited, part of Springer Nature. All rights reserved. Ongoing declines in the structure and function of the world's coral reefs require novel approaches to sustain these ecosystems and the millions of people who depend on them. A presently unexplored approach that draws on theory and practice in human health and rural development is to systematically identify and learn from the 'outliers' - places where ecosystems are substantially better ('bright spots') or worse ('dark spots') than expected, given the environmental conditions and socioeconomic drivers they are exposed to. Here we compile data from more than 2,500 reefs worldwide and develop a Bayesian hierarchical model to generate expectations of how standing stocks of reef fish biomass are related to 18 socioeconomic drivers and environmental conditions. We identify 15 bright spots and 35 dark spots among our global survey of coral reefs, defined as sites that have biomass levels more than two standard deviations from expectations. Importantly, bright spots are not simply comprised of remote areas with low fishing pressure; they include localities where human populations and use of ecosystem resources is high, potentially providing insights into how communities have successfully confronted strong drivers of change. Conversely, dark spots are not necessarily the sites with the lowest absolute biomass and even include some remote, uninhabited locations often considered near pristine. We surveyed local experts about social, institutional, and environmental conditions at these sites to reveal that bright spots are characterized by strong sociocultural institutions such as customary taboos and marine tenure, high levels of local engagement in management, high dependence on marine resources, and beneficial environmental conditions such as deep-water refuges. Alternatively, dark spots are characterized by intensive capture and storage technology and a recent history of environmental shocks. Our results suggest that investments in strengthening fisheries governance, particularly aspects such as participation and property rights, could facilitate innovative conservation actions that help communities defy expectations of global reef degradation.

Ocean warming under climate change threatens coral reefs directly, through fatal heat stress to corals and indirectly, by boosting the energy of cyclones that cause coral destruction and loss of associated organisms. Although cyclone frequency is unlikely to rise, cyclone intensity is predicted to increase globally, causing more frequent occurrences of the most destructive cyclones with potentially severe consequences for coral reef ecosystems. While increasing heat stress is considered a pervasive risk to coral reefs, quantitative estimates of threats from cyclone intensification are lacking due to limited data on cyclone impacts to inform projections. Here, using extensive data from Australia's Great Barrier Reef (GBR), we show that increases in cyclone intensity predicted for this century are sufficient to greatly accelerate coral reef degradation. Coral losses on the outer GBR were small, localized and offset by gains on undisturbed reefs for more than a decade, despite numerous cyclones and periods of record heat stress, until three unusually intense cyclones over 5 years drove coral cover to record lows over >1500 km. Ecological damage was particularly severe in the central-southern region where 68% of coral cover was destroyed over >1000 km, forcing record declines in the species richness and abundance of associated fish communities, with many local extirpations. Four years later, recovery of average coral cover was relatively slow and there were further declines in fish species richness and abundance. Slow recovery of community diversity appears likely from such a degraded starting point. Highly unusual characteristics of two of the cyclones, aside from high intensity, inflated the extent of severe ecological damage that would more typically have occurred over 100s of km. Modelling published predictions of future cyclone activity, the likelihood of more intense cyclones within time frames of coral recovery by mid-century poses a global threat to coral reefs and dependent societies.

Coral reef fisheries support the livelihoods of millions of people but have been severely and negatively affected by anthropogenic activities. We conducted a systematic review of published data on the biomass of coral reef fishes to explore how the condition of reef fisheries is related to the density of local human populations, proximity of the reef to markets, and key environmental variables (including broad geomorphologic reef type, reef area, and net productivity). When only population density and environmental covariates were considered, high variability in fisheries conditions at low human population densities resulted in relatively weak explanatory models. The presence or absence of human settlements, habitat type, and distance to fish markets provided a much stronger explanatory model for the condition of reef fisheries. Fish biomass remained relatively low within 14 km of markets, then biomass increased exponentially as distance from reefs to markets increased. Our results suggest the need for an increased science and policy focus on markets as both a key driver of the condition of reef fisheries and a potential source of solutions.

Cost-effective proxies of biodiversity and species abundance, applicable across a range of spatial scales, are needed for setting conservation priorities and planning action. We outline a rapid, efficient, and low-cost measure of spectral signal from digital habitat images that, being an effective proxy for habitat complexity, correlates with species diversity and requires little image processing or interpretation. We validated this method for coral reefs of the Great Barrier Reef (GBR), Australia, across a range of spatial scales (1 m to 10 km), using digital photographs of benthic communities at the transect scale and high-resolution Landsat satellite images at the reef scale. We calculated an index of image-derived spatial heterogeneity, the mean information gain (MIG), for each scale and related it to univariate (species richness and total abundance summed across species) and multivariate (species abundance matrix) measures of fish community structure, using two techniques that account for the hierarchical structure of the data: hierarchical (mixed-effect) linear models and distance-based partial redundancy analysis. Over the length and breadth of the GBR, MIG alone explained up to 29% of deviance in fish species richness, 33% in total fish abundance, and 25% in fish community structure at multiple scales, thus demonstrating the possibility of easily and rapidly exploiting spatial information contained in digital images to complement existing methods for inferring diversity and abundance patterns among fish communities. Thus, the spectral signal of unprocessed remotely sensed images provides an efficient and low-cost way to optimize the design of surveys used in conservation planning. In data-sparse situations, this simple approach also offers a viable method for rapid assessment of potential local biodiversity, particularly where there is little local capacity in terms of skills or resources for mounting in-depth biodiversity surveys.

In an effort to deliver better outcomes for people and the ecosystems they depend on, many governments and civil society groups are engaging natural resource users in collaborative management arrangements (frequently called comanagement). However, there are few empirical studies demonstrating the social and institutional conditions conducive to successful comanagement outcomes, especially in small-scale fisheries. Here, we evaluate 42 comanagement arrangements across five countries and show that: ( i ) comanagement is largely successful at meeting social and ecological goals; ( ii ) comanagement tends to benefit wealthier resource users; ( iii ) resource overexploitation is most strongly influenced by market access and users’ dependence on resources; and ( iv ) institutional characteristics strongly influence livelihood and compliance outcomes, yet have little effect on ecological conditions.

Sustainably managing ecosystems is challenging, especially for complex systems such as coral reefs. This study develops critical reference points for sustainable management by using a large empirical dataset on the coral reefs of the western Indian Ocean to investigate associations between levels of target fish biomass (as an indicator of fishing intensity) and eight metrics of ecosystem state. These eight ecological metrics each exhibited specific thresholds along a continuum of fishable biomass ranging from heavily fished sites to old fisheries closures. Three thresholds lay above and five below a hypothesized window of fishable biomass expected to produce a maximum multispecies sustainable yield ( B MMSY ). Evaluating three management systems in nine countries, we found that unregulated fisheries often operate below the B MMSY , whereas fisheries closures and, less frequently, gear-restricted fisheries were within or above this window. These findings provide tangible management targets for multispecies coral reef fisheries and highlight key tradeoffs required to achieve different fisheries and conservation goals.

With rapidly increasing rates of contemporary extinction, predicting extinction vulnerability and identifying how multiple stressors drive non-random species loss have become key challenges in ecology. These assessments are crucial for avoiding the loss of key functional groups that sustain ecosystem processes and services. We developed a novel predictive framework of species extinction vulnerability and applied it to coral reef fishes. Although relatively few coral reef fishes are at risk of global extinction from climate disturbances, a negative convex relationship between fish species locally vulnerable to climate change vs. fisheries exploitation indicates that the entire community is vulnerable on the many reefs where both stressors co-occur. Fishes involved in maintaining key ecosystem functions are more at risk from fishing than climate disturbances. This finding is encouraging as local and regional commitment to fisheries management action can maintain reef ecosystem functions pending progress towards the more complex global problem of stabilizing the climate.

A recent literature review reported negative relationships between diet discrimination factors (DDFs = X(fish) - X(food) ; X = δ(15) N or δ(13) C) and the values of δ(15) N and δ(13) C in the food of wild organisms but there has been no laboratory-based confirmation of these relationships to date. Laboratory reared guppies (Poecilia reticulata) fed a series of diets with a range of δ(13) C (-22.9 to -6.6‰) and δ(15) N (6.5 to 1586‰) values were used to magnify diet-tissue dynamics in order to calculate DDFs once the fish had achieved equilibrium with each of the diets. Values of DDFs range widely for δ(15) N (7.1 to -849‰) and δ(13) C (1.1 to -7.0‰) and showed a strong negative correlation with the stable isotope value in the food for δ(15) N (slope = -0.59 ± 0.02, r(2) = 0.95) and δ(13) C (slope = -0.56 ± 0.02, r(2) = 0.94). Based on these relationships, the magnitude of DDF change over environmentally relevant values of δ(15) N or δ(13) C would be significant and could confound the interpretation of stable isotopes in the environment. Using highly enriched experimental diets, our study adds to a growing number of studies that undermine the consistent trophic enrichment paradigm with results that demonstrate the currently poor mechanistic understanding of how DDFs arise. The results of our study highlight that the magnitude of the stable isotope values in prey must be considered when choosing DDF values. Future laboratory studies should therefore be directed at uncovering the mechanistic basis of DDFs and, like others before, we recommend the determination of diet-dependent DDFs under laboratory conditions before modeling dietary proportions or calculating trophic positions.

Changes from coral to macroalgal dominance following disturbances to corals symbolize the global degradation of coral reefs. The development of effective conservation measures depends on understanding the causes of such phase shifts. The prevailing view that coral–macroalgal phase shifts commonly occur due to insufficient grazing by fishes is based on correlation with overfishing and inferences from models and small-scale experiments rather than on long-term quantitative field studies of fish communities at affected and resilient sites. Consequently, the specific characteristics of herbivorous fish communities that most promote reef resilience under natural conditions are not known, though this information is critical for identifying vulnerable ecosystems. In this study, 11 years of field surveys recorded the development of the most persistent coral–macroalgal phase shift (>7 years) yet observed on Australia’s Great Barrier Reef (GBR). This shift followed extensive coral mortality caused by thermal stress (coral bleaching) and damaging storms. Comparisons with two similar reefs that suffered similar disturbances but recovered relatively rapidly demonstrated that the phase shift occurred despite high abundances of one herbivore functional group (scraping/excavating parrotfishes: Labridae). However, the shift was strongly associated with low fish herbivore diversity and low abundances of algal browsers (predominantly Siganidae) and grazers/detritivores (Acanthuridae), suggesting that one or more of these factors underpin reef resilience and so deserve particular protection. Herbivorous fishes are not harvested on the GBR, and the phase shift was not enhanced by unusually high nutrient levels. This shows that unexploited populations of herbivorous fishes cannot ensure reef resilience even under benign conditions and suggests that reefs could lose resilience under relatively low fishing pressure. Predictions of more severe and widespread coral mortality due to global climate change emphasize the need for more effective identification and protection of ecosystem components that are critical for the prevention of coral reef phase shifts.

Stable isotopes of nitrogen and carbon (δ15N and δ13C) provide an important tool to examine diet, trophic position and movement/migration of both aquatic and terrestrial animals. Over the past 10 years, there have been repeated calls to tighten up basic assumptions when applying stable isotopes, one of the most important being the application of accurate, species-specific diet-tissue discrimination factors (DTDFs). Taxa- or species-specific DTDFs are required for (i) predicting dietary sources to a consumer using stable isotope mixing models and (ii) for estimating trophic position relative to primary consumers or known base species. Logan & Lutcavage (2010) recently presented data on stable isotope dynamics in elasmobranch fishes and concluded that DTDFs for teleost fish were suitable for elasmobranch fish, endorsing the generally applied value of 3.4‰. When considering (i) a recent study which found that DTDFs were lower for large sharks than teleost fish (Hussey et al., 2010) and (ii) that the Logan and Lutcavage study did not experimentally address the issue of DTDFs, we would argue that this conclusion is misleading. We demonstrate this point by estimating the proportion of prey items of a captive shark with a known diet history by modelling the δ15N values of the shark and its prey. The often repeated implication of inaccurate DTDFs is clear, with model results highly variable depending on the selected DTDF. In addition, model results for the standard teleost DTDF of 3.4‰ provided erroneous estimates of prey consumption. The suggestion that DTDFs for teleost fish are suitable for elasmobranchs may mislead investigators to choose DTDFs which are likely not applicable to their study species. Caution is therefore warranted in advocating this approach. Continued experimental work to examine stable isotopes in sharks is required and recommendations are made.

Ecological monitoring programs typically aim to detect changes in the abundance of species of conservation concern or which reflect system status. Coral reef fish assemblages are functionally important for reef health and these are most commonly monitored using underwater visual surveys (UVS) by divers. In addition to estimating numbers, most programs also collect estimates of fish lengths to allow calculation of biomass, an important determinant of a fish’s functional impact. However, diver surveys may be biased because fishes may either avoid or are attracted to divers and the process of estimating fish length could result in fish counts that differ from those made without length estimations. Here we investigated whether (1) general diver disturbance and (2) the additional task of estimating fish lengths affected estimates of reef fish abundance and species richness during UVS, and for how long. Initial estimates of abundance and species richness were significantly higher than those made on the same section of reef after diver disturbance. However, there was no evidence that estimating fish lengths at the same time as abundance resulted in counts different from those made when estimating abundance alone. Similarly, there was little consistent bias among observers. Estimates of the time for fish taxa that avoided divers after initial contact to return to initial levels of abundance varied from three to 17 h, with one group of exploited fishes showing initial attraction to divers that declined over the study period. Our finding that many reef fishes may disperse for such long periods after initial contact with divers suggests that monitoring programs should take great care to minimise diver disturbance prior to surveys.

Aim Quantifying and predicting change in large ecosystems is an important research objective for applied ecologists as human disturbance effects become increasingly evident at regional and global scales. However, studies used to make inferences about large-scale change are frequently of uneven quality and few in number, having been undertaken to study local, rather than global, change. Our aim is to improve the quality of inferences that can be made in meta-analyses of large-scale disturbance by integrating studies of varying quality in a unified modelling framework that is informative for both local and regional management. Innovation Here we improve conventionally structured meta-analysis methods by including imputation of unknown study variances and the use of Bayesian factor potentials. The approach is a coherent framework for integrating data of varying quality across multiple studies while facilitating belief statements about the uncertainty in parameter estimates and the probable outcome of future events. The approach is applied to a regional meta-analysis of the effects of loss of coral cover on species richness and the abundance of coral-dependent fishes in the western Indian Ocean (WIO) before and after a mass bleaching event in 1998. Main conclusions Our Bayesian approach to meta-analysis provided greater precision of parameter estimates than conventional weighted linear regression meta-analytical techniques, allowing us to integrate all available data from 66 available study locations in the WIO across multiple scales. The approach thereby: (1) estimated uncertainty in site-level estimates of change, (2) provided a regional estimate for future change at any given site in the WIO, and (3) provided a probabilistic belief framework for future management of reef resources at both local and regional scales.

Dennard, S. T., MacNeil, M. A., Treble, M. A., Campana, S., and Fisk, A. T. 2010. Hierarchical analysis of a remote, Arctic, artisanal longline fishery. – ICES Journal of Marine Science, 67: 41–51. This is the first paper to explore trends in catch per unit effort (cpue) through time of a Greenland halibut Reinhardtius hippoglossoides stock targeted by an artisanal, winter fishery in Cumberland Sound on southern Baffin Island, Canada. We modelled cpue data from 1987 to 2003, looking at two questions: what factors have driven cpue trends, and is cpue an accurate index of a stock's abundance? In the context of limited data availability, we used generalized linear models (GLMs) and hierarchical models to assess important predictors of cpue. Hierarchical models with multiple fixed environmental effects contained fishing location or individual fisher as random effects. A month effect showed greatest catch rates during February and March; the monthly North Atlantic Oscillation index was positively associated with catch rates; and a change from decreasing to increasing cpue after 1996 was linked to reduced fishery participation following a large storm. The best Akaike's information criterion-ranked GLM identified a negative relationship of cpue with shark bycatch. Although data limitations precluded conventional stock assessment, our models implicated the environment and fisher behaviour as drivers of cpue trends. Additionally, using multiple hierarchical models to predict cpue provided a more informative analysis for understanding trends in cpue than a GLM alone.

MacNeil, M. A., Carlson, J. K., and Beerkircher, L. R. 2009. Shark depredation rates in pelagic longline fisheries: a case study from the Northwest Atlantic. – ICES Journal of Marine Science, 66: 708–719. A suite of modelling approaches was employed to analyse shark depredation rates from the US Atlantic pelagic longline fishery. As depredation events are relatively rare, there are a large number of zeroes in pelagic longline data and conventional generalized linear models (GLMs) may be ineffective as tools for statistical inference. GLMs (Poisson and negative binomial), two-part (delta-lognormal and truncated negative binomial, T-NB), and mixture models (zero-inflated Poisson, ZIP, and zero-inflated negative binomial, ZINB) were used to understand the factors that contributed most to the occurrence of depredation events that included a small proportion of whale damage. Of the six distribution forms used, only the ZIP and T-NB models performed adequately in describing depredation data, and the T-NB and ZINB models outperformed the ZIP models in bootstrap cross-validation estimates of prediction error. Candidate T-NB and ZINB model results showed that encounter probabilities were more strongly related to large-scale covariates (space, season) and that depredation counts were correlated with small-scale characteristics of the fishery (temperature, catch composition). Moreover, there was little evidence of historical trends in depredation rates. The results show that the factors contributing to most depredation events are those already controlled by ships' captains and, beyond novel technologies to repel sharks, there may be little more to do to reduce depredation loss in the fishery within current economic and operational constraints.

Assessments of the biodiversity and structure of coral reef fish communities are often plagued by inadequate sampling and biases inherent in commonly used Underwater Visual Census (UVC) methods. Of these biases, heterogeneity in the detectability of reef-fish species is often ignored, even though it may have substantial effects on biodiversity estimates. Using highly repli- cated UVC sampling of all fish species at 4 sites in Tanzania, East Africa, we show that detectability varies greatly across species and is affected by traits such as body size and schooling behaviour, and that detectability of reef fishes can be readily accounted for by the application of Capture-Mark- Recapture (CMR) models. Based on our results, we recommend that approximately 24 point counts are necessary to assess full reef-fish species richness at sites in the Western Indian Ocean.

Epistemology, the theory of how knowledge arises, is an issue that ecologists and environmental scientists may not often consider in their work. However, beliefs about epistemology play a direct role in how they conduct research and, consciously or not, the conclusions made through analysis reflect some form of epistemology. I argue that the Popperian epistemology by which most environmental scientists are trained is generally incompatible with research on observational data and that observation-based studies can be improved by modifying Popper's notion of falsification.

Diet-tissue fractionation factors and metabolic turnover rates of delta15N and delta13C were assessed in laboratory-reared black fly (Simulium vittatum IS-7) larvae fed isotopically distinct diets. Five treatments consisted of using food with different delta15N signatures throughout the experiments (19-26 days), a sixth shifted from a low to high delta15N signature diet (uptake) on day 14, and the last shifted from a high to low delta15N signature diet (elimination) on day 14. In the larvae, diet-tissue fractionation factors for delta13C, which were in steady state with food, ranged from -0.61 to 2.0, with a median of 1.87. The delta15N diet-tissue fractionation factors were mostly negative, ranging from +2.85 to -24.96 per thousand, with a single positive value from the elimination treatment in which larval delta15N did not achieve steady state with the food. Diet-tissue fractionation factors also had a significant negative relationship (r2 = 0.98) with delta15N values in the food suggesting that nitrogen diet-tissue fractionation factors are 15N concentration-dependent. The delta15N of shed head capsules and feces were enriched in 15N and could be mechanisms for elimination of 15N by the larvae. For delta15N, metabolic turnover values based on the Hesslein model were highly consistent (0.40 to 0.43 delta15N*day(-1)) between uptake and elimination phases and across experiments and were an order of magnitude greater than growth rates. The rapid turnover of nitrogen in black fly larvae, which was orders of magnitude greater than measured in vertebrates, makes them an excellent indicator of short-term changes in nitrogen inputs to aquatic systems.

Stable isotope analysis (SIA) is recognized as a powerful analytical tool with numerous ecological applications. This has been highlighted by the increase in popularity of the isotope ratio mass spectrometry (IRMS) technique and the large number of studies reporting isotopic data. Comparisons of new isotopic data with previously published results and the use of large volumes of isotopic ratios in meta-analyses to explain isotopic variance are commonplace. Such data often originate from different IRMS instruments and are assumed to be readily comparable as all instruments are calibrated to International Atomic Energy Agency (IAEA) standards. To test the validity of this assumption, we analyzed a single ecological sample (homogenized cod muscle, Gadus morhua) on eight anonymous IRMS instruments and found significant variation in both δ15N and δ13C. We used a one-way analysis of variance (ANOVA) with random effects to estimate the average variability of laboratory results within and among instruments. Overall, 74% of variation in δ15N and 35% of variation in δ13C of a single ecological sample was explained by differences in the IRMS instrument used. In light of these findings, researchers are encouraged to submit their own sample reference to provide an independent check on variation between runs and between instruments; consistent discrepancies between instruments should be corrected through linear regression. Comparisons of data obtained from multiple instruments should acknowledge inter-instrument variation as a potential source of error.

Identifying the rates of recovery of fish in no-take areas is fundamental to designing protected area networks, managing fisheries, estimating yields, identifying ecological interactions, and informing stakeholders about the outcomes of this management. Here we study the recovery of coral reef fishes through 37 years of protection using a space-for-time chronosequence of four marine national parks in Kenya. Using AIC model selection techniques, we assessed recovery trends using five ecologically meaningful production models: asymptotic, Ricker, logistic, linear, and exponential. There were clear recovery trends with time for species richness, total and size class density, and wet masses at the level of the taxonomic family. Species richness recovered rapidly to an asymptote at 10 years. The two main herbivorous families displayed differing responses to protection, scarids recovering rapidly, but then exhibiting some decline while acanthurids recovered more slowly and steadily throughout the study. Recovery of the two invertebrate-eating groups suggested competitive interactions over resources, with the labrids recovering more rapidly before a decline and the balistids demonstrating a slower logistic recovery. Remaining families displayed differing trends with time, with a general pattern of decline in smaller size classes or small-bodied species after an initial recovery, which suggests that some species- and size-related competitive and predatory control occurs in older closures. There appears to be an ecological succession of dominance with an initial rapid rise in labrids and scarids, followed by a slower rise in balistids and acanthurids, an associated decline in sea urchins, and an ultimate dominance in calcifying algae. Our results indicate that the unfished ''equilibrium'' biomass of the fish assemblage .10 cm is 1100-1200 kg/ha, but these small parks (,10 km 2 ) are likely to underestimate pre- human influence values due to edge effects and the rarity of taxa with large area requirement, such as apex predators, including sharks.

With marine biodiversity declining globally at accelerating rates, maximising the effectiveness of conservation has become a key goal for local, national and international regulators. Marine protected areas (MPAs) have been widely advocated for conserving and managing marine biodiversity yet, despite extensive research, their benefits for conserving non-target species and wider ecosystem functions remain unclear. Here, we demonstrate that MPAs can increase the resilience of coral reef communities to natural disturbances, including coral bleaching, coral diseases, Acanthaster planci outbreaks and storms. Using a 20-year time series from Australia's Great Barrier Reef, we show that within MPAs, (1) reef community composition was 21-38% more stable; (2) the magnitude of disturbance impacts was 30% lower and (3) subsequent recovery was 20% faster that in adjacent unprotected habitats. Our results demonstrate that MPAs can increase the resilience of marine communities to natural disturbance possibly through herbivory, trophic cascades and portfolio effects.

The primary measurement made of reef fishes is abundance, which is used to compare populations and understand the processes affecting their dynamics. Abundance is typically expressed as counts of individuals or total biomass, conveying distinct but related information about the state of a fish population or community at a given point in time. Total community abundance varies at scales ranging from entire ocean basins to habitat patches on individual reefs, due to a range of processes that vary in relative importance at different scales. At local to regional scales, abundance changes between and within species in accordance with well-established macro-ecological patterns: variation in abundance among species typically follows a log-normal distribution, while temporal variation within species conforms to Taylor's power law. Changes in the relative abundance of species occur at all scales and reflect the aggregate effects of species-specific responses to scale-specific processes. The diverse and multi-scale patterns of variation in fish abundance suggest that the application of hierarchical models, which explicitly specify the scales at which different processes influence abundance, will lead to a more holistic understanding of reef fish ecology. Abundance is the most commonly measured quantity in studies of reef fishes. It is also a major determinant of the effect that a population of reef fishes has in a coral reef ecosystem. Reef fish abundance may be measured in numbers of individuals or estimates of population biomass, conveying distinct but related information about the state of a reef fish community. Counts (or densities, if normalized to a sample area) are more common, presumably due to their greater ease of collection. However, there is growing evidence that trained observers are able to estimate fish lengths with only minimal bias [736], and that, in conjunction with reliable taxon-specific length–weight relationships, biomass estimates can be reliably obtained [74]. Because the extent to which a species can perform ecological functions (e.g. consume algae, or provide nutrition for humans) often depends upon population biomass more strongly than numerical abundance, biomass has become increasingly important in reef ecosystem research.

White sharks are highly migratory and segregate by sex, age and size. Unlike marine mammals, they neither surface to breathe nor frequent haul-out sites, hindering generation of abundance data required to estimate population size. A recent tag-recapture study used photographic identifications of white sharks at two aggregation sites to estimate abundance in “central California” at 219 mature and sub-adult individuals. They concluded this represented approximately one-half of the total abundance of mature and sub-adult sharks in the entire eastern North Pacific Ocean (ENP). This low estimate generated great concern within the conservation community, prompting petitions for governmental endangered species designations. We critically examine that study and find violations of model assumptions that, when considered in total, lead to population underestimates. We also use a Bayesian mixture model to demonstrate that the inclusion of transient sharks, characteristic of white shark aggregation sites, would substantially increase abundance estimates for the adults and sub-adults in the surveyed sub-population. Using a dataset obtained from the same sampling locations and widely accepted demographic methodology, our analysis indicates a minimum all-life stages population size of >2000 individuals in the California subpopulation is required to account for the number and size range of individual sharks observed at the two sampled sites. Even accounting for methodological and conceptual biases, an extrapolation of these data to estimate the white shark population size throughout the ENP is inappropriate. The true ENP white shark population size is likely several-fold greater as both our study and the original published estimate exclude non-aggregating sharks and those that independently aggregate at other important ENP sites. Accurately estimating the central California and ENP white shark population size requires methodologies that account for biases introduced by sampling a limited number of sites and that account for all life history stages across the species' range of habitats.

Meta-analysis and decision analysis are underpinned by well-developed methods that are commonly applied to a variety of problems and disciplines. While these two fields have been closely linked in some disciplines such as medicine, comparatively little attention has been paid to the potential benefits of linking them in ecology, despite reasonable expectations that benefits would be derived from doing so. Meta-analysis combines information from multiple studies to provide more accurate parameter estimates and to reduce the uncertainty surrounding them. Decision analysis involves selecting among alternative choices using statistical information that helps to shed light on the uncertainties involved. By linking meta-analysis to decision analysis, improved decisions can be made, with quantification of the costs and benefits of alternate decisions supported by a greater density of information. Here, we briefly review concepts of both meta-analysis and decision analysis, illustrating the natural linkage between them and the benefits from explicitly linking one to the other. We discuss some examples in which this linkage has been exploited in the medical arena and how improvements in precision and reduction of structural uncertainty inherent in a meta-analysis can provide substantive improvements to decision analysis outcomes by reducing uncertainty in expected loss and maximising information from across studies. We then argue that these significant benefits could be translated to ecology, in particular to the problem of making optimal ecological decisions in the face of uncertainty.

Many ecosystems face degradation unless factors that underpin their resilience can be effectively managed. In tropical reef ecosystems, grazing by herbivorous fishes can prevent coral-macroalgal phase shifts that commonly signal loss of resilience. However, knowledge of grazing characteristics that most promote resilience is typically experimental, localized, and sparse, which limits broad management applications. Applying sound ecological theory to broad-scale data may provide an alternative basis for ecosystem management. We explore the idea that resilience is positively related to the diversity within and among functional groups of organisms. Specifically, we infer the relative vulnerability of different subregions of the Great Barrier Reef (GBR) to phase shifts based on functional characteristics of the local herbivorous fish communities. Reef slopes on 92 reefs set in three zones of the continental shelf in eight latitudinal sectors of the GBR were surveyed on multiple occasions between 1995 and 2009. Spatial variation in fish community structure was high and driven primarily by shelf position. Measures of functional diversity, functional redundancy, and abundance were generally higher offshore and lower inshore. Two turbid inshore subregions were considered most vulnerable based on very low measures of herbivore function, and this was supported by the occurrence of phase shifts within one of three subregions. Eleven reefs that resisted phase shifts after major coral mortality included some with very low measures of herbivore function. The fact that phase shifts did not necessarily occur when large herbivores were scarce indicates that other environmental factors compensated to preserve resilience. Estimates of vulnerability based solely on herbivore function may thus prove conservative, but caution is appropriate, since compensatory factors are largely unknown and could be eroded unwittingly by anthropogenic stresses. Our data suggest that managing the threat of phase shifts in coral reef ecosystems successfully will require spatially explicit strategies that consider both the functional characteristics of local herbivore communities and environmental factors that may raise or lower resilience thresholds. A strong positive correlation between water clarity and the species richness and abundance of herbivorous fishes suggests that management of water quality is of generic importance to ensure the ecosystem services of this important group of herbivores.

Managing coral reefs for resilience to climate change is a popular concept but has been difficult to implement because the empirical scientific evidence has either not been evaluated or is sometimes unsupportive of theory, which leads to uncertainty when considering methods and identifying priority reefs. We asked experts and reviewed the scientific literature for guidance on the multiple physical and biological factors that affect the ability of coral reefs to resist and recover from climate disturbance. Eleven key factors to inform decisions based on scaling scientific evidence and the achievability of quantifying the factors were identified. Factors important to resistance and recovery, which are important components of resilience, were not strongly related, and should be assessed independently. The abundance of resistant (heat-tolerant) coral species and past temperature variability were perceived to provide the greatest resistance to climate change, while coral recruitment rates, and macroalgae abundance were most influential in the recovery process. Based on the 11 key factors, we tested an evidence-based framework for climate change resilience in an Indonesian marine protected area. The results suggest our evidence-weighted framework improved upon existing un-weighted methods in terms of characterizing resilience and distinguishing priority sites. The evaluation supports the concept that, despite high ecological complexity, relatively few strong variables can be important in influencing ecosystem dynamics. This is the first rigorous assessment of factors promoting coral reef resilience based on their perceived importance, empirical evidence, and feasibility of measurement. There were few differences between scientists' perceptions of factor importance and the scientific evidence found in journal publications but more before and after impact studies will be required to fully test the validity of all the factors. The methods here will increase the feasibility and defensibility of including key resilience metrics in evaluations of coral reefs, as well as reduce costs. Adaptation, marine protected areas, priority setting, resistance, recovery.

Characterizing dietary resources and species interactions in estuaries is challenging, particularly when considering the dynamic nature of these ecosystems, the ranges in body sizes of species, and the potential for trophic roles to vary with ontogeny. We examined the influence of season and location on relationships between body size and δ 15N, δ 13C, and δ 34S values across a range of fishes from two subtropical estuaries. The results suggest that isotopic values of estuarine fishes are independent of body size. However, seasonal variation propagated throughout the assemblage as the majority of fishes integrated different δ 15N, δ 13C, or δ 34S values. The absence of δ 15N-, δ 13C-, and δ 34S-body size relationships suggests that either (1) dietary preference of these fishes do not shift within the range of body sizes sampled, (2) these fishes shift to an alternate diet that is not isotopically distinct, or (3) that spatial and temporal variation in isotopic signatures of prey negate any size-based relationships. Seasonal variability in the isotopic values of these fishes suggests either movement to an alternative habitat or a shift in organic matter source associated with the transition of dry to wet seasons. Moreover, variance distributions of the best-fit models indicate that seasonal dietary preferences of conspecifics do not vary over moderate spatial scales. Seasonal variability among fishes in these estuaries suggests plasticity in feeding strategies that may afford greater adaptive flexibility to these species in response to changes in food availability resulting from variable environmental conditions. © 2011 Coastal and Estuarine Research Federation.

Global climate change has the potential to substantially alter the production and community structure of marine fisheries and modify the ongoing impacts of fishing. Fish community composition is already changing in some tropical, temperate and polar ecosystems, where local combinations of warming trends and higher environmental variation anticipate the changes likely to occur more widely over coming decades. Using case studies from the Western Indian Ocean, the North Sea and the Bering Sea, we contextualize the direct and indirect effects of climate change on production and biodiversity and, in turn, on the social and economic aspects of marine fisheries. Climate warming is expected to lead to (i) yield and species losses in tropical reef fisheries, driven primarily by habitat loss; (ii) community turnover in temperate fisheries, owing to the arrival and increasing dominance of warm-water species as well as the reduced dominance and departure of cold-water species; and (iii) increased diversity and yield in Arctic fisheries, arising from invasions of southern species and increased primary production resulting from ice-free summer conditions. How societies deal with such changes will depend largely on their capacity to adapt - to plan and implement effective responses to change - a process heavily influenced by social, economic, political and cultural conditions. This journal is © 2010 The Royal Society.

A recent literature review reported negative relationships between diet discrimination factors (DDFs = X(fish) - X(food) ; X = δ(15) N or δ(13) C) and the values of δ(15) N and δ(13) C in the food of wild organisms but there has been no laboratory-based confirmation of these relationships to date. Laboratory reared guppies (Poecilia reticulata) fed a series of diets with a range of δ(13) C (-22.9 to -6.6‰) and δ(15) N (6.5 to 1586‰) values were used to magnify diet-tissue dynamics in order to calculate DDFs once the fish had achieved equilibrium with each of the diets. Values of DDFs range widely for δ(15) N (7.1 to -849‰) and δ(13) C (1.1 to -7.0‰) and showed a strong negative correlation with the stable isotope value in the food for δ(15) N (slope = -0.59 ± 0.02, r(2) = 0.95) and δ(13) C (slope = -0.56 ± 0.02, r(2) = 0.94). Based on these relationships, the magnitude of DDF change over environmentally relevant values of δ(15) N or δ(13) C would be significant and could confound the interpretation of stable isotopes in the environment. Using highly enriched experimental diets, our study adds to a growing number of studies that undermine the consistent trophic enrichment paradigm with results that demonstrate the currently poor mechanistic understanding of how DDFs arise. The results of our study highlight that the magnitude of the stable isotope values in prey must be considered when choosing DDF values. Future laboratory studies should therefore be directed at uncovering the mechanistic basis of DDFs and, like others before, we recommend the determination of diet-dependent DDFs under laboratory conditions before modeling dietary proportions or calculating trophic positions.

International audience; Coral reefs are highly complex ecological systems, where multiple processes interact across scales in space and time to create assemblages of exceptionally high biodiversity. Despite the increasing frequency of hierarchically structured sampling programs used in coral-reef science, little progress has been made in quantifying the relative importance of processes operating across multiple scales. The vast majority of reef studies are conducted, or at least analyzed, at a single spatial scale, ignoring the implicitly hierarchical structure of the overall system in favor of small-scale experiments or large-scale observations. Here we demonstrate how alpha (mean local number of species), beta diversity (degree of species dissimilarity among local sites), and gamma diversity (overall species richness) vary with spatial scale, and using a hierarchical, information-theoretic approach, we evaluate the relative importance of site-, reef-, and atoll-level processes driving the fish metacommunity structure among 10 atolls in French Polynesia. Process-based models, representing well-established hypotheses about drivers of reef-fish community structure, were assembled into a candidate set of 12 hierarchical linear models. Variation in fish abundance, biomass, and species richness were unevenly distributed among transect, reef, and atoll levels, establishing the relative contribution of variation at these spatial scales to the structure of the metacommunity. Reef-fish biomass, species richness, and the abundance of most functional-groups corresponded primarily with transect-level habitat diversity and atoll-lagoon size, whereas detritivore and grazer abundances were largely correlated with potential covariates of larval dispersal. Our findings show that (1) within-transect and among-atoll factors primarily drive the relationship between alpha and gamma diversity in this reef-fish metacommunity; (2) habitat is the primary correlate with reef fish metacommunity structure at multiple spatial scales; and (3) inter-atoll connectedness was poorly correlated with the nonrandom clustering of reef-fish species. These results demonstrate the importance of modeling hierarchical data and processes in understanding reef-fish metacommunity structure

Metabolic turnover rates (m) of delta(15)N and delta(13)C were assessed in different tissues of newly hatched captive-raised corn snakes (Elaphe guttata guttata) fed maintenance diets consisting of earthworms (Eisenia foetida) that varied substantially in delta(15)N (by 644 per thousand) and delta(13)C (by 5.0 per thousand). Three treatments were used during this 144 day experiment that consisted of the same diet throughout (control), shifting from a depleted to an enriched stable isotope signature diet (uptake), and shifting from an enriched to depleted stable isotope signature diet (elimination). Values of delta(13)C in the liver, blood, and muscle of the control snakes reached equilibrium with and were, respectively, 1.73, 2.25 and 2.29 greater than in their diet, this increase is called an isotopic discrimination factor (Deltadelta(13)C = delta(13)C(snake) - delta(13)C(food)). Values of delta(15)N in snake tissues did not achieve equilibrium with the diets in any of the exposures and thus Delta(15)N could not be estimated. Values of metabolic turnover rates (m) for delta(13)C and delta(15)N were greater in liver than in muscle and blood, which were similar, and relative results remained the same if the fraction of (15)N and (13)C were modeled. Although caution is warranted because equilibrium values of stable isotopes in the snakes were not achieved, values of m were greater for delta(13)C than delta(15)N, resulting in shorter times to dietary equilibrium for delta(13)C upon a diet shift, and for both stable isotopes in all tissues, greater during an elimination than in an uptake shift in diet stable isotope signature. Multiple explanations for the observed differences between uptake and elimination shifts raise new questions about the relationship between animal and diet stable isotope concentrations. Based on this study, interpretation of feeding ecology using stable isotopes is highly dependent on the kind of stable isotope, tissue, direction of diet switch (uptake versus elimination), and the growth rate of the animal.

Diet-tissue fractionation factors and metabolic turnover rates of delta15N and delta13C were assessed in laboratory-reared black fly (Simulium vittatum IS-7) larvae fed isotopically distinct diets. Five treatments consisted of using food with different delta15N signatures throughout the experiments (19-26 days), a sixth shifted from a low to high delta15N signature diet (uptake) on day 14, and the last shifted from a high to low delta15N signature diet (elimination) on day 14. In the larvae, diet-tissue fractionation factors for delta13C, which were in steady state with food, ranged from -0.61 to 2.0, with a median of 1.87. The delta15N diet-tissue fractionation factors were mostly negative, ranging from +2.85 to -24.96 per thousand, with a single positive value from the elimination treatment in which larval delta15N did not achieve steady state with the food. Diet-tissue fractionation factors also had a significant negative relationship (r2 = 0.98) with delta15N values in the food suggesting that nitrogen diet-tissue fractionation factors are 15N concentration-dependent. The delta15N of shed head capsules and feces were enriched in 15N and could be mechanisms for elimination of 15N by the larvae. For delta15N, metabolic turnover values based on the Hesslein model were highly consistent (0.40 to 0.43 delta15N*day(-1)) between uptake and elimination phases and across experiments and were an order of magnitude greater than growth rates. The rapid turnover of nitrogen in black fly larvae, which was orders of magnitude greater than measured in vertebrates, makes them an excellent indicator of short-term changes in nitrogen inputs to aquatic systems.

We conducted a diet-switching experiment using freshwater ocellate river stingrays (Potamotrygon motoro) fed a novel earthworm (Eisenia foetida) diet to establish the relative contributions of growth and metabolism to δ 15 N values in an elasmobranch species. We specifically controlled for the potential effects of protein composition of experi- mental diets on δ 15 N turnover to determine whether δ 15 N turnover after a low to high δ 15 N diet switch (uptake) and a high to low δ 15 N diet switch (elimination) will occur at the same rate within each consumer tissue. Our results showed that the turnover of δ 15 N from metabolism and growth differed between uptake and elimination phases in the liver, blood, cartilage, and muscle of freshwater stingrays. During uptake, liver was found to track dietary δ 15 N more closely than the other tissues, with the highest metabolic turnover rate of δ 15 N (0.015 day -1 ), whereas cartilage had the slowest rate of metabolic δ 15 N turnover (0.0022 day -1 ) relative to a constant rate of growth among tissues (0.003 day -1 ). We propose that estimates of trophic position from muscle sampling alone have considerable uncertainty, particularly for scavenging or omnivorous species. We suggest that multitissue sampling can identify this problem and lead to a more robust evaluation of trophic dynamics for individual species. Resume : Nous avons mene une experience de changement de regime alimentaire chez la pastenague d'eau douce ocellee (Potamotrygon motoro) nourrie d'un regime inusite de vers de terre (Eisenia foetida) afin d'etablir les contribu- tions relatives de la croissance et du metabolisme aux valeurs de 15 N chez une espece d'elasmobranches. Nous avons

The authors provide corrections for two equation errors, one in the main manuscript text and one in Supplementary Material File S4 of Hussey et al. (2014). A spelling mistake in one of the figure axes is also corrected. The errors are as follows: 1. Within the main manuscript (page 241; bottom of text column two), the following equation to calculate trophic position (TP) using a scaled Δ15N framework based on a dietary δ15N value‐dependent Δ15N model was presented; TP=log(δ15Nlim−δ15Nbase)−log(δ15Nlim−δ15NTP)k The TP of the baseline organism was omitted from this equation and must be added to obtain an absolute TP value for the organism of interest. The corrected equation is consequently; TP=log(δ15Nlim−δ15Nbase)−log(δ15Nlim−δ15NTP)k+TPbase where TPbase is the trophic position of the consumer used to define δ15Nbase (i.e. TP = 2 or 3). 2. In the supplementary material file titled, ‘ele12226‐sup‐0004‐SupplementaryMaterialS4’, equation (S3) was written as follows which is incorrect; k=−log(β0−δ15Nlim)−δ15Nlim The above equation has now been corrected to; k=−logβ0−δ15Nlim−δ15Nlim following the same equation presented in the manuscript text (page 242; top of text column one). In addition, the equations in Supplementary Material File S4 have been reordered; the above equation is now listed as (S4). The corrected Supplementary Material File S4 has been provided as the online Supporting Information of this corrigendum (entitled ‘ele_12270‐sup‐0001‐SupplementaryMaterialS4 CORRECTED’) 3. In Figure 6, a spelling mistake in the x‐axis legends of (a), (c), (e) and (g) reads ‘basline organism’ and should be corrected to ‘baseline organism’.

Coral reefs have emerged as one of the ecosystems most vulnerable to climate variation and change. While the contribution\ud of a warming climate to the loss of live coral cover has been well documented across large spatial and temporal scales, the\ud associated effects on fish have not. Here, we respond to recent and repeated calls to assess the importance of local\ud management in conserving coral reefs in the context of global climate change. Such information is important, as coral reef\ud fish assemblages are the most species dense vertebrate communities on earth, contributing critical ecosystem functions\ud and providing crucial ecosystem services to human societies in tropical countries. Our assessment of the impacts of the\ud 1998 mass bleaching event on coral cover, reef structural complexity, and reef associated fishes spans 7 countries, 66 sites\ud and 26 degrees of latitude in the Indian Ocean. Using Bayesian meta-analysis we show that changes in the size structure,\ud diversity and trophic composition of the reef fish community have followed coral declines. Although the ocean scale\ud integrity of these coral reef ecosystems has been lost, it is positive to see the effects are spatially variable at multiple scales,\ud with impacts and vulnerability affected by geography but not management regime. Existing no-take marine protected areas\ud still support high biomass of fish, however they had no positive affect on the ecosystem response to large-scale disturbance.\ud This suggests a need for future conservation and management efforts to identify and protect regional refugia, which should\ud be integrated into existing management frameworks and combined with policies to improve system-wide resilience to\ud climate variation and change.

SummaryNetworks of no-take marine reserves (NTMRs) are widely advocated for preserving exploited fish stocks and for conserving biodiversity. We used underwater visual surveys of coral reef fish and benthic communities to quantify the short- to medium-term (5 to 30 years) ecological effects of the establishment of NTMRs within the Great Barrier Reef Marine Park (GBRMP). The density, mean length, and biomass of principal fishery species, coral trout (Plectropomus spp., Variola spp.), were consistently greater in NTMRs than on fished reefs over both the short and medium term. However, there were no clear or consistent differences in the structure of fish or benthic assemblages, non-target fish density, fish species richness, or coral cover between NTMR and fished reefs. There was no indication that the displacement and concentration of fishing effort reduced coral trout populations on fished reefs. A severe tropical cyclone impacted many survey reefs during the study, causing similar declines in coral cover and fish density on both NTMR and fished reefs. However, coral trout biomass declined only on fished reefs after the cyclone. The GBRMP is performing as expected in terms of the protection of fished stocks and biodiversity for a developed country in which fishing is not excessive and targets a narrow range of species. NTMRs cannot protect coral reefs directly from acute regional-scale disturbance but, after a strong tropical cyclone, impacted NTMR reefs supported higher biomass of key fishery-targeted species and so should provide valuable sources of larvae to enhance population recovery and long-term persistence.

International audience; Climate-induced coral bleaching is among the greatest current threats to coral reefs, causing widespread loss of live coral cover1. Conditions under which reefs bounce back from bleaching events or shift from coral to algal dominance are unknown, making it difficult to predict and plan for differing reef responses under climate change2. Here we document and predict long-term reef responses to a major climate-induced coral bleaching event that caused unprecedented region-wide mortality of Indo-Pacific corals. Following loss of >90% live coral cover, 12 of 21 reefs recovered towards pre-disturbance live coral states, while nine reefs underwent regime shifts to fleshy macroalgae. Functional diversity of associated reef fish communities shifted substantially following bleaching, returning towards pre-disturbance structure on recovering reefs, while becoming progressively altered on regime shifting reefs. We identified threshold values for a range of factors that accurately predicted ecosystem response to the bleaching event. Recovery was favoured when reefs were structurally complex and in deeper water, when density of juvenile corals and herbivorous fishes was relatively high and when nutrient loads were low. Whether reefs were inside no-take marine reserves had no bearing on ecosystem trajectory. Although conditions governing regime shift or recovery dynamics were diverse, pre-disturbance quantification of simple factors such as structural complexity and water depth accurately predicted ecosystem trajectories. These findings foreshadow the likely divergent but predictable outcomes for reef ecosystems in response to climate change, thus guiding improved management and adaptation.