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Fishes are commercially, recreationally and functionally important inhabitants of coral reefs. Accordingly, accurate assessments of fish abundance and diversity are necessary for effective reef management. While some reef fish monitoring programmes target all fishes, many survey a subset of common and visually obvious species. Changing to counts of all species, while desirable, risks new and unwelcome biases from altered observer swimming speeds and search patterns. Here we test whether substantially increasing the number of target species in an established fish monitoring programme biases counts of the original subset, so precluding ongoing comparisons with historical data. A subset of 141 fish species have been visually surveyed along 50 × 5 m transects over 27 years throughout Australia's Great Barrier Reef. We experimentally compared counts of the subset from standard subset-only surveys and from surveys of all species (excluding small site-attached fishes that are surveyed separately) at three diverse reefs. Subset species richness and abundance, in total and of major families, and assemblage structure did not differ due to survey method. The high-level experience of the one observer appeared to overcome new biases from counting more species and the extra 2 min/transect was not logistically excessive. Surveys of all fishes recorded almost 80% more species than subset-only surveys and >130% higher total abundance on average from >150% more genera that included abundant and functionally important taxa. Overall, fish counts by an experienced observer were not biased by the number of species surveyed and counts of all species markedly improved assessments of reef fish diversity and function.

The relative roles of top‐down (consumer‐driven) and bottom‐up (resource‐driven) forcing in exploited marine ecosystems have been much debated. Examples from a variety of marine systems of exploitation‐induced, top‐down trophic forcing have led to a general view that human‐induced predator perturbations can disrupt entire marine food webs, yet other studies that have found no such evidence provide a counterpoint. Though evidence continues to emerge, an unresolved debate exists regarding both the relative roles of top‐down versus bottom‐up forcing and the capacity of human exploitation to instigate top‐down, community‐level effects. Using time‐series data for 104 reef communities spanning tropical to temperate Australia from 1992 to 2013, we aimed to quantify relationships among long‐term trophic group population density trends, latitude, and exploitation status over a continental‐scale biogeographic range. Specifically, we amalgamated two long‐term monitoring databases of marine community dynamics to test for significant positive or negative trends in density of each of three key trophic levels (predators, herbivores, and algae) across the entire time series at each of the 104 locations. We found that trophic control tended toward bottom‐up driven in tropical systems and top‐down driven in temperate systems. Further, alternating long‐term population trends across multiple trophic levels (a method of identifying trophic cascades), presumably due to top‐down trophic forcing, occurred in roughly fifteen percent of locations where the prerequisite significant predator trends occurred. Such alternating trophic trends were significantly more likely to occur at locations with increasing predator densities over time. Within these locations, we found a marked latitudinal gradient in the prevalence of long‐term, alternating trophic group trends, from rare in the tropics (, Using time‐series data for 104 reef communities spanning tropical to temperate Australia from 1992 to 2013, we quantified relationships among long‐term trophic group population density trends, latitude, and exploitation status over a continental‐scale biogeographic range. These data suggest that the type and degree of trophic forcing in this system are likely related to one or more covariates of latitude, and that ecosystem resiliency to top‐down control does not universally vary in this system based on exploitation level.

International audience; Few studies assess the effects of recreational fishing in isolation from commercial fishing. We used meta-analysis to synthesise 4444 samples from 30 years (1987–2017) of fish surveys inside and outside a large network of highly protected reserves in the Ningaloo Marine Park, Western Australia, where the major fishing activity is recreational. Data were collected by different agencies, using varied survey designs and sampling methods. We contrasted the relative abundance and biomass of target and non-target fish groups between fished and reserve locations. We considered the influence of, and possible interactions between, seven additional variables: age and size of reserve, one of two reserve network configurations, reef habitat type, recreational fishing activity, shore-based fishing regulations and survey method. Taxa responded differently: the abundance and biomass inside reserves relative to outside was higher for targeted lethrinids, while other targeted (and non-targeted) fish groups were indistinguishable. Reef habitat was important for explaining lethrinid response to protection, and this factor interacted with reserve size, such that larger reserves were demonstrably more effective in the back reef and lagoon habitats. There was little evidence of changes in relative abundance and biomass of fishes with reserve age, or after rezoning and expansion of the reserve network. Our study demonstrates the complexities in quantifying fishing effects, highlighting some of the key factors and interactions that likely underlie the varied results in reserve assessments that should be considered in future reserve design and assessment.

The much-publicized threats to coral reef systems necessitate a considered management response based on comprehensive ecological data. However, data from large reef systems commonly originate from multiple monitoring programs that use different methods, each with distinct biases that limit united assessments of ecological status. The effective integration of data from different monitoring methods would allow better assessment of system status and hence, more informed management. Here we examine the scope for comparability and complementarity of fish data from two different methods used on Australia's Great Barrier Reef (GBR): underwater visual census (UVC) and baited remote underwater video stations (BRUVS). We compared commonly reported reef fish measures from UVC and BRUVS on similar reef slope habitats of three central GBR reefs. Both methods recorded similar estimates of total species richness, although ~30% of recorded species were not common to both methods. There were marked differences between methods in sub-group species richness, frequency of species occurrences, relative abundances of taxa and assemblage structure. The magnitude and orientation of inter-method differences were often inconsistent among taxa. However, each method better categorized certain components of fish communities: BRUVS sampled more predatory species in higher numbers while UVC was similarly better at sampling damselfishes (Pomacentridae). Our results suggest limited scope for direct or adjusted comparisons of data from UVC and BRUVS. Conversely, complementary aspects of the two methods confirm that their integration in monitoring programs will provide a more complete and extensive assessment of reef fish status for managers than from either method alone.

Climate change threatens coral reefs across the world. Intense bleaching has caused dramatic coral mortality in many tropical regions in recent decades, but less obvious chronic effects of temperature and other stressors can be equally threatening to the long-term persistence of diverse coral-dominated reef systems. Coral reefs persist if coral recovery rates equal or exceed average rates of mortality. While mortality from acute destructive events is often obvious and easy to measure, estimating recovery rates and investigating the factors that influence them requires long-term commitment. Coastal development is increasing in many regions, and sea surface temperatures are also rising. The resulting chronic stresses have predictable, adverse effects on coral recovery, but the lack of consistent long-term data sets has prevented measurement of how much coral recovery rates are actually changing. Using long-term monitoring data from 47 reefs spread over 10 degrees of latitude on Australia's Great Barrier Reef (GBR), we used a modified Gompertz equation to estimate coral recovery rates following disturbance. We compared coral recovery rates in two periods: 7 years before and 7 years after an acute and widespread heat stress event on the GBR in 2002. From 2003 to 2009, there were few acute disturbances in the region, allowing us to attribute the observed shortfall in coral recovery rates to residual effects of acute heat stress plus other chronic stressors. Compared with the period before 2002, the recovery of fast-growing Acroporidae and of "Other" slower growing hard corals slowed after 2002, doubling the time taken for modest levels of recovery. If this persists, recovery times will be increasing at a time when acute disturbances are predicted to become more frequent and intense. Our study supports the need for management actions to protect reefs from locally generated stresses, as well as urgent global action to mitigate climate change.

Predatory fishes are important components of coral-reef ecosystems of the Great Barrier Reef (GBR) through both the ecological functions they perform and their high value to recreational and commercial fisheries, estimated at $30 million in 2014. However, management of GBR predatory fish populations is hampered by a lack of knowledge of their distribution and abundance, aside from that of the highly targeted coral trout (Plectropomus spp. and Variola spp.). Furthermore, there is little information on how these fishes respond to environmental stressors such as coral bleaching, outbreaks of coral-feeding starfishes (Acanthaster planci) and storms, which limits adaptive management of their populations as the frequency or severity of such natural disturbances increases under climate change. Here, we document the distribution and abundance of 48 species of reef-associated predatory fishes and assess their vulnerability to a range of natural disturbances. There were clear differences in predatory fish assemblages across the continental shelf, but many species were widespread, with few species restricted to either inshore or offshore waters. There was weak latitudinal structure with only a few species restricted to either the northern or southern GBR. On the whole, predatory fishes were surprisingly resistant to the effects of disturbance, with few clear changes in abundance or species richness following 66 documented disturbances of varying magnitudes.

Laboratory experiments have shown that the behaviour of reef fishes can be impaired by the CO2 levels projected to occur in the ocean by the end of this century. Research now shows that reef fishes at natural volcanic CO2 seeps also exhibit behavioural abnormalities, and that behaviour does not acclimate with extended exposure to high CO2. Fish communities are therefore likely to face a serious threat from CO2-induced behavioural abnormalities in the future as ocean acidification becomes widespread.

Planktivorous damselfishes (Pomacentridae) are diverse and abundant on the Great Barrier Reef (GBR), are important prey for commercially harvested coral trout (Plectropomus spp.) and their feeding mode plays a central role in transferring energy from the plankton to the reef. However, little is known about their distribution patterns throughout the GBR and how those patterns are influenced by predators and habitat despite increasing pressures on both. Here we quantify the distribution and abundance of GBR planktivorous damselfishes, then examine the role of coral trout and habitat in shaping their assemblages. The assemblage structure of planktivorous damselfishes varied across the continental shelf, yet their total abundances varied sub-regionally, dependent on differences in coral habitat. Latitudinal patterns were relatively weak. Damselfish assemblages generally retained characteristics of their sub-regional setting over 20 years and assemblage degradation was only associated with major coral losses. Damselfish numbers were not negatively influenced by top-down control from coral trout. Instead, numbers of coral trout and damselfishes were both positively associated with coral habitat and each other. Our findings suggest that a complexity of factors and interactions shape reef fish assemblages and reinforce the fundamental importance of coral as the foundation of healthy reef communities.

Crown-of-thorns starfish (CoTS;Acanthaster spp.) are an outbreaking pest among many Indo-Pacific coral reefs that cause substantial ecological and economic damage. Despite ongoing CoTS research, there remain critical gaps in observing CoTS populations and accurately estimating their numbers, greatly limiting understanding of the causes and sources of CoTS outbreaks. Here we address two of these gaps by (1) estimating the detectability of adult CoTS on typical underwater visual count (UVC) surveys using covariates and (2) inter-calibrating multiple data sources to estimate CoTS densities within the Cairns sector of the Great Barrier Reef (GBR). We find that, on average, CoTS detectability is high at 0.82 [0.77, 0.87] (median highest posterior density (HPD) and [95% uncertainty intervals]), with CoTS disc width having the greatest influence on detection. Integrating this information with coincident surveys from alternative sampling programs, we estimate CoTS densities in the Cairns sector of the GBR averaged 44 [41, 48] adults per hectare in 2014.

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.

Territorial damselfishes that manipulate (“farm”) the algae in their territories can have a marked effect on benthic community structure and may influence coral recovery following disturbances. Despite the numerical dominance of farming species on many reefs, the importance of their grazing activities is often overlooked, with most studies only examining their roles over restricted spatial and temporal scales. We used the results of field surveys covering 9.5° of latitude of the Great Barrier Reef to describe the distribution, abundance and temporal dynamics of farmer communities. Redundancy analysis revealed unique subregional assemblages of farming species that were shaped by the combined effects of shelf position and, to a lesser extent, by latitude. These spatial patterns were largely stable through time, except when major disturbances altered the benthic community. Such disturbances affected the functional guilds of farmers in different ways. Since different guilds of farmers modify benthic community structure and affect survival of juvenile corals in different ways, these results have important implications for coral recovery following disturbances.

The composition and functionality of ecologically important herbivorous fish assemblages were examined throughout much of Australia’s Great Barrier Reef (GBR). Diversity and abundance of surgeonfishes (Acanthuridae), parrotfishes (Labridae) and rabbitfishes (Siganidae) were strongly associated with position on the continental shelf, whilst effects of latitude were weaker and inconsistent. Species distributions varied considerably amongst taxonomic groups; parrotfishes were mostly widespread whilst distributions of surgeonfishes were often restricted. Most inshore environments supported depauperate herbivore assemblages dominated by different taxa and functional groups compared with assemblages in offshore environments. There were also strong cross-shelf transitions in the main taxa performing each functional role. Overall, this study show that the functional contributions of herbivorous fish assemblages to important ecosystem processes and the contributing taxa vary considerably amongst different GBR environments. Additionally, the two most numerically dominant herbivores actively select detritus, not algae, supporting increasing evidence for the importance of detritus in coral reef ecology.

The effects of disturbances on coral reef fishes have been extensively documented but most studies have relied on opportunistic sampling following single events. Few studies have the spatial and temporal extent to directly compare the effects of multiple disturbances over a large geographic scale. Here, benthic communities and butterflyfishes on 47 reefs of the Great Barrier Reef were surveyed annually to examine their responses to physical disturbances (cyclones and storms) and/or biological disturbances (bleaching, outbreaks of crown-of-thorns starfish and white syndrome disease). The effects on benthic and butterflyfish communities varied among reefs depending on the structure and geographical setting of each community, on the size and type of disturbance, and on the disturbance history of that reef. There was considerable variability in the response of butterflyfishes to different disturbances: physical disturbances (occurring with or without biological disturbances) produced substantial declines in abundance, whilst biological disturbances occurring on their own did not. Butterflyfishes with the narrowest feeding preferences, such as obligate corallivores, were always the species most affected. The response of generalist feeders varied with the extent of damage. Wholesale changes to the butterflyfish community were only recorded where structural complexity of reefs was drastically reduced. The observed effects of disturbances on butterflyfishes coupled with predictions of increased frequency and intensity of disturbances sound a dire warning for the future of butterflyfish communities in particular and reef fish communities in general.

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.

This manuscript was greatly improved with constructive feedback from Dr. Mark Carr and two anonymous reviewers. We thank all past and present members of the Long-term Monitoring Program (LTMP) at the Australian Institute of Marine Science (AIMS) who helped to gather the data used in this study. Thanks to the staff of the AIMS Marine Monitoring Program, AIMS National Sea Simulator, Orpheus Island Research Station, AIMS Data Centre, and AIMS Marine Operations for the use of their facilities and their assistance. The Long-Term Monitoring Program is supported by AIMS and has been funded in part by the Australian Government's National Environmental Research Program and National Environmental Science Program.

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.

The extent to which fish communities are structured by spatial variability in coral reef habitats versus stochastic processes (such as larval supply) is very important in predicting responses to sustained and ongoing habitat degradation. In this study, butterflyfish and benthic communities were surveyed annually over 15 years on 47 reefs (spanning 12° of latitude) of the Great Barrier Reef (GBR). Spatial autocorrelation in the structure of butterflyfish communities versus key differences in reef habitats was investigated to assess the extent to which the structure of these fish communities is influenced by habitat conditions. Benthic communities on each of the 47 reefs were broadly categorised as either: 1. Poritidae/Alcyoniidae, 2. mixed taxa, 3. soft coral or 4. Acropora-dominated habitats. These habitat types most reflected increases in water clarity and wave exposure, moving across the GBR shelf from coastal to outer-shelf environments. In turn, each habitat type also supported very distinct butterflyfish communities. Hard coral feeders were always the dominant butterflyfish species in each community type. However, the numerically dominant species changed according to habitat type, representing spatial replacement of species across the shelf. This study reveals clear and consistent differences in the structure of fish communities among reefs associated with marked differences in habitat structure.

The functional roles of certain reef fishes are considered to facilitate recovery of reef ecosystems following coral mortality. Maintenance of high fish species diversity and associated func- tional diversity are thought to represent an 'ecological insurance' against ecosystem degradation. We examined responses of reef fish communities to varied levels of coral decline on 22 individual reefs of the Great Barrier Reef over an 11 yr period. Using 7 measures of species diversity, we found that fish diversity rarely decreased due to coral declines, even on 7 reefs that suffered massive coral losses (cover decreased by >75%). However, maintenance of fish diversity on those 7 reefs belied major changes in fish communities that involved increases in abundance of large herbivores and decreases in abundance of both coral-dependent fishes and species with no obvious dependence on coral. The magnitude of change in species abundances increased linearly with the magnitude of coral decline. While the proportion of species that increased or decreased in abundance varied considerably among reefs, 45 to 71% of fish species decreased in abundance on some reefs. Ecological function is related to abundance, so such decreases are likely to indicate reduced ecosystem function. Our results sug- gest that: (1) reef fish diversity may not be a reliable indicator of reef resilience and (2) predicted declines in coral cover due to global warming are likely to cause changes in the structure of reef fish communities, but the nature of these changes and associated capacity of reef fishes to assist eco- system recovery will vary among reefs.

Coral reefs are consistently and increasingly subject to acute disturbance events that often lead to a reduction in live coral cover with concomitant effects on the diversity and abundance of coral reef fishes. Here we examine changes in both hard coral and reef-fish assemblages over 15 yr following major losses of coral from exposed reefs in 2 widely separated sectors of the Great Barrier Reef (GBR), Australia. While the rate and extent of increase in coral cover (from 60%) was similar in the 2 sectors, differences in the rugosity of the underlying reef framework influenced the structure of fish communities. Soon after disturbance, when coral cover was very low and the lime- stone reef framework constituted most of the surface relief, the relatively featureless substrate on reefs of the southern sector supported fewer fish species than reefs of the northern sector, which had a more rugose substrate. At first, northern reefs also had a higher proportion of herbivorous fish spe- cies, presumably because the more complex reef surface provided shelter and allowed them to exploit the abundant algal turf. With increasing coral cover, coral colonies came to provide most of the surface relief in both sectors, and species richness and the trophic structure of the fish communi- ties converged. Variation in the cover of branching corals explained significant variation in the fish communities in both sectors over time, reflecting the importance of this growth form to small coral- associated fishes. These results show that the recovery of the coral community and the complexity of underlying reef framework interact to determine the functional structure of associated fish communi- ties despite differences in regional settings.

Habitat perturbations play a major role in shaping community structure; however, the elements of disturbance-related habitat change that affect diversity are not always apparent. This study examined the effects of habitat disturbances on species richness of coral reef fish assemblages using annual surveys of habitat and 210 fish species from 10 reefs on the Great Barrier Reef (GBR). Over a period of 11 years, major disturbances, including localised outbreaks of crown-of-thorns sea star (Acanthaster planci), severe storms or coral bleaching, resulted in coral decline of 46–96% in all the 10 reefs. Despite declines in coral cover, structural complexity of the reef framework was retained on five and species richness of coral reef fishes maintained on nine of the disturbed reefs. Extensive loss of coral resulted in localised declines of highly specialised coral-dependent species, but this loss of diversity was more than compensated for by increases in the number of species that feed on the epilithic algal matrix (EAM). A unimodal relationship between areal coral cover and species richness indicated species richness was greatest at approximately 20% coral cover declining by 3–4 species (6–8% of average richness) at higher and lower coral cover. Results revealed that declines in coral cover on reefs may have limited short-term impact on the diversity of coral reef fishes, though there may be fundamental changes in the community structure of fishes.

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 crown-of-thorns starfish (COTS) is a major predator of hard corals. Repeated COTS outbreaks in the Cairns and Central sections of the Great Barrier Reef (GBR) have been responsible for greater declines in coral cover than any other type of disturbance, including cyclones, disease, and coral bleaching. Knowledge of the precise timing and location of primary outbreaks could reveal the initial drivers of outbreaks and so could indicate possible management measures. In the central GBR, COTS outbreaks appear to follow major flooding events, but despite many years of observations, no primary outbreak has ever been unequivocally identified in the central and northern GBR. Here we locate a primary outbreak of COTS on the southern GBR which is not correlated with flooding. Instead it appears to have been the result of a combination of life history traits of COTS and prevailing oceanographic conditions. The hydrodynamic setting implies that the outbreak could disperse larvae to other reefs in the region.

Recognition of the complex spatial and temporal variability of abundance and diversity found in many populations has led to a greater focus on the roles of heterogeneity, stochasticity, and disturbance in the structure and persistence of communities. This focus is directly relevant to coral reef communities that are characterized by very high species diversity in a spatially heterogeneous environment, display stochastic variability in community structure at small spatial and temporal scales, and are subject to major disturbances. We monitored coral and fish assemblages over 14 years on fixed sites spread over 80 km of the southern Great Barrier Reef (GBR), Australia, and found evidence of large-scale resilience and predictable recovery of these assemblages. Sometime between November 1987 and October 1989, live coral cover on the shallow northeast flanks of some reefs in the southern GBR decreased from >80% to

Changes in reef assemblages of corals and fishes following a tropical cyclone were assessed using data sets from (1) manta tow surveys of entire reef perimeters and (2) intensive surveys of specific sites, across 11 reefs lying close to the cyclone's track. Only one of the reefs experienced an obvious and immediate decline in mean coral cover (from 24 to 8%) due to the cyclone. The abundance and species richness of adult damselfish assemblages on intensive survey sites at this reef were not affected in the short term (6–8 weeks), despite the removal of 48% of living hard coral. Assemblages of adult fishes showed a similar lack of response at three other reefs where no significant habitat changes had occurred. Eleven to twelve months later, the total abundance of damselfishes had decreased substantially at eight of the sampled reefs, while the abundance of larger mobile fishes remained stable. We infer that the effects on coral assemblages reflect the short duration and orientation of the cyclone, the history of exposure to wave energy (influencing life-form structure and therefore degree of fragility), and the degree of consolidation of the reef matrix. The lack of short-term effects of the cyclone on adult fishes shows that these fishes can endure periods of intense underwater turbulence. The lack of change in damselfish assemblages weeks after loss of coral cover implies that this resource was not limiting adult fish densities. The reasons for widespread decreases in damselfish numbers 11–12 months after the cyclone are unknown.

High biodiversity ecosystems are commonly associated with complex habitats. Coral reefs are highly diverse ecosystems, but are under increasing pressure from numerous stressors, many of which reduce live coral cover and habitat complexity with concomitant effects on other organisms such as reef fishes. While previous studies have highlighted the importance of habitat complexity in structuring reef fish communities, they employed gradient or meta-analyses which lacked a controlled experimental design over broad spatial scales to explicitly separate the influence of live coral cover from overall habitat complexity. Here a natural experiment using a long term (20 year), spatially extensive (∼ 115,000 kms(2)) dataset from the Great Barrier Reef revealed the fundamental importance of overall habitat complexity for reef fishes. Reductions of both live coral cover and habitat complexity had substantial impacts on fish communities compared to relatively minor impacts after major reductions in coral cover but not habitat complexity. Where habitat complexity was substantially reduced, species abundances broadly declined and a far greater number of fish species were locally extirpated, including economically important fishes. This resulted in decreased species richness and a loss of diversity within functional groups. Our results suggest that the retention of habitat complexity following disturbances can ameliorate the impacts of coral declines on reef fishes, so preserving their capacity to perform important functional roles essential to reef resilience. These results add to a growing body of evidence about the importance of habitat complexity for reef fishes, and represent the first large-scale examination of this question on the Great Barrier Reef.

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.

SUMMARY Expert opinion was canvassed to identify crucial knowledge gaps in current understanding of climate change impacts on coral reef fishes. Scientists that had published three or more papers on the effects of climate and environmental factors on reef fishes were invited to submit five questions that, if addressed, would improve our understanding of climate change effects on coral reef fishes. Thirty-three scientists provided 155 questions, and 32 scientists scored these questions in terms of: (i) identifying a knowledge gap, (ii) achievability, (iii) applicability to a broad spectrum of species and reef habitats, and (iv) priority. Forty-two per cent of the questions related to habitat associations and community dynamics of fish, reflecting the established effects and immediate concern relating to climate-induced coral loss and habitat degradation. However, there were also questions on fish demographics, physiology, behaviour and management, all of which could be potentially affected by climate change. Irrespective of their individual expertise and background, scientists scored questions from different topics similarly, suggesting limited bias and recognition of a need for greater interdisciplinary and collaborative research. Presented here are the 53 highest-scoring unique questions. These questions should act as a guide for future research, providing a basis for better assessment and management of climate change impacts on coral reefs and associated fish communities.

Body mass (BM) was recorded regularly during pregnancy in four female Indian Ocean bottlenose dolphins (Tursiops truncatus). Daily food intakes were recorded for each animal before and after parturition. BM increase occurred variably between 2 and 5 months of gestation, and at parturition mass increases averaged 41.2% of initial prepregnancy mass. Changes in mass can thus be used as an early indicator of pregnancy. During the 12 months of pregnancy, no significant changes occurred in the amount of food ingested compared with previous years. Daily food intake during lactation (X = 13.2 kg, 8% of BM) proved significantly higher (P < 0.001) than during pregnancy (X = 8.7 kg, 5.2% of BM).

SummaryNo-take marine reserves (NTMRs) are much advocated as a solution to managing marine ecosystems, protecting exploited species and restoring natural states of biodiversity [1,2]. Increasingly, it is becoming clear that effective marine conservation and management at ecosystem and regional scales requires extensive networks of NTMRs [1,2]. The world's largest network of such reserves was established on Australia's Great Barrier Reef (GBR) in 2004. Closing such a large area to all fishing has been socially and politically controversial, making it imperative that the effectiveness of this new reserve network be assessed. Here we report evidence, first, that the densities of the major target species of the GBR reef line fisheries were significantly higher in the new NTMRs, compared with fished sites, in just two years; and second, that the positive differences were consistent for multiple marine reserves over an unprecedented spatial scale (>1,000 km).