Comparability and complementarity of reef fish measures from underwater visual census (UVC) and baited remote underwater video stations (BRUVS).

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.

Latitude and protection affect decadal trends in reef trophic structure over a continental scale.

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 (<5% of cases) to relatively common in temperate areas (~45%). Lastly, the strongest trends in predator and algal density occurred in older no-take marine reserves; however, exploitation status did not affect the likelihood of alternating long-term trophic group trends occurring. Our 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.

Counts of coral reef fishes by an experienced observer are not biased by the number of target species.

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.

Reef fish communities are spooked by scuba surveys and may take hours to recover.

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.

Delayed coral recovery in a warming ocean.

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.

The threat to coral reefs from more intense cyclones under climate change.

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.

Joint estimation of crown of thorns (Acanthaster planci) densities on the Great Barrier Reef.

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.

Marine protected areas increase resilience among coral reef communities.

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.

Expectations and Outcomes of Reserve Network Performance following Re-zoning of the Great Barrier Reef Marine Park.

Networks 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.

Retention of habitat complexity minimizes disassembly of reef fish communities following disturbance: a large-scale natural experiment.

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.

Spatial variation in the functional characteristics of herbivorous fish communities and the resilience of coral reefs.

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.

Ongoing effects of no-take marine reserves on commercially exploited coral trout populations on the Great Barrier Reef.

Networks of no-take marine reserves (NTMRs) are widely used for managing marine resources. Because they restrict fishing, managers need to monitor reserves to reassure stakeholders that they are achieving the intended results. In 2004, the Great Barrier Reef (GBR) Marine Park was rezoned and the area of NTMRs was greatly increased. Using manta tow we assessed the effectiveness of the new NTMRs in conserving coral trout (Plectropomus and Variola spp.), the principle targets of the GBR reef line fishery. Over a six year period, we sampled regional groups of matched pairs of similar reefs, ones closed to fishing under the rezoning and ones that remained open. Coral trout populations were significantly higher in NTMRs. While coral trout populations declined on reefs open to fishing, stocks were maintained in NTMRs, highlighting the ongoing benefits of marine reserves.

Rapid increase in fish numbers follows creation of world's largest marine reserve network.

No-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).

Habitat utilization by coral reef fish: implications for specialists vs. generalists in a changing environment.

1. The impact of environmental disturbance and habitat loss on associated species is expected to be dependent on a species' level of specialization. We examined habitat use and specialization of coral reef fish from the diverse and ecologically important family Pomacentridae, and determined which species are susceptible to declines in coral cover due to disturbance induced by crown-of-thorns seastar (COTS, Acanthaster planci L.). 2. A high proportion of pomacentrid species live in association with live coral as adults (40%) or juveniles (53%). Adults of many species had strong affiliations with branching corals, while juveniles favoured plating growth forms, reflecting the sizes of refuge provided by coral types. 3. Juveniles of species that associated with coral had narrower niche breadths than adult conspecifics, due to associations with specific coral types. The especially high coral association and narrower niche breadth of juveniles suggest that the presence of live coral is crucial for many species during early life history, and that disturbance-induced coral loss may have serious flow-on effects on adult abundance. 4. Microhabitat availability was a poor predictor of fish species abundance. Significant correlations between coverage of coral types and abundance of five adults and two juvenile species were detected; however, these relationships explained <35% and <10% of the variation in abundance of adult and juvenile species, respectively. 5. Niche breadth explained 74% of the variation in species' mean response to coral decline and it is clear that disturbance has a greater impact on resource specialists, suggesting that increasing frequency and intensity of coral loss will cause reef fish communities to become dominated by habitat generalists at the expense of coral-dwelling specialists.