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With the ongoing loss of coral cover and the associated flattening of reef architecture, understanding the links between coral habitat and reef fishes is of critical importance. Here, we investigate whether considering coral traits and functional diversity provides new insights into the relationship between structural complexity and reef fish communities, and whether coral traits and community composition can predict structural complexity. Across 157 sites in Seychelles, Maldives, the Chagos Archipelago, and Australia’s Great Barrier Reef, we find that structural complexity and reef zone are the strongest and most consistent predictors of reef fish abundance, biomass, species richness, and trophic structure. However, coral traits, diversity, and life histories provided additional predictive power for models of reef fish assemblages, and were key drivers of structural complexity. Our findings highlight that reef complexity relies on living corals—with different traits and life histories—continuing to build carbonate skeletons, and that these nuanced relationships between coral assemblages and habitat complexity can affect the structure of reef fish assemblages. Seascape-level estimates of structural complexity are rapid and cost effective with important implications for the structure and function of fish assemblages, and should be incorporated into monitoring programs.

Remote underwater videos (RUVs) are valuable for studying fish assemblages and behaviors, but analyzing them is time-consuming. To effectively extract data from RUVs while minimizing sampling errors, this study developed optimal subsampling strategies for assessing relative abundance, richness, and bite rates of corallivorous fish across eight geographically dispersed reef sites on the Great Barrier Reef and in the Torres Strait. Analyzing 40 frames per 60-min video yielded precise and accurate estimates of the mean number of individuals per frame (i.e., MeanCount), with systematic sampling (one frame every 90 s) proved as effective as or better than random sampling, depending on the survey sites. However, this approach underestimated species richness by ~ 40%, missing the less common species. For estimating bite rates, 30 min or 15 feeding events were optimal, with no significant gains in precision and accuracy with further effort. These strategies enhance data standardization and process efficiency, reducing the time required for MeanCount and bite rate estimates by nine and two times, respectively, compared to full video annotation.

An influential paradigm in coral reef ecology is that fishing causes trophic cascades through reef fish assemblages, resulting in reduced herbivory and thus benthic phase shifts from coral to algal dominance. Few long-term field tests exist of how fishing affects the trophic structure of coral reef fish assemblages, and how such changes affect the benthos. Alternatively, benthic change itself may drive the trophic structure of reef fish assemblages. Reef fish trophic structure and benthic cover were quantified almost annually from 1983 to 2014 at two small Philippine islands (Apo, Sumilon). At each island a No-Take Marine Reserve (NTMR) site and a site open to subsistence reef fishing were monitored. Thirteen trophic groups were identified. Large planktivores often accounted for >50% of assemblage biomass. Significant NTMR effects were detected at each island for total fish biomass, but for only 2 of 13 trophic components: generalist large predators and large planktivores. Fishing-induced changes in biomass of these components had no effect on live hard coral (HC) cover. In contrast, HC cover affected biomass of 11 of 13 trophic components significantly. Positive associations with HC cover were detected for total fish biomass, generalist large predators, piscivores, obligate coral feeders, large planktivores, and small planktivores. Negative associations with HC cover were detected for large benthic foragers, detritivores, excavators, scrapers, and sand feeders. These associations of fish biomass to HC cover were most clear when environmental disturbances (e.g., coral bleaching, typhoons) reduced HC cover, often quickly (1–2 yr), and when HC recovered, often slowly (5–10 yr). As HC cover changed, the biomass of 11 trophic components of the fish assemblage changed. Benthic and fish assemblages were distinct at all sites from the outset, remaining so for 31 yr, despite differences in fishing pressure and disturbance history. HC cover alone explained ~30% of the variability in reef fish trophic structure, whereas fishing alone explained 24%. Furthermore, HC cover affected more trophic groups more strongly than fishing. Management of coral reefs must include measures to maintain coral reef habitats, not just measures to reduce fishing by NTMRs.

Baselines and benchmarks (B&Bs) are needed to evaluate the ecological status and fisheries potential of coral reefs. B&Bs may depend on habitat features and energetic limitations that constrain biomass within the natural variability of the environment and fish behaviors. To evaluate if broad B&Bs exist, we compiled data on the biomass of fishes in ~1000 reefs with no recent history of fishing in 19 ecoregions. These reefs spanned the full longitude and latitude of Indian and Pacific Ocean reefs and included older high-compliance fisheries closures (>15 yr closure) and remote reef areas (>9 h travel time from fisheries markets). There was no significant change in biomass over the 15 to 48 yr closure period but closures had only ~40% of the biomass (740 kg ha−1, lower confidence interval [LCI] = 660 kg ha−1, upper confidence interval [UCI] = 810 kg ha−1, n = 157) of remote tropical reefs (1870 [1730, 2000] kg ha−1, n = 503). Remote subtropical reefs had lower biomass (950 [860, 1040] kg ha−1, n = 329) than tropical reefs. Closures and remote reef fish biomass responded differently to environmental variables of coral cover, net primary productivity, and light, indicating that remote reefs are more limited by productivity and habitat than closures. Closures in fished seascapes are unlikely to achieve the biomass and community composition of remote reefs, which suggests fisheries benchmarks will differ substantially from wilderness baselines. A fishery benchmark (B₀) of ~1000 kg ha−1 adjusted for geography is suggested for fisheries purposes. For ecological purposes, a wilderness baseline of ~1900 kg ha−1 is appropriate for including large and mobile species not well protected by closures.

Repeated bouts of coral bleaching threaten the long-term persistence of coral reefs and associated communities. Here, we document the short- and long-term impacts of heatwave events on coral and fish assemblages, based on regular surveys of 18 reefs of the granitic islands of Seychelles over 23 yr. Extreme heat events in 1998 and 2016 led to bleaching-associated declines in coral cover, whilst between these years there was an interim period of coral recovery on some reefs. Coral decline and recovery were primarily due to changes in the cover of branching coral, particularly those from the families Acroporidae and Pocilloporidae. Surveys during the 2016 bleaching found that 95% of the 468 Acropora and Pocillopora colonies observed were either bleached or recently dead. The extent of bleaching and subsequent mortality were best explained by a priori assessments of community susceptibility to heat stress. One year later (2017), coral cover had fallen by 70% and average coverage across the 18 reefs was at 6%, similar to levels recorded in 2005, 7 yr after the 1998 bleaching. Decline in coral following the 2016 bleaching coincided with reduced abundance of fish < 11 cm TL, particularly corallivores, invertivores and mixed diet feeders. These changes are likely to foreshadow more widespread loss once the habitat structure erodes. Accordingly, 7 yr after the 1998 bleaching, when coral skeletons and reef structure had collapsed on some reefs, abundance of both large- and small-bodied fish had declined. We show that fluctuation in the cover of branching coral is positively associated with changes in the abundance of small-bodied fish which contribute to ecological processes and high diversity, suggesting branching corals are a keystone structure. Increased frequency of bleaching threatens the capacity of branching corals to fully recover after disturbances, reducing the amplitude of boom bust cycles of these corals and the keystone habitat structure they provide reef fish.

Alteration of benthic reef habitat after coral bleaching and mortality induces changes in fish assemblages, with implications for fisheries. Our understanding of climate impacts to coral reef fisheries is largely based on fish abundance and biomass. The rates at which biomass is produced and replenished (productivity and turnover) are also important to sustaining fisheries, yet the responses of these metrics following bleaching are largely unknown. Here, we examine changes in fish productivity and turnover after mass coral bleaching events in Seychelles, on reefs that were recovering to coral-dominated habitats and those that shifted to macroalgae-dominated regimes. Productivity of fish assemblages increased on all recovering reefs, particularly on fished reefs resulting in levels similar to protected reefs 19 years after bleaching. Herbivore-detritivores, such as scraping and excavating parrotfish, appeared to drive biomass production through increased abundance on recovering reefs. Productivity on regime-shifted reefs remained stable at 1994 levels in fished areas, with increases observed on protected reefs. Large increases in browser productivity (particularly on protected reefs), combined with increases for invertivores, maintained post-bleaching productivity on macroalgal reefs. For all diet groups, net turnover was generally higher on fished regime-shifted reefs than on recovering reefs, suggesting fish biomass is more readily replenished on macroalgal reefs. Reef structural complexity was a positive predictor of productivity for all diet groups. These findings indicate that post-bleaching reef fish productivity is strongly influenced by benthic recovery trajectories, and demonstrates the importance of herbivore and invertivore species in sustaining small-scale inshore fisheries following climatic disturbances.

Cryptobenthic fishes are abundant on coral reefs, and their larvae dominate the ichthyoplankton in near reef waters. However, we have a limited understanding of how pelagic and on-reef processes are linked, especially how late-stage cryptobenthic fish larvae use near reef waters. We therefore used depth-stratified light trap sampling from 2 to 27 m at Lizard Island, Great Barrier Reef. This revealed clear depth variation in late-stage larval fish assemblages. Gobiidae larvae characterised mid-depth (13 m) samples. By contrast, larval Apogonidae were only abundant in shallow samples. Deep samples were typified by (non-target) adult apogonids. Contrary to expectations that poor-swimming cryptobenthic larvae would be flow-sheltering in deeper water, our results suggest that late-stage cryptobenthic larvae use large portions of the water column, although their preferred positions may be taxon-specific.

Efforts to confront the challenges of environmental change and uncertainty include attempts to adaptively manage social–ecological systems. However, critical questions remain about whether adaptive management can lead to sustainable outcomes for both ecosystems and society. Here, we make a contribution to these efforts by presenting a 16-y analysis of ecological outcomes and perceived livelihood impacts from adaptive coral reef management in Papua New Guinea. The adaptive management system we studied was a customary rotational fisheries closure system (akin to fallow agriculture), which helped to increase the biomass of reef fish and make fish less wary (more catchable) relative to openly fished areas. However, over time the amount of fish in openly fished reefs slowly declined. We found that, overall, resource users tended to have positive perceptions about this system, but there were negative perceptions when fishing was being prohibited. We also highlight some of the key traits of this adaptive management system, including 1) strong social cohesion, whereby leaders played a critical role in knowledge exchange; 2) high levels of compliance, which was facilitated via a “carrot-and-stick” approach that publicly rewarded good behavior and punished deviant behavior; and 3) high levels of participation by community actors.

Reef fisheries are multispecific and employ a variety of fishing gears across marine environments, even in remote areas. This intricate and multifaceted nature of reef fisheries is often overlooked in management strategies, leading to global management failures. In Brazil, information about reef fisheries is often scarce and scattered. This stems from inadequate policies and an unrecognized societal value of reef fisheries. Here, we combine nationwide reef fish landing data (1950–2015) with an extensive literature review on Brazilian reef fisheries. We explore temporal and spatial patterns in total landings, species traits, functional diversity and composition to understand the current scenario, identify drivers of change and highlight information gaps. Brazilian reef fisheries rapidly increased in landing volume, number of targeted species and exploited traits in the 1980’s, despite mainly targeting carnivorous fish (groupers, snappers, jacks and trevallies). Exploited functional space increased over time, mainly due to the incorporation of smaller and lower-trophic level species that gradually were added to the pool of fished species. Local and international markets have been the main drivers behind these patterns, while subsistence fishing is marginal. Lack of proper management and enforcement of existing regulations have led to population declines, dwindling total catches since the early 2000’s, and numerous threatened species. Artisanal fishing accounts for the majority of catches, raising concern on the social impacts of degraded reef fisheries. We highlight the urgent need for adequate fishing statistics, and the use/application of science-based management and policy actions to secure productive fisheries and healthy reef ecosystems in Brazil.