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Marine fisheries in coastal ecosystems in many areas of the world have historically removed large-bodied individuals, potentially impairing ecosystem functioning and the long-term sustainability of fish populations. Reporting on size-based indicators that link to food-web structure can contribute to ecosystem-based management, but the application of these indicators over large (cross-ecosystem) geographical scales has been limited to either fisheries-dependent catch data or diver-based methods restricted to shallow waters (20 m) that can misrepresent the abundance of large-bodied fished species. We obtained data on the body-size structure of 82 recreationally or commercially targeted marine demersal teleosts from 2904 deployments of baited remote underwater stereo-video (stereo-BRUV). Sampling was at up to 50 m depth and covered approximately 10,000 km of the continental shelf of Australia. Seascape relief, water depth, and human gravity (i.e., a proxy of human impacts) were the strongest predictors of the probability of occurrence of large fishes and the abundance of fishes above the minimum legal size of capture. No-take marine reserves had a positive effect on the abundance of fishes above legal size, although the effect varied across species groups. In contrast, sublegal fishes were best predicted by gradients in sea surface temperature (mean and variance). In areas of low human impact, large fishes were about three times more likely to be encountered and fishes of legal size were approximately five times more abundant. For conspicuous species groups with contrasting habitat, environmental, and biogeographic affinities, abundance of legal-size fishes typically declined as human impact increased. Our large-scale quantitative analyses highlight the combined importance of seascape complexity, regions with low human footprint, and no-take marine reserves in protecting large-bodied fishes across a broad range of species and ecosystem configurations.Las pesquerías marinas de los ecosistemas costeros en muchas áreas del mundo históricamente han removido a individuos de gran tamaño, potencialmente perjudicando el funcionamiento ambiental y la sostenibilidad a largo plazo de las poblaciones de peces. Los reportes sobre los indicadores basados en el tamaño que se vinculan con la estructura de la red alimenticia pueden contribuir al manejo basado en el ecosistema, aunque la aplicación de estos indicadores a grandes (inter-ecosistemas) escalas geográficas ha estado limitada a datos de captura dependientes de las pesquerías o métodos basados en el buceo restringidos a aguas someras (20 m), lo cual puede representar erróneamente la abundancia de peces de gran tamaño capturados para la pesca. Obtuvimos los datos de la estructura del tamaño corporal de 82 teleósteos marinos demersales focalizados por razones recreativas o comerciales tomados de 2,904 despliegues de video estéreo subacuático remoto con cebo (stereo-BRUV, en inglés). El muestreo se realizó hasta los 50 metros de profundidad y abarcó aproximadamente 10,000 km del talud continental de Australia. El relieve marino, la profundidad del agua y la gravedad humana (es decir, un indicador de los impactos humanos) fueron los pronosticadores más sólidos de la probabilidad de incidencia de los peces de gran tamaño y de la abundancia de peces por encima del tamaño legal mínimo de captura. Las reservas marinas de protección total tienen un efecto positivo sobre la abundancia de los peces que están por encima del tamaño legal, aunque el efecto varió según el grupo de especies. Como contraste, los peces de tamaño sublegal fueron pronosticados de mejor manera usando gradientes de la temperatura de la superficie marina (media y varianza). En las áreas con un impacto humano reducido, los peces de gran tamaño corporal tenían hasta tres veces mayor probabilidad de aparecer y los peces de tamaño legal eran aproximadamente cinco veces más abundantes. Para los grupos de especies conspicuas con afinidades contrastantes de hábitat, ambiente y biogeografía, la abundancia de peces de tamaño legal normalmente declinó conforme aumentó el impacto humano. Nuestros análisis cuantitativos a gran escala resaltan la importancia conjunta que tienen la complejidad marina, las regiones con una huella humana reducida y las reservas marinas de protección total para la protección de los peces de gran tamaño corporal en una extensa gama de especies y configuraciones ecosistémicas. Efectos de la Huella Humana y los Factores Biofísicos sobre la Estructura del Tamaño Corporal de Especies Marinas Capturadas para la Pesca.

Marine reserves are a key tool for the conservation of marine biodiversity, yet only ~2.5% of the world's oceans are protected. The integration of marine reserves into connected networks representing all habitats has been encouraged by international agreements, yet the benefits of this design has not been tested empirically. Australia has one of the largest systems of marine reserves, providing a rare opportunity to assess how connectivity influences conservation success. An Australia‐wide dataset was collected using baited remote underwater video systems deployed across a depth range from 0 to 100 m to assess the effectiveness of marine reserves for protecting teleosts subject to commercial and recreational fishing. A meta‐analytical comparison of 73 fished species within 91 marine reserves found that, on average, marine reserves had 28% greater abundance and 53% greater biomass of fished species compared to adjacent areas open to fishing. However, benefits of protection were not observed across all reserves (heterogeneity), so full subsets generalized additive modelling was used to consider factors that influence marine reserve effectiveness, including distance‐based and ecological metrics of connectivity among reserves. Our results suggest that increased connectivity and depth improve the aforementioned marine reserve benefits and that these factors should be considered to optimize such benefits over time. We provide important guidance on factors to consider when implementing marine reserves for the purpose of increasing the abundance and size of fished species, given the expected increase in coverage globally. We show that marine reserves that are highly protected (no‐take) and designed to optimize connectivity, size and depth range can provide an effective conservation strategy for fished species in temperate and tropical waters within an overarching marine biodiversity conservation framework., An Australia‐wide dataset was collected using baited remote underwater video systems deployed across a depth range from 0 to 100 m to assess the effectiveness of marine reserves for protecting fished species. A meta‐analytical comparison of 73 fished species within 91 marine reserves found that, on average, marine reserves had 28% greater abundance and 53% greater biomass of fished species compared to adjacent areas open to fishing. We show that marine reserves that are highly protected (no‐take) and designed to optimize connectivity, size and depth range can provide an effective conservation strategy for fished species in temperate and tropical waters.

Made available in DSpace on 2021-06-25T12:19:58Z (GMT). No. of bitstreams: 0 Previous issue date: 2020-09-24 Australian Government's National Environmental Science Program Australian Research Data Commons GorgonBarrow Island Gorgon Barrow Island Net Conservation Benefits Fund Baited remote underwater stereo-video systems (stereo-BRUVs) are a popular tool to sample demersal fish assemblages and gather data on their relative abundance and body size structure in a robust, cost-effective and non-invasive manner. Given the rapid uptake of the method, subtle differences have emerged in the way stereo-BRUVs are deployed and how the resulting imagery is annotated. These disparities limit the interoperability of datasets obtained across studies, preventing broadscale insights into the dynamics of ecological systems. We provide the first globally accepted guide for using stereo-BRUVs to survey demersal fish assemblages and associated benthic habitats. Information on stereo-BRUVs design, camera settings, field operations and image annotation are outlined. Additionally, we provide links to protocols for data validation, archiving and sharing. Globally, the use of stereo-BRUVs is spreading rapidly. We provide a standardized protocol that will reduce methodological variation among researchers and encourage the use of Findable, Accessible, Interoperable and Reusable workflows to increase the ability to synthesize global datasets and answer a broad suite of ecological questions. Univ Western Australia, UWA Oceans Inst, Perth, WA, Australia Univ Western Australia, Sch Biol Sci, Perth, WA, Australia Dept Biodivers Conservat & Attract, Marine Sci Program, Biodivers & Conservat Sci, Kensington, WA, Australia Curtin Univ, Sch Mol & Life Sci, Perth, WA, Australia Univ Tasmania, Inst Marine & Antarctic Studies, Hobart, Tas, Australia Silliman Univ, Angelo King Ctr Res & Environm Management, Dumaguete, Philippines NOAA Inouye Reg Ctr, NOAA Fisheries, Pacific Isl Fisheries Sci Ctr, Sci Operat Div, Honolulu, HI USA Univ Hawaii Manoa, Joint Inst Marine & Atmospher Res, Honolulu, HI 96822 USA South African Inst Aquat Biodivers, Grahamstown, South Africa Rhodes Univ, Dept Zool & Entomol, Grahamstown, South Africa Univ St Andrews, Ctr Res Ecol & Environm Modelling, Sch Math & Stat, St Andrews, Fife, Scotland Indian Ocean Marine Res Ctr, Australian Inst Marine Sci, Perth, WA, Australia Australian Inst Marine Sci, Townsville, Qld, Australia Govt Western Australia, Western Australian Fisheries & Marine Res Labs, Dept Primary Ind & Reg Dev, North Beach, WA, Australia NSW Dept Primary Ind, Fisheries Res, Taylors Beach, NSW, Australia Dept Environm & Water, Marine Sci Program, Sci & Corp Serv Div, Adelaide, SA, Australia Flinders Univ S Australia, Southern Shark Ecol Grp, Coll Sci & Engn, Bedford Pk, SA, Australia Deakin Univ, Sch Life & Environm Sci, Ctr Integrat Ecol, Warrnambool, Vic, Australia NSW Dept Primary Ind, Fisheries Res, Huskisson, NSW, Australia Coral Reef Res Fdn, Koror, Palau NSW Dept Primary Ind, Fisheries Res, Coffs Harbour, NSW, Australia Ctr Environm Fisheries & Aquaculture Sci, Lowestoft, Suffolk, England Sao Paulo State Univ, Elasmobranch Res Lab, Inst Biosci, Sao Vicente, SP, Brazil Massey Univ, Sch Nat & Computat Sci, Auckland, New Zealand Sao Paulo State Univ, Elasmobranch Res Lab, Inst Biosci, Sao Vicente, SP, Brazil

As pressure on coastal marine resources is increasing globally, the need to quantitatively assess vulnerable fish stocks is crucial in order to avoid the ecological consequences of stock depletions. Species of Sciaenidae (croakers, drums) are important components of tropical and temperate fisheries and are especially vulnerable to exploitation. The black-spotted croaker, Protonibea diacanthus, is the only large sciaenid in coastal waters of northern Australia where it is targeted by commercial, recreational and indigenous fishers due to its food value and predictable aggregating behaviour. Localized declines in the abundance of this species have been observed, highlighting the urgent requirement by managers for information on fine- and broad-scale population connectivity. This study examined the population structure of P. diacanthus across north-western Australia using three complementary methods: genetic variation in microsatellite markers, otolith elemental composition and parasite assemblage composition. The genetic analyses demonstrated that there were at least five genetically distinct populations across the study region, with gene flow most likely restricted by inshore biogeographic barriers such as the Dampier Peninsula. The otolith chemistry and parasite analyses also revealed strong spatial variation among locations within broad-scale regions, suggesting fine-scale location fidelity within the lifetimes of individual fish. The complementarity of the three techniques elucidated patterns of connectivity over a range of spatial and temporal scales. We conclude that fisheries stock assessments and management are required at fine scales (100 s of km) to account for the restricted exchange among populations (stocks) and to prevent localized extirpations of this species. Realistic management arrangements may involve the successive closure and opening of fishing areas to reduce fishing pressure.

Dredging can have significant impacts on aquatic environments, but the direct effects on fish have not been critically evaluated. Here, a meta-analysis following a conservative approach is used to understand how dredging-related stressors, including suspended sediment, contaminated sediment, hydraulic entrainment and underwater noise, directly influence the effect size and the response elicited in fish across all aquatic ecosystems and all life-history stages. This is followed by an in-depth review summarizing the effects of each dredging-related stressor on fish. Across all dredging-related stressors, studies that reported fish mortality had significantly higher effect sizes than those that describe physiological responses, although indicators of dredge impacts should endeavour to detect effects before excessive mortality occurs. Studies examining the effects of contaminated sediment also had significantly higher effect sizes than studies on clean sediment alone or noise, suggesting additive or synergistic impacts from dredging-related stressors. The early life stages such as eggs and larvae were most likely to suffer lethal impacts, while behavioural effects were more likely to occur in adult catadromous fishes. Both suspended sediment concentration and duration of exposure greatly influenced the type of fish response observed, with both higher concentrations and longer exposure durations associated with fish mortality. The review highlights the need for in situ studies on the effects of dredging on fish which consider the interactive effects of multiple dredging-related stressors and their impact on sensitive species of ecological and fisheries value. This information will improve the management of dredging projects and ultimately minimize their impacts on fish.

An Amendment to this paper has been published and can be accessed via a link at the top of the paper.

Fishing has had a profound impact on global reef shark populations, and the absence or presence of sharks is strongly correlated with national socio-economic conditions and reef governance. Decades of overexploitation have devastated shark populations, leaving considerable doubt as to their ecological status(1,2). Yet much of what is known about sharks has been inferred from catch records in industrial fisheries, whereas far less information is available about sharks that live in coastal habitats(3). Here we address this knowledge gap using data from more than 15,000 standardized baited remote underwater video stations that were deployed on 371 reefs in 58 nations to estimate the conservation status of reef sharks globally. Our results reveal the profound impact that fishing has had on reef shark populations: we observed no sharks on almost 20% of the surveyed reefs. Reef sharks were almost completely absent from reefs in several nations, and shark depletion was strongly related to socio-economic conditions such as the size and proximity of the nearest market, poor governance and the density of the human population. However, opportunities for the conservation of reef sharks remain: shark sanctuaries, closed areas, catch limits and an absence of gillnets and longlines were associated with a substantially higher relative abundance of reef sharks. These results reveal several policy pathways for the restoration and management of reef shark populations, from direct top-down management of fishing to indirect improvement of governance conditions. Reef shark populations will only have a high chance of recovery by engaging key socio-economic aspects of tropical fisheries.

Many marine fish populations have declined due to the individual or cumulative impacts of increasing water temperatures, ocean acidification, overfishing and other human-induced impacts such as land run-off, dredging and habitat alteration. Some solutions may be offered by ecosystem-based fisheries and conservation management. However, understanding their effectiveness relies on the availability of good quality data on the size distributions and abundance of fish populations and assemblages, collected at appropriate temporal and spatial scales. Since the early 2000s, baited remote underwater video systems (BRUVs) have become a popular tool for collecting data on fish assemblages across a range of depths and habitats. In Australia, this technique has been adopted by many different agencies and institutions, creating a unique opportunity to compile a continental-scale synthesis of fish data using a standardised sampling technique. Key Australian researchers and managers were invited to contribute to a synthesis workshop on baited underwater video in Albany, Western Australia between the 4th and 8th of February 2018. Data from 19,939 BRUVs deployments, collected between 2000 and 2017 around Australia, were compiled using GlobalArchive (globalarchive.org). The workshop identified and prioritised several key research themes that would contribute to the conservation and sustainable management of focal species and broad assemblages. Our goal is to describe where and when the data were collected, the type of equipment used and how the imagery was analysed. We also discuss the types of questions that can be addressed by analysing these standardised datasets and the potential benefits to conservation and fisheries management.

Knowledge of the factors that influence spatial patterns in fish abundance, distribution and diversity are essential for informing fisheries and conservation management. The present study was conducted in the nearshore Pilbara bioregion of north-western Australia where the dynamic marine environment is characterised by large embayments, numerous islands and islets, coexisting with globally significant petrochemical and mineral industries. Within Western Australia, this nearshore bioregion has high biodiversity and is considered to play an essential role in the recruitment of species of commercial importance. To better inform future investigations into both ecological processes and planning scenarios for management, a rapid assessment of the distribution, abundance and associations with nearshore habitats of fishes across the region was conducted. Baited remote underwater stereo-video systems (stereo-BRUVs) were used to simultaneously sample the fish assemblage and habitat composition. Generalised additive mixed models (GAMMs) were used to determine whether the abundance of fishes were related to habitat and a range of environmental variables (visibility, depth, distance to 30 m and 200 m depth isobars, boat ramps and the nearest large embayment (Exmouth Gulf). A diverse fish assemblage comprising 343 species from 58 families was recorded. The abundance and distribution patterns of fishery-target species and of the five most common and abundant species and families were linked positively with areas of high relief, hard coral cover, reef and macroalgae and negatively with the distance to the nearest oceanic waters (200 m depth isobar). This study provides information that can contribute to future marine spatial planning scenarios for management of the Pilbara using a unique, analytical approach that has broad application in biogeography.

Monitoring programs that aim to measure the diversity, abundance and biomass of fishes depend on accurate and reliable biological data to guide the development of robust management plans. It is important to implement an appropriate sampling technique that provides a comprehensive assessment, while reducing associated biases in the data collection process. We compared the sampling abilities of four different underwater stereo-video techniques; baited remote underwater stereo-video systems (BRUV), diver operated stereo-video (DOV), and two relatively new methodologies; slow towed stereo-video (STV) and remotely operated vehicle (ROV) fitted with a stereo-video. Comparisons were conducted in a temperate reef system along a single limestone ridge within Geographe Bay, Western Australia. More fish species and individuals were sampled by BRUVs, while transect based methods (DOV, STV, and ROV) were comparable. Combining BRUVs with a transect method resulted in a ~10% increase in observed diversity. BRUVs had a higher statistical power to detect change in comparison to the transect methods. This was due to the higher variability observed in transect methods that may sample greater habitat heterogeneity within a sample unit compared to BRUVs. Although differences did exist, data collected with the ROV was generally comparable to the other transect methods. We believe further research into ROV use is warranted as they provide a safer alternative to diver-based techniques and have the ability to extend into deeper-waters. We recommend that for fish diversity and abundance assessments a sampling strategy that combines BRUVs and a transect method should be adopted.

In this study, a total of 212 eggs were visually identified as snapper Chrysophrys auratus. Real-time PCR confirmed visual identification in 69% of cases but corroboration varied widely among plankton samples. The use of molecular tools to support visual identification prior to adopting daily egg production stock assessment methods should be considered.

Understanding the drivers of dispersal among populations is a central topic in marine ecology and fundamental for spatially explicit management of marine resources. The extensive coast of Northwestern Australia provides an emerging frontier for implementing new genomic tools to comparatively identify patterns of dispersal across diverse and extreme environmental conditions. Here, we focused on the stripey snapper (Lutjanus carponotatus), which is important to recreational, charter-based and customary fishers throughout the Indo-West Pacific. We collected 1,016 L. carponotatus samples at 51 locations in the coastal waters of Northwestern Australia ranging from the Northern Territory to Shark Bay and adopted a genotype-by-sequencing approach to test whether realized connectivity (via larval dispersal) was related to extreme gradients in coastal hydrodynamics. Hydrodynamic simulations using CONNIE and a more detailed treatment in the Kimberley Bioregion provided null models for comparison. Based on 4,402 polymorphic single nucleotide polymorphism loci shared across all individuals, we demonstrated significant genetic subdivision between the Shark Bay Bioregion in the south and all locations within the remaining, more northern bioregions. More importantly, we identified a zone of admixture spanning a distance of 180 km at the border of the Kimberley and Canning bioregions, including the Buccaneer Archipelago and adjacent waters, which collectively experiences the largest tropical tidal range and some of the fastest tidal currents in the world. Further testing of the generality of this admixture zone in other shallow water species across broader geographic ranges will be critical for our understanding of the population dynamics and genetic structure of marine taxa in our tropical oceans.

Marine macroinvertebrates support important fisheries throughout the Indo-Pacific, but stocks of species such as trochus (Rochia nilotica) are easily overharvested. In north-western Australia, trochus are taken from inshore reefs by Indigenous Australians and oceanic reefs by artisanal Indonesian fishers. The management of these environmentally distinct regions relies on understanding their spatial interdependencies, yet connectivity between them has not been evaluated empirically. Here, we used genotype-by-sequencing analysis of 514 trochus samples collected from 17 locations (15 in the inshore Kimberley, 2 offshore oceanic sites). Analysis of 5428 polymorphic single nucleotide polymorphism loci revealed significant genetic subdivision between the oceanic and coastal sites, and a subset of loci exhibited significantly higher subdivision, suggesting they are subject to directional selection. Population differentiation was also evident between the two oceanic sites, but not between coastal sites. Trochus populations from the coastal Kimberley and oceanic reefs represent two genetically and demographically independent units, with preliminary evidence for local adaptation to these distinctive environments. Management strategies for R. nilotica reflect these divisions, but the limited connectivity among oceanic populations indicates that they are vulnerable to overexploitation. Furthermore, their potential adaptive distinctiveness indicates that coastal stocks may be unsuitable for replenishing oceanic stocks.

Accelerating coastal development and shipping activities dictate that dredging operations will intensify, increasing potential impacts to fishes. Coastal fishes have high economic, ecological, and conservation significance and there is a need for evidence-based, quantitative guidelines on how to mitigate the impacts of dredging activities. We assess the potential risk from dredging to coastal fish and fisheries on a global scale. We then develop quantitative guidelines for two management strategies: threshold reference values and seasonal restrictions. Globally, threatened species and nearshore fisheries occur within close proximity to ports. We find that maintaining suspended sediment concentrations below 44 mg/L (15–121 bootstrapped CI) and for less than 24 hours would protect 95% of fishes from dredging-induced mortality. Implementation of seasonal restrictions during peak periods of reproduction and recruitment could further protect species from dredging impacts. This study details the first evidence-based defensible approach to minimize impacts to coastal fishes from dredging activities.

Trap sampling over reefs in deep (mean = 20 m) and shallow (mean = 10 m) waters along c. 1500 km of coastline in tropical north-western Australia during both day and night and in wet and dry periods yielded 23 377 fishes, representing 32 families, 58 genera and 119 species. Individuals of the Serranidae, Lutjanidae, Lethrinidae and Carangidae contributed 88.9% to the total catch. The ichthyofaunal compositions of the Kimberley, Canning and Pilbara bioregions were relatively discrete. Species composition was influenced far more by location (latitude) than by water depth, period and time of day, and underwent a gradational change southwards. The latter change reflected differences in the trends exhibited by the relative abundances of certain species with increasing latitude and the confinement of other species largely to particular regions. The three most abundant species, i.e. Lethrinus sp. 3, Lutjanus carponotatus and Lethrinus laticaudis contributed 34.8, 20.8 and 11.6% to the total catch, respectively. The first species was rarely recorded in the two most northern locations and was abundant in the four most southern locations, whereas the last two species were relatively more abundant in northern than in southern locations. Lutjanus bitaeniatus and Lutjanus johnii were found exclusively at the two locations in the Kimberley region, whereas Abalistes stellatus, Pentapodus emeryii and Lethrinus nebulosus were not caught in this region but were found in both locations of the Canning and Pilbara regions. The species composition in deep and shallow waters at each location almost invariably differed significantly between day and night and between dry and wet periods, with species such as L. bitaeniatus, L. johnii, Lutjanus sebae and A. stellatus being more abundant over deep reefs, whereas L. carponotatus, L. laticaudis, Siganus fuscescens and Lethrinus lentjan were more numerous over shallow reefs. Species such as L. johnii and Lethrinus atkinsoni were relatively more important in night-time than daytime catches, whereas the reverse applied to Lethrinus lentjan, L. laticaudis and Choerodon cyanodus. Lethrinus sp. 3 and L. laticaudis were relatively more important in catches during the dry than wet period.

The grass emperor Lethrinus laticaudis is a conspicuous element of the commercial and recreational catch from nearshore reef systems across northern Australia. The nearshore reef systems across northern Australia are exposed to increasing levels of fishing pressure from commercial and recreational fishers. To inform ongoing management of this species, the present study examined the stock structure of L. laticaudis across northern Australia using a combination of complementary techniques. In all, 342 L. laticaudis samples were collected from 13 locations in the coastal waters of northern Australia ranging from the Pilbara region of Western Australia to Moreton Bay in south-east Queensland. Population genetic analyses using microsatellite markers demonstrated that there were at least four genetically distinct populations across northern Australia with gene flow between management jurisdictions (with significantly more separation between Western Australian and Northern Territory locations than between Northern Territory and Queensland locations). An isolation by distance effect was evident (genetic differences increasing linearly with distance). Otolith microchemistry and parasitology analyses indicated some spatial structuring of populations within broader regions. These findings of restricted connectivity at small spatial scales suggest that L. laticaudis is vulnerable to localised depletion in areas where fishing effort is concentrated. This conclusion is consistent with recent observations of fishery declines in heavily fished locations.

Thirty-four microsatellite loci were isolated from three reef fish species; golden snapperLutjanus johnii, blackspotted croakerProtonibea diacanthusand grass emperorLethrinus laticaudisusing a next generation sequencing approach. Both IonTorrent single reads and Illumina MiSeq paired-end reads were used, with the latter demonstrating a higher quality of reads than the IonTorrent. From the 1–1.5 million raw reads per species, we successfully obtained 10–13 polymorphic loci for each species, which satisfied stringent design criteria. We developed multiplex panels for the amplification of the golden snapper and the blackspotted croaker loci, as well as post-amplification pooling panels for the grass emperor loci. The microsatellites characterized in this work were tested across three locations of northern Australia. The microsatellites we developed can detect population differentiation across northern Australia and may be used for genetic structure studies and stock identification.

Due to human activities, marine and terrestrial ecosystems face a future where disturbances are predicted to occur at a frequency and severity unprecedented in the recent past. Of particular concern is the ability of systems to recover where multiple stressors act simultaneously. We examine this issue in the context of a coral reef ecosystem where increases in stressors, such as fisheries, benthic degradation, cyclones and coral bleaching, are occurring at global scales. By utilizing long-term (decadal) monitoring programs, we examined the combined effects of chronic (removal of sharks) and pulse (cyclones, bleaching) disturbances on the trophic structure of coral reef fishes at two isolated atoll systems off the coast of northwest Australia. We provide evidence consistent with the hypothesis that the loss of sharks can have an impact that propagates down the food chain, potentially contributing to mesopredator release and altering the numbers of primary consumers. Simultaneously, we show how the effects of bottom-up processes of bleaching and cyclones appear to propagate up the food chain through herbivores, planktivores and corallivores, but do not affect carnivores. Because their presence may promote the abundance of herbivores, the removal of sharks by fishing has implications for both natural and anthropogenic disturbances involving the loss of corals, as herbivores are critical to the progress and outcome of coral recovery.