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Environmental disturbances and fishing are well known drivers of coral reef fish population size, length-frequency, and assemblage structure. However, few studies have partitioned the spatial and temporal impacts of multiple disturbance events and long-term no-take marine reserve (NTMR) protection on the biomass of juvenile and adult reef-fishes based on the known size of sexual maturity. Here, we document responses in the biomass of juvenile and adult wrasses (Labridae) Hemigymnus melapterus, H. fasciatus, Cheilinus fasciatus, and Oxycheilinus digramma, to environmental disturbance events, NTMR protection, and predator density on inshore fringing coral reefs at the Palm and Whitsunday Island groups, Great Barrier Reef (GBR), Australia from 2007 to 2018 (12 years). The biomass of juvenile and adult wrasses on inshore GBR reefs were driven predominantly by benthic habitat associations, rather than by NTMR protection or density of wrasse predators (Plectropomus spp.). Despite similar species-specific associations of juvenile and adult wrasses with benthic cover, juvenile wrasse biomass consistently declined following coral bleaching and cyclone events. Conversely, adult wrasses had variable responses to disturbance events, including some increases in biomass. Disturbance-mediated declines in the biomass of juvenile wrasses are likely to generate ongoing reductions in the abundance of these species on inshore GBR reefs. Our findings provide further evidence that habitat loss impacts a range of coral reef fishes beyond those that are directly reliant upon live coral. Shifts in assemblage structure, loss of biodiversity, and reductions in fishery productivity will become increasingly apparent in coral reef ecosystems if anthropogenic global warming continues unabated.

For over 40 years, management of the Great Barrier Reef Marine Park (GBRMP) in Australia has focused on limiting human-use impacts to facilitate natural resilience and recovery. Compounding acute disturbances and chronic stressors have resulted in degradation of coral reef habitats in many areas of the Marine Park. Given current trends and predictions of escalating climate-driven disturbances, it is increasingly evident that effective management of the GBRMP requires adaptive and novel approaches to protect and restore coral reef health. Here, we provide an overview of the logistical requirements and early-stage ecological benefits of repositioning 400 tonnes of moderately sized (1–3 m diameter) Porites spp. coral colonies (bommies) that were displaced by cyclone-generated swells that impacted reefs in the Whitsunday Islands during March 2017. An ecological survey conducted 16 months after the bommie repositioning revealed that several genera of hard coral had settled onto the bommies and that a range of reef fish species were associating with the restored habitat. Early findings suggest that the repositioning of the displaced bommies has assisted in restoring reef habitat structure and settlement habitat for juvenile corals, while improving natural aesthetics, vessel access and tourist experiences at Manta Ray Bay.

Coral reef ecosystems are under increasing pressure from local and regional stressors and a changing climate. Current management focuses on reducing stressors to allow for natural recovery, but in many areas where coral reefs are damaged, natural recovery can be restricted, delayed or interrupted because of unstable, unconsolidated coral fragments, or rubble. Rubble fields are a natural component of coral reefs, but repeated or high-magnitude disturbances can prevent natural cementation and consolidation processes, so that coral recruits fail to survive. A suite of interventions have been used to target this issue globally, such as using mesh to stabilise rubble, removing the rubble to reveal hard substrate and deploying rocks or other hard substrates over the rubble to facilitate recruit survival. Small, modular structures can be used at multiple scales, with or without attached coral fragments, to create structural complexity and settlement surfaces. However, these can introduce foreign materials to the reef, and a limited understanding of natural recovery processes exists for the potential of this type of active intervention to successfully restore local coral reef structure. This review synthesises available knowledge about the ecological role of coral rubble, natural coral recolonisation and recovery rates and the potential benefits and risks associated with active interventions in this rapidly evolving field. Fundamental knowledge gaps include baseline levels of rubble, the structural complexity of reef habitats in space and time, natural rubble consolidation processes and the risks associated with each intervention method. Any restoration intervention needs to be underpinned by risk assessment, and the decision to repair rubble fields must arise from an understanding of when and where unconsolidated substrate and lack of structure impair natural reef recovery and ecological function. Monitoring is necessary to ascertain the success or failure of the intervention and impacts of potential risks, but there is a strong need to specify desired outcomes, the spatial and temporal context and indicators to be measured. With a focus on the Great Barrier Reef, we synthesise the techniques, successes and failures associated with rubble stabilisation and the use of small structures, review monitoring methods and indicators, and provide recommendations to ensure that we learn from past projects.

Combining no-take marine reserves with exclusive access by communities to unreserved waters could provide the required incentives for community management to achieve positive impacts. However, few protected areas have been critically evaluated for their impact, which involves applying counterfactual thinking to predict conditions within protected areas if management had never occurred. Here, we use statistical matching to conduct a rigorous impact evaluation of dual management systems on coral reef fishes in Tonga, with communities having both full no-take areas and areas of exclusive fishing rights. No-take areas generally had positive impacts on the species richness, biomass, density, and size of target reef fish, while exclusive access areas were similar to predicted counterfactual conditions. The latter is likely because overall fishing pressure in exclusive access areas might not actually change, although more fish could be exploited by communities with access rights. Our findings suggest that dual management is effective at incentivizing effective community-based no-take areas for biodiversity conservation and resource management.

Coral reef ecosystems have suffered an unprecedented loss of habitat-forming hard corals in recent decades. While marine conservation has historically focused on passive habitat protection, demand for and interest in active restoration has been growing in recent decades. However, a disconnect between coral restoration practitioners, coral reef managers and scientists has resulted in a disjointed field where it is difficult to gain an overview of existing knowledge. To address this, we aimed to synthesise the available knowledge in a comprehensive global review of coral restoration methods, incorporating data from the peer-reviewed scientific literature, complemented with grey literature and through a survey of coral restoration practitioners. We found that coral restoration case studies are dominated by short-term projects, with 60% of all projects reporting less than 18 months of monitoring of the restored sites. Similarly, most projects are relatively small in spatial scale, with a median size of restored area of 100 m2. A diverse range of species are represented in the dataset, with 229 different species from 72 coral genera. Overall, coral restoration projects focused primarily on fast-growing branching corals (59% of studies), and report survival between 60 and 70%. To date, the relatively young field of coral restoration has been plagued by similar ‘growing pains’ as ecological restoration in other ecosystems. These include 1) a lack of clear and achievable objectives, 2) a lack of appropriate and standardised monitoring and reporting and, 3) poorly designed projects in relation to stated objectives. Mitigating these will be crucial to successfully scale up projects, and to retain public trust in restoration as a tool for resilience based management. Finally, while it is clear that practitioners have developed effective methods to successfully grow corals at small scales, it is critical not to view restoration as a replacement for meaningful action on climate change.

Quantifying the role of biophysical and anthropogenic drivers of coral reef ecosystem processes can inform management strategies that aim to maintain or restore ecosystem structure and productivity. However, few studies have examined the combined effects of multiple drivers, partitioned their impacts, or established threshold values that may trigger shifts in benthic cover. Inshore fringing reefs of the Great Barrier Reef Marine Park (GBRMP) occur in high-sediment, high-nutrient environments and are under increasing pressure from multiple acute and chronic stressors. Despite world-leading management, including networks of no-take marine reserves, relative declines in hard coral cover of 40–50% have occurred in recent years, with localized but persistent shifts from coral to macroalgal dominance on some reefs. Here we use boosted regression tree analyses to test the relative importance of multiple biophysical drivers on coral and macroalgal cover using a long-term (12–18 yr) data set collected from reefs at four island groups. Coral and macroalgal cover were negatively correlated at all island groups, and particularly when macroalgal cover was above 20%. Although reefs at each island group had different disturbance-and-recovery histories, degree heating weeks (DHW) and routine wave exposure consistently emerged as common drivers of coral and macroalgal cover. In addition, different combinations of sea-surface temperature, nutrient and turbidity parameters, exposure to high turbidity (primary) floodwater, depth, grazing fish density, farming damselfish density, and management zoning variously contributed to changes in coral and macroalgal cover at each island group. Clear threshold values were apparent for multiple drivers including wave exposure, depth, and degree heating weeks for coral cover, and depth, degree heating weeks, chlorophyll a, and cyclone exposure for macroalgal cover, however, all threshold values were variable among island groups. Our findings demonstrate that inshore coral reef communities are typically structured by broadscale climatic perturbations, superimposed upon unique sets of local-scale drivers. Although rapidly escalating climate change impacts are the largest threat to coral reefs of the GBRMP and globally, our findings suggest that proactive management actions that effectively reduce chronic stressors at local scales should contribute to improved reef resistance and recovery potential following acute climatic disturbances.

Aim: Marine protected areas (MPAs) are increasingly implemented to conserve or restore coral reef biodiversity, yet evidence of their benefits for enhancing coral cover is limited and variable. Location: 30 MPAs worldwide and nearby sites (within 10 km). Taxa: Cover of key functional groups for coral (total, branching, massive and tabular), and algae (total, filamentous, foliose) and total biomass of reef fish trophic groups (excavator, scraper, browser, higher carnivore). Methods: We used a global dataset obtained using standardized survey methods at 465 sites associated with 30 MPAs in 28 ecoregions to test the effects of five key MPA attributes (>10 years old, well‐enforced, no‐take, large and isolated) on coral cover, algal cover and reef fish biomass. We also tested the direct (reducing disturbance by human activities) versus indirect pathways (increasing grazing potential through recovering populations of herbivorous fishes) by which MPAs can influence coral and algal cover. Results: Only well‐enforced, no‐take and old (>10 years) MPAs had higher total coral cover (response ratio 1.08–1.19×) than fished sites, mostly due to the increased cover of massive coral growth forms (1.34–2.06×). This effect arose through both the direct influence of protection and indirect benefits of depressed algal cover by recovering herbivorous fish biomass. Neither the direct (standardized coefficient = 0.06) nor indirect effects (standardized coefficient = 0.04) of no‐take protection on coral cover were particularly strong, likely reflecting regional differences in fishing gear, targeted species and trophic webs. Conclusions: MPAs promote the persistence of some functional groups of corals, and thus represent an important management tool, globally.

We thank the staff of WorldFish Center and the Secretariat of the Pacific Community for their administrative support. Helpful comments were given by N. Andrew, J. Bell, W. Nash and S. Uthicke. We thank N. Agudo, P. Blazer, B. Blockmans, J. Le Dreau and M. Simutoga for their helpful assistance. The project was funded by the Australian Centre for International Agricultural Research (ACIAR) through project FIS/1999/025, the 3 provinces of New Caledonia and the government of France.

Market price trends of seafood can inform fishery management measures and strengthen the bargaining power of fishers. The four-sided sea cucumber Isostichopus badionotus and donkey dung sea cucumber Holothuria mexicana are heavily exploited in small-scale fisheries in the Gulf of Mexico and Caribbean for export to China. We recorded prices and sizes of the dried sea cucumbers from 41 lots in 28 shops in Hong Kong and Guangzhou, China. Market value ranged 132–358 US$ kg−1 for I. badionotus, and 16–209 US$ kg−1 for H. mexicana. The relationship between product length and price per kg was weak for both species, revealing large variability in the marketplace. Price per individual increased linearly with product length for H. mexicana, and increased nonlinearly for I. badionotus indicating that large specimens were disproportionately more valuable than small ones. Thus, the economic performance of fisheries, especially those for I. badionotus, could be optimised by strictly enforcing large minimum size limits. High market value identifies I. badionotus as a species of conservation concern. A large difference between reported prices received by fishers and market retail prices suggests substantial scope for upgrading value chains of small-scale export fisheries.

Fisheries usually first remove large predators before switching to smaller species, causing lasting changes to fish community structure. Reef fish provide essential protein and income for many people, and the impacts of commercial and high-intensity subsistence fishing on reef fish are well documented. However, how fish communities respond to low levels of subsistence fishing using traditional techniques (fishing for food, few fishers) is less well understood. We use three atolls in the Marshall Islands as a model system to quantify effects of commercial and subsistence fishing on reef fish communities, compared to a near-pristine baseline. Unexpectedly, fish biomass was highest on the commercially-fished atoll where the assemblage was dominated by herbivores (50% higher than other atolls) and contained few top predators (70% lower than other atolls). By contrast, fish biomass and trophic composition did not differ between pristine and subsistence-fished atolls – top predators were abundant on both. We show that in some cases, reefs can support fishing by small communities to provide food but still retain intact fish assemblages. Low-intensity subsistence fishing may not always harm marine food webs, and we suggest that its effects depend on the style and intensity of fishing practised and the type of organisms targeted.

Coral reefs are periodically impacted by disturbance events that reduce live coral cover and habitat complexity, with concomitant effects on fish assemblage structure. While the density of some fish species may increase following coral loss, most species decline. Determining which species are ‘winners’ and ‘losers’ following disturbances is fundamental to inform projections of future reef community structure, biodiversity, and productivity. Here, we analyse a long-term (2006–2018), spatially extensive (≈ 700 km) ‘natural experiment’ in which the responses of 11 wrasse taxa to acute disturbance events and no-take marine reserve (NTMR) protection were quantified on fringing coral reefs in the Palm (18°34′ S, 146°29′ E), Whitsunday (20°08′ S, 148°56′ E), and Keppel Island (23°10′ S, 150°57′ E) groups, Great Barrier Reef, Australia. The responses of wrasse densities to benthic habitat change were taxa specific and temporally consistent. Disturbance-mediated reductions in live hard coral cover and/or habitat complexity resulted in density declines for Hemigymnus melapterus, Hemigymnus fasciatus, Cheilinus fasciatus, Labroides spp., Oxycheilinus digramma, and Thalassoma spp. Conversely, Halichoeres spp. densities correlated positively with increased relative cover of sand and rubble, while Stethojulis spp., Anampses spp., Epibulus insidiator, and Bodianus spp. displayed variable responses to habitat changes. No wrasses exhibited an NTMR effect and predator density, irrespective of NTMR status, only influenced five taxa across all island groups. The lack of NTMR effects and variable top-down predator effects suggest that taxa-specific benthic habitat associations were the predominant drivers of wrasse densities on inshore GBR reefs.

The Coral Sea is a marginal sea of the southwestern Pacific, bounded by the Australian continental shelf to the west, southeastern Papua New Guinea (PNG) and the southeastern Solomon Islands to the north, the Vanuatu archipelago to the east, and the hydrographic barrier of the Tasman Front to the south. Its underlying geology consists of a series of basins interrupted by plateaux and rises, and is bordered by volcanic island arcs to the east. Its oceanography is dominated by the east-to-west South Equatorial Current (SEC) and its bifurcation at the edge of the Australian continental shelf. This area is relatively unimpacted, and connects the tropical center of marine biodiversity with subtropical and temperate seas, and with the extensive continental shelf habitats off the Australian margin with the rich island archipelagos to the east. The Coral Sea offers a rare opportunity to explore a tropical sea as close to its “baseline” conditions as any marine area in the world.

Reef Life Survey (RLS) provides a new model for ecological monitoring through training experienced recreational divers in underwater visual census methods to the level of skilled scientists. Detail produced is similar to that of programs with professional scientific teams, at low cost to allow global coverage. RLS differs from most other citizen science initiatives in its emphasis on rigorous training and data quality rather than open participation, selectively involving the most skilled and committed members. Volunteers participate primarily because they appreciate the close relationship with scientists, other divers, and managers, and see their efforts directly contributing to improved environmental outcomes. RLS works closely with Australian management agencies, scheduling annual events at core monitoring sites associated with 10 inshore marine protected areas Australia-wide. Surveys of 12 offshore Australian Marine Parks (AMPs) are realized through 2-4 week voyages in a sailing catamaran crewed by volunteers. Across the AMP network, RLS surveys have quantified densities of fishes, mobile invertebrates, macroalgae and corals at 350 shallow coral reef sites (180 sites surveyed on two or more occasions), providing an understanding of (i) population changes amongst threatened species including sea snakes, (ii) responses of fish and invertebrate populations following fisheries closures, (iii) ecosystem-wide impacts of marine heat-waves, and (iv) the extent that AMPs spanning the network comprehensively encompass national coral reef biodiversity. This scientist/volunteer/manager collaboration could be greatly expanded globally (presently 3537 sites in 53 countries).

Despite increasing threats to Tonga’s coral reefs from stressors that are both local (e.g. overfishing and pollution) and global (e.g. climate change), there is yet to be a systematic assessment of the status of the country’s coral reef ecosystem and reef fish fishery stocks. Here, we provide a national ecological assessment of Tonga’s coral reefs and reef fish fishery using ecological survey data from 375 sites throughout Tonga’s three main island groups (Ha’apai, Tongatapu and Vava’u), represented by seven key metrics of reef health and fish resource status. Boosted regression tree analysis was used to assess and describe the relative importance of 11 socio-environmental variables associated with these key metrics of reef condition. Mean live coral cover across Tonga was 18%, and showed a strong increase from north to south correlated with declining sea surface temperature, as well as with increasing distance from each provincial capital. Tongatapu, the southernmost island group, had 2.5 times greater coral cover than the northernmost group, Vava’u (24.9% and 10.4% respectively). Reef fish species richness and density were comparable throughout Tongatapu and the middle island group, Ha’apai (~35 species/transect and ~2500 fish/km2), but were significantly lower in Vava’u (~24 species/transect and ~1700 fish/km2). Spatial patterns in the reef fish assemblage were primarily influenced by habitat-associated variables (slope, structural complexity, and hard coral cover). The biomass of target reef fish was greatest in Ha’apai (~820 kg/ha) and lowest in Vava’u (~340 kg/ha), and was negatively associated with higher human influence and fishing activity. Overall mean reef fish biomass values suggest that Tonga’s reef fish fishery can be classified as moderately to heavily exploited, with 64% of sites having less than 500 kg/ha. This study provides critical baseline ecological information for Tonga’s coral reefs that will: (1) facilitate ongoing management and research; and (2) enable accurate reporting on conservation targets locally and internationally.

Giant clams have been over-exploited throughout their wide geographical range in the Indo-Pacific. Marine reserves could be one tool to potentially safeguard broodstock, but their effect on giant clam abundance and the differential benefits of lagoon reserves compared to barrier reef reserves is still unclear. We assessed abundances of four species of giant clams across 20 barrier reef and 30 lagoon reef sites across 600 km of coastline in New Caledonia using stratified underwater visual censuses. Tridacna maxima was the most common species. T. derasa was significantly more abundant in marine reserves than at sites open to fishing, but there was no effect of marine reserves on total abundance pooled across the four species. T. squamosa was significantly more abundant on barrier reefs, while Hippopus hippopus was found solely on lagoon reefs. National data from fisher logbooks shows a marked reduction in commercial catches of giant clam following implementation of daily catch limits of 5 giant clams per vessel per trip. Despite small daily bag limits of 2 giant clams per recreational fisher per trip, the recreational catch appears to be significant and much greater than the commercial catch. The utility of marine reserves on giant clams appears to be species specific, and might be diminished for the group as a whole by the concomitant protection of their natural predators. Both lagoon and barrier reef sites should be included in reserve networks. Our data suggest that daily boat/trip limits are an effective output control, at least for commercial fishers, but might not safeguard giant clams if recreational fishers are numerous. Further fishery restrictions on the less common species might be needed to ensure their persistence in the Indo-Pacific.

Existing marine bioregions covering the Pacific Ocean are conceptualised at spatial scales that are too broad for national marine spatial planning. Here, we developed the first combined oceanic and coastal marine bioregionalisation at national scales, delineating 262 deep-water and 103 reef-associated bioregions across the southwest Pacific. The deep-water bioregions were informed by thirty biophysical environmental variables. For reef-associated environments, records for 806 taxa at 7369 sites were used to predict the probability of observing taxa based on environmental variables. Both deep-water and reef-associated bioregions were defined with cluster analysis applied to the environmental variables and predicted species observation probabilities, respectively to classify areas with high taxonomic similarity. Local experts further refined the delineation of the bioregions at national scales for four countries. This work provides marine bioregions that enable the design of ecologically representative national systems of marine protected areas within offshore and inshore environments in the Pacific.

Near-shore marine environments are increasingly subjected to reduced water quality, and their ability to withstand it is critical to their persistence. The potential role marine reserves may play in mitigating the effects of reduced water quality has received little attention. We investigated the spatial and temporal variability in live coral and macro-algal cover and water quality during moderate and major flooding events of the Fitzroy River within the Keppel Bay region of the Great Barrier Reef Marine Park from 2007 to 2013. We used 7 years of remote sensing data on water quality and data from long-term monitoring of coral reefs to quantify exposure of coral reefs to flood plumes. We used a distance linear model to partition the contribution of abiotic and biotic factors, including zoning, as drivers of the observed changes in coral and macro-algae cover. Moderate flood plumes from 2007 to 2009 did not affect coral cover on reefs in the Keppel Islands, suggesting the reef has intrinsic resistance against short-term exposure to reduced water quality. However, from 2009 to 2013, live coral cover declined by ∼50% following several weeks of exposure to turbid, low salinity water from major flood plume events in 2011 and subsequent moderate events in 2012 and 2013. Although the flooding events in 2012 and 2013 were smaller than the flooding events between 2007 to 2009, the ability of the reefs to withstand these moderate floods was lost, as evidenced by a ∼20% decline in coral cover between 2011 to 2013. Although zoning (no-take reserve or fished) was identified a significant driver of coral cover, we recorded consistently lower coral cover on reserve reefs than on fished reefs throughout the study period and significantly lower cover in 2011. Our findings suggest that even reefs with an inherent resistance to reduced water quality are not able to withstand repeated disturbance events. The limitations of reserves in mitigating the effects of reduced water quality on near-shore coral reefs underscores the importance of integrated management approaches that combine effective land-based management with networks of no-take reserves.

Spatial management of the highly dynamic pelagic realm, and the highly mobile species it supports, requires dynamic processes to be incorporated into reserve design. To achieve this, planners need information on how these processes vary across space and time, and how this variation relates to species of conservation interest. This study presents a new method of quantifying variability that captures both between- and within-year changes in variables of interest. We applied this method to remotely-sensed chlorophyll-a in the Coral Sea to find five distinct regimes of variation that serve as surrogates for assemblages of species of conservation interest. We performed a gap analysis to determine protection of the regimes both internationally and nationally within Australia's network of marine reserves in the Coral Sea. We also identified key areas for protection within each regime, in terms of chlorophyll-a variability and species associations, and examined their protection status. Depending on conservation objectives, reserve systems that span multiple national jurisdictions and a rezoning of Australian national waters might be necessary to meet protection requirements for the regimes and for key areas within them. The current suspension and review of the Coral Sea Commonwealth Marine Reserve management plans and the recent proclamation of New Caledonia's as yet unzoned Coral Sea Nature Park offer planners an opportunity to incorporate dynamic processes into conservation planning for the Coral Sea. The method we present can be applied at other locations for time-series of any variable/s of interest, aiding the spatial management of dynamic features in both marine and terrestrial contexts.

Global warming is markedly changing diverse coral reef ecosystems through an increasing frequency and magnitude of mass bleaching events1–3. How local impacts scale up across affected regions depends on numerous factors, including patchiness in coral mortality, metabolic effects of extreme temperatures on populations of reef-dwelling species4 and interactions between taxa. Here we use data from before and after the 2016 mass bleaching event to evaluate ecological changes in corals, algae, fishes and mobile invertebrates at 186 sites along the full latitudinal span of the Great Barrier Reef and western Coral Sea. One year after the bleaching event, reductions in live coral cover of up to 51% were observed on surveyed reefs that experienced extreme temperatures; however, regional patterns of coral mortality were patchy. Consistent declines in coral-feeding fishes were evident at the most heavily affected reefs, whereas few other short-term responses of reef fishes and invertebrates could be attributed directly to changes in coral cover. Nevertheless, substantial region-wide ecological changes occurred that were mostly independent of coral loss, and instead appeared to be linked directly to sea temperatures. Community-wide trophic restructuring was evident, with weakening of strong pre-existing latitudinal gradients in the diversity of fishes, invertebrates and their functional groups. In particular, fishes that scrape algae from reef surfaces, which are considered to be important for recovery after bleaching2, declined on northern reefs, whereas other herbivorous groups increased on southern reefs. The full impact of the 2016 bleaching event may not be realized until dead corals erode during the next decade5,6. However, our short-term observations suggest that the recovery processes, and the ultimate scale of impact, are affected by functional changes in communities, which in turn depend on the thermal affinities of local reef-associated fauna. Such changes will vary geographically, and may be particularly acute at locations where many fishes and invertebrates are close to their thermal distribution limits7. Fish and invertebrate communities transformed across the span of the Great Barrier Reef following the 2016 bleaching event due to a decline in coral-feeding fishes resulting from coral loss, and because of different regional responses of key trophic groups to the direct effect of temperature.

Severe climatic disturbance events often have major impacts on coral reef communities, generating cycles of decline and recovery, and in some extreme cases, community-level phase shifts from coral- to algal-dominated states. Benthic habitat changes directly affect reef fish communities, with low coral cover usually associated with low fish diversity and abundance. No-take marine reserves (NTRs) are widely advocated for conserving biodiversity and enhancing the sustainability of exploited fish populations. Numerous studies have documented positive ecological and socio-economic benefits of NTRs; however, the ability of NTRs to ameliorate the effects of acute disturbances on coral reefs has seldom been investigated. Here, we test these factors by tracking the dynamics of benthic and fish communities, including the important fishery species, coral trout (Plectropomus spp.), over 8 years in both NTRs and fished areas in the Keppel Island group, Great Barrier Reef, Australia. Two major disturbances impacted the reefs during the monitoring period, a coral bleaching event in 2006 and a freshwater flood plume in 2011. Both disturbances generated significant declines in coral cover and habitat complexity, with subsequent declines in fish abundance and diversity, and pronounced shifts in fish assemblage structure. Coral trout density also declined in response to the loss of live coral, however, the approximately 2:1 density ratio between NTRs and fished zones was maintained over time. The only post-disturbance refuges for coral trout spawning stocks were within the NTRs that escaped the worst effects of the disturbances. Although NTRs had little discernible effect on the temporal dynamics of benthic or fish communities, it was evident that the post-disturbance refuges for coral trout spawning stocks within some NTRs may be critically important to regional-scale population persistence and recovery.

Tropical marginal seas (TMSs) are natural subregions of tropical oceans containing biodiverse ecosystems with conspicuous, valued, and vulnerable biodiversity assets. They are focal points for global marine conservation because they occur in regions where human populations are rapidly expanding. Our review of 11 TMSs focuses on three key ecosystems—coral reefs and emergent atolls, deep benthic systems, and pelagic biomes—and synthesizes, illustrates, and contrasts knowledge of biodiversity, ecosystem function, interaction between adjacent habitats, and anthropogenic pressures. TMSs vary in the extent that they have been subject to human influence—from the nearly pristine Coral Sea to the heavily exploited South China and Caribbean Seas—but we predict that they will all be similarly complex to manage because most span multiple national jurisdictions. We conclude that developing a structured process to identify ecologically and biologically significant areas that uses a set of globally agreed criteria is a tractable first step toward effective multinational and transboundary ecosystem management of TMSs.

As anthropogenic and natural disturbances intensify, there is mounting concern about the loss of functionally important or unique species. Functional redundancy, or the presence of several different species occupying similar functional niches, can provide insurance against diversity loss, but evidence for this effect is rare. Likewise, the ways in which functional redundancy patterns respond to disturbances are poorly known, impeding a thorough understanding of community‐level dynamics post disturbance. Here, we use an extensive reduction of hard coral cover following a tropical cyclone to explore the response of a highly diverse reef fish assemblage to habitat degradation. We demonstrate that despite clear trait value‐specific susceptibility of fishes to the disturbance, five of six functional indices (including functional richness and evenness) showed no relationship with habitat degradation. In contrast, functional originality, which quantifies the average functional uniqueness of species within an assemblage, increased post disturbance, exhibiting a negative, albeit weak, relationship with decreasing coral cover. The increase in functional originality is simultaneously driven by the loss of functionally similar species in susceptible groups (predominantly small planktivorous and omnivorous species that associate with live coral habitat) and the addition of functionally unique species in groups that benefit from the disturbance (large, non‐territorial species feeding on algal turfs, detritus, and invertebrates). Our findings suggest that coral reefs with high coral cover can foster fish assemblages with low functional originality (i.e., high functional redundancy), therefore preventing detectible changes in some of the most commonly applied functional indices post disturbance. However, we caution that the limited resolution of trait‐based approaches may mask the loss of functionally unique species and that, with an increase in functional originality, post disturbance assemblages may be less suited to adequately maintain certain ecosystem functions in the face of future disturbances. Thus, there is an urgent need for further exploration of the dynamics between disturbances, functional redundancy, and ecosystem functioning.

Declines in the abundance of marine vertebrates are of considerable concern, especially when they occur in isolated locations relatively protected from most major anthropogenic disturbances. This paper reports on sustained declines in the abundance and diversity of sea snakes at Ashmore Reef, a renowned biodiversity hotspot in Australia’s Timor Sea. Surveys conducted in eight years between 1973 and 2010 recorded the highest abundances (average 42–46 snakes day−1) and species richness (nine species) in 1973 and 1994. In 2002 abundance had declined by more than 50% (21 snakes day−1) and only five species were recorded. Since 2005 abundances have been consistently low (1–7 snakes day−1), with just two species, Aipysurus laevis andEmydocephalus annulatus, recorded in significant numbers. Despite extensive searches since 2005 (especially in 2010) five species of sea snake historically abundant at Ashmore Reef have not been sighted and are presumed to have become locally extinct. These species include three Timor Sea endemics Aipysurus apraefrontalis, Aipysurus foliosquama, Aipysurus fuscus, and one Australasian endemic Aipysurus duboisii. Declines in the abundance and diversity of sea snakes at Ashmore Reef cannot be attributed to differences in survey methods among years. Ashmore Reef was declared a National Nature Reserve (IUCN Category 1a) in 1983 and, although the causes for the declines are not known, this protection has not prevented their occurrence. We discuss possible causes for these enigmatic declines however, in order to implement effective management strategies, studies are needed to determine why sea snakes have disappeared from Ashmore Reef.

Sharks present a critical conservation challenge, but little is known about their spatial distribution and vulnerability, particularly in complex seascapes such as Australia's Great Barrier Reef Marine Park (GBRMP). We review (1) the distribution of shark species among the primary habitats of the GBRMP (coral reefs, inshore/shelf, pelagic and deep-water habitats) (2) the relative exploitation of each species by fisheries, and (3) how current catch rates interact with their vulnerability and trophic index. Excluding rays and chimaeras, we identify a total of 82 shark species in the GBRMP. We find that shark research in the GBRMP has yielded little quantitative information on most species. Reef sharks are largely site-fidelic, but can move large distances and some regularly use non-reef habitats. Inshore and shelf sharks use coastal habitats either exclusively or during specific times in their life cycle (e.g. as nurseries). Virtually nothing is known about the distribution and habitat use of the GBRMP's pelagic and deep-water sharks. At least 46 species (53.5 %) are caught in one or more fisheries, but stock assessments are lacking for most. At least 17 of the sharks caught are considered highly vulnerable to exploitation. We argue that users of shark resources should be responsible for demonstrating that a fishery is sustainable before exploitation is allowed to commence or continue. This fundamental change in management principle will safeguard against stock collapses that have characterised many shark fisheries.

Quantifying changes to coral reef fish assemblages in the wake of cyclonic disturbances is challenging due to spatial variability of damage inherent in such events. Often, fish abundance appears stable at one spatial scale (e.g. reef-wide), but exhibits substantial change at finer scales (e.g. site-specific decline or increase). Taxonomic resolution also plays a role; overall stability at coarse taxonomic levels (e.g. family) may mask species-level turnover. Here we document changes to reef fish communities after severe Tropical Cyclone Ita crossed Lizard Island, Great Barrier Reef. Coral and reef fish surveys were conducted concurrently before and after the cyclone at four levels of exposure to the prevailing weather. Coral cover declined across all exposures except sheltered sites, with the largest decline at exposed sites. There was no significant overall reduction in the total density, biomass and species richness of reef fishes between 2011 and 2015, but individual fish taxa (families and species) changed in complex and unpredictable ways. For example, more families increased in density and biomass than decreased following Cyclone Ita, particularly at exposed sites whilst more fish families declined at lagoon sites even though coral cover did not decline. All sites lost biomass of several damselfish species, and at most sites there was an increase in macroinvertivores and grazers. Overall, these results suggest that the degree of change measured at coarse taxonomic levels masked high species-level turnover, although other potential explanations include that there was no impact of the storm, fish assemblages were impacted but underwent rapid recovery or that there is a time lag before the full impacts become apparent. This study confirms that in high-complexity, high diversity ecosystems such as coral reefs, species level analyses are essential to adequately capture the consequences of disturbance events.

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.

This report summarizes a workshop on the Coral Sea to determine key research findings and identify the research gaps needed to support sustainable management of a proposed Coral Sea Marine Reserve. Key research questions included determining the connectivity of apex predators with the broader southwest Pacific Ocean, and assessing the regions’ biodiversity in relation to seabed topography and oceanographic processes. The workshop concluded noting the importance of engaging surrounding countries in maintaining the sustainability and uniqueness of the Coral Sea.

Herbivory is an important mechanism affecting algal succession, particularly on coral reefs where the relationship between algae and corals is largely controlled by herbivores. However, different functional groups of herbivores may have contrasting effects on succession, which may explain different trajectories of coral reef recovery after disturbance. Here, the effects of different herbivore groups (roving herbivores = foragers and territorial damselfish = farmers) were isolated by a multi-factorial experiment carried out on a coastal coral reef with high macroalgal cover, high farmer densities and relatively low forager abundance. The effects of foragers and farmers were distinguished by monitoring algal succession on settlement tiles placed inside and outside exclusion cages, with orthogonal treatments established inside and outside damselfish territories (with appropriate cage controls). Within 12 months, algal assemblages on ungrazed tiles inside exclusion cages proceeded rapidly from fine filamentous turfs, to corticated algae, to tough erect (e.g. Amphiroa spp.) and foliose (e.g. Peyssonnellidae) calcified algae. Farmers had a dramatic impact on succession, essentially arresting the development of the algal community at a point where it was dominated by palatable filamentous algae of the genus Polysiphonia. Fleshy macroalgae such as Sargassum spp. were excluded from farmer territories. In contrast, foragers did not suppress fleshy macroalgae, but rather, appeared to decelerate succession and promote a relatively diverse assemblage. In contrast to forager-dominated reefs, farmer territories did not appear to function solely as forager exclusion areas or promote algal diversity as a result of intermediate grazing pressure. The relatively strong effects of farmers observed here may represent a future scenario for coral reefs that are increasingly subject to overfishing of large grazing fishes.

The present study provides the first analysis of the feeding macroecology of territorial damselfishes (Perciformes: Pomacentridae), a circumtropical family whose feeding and behavioral activities are important in structuring tropical and subtropical reef benthic communities. The analyses were conducted from data collected by the authors and from the literature. A strong positive correlation was observed between bite rates and sea surface temperature (SST) for the genus Stegastes. A negative correlation was found between bite rates and mean body size for the genera Stegastes and Pomacentrus, but this relationship was not significant when all territorial pomacentrids were analyzed together. A negative correlation between body size and SST was observed for the whole group and for the genera Stegastes, and Pomacentrus. No relationship was found between territory size and feeding rates. Principal Components Analysis showed that differences in feeding rates accounted for most of the variability in the data. It also suggested that body size may be important in characterizing the different genera. In general, tropical species are smaller and have higher bite rates than subtropical ones. This study extended the validity of Bergmann’s rule, which states that larger species or larger individuals within species occur towards higher latitudes and/or lower temperatures, for an important group of reef fishes. The identification of large-scale, robust ecological patterns in the feeding ecology of pomacentrid fishes may establish a foundation for predicting large-scale changes in reef fish assemblages with expected future changes in global SST.

The effects of territorial damselfish on coral reef benthos have been well-studied for a few relatively large-bodied species with visually distinct territories. Despite a growing body of research demonstrating their abundance, and their effects on algae, corals and other grazers, there has been little research on the effects of the territorial damselfish community as a whole. This study investigated the space occupation, territory composition, and diet of ten damselfish species at three locations: Magnetic and Orpheus Islands (Great Barrier Reef), and Kimbe Bay (Papua New Guinea). Territories were measured, and the composition of benthic communities inside and outside territories was assessed both in situ and from algal collections. The stomach contents of territorial damselfishes were also quantified. Although the larger, previously well-studied species had the most visible effect on the benthic community in their territories, all the smaller species also significantly affected the algal composition, normally with an increase of palatable algae. However, the composition of algal assemblages inside the territories of different species varied considerably. Damselfish territories were highly individual, not just among species, but also among locations. Diets were diverse and indicated a greater degree of omnivory and detritivory than previously thought. At all locations, territories occupied a substantial proportion of the substratum: >25% on Magnetic Island, >50% at Orpheus Island, and ∼50% in Kimbe Bay. Within individual zones, this figure was as high as 70%. The contribution of territorial damselfishes to a range of benthic patterns and processes is considerable, and future benthic studies may need to distinguish more closely between territory and non-territory areas.

International audience; We review present understanding of the spatial and temporal diet variability (trophodynamics) of a range of pelagic marine top predators, at both early and adult life history stages. We begin with a review of methodologies used to advance our understanding of the trophodynamics of marine top predators, particularly in relation to climate change. We then explore how these developments are informing our understanding of the major trophic groups in food webs leading to, and including, marine top predators. We examine through specific examples how the impacts of ocean warming may affect pelagic food web relationships from both top-down and bottom-up perspectives. We examine the potential, in the absence of long-term data sets, of using large-scale spatial studies to examine how potential changes in biological oceanography could impact the biomass and composition of prey species, particularly the role of phytoplankton size spectra. We focus on examples from regions where biotic change with respect to climate change is likely. In particular, we detail the effects of climate change on oceanographic and bathymetric "hotspots" and provide the example involving seabirds in the Benguela Current system. We end by urging the development of international collaborations and databases to facilitate comprehensive ocean-scale understanding of climate impacts on marine top predators.

The loss of large fishes from coral reefs can alter the composition of benthic assemblages and increase the abundance of smaller fishes at lower trophic levels. An experimental exclusion of medium and large fishes, maintained over 30 mo, had a major impact on the dynamics of 2 abundant damselfishes (Pomacentrus adelus and P. wardi) and altered their relative abundance in favour of the larger species, P. wardi. The territory size of both species inside exclusion cages increased by 20 to 50% in the first year, but then declined to their original size after a further 6 mo. The exclusion of larger fishes also led to an increase in the quantity and quality of food algae within damselfish territories. These results suggest that larger predatory and herbivorous fish influence the composition of coral reef communities not only directly, but also indirectly, by controlling the abundance and territorial activities of damselfish.

Territorial damselfish are important herbivores on coral reefs because they can occupy a large proportion of the substratum and modify the benthic community to promote the cover of food algae. However, on coastal coral reefs damselfish occupy habitats that are often dominated by unpalatable macroalgae. The aim of this study was to examine whether damselfish can maintain distinctive algal assemblages on a coastal reef that is seasonally dominated by Sargassum (Magnetic Island, Great Barrier Reef). Here, three abundant species (Pomacentrus tripunctatus, P. wardi and Stegastes apicalis) occupied up to 60% of the reef substrata. All three species promoted the abundance of food algae in their territories. The magnitudes of the effects varied among reef zones, but patterns were relatively stable over time. Damselfish appear to readily co-exist with large unpalatable macroalgae as they can use it as a substratum for promoting the growth of palatable epiphytes. Damselfish territories represent patches of increased epiphyte load on macroalgae, decreased sediment cover, and enhanced cover of palatable algal turf.

Near-shore marine environments are increasingly subjected to reduced water quality, and their ability to withstand it is critical to their persistence. The potential role marine reserves may play in mitigating the effects of reduced water quality has received little attention. We investigated the spatial and temporal variability in live coral and macro-algal cover and water quality during moderate and major flooding events of the Fitzroy River within the Keppel Bay region of the Great Barrier Reef Marine Park from 2007 to 2013. We used 7 years of remote sensing data on water quality and data from long-term monitoring of coral reefs to quantify exposure of coral reefs to flood plumes. We used a distance linear model to partition the contribution of abiotic and biotic factors, including zoning, as drivers of the observed changes in coral and macro-algae cover. Moderate flood plumes from 2007 to 2009 did not affect coral cover on reefs in the Keppel Islands, suggesting the reef has intrinsic resistance against short-term exposure to reduced water quality. However, from 2009 to 2013, live coral cover declined by ∼ 50% following several weeks of exposure to turbid, low salinity water from major flood plume events in 2011 and subsequent moderate events in 2012 and 2013. Although the flooding events in 2012 and 2013 were smaller than the flooding events between 2007 to 2009, the ability of the reefs to withstand these moderate floods was lost, as evidenced by a ∼ 20% decline in coral cover between 2011 to 2013. Although zoning (no-take reserve or fished) was identified a significant driver of coral cover, we recorded consistently lower coral cover on reserve reefs than on fished reefs throughout the study period and significantly lower cover in 2011. Our findings suggest that even reefs with an inherent resistance to reduced water quality are not able to withstand repeated disturbance events. The limitations of reserves in mitigating the effects of reduced water quality on near-shore coral reefs underscores the importance of integrated management approaches that combine effective land-based management with networks of no-take reserves.

No-take marine reserves (NTMRs) are increasingly being established to conserve or restore biodiversity and to enhance the sustainability of fisheries. Although effectively designed and protected NTMR networks can yield conservation and fishery benefits, reserve effects often fail to manifest in systems where there are high levels of non-compliance by fishers (poaching). Obtaining reliable estimates of NTMR non-compliance can be expensive and logistically challenging, particularly in areas with limited or non-existent resources for conducting surveillance and enforcement. Here we assess the utility of density estimates and re-accumulation rates of derelict (lost and abandoned) fishing line as a proxy for fishing effort and NTMR non-compliance on fringing coral reefs in three island groups of the Great Barrier Reef Marine Park (GBRMP), Australia. Densities of derelict fishing line were consistently lower on reefs within old (>20 year) NTMRs than on non-NTMR reefs (significantly in the Palm and Whitsunday Islands), whereas line densities did not differ significantly between reefs in new NTMRs (5 years of protection) and non-NTMR reefs. A manipulative experiment in which derelict fishing lines were removed from a subset of the monitoring sites demonstrated that lines re-accumulated on NTMR reefs at approximately one third (32.4%) of the rate observed on non-NTMR reefs over a thirty-two month period. Although these inshore NTMRs have long been considered some of the best protected within the GBRMP, evidence presented here suggests that the level of non-compliance with NTMR regulations is higher than previously assumed.

The Coral Sea, located at the southwestern rim of the Pacific Ocean, is the only tropical marginal sea where human impacts remain relatively minor. Patterns and processes identified within the region have global relevance as a baseline for understanding impacts in more disturbed tropical locations. Despite 70 years of documented research, the Coral Sea has been relatively neglected, with a slower rate of increase in publications over the past 20 years than total marine research globally. We review current knowledge of the Coral Sea to provide an overview of regional geology, oceanography, ecology and fisheries. Interactions between physical features and biological assemblages influence ecological processes and the direction and strength of connectivity among Coral Sea ecosystems. To inform management effectively, we will need to fill some major knowledge gaps, including geographic gaps in sampling and a lack of integration of research themes, which hinder the understanding of most ecosystem processes.

The Coral Sea, located at the southwestern rim of the Pacific Ocean, is the only tropical marginal sea where human impacts remain relatively minor. Patterns and processes identified within the region have global relevance as a baseline for understanding impacts in more disturbed tropical locations. Despite 70 years of documented research, the Coral Sea has been relatively neglected, with a slower rate of increase in publications over the past 20 years than total marine research globally. We review current knowledge of the Coral Sea to provide an overview of regional geology, oceanography, ecology and fisheries. Interactions between physical features and biological assemblages influence ecological processes and the direction and strength of connectivity among Coral Sea ecosystems. To inform management effectively, we will need to fill some major knowledge gaps, including geographic gaps in sampling and a lack of integration of research themes, which hinder the understanding of most ecosystem processes.

Marine protected areas can prevent over-exploitation, but their effect on marine diseases is less clear. We examined how marine reserves can reduce diseases affecting reef-building corals following acute and chronic disturbances. One year after a severe tropical cyclone, corals inside reserves had sevenfold lower levels of disease than those in non-reserves. Similarly, disease prevalence was threefold lower on reserve reefs following chronic exposure to terrestrial run-off from a degraded river catchment, when exposure duration was below the long-term site average. Examination of 35 predictor variables indicated that lower levels of derelict fishing line and injured corals inside reserves were correlated with lower levels of coral disease in both case studies, signifying that successful disease mitigation occurs when activities that damage reefs are restricted. Conversely, reserves were ineffective in moderating disease when sites were exposed to higher than average levels of run-off, demonstrating that reductions in water quality undermine resilience afforded by reserve protection. In addition to implementing protected areas, we highlight that disease management efforts should also target improving water quality and limiting anthropogenic activities that cause injury.

Herbivorous fishes have been attributed a central role in structuring benthic communities on coral reefs. However, the relative importance of different behavioural groups of herbivores may differ and their interactions may be complex. This study focuses on an experiment that discriminates between two groups of herbivorous fish: (1) “Foragers” (relatively mobile, schooling grazers, including parrotfishes and surgeonfishes) and (2) “Farmers” (highly site-attached, territorial species, primarily damselfishes). Preliminary observations at Kimbe Bay (Papua New Guinea) showed that both groups were common, and that farmers defended areas from foragers and maintained algal communities that were distinct from the surrounding undefended substratum. An orthogonal combination of a farmer removal treatment and a forager exclusion treatment was applied to isolate their separate effects on algae and corals, and to determine whether farmer territory composition results from forager exclusion or algal cultivation. The experiment showed that foragers had quantitatively greater and qualitatively different effects on sessile benthic community structure than farmers. Where foragers were excluded, there were substantial increases in the cover and biomass of macro-algae and a decline in some corals, regardless of the presence of farmers. Where farmers were removed there was a moderate decline in the cover of some food algal species, regardless of whether foragers had access. No effect of the exclusion of foragers by farmers could be detected. Our results support prevailing views that foragers have a major impact on coral reefs and farmers cultivate selected algae, but challenge the hypothesis that damselfish influence habitat structure by moderating forager disturbance.

Territorial damselfishes, or ‘farmers’, modify the benthic communities in their territories in favour of preferred food species, usually filamentous algae. Behavioural observations of the farming Ward’s damselfish, Pomacentrus wardi, on Lizard Island, Great Barrier Reef, revealed that 55% of the observed individuals had high bite rates on the surface of soft corals (genera Sinularia, Isis and Sarcophyton). Furthermore, numerous soft corals within P. wardi territories were observed to have algal turfs growing on them. Such observations suggest an unprecedented versatility in the choice of seemingly healthy soft corals as a substrate for algal farms. This behaviour may be a novel technique for reducing competitive interactions from roving herbivores, and may have sublethal consequences for the soft corals that remain to be tested.