AbstractAimWidespread coral bleaching, crown-of-thorns seastar outbreaks, and tropical storms all threaten foundational coral species of the Great Barrier Reef, with impacts differing over time and space. Yet, dispersal via larval propagules could aid reef recovery by supplying new settlers and enabling the spread of adaptive variation among regions. Documenting and predicting spatial connections arising from planktonic larval dispersal in marine species, however, remains a formidable challenge.LocationThe Great Barrier Reef, AustraliaMethodsContemporary biophysical larval dispersal models were used to predict longdistance multigenerational connections for two common and foundational coral species (Acropora tenuisandAcropora millepora). Spatially extensive genetic surveys allowed us to infer signatures of asymmetric dispersal for these species and evaluate concordance against expectations from biophysical models using coalescent genetic simulations, directions of inferred gene flow, and spatial eigenvector modelling.ResultsAt long distances, biophysical models predicted a preponderance of north to south connections and genetic results matched these expectations: coalescent genetic simulations rejected an alternative scenario of historical isolation; the strongest signals of inferred gene flow were from north to south; and asymmetric eigenvectors derived from north to south connections in the biophysical models were significantly better predictors of spatial genetic patterns than eigenvectors derived from symmetric null spatial models.Main conclusionsResults are consistent with biophysical dispersal models yielding approximate summaries of past multigenerational gene flow conditioned upon directionality of connections. ForA. tenuisandA. millepora, northern and central reefs have been important sources to downstream southern reefs over the recent evolutionary past and should continue to provide southward gene flow. Endemic genetic diversity of southern reefs suggests substantial local recruitment and lack of long distance gene flow from south to north.

AbstractCorals are experiencing unprecedented decline from climate change-induced mass bleaching events. Dispersal not only contributes to coral reef persistence through demographic rescue but can also hinder or facilitate evolutionary adaptation. Locations of reefs that are likely to survive future warming therefore remain largely unknown, particularly within the context of both ecological and evolutionary processes across complex seascapes that differ in temperature range, strength of connectivity, network size, and other characteristics. Here, we used eco-evolutionary simulations to examine coral adaptation to warming across reef networks in the Caribbean, the Southwest Pacific, and the Coral Triangle. We assessed the factors associated with coral persistence in multiple reef systems to understand which results are general and which are sensitive to particular geographic contexts. We found that evolution can be critical in preventing extinction and facilitating the long-term recovery of coral communities in all regions. Furthermore, the strength of immigration to a reef (destination strength) and current sea surface temperature robustly predicted reef persistence across all reef networks and across temperature projections. However, we found higher initial coral cover, slower recovery, and more evolutionary lag in the Coral Triangle, which has a greater number of reefs and more larval settlement than the other regions. We also found the lowest projected future coral cover in the Caribbean. These findings suggest that coral reef persistence depends on ecology, evolution, and habitat network characteristics, and that, under an emissions stabilization scenario (RCP 4.5), recovery may be possible over multiple centuries.

AbstractIncreasingly severe marine heatwaves under climate change threaten the persistence of many marine ecosystems. Mass coral bleaching events, caused by periods of anomalously warm sea surface temperatures (SST), have led to catastrophic levels of coral mortality globally. Remotely monitoring and forecasting such biotic responses to heat stress is key for effective marine ecosystem management. The Degree Heating Week (DHW) metric, designed to monitor coral bleaching risk, reflects the duration and intensity of heat stress events, and is computed by accumulating SST anomalies (HotSpot) relative to a stress threshold over a 12-week moving window. Despite significant improvements in the underlying SST datasets, corresponding revisions of the HotSpot threshold and accumulation window are still lacking. Here, we fine-tune the operational DHW algorithm to optimise coral bleaching predictions using the 5km satellite-based SSTs (CoralTemp v3.1) and a global coral bleaching dataset (37,871 observations, National Oceanic and Atmospheric Administration). After developing 234 test DHW algorithms with different combinations of HotSpot threshold and accumulation window, we compared their bleaching-prediction ability using spatiotemporal Bayesian hierarchical models and sensitivity-specificity analyses. Peak DHW performance was reached using HotSpot thresholds less than or equal to Maximum Monthly Mean SST and accumulation windows of 4 – 8 weeks. This new configuration correctly predicted up to an additional 310 bleaching observations compared to the operational DHW algorithm, an improved hit rate of 7.9 %. Given the detrimental impacts of marine heatwaves across ecosystems, heat stress algorithms could also be fine-tuned for other biological systems, improving scientific accuracy, and enabling ecosystem governance.

Herbivory and nutrient availability are fundamental drivers of benthic community succession in shallow marine systems, including coral reefs. Despite the importance of early community succession for coral recruitment and recovery, studies characterizing the impact of top-down and bottom-up drivers on micro- and macrobenthic communities at scales relevant to coral recruitment are lacking. Here, a combination of tank and field experiments were used to assess the effects of herbivore exclusion and nutrient enrichment on micro- to macrobenthic community succession and subsequent coral recruitment success. Herbivore exclusion had the strongest effect on micro- and macrobenthic community succession, including a community shift toward copiotrophic and potentially opportunistic/pathogenic microorganisms, an increased cover of turf and macroalgae, and decreased cover of crustose coralline algae. Yet, when corals settled prior to the development of a macrobenthic community, rates of post-settlement survival increased when herbivores were excluded, benefiting from the predation refugia provided by cages during their vulnerable early post-settlement stage. Interestingly, survival on open tiles was negatively correlated with the relative abundance of the bacterial order Rhodobacterales, an opportunistic microbial group previously associated with stressed and diseased corals. Development of micro- and macrobenthic communities in the absence of herbivory, however, led to reduced coral settlement. In turn, there were no differences in post-settlement survival between open and caged treatments for corals settled on tiles with established benthic communities. As a result, open tiles experienced marginally higher recruitment rates, driven primarily by the higher initial number of settlers on open tiles compared to caged tiles. Overall, we reveal that the primary interaction driving coral recruitment is the positive effect of herbivory in creating crustose coralline algae (CCA)-dominated habitats, free of fleshy algae and associated opportunistic microbes, to enhance coral settlement. The negative direct and indirect impact of fish predation on newly settled corals was outweighed by the positive effect of herbivory on the initial rate of coral settlement. In turn, the addition of nutrients further altered benthic community succession in the absence of herbivory, reducing coral post-settlement survival. However, the overall impact of nutrients on coral recruitment dynamics was minor relative to herbivory.

Unraveling the processes that drive diversity patterns remains a central challenge for ecology, and an increased understanding is especially urgent to address and mitigate escalating diversity loss. Studies have primarily focused on singular taxonomic groups, but recent research has begun evaluating spatial diversity patterns across multiple taxonomic groups and suggests taxa may have congruence in their diversity patterns. Here, we use surveys of the coral reef benthic groups: scleractinian corals, macroalgae, sponges and gorgonians conducted in the Bahamian Archipelago across 27 sites to determine if there is congruence between taxonomic groups in their site-level diversity patterns (i.e. alpha diversity: number of species, and beta diversity: differences in species composition) while accounting for environmental predictors (i.e. depth, wave exposure, market gravity (i.e. human population size and distance to market), primary productivity, and grazing). Overall, we found that the beta diversities of these benthic groups were significant predictors of each other. The most consistent relationships existed with algae and coral, as their beta diversity was a significant predictor of every other taxa's beta diversity, potentially due to their strong biotic interactions and dominance on the reef. Conversely, we found no congruence patterns in the alpha diversity of the taxa. Market gravity and exposure showed the most prevalent correlation with both alpha and beta diversity for the taxa. Overall, our results suggest that coral reef benthic taxa can have spatial congruence in species composition, but not number of species, and that future research on biodiversity trends should consider that taxa may have non-independent patterns.

Climate change and ENSO have triggered five mass coral bleaching events on Australia's Great Barrier Reef (GBR), three of which occurred in the last 5 years.1-5 Here, we explore the cumulative nature of recent impacts and how they fragment the reef's connectivity. The coverage and intensity of thermal stress have increased steadily over time. Cumulative bleaching in 2016, 2017, and 2020 is predicted to have reduced systemic larval supply by 26%, 50%, and 71%, respectively. Larval disruption is patchy and can guide interventions. The majority of severely bleached reefs (75%) are predicted to have experienced an 80%-100% loss of larval supply. Yet restoration would not be cost-effective in the 2% of such reefs (∼30) that still experience high larval supply. Managing such climate change impacts will benefit from emerging theory on the facilitation of genetic adaptation,6,7 which requires the existence of regions with predictably high or low thermal stress. We find that a third of reefs constitute warm spots that have consistently experienced bleaching stress. Moreover, 13% of the GBR are potential refugia that avoid significant warming more than expected by chance, with a modest proportion (14%) within highly protected areas. Coral connectivity is likely to become increasingly disrupted given the predicted escalation of climate-driven disturbances,8 but the existence of thermal refugia, potentially capable of delivering larvae to 58% of the GBR, may provide pockets of systemic resilience in the near-term. Theories of conservation planning for climate change will need to consider a shifting portfolio of thermal environments over time.

Maintaining coral reef ecosystems is a social imperative, because so many people depend on coral reefs for food production, shoreline protection, and livelihoods. The survival of reefs this century, however, is threatened by the mounting effects of climate change. Climate mitigation is the foremost and essential action to prevent coral reef ecosystem collapse. Without it, reefs will become extremely diminished within the next 20–30 years. Even with strong climate mitigation, however, existing conservation measures such as marine protected areas and fisheries management are no longer sufficient to sustain the ecosystem and many additional and innovative actions to increase reef resilience must also be taken. In this paper we assess the suite of protections and actions in terms of their potential to be effective according to a set of criteria that include effectiveness, readiness, co-benefits and disbenefits. Even with the best scientific innovation, saving coral reefs will require a well-funded, well-designed, and rapidly executed strategy with political and social commitments at the level of other grand challenges.

Once spectacular coral reefs have often become overrun by persistent seaweed. A new study reveals that elevating the density of herbivorous spider crabs to unnatural levels can reduce seaweed and help corals recover. Once spectacular coral reefs have often become overrun by persistent seaweed. A new study reveals that elevating the density of herbivorous spider crabs to unnatural levels can reduce seaweed and help corals recover.

Corals are experiencing unprecedented decline from climate change-induced mass bleaching events. Dispersal not only contributes to coral reef persistence through demographic rescue but can also hinder or facilitate evolutionary adaptation. Locations of reefs that are likely to survive future warming therefore remain largely unknown, particularly within the context of both ecological and evolutionary processes across complex seascapes that differ in temperature range, strength of connectivity, network size, and other characteristics. Here, we used eco-evolutionary simulations to examine coral adaptation to warming across reef networks in the Caribbean, the Southwest Pacific, and the Coral Triangle. We assessed the factors associated with coral persistence in multiple reef systems to understand which results are general and which are sensitive to particular geographic contexts. We found that evolution can be critical in preventing extinction and facilitating the long-term recovery of coral communities in all regions. Furthermore, the strength of immigration to a reef (destination strength) and current sea surface temperature robustly predicted reef persistence across all reef networks and across temperature projections. However, we found higher initial coral cover, slower recovery, and more evolutionary lag in the Coral Triangle, which has a greater number of reefs and more larval settlement than the other regions. We also found the lowest projected future coral cover in the Caribbean. These findings suggest that coral reef persistence depends on ecology, evolution, and habitat network characteristics, and that, under an emissions stabilization scenario (RCP 4.5), recovery may be possible over multiple centuries.

Global environmental change is challenging species with novel conditions, such that demographic and evolutionary trajectories of populations are often shaped by the exchange of organisms and alleles across landscapes. Current ecological theory predicts that random networks with dispersal shortcuts connecting distant sites can promote persistence when there is no capacity for evolution. Here, we show with an eco-evolutionary model that dispersal shortcuts across environmental gradients instead hinder persistence for populations that can evolve because long-distance migrants bring extreme trait values that are often maladaptive, short-circuiting the adaptive response of populations to directional change. Our results demonstrate that incorporating evolution and environmental heterogeneity fundamentally alters theoretical predictions regarding persistence in ecological networks.

Crown-of-thorns sea stars (Acanthaster sp.) are among the most studied coral reef organisms, owing to their propensity to undergo major population irruptions, which contribute to significant coral loss and reef degradation throughout the Indo-Pacific. However, there are still important knowledge gaps pertaining to the biology, ecology, and management of Acanthaster sp. Renewed efforts to advance understanding and management of Pacific crown-of-thorns sea stars (Acanthaster sp.) on Australia’s Great Barrier Reef require explicit consideration of relevant and tractable knowledge gaps. Drawing on established horizon scanning methodologies, this study identified contemporary knowledge gaps by asking active and/or established crown-of-thorns sea star researchers to pose critical research questions that they believe should be addressed to improve the understanding and management of crown-of-thorns sea stars on the Great Barrier Reef. A total of 38 participants proposed 246 independent research questions, organized into 7 themes: feeding ecology, demography, distribution and abundance, predation, settlement, management, and environmental change. Questions were further assigned to 48 specific topics nested within the 7 themes. During this process, redundant questions were removed, which reduced the total number of distinct research questions to 172. Research questions posed were mostly related to themes of demography (46 questions) and management (48 questions). The dominant topics, meanwhile, were the incidence of population irruptions (16 questions), feeding ecology of larval sea stars (15 questions), effects of elevated water temperature on crown-of-thorns sea stars (13 questions), and predation on juveniles (12 questions). While the breadth of questions suggests that there is considerable research needed to improve understanding and management of crown-of-thorns sea stars on the Great Barrier Reef, the predominance of certain themes and topics suggests a major focus for new research while also providing a roadmap to guide future research efforts.

By 2004, Belize was exhibiting classic fishing down of the food web. Groupers (Serranidae) and snappers (Lutjanidae) were scarce and fisheries turned to parrotfishes (Scarinae), leading to a 41% decline in their biomass. Several policies were enacted in 2009-2010, including a moratorium on fishing parrotfish and a new marine park with no-take areas. Using a 20-year time series on reef fish and benthos, we evaluated the impact of these policies approximately 10 years after their implementation. Establishment of the Southwater Caye Marine Reserve led to a recovery of snapper at 2 out of 3 sites, but there was no evidence of recovery outside the reserve. Snapper populations in an older reserve continued to increase, implying that at least 9 years is required for their recovery. Despite concerns over the feasibility of banning parrotfish harvest once it has become a dominant fin fishery, parrotfishes returned and exceeded biomass levels prior to the fishery. The majority of these changes involved an increase in parrotfish density; species composition and adult body size generally exhibited little change. Recovery occurred equally well in reserves and areas open to other forms of fishing, implying strong compliance. Temporal trends in parrotfish grazing intensity were strongly negatively associated with the cover of macroalgae, which by 2018 had fallen to the lowest levels observed since measurements began in 1998. Coral populations remained resilient and continued to exhibit periods of net recovery after disturbance. We found that a moratorium on parrotfish harvesting is feasible and appears to help constrain macroalgae, which can otherwise impede coral resilience.

Global overfishing of higher-level predators has caused cascading effects to lower trophic levels in many marine ecosystems. On coral reefs, which support highly diverse food webs, the degree to which top-down trophic cascades can occur remains equivocal. Using extensive survey data from coral reefs across the relatively unfished northern Great Barrier Reef (nGBR), we quantified the role of reef sharks in structuring coral reef fish assemblages. Using a structural equation modeling (SEM) approach, we explored the interactions between shark abundance and teleost mesopredator and prey functional group density and biomass, while explicitly accounting for the potentially confounding influence of environmental variation across sites. Although a fourfold difference in reef shark density was observed across our survey sites, this had no impact on either the density or biomass of teleost mesopredators or prey, providing evidence for a lack of trophic cascading across nGBR systems. Instead, many functional groups, including sharks, responded positively to environmental drivers. We found reef sharks to be positively associated with habitat complexity. In turn, physical processes such as wave exposure and current velocity were both correlated well with multiple functional groups, reflecting how changes to energetic conditions and food availability, or modification of habitat affect fish distribution. The diversity of species within coral reef food webs and their associations with bottom-up drivers likely buffers against trophic cascading across GBR functional guilds when reef shark assemblages are depleted, as has been demonstrated in other complex ecosystems.

Innovative solutions to improve the condition and resilience of ecosystems are needed to address societal challenges and pave the way towards a climate-resilient future. Nature-based solutions offer the potential to protect, sustainably manage and restore natural or modified ecosystems while providing multiple other benefits for health, the economy, society and the environment. However, the implementation of nature-based solutions stems from a discourse that is almost exclusively derived from a terrestrial and urban context and assumes that risk reduction is resolved locally. We argue that this position ignores the importance of complex ecological interactions across a range of temporal and spatial scales and misses the substantive contribution from marine ecosystems, which are notably absent from most climate mitigation and adaptation strategies that extend beyond coastal disaster management. Here, we consider the potential of sediment-dwelling fauna and flora to inform and support nature-based solutions, and how the ecology of benthic environments can enhance adaptation plans. We illustrate our thesis with examples of practice that are generating, or have the potential to deliver, transformative change and discuss where further innovation might be applied. Finally, we take a reflective look at the realized and potential capacity of benthic-based solutions to contribute to adaptation plans and offer our perspectives on the suitability and shortcomings of past achievements and the prospective rewards from sensible prioritization of future research.
. This article is part of the theme issue ‘Climate change and ecosystems: threats, opportunities and solutions'.

Protection of coastal ecosystems from deforestation may be the best way to protect coral reefs from sediment runoff. However, given the importance of generating economic activities for coastal livelihoods, the prohibition of development is often not feasible. In light of this, logging codes of practice have been developed to mitigate the impacts of logging on downstream ecosystems. However, no studies have assessed whether managed land-clearing can occur in tandem with coral reef conservation goals. This study quantifies the impacts of current land use and the risk of potential logging activities on downstream coral reef condition and fisheries using a novel suite of linked land-sea models, using Kolombangara Island in the Solomon Islands as a case study. Further, we examine the ability of erosion reduction strategies stipulated in logging codes of practice to reduce these impacts as clearing extent increases. We found that with present-day land use, reductions in live and branching coral cover and increases in turf algae were associated with exposure to sediment runoff from catchments and log ponds. Critically, reductions in fish grazer abundance and biomass were associated with increasing sediment runoff, a functional group that accounts for ~25% of subsistence fishing. At low clearing extents, although best management practices minimize the exposure of coral reefs to increased runoff, it would still result in 32% of the reef experiencing an increase in sediment exposure. If clearing extent increased, best management practices would have no impact, with a staggering 89% of coral reef area at risk compared to logging with no management. Synthesis and applications. Assessing trade-offs between coastal development and protection of marine resources is a challenge for decision makers globally. Although development activities requiring clearing can be important for livelihoods, our results demonstrate that new logging in intact forest risks downstream resources important for both food and livelihood security. Importantly, our approach allows for spatially explicit recommendations for where terrestrial management might best complement marine management. Finally, given the critical degradation feedback loops that increased sediment runoff can reinforce on coral reefs, minimizing sediment runoff could play an important role in helping coral reefs recover from climate-related disturbances.

Sustainable development (SD) policies targeting marine economic sectors, designed to alleviate poverty and conserve marine ecosystems, have proliferated in recent years. Many developing countries are providing poor fishing households with new fishing boats (fishing capital) that can be used further offshore as a means to improve incomes and relieve fishing pressure on nearshore fish stocks. These kinds of policies are a marine variant of traditional SD policies focused on agriculture. Here, we evaluate ex ante economic and environmental impacts of provisions of fishing and agricultural capital, with and without enforcement of fishing regulations that prohibit the use of larger vessels in nearshore habitats. Combining methods from development economics, natural resource economics, and marine ecology, we use a unique dataset and modeling framework to account for linkages between households, business sectors, markets, and local fish stocks. We show that the policies investing capital in local marine fisheries or agricultural sectors achieve income gains for targeted households, but knock-on effects lead to increased harvest of nearshore fish, making them unlikely to achieve conservation objectives in rural coastal economies. However, pairing an agriculture stimulus with increasing enforcement of existing fisheries’ regulations may lead to a win–win situation. While marine-based policies could be an important tool to achieve two of the United Nations Sustainable Development Goals (alleviate poverty and protect vulnerable marine resources), their success is by no means assured and requires consideration of land and marine socioeconomic linkages inherent in rural economies.

As oceans continue to warm under climate change, understanding the differential growth responses of corals is increasingly important. Scleractinian corals exhibit a broad range of life-history strategies, yet few studies have explored interspecific variation in long-term growth rates under a changing climate. Here we studied growth records of two coral species with different growth forms, namely branching Isopora palifera and massive Porites spp. at an offshore reef (Myrmidon Reef) of the central Great Barrier Reef (GBR), Australia. Skeletal growth chronologies were constructed using a combination of X-radiographs, gamma densitometry, and trace element (Sr/Ca) analysis. General additive mixed-effect models (GAMMs) revealed that skeletal density of I. palifera declined linearly and significantly at a rate of 1.2% yr−1 between 2002 and 2012. Calcification was stable between 2002 and 2009, yet declined significantly at a rate of 12% yr−1 between 2009 and 2012 following anomalously high sea surface temperatures (SST). Skeletal density of massive Porites exhibited a significant non-linear response over the 11-year study period (2002−2012) in that density was temporarily reduced during the 2009–2010 anomalously hot years, while linear extension and calcification showed no significant trends. Linear extension, density and calcification rates of I. palifera increased to maximum growth of 26.7–26.9 °C, beyond which they declined. In contrast, calcification and linear extension of Porites exhibited no response to SST, but exhibited a significant linear decline in skeletal density with increasing SST. Our results reveal significant differences in coral growth patterns among coral growth forms, and highlight both the resistant nature of massive Porites and sensitivity of branching I. palifera. Future research should target a broad range of coral taxa within similar environments to provide a community-level response of ocean warming on coral reef communities.

The Great Barrier Reef (GBR) is of immense biological, cultural and economic importance, but has also rapidly degraded over the last 30 years. Improved spatial information on reef geomorphic zonation and benthic cover type (including coral type) is critical to support scientific work to understand how the GBR is changing, and to support resource management decisions that enable conservation of the reef and its essential ecosystem services. Yet, no comprehensive maps exist that detail the geomorphic zonation or benthic cover for the GBR’s ~ 3000 reefs. This study presents three new types of shallow reef maps for 237 reefs in the central Cairns Management Region of the GBR Marine Park (GBRMP), explores how the detailed habitat maps created compared to current maps and posits how the new maps may support and refine current critical key science outputs and management challenges. Geomorphic Zonation, Benthic Cover and Coral Type habitat maps were created using a unique combined object-based image analysis and ecological modelling approach that incorporated satellite imagery, limited field data and key reef physical attributes (depth, slope, waves) using a previously peer-reviewed mapping approach developed for the Capricorn Bunker Group reefs, Southern GBR. The mapping approach was consistent and repeatable, suggesting applicability to mapping all 3000 reefs in the GBRMP. Compared to existing maps that only outline each reef, the increase in detail provided by these new habitat maps enabled discrete characterisation of each reef’s geomorphology and benthic composition. With the new habitat maps, areas within each reef can be identified as either coral habitat or not coral habitat. This has not been possible previously. As such, a model of coral ecological and biophysical processes that depends on bottom reflectance of sand and coral areas can be fine-tuned. Similarly, for reef restoration, nursery structures are commonly placed in non-coral habitats, and/or coral larvae are dispersed in areas of known coral habitat. The new habitat maps presented permit more accurate identification of these areas such that restoration projects can be targeted more effectively. These findings confirm the need to now apply this mapping approach to the full extent of the GBR.

The third global bleaching event caused prolonged elevated sea surface temperatures from 2014 to 2017 that heavily impacted coral reefs worldwide. This study determines changes in benthic community following this bleaching event at a remote UNESCO World Heritage Site in the Western Indian Ocean. Aldabra Atoll offers a rare opportunity to study global impacts in the absence of local anthropogenic stressors. Analysis of satellite-derived temperature data indicated that Aldabra was exposed to the highest bleaching-risk intensity of the past 20 years during this bleaching event. Bleaching-risk conditions lasted from December 2015 to June 2016 close to the 4 °C-week threshold, when bleaching is expected. Benthic cover was established pre- and post-bleaching from 21 transects across two reef locations (lagoonal reef, 2 m depth; seaward reef, 5 and 15 m depth). From a pre-bleaching benthic community in which living corals and epilithic algal matrix (EAM) predominated, Aldabra’s reefs switched to an EAM-dominated community 8 months after bleaching. Soft corals declined by 93% of their overall pre-bleaching cover to < 1%. Although overall hard-coral cover was also reduced, the decline varied among depths and might indicate local adaptations of the lagoonal reef, due to greater variability in sea surface temperature compared to the seaward reef. With the exception of Isopora palifera, all taxomorphic coral groups experienced a decline following bleaching. Overall, Rhytisma experienced a near-complete extirpation, Acroporids (excluding I. palifera) and branching Poritids declined by more than 80%, Merulinidae lost ca. 60% of their pre-bleaching cover, while massive Poritids cover slightly decreased. Aldabra’s benthic community therefore underwent substantial changes following the 2014–2017 bleaching event and showed that live coral cover declines significantly even in protected areas isolated from local anthropogenic pressures.

Climate change is impacting coral reefs now. Recent pan-tropical bleaching events driven by unprecedented global heat waves have shifted the playing field for coral reef management and policy. While best-practice conventional management remains essential, it may no longer be enough to sustain coral reefs under continued climate change. Nor will climate change mitigation be sufficient on its own. Committed warming and projected reef decline means solutions must involve a portfolio of mitigation, best-practice conventional management and coordinated restoration and adaptation measures involving new and perhaps radical interventions, including local and regional cooling and shading, assisted coral evolution, assisted gene flow, and measures to support and enhance coral recruitment. We propose that proactive research and development to expand the reef management toolbox fast but safely, combined with expedient trialling of promising interventions is now urgently needed, whatever emissions trajectory the world follows. We discuss the challenges and opportunities of embracing new interventions in a race against time, including their risks and uncertainties. Ultimately, solutions to the climate challenge for coral reefs will require consideration of what society wants, what can be achieved technically and economically, and what opportunities we have for action in a rapidly closing window. Finding solutions that work for coral reefs and people will require exceptional levels of coordination of science, management and policy, and open engagement with society. It will also require compromise, because reefs will change under climate change despite our best interventions. We argue that being clear about society's priorities, and understanding both the opportunities and risks that come with an expanded toolset, can help us make the most of a challenging situation. We offer a conceptual model to help reef managers frame decision problems and objectives, and to guide effective strategy choices in the face of complexity and uncertainty.

Length–weight relationships (LWRs) are a fundamental tool for the non-intrusive determination of biomass, a unit of measure that facilitates the quantification of ecosystem and fisheries productivity. LWRs have been defined and broadly applied for many marine species across a range of ecosystems, especially regarding fishes. However, LWRs are yet to be determined for the majority of marine taxa, particularly for small cryptic organisms that are difficult to census and poorly described. On coral reefs, the motile cryptofauna represent the greatest density and diversity of metazoan taxa that likely support critical steps in trophic pathways, but little empirical data exist beyond biodiversity assessments. We evaluated LWRs for 42 groups of motile cryptofauna across four microhabitats (live Acropora, live Pocillopora, dead branching coral and coral rubble) in Palau, Western Micronesia. We employed a robust methodology to determine LWRs by comparing the suitability of a series of linear, quadratic, polynomial and power models. Using the best-fit equations for each group, we provide the first documented LWRs for motile cryptofauna, namely at the level of family. LWRs were well fit (R2 > 0.90) for 45% of the groups and reasonable (R2 > 0.70) for 76%. The presence, size and weight of cryptofauna varied among microhabitats with the size distribution of 13 groups significantly influenced by habitat type. Establishment of these LWRs provides critical baseline information regarding an overlooked group on coral reefs, making population data on the cryptofauna more accessible to support future research aiming to characterise the roles of these taxa in ecosystem functioning and trophodynamics.

The Great Barrier Reef (GBR) coral coverage is in rapid decline from severe and sustained pressures from lagoon water quality, crown-of-thorns starfish (COTS), coral bleaching, tropical cyclones, pollution and diseases. The two recent GBR coral bleaching events (2016–2017) lead to Great Barrier Reef Marine Park Authority (GBRMPA) shifting their focus from passive management to active intervention (Great Barrier Reef Blueprint for resilience by GBRMPA). These active interventions, potentially able to increase GBR resilience, as there are reefs that, due to their physical location relative to all other reefs, river and estuary entrances, ocean currents, have favourable coral growth conditions. To undertake such interventions, various information is required including tropical cyclone wave climates. This paper develops tropical cyclone wave climates for the entire GBR. These wave climates were developed by simulating several thousand synthetic cyclones derived from the “HadGEM” general circulation model with RCP8.5 climate change scenario. The synthetic cyclones adopted herein include the following climate changes assessed by comparing averages of key forcing parameters between 1950 to 1999 and 2050 to 2099. Their average arrival rate increases from 2.25 to 2.41 cyclones/year and their average maximum wind speed increases from 24 to 28 m/s. Their average radius to maximum winds remains constant at 51 km. Two key challenges were resolved, namely, long runtimes and large files (600 m grid increment covering 1800 km by 280 km). Runtimes were reduced by excluding cyclones where their wind speeds over the entire event never exceeded 10 m/s within GBR itself or within 100 km of the GBR over water. Maximum wave heights were compared with an extended fetch empirical expression, which was based on satellite data of tropical cyclones in open waters, when cyclones were outside the GBR lagoon. These comparisons indicate that predicted wave heights have a lower bias using default wave generation parameters when compared with the extended fetch empirical expression. Prediction uncertainty was estimated at no more than 10% from various cyclonic wind-field models. The existing GBR reefs reduce nearshore wave or runup height by between 1.5 and 2 times compared to the no reef case. The reduction in wave or runup height was found to be minimal for 1 m sea level rise. These two findings indicate that there is more flooding potential from coral removal than SLR within the GBR lagoon.

Ecosystem-based management on coral reefs has historically focussed on biodiversity conservation through the establishment of marine reserves, but it is increasingly recognised that a subset of species can be key to the maintenance of ecosystem processes and functioning. Specific provisions for these key taxa are essential to biodiversity conservation and resilience-based adaptive management. While a wealth of literature addresses ecosystem functioning on coral reefs, available information covers only a subset of specific taxa, ecological processes and environmental stressors. What is lacking is a comparative assessment across the diverse range of coral reef species to synthesise available knowledge to inform science and management. Here we employed expert elicitation coupled with a literature review to generate the first comprehensive assessment of 70 taxonomically diverse and functionally distinct coral reef species from microbes to top predators to summarise reef functioning. Although our synthesis is largely through the lens of the Great Barrier Reef, Australia, a particularly data-rich system, it is relevant to coral reefs in general. We use this assessment to evaluate which taxa drive processes that maintain a healthy reef and whether management of these taxa is considered a priority (i.e. are they vulnerable?) or is feasible (i.e. can they be managed?). Scientific certainty was scored to weight our recommendations, particularly when certainty was low. We use five case studies to highlight critical gaps in knowledge that limit our understanding of ecosystem functioning. To inform the development of novel management strategies and research objectives, we identify taxa that support positive interactions and enhance ecosystem performance, including those where these roles are currently underappreciated. We conclude that current initiatives effectively capture many priority taxa but that there is significant room to increase opportunities for underappreciated taxa in both science and management to maximally safeguard coral reef functioning.

Small-scale structural complexity shapes how consumers and primary producers interact, which can influence ecosystem trajectories. Coral reefs are some of the most structurally complex ecosystems, though their complexity is threatened owing to anthropogenic influences. Some reefs shift towards macroalgal dominance following mass coral mortality, which can hinder the recovery of corals because they compete with the faster growing macroalgae for space. Using video observations, surveys and in situ experiments on a forereef in eastern Palau, we investigated the role different microhabitats play in facilitating the persistence of the macroalga Lobophora, which is one of the strongest negative interactors with corals. Collectively, our observational and experimental data show that small crevices provide a refuge to Lobophora recruits by excluding most adult herbivorous fishes. Consequently, Lobophora is disproportionately more abundant within these concealed microhabitats on the reef, which highlights the important role of microhabitats as macroalgal nurseries from which macroalgae can spread following mass coral mortality. While a large proportion of our current understanding of grazer–algae interactions is based on research using flat surfaces, our findings demonstrate that the interactions between herbivorous fishes and benthic organisms are strongly mediated by microhabitats. It is thus important to consider the influence of structural complexity in order to understand the nuances that govern benthic regimes.

The concept of resilience is long established across a wide-range of disciplines, but its evaluation in many ecosystems has been challenging due to the complexities involved in quantifying a somewhat abstract dynamical phenomenon. We develop a framework of resilience-related concepts and describe their methodological approaches. Seven broad approaches were identified under the three principle concepts of (1) ecological resilience (ecological resilience, precariousness and current attractor), (2) engineering resilience (short-term recovery rate and long-term reef performance), and (3) vulnerability (absolute and relative vulnerability) respectively. Using specific examples, we assess the strengths and limitations of each approach and their capacity to answer common management questions. The current synthesis provides new directions for resilience assessments to be incorporated into management decisions and has implications on the research agenda for advances in resilience assessments.

Sedimentation and overfishing are important local stressors on coral reefs that can independently result in declines in coral recruitment and shifts to algal-dominated states. However, the role of herbivory in driving recovery across environmental gradients is often unclear. Here we investigate early successional benthic communities and coral recruitment across a sediment gradient in Palau, Micronesia over a 12-month period. Total sedimentation rates measured by 'TurfPods' varied from 0.03 ± 0.1 SE mg cm-2 d-1 at offshore sites to 1.32 ± 0.2 mg cm-2 d-1 at inshore sites. To assess benthic succession, three-dimensional settlement tiles were deployed at sites with experimental cages used to exclude tile access to larger herbivorous fish. Benthic assemblages exhibited rapid transitions across the sediment gradient within three months of deployment. At low levels of sedimentation (less than 0.6 mg cm-2 d-1), herbivory resulted in communities dominated by coral recruitment inducers (short turf algae and crustose coralline algae), whereas exclusion of herbivores resulted in the overgrowth of coral inhibitors (encrusting and upright foliose macroalgae). An 'inducer threshold' was found under increasing levels of sedimentation (greater than 0.6 mg cm-2 d-1), with coral inducers having limited to no presence in communities, and herbivore access to tiles resulted in sediment-laden turf algal assemblages, while exclusion of herbivores resulted in invertebrates (sponges, ascidians) and terrestrial sediment accumulation. A 'coral recruitment threshold' was found at 0.8 mg cm-2 d-1, below which net coral recruitment was reduced by 50% in the absence of herbivores, while recruitment was minimal above the threshold. Our results highlight nonlinear trajectories of benthic succession across sediment gradients and identify strong interactions between sediment and herbivory that have cascading effects on coral recruitment. Local management strategies that aim to reduce sedimentation and turbidity and manage herbivore fisheries can have measurable effects on benthic community succession and coral recruitment, enhancing reef resilience and driving coral recovery.

Microorganisms are fundamental drivers of biogeochemical cycling, though their contribution to coral reef ecosystem functioning is poorly understood. Here, we infer predictors of bacterioplankton community dynamics across surface-waters of the Great Barrier Reef (GBR) through a meta-analysis, combining microbial with environmental data from the eReefs platform. Nutrient dynamics and temperature explained 41.4% of inter-seasonal and cross-shelf variation in bacterial assemblages. Bacterial families OCS155, Cryomorphaceae, Flavobacteriaceae, Synechococcaceae and Rhodobacteraceae dominated inshore reefs and their relative abundances positively correlated with nutrient loads. In contrast, Prochlorococcaceae negatively correlated with nutrients and became increasingly dominant towards outershelf reefs. Cyanobacteria in Prochlorococcaceae and Synechococcaceae families occupy complementary cross-shelf biogeochemical niches; their abundance ratios representing a potential indicator of GBR nutrient levels. One Flavobacteriaceae-affiliated taxa was putatively identified as diagnostic for ecosystem degradation. Establishing microbial observatories along GBR environmental gradients will facilitate robust assessments of microbial contributions to reef health and inform tipping-points in reef condition.

Spatial management of fish populations can potentially be optimized by determining the area of influence of a particular species. We performed an acoustic tagging study implemented on Denis Island in the Seychelles to assess the area of influence of the heavily targeted shoemaker spinefoot, Siganus sutor. We investigated whether this species acts as a mobile link between coral patches and seagrass meadows, and whether their movements differed between day and night. The study incorporated an array of 22 acoustic stations deployed within dense coral patches, seagrass meadows and mixed habitats of both seagrass and coral. Fifteen S. sutor carrying internal acoustic tags were monitored from November 2016 until May 2017. Detection patterns revealed them to be diurnal herbivores, with only rare nocturnal movements. Home-range estimates showed that individuals differed in their spatial range extents and habitats used, covering ~15% of the total shallow subtidal coastline of the island. However, they displayed very small daily movements (

The sliding and overturning of unconsolidated rubble by hydrodynamic forcing is expected to cause physical damage to settled coral recruits and asexual fragments by scouring and smothering. Yet, few empirical studies have tested the relationship between rubble mobilisation frequency and the survival and growth of these corals. Here, we tested the response of small coral fragments to varying levels of experimental scouring and smothering, proxies for rubble mobilisation impacts, on two coral species with distinct functional traits; Porites rus (robust, encrusting) and Pocillopora verrucosa (sensitive, branching). This study investigated: 1) how coral fragment survival was affected by inversion on rubble or sand substratum over ~2 w (i.e. smothering); and 2) how the survival, growth and tissue properties of fragments were affected by rubble being overturned (i.e. experiencing scouring or abrasion) at different frequencies over ~10 w. Smothering substratum had a profound influence on the probability of fragment survival. For both species, survival was

Two-dimensional numerical modelling of swell wave dynamics on idealized fringing reefs is performed using SWAN, covering a wide range of bathymetries, climate forcing conditions and water depths over the reefs. The results illustrate the impact of reef geometry and bathymetry, coral species and sea level rise on key hydrodynamic parameters on the reef and on forces on corals. The modelling demonstrates that one-dimensional models underestimate the wave action on the reef flat. Wide short reefs and narrow long reefs have similar wave heights at the centre of the reef flat. For a given reef length, the wave height first decreases with increasing reef width, then increases to a local maximum when reef width is approximately equal to the reef length, and then decreases for further increases in width. This pattern is a result of combined dissipation and refraction processes, which combine to lead to different zones of cross-reef wave transformation. Provided that a reef retains its hydrodynamic functions in breaking and refracting the waves, sea level rise enhances the wave heights and wave orbital velocities on the reef flat. If vertical coral growth does not keep pace with sea level rise, loss of the hydrodynamic functions of the reef may occur on deeper reefs, and result in a reduction of near bed velocities with sea level rise. Hydrodynamic forces on corals vary by coral species and SLR changes the magnitude of the forces on different species in different ways, which may lead to less favourable conditions for certain coral species. For long period swell, the intermediate size corals are drag-dominated and behave similarly to branching corals, whereas for short period swell their behavior is similar to that of the inertia-dominated massive corals. For intermediate corals different responses to SLR may therefore be expected for different overall regional wave climates. Over time, this process may contribute to changes in the structural complexity of reefs. The influence of sea level rise on the forces on corals on the reef flat is different under swell and cyclonic wind conditions since wind influences wave period in the latter case.

Pollution from land-based run-off threatens coastal ecosystems and the services they provide, detrimentally affecting the livelihoods of millions people on the world's coasts. Planning for linkages among terrestrial, freshwater and marine ecosystems can help managers mitigate the impacts of land-use change on water quality and coastal ecosystem services. We examine the approaches used for land-sea planning, with particular focus on the models currently used to estimate the impacts of land-use change on water quality and fisheries. Our findings could also be applied to other ecosystem services. This Review encompasses modelling of: large scale drivers of land-use change; local activities that cause such change; run-off, dispersal and transformation of pollutants in the coastal ocean; ecological responses to pollutants; socio-economic responses to ecological change; and finally, the design of a planning response. We find that there is a disconnect between the dynamical models that can be used to link land to sea processes and the simple tools that are typically used to inform planning. This disconnect may weaken the robustness of plans to manage dynamic processes. Land-sea planning is highly interdisciplinary, making the development of effective plans a challenge for small teams of managers and decision makers. Synthesis and applications. We propose some guiding principles for where and how dynamic land-sea connections can most effectively be built into planning tools. Tools that can capture pertinent processes are needed, but they must be simple enough to be implemented in regions with limited resources for collecting data, developing models and developing integrated land-sea plans.

Larval settlement to the benthos can be influenced by physical and chemical cues. On coral reefs, the macroalga Lobophora is known to negatively impact coral recruitment, though the scales at which it affects coral larvae is unclear. We used aquarium experiments to mechanistically assess the response of larvae from 3 Acropora species to Lobophora at multiple spatial scales, and complemented these experiments with an analysis of the effects of Lobophora on Acropora spp. field recruitment patterns. The smallest scale (0−10 cm) focused on the effects of the distribution of Lobophora across an experimental tile, with settlement declining 60% for 2 of the species when a 15 cm 2 piece of Lobophora was distributed throughout a 100 cm 2 tile, compared to the control. The intermediate scale (5−15 cm) focused on the effects of increasing algal biomass on settlement, with settlement for all species negatively associated with algal biomass. Settlement decreased almost 50% in the highest treatment (6.2 g of Lobophora in the tanks), compared to the control. The mechanism of settlement inhibition was also tested at this scale, with waterborne compounds highlighted as a key settlement inhibitor. Lobophora also impaired overall settlement at the largest scale (0−100 cm), decreasing settlement by 40−50%, regardless of its location relative to the settlement substrate. Finally, Acropora field recruitment patterns also demonstrated a negative effect of Lobophora on coral recruitment in situ. Our results reveal the ability of Lobophora to inhibit coral settlement at multiple spatial scales, which may contribute to large-scale recruitment failure on coral reefs following disturbances.

Previous studies have reported recent substantial declines in the growth rates of massive Porites corals under warming oceans. However, the majority of these reports are from inshore reefs, and few have explored growth responses in offshore reefs from remote locations with low levels of pollution, sedimentation or nutrient loading. Here, we examined continuous growth records of massive Porites from remote locations spanning a 25° latitudinal gradient in the Indo-Pacific, including Palau, central Sulawesi, West Papua and the central Great Barrier Reef (GBR). Between 1982 and 2012, no significant changes in calcification or extension anomalies were observed at any study location, despite significant increases in sea surface temperature (SST) at all sites. Skeletal density increased linearly by ∼0.4% yr-1 in Palau, but no change was found in Sulawesi, yet skeletal density showed a significant nonlinear change in West Papua and the GBR. Skeletal density displayed a significant positive linear relationship with SST at Palau and West Papua, whereas no relationship was observed in Sulawesi. In the GBR, skeletal density exhibited a nonlinear parabolic relationship with SST, with strong negative anomalies occurring following major thermal events. Unlike the ongoing declines in growth rates of inshore corals that have been widely reported, we found that calcification and extension anomalies of the majority of Porites from offshore remote locations do not appear to be exhibiting negative growth responses to warming SST. Our results suggest that reefs experiencing low levels of local stressors may show increased resilience to warming SST in an era of rapidly warming oceans.

Ecosystems around the world are reorganizing due to climate change1, motivating management responses to facilitate species persistence and maintain ecological functions. Spatial management actions are generally undertaken to relieve local stressors on populations and have recently been suggested as an approach to facilitate species range shifts, provide refugia and enhance resilience to climate change2,3. Efforts to identify which habitats to protect, however, typically assume that organisms do not evolve in response to shifting environmental conditions4,5 despite growing evidence that rapid evolutionary responses occur under new selective regimes in the wild6,7. It is not clear whether conservation strategies would be different if evolutionary dynamics were considered during conservation planning. Here, we show that evolutionary responses fundamentally change recommendations for conservation actions. With spatially explicit simulations of a simple three-species coral reef ecosystem, we show that the preferred management strategies changed from those focusing on thermal refugia when evolutionary capacity was absent to those prioritizing trait and habitat diversity or high cover when adaptive evolution was possible. Prioritizing habitat diversity protects heat resistant populations and protects cooler refuges and the stepping stones between them. The protection of habitat heterogeneity and connectivity also produced substantially larger benefits outside reserves than refugia-based strategies, providing conservation planners an opportunity to facilitate adaptation to ongoing and unpredictable change.

Despite general and wide-ranging negative effects of coral reef degradation on reef communities, hope might exist for reef-associated predators that use nursery habitats. When reef structural complexity is lost, refuge density declines and prey vulnerability increases. Here, we explore whether the presence of nursery habitats can promote high predator productivity on degraded reefs by mitigating the costs of increased vulnerability in early life, whilst allowing for the benefits of increased food availability in adulthood. We apply size-based ecosystem models of coral reefs with high and low structural complexity to predict fish biomass and productivity in the presence and absence of mangrove nurseries. Our scenarios allow us to elucidate the interacting effects of refuge availability and ontogenetic habitat shifts for fisheries productivity. We find that low complexity, degraded reefs with nurseries can support fisheries productivity that is equal to or greater than that in complex reefs that lack nurseries. We compare and validate model predictions with field data from Belize. Our results should inform reef fisheries management strategies and protected areas now and into the future.

Coral reef restoration is an increasingly important part of tropical marine conservation. Information about what motivates coral reef restoration as well as its success and cost is not well understood but is needed to inform restoration decisions. We systematically review and synthesize data from mostly scientific studies published in peer-reviewed and gray literature on the motivations for coral reef restoration, the variables measured, outcomes reported, the cost per hectare of the restoration project, the survival of restored corals, the duration of the project, and its overall spatial extent depending on the restoration technique employed. The main motivation to restore coral reefs for the projects assessed was to further our ecological knowledge and improve restoration techniques, with coral growth, productivity, and survival being the main variables measured. The median project cost was 400,000 US$/ha (2010 US$), ranging from 6,000 US$/ha for the nursery phase of coral gardening to 4,000,000 US$/ha for substrate addition to build an artificial reef. Restoration projects were mostly of short duration (1–2 years) and over small spatial extents (0.01 ha or 108 m2). Median reported survival of restored corals was 60.9%. Future research to survey practitioners who do not publish their discoveries would complement this work. Our findings and database provide critical data to inform future research in coral reef restoration.

Recreational fishing practices can have significant impacts on marine ecosystems but their catch dynamics are often difficult to quantify, particularly for spearfishing. On coral reefs, the impacts of recreational spearfishing are often considered to be negligible compared to other practices, but the highly selective method adopted by spearfishers can result in locally distinct ecological consequences. Here we investigated the spatial patterns and catch composition of recreational spearfishers on the Great Barrier Reef using an online survey (n = 141 participants) targeted at spearfishers active along the coastline of Queensland. Observations from within the Queensland spearfishing community were also used to explore perceived changes in catches of three functionally distinct spearing targets. Preferred reef regions (coastal, inshore, offshore) differed among spearfishers from Bundaberg (south) to Cooktown (north). The piscivorous coral trout, Plectropomus leopardus, was suggested to be the preferred target comprising 34% (±1.5 SE) of spearfishers' reported catch composition. Spearfishers also noted a variety of changes in their catch composition over time, particularly regarding parrotfishes (decreased landings) and tuskfishes (increased landings). How this relates to the relative abundance and population biology of these taxa on the Great Barrier Reef requires attention. Spearfishers can provide important information regarding the status of their fishery through direct observations, which can inform legislation when acknowledged.

Marine protected areas (MPAs) are increasingly used to support both biodiversity conservation and fisheries management. However, MPA performance is likely to be compromised if people who depend on fishing are excluded from MPA design decision making. Participatory MPA design helps to address this problem by engaging local stakeholders in all critical decisions, including the total coverage, placement, and local size of no-take marine reserves. Here, we report the findings from a participatory MPA design project on Selayar Island, Indonesia, in which a community initiated collaborations with scientists to access modern quantitative tools for community-led MPA scenario testing. The outcomes highlight a local disagreement between ecologically and socially desirable MPA designs. Focused on social considerations, the initial community-supported MPA design consisted of four small reserves (0.5–1 km wide) in predominately southern community waters, where they were intended to restrict external fishers. Ecologically optimal MPA designs, in contrast, consisted of one or two large reserves (4–6 km wide) in northern community waters, where they were expected to restrict primarily local fishers but better support the rebuilding of fish populations and fisheries. However, ecologically optimal MPA designs were socially infeasible. Using quantitative MPA performance assessments, the community negotiated an alternative MPA design consisting of two 1.5–2 km wide reserves at socially and ecologically favorable locations. Compared to the initial proposal, this revised MPA design was estimated (1) to protect three to four times more individuals of key fishery species within reserve boundaries and (2) to double local fishery catches. We conclude that even simple MPA design tools, which quantify and visualize local conservation and fishery outcomes under alternative MPA scenarios, add value to participatory decision making and likely MPA performance.

Notionally herbivorous fishes maintains a critical ecosystem function on coral reefs by grazing algae and maintaining highly productive algal turf assemblages. Current paradigms implicate habitat complexity, predation, and primary productivity as major drivers of the distribution and abundance of herbivorous fish, yet little is known about the relative contribution of these factors. Here, we compare bottom-up and top-down drivers of notional herbivore assemblages across an environmental gradient of wave exposure in the Palau archipelago. We surveyed herbivore assemblages at reef slopes (6–9 m) across 18 sites, and quantified proxies of top-down control (predator biomass, habitat complexity) and bottom-up drivers (net primary production, nutrients) at each site. Despite substantial variability in herbivore biomass throughout the archipelago (6–65 g/m 2 ), general additive models indicate that neither top-down nor bottom-up drivers significantly predicted biomass or density of herbivores among sites. In contrast to expectations, herbivore biomass was highest at sites with high predator biomass, low structural complexity, and low benthic productivity. Rather, the highest biomass of herbivores was associated with shallow, tidally emergent, productive reef flats located adjacent to steep vertical walls (“drop-offs”). The emergent nature of this neighboring habitat precluded occupation by territorial fishes and multiple species of herbivores were observed to make foraging runs into this habitat once tidally inundated. We hypothesize that this habitat configuration provides an important cross-habitat resource subsidy. Multivariate ordination and permutation of herbivore communities revealed strong evidence for biogeographic partitioning throughout the archipelago (western, southwestern, inner eastern, and outer eastern clusters), contributing to an emerging picture that the habitat heterogeneity of seascapes can overwhelm the effects of conventional top-down and bottom-up structuring of herbivory on coral reefs.

Many habitat-building corals undergo mass synchronous spawning events. Yet, despite the enormous amounts of larvae produced, larval dispersal from a single spawning event and the reliability of larval supply are highly dependent on vagaries of ocean currents. However, colonies from the same population will occasionally spawn over successive months. These split spawning events likely help to realign reproduction events to favourable environmental conditions. Here, we show that split spawning may benefit corals by increasing the reliability of larval supply. By modelling the dispersal of coral larvae across Australia's Great Barrier Reef, we find that split spawning increased the diversity of sources and reliability of larval supply the reefs could receive, especially in regions with low and intrinsically variable connectivity. Such increased larval supply might help counteract the expected declines in reproductive success associated with split spawning events.

Benthic marine organisms rely on the dispersal and recruitment of propagules to replenish depleted populations following disturbances. Yet, ecological interactions between colonizing larvae and benthic competitors that become established following a disturbance can be a primary driver of recruitment success. On some coral reefs, local and global stressors have led to a proliferation of macroalgae that can inhibit the recruitment and recovery of corals. The brown macroalga Lobophora is considered a particularly strong inhibitor of coral recruitment, yet there is little information on how the alga affects demographic bottlenecks across early life-history stages. In the present study, we conducted a series of experiments to determine the effects of Lobophora sp. on three distinct life-history stages of the coral Acropora digitifera: larval settlement, early post-settlement survival, and survival and growth of small nubbins (1 cm) created from adult colonies. Our results demonstrate a high sensitivity of coral larvae to Lobophora, with settlement decreasing 16-fold when the alga was present on tiles compared to controls. Moreover, larvae did not settle on tiles when Lobophora cover > 50%. A negative, albeit minor, effect of Lobophora on the early post-settlement survival was evident, despite few recorded incidents of direct competition between settled corals and Lobophora because of low larval settlement in proximity to the alga. Conversely, there was no effect of Lobophora on the growth and survival of coral nubbins. Our results indicate that Lobophora most heavily impacts coral recruitment by inhibiting larval settlement, with the impact of the alga on recruitment decreasing through later life-history stages. These findings are concurrent with recent studies that demonstrate the ability of particular macroalgal species to deter coral larvae from settling on degraded reefs, likely through the release of chemical compounds, thereby impacting the recovery of coral populations following disturbances.

An adult, female grey reef shark Carcharhinus amblyrhnchos was observed missing its first dorsal fin in 2014. The same individual was re-photographed 4 years later indicating that this numerically dominant reef shark can survive total loss of its first dorsal fin. While this disability may impair the shark's ability to undertake pursuit predation, the species has a diversity of foraging modes that probably facilitates survival.

Orbicella annularis (Ellis and Solander,
1786), a key reef building species, is unusual among
Caribbean corals in the flexibility it displays in its symbioses
with dinoflagellates in the family Symbiodiniaceae. This
variability has been documented at a range of spatial scales;
from within and between colonies to scales spanning the
entire species range. However, temporal variability in
Symbiodiniaceae communities found within O. annularis
colonies is not well understood. Evidence suggests that
symbiont communities in this coral species fluctuate
temporally in response to environmental stressors (sporadic
changes in abundance and in community composition). In
this study, we investigated temporal stability of symbiont
communities in O. annularis at four sites in the Bahamas
over a period spanning 6 yrs. While the dominant symbiont
species, Breviolum minutum (LaJeunesse et al.) J.E.Parkinson
& LaJeunesse (formerly ITS2-type B1), remained stable
across four patch-reef study sites, finer resolution molecular
techniques revealed inter-annual variability in the presence/
absence of cryptic species Durusdinium trenchii (LaJeunesse)
LaJeunesse (formerly ITS2-type D1a). Durusdinium trenchii
is known to play a role in resistance to environmental stress
and may have a protective effect under warm conditions.
These results suggest that, while it might take an extreme
environmental perturbation to trigger a long-term shift in
the dominant symbiont, at background levels, less prevalent
symbiont taxa are likely to be continually shuffling their
relative abundances as they change in response to seasonal
or environmental changes.

Resilience underpins the sustainability of both ecological and social systems. Extensive loss of reef corals following recent mass bleaching events have challenged the notion that support of system resilience is a viable reef management strategy. While resilience-based management (RBM) cannot prevent the damaging effects of major disturbances, such as mass bleaching events, it can support natural processes that promote resistance and recovery. Here, we review the potential of RBM to help sustain coral reefs in the 21st century. We explore the scope for supporting resilience through existing management approaches and emerging technologies and discuss their opportunities and limitations in a changing climate. We argue that for RBM to be effective in a changing world, reef management strategies need to involve both existing and new interventions that together reduce stress, support the fitness of populations and species, and help people and economies to adapt to a highly altered ecosystem.

Extreme disturbances often lead to community reorganisations, yet sometimes ecosystems unexpectedly fail to recover. Such surprising outcomes may pinpoint important yet overlooked mechanisms that drive ecosystems into undesirable states. Using long-term field observations, experimental manipulations and mechanistic modelling, we document the drivers of an unexpected phase shift from coral to macroalgal dominance following typhoon disturbance on reefs in Palau (Micronesia). After extensive coral mortality, an ephemeral bloom of a canopy-forming macroalga (Liagora sp.) provided physical refuge from herbivore grazing, resulting in the establishment of a secondary, understory macroalga (Lobophora spp.). After disappearance of Liagora canopies and resulting loss of grazing refuge, the Lobophora patches continued to expand and led to a macroalgal (Lobophora-) dominated state that has persisted for more than 2 years. We developed a mechanistic model of Lobophora patch dynamics parameterised with rates of growth measured in situ to simulate the observed proliferation of Lobophora under variable grazing refuges in space and time. Model simulations showed that short-term escapes from grazing were pivotal in allowing establishment of patches of Lobophora. Ephemeral grazing refuges created an opportunity to reach a cover above which Lobophora growth exceeds grazing, so that Lobophora could expand after disappearance of Liagora canopies. Critically, in the absence of grazing refuge, herbivore biomass was sufficient to prevent the establishment of Lobophora patches. Our model demonstrates that with rapid algal growth and low grazing, a relatively minor grazing refuge (6 month) is sufficient to escape herbivore control after extensive coral mortality, leading to unexpected recovery failure. Transient fluctuations in the intensity of control mechanisms, such as herbivore grazing, can have disproportionate and long-lasting effects on community structure. Overall, this study stresses that our perception of reef dynamics must integrate the time scales at which reefs can be sensitive to transient changes in mechanisms promoting coral dominance.

Understanding the dynamics of habitat-forming organisms is fundamental to managing natural ecosystems. Most studies of coral reef dynamics have focused on clear-water systems though corals inhabit many turbid regions. Here, we illustrate the key drivers of an inshore coral reef ecosystem using 10 years of biological, environmental, and disturbance data. Tropical cyclones, crown-of-thorns starfish, and coral bleaching are recognized as the major drivers of coral loss at mid- and offshore reefs along the Great Barrier Reef (GBR). In comparison, little is known about what drives temporal trends at inshore reefs closer to major anthropogenic stress. We assessed coral cover dynamics using state-space models within six major inshore GBR catchments. An overall decline was detected in nearly half (46%) of the 15 reefs at two depths (30 sites), while the rest exhibited fluctuating (23%), static (17%), or positive (13%) trends. Inshore reefs responded similarly to their offshore counterparts, where contemporary trends were predominantly influenced by acute disturbance events. Storms emerged as the major driver affecting the inshore GBR, with the effects of other drivers such as disease, juvenile coral density, and macroalgal and turf per cent cover varying from one catchment to another. Flooding was also associated with negative trends in live coral cover in two southern catchments, but the mechanism remains unclear as it is not reflected in available metrics of water quality and may act through indirect pathways.

Managing diverse ecosystems is challenging because structuring drivers are often processes having diffuse impacts that attenuate from the people who were "managed" to the expected ecosystem-wide outcome. Coral reef fishes targeted for management only indirectly link to the ecosystem's foundation (reef corals). Three successively weakening interaction tiers separate management of fishing from coral abundance. We studied 12 islands along the 700-km eastern Caribbean archipelago, comparing fished and unfished coral reefs. Fishing reduced biomass of carnivorous (snappers and groupers) and herbivorous (parrotfish and surgeonfish) fishes. We document attenuating but important effects of managing fishing, which explained 37% of variance in parrotfish abundance, 20% of variance in harmful algal abundance, and 17% of variance in juvenile coral abundance. The explained variance increased when we quantified herbivory using area-specific bite rates. Local fisheries management resulted in a 62% increase in the archipelago's juvenile coral density, improving the ecosystem's recovery potential from major disturbances.

The use of physics-based wave propagation predictions requires a considerable time commitment, a high level of expertise and extensive climate and reef data that are not always available when undertaking planning for management of coasts and coral reef ecosystems. Bayesian belief networks (BBNs) have at least three attributes that make them an excellent choice to communicate physics-based wave model predictions. First, BBNs subsume thousands of predictions to provide probabilistic outcomes. Second, by using prior probabilities, a practitioner can still obtain predictions of wave outcomes even when their knowledge of input parameters is incomplete. Third, BBNs can propagate evidence from outputs to inputs, which can be used to identify input conditions that are most likely to deliver a chosen outcome. These three attributes are tested and found to hold for a BBN developed for this purpose.

Dissolved inorganic nitrogen (DIN) runoff from Great Barrier Reef (GBR) catchments is a threat to coral reef health. Several initiatives address this threat, including the Australian Government's Reef 2050 Plan. However, environmental decision makers face an unsolved prioritization challenge: determining the exposure of reefs to DIN from individual rivers. Here, we use virtual river tracers embedded within a GBR-wide hydrodynamic model to resolve the spatial and temporal dynamics of 16 individual river plumes during three wet seasons (2011−2013). We then used in-situ DIN observations to calibrate tracer values, allowing us to estimate the contribution of each river to reef-scale DIN exposure during each season. Results indicate that the Burdekin, Fitzroy, Tully and Daintree rivers pose the greatest DIN exposure risk to coral reefs during the three seasons examined. Results were used to demonstrate a decision support framework that combines reef exposure risk with river dominance (threat diversity).

The Sentinel-2A and 2B Multi-Spectral Instrument (MSI) offers a specification of potential value toward a number of objectives in remote sensing of coral reefs. Coral reefs represent a unique challenge for remote sensing, being highly heterogeneous at metre scales and occurring at variable depths and water clarity regimes. However, conservation initiatives, such as the United Nations Sustainable Development Goals, add urgency to the need for the large scale environmental monitoring information that remote sensing can provide. In the quest to meet this challenge a range of satellite instruments have been leveraged, from Landsat to high spatial resolution sensors such as WorldView-2, toward objectives such as: mapping of bottom types, bathymetry, change detection, and detection of coral bleaching events. Sentinel-2A and 2B offer a new paradigm of available instruments, with a 5-day revisit, 10 m multispectral spatial resolution and freely available data. Pre-launch simulation analyses by several of the authors suggested Sentinel-2 would have good performance for reef applications, in this paper we follow up on this study by reviewing the potential based on the substantial archive of actual data now available. First we determine to what extent the World's reefs are covered by Sentinel-2, since the mission requirements do not by default include all reefs. Secondly we review how a 5-day revisit translates to a usable acquisition rate of clear images, given that cloud and surface glint are common confounding factors. The usable acquisition rate is the real determinant of the objectives to which the data can be applied. Finally we apply current processing algorithms to Sentinel-2 data of several sites over the Great Barrier Reef, including physics-based bathymetry inversion and object-orientated benthic mapping. Landsat 8 OLI is most comparable current sensor to Sentinel-2 MSI, so direct comparisons and the possibilities for data synthesis are explored. Our findings confirm that Sentinel-2 has excellent performance for meeting several essential coral reef scientific and monitoring objectives. Taking into account cloud and sun glint, the usable acquisition rate for a large proportion of reefs is likely to be around 20 clear images a year on average, giving a new potential for evaluation of short time-scale disturbances and impacts. The spatial resolution of 10 m is a key threshold for delineating benthic features of interest such as coral structures, and there is evidence from image and field data that bleaching is detectable. Radiometrically Sentinel-2 data can support good results in physics-based methods, such as bathymetric mapping, comparable to Landsat 8 and WorldView-2. In addition the large scale acquisition area, provided by the 290 km wide swath, offers advantages over high spatial resolution imagery for mapping at multi-reef scales. Sentinel-2 data can be immediately leveraged with existing methods, to provide a new level of reef monitoring information compared to that previously available by remote sensing. Combined with Landsat 8 and the historical Landsat archive, the data collected today will be invaluable for decades or even centuries to come. In this context, the main downside of the Sentinel-2 mission is that approximately 12% of the World's reefs currently lie outside the acquisition plan and are not imaged. Surprisingly, for a European initiative, coral reefs in European governed territories are among the worst served globally. These omissions, approximately only 1/200th of the currently imaged area, limit the global scope which otherwise would be one of Sentinel-2's greatest strengths.

Despite being one of the most important and well-studied coral reefs in the world, the full extent of coral habitat of the Great Barrier Reef (GBR) is not well mapped and there is no current and comprehensive map of the GBR's geomorphic zonation or benthic composition. This paper demonstrates an approach that integrates ecological coral habitat mapping with empirical modelling to map the geomorphic zonation and benthic composition of the “shallow offshore reefs” of the GBR, using the Capricorn Bunker Group (CBG) as a case study. The approach combined environmental data sets and geo-ecological rule sets to identify geomorphic zones. The benthic composition of individual geomorphic zones was mapped for: shallow reef flat zones, using object-based image analysis with context driven rules based on coral reef ecology; and reef slope zones, using levels of wave exposure to predict the distribution of coral types. The environmental data sets used were field-based benthic composition data, Landsat 8 OLI satellite image-derived bottom reflectance, water depth and slope (15 m × 15 m pixel size) data, reef impact data, and modelled wave exposure. The study showed that the combination of geomorphic-ecological rules and models with remote sensing imagery provided robust mapping results over a large (~2500 km2) reef system, of which 245 km2 was mapped as shallow coral reefs and 88 km2 of that was mapped as areas containing coral. Most importantly, the method produced defined the geomorphic zones and benthic composition of a study area that is significantly larger than the majority of coral reef remote sensing mapping projects previously published. With some modifications, the methods presented have the potential to be applied to the full extent of the shallow offshore reefs of the GBR, or any large reef globally. Monitoring and management of coral reefs for conservation and other purposes, at regional to global scales will benefit from the ability to produce and use this type of essential information on a regular basis.

Overexploitation of large apex marine predators is widespread in the world's oceans, yet the timing and extent of declines are poorly understood. Here we reconstruct a unique fisheries-independent dataset from a shark control programme spanning 1760 km of the Australian coastline over the past 55 years. We report substantial declines (74-92%) of catch per unit effort of hammerhead (Sphyrnidae), whaler (Carcharhinidae), tiger shark (Galeocerdo cuvier) and white sharks (Carcharodon carcharias). Following onset of the program in the 1960s, catch rates in new installations in subsequent decades occurred at a substantially lower rate, indicating regional depletion of shark populations over the past half a century. Concurrent declines in body size and the probability of encountering mature individuals suggests that apex shark populations are more vulnerable to exploitation than previously thought. Ongoing declines and lack of recovery of vulnerable and protected shark species are a cause for concern.

In response to multiple stressors, coral reef health has declined in recent decades, with reefs exhibiting reduced living coral and structural complexity, and a concomitant rise in the dominance of algal resources. Reef degradation alters food availability and reduces the diversity and density of refuges for prey. These changes affect predator–prey interactions and can have cascading impacts on food webs and fisheries productivity. We use a size-based ecosystem model of coral reefs that incorporates the influence of structural complexity, benthic primary production and detrital recycling to explore how predator–prey interactions and fisheries productivity respond to a gradient of reef degradation. We show that fisheries productivity overall may be robust to initial stages of reef degradation because the benefits of increased resources outweigh the costs of moderate refuge decline. However, the assemblage composition and size structure of reef fish will differ on degraded reefs, with herbivores and invertivores contributing relatively more to productivity. More significant losses of refuges associated with the erosion of structural complexity correspond to fisheries productivity losses of at least 35% compared to healthy reefs. Synthesis and applications. Our model provides fisheries managers with quantitative predictions about how fisheries productivity may change in response to the ongoing degradation of coral reefs. We predict an initial increase in productivity at intermediate reef degradation, followed by a drastic decline when structural complexity is lost. We also capture subtle changes to potential catch composition and fish size, including increases in smaller herbivorous and invertivorous fish from degraded reefs, which will undoubtedly impact fisheries value. On the one hand, our results reassure for continued productivity in the short term, but on the other, we warn against complacency. Management must change to capture any potential benefits to fisheries, and long-term sustainability still depends on the maintenance of complex coral reef habitats.

With over 1 billion people currently relying on the services provided by marine ecosystems – e.g. food, fibre and coastal protection – governments, scientists and international bodies are searching for innovative research to support decision-makers in achieving the Sustainable Development Goals (SDGs). Valuing past and present ecosystem services allows investigation into how different scenarios impact the SDGs, such as economic growth, sustainability, poverty and equity among stakeholders. This paper investigates the past and current value of the lobster fishery located in the Table Mountain National Park Marine Protected Area. It then uses InVEST to highlight future changes under different scenarios. While we found a significant decline in fishery value over the next ten years under all three scenarios, the exclusion of large-scale fisheries from the marine protected area seems to yield the most positive results in regard to South Africa's SDG commitments. This scenario has the potential to generate approximately 50% more revenue, while also producing the highest available protein to local communities, highest quantity of spawners and highest economic distribution to small-scale fisheries. It is clear through this research that valuing ecosystem services can enable a future of healthy economies, people and environments; the highly sought-after triple-bottom line.

Refuge availability and fishing alter predator-prey interactions on coral reefs, but our understanding of how they interact to drive food web dynamics, community structure and vulnerability of different trophic groups is unclear. Here, we apply a size-based ecosystem model of coral reefs, parameterized with empirical measures of structural complexity, to predict fish biomass, productivity and community structure in reef ecosystems under a broad range of refuge availability and fishing regimes. In unfished ecosystems, the expected positive correlation between reef structural complexity and biomass emerges, but a non-linear effect of predation refuges is observed for the productivity of predatory fish. Reefs with intermediate complexity have the highest predator productivity, but when refuge availability is high and prey are less available, predator growth rates decrease, with significant implications for fisheries. Specifically, as fishing intensity increases, predators in habitats with high refuge availability exhibit vulnerability to over-exploitation, resulting in communities dominated by herbivores. Our study reveals mechanisms for threshold dynamics in predators living in complex habitats and elucidates how predators can be food-limited when most of their prey are able to hide. We also highlight the importance of nutrient recycling via the detrital pathway, to support high predator biomasses on coral reefs.

Corals of the Great Barrier Reef (GBR) have declined over the past 30 years. While reef state depends on the balance between disturbance and recovery, most studies have focused on the effects of disturbance on reef decline. We show that coral recovery rates across the GBR declined by an average of 84% between 1992 and 2010. Recovery was variable: Some key coral types had close to zero recovery by the end of that period, whereas some reefs exhibited high recovery. Our results indicate that coral recovery is sensitive to chronic but manageable pressures, and is suppressed for several years following acute disturbances. Loss of recovery capacity was partly explained by the cumulative effects of chronic pressures including water quality, warming, and sublethal effects of acute disturbances (cyclones, outbreaks of crown-of-thorns starfish, and coral bleaching). Modeled projections indicate that recovery rates can respond rapidly to reductions in acute and chronic stressors, a result that is consistent with fast recovery observed on some reefs in the central and southern GBR since the end of the study period. A combination of local management actions to reduce chronic disturbances and global action to limit the effect of climate change is urgently required to sustain GBR coral cover and diversity.

Herbivory plays an important role in controlling benthic dynamics on coral reefs. The previous studies have highlighted the importance of grazing herbivorous fishes in removing algal turf biomass, but fewer studies have investigated the impact of invertebrate microherbivore grazing. This study examined the impact of microherbivore grazing in areas of high- and low-wave exposure on the forereefs of Palau, Micronesia, in June 2015. Experimental tiles were placed on open benthos, and in benthic and suspended herbivore exclusion cages at exposed and sheltered sites to partition the grazing impacts of microherbivores from fish grazers while examining the effect of exposure on algal turf productivity. Microherbivore grazing significantly impacted algal turf biomass, and this impact was greater in exposed sites than sheltered sites. Exposure did not significantly affect algal turf biomass on experimental tiles in the suspended exclusion cages. Surveys of microherbivore density revealed only Paguroidea (hermit crabs, especially of family Diogenidae) were more abundant at exposed sites than sheltered sites. Furthermore, tank trials of grazing rates showed diogenid hermit crabs removed over four times as much algal turf biomass as Columbellidae (marine gastropods), the second most abundant microherbivores. These results show that microherbivores are significant grazers on Palau’s forereefs, and may play an important role in maintaining reef resilience as reef health continues to decline worldwide. The significant role of invertebrate microherbivores in removing algal turf biomass should be investigated when considering the ecological role of herbivory on coral reefs.

Aim: Use a fishery-independent metric to model and map regional-scale fishing impact, and demonstrate how this metric assists with modelling current and potential fish biomass to support coral-reef management. We also examine the relative importance of anthropogenic and natural factors on fishes at biogeographical scales. Location: Reefs of five jurisdictions in Micronesia. Methods: a subset of 1,127 fish surveys (470 surveys) was used to calculate site-specific mean parrotfish lengths (a proxy for cumulative fishing impact), which were modelled against 20 biophysical and anthropogenic variables. The resulting model was extrapolated to each 1 ha reef cell in the region to generate a fishing impact map. The remaining data (657 surveys) were then used to model fish biomass using 15 response variables, including fishing impact. This model was used to map estimated current regional fish standing stocks and, by setting fishing impact to 0, potential standing stocks. Results: Human population pressure and distance to port were key anthropogenic variables predicting fishing impact. Total fish biomass was negatively correlated with fishing, but the influence of natural gradients of primary productivity, sea surface temperature, habitat quality and larval supply was regionally more important. Main conclusions: Mean parrotfish length appears to be a useful fishery-independent metric for modelling Pacific fishing impact, but considering environmental covariates is critical. Explicitly modelling fishing impact has multiple benefits, including generation of the first large-scale map of tropical fishing impacts that can inform conservation planning. Using fishing impact data to map current and potential fish stocks provides further benefits, including highlighting the relative importance of fishing on fish biomass and identifying key biophysical variables that cause maximum potential biomass to vary significantly across the region. Regional-scale maps of fishing, fish standing stocks and the potential benefits of protection are likely to lead to improved conservation outcomes during reserve network planning.

Classically, biomass partitioning across trophic levels was thought to add up to a pyramidal distribution. Numerous exceptions have, however, been noted including complete pyramidal inversions. Elevated levels of biomass top-heaviness (i.e. high consumer/resource biomass ratios) have been reported from Arctic tundra communities to Brazilian phytotelmata, and in species assemblages as diverse as those dominated by sharks and ants. We highlight two major pathways for creating top-heaviness, via: (1) endogenous channels that enhance energy transfer across trophic boundaries within a community and (2) exogenous pathways that transfer energy into communities from across spatial and temporal boundaries. Consumer-resource models and allometric trophic network models combined with niche models reveal the nature of core mechanisms for promoting top-heaviness. Outputs from these models suggest that top-heavy communities can be stable, but they also reveal sources of instability. Humans are both increasing and decreasing top-heaviness in nature with ecological consequences. Current and future research on the drivers of top-heaviness can help elucidate fundamental mechanisms that shape the architecture of ecological communities and govern energy flux within and between communities. Questions emerging from the study of top-heaviness also usefully draw attention to the incompleteness and inconsistency by which ecologists often establish definitional boundaries for communities.

The National Oceanic and Atmospheric Administration's Coral Reef Watch program developed and operates several global satellite products to monitor bleaching-level heat stress. While these products have a proven ability to predict the onset of most mass coral bleaching events, they occasionally miss events; inaccurately predict the severity of some mass coral bleaching events; or report false alarms. These products are based solely on temperature and yet coral bleaching is known to result from both temperature and light stress. This study presents a novel methodology (still under development), which combines temperature and light into a single measure of stress to predict the onset and severity of mass coral bleaching. We describe here the biological basis of the Light Stress Damage (LSD) algorithm under development. Then by using empirical relationships derived in separate experiments conducted in mesocosm facilities in the Mexican Caribbean we parameterize the LSD algorithm and demonstrate that it is able to describe three past bleaching events from the Great Barrier Reef (GBR). For this limited example, the LSD algorithm was able to better predict differences in the severity of the three past GBR bleaching events, quantifying the contribution of light to reduce or exacerbate the impact of heat stress. The new Light Stress Damage algorithm we present here is potentially a significant step forward in the evolution of satellite-based bleaching products.

Marine reserves are a commonly applied conservation tool, but their size is often chosen based on considerations of socioeconomic rather than ecological impact. Here, we use a simple individual-based model together with the latest empirical information on home ranges, densities and schooling behaviour in 66 coral reef fishes to quantify the conservation effectiveness of various reserve sizes. We find that standard reserves with a diameter of 1–2 km can achieve partial protection (≥50% of the maximum number of individuals) of 56% of all simulated species. Partial protection of the most important fishery species, and of species with diverse functional roles, required 2–10 km wide reserves. Full protection of nearly all simulated species required 100 km wide reserves. Linear regressions based on the mean home range and density, and even just the maximum length, of fish species approximated these results reliably, and can therefore be used to support locally effective decision making.

Marine protected areas (MPAs) form the cornerstone of marine conservation. Identifying which factors contribute to their success or failure is crucial considering the international conservation targets for 2020 and the limited funds generally available for marine conservation. We identified common factors of success and/or failure of MPA effectiveness using peer-reviewed publications and first-hand expert knowledge for 27 case studies around the world. We found that stakeholder engagement was considered to be the most important factor affecting MPA success, and equally, its absence, was the most important factor influencing failure. Conversely, while some factors were identified as critical for success, their absence was not considered a driver of failure, and vice versa. This mismatch provided the impetus for considering these factors more critically. Bearing in mind that most MPAs have multiple objectives, including non-biological, this highlights the need for the development and adoption of standardized effectiveness metrics, besides biological considerations, to measure factors contributing to the success or failure of MPAs to reach their objectives. Considering our conclusions, we suggest the development of specific protocols for the assessment of stakeholder engagement, the role of leadership, the capacity of enforcement and compliance with MPAs objectives. Moreover, factors defining the success and failure of MPAs should be assessed not only by technical experts and the relevant authorities, but also by other stakeholder groups whose compliance is critical for the successful functioning of an MPA. These factors should be considered along with appropriate ecological, social, and economic data and then incorporated into adaptive management to improve MPA effectiveness.

Blue carbon initiatives require accurate monitoring of carbon stocks. We examined sources of variability in seagrass organic carbon (Corg) stocks, contrasting spatial with short temporal scales. Seagrass morphology and sediment Corg stocks were measured from biomass and shallow sediment cores collected in Moreton Bay, Australia. Samples were collected between 2012 and 2013, from a total of 77 sites that spanned a gradient of water turbidity. Environmental measures of water quality between 2000 and 2013 revealed strong seasonal fluctuations from summer to winter, yet seagrass biomass exhibited no temporal variation. There was no temporal variability in Corg stocks, other than below ground biomass stocks were slightly higher in June 2013. Seagrass locations were grouped into riverine, coastal, and seagrass loss locations and short temporal variability of Corg stocks was analysed within these categories to provide clearer insights into temporal patterns. Above ground Corg stocks were similar between coastal and riverine meadows. Below ground Corg stocks were highest in coastal meadows, followed by riverine meadows. Sediment Corg stocks within riverine meadows were much higher than at coastal meadows and areas of seagrass loss, with no difference in sediment Corg stocks between these last two categories. Riverine seagrass meadows, of higher turbidity, had greater total Corg stocks than meadows in offshore areas irrespective of time. We suggest that Corg stock assessment should prioritise sampling over spatial gradients, but repeated monitoring over short time scales is less likely to be warranted if environmental conditions remain stable.

Seagrass ecosystems are inherently dynamic, responding to environmental change across a range of scales. Habitat requirements of seagrass are well defined, but less is known about their ability to resist disturbance. Specific means of recovery after loss are particularly difficult to quantify. Here we assess the resistance and recovery capacity of 12 seagrass genera. We document four classic trajectories of degradation and recovery for seagrass ecosystems, illustrated with examples from around the world. Recovery can be rapid once conditions improve, but seagrass absence at landscape scales may persist for many decades, perpetuated by feedbacks and/or lack of seed or plant propagules to initiate recovery. It can be difficult to distinguish between slow recovery, recalcitrant degradation, and the need for a window of opportunity to trigger recovery. We propose a framework synthesizing how the spatial and temporal scales of both disturbance and seagrass response affect ecosystem trajectory and hence resilience.

Global climate change and localized anthropogenic stressors are driving rapid declines in coral reef health. In vitro experiments have been fundamental in providing insight into how reef organisms will potentially respond to future climates. However, such experiments are inevitably limited in their ability to reproduce the complex interactions that govern reef systems. Studies examining coral communities that already persist under naturally-occurring extreme and marginal physicochemical conditions have therefore become increasingly popular to advance ecosystem scale predictions of future reef form and function, although no single site provides a perfect analog to future reefs. Here we review the current state of knowledge that exists on the distribution of corals in marginal and extreme environments, and geographic sites at the latitudinal extremes of reef growth, as well as a variety of shallow reef systems and reef-neighboring environments (including upwelling and CO2 vent sites). We also conduct a synthesis of the abiotic data that have been collected at these systems, to provide the first collective assessment on the range of extreme conditions under which corals currently persist. We use the review and data synthesis to increase our understanding of the biological and ecological mechanisms that facilitate survival and success under sub-optimal physicochemical conditions. This comprehensive assessment can begin to: (i) highlight the extent of extreme abiotic scenarios under which corals can persist, (ii) explore whether there are commonalities in coral taxa able to persist in such extremes, (iii) provide evidence for key mechanisms required to support survival and/or persistence under sub-optimal environmental conditions, and (iv) evaluate the potential of current sub-optimal coral environments to act as potential refugia under changing environmental conditions. Such a collective approach is critical to better understand the future survival of corals in our changing environment. We finally outline priority areas for future research on extreme and marginal coral environments, and discuss the additional management options they may provide for corals through refuge or by providing genetic stocks of stress tolerant corals to support proactive management strategies.

Seagrass meadows serve as marine carbon sinks, though rates of carbon burial and sediment accretion may vary within and among seagrass meadows due to spatial and temporal variability in sedimentary and biophysical conditions. However, few data are available to evaluate variation in carbon burial over decades to centuries, particularly in subtropical seagrass meadows. Here we assess historical trends in rates of vertical accretion and carbon burial in subtropical seagrass sediments in Moreton Bay, Australia. A total of 19 sediment cores varying in length from 22 to 205 cm were collected from six locations, including two locations where seagrass meadows occurred historically but were lost in recent decades. Cores were dated using 210Pb and 14C. Geochronologies were modelled based on the successful 210Pb dates for two of the locations combined with 14C at five locations. Organic and inorganic carbon content, dry bulk density and stable carbon and nitrogen isotope composition (δ13Corg, δ15N) were measured throughout the cores. Sediments underlying seagrass meadows in Moreton Bay have organic carbon stored up to a depth of at least 2 m which dates to over 7000 yr BP. Across the entire time series, organic carbon burial rates averaged 19 g m−2 yr−1 and inorganic carbon burial rates averaged 27 g m−2 yr−1. Overall mean rates of vertical accretion were estimated to be 0.2 cm yr−1. Rates of vertical accretion accelerated 10-fold following European colonisation which commenced in 1824, from 0.06 ± 0.06 cm yr−1 to 0.66 ± 1.19 cm yr−1. Similarly, rates of organic carbon burial averaged 7.2 ± 5.5 g m−2 yr−1 but then increased 7-fold post-colonisation to 50.5 ± 82.1 g m−2 yr−1. Thus, in Moreton Bay, European settlement and associated land-use change has enhanced sediment accretion and carbon burial in seagrass sediments.

Australia's Great Barrier Reef (GBR) is under pressure from a suite of stressors including cyclones, crown-of-thorns starfish (COTS), nutrients from river run-off and warming events that drive mass coral bleaching. Two key questions are: how vulnerable will the GBR be to future environmental scenarios, and to what extent can local management actions lower vulnerability in the face of climate change? to address these questions, we use a simple empirical and mechanistic coral model to explore six scenarios that represent plausible combinations of climate change projections (from four Representative Concentration Pathways, RCPs), cyclones and local stressors. Projections (2017-2050) indicate significant potential for coral recovery in the near-term, relative to current state, followed by climate-driven decline. Under a scenario of unmitigated emissions (RCP8.5) and business-as-usual management of local stressors, mean coral cover on the GBR is predicted to recover over the next decade and then rapidly decline to only 3% by year 2050. In contrast, a scenario of strong carbon mitigation (RCP2.6) and improved water quality, predicts significant coral recovery over the next two decades, followed by a relatively modest climate-driven decline that sustained coral cover above 26% by 2050. In an analysis of the impacts of cumulative stressors on coral cover relative to potential coral cover in the absence of such impacts, we found that GBR-wide reef performance will decline 27%-74% depending on the scenario. Up to 66% of performance loss is attributable to local stressors. The potential for management to reduce vulnerability, measured here as the mean number of years coral cover can be kept above 30%, is spatially variable. Management strategies that alleviate cumulative impacts have the potential to reduce the vulnerability of some midshelf reefs in the central GBR by 83%, but only if combined with strong mitigation of carbon emissions.

To support fishing communities, reserves should ensure the persistence of meta-populations while boosting fisheries yield. However, so far their design from the onset has rarely considered both objectives simultaneously. Here we overcome this barrier in designing a network of reserves for the Caribbean spiny lobster, a species with long larval duration for which local management is considered pointless because the benefits of protection are believed to be accrued elsewhere. Our reserve design approach uses spatially explicit population models and considers ontogenetic migration, larval and adult movement. We show that yield and persistence are negatively related, but that both objectives can be maximized simultaneously during planning. Importantly, we also show that local efforts to manage spiny lobster, the most economically valuable marine resource in the Caribbean, can result in locally accrued benefits, overcoming a major barrier to investing effort in the appropriate management of this species.

Environmental conservation initiatives, including marine protected areas (MPAs), have proliferated in recent decades. Designed to conserve marine biodiversity, many MPAs also seek to foster sustainable development. As is the case for many other environmental policies and programs, the impacts of MPAs are poorly understood. Social-ecological systems, impact evaluation, and common-pool resource governance are three complementary scientific frameworks for documenting and explaining the ecological and social impacts of conservation interventions. We review key components of these three frameworks and their implications for the study of conservation policy, program, and project outcomes. Using MPAs as an illustrative example, we then draw upon these three frameworks to describe an integrated approach for rigorous empirical documentation and causal explanation of conservation impacts. This integrated three-framework approach for impact evaluation of governance in social-ecological systems (3FIGS) accounts for alternative explanations, builds upon and advances social theory, and provides novel policy insights in ways that no single approach affords. Despite the inherent complexity of social-ecological systems and the difficulty of causal inference, the 3FIGS approach can dramatically advance our understanding of, and the evidentiary basis for, effective MPAs and other conservation initiatives.

Climate change and ocean acidification are altering marine ecosystems and, from a human perspective, creating both winners and losers. Human responses to these changes are complex, but may result in reduced government investments in regulation, resource management, monitoring and enforcement. Moreover, a lack of peoples' experience of climate change may drive some towards attributing the symptoms of climate change to more familiar causes such as management failure. Taken together, we anticipate that management could become weaker and less effective as climate change continues. Using diverse case studies, including the decline of coral reefs, coastal defences from flooding, shifting fish stocks and the emergence of new shipping opportunities in the Arctic, we argue that human interests are better served by increased investments in resource management. But greater government investment in management does not simply mean more of "business-as-usual." Management needs to become more flexible, better at anticipating and responding to surprise, and able to facilitate change where it is desirable. A range of technological, economic, communication and governance solutions exists to help transform management. While not all have been tested, judicious application of the most appropriate solutions should help humanity adapt to novel circumstances and seek opportunity where possible.

Marine protected areas (MPAs) are increasingly being used globally to conserve marine resources. However, whether many MPAs are being effectively and equitably managed, and how MPA management influences substantive outcomes remain unknown. We developed a global database of management and fish population data (433 and 218 MPAs, respectively) to assess: MPA management processes; the effects of MPAs on fish populations; and relationships between management processes and ecological effects. Here we report that many MPAs failed to meet thresholds for effective and equitable management processes, with widespread shortfalls in staff and financial resources. Although 71% of MPAs positively influenced fish populations, these conservation impacts were highly variable. Staff and budget capacity were the strongest predictors of conservation impact: MPAs with adequate staff capacity had ecological effects 2.9 times greater than MPAs with inadequate capacity. Thus, continued global expansion of MPAs without adequate investment in human and financial capacity is likely to lead to sub-optimal conservation outcomes.

Australia's iconic Great Barrier Reef (GBR) continues to suffer from repeated impacts of cyclones, coral bleaching, and outbreaks of the coral-eating crown-of-thorns starfish (COTS), losing much of its coral cover in the process. This raises the question of the ecosystem's systemic resilience and its ability to rebound after large-scale population loss. Here, we reveal that around 100 reefs of the GBR, or around 3%, have the ideal properties to facilitate recovery of disturbed areas, thereby imparting a level of systemic resilience and aiding its continued recovery. These reefs (1) are highly connected by ocean currents to the wider reef network, (2) have a relatively low risk of exposure to disturbances so that they are likely to provide replenishment when other reefs are depleted, and (3) have an ability to promote recovery of desirable species but are unlikely to either experience or spread COTS outbreaks. The great replenishment potential of these 'robust source reefs', which may supply 47% of the ecosystem in a single dispersal event, emerges from the interaction between oceanographic conditions and geographic location, a process that is likely to be repeated in other reef systems. Such natural resilience of reef systems will become increasingly important as the frequency of disturbances accelerates under climate change.

The Great Barrier Reef Marine Park (GBRMP) is the largest network of marine reserves in the world, yet little is known of the efficacy of no-fishing zones in the relatively lightly-exploited remote parts of the system (i.e. northern regions). Here, we find that the detection of reserve effects is challenging and that heterogeneity in benthic habitat composition, specifically branching coral cover, is one of the strongest driving forces of fish assemblages. As expected, the biomass of targeted fish species was generally greater (up to 5-fold) in no-take zones than in fished zones, but we found no differences between the two forms of no-take zone: 'no-take' versus 'no-entry'. Strong effects of zoning were detected in the remote Far-North inshore reefs and more central outer reefs, but surprisingly fishing effects were absent in the less remote southern locations. Moreover, the biomass of highly targeted species was nearly 2-fold greater in fished areas of the Far-North than in any reserve (no-take or no-entry) further south. Despite high spatial variability in fish biomass, our results suggest that fishing pressure is greater in southern areas and that poaching within reserves may be common. Our results also suggest that fishers 'fish the line' as stock sizes in exploited areas decreased near larger no-take zones. Interestingly, an analysis of zoning effects on small, non-targeted fishes appeared to suggest a top-down effect from mesopredators, but was instead explained by variability in benthic composition. Thus, we demonstrate the importance of including appropriate covariates when testing for evidence of trophic cascades and reserve successes or failures.

Many coral reefs have phase shifted from coral to macroalgal dominance. Ocean acidification (OA) due to elevated CO2 is hypothesised to advantage macroalgae over corals, contributing to these shifts, but the mechanisms affecting coral-macroalgal interactions under OA are unknown. Here, we show that (i) three common macroalgae are more damaging to a common coral when they compete under CO2 concentrations predicted to occur in 2050 and 2100 than under present-day conditions, (ii) that two macroalgae damage corals via allelopathy, and (iii) that one macroalga is allelopathic under conditions of elevated CO2, but not at ambient levels. Lipid-soluble, surface extracts from the macroalga Canistrocarpus (=Dictyota) cervicornis were significantly more damaging to the coral Acropora intermedia growing in the field if these extracts were from thalli grown under elevated vs ambient concentrations of CO2. Extracts from the macroalgae Chlorodesmis fastigiata and Amansia glomerata were not more potent when grown under elevated CO2. Our results demonstrate increasing OA advantages seaweeds over corals, that algal allelopathy can mediate coral-algal interactions, and that OA may enhance the allelopathy of some macroalgae. Other mechanisms also affect coral-macroalgal interactions under OA, and OA further suppresses the resilience of coral reefs suffering blooms of macroalgae.

Climate change will homogenise the environment and generate a preponderance of mediocre reefs. Managing seascapes of mediocrity will be challenging because our science is ill prepared to deal with the ‘shades of grey’ of reef health; we tend to study natural processes in the healthiest reefs available. Yet much can be gained by examining the drivers and implications of even subtle changes in reef state. Where strong ecological interactions are discovered, even small changes in abundance can have profound impacts on coral resilience. Indeed, if we are to develop effective early warnings of critical losses of resilience, then monitoring must place greater emphasis on measuring and interpreting changes in reef recovery rates. In terms of mechanism, a more nuanced approach is needed to explore the generality of what might be considered ‘dogma’. A more nuanced approach to science will serve managers needs well and help minimise the rise of mediocrity in coral reef ecosystems.

Herbivores greatly influence the productivity of algae but their impact can depend on the nuances of the timing, location, and intensity of herbivory. While plants can escape herbivory in spatial refugia, small-scale variations in habitat quality play a critical role in plant tolerance to herbivory and might generate complex trade-offs. On coral reefs, overstory branching corals provide a refuge from fish herbivory but also provide refugia for many small fish that excrete nutrients. Therefore, algae living in this habitat might also benefit from higher nutrient delivery. However, because coral branches occlude sunlight, algal growth rates might be impaired despite experiencing elevated nutrients and lower herbivory. In lab-based experiments, light, nutrients, and simulated herbivory were manipulated in summer and winter to investigate how these processes interact to influence the tolerance of herbivory in the calcifying green algae Halimeda, an important producer of reef carbonate sediments worldwide. Halimeda heteromorpha which is commonly found associated with branching corals tolerated tissue damage by increasing rates of segment production. Greater tolerance was observed at levels of light resembling those experienced under the coral’s canopy. Nutrient additions increased compensatory segment growth in winter but not summer. Levels of tolerance were seasonal and nutrient dependent. Results show that small-scale variations in habitat quality may influence tolerance to herbivory in Halimeda. This suggests that if coral habitats are degraded or lost and oceans continue to warm, a likely negative impact on Halimeda populations and its contribution to carbonate sediments could be expected if high levels of herbivory are maintained.

Coastal fish populations are typically threatened by multiple human activities, including fishing pressure and run-off of terrestrial pollution. Linking multiple threats to their impacts on fish populations is challenging because the threats may influence a species directly, or indirectly, via its habitats and its interactions with other species. Here we examine spatial variation in abundance of coral reef fish across gradients of fishing pressure and turbidity in Fiji. We explicitly account for multiple pathways of influence to test the alternative hypotheses that (1) habitat moderates predation by providing shelter, so habitat loss only affects prey fish populations if there are abundant predators, (2) habitat change co-drives biomass of both prey and predator functional groups. We examined responses of 7 fish functional groups and found that habitat change co-drives both predator and prey responses to turbidity. Abundances of all functional groups were associated with changes in habitat cover; however, the responses of their habitats to turbidity were mixed. Planktivore and piscivore abundance were lower in areas of high turbidity, because cover of their preferred habitats was lower. Invertivore, browser and grazer abundance did not change strongly over the turbidity gradient, because different components of their habitats exhibited both increases and decreases with turbidity. The effects of turbidity on fish populations were minor in areas where fish populations were already depleted by fishing. These findings suggest that terrestrial run-off modifies the composition of reef fish communities indirectly by affecting the benthic habitats that reef fish use.

Larval dispersal by ocean currents is a critical component of systematic marine protected area (MPA) design. However, there is a lack of quantitative methods to incorporate larval dispersal in support of increasingly diverse management objectives, including local population persistence under multiple types of threats (primarily focused on larval retention within and dispersal between protected locations) and benefits to unprotected populations and fisheries (primarily focused on larval export from protected locations to fishing grounds). Here, we present a flexible MPA design approach that can reconcile multiple such potentially conflicting management objectives by balancing various associated treatments of larval dispersal information. We demonstrate our approach based on alternative dispersal patterns, combinations of threats to populations, management objectives, and two different optimization strategies (site vs. network-based). Our outcomes highlight a consistently high effectiveness in selecting priority locations that are self-replenishing, inter-connected, and/or important larval sources. We find that the opportunity to balance these three dispersal attributes flexibly can help not only to prevent meta-population collapse, but also to ensure effective fisheries recovery, with average increases in the number of recruits at fishing grounds at least two times higher than achieved by standard habitat-based or ad-hoc MPA designs. Future applications of our MPA design approach should therefore be encouraged, specifically where management tools other than MPAs are not feasible.

Coral reef monitoring programmes exist in all regions of the world, recording reef attributes such as coral cover, fish biomass and macroalgal cover. Given the cost of such monitoring programs, and the degraded state of many of the world's reefs, understanding how reef monitoring data can be used to shape management decisions for coral reefs is a high priority. However, there is no general guide to understanding the ecological implications of the data in a format that can trigger a management response. We attempt to provide such a guide for interpreting the temporal trends in 41 coral reef monitoring attributes, recorded by seven of the largest reef monitoring programmes. We show that only a small subset of these attributes is required to identify the stressors that have impacted a reef (i.e. provide a diagnosis), as well as to estimate the likely recovery potential (prognosis). Two of the most useful indicators, turf algal canopy height and coral colony growth rate are not commonly measured, and we strongly recommend their inclusion in reef monitoring. The diagnosis and prognosis system that we have developed may help guide management actions and provides a foundation for further development as biological and ecological insights continue to grow.

Overfishing threatens the sustainability of coastal marine biodiversity, especially in tropical developing countries. To counter this problem, about 200 governments worldwide have committed to protecting 10%-20% of national coastal marine areas. However, associated impacts on fisheries productivity are unclear and could weaken the food security of hundreds of millions of people who depend on diverse and largely unregulated fishing activities. Here, we present a systematic theoretic analysis of the ability of reserves to rebuild fisheries under such complex conditions, and we identify maximum reserve coverages for biodiversity conservation that do not impair long-term fisheries productivity. Our analysis assumes that fishers have no viable alternative to fishing, such that total fishing effort remains constant (at best). We find that realistic reserve networks, which protect 10%-30% of fished habitats in 1-20 km wide reserves, should benefit the long-term productivity of almost any complex fishery. We discover a "rule of thumb" to safeguard against the long-term catch depletion of particular species: individual reserves should export 30% or more of locally produced larvae to adjacent fishing grounds. Specifically on coral reefs, where fishers tend to overexploit species whose dispersal distances as larvae exceed the home ranges of adults, decisions on the size of reserves needed to meet the 30% larval export rule are unlikely to compromise the protection of resident adults. Even achieving the modest Aichi Target 11 of 10% "effective protection" can then help rebuild depleted catch. However, strictly protecting 20%-30% of fished habitats is unlikely to diminish catch even if overfishing is not yet a problem while providing greater potential for biodiversity conservation and fishery rebuilding if overfishing is substantial. These findings are important because they suggest that doubling or tripling the only globally enforced marine reserve target will benefit biodiversity conservation and higher fisheries productivity where both are most urgently needed.

The present study reports a previously undocumented mass spawning aggregation and group spawning phenomena of c. 1200 individual bumphead parrotfish Bolbometopon muricatum in Palau, Micronesia. Although B. muricatum are protected in Palau, it is further recommended that management strategies should consider establishment of no-take zones at B. muricatum spawning aggregations and concomitant sleeping grounds elsewhere.

Coral reefs provide critical services to coastal communities, and these services rely on ecosystem functions threatened by stressors. By summarizing the threats to the functioning of reefs from fishing, climate change, and decreasing water quality, we highlight that these stressors have multiple, conflicting effects on functionally similar groups of species and their interactions, and that the overall effects are often uncertain because of a lack of data or variability among taxa. The direct effects of stressors on links among functional groups, such as predator-prey interactions, are particularly uncertain. Using qualitative modeling, we demonstrate that this uncertainty of stressor impacts on functional groups (whether they are positive, negative, or neutral) can have significant effects on models of ecosystem stability, and reducing uncertainty is vital for understanding changes to reef functioning. This review also provides guidance for future models of reef functioning, which should include interactions among functional groups and the cumulative effect of stressors.

Seagrass above, below and total biomass, density and leaf area, length and width were quantified at a species level for 122 sites over three sampling periods in Moreton Bay, Australia. Core samples were collected in two regions: (1) a high water quality region with varying species assemblages and canopy complexity (98 sites); and (2) along a turbidity gradient in the bay (24 sites within four locations). Core samples were collected using a 15 cm diameter×20 cm long corer. Seagrass dry biomass per component was quantified per species present in each sample. A total of 220 biomass and density data records are included, 130 from the high water quality region and 90 from the turbidity gradient. These data provide a detailed assessment of biomass, density and leaf metrics per species sampled from Moreton Bay over 2012-2013. In future, these can be used as a baseline to assess seasonal and spatial variation within the bay, within the region and among regions.

Community succession following disturbance depends on positive and negative interactions, the strength of which change along environmental gradients. To investigate how early succession affects coral reef recovery, we conducted an 18-month experiment in Palau, using recruitment tiles and herbivore exclusion cages. One set of reefs has higher wave exposure and had previously undergone a phase shift to macroalgae following a major typhoon, whereas the other set of reefs have lower wave exposure and did not undergo a macroalgal phase shift. Similar successional trajectories were observed at all sites when herbivores were excluded: turf algae dominated early succession, followed by shifts to foliose macroalgae and heterotrophic invertebrates. However, trajectories differed in the presence of herbivores. At low wave exposure reefs, herbivores promoted coralline algae and limited turf and encrusting fleshy algae in crevice microhabitats, facilitating optimal coral recruitment. Under medium wave exposure, relatively higher but still low coverage of turf and encrusting fleshy algae (15-25%) found in crevice microhabitats inhibited coral recruitment, persisting throughout multiple recruitment events. Our results indicate that altered interaction strength in different wave environments following disturbance can drive subtle changes in early succession that cascade to alter secondary succession to coral recruitment and system recovery.

With rapid changes taking place on coral reefs, managers and scientists are faced with prioritising interventions that might avoid undesirable losses in ecosystem health. The property of resilience captures how reefs react and respond to stressors and environmental changes. Therefore, in principle, management goals are more likely to be realised if resilience theory is used to inform decision making and help set realistic expectations for reef outcomes. Indeed, a new approach to reef management has been termed 'resilience-based management' (RBM). Yet, resilience concepts have often been criticised for being vague, difficult to operationalise, and beset by multiple definitions. Here, we evaluate how the advent of RBM has changed one aspect of reef management: assessment and monitoring. We compare the metrics used in conventional monitoring programs with those developed through resilience assessments and find that the latter have a stronger focus on ecological processes and exposure to environmental drivers. In contrast, monitoring tends to focus on metrics of reef state and has greater taxonomic resolution, which provides comprehensive information on the nature of changes but does not predict the future responses of reefs in part because it is difficult to extrapolate statistical trends of complex ecological systems. In addition, metrics measured by resilience studies are more diverse, owing in part to the reliance of state metrics as proxies of processes given the difficulty in quantifying key ecological processes directly. We conclude by describing practical ways of improving resilience assessments, and avenues for future research.

While environmental filters are well-known factors influencing community assembly, the extent to which these modify species functions, and entire ecosystem processes, is poorly understood. Focusing on a high-diversity system, we ask whether environmental filtering has ecosystem-wide effects beyond community assembly. We characterise a coral reef herbivorous fish community for swimming performance based on ten functional traits derived from fish morphology. We then investigate whether wave exposure modifies the functional make-up of herbivory, and the absolute and relative feeding frequency of distinct feeding functional groups. Herbivorous fish species conformed to either laterally compressed or fusiform body plans, which differ in their morphological design to minimise drag. High wave exposure selectively limited the feeding function of the deepest body shapes with highest caudal thrust efficiency, and favoured fusiform bodies irrespective of pectoral fin shape. Traditionally recognised herbivore feeding functional groups (i.e. grazers–detritivores and scrapers–small excavators) differed in swimming performance, and in their capacity to feed consistently across levels of wave exposure. We therefore emphasise the distinctness of their ecological niche and functional complementarity. Species within the same feeding functional group also had contrasting responses to wave exposure. We thereby reveal a further ecological dimension of niche partitioning, and reiterate the risk of assuming functional redundancy among species with a common feeding mode. Contrasting responses of species within feeding functional roles (i.e. response diversity) allowed the preservation of critical trophic functions throughout the gradient (e.g. macroalgal browsing), and likely explained why overall levels of herbivory were robust to filtering. Whether ecosystem functioning will remain robust under the additive effects of environmental stress and human-induced disturbances remains to be tested. A lay summary is available for this article.

Coastal ecosystems can be degraded by poor water quality. Tracing the causes of poor water quality back to land-use change is necessary to target catchment management for coastal zone management. However, existing models for tracing the sources of pollution require extensive data-sets which are not available for many of the world's coral reef regions that may have severe water quality issues. Here we develop a hierarchical Bayesian model that uses freely available satellite data to infer the connection between land-uses in catchments and water clarity in coastal oceans. We apply the model to estimate the influence of land-use change on water clarity in Fiji. We tested the model's predictions against underwater surveys, finding that predictions of poor water quality are consistent with observations of high siltation and low coverage of sediment-sensitive coral genera. The model thus provides a means to link land-use change to declines in coastal water quality.

People have an enduring fascination with the biology of the oceans. When the BBC's 'Blue Planet' series first aired on British television almost a quarter of the nation tuned in. As the diversity of science in this special issue of Current Biology attests, the ocean presents a challenging environment for study while also exhibiting some of the most profound and disruptive symptoms of global change. Marine science has made major advances in the past few decades, which were primarily made possible through important technological innovations. This progress notwithstanding, there are persistent challenges in achieving an understanding of marine processes at appropriate scales and delivering meaningful insights to guide ocean policy and management. Naturally, the examples chosen below betray my ecological leanings, but I hope that many of the issues raised resonate with readers in many different disciplines.

Studies on the growth response of corals to changing climate have largely focused on long-lived corals with relatively distinct density bands such as massive Porites corals. Little is known about the climatic response of other more abundant growth forms, such as branching Acropora corals, largely because of the absence of a clear annual density banding pattern. Using a combination of X-radiography, gamma densitometry, Sr/Ca analysis, and Uranium–Thorium (U-Th) dating, we quantified patterns of annual growth in the robust branching coral Isopora palifera from the central Great Barrier Reef (GBR), Australia (18°16′S 147°22′E) collected in May 2013. While visual analysis of the positive X-radiographs revealed alternating patterns of high- and low-density bands along the central growth axis, gamma-densitometry analysis suggests that these bands do not exhibit a clear annual cycle. In contrast, skeletal Sr/Ca ratios consistently revealed clear patterns of seasonality matching local sea surface temperatures (SST), and provided a growth chronology to calculate linear extension rate, skeletal density and calcification rate. Comparisons between SST-Sr/Ca calibrations derived from our I. palifera samples with (i) massive Porites from the same location and (ii) Isopora spp. from the GBR and Papua New Guinea revealed significant differences of up to 3.5 °C, implying palaeoclimate reconstructions should use site-specific and species-specific Sr/Ca-SST calibrations. Our approach provides a robust method for assessing changes in growth for a common Indo-Pacific branching coral, and provides a valuable framework for quantifying past and future changes in skeletal growth in response to climate change.

A 2007 earthquake in the western Solomon Islands resulted in a localised subsidence event in which sea level (relative to the previous coastal settings) rose approximately 30-70 cm, providing insight into impacts of future rapid changes to sea level on coastal ecosystems. Here, we show that increasing sea level by 30-70 cm can have contrasting impacts on mangrove, seagrass and coral reef ecosystems. Coral reef habitats were the clear winners with a steady lateral growth from 2006-2014, yielding a 157% increase in areal coverage over seven years. Mangrove ecosystems, on the other hand, suffered the largest impact through a rapid dieback of 35% (130 ha) of mangrove forest in the study area after subsidence. These forests, however, had partially recovered seven years after the earthquake albeit with a different community structure. The shallow seagrass ecosystems demonstrated the most dynamic response to relative shifts in sea level with both losses and gains in areal extent at small scales of 10-100 m. The results of this study emphasize the importance of considering the impacts of sea-level rise within a complex landscape in which winners and losers may vary over time and space.

Ecological systems often operate on time scales significantly longer or shorter than the time scales typical of human decision making, which causes substantial difficulty for conservation and management in socioecological systems. For example, invasive species may move faster than humans can diagnose problems and initiate solutions, and climate systems may exhibit long-term inertia and short-term fluctuations that obscure learning about the efficacy of management efforts in many ecological systems. We adopted a management-decision framework that distinguishes decision makers within public institutions from individual actors within the social system, calls attention to the ways socioecological systems respond to decision makers' actions, and notes institutional learning that accrues from observing these responses. We used this framework, along with insights from bedeviling conservation problems, to create a typology that identifies problematic time-scale mismatches occurring between individual decision makers in public institutions and between individual actors in the social or ecological system. We also considered solutions that involve modifying human perception and behavior at the individual level as a means of resolving these problematic mismatches. The potential solutions are derived from the behavioral economics and psychology literature on temporal challenges in decision making, such as the human tendency to discount future outcomes at irrationally high rates. These solutions range from framing environmental decisions to enhance the salience of long-term consequences, to using structured decision processes that make time scales of actions and consequences more explicit, to structural solutions aimed at altering the consequences of short-sighted behavior to make it less appealing. Additional application of these tools and long-term evaluation measures that assess not just behavioral changes but also associated changes in ecological systems are needed.

Ecological systems often operate on time scales significantly longer or shorter than the time scales typical of human decision making, which causes substantial difficulty for conservation and management in socioecological systems. For example, invasive species may move faster than humans can diagnose problems and initiate solutions, and climate systems may exhibit long-term inertia and short-term fluctuations that obscure learning about the efficacy of management efforts in many ecological systems. We adopted a management-decision framework that distinguishes decision makers within public institutions from individual actors within the social system, calls attention to the ways socioecological systems respond to decision makers' actions, and notes institutional learning that accrues from observing these responses. We used this framework, along with insights from bedeviling conservation problems, to create a typology that identifies problematic time-scale mismatches occurring between individual decision makers in public institutions and between individual actors in the social or ecological system. We also considered solutions that involve modifying human perception and behavior at the individual level as a means of resolving these problematic mismatches. The potential solutions are derived from the behavioral economics and psychology literature on temporal challenges in decision making, such as the human tendency to discount future outcomes at irrationally high rates. These solutions range from framing environmental decisions to enhance the salience of long-term consequences, to using structured decision processes that make time scales of actions and consequences more explicit, to structural solutions aimed at altering the consequences of short-sighted behavior to make it less appealing. Additional application of these tools and long-term evaluation measures that assess not just behavioral changes but also associated changes in ecological systems are needed.

Disturbance releases space and allows the growth of opportunistic species, excluded by the old stands, with a potential to alter community dynamics. In coral reefs, abundances of fast-growing, and disturbance-tolerant sponges are expected to increase and dominate as space becomes available following acute coral mortality events. Yet, an increase in abundance of these opportunistic species has been reported in only a few studies, suggesting certain mechanisms may be acting to regulate sponge populations. To gain insights into mechanisms of population control, we simulated the dynamics of the common reef-excavating sponge Cliona tenuis in the Caribbean using an individual-based model. An orthogonal hypothesis testing approach was used, where four candidate mechanisms-algal competition, stock-recruitment limitation, whole and partial mortality-were incorporated sequentially into the model and the results were tested against independent field observations taken over a decade in Belize, Central America. We found that releasing space after coral mortality can promote C. tenuis outbreaks, but such outbreaks can be curtailed by macroalgal competition. The asymmetrical competitive superiority of macroalgae, given by their capacity to pre-empt space and outcompete with the sponge in a size-dependant fashion, supports their capacity to steal the opportunity from other opportunists. While multiple system stages can be expected in coral reefs following intense perturbation macroalgae may prevent the growth of other space-occupiers, such as bioeroding sponges, under low grazing pressure.

Drivers of recruitment in sessile marine organisms are often poorly understood, due to the rapidly changing requirements experienced during early ontogeny. The complex suite of physical, biological, and ecological interactions beginning at larval settlement involves a series of trade-offs that influence recruitment success. For example, while cryptic settlement within complex microhabitats is a commonly observed phenomenon in sessile marine organisms, it is unclear whether trade-offs between competition in cryptic refuges and predation on exposed surfaces leads to higher recruitment. To explore the trade-offs during the early ontogeny of scleractinian corals, we combined field observations with laboratory and field experiments to develop a mechanistic understanding of coral recruitment success. Multiple experiments conducted over 15 months in Palau (Micronesia) allowed a mechanistic approach to study the individual factors involved in recruitment: settlement behavior, growth, competition, and predation, as functions of microhabitat and ontogeny. We finally developed and tested a predictive recruitment model with the broader aim of testing whether our empirical insights explained patterns of coral recruitment and quantifying the relative importance of each trade-off. Coral settlement was higher in crevices than exposed microhabitats, but post-settlement bottlenecks differed markedly in the presence (uncaged) and absence (caged) of predators. Incidental predation by herbivores on exposed surfaces at early post-settlement (

Coral bleaching events threaten the sustainability of the Great Barrier Reef (GBR). Here we show that bleaching events of the past three decades have been mitigated by induced thermal tolerance of reef-building corals, and this protective mechanism is likely to be lost under near-future climate change scenarios. We show that 75% of past thermal stress events have been characterized by a temperature trajectory that subjects corals to a protective, sub-bleaching stress, before reaching temperatures that cause bleaching. Such conditions confer thermal tolerance, decreasing coral cell mortality and symbiont loss during bleaching by over 50%. We find that near-future increases in local temperature of as little as 0.5°C result in this protective mechanism being lost, which may increase the rate of degradation of the GBR.

Controlling the spread of invasive species, pests, and pathogens is often logistically limited to interventions that target specific locations at specific periods. However, in complex, highly connected systems, such as marine environments connected by ocean currents, populations spread dynamically in both space and time via transient connectivity links. This results in nondeterministic future distributions of species in which local populations emerge dynamically and concurrently over a large area. The challenge, therefore, is to choose intervention locations that will maximize the effectiveness of the control efforts. We propose a novel method to manage dynamic species invasions and outbreaks that identifies the intervention locations most likely to curtail population expansion by selectively targeting local populations most likely to expand their future range. Critically, at any point during the development of the invasion or outbreak, the method identifies the local intervention that maximizes the long-term benefit across the ecosystem by restricting species' potential to spread. In so doing, the method adaptively selects the intervention targets under dynamically changing circumstances. To illustrate the effectiveness of the method we applied it to controlling the spread of crown-of-thorns starfish (Acanthaster sp.) outbreaks across Australia's Great Barrier Reef. Application of our method resulted in an 18-fold relative improvement in management outcomes compared with a random targeting of reefs in putative starfish control scenarios. Although we focused on applying the method to reducing the spread of an unwanted species, it can also be used to facilitate the spread of desirable species through connectivity networks. For example, the method could be used to select those fragments of habitat most likely to rebuild a population if they were sufficiently well protected.

Migrating species are common within seascapes, but the potential for these movements to alter the populations and functional roles of non-migrating species (e.g. by increasing predation) is rarely investigated. This study considers whether the presence of nursery habitats (mangroves and seagrass) simply enhances the abundance of nursery-using parrotfishes and piscivores on nearby coral reefs, or also affects other parrotfishes. Data from 131 reef sites and multiple seascape configurations across 13 degrees of latitude were used to model correlations between biophysical variables, including nursery habitat connectivity, and the abundance and grazing pressure of both nursery-using species and other parrotfishes and piscivore biomass. Connectivity to mangroves and dense seagrass was positively correlated with the biomass of nursery-using species, but was also negatively correlated with non-nursery parrotfish populations. This reduction may be caused indirectly by nursery habitats increasing confamilial competition and predation by nursery-using piscivores, particularly affecting small parrotfishes settling directly onto reefs. As key reef grazers, parrotfishes affect coral demographics. Consequently, a spatial simulation model predicted the impacts after five years of changes in grazing pressure because of nursery habitat connectivity. The model demonstrated that high nursery connectivity was correlated to changes in grazing pressure on nearby reefs that could potentially lead to differences in coral cover of ∼3–4% when compared to low connectivity reefs. However, the direction of this change depended on the seascapes’ characteristics. Historically, large-bodied, nursery-using parrotfish would have increased grazing in all nursery-rich seascapes. Overfishing means that nursery availability may have spatially variable impacts on coral cover, influencing reserve design. This study suggests that nursery availability may directly and indirectly modify an ecological process, and alter an ecological cascade (migrating species increase predator and competitor abundances, affecting other grazers and consequently corals). Therefore, elucidating the multi-species impacts of animal movements is required to better understand ecosystem functioning.

A single ecosystem can exhibit great biogeographic and environmental variability. While a given ecological driver might have a strong impact in one region, it does not necessarily hold that its importance will extend elsewhere. Coral reefs provide a striking example in that coral communities have low resilience in the Atlantic and remarkable resilience in parts of the species-rich Pacific. Recent experimental evidence from the Atlantic finds that fishing of large herbivorous fish can be a strong driver of coral resilience. Here, we repeat the Atlantic experiment in the highly resilient forereef of Moorea (French Polynesia), which has repeatedly recovered from disturbances. A combination of cages, fish deterrents (FDs), and controls allowed us to simulate the consequences of fishing large herbivores on algal assemblages, coral recruitment, and the demographic rates of coral juveniles. We find that the impacts of removing large herbivorous reef fish vary with early coral ontogeny. Reduced herbivore access led to a modest macroalgal bloom and reduction in coral recruitment. However, larger juvenile corals ( 1 cm diameter) survived better and grew faster under these conditions because of a reduction in corallivory. To determine the net impact of losing larger herbivorous fish, we combined experimental results with estimated demographic parameters in an individual-based model. Simulating coral recovery trajectories for five years, we find that protecting larger reef fish led to better recovery in 66-99% of simulations, depending on underlying assumptions (with the more credible assumptions being associated with greater likelihood of net positive impacts). While we find that fishing effects are detrimental to corals in both the Atlantic and Pacific systems studied, the nature of the interactions varied markedly. In the identical previously-published study in the Atlantic, macroalgae exhibited a rapid bloom and caused a sufficiently large reduction in coral recruitment to force a predicted ecosystem shift to an alternative attractor. The commensurate macroalgal bloom in Moorea was weak yet the corals were two orders of magnitude more sensitive to its presence. We do not suggest that a reduction in recruitment in Moorea will lead to alternative attractors but the long-term risks of a reduction in recovery rate are cause for concern as rates of coral mortality are projected to increase. The emerging picture is that Pacific reefs are less likely to experience macroalgal blooms but are surprisingly sensitive to such blooms if they occur.

Naso lituratus (orangespine unicornfish) and Naso unicornis (bluespine unicornfish) are widespread species that are heavily targeted in many nearshore fisheries of Pacific Island countries. In addition to providing a critical food and income source, both species fulfil critical ecological functions in the top-down control of coral reef macroalgae; particularly fleshy brown algae (i.e. Sargassum spp.) which can out-compete and smother corals. Despite heavy long-term harvesting, there are currently very limited species-specific management measures. This review assesses the biology and ecology of both species, and combines this with the current status of the fisheries in the Pacific, and proposes realistic ecosystem-based species-specific fisheries policies. Although unicornfish populations have displayed continuing resilience to heavy fishing pressure, reports of declining stocks combined with a range of life-history traits (i.e. longevity, habitat-specificity, easily targeted aggregations), indicate that both species are vulnerable to overexploitation. Modern day common fishing practices such as scuba and night-time spearfishing are intensifying their exploitation. The most effective management measure would be fishing effort constraints, including banning modern and unsustainable methods. However, owing to enforcement limitations in Pacific Islands, the most practical approach to management would include a combination of management tools, including periodic sales bans around identified spawning times (i.e. Hawaii; May–June), and size/catch limits. Furthermore, home range data suggest that even with limited knowledge, small MPAs ( 10 km linear distance are recommended for N. lituratus. This comprehensive review confirms the pressing need for implementation of the aforementioned management practices to protect these species in regions where they are heavily targeted, and prevent the impairment of their critical ecological function and importance as a food and income source. Copyright © 2016 John Wiley & Sons, Ltd.

Seagrass meadows are important marine carbon sinks, yet they are threatened and declining worldwide. Seagrass management and conservation requires adequate understanding of the physical and biological factors determining carbon content in seagrass sediments. Here, we identified key factors that influence carbon content in seagrass meadows across several environmental gradients in Moreton Bay, SE Queensland. Sampling was conducted in two regions: (1) Canopy Complexity, 98 sites on the Eastern Banks, where seagrass canopy structure and species composition varied while turbidity was consistently low; and (2) Turbidity Gradient, 11 locations across the entire bay, where turbidity varied among sampling locations. Sediment organic carbon content and seagrass structural complexity (shoot density, leaf area, and species specific characteristics) were measured from shallow sediment and seagrass biomass cores at each location, respectively. Environmental data were obtained from empirical measurements (water quality) and models (wave height). The key factors influencing carbon content in seagrass sediments were seagrass structural complexity, turbidity, water depth, and wave height. In the Canopy Complexity region, carbon content was higher for shallower sites and those with higher seagrass structural complexity. When turbidity varied along the Turbidity Gradient, carbon content was higher at sites with high turbidity. In both regions carbon content was consistently higher in sheltered areas with lower wave height. Seagrass canopy structure, water depth, turbidity, and hydrodynamic setting of seagrass meadows should therefore be considered in conservation and management strategies that aim to maximize sediment carbon content.

Parrotfishes are an ecologically and commercially important teleost group whose grazing contributes to maintaining coral-dominated states on hermatypic reefs. However, overfishing has skewed sex ratios of Atlantic parrotfishes because fishing has disproportionate impacts on larger individuals, and males are generally larger than females. Whether protection from fishing may allow sex ratios to return to equilibrium is unknown, as fishing can induce irreversible ecological and/or evolutionary shifts. Bermuda banned trap fishing in 1990, creating a unique opportunity to analyse long-term responses of Atlantic parrotfishes to release from fishing. We found that sex ratios of four common parrotfishes were initially skewed, with male proportions ranging from 0.04 to 0.18. However, male proportions rebounded within 3–4 yr, equilibrating at values ranging from 0.36 to 0.54, similar to those reported at unfished sites in the region. Our results are encouraging for regional efforts to recover lost grazing function by restoring overfished herbivore populations.

Coral reef habitat structural complexity influences key ecological processes, ecosystem biodiversity, and resilience. Measuring structural complexity underwater is not trivial and researchers have been searching for accurate and cost-effective methods that can be applied across spatial extents for over 50 years. This study integrated a set of existing multi-view, image-processing algorithms, to accurately compute metrics of structural complexity (e.g. ratio of surface to planar area) underwater solely from images. This framework resulted in accurate, high-speed 3D habitat reconstructions at scales ranging from small corals to reef-scapes (10s km2). Structural complexity was accurately quantified from both contemporary and historical image datasets across three spatial scales: (i) branching coral colony (Acropora spp.); (ii) reef area (400 m2); and (iii) reef transect (2 km). At small scales, our method delivered models with

The designation of no-take marine reserves involves social and economic concerns due to the resulting displacement of fishing effort, when fishing rights are removed from those who traditionally fished within an area. Displacement can influence the functioning of the fishery and success of the reserve, yet levels of displacement are seldom quantified after reserve implementation and very rarely before that. We devised a simple analytical framework based on set theory to facilitate reserve placement. Implementation of the framework requires maps of fishing grounds, fishing effort, or catch per unit effort for at least 2 years. The framework quantifies the level of conflict that a reserve designation might cause in the fishing sector due to displacement and the opportunities to offset the conflict through fisher spatial mobility (i.e. ability of fishers to fish elsewhere). We also considered how the outputs of the framework can be used to identify targeted management interventions for each fishery. We applied the method in Honduras, where the largest marine protected area in Central America is being placed, for which spatial data on fishing effort were available for 6 fisheries over 3 years. The proposed closure had a greater negative impact on the shrimp and lobster scuba fisheries, which concentrated respectively 28% and 18% of their effort inside the reserve. These fisheries could not accommodate the displacement within existing fishing grounds. Both would be forced to stretch into new fishing grounds, which are available but are of unknown quality. These stakeholders will likely require compensation to offset costly exploratory fishing or to travel to fishing grounds farther away from port.

The designation of no-take marine reserves involves social and economic concerns due to the resulting displacement of fishing effort, when fishing rights are removed from those who traditionally fished within an area. Displacement can influence the functioning of the fishery and success of the reserve, yet levels of displacement are seldom quantified after reserve implementation and very rarely before that. We devised a simple analytical framework based on set theory to facilitate reserve placement. Implementation of the framework requires maps of fishing grounds, fishing effort, or catch per unit effort for at least 2 years. The framework quantifies the level of conflict that a reserve designation might cause in the fishing sector due to displacement and the opportunities to offset the conflict through fisher spatial mobility (i.e. ability of fishers to fish elsewhere). We also considered how the outputs of the framework can be used to identify targeted management interventions for each fishery. We applied the method in Honduras, where the largest marine protected area in Central America is being placed, for which spatial data on fishing effort were available for 6 fisheries over 3 years. The proposed closure had a greater negative impact on the shrimp and lobster scuba fisheries, which concentrated respectively 28% and 18% of their effort inside the reserve. These fisheries could not accommodate the displacement within existing fishing grounds. Both would be forced to stretch into new fishing grounds, which are available but are of unknown quality. These stakeholders will likely require compensation to offset costly exploratory fishing or to travel to fishing grounds farther away from port.

Among the biggest global challenges for policymakers is the development of land use policies robust to climate change impacts. While diverse fields can inform adaptation, integrated social-ecological assessment of the multiple adaptation options are rare and cannot be easily applied. Here, we build on past studies by undertaking an integrated fine scale and strategic allocation of sea level rise (SLR) adaptation options that can direct policy making. We use models of probabilistic SLR inundation, urban growth, and sub- and intertidal ecosystem migration, to investigate the impacts of different SLR adaptation strategies, and how these can be allocated to best achieve both development and conservation goals. Coastal adaptation will involve trade-offs among development and conservation objectives and these will vary based on the extent to which sea levels rise. There will be trade-offs between conservation objectives regardless of the adaptation options chosen, however, retreat does provide opportunities for enabling the expansion of coastal ecosystems inland. Local governments can save billions of dollars and minimize political conflict between conservation and development goals through integrated strategic spatial planning. Our planning approach both informs policy and is transferable to other coastal regions faced with a rising sea.

Coral reefs are in decline worldwide and monitoring activities are important for assessing the impact of disturbance on reefs and tracking subsequent recovery or decline. Monitoring by field surveys provides accurate data but at highly localised scales and so is not cost-effective for reef scale monitoring at frequent time points. Remote sensing from satellites is an alternative and complementary approach. While remote sensing cannot provide the level of detail and accuracy at a single point than a field survey, the statistical power for inferring large scale patterns benefits in having complete areal coverage. This review considers the state of the art of coral reef remote sensing for the diverse range of objectives relevant for management, ranging from the composition of the reef: physical extent, benthic cover, bathymetry, rugosity; to environmental parameters: sea surface temperature, exposure, light, carbonate chemistry. In addition to updating previous reviews, here we also consider the capability to go beyond basic maps of habitats or environmental variables, to discuss concepts highly relevant to stakeholders, policy makers and public communication: such as biodiversity, environmental threat and ecosystem services. A clear conclusion of the review is that advances in both sensor technology and processing algorithms continue to drive forward remote sensing capability for coral reef mapping, particularly with respect to spatial resolution of maps, and synthesis across multiple data products. Both trends can be expected to continue.

The problem of ecosystem overfishing has mostly focused on the function of forage fish as prey for apex predators. Here, I consider another ecosystem function, herbivory, that affects habitat quality. Parrotfish are an important fishery in many parts of the Caribbean and the dominant herbivorous fish on its coral reefs. Herbivory helps to control macroalgae which compete with coral and can impede reef resilience if allowed to bloom. Thus, long-term maintenance of reef habitat quality, which underpins fisheries, requires sufficient parrotfish stock. Ecosystem models predict that reductions in parrotfish grazing could have deleterious impacts on reef habitat yet the determination of ecologically sustainable levels of parrotfish harvest remains elusive. An initial solution to this dilemma is proposed for areas where an outright ban on herbivore exploitation is considered infeasible. Fisheries management has tended to consider coral reefs as a single habitat such that regulations apply evenly throughout exploitable areas. But reef habitats are not equally susceptible to ecosystem overfishing and some do not appear to have a strong requirement for parrotfish grazing. One habitat, Orbicella reef, has a high dependence on herbivory, whereas the state of another dominant habitat – gorgonian plain – appears to be driven by environmental factors (e.g. wave exposure). Ecosystem-based fisheries management could be improved by restricting parrotfish harvest on Orbicella reefs yet allowing exploitation on gorgonian plain. Management could then focus on achieving a sustainable yield on gorgonian plains without the added complexity of estimating catch levels that avoid ecosystem overfishing.

The physiological performance of a reef-building coral is a combined outcome of both the coral host and its algal endosymbionts, Symbiodinium While Orbicella annularis-a dominant reef-building coral in the Wider Caribbean-is known to be a flexible host in terms of the diversity of Symbiodinium types it can associate with, it is uncertain how this diversity varies across the Caribbean, and whether spatial variability in the symbiont community is related to either O. annularis genotype or environment. Here, we target the Symbiodinium-ITS2 gene to characterize and map dominant Symbiodinium hosted by O. annularis at an unprecedented spatial scale. We reveal northwest-southeast partitioning across the Caribbean, both in terms of the dominant symbiont taxa hosted and in assemblage diversity. Multivariate regression analyses incorporating a suite of environmental and genetic factors reveal that observed spatial patterns are predominantly explained by chronic thermal stress (summer temperatures) and are unrelated to host genotype. Furthermore, we were able to associate the presence of specific Symbiodinium types with local environmental drivers (for example, Symbiodinium C7 with areas experiencing cooler summers, B1j with nutrient loading and B17 with turbidity), associations that have not previously been described.

Tropical cyclones have been a major cause of reef coral decline during recent decades, including on the Great Barrier Reef (GBR). While cyclones are a natural element of the disturbance regime of coral reefs, the role of temporal clustering has previously been overlooked. Here, we examine the consequences of different types of cyclone temporal distributions (clustered, stochastic or regular) on reef ecosystems. We subdivided the GBR into 14 adjoining regions, each spanning roughly 300 km, and quantified both the rate and clustering of cyclones using dispersion statistics. To interpret the consequences of such cyclone variability for coral reef health, we used a model of observed coral population dynamics. Results showed that clustering occurs on the margins of the cyclone belt, being strongest in the southern reefs and the far northern GBR, which also has the lowest cyclone rate. In the central GBR, where rates were greatest, cyclones had a relatively regular temporal pattern. Modelled dynamics of the dominant coral genus, Acropora, suggest that the long-term average cover might be more than 13 % greater (in absolute cover units) under a clustered cyclone regime compared to stochastic or regular regimes. Thus, not only does cyclone clustering vary significantly along the GBR but such clustering is predicted to have a marked, and management-relevant, impact on the status of coral populations. Additionally, we use our regional clustering and rate results to sample from a library of over 7000 synthetic cyclone tracks for the GBR. This allowed us to provide robust reef-scale maps of annual cyclone frequency and cyclone impacts on Acropora. We conclude that assessments of coral reef vulnerability need to account for both spatial and temporal cyclone distributions.

Sharks are considered the apex predator of coral reefs, but the consequences of their global depletion are uncertain. Here we explore the ecological roles of sharks on coral reefs and, conversely, the importance of reefs for sharks. We find that most reef-associated shark species do not act as apex predators but instead function as mesopredators along with a diverse group of reef fish. While sharks perform important direct and indirect ecological roles, the evidence to support hypothesised shark-driven trophic cascades that benefit corals is weak and equivocal. Coral reefs provide some functional benefits to sharks, but sharks do not appear to favour healthier reef environments. Restoring populations of sharks is important and can yet deliver ecological surprise. Stable isotopes reveal that sharks span an extended range of trophic levels with true apex species being higher than most common reef sharks.Dietary analysis reveals that most common reef sharks are mesopredators occupying a similar trophic level to large piscivorous fishes.Evidence for shark-induced trophic cascades that benefit herbivorous fishes is weak or equivocal on coral reefs.Sharks can exert non-consumptive or 'fear' effects that disrupt the foraging of potential prey.While coral reefs provide a range of ecological benefits for sharks, the link between healthy reefs and shark abundance is unclear.

Land-use change in the coastal zone has led to worldwide degradation of marine coastal ecosystems and a loss of the goods and services they provide. Restoration is the process of assisting the recovery of an ecosystem that has been degraded, damaged, or destroyed and is critical for habitats where natural recovery is hindered. Uncertainties about restoration cost and feasibility can impede decisions on whether, what, how, where, and how much to restore. Here, we perform a synthesis of 235 studies with 954 observations from restoration or rehabilitation projects of coral reefs, seagrass, mangroves, saltmarshes, and oyster reefs worldwide, and evaluate cost, survival of restored organisms, project duration, area, and techniques applied. Findings showed that while the median and average reported costs for restoration of one hectare of marine coastal habitat were around US$80 000 (2010) and US$1 600 000 (2010), respectively, the real total costs (median) are likely to be two to four times higher. Coral reefs and seagrass were among the most expensive ecosystems to restore. Mangrove restoration projects were typically the largest and the least expensive per hectare. Most marine coastal restoration projects were conducted in Australia, Europe, and USA, while total restoration costs were significantly (up to 30 times) cheaper in countries with developing economies. Community-or volunteer-based marine restoration projects usually have lower costs. Median survival of restored marine and coastal organisms, often assessed only within the first one to two years after restoration, was highest for saltmarshes (64.8%) and coral reefs (64.5%) and lowest for seagrass (38.0%). However, success rates reported in the scientific literature could be biased towards publishing successes rather than failures. The majority of restoration projects were short-lived and seldom reported monitoring costs. Restoration success depended primarily on the ecosystem, site selection, and techniques applied rather than on money spent. We need enhanced investment in both improving restoration practices and large-scale restoration.

The calcareous green alga Halimeda is a key contributor to carbonate sediment production on coral reefs. As herbivores have a direct negative effect on the abundance of Halimeda, protection from herbivory is critical for Halimeda growth. Branching corals such as Acropora are likely to provide refugia for Halimeda from grazers, yet studies are scarce. Here, we investigated the vulnerability of two Halimeda species to herbivory using fish exclusion cages and assessed the contribution of coral structural complexity to seasonal changes in Halimeda biomass and morphometrics. While up to 50 % Halimeda abundance was depleted outside cages due to herbivory and the exclusion of large herbivores resulted in an increase in net growth up to threefold, Halimeda recruitment was positively affected by herbivory, more than two times greater outside cages. However, these responses differed between species and seasons; only one species was affected in winter but not summer. Coral structural complexity facilitated an increase of total algal biomass particularly in summer. At the individual level, thalli growing inside the Acropora canopy were always significantly larger (thallus biomass, volume and height) than those growing in exposed areas. We estimated that the carbonate production of Halimeda was nearly three times greater inside refuges provided by Acropora. Because Halimeda species differ in growth rates and susceptibility to grazing, we predict that the ongoing degradation of the habitat complexity provided by branching corals will alter Halimeda community structure and its contribution to local sediment budgets.

Many countries are legally obliged to embrace ecosystem-based approaches to fisheries management. Reductions in bycatch and physical habitat damage are now commonplace, but mitigating more sophisticated impacts associated with the ecological functions of target fisheries species are in their infancy. Here we model the impacts of a parrotfish fishery on the future state and resilience of Caribbean coral reefs, enabling us to view the tradeoff between harvest and ecosystem health. We find that the implementation of a simple and enforceable size restriction of >30 cm provides a win:win outcome in the short term, delivering both ecological and fisheries benefits and leading to increased yield and greater coral recovery rate for a given harvest rate. However, maintaining resilient coral reefs even until 2030 requires the addition of harvest limitations (

The connectivity of marine organisms among habitat patches has been dominated by two independent paradigms with distinct conservation strategies. One paradigm is the dispersal of larvae on ocean currents, which suggests networks of marine reserves. The other is the demersal migration of animals from nursery to adult habitats, requiring the conservation of connected ecosystem corridors. Here, we suggest that a common driver, wave exposure, links larval and demersal connectivity across the seascape. To study the effect of linked connectivities on fish abundance at reefs, we parameterize a demographic model for the Bahamas seascape using maps of habitats, empirically forced models of wave exposure and spatially realistic three-dimensional hydrological models of larval dispersal. The integrated empirical-modeling approach enabled us to study linked connectivity on a scale not currently possible by purely empirical studies. We find sheltered environments not only provide greater nursery habitat for juvenile fish but larvae spawned on adjacent reefs have higher retention, thereby creating a synergistic increase in fish abundance. Uniting connectivity paradigms to consider all life stages simultaneously can help explain the evolution of nursery habitat use and simplifies conservation advice: Reserves in sheltered environments have desirable characteristics for biodiversity conservation and can support local fisheries through adult spillover.

Understanding marine regime shifts is important not only for ecology but also for developing marine management that assures the provision of ecosystem services to humanity. While regime shift theory is well developed, there is still no common understanding on drivers, mechanisms and characteristic of abrupt changes in real marine ecosystems. Based on contributions to the present theme issue, we highlight some general issues that need to be overcome for developing a more comprehensive understanding of marine ecosystem regime shifts. We find a great divide between benthic reef and pelagic ocean systems in how regime shift theory is linked to observed abrupt changes. Furthermore, we suggest that the long-lasting discussion on the prevalence of top-down trophic or bottom-up physical drivers in inducing regime shifts may be overcome by taking into consideration the synergistic interactions of multiple stressors, and the special characteristics of different ecosystem types. We present a framework for the holistic investigation of marine regime shifts that considers multiple exogenous drivers that interact with endogenous mechanisms to cause abrupt, catastrophic change. This framework takes into account the time-delayed synergies of these stressors, which erode the resilience of the ecosystem and eventually enable the crossing of ecological thresholds. Finally, considering that increased pressures in the marine environment are predicted by the current climate change assessments, in order to avoid major losses of ecosystem services, we suggest that marine management approaches should incorporate knowledge on environmental thresholds and develop tools that consider regime shift dynamics and characteristics. This grand challenge can only be achieved through a holistic view of marine ecosystem dynamics as evidenced by this theme issue.

Under projections of global climate change and other stressors, significant changes in the ecology, structure and function of coral reefs are predicted. Current management strategies tend to look to the past to set goals, focusing on halting declines and restoring baseline conditions. Here, we explore a complementary approach to decision making that is based on the anticipation of future changes in ecosystem state, function and services. Reviewing the existing literature and utilizing a scenario planning approach, we explore how the structure of coral reef communities might change in the future in response to global climate change and overfishing. We incorporate uncertainties in our predictions by considering heterogeneity in reef types in relation to structural complexity and primary productivity. We examine 14 ecosystem services provided by reefs, and rate their sensitivity to a range of future scenarios and management options. Our predictions suggest that the efficacy of management is highly dependent on biophysical characteristics and reef state. Reserves are currently widely used and are predicted to remain effective for reefs with high structural complexity. However, when complexity is lost, maximizing service provision requires a broader portfolio of management approaches, including the provision of artificial complexity, coral restoration, fish aggregation devices and herbivore management. Increased use of such management tools will require capacity building and technique refinement and we therefore conclude that diversification of our management toolbox should be considered urgently to prepare for the challenges of managing reefs into the 21st century.

Small-scale experiments and theory suggest that ecological functions provided by communities become more stable with increased species richness. Whether these patterns manifest at regional spatial scales and within species-rich communities (e.g. coral reefs) is largely unknown. We quantified five biogeochemical processes, and an aggregate measure of multifunctionality, in species-rich coastal fish communities to test three questions: (1) Do previously predicted biodiversity-ecosystem-function relationships hold across large spatial scales and in highly diverse communities? (2) can additional covariates of community structure improve these relationships? (3) What is the role of community biomass and functional group diversity in maintaining biogeochemical processes under various scenarios of species loss across ecosystem types? These questions were tested across a large regional gradient of coral reef, mangrove and seagrass ecosystems. Statistical models demonstrated that species richness and the mean maximum body size per species strongly predicted biogeochemical processes in all ecosystem types, but functional group diversity was only a weak predictor. Simulating three scenarios of species loss demonstrated that conserving community biomass alone increased the ability for communities to maintain ecosystem processes. Multifunctionality of biogeochemical processes was maintained least in simulations that conserved biomass and community structure, underscoring the relative lack of importance of community structure in maintaining multiple simultaneous ecosystem functions in this system. Findings suggest that conserving community biomass alone may be sufficient to sustain certain biogeochemical processes, but when considering conservation of multiple simultaneous biogeochemical processes, management efforts should focus first on species richness.

Anthropogenic stress has been shown to reduce coral coverage in ecosystems all over the world. A phase shift towards an algae-dominated system may accompany coral loss. In this case, the composition of the reef-associated fish assemblage will change and human communities relying on reef fisheries for income and food security may be negatively impacted. We present a case study based on the Raja Ampat Archipelago in Eastern Indonesia. Using a dynamic food web model, we simulate the loss of coral reefs with accompanied transition towards an algae-dominated state and quantify the likely change in fish populations and fisheries productivity. One set of simulations represents extreme scenarios, including 100% loss of coral. In this experiment, ecosystem changes are driven by coral loss itself and a degree of habitat dependency by reef fish is assumed. An alternative simulation is presented without assumed habitat dependency, where changes to the ecosystem are driven by historical observations of reef fish communities when coral is lost. The coral-algal phase shift results in reduced biodiversity and ecosystem maturity. Relative increases in the biomass of small-bodied fish species mean higher productivity on reefs overall, but much reduced landings of traditionally targeted species.

Anthropogenic stress has been shown to reduce coral coverage in ecosystems all over the world. A phase shift towards an algae-dominated system may accompany coral loss. In this case, the composition of the reef-associated fish assemblage will change and human communities relying on reef fisheries for income and food security may be negatively impacted. We present a case study based on the Raja Ampat Archipelago in Eastern Indonesia. Using a dynamic food web model, we simulate the loss of coral reefs with accompanied transition towards an algae-dominated state and quantify the likely change in fish populations and fisheries productivity. One set of simulations represents extreme scenarios, including 100% loss of coral. In this experiment, ecosystem changes are driven by coral loss itself and a degree of habitat dependency by reef fish is assumed. An alternative simulation is presented without assumed habitat dependency, where changes to the ecosystem are driven by historical observations of reef fish communities when coral is lost. The coral-algal phase shift results in reduced biodiversity and ecosystem maturity. Relative increases in the biomass of small-bodied fish species mean higher productivity on reefs overall, but much reduced landings of traditionally targeted species.

As the frequency and intensity of coral mortality events increase under climate change, understanding how declines in coral cover may affect the bioerosion of reef frameworks is of increasing importance. Here, we explore decadal-scale rates of bioerosion of the framework building coral Orbicella annularis by grazing parrotfish following the 1997/1998 El Niño-related mass mortality event at Long Cay, Belize. Using high-precision U-Th dating and CT scan analysis, we quantified in situ rates of external bioerosion over a 13-year period (1998-2011). Based upon the error-weighted average U-Th age of dead O. annularis skeletons, we estimate the average external bioerosion between 1998 and 2011 as 0.92 ± 0.55 cm depth. Empirical observations of herbivore foraging, and a nonlinear numerical response of parrotfish to an increase in food availability, were used to create a model of external bioerosion at Long Cay. Model estimates of external bioerosion were in close agreement with U-Th estimates (0.85 ± 0.09 cm). The model was then used to quantify how rates of external bioerosion changed across a gradient of coral mortality (i.e. from few corals experiencing mortality following coral bleaching to complete mortality). Our results indicate that external bioerosion is remarkably robust to declines in coral cover, with no significant relationship predicted between the rate of external bioerosion and the proportion of O. annularis that died in the 1998 bleaching event. The outcome was robust because the reduction in grazing intensity that follows coral mortality was compensated for by a positive numerical response of parrotfish to an increase in food availability. Our model estimates further indicate that for an O. annularis-dominated reef to maintain a positive state of reef accretion, a necessity for sustained ecosystem function, live cover of O. annularis must not drop below a ~5-10% threshold of cover.

As the frequency and intensity of coral mortality events increase under climate change, understanding how declines in coral cover may affect the bioerosion of reef frameworks is of increasing importance. Here, we explore decadal-scale rates of bioerosion of the framework building coral Orbicella annularis by grazing parrotfish following the 1997/1998 El Niño-related mass mortality event at Long Cay, Belize. Using high-precision U-Th dating and CT scan analysis, we quantified in situ rates of external bioerosion over a 13-year period (1998-2011). Based upon the error-weighted average U-Th age of dead O. annularis skeletons, we estimate the average external bioerosion between 1998 and 2011 as 0.92 ± 0.55 cm depth. Empirical observations of herbivore foraging, and a nonlinear numerical response of parrotfish to an increase in food availability, were used to create a model of external bioerosion at Long Cay. Model estimates of external bioerosion were in close agreement with U-Th estimates (0.85 ± 0.09 cm). The model was then used to quantify how rates of external bioerosion changed across a gradient of coral mortality (i.e. from few corals experiencing mortality following coral bleaching to complete mortality). Our results indicate that external bioerosion is remarkably robust to declines in coral cover, with no significant relationship predicted between the rate of external bioerosion and the proportion of O. annularis that died in the 1998 bleaching event. The outcome was robust because the reduction in grazing intensity that follows coral mortality was compensated for by a positive numerical response of parrotfish to an increase in food availability. Our model estimates further indicate that for an O. annularis-dominated reef to maintain a positive state of reef accretion, a necessity for sustained ecosystem function, live cover of O. annularis must not drop below a ~5-10% threshold of cover.

Establishing the effectiveness of habitat features to act as surrogate measures of diversity and abundance of juvenile reef fish provides information that is critical to coral reef management. When accurately set on a broader spatial context, microhabitat information becomes more meaningful and its management application becomes more explicit. The goal of the study is to identify coral reef areas potentially important to juvenile fishes in Ngederrak Reef, Republic of Palau, across different spatial scales. To achieve this, the study requires the accomplishment of the following tasks: (1) structurally differentiate the general microhabitat types using acoustics; (2) quantify microhabitat association with juvenile reef fish community structure; and (3) conduct spatial analysis of the reef-wide data and locate areas optimal for juvenile reef fish settlement. The results strongly suggest the importance of branching structures in determining species count and abundance of juvenile reef fish at the outer reef slope of Ngederrak Reef. In the acoustic map, the accurate delineation of these features allowed us to identify reef areas with the highest potential to harbor a rich aggregation of juvenile reef fish. Using a developed spatial analysis tool that ranks pixel groups based on user-defined parameters, the reef area near the Western channel of Ngederrak is predicted to have the most robust aggregation of juvenile reef fish. The results have important implications not only in management, but also in modeling the impacts of habitat loss on reef fish community. At least for Ngederrak Reef, the results advanced the utility of acoustic systems in predicting spatial distribution of juvenile fish.

Establishing the effectiveness of habitat features to act as surrogate measures of diversity and abundance of juvenile reef fish provides information that is critical to coral reef management. When accurately set on a broader spatial context, microhabitat information becomes more meaningful and its management application becomes more explicit. The goal of the study is to identify coral reef areas potentially important to juvenile fishes in Ngederrak Reef, Republic of Palau, across different spatial scales. To achieve this, the study requires the accomplishment of the following tasks: (1) structurally differentiate the general microhabitat types using acoustics; (2) quantify microhabitat association with juvenile reef fish community structure; and (3) conduct spatial analysis of the reef-wide data and locate areas optimal for juvenile reef fish settlement. The results strongly suggest the importance of branching structures in determining species count and abundance of juvenile reef fish at the outer reef slope of Ngederrak Reef. In the acoustic map, the accurate delineation of these features allowed us to identify reef areas with the highest potential to harbor a rich aggregation of juvenile reef fish. Using a developed spatial analysis tool that ranks pixel groups based on user-defined parameters, the reef area near the Western channel of Ngederrak is predicted to have the most robust aggregation of juvenile reef fish. The results have important implications not only in management, but also in modeling the impacts of habitat loss on reef fish community. At least for Ngederrak Reef, the results advanced the utility of acoustic systems in predicting spatial distribution of juvenile fish.

Size and age are fundamental organismal traits, and typically, both are good predictors of mortality. For many species, however, size and age predict mortality in ontogenetically opposing directions. Specifically, mortality due to predation is often more intense on smaller individuals whereas mortality due to senescence impacts, by definition, on older individuals. When size-based and age-based mortality are independent in this manner, modelling mortality in both traits is often necessary. Classical approaches, such as Leslie or Lefkovitch matrices, usually require the model to infer the state of one trait from the state of the other, for example by assuming that explicitly modelled age (or stage) class structure provides implicit information on underlying size-class structure, as is the case in many species. However, the assumption that one trait informs on the other is challenged when size and age are decoupled, as often occurs in invertebrates, amphibians, fish, reptiles and plants. In these cases, age-structured models may perform poorly at capturing size-based mortality, and vice versa. We offer a solution to this dilemma, relaxing the assumption that class structure in one trait is inferable from class structure in another trait. Using empirical data from a reef fish, Sparisoma viride (Scaridae), we demonstrate how an individual-based model (IBM) can be implemented to model mortality as explicit, independent and simultaneous functions of individual size and age - an approach that mimics the effects of mortality in many wild populations. By validating this 'multitrait IBM' against three independent lines of empirical data, we determine that the approach produces more convincing predictions of size-class structure, longevity and post-settlement mortality for S. viride than do the trait-independent or single-trait mortality models tested. Multitrait IBMs also allow trait-based mortality to be modelled either additively or multiplicatively, and individual variability in growth rates can be accommodated. Consequently, we propose that the approach may be useful in fields that may benefit from disentangling, or investigating interactions among, size-based and age-based demographic processes, including comparative demography (e.g. life-history consequences of resource patchiness) and conservation biology (e.g. impacts of invasive predators on size structure but not life span of natives).

1. Size and age are fundamental organismal traits, and typically, both are good predictors of mortality. For many species, however, size and age predict mortality in ontogenetically opposing directions. Specifically, mortality due to predation is often more intense on smaller individuals whereas mortality due to senescence impacts, by definition, on older individuals. 2. When size-based and age-based mortality are independent in this manner, modelling mortality in both traits is often necessary. Classical approaches, such as Leslie or Lefkovitch matrices, usually require the model to infer the state of one trait from the state of the other, for example by assuming that explicitly modelled age (or stage) class structure provides implicit information on underlying size-class structure, as is the case in many species. 3. However, the assumption that one trait informs on the other is challenged when size and age are decoupled, as often occurs in invertebrates, amphibians, fish, reptiles and plants. In these cases, age-structured models may perform poorly at capturing size-based mortality, and vice versa. 4. We offer a solution to this dilemma, relaxing the assumption that class structure in one trait is inferable from class structure in another trait. Using empirical data from a reef fish, Sparisoma viride (Scaridae), we demonstrate how an individual-based model (IBM) can be implemented to model mortality as explicit, independent and simultaneous functions of individual size and age - an approach that mimics the effects of mortality in many wild populations. By validating this 'multitrait IBM' against three independent lines of empirical data, we determine that the approach produces more convincing predictions of size-class structure, longevity and post-settlement mortality for S. viride than do the trait-independent or single-trait mortality models tested. 5. Multitrait IBMs also allow trait-based mortality to be modelled either additively or multiplicatively, and individual variability in growth rates can be accommodated. Consequently, we propose that the approach may be useful in fields that may benefit from disentangling, or investigating interactions among, size-based and age-based demographic processes, including comparative demography (e.g. life-history consequences of resource patchiness) and conservation biology (e.g. impacts of invasive predators on size structure but not life span of natives).

The business community has been frequently criticized for its lack of engagement with climate change, not just in terms of mitigation but increasingly also in terms of adaptation. One reason why executives may not take more decisive action on adaptation is the type of information they rely on for decision-making purposes. From this perspective, executives who engage more with scientific information sources for decision-making purposes would be likely to have a more comprehensive understanding of climate change, and would consequently be more concerned about their company’s vulnerability and adaptation needs. So far, however, there is limited evidence showing that executives’ lack of engagement with scientific information influences their perception that climate change is a serious issue. In this paper, we use survey data collected from 125 executives across the top 500 companies on the Australian Stock Exchange (ASX-500) to examine the links between how executives obtain information on climate change and their perceived need for adaptation action. Findings show that executives who report greater engagement with scientific information express greater concern about their company’s vulnerability, which also translates into a greater perceived need for adaptation action. Making scientific information accessible to executives is therefore important for communicating climate science to a business audience.

Environmental conditions play an important role in post-disturbance dynamics of ecosystems by modulating recovery of surviving communities and influencing patterns of succession. Here, we document the effects of wave exposure following a catastrophic disturbance on coral reefs in driving a phase shift to macroalgal dominance. In December 2012, a Category 5 super typhoon (‘Typhoon Bopha’) passed 50 km to the south of Palau (Micronesia), causing a major loss of reef corals. Immediately post-disturbance, a rapid and extensive phase shift of the macroalgae Liagora sp. (Rhodophyta) was observed at sites exposed to chronic wave exposure. To quantify the influence of biotic and abiotic drivers in modulating the extent of post-disturbance Liagora blooms, we compared benthic substrates and herbivore assemblages at sites surveyed pre- and post-disturbance across a gradient of wave exposure. Relative changes in herbivore biomass and coral cover before and after disturbance did not significantly predict the extent of Liagora cover, indicating that changes in herbivore biomass or reductions in grazing pressure were not directly responsible for driving the Liagora blooms. By contrast, the degree of wave exposure experienced at sites post-disturbance explained >90 % of model variance (p < 0.001, R2 = 0.69), in that Liagora was absent at low exposure sites, while most extensive blooms were observed at highly exposed sites. At regional scales, spatial maps of wave exposure accurately predicted the presence of Liagora at impacted sites throughout the Palau archipelago (>150 km distance), highlighting the predictive capacity of wave exposure as an explanatory variable and the deterministic nature of post-disturbance macroalgal blooms. Understanding how physical conditions modulate recovery of ecosystems after disturbance allows insight into post-disturbance dynamics and succession of communities, ultimately allowing management strategies to prioritise restoration efforts in regions that are most effective.

Environmental conditions play an important role in post-disturbance dynamics of ecosystems by modulating recovery of surviving communities and influencing patterns of succession. Here, we document the effects of wave exposure following a catastrophic disturbance on coral reefs in driving a phase shift to macroalgal dominance. In December 2012, a Category 5 super typhoon (‘Typhoon Bopha’) passed 50 km to the south of Palau (Micronesia), causing a major loss of reef corals. Immediately post-disturbance, a rapid and extensive phase shift of the macroalgae Liagora sp. (Rhodophyta) was observed at sites exposed to chronic wave exposure. To quantify the influence of biotic and abiotic drivers in modulating the extent of post-disturbance Liagora blooms, we compared benthic substrates and herbivore assemblages at sites surveyed pre- and post-disturbance across a gradient of wave exposure. Relative changes in herbivore biomass and coral cover before and after disturbance did not significantly predict the extent of Liagora cover, indicating that changes in herbivore biomass or reductions in grazing pressure were not directly responsible for driving the Liagora blooms. By contrast, the degree of wave exposure experienced at sites post-disturbance explained >90 % of model variance (p 150 km distance), highlighting the predictive capacity of wave exposure as an explanatory variable and the deterministic nature of post-disturbance macroalgal blooms. Understanding how physical conditions modulate recovery of ecosystems after disturbance allows insight into post-disturbance dynamics and succession of communities, ultimately allowing management strategies to prioritise restoration efforts in regions that are most effective.

Marine reserves are widely used to manage for the potentially conflicting objectives of conserving biodiversity and improving fisheries. The fisheries and conservation benefits of alternative reserve designs would ideally be assessed using dynamic models, which consider spillover of fish and larvae to fished areas, and the displacement of fishers to unprotected sites. In practice, however, decisions about the location of marine reserves generally rely on cheaper and faster static models. Static models analyze only spatial patterns in habitats, and typically assume fisheries profits are reduced by the amount that was generated in areas designated as reserves. To help determine the benefits of developing dynamic fisheries models, we assessed how well static models estimate costs of reserve systems to fisheries and how outcomes from reserves designed using either static or dynamic models differ. We tested these questions in two case studies, the network of marine protected areas in southern California, USA and the proposed Tun Mustapha Marine Park in Malaysia. Static models could either under or over-estimate the cost of reserve plans to fisheries, depending on the relative importance of fisher movement and larval dispersal dynamics. Despite the inaccuracy of static models for estimating costs, reserves designed using static models were similar to those designed with dynamic models if fisheries were well managed; or larval dispersal networks were simple. If larval networks were complex or there was overfishing, dynamic models generated substantially different reserve networks from static models, which improved conservation outcomes by up to 10% and fishing profits by up 20%. The time-scale of management was also important, because only dynamic models accounted for larval dispersal, so could find reserves that maximized the long-term benefits of larval spillover. Our case studies provide quantitative support for the assertion that static models can be useful for planning marine reserves for short-term objectives in well managed fisheries, but are not reliable for evaluating the relative costs of reserves to fisheries. Copyright:

For many ecosystem services, it remains uncertain whether the impacts of climate change will be mostly negative or positive and how these changes will be geographically distributed. These unknowns hamper the identification of regional winners and losers, which can influence debate over climate policy. Here, we use coral reefs to explore the spatial variability of climate stress by modelling the ecological impacts of rising sea temperatures and ocean acidification, two important coral stressors associated with increasing greenhouse gas (GHG) emissions. We then combine these results with national per capita emissions to quantify inequities arising from the distribution of cause (CO2 emissions) and effect (stress upon reefs) among coral reef countries. We find pollution and coral stress are spatially decoupled, creating substantial inequity of impacts as a function of emissions. We then consider the implications of such inequity for international climate policy. Targets for GHG reductions are likely to be tied to a country's emissions. Yet within a given level of GHG emissions, our analysis reveals that some countries experience relatively high levels of impact and will likely experience greater financial cost in terms of lost ecosystem productivity and more extensive adaptation measures. We suggest countries so disadvantaged be given access to international adaptation funds proportionate with impacts to their ecosystem. We raise the idea that funds could be more equitably allocated by formally including a metric of equity within a vulnerability framework.

Aim: Coral assemblages on Caribbean reefs have largely been considered to be biogeographically homogeneous at a regional scale. We reassess this in three taxa (corals, sponges and octocorals) using three community attributes with increasing levels of information (species richness, composition and relative abundance) across hierarchical spatial scales, and identify the key environmental drivers associated with this variation. Location: Caribbean Basin. Methods: We assessed reefs along 546 transects positioned within the same forereef habitat (Orbicella reef) in 11 countries, using a consistent methodology and surveyors. Spatial variability in richness, composition and relative abundance was assessed at four hierarchical spatial scales - transects (metres), sites (kilometres), areas (tens of kilometres) and regions (hundreds of kilometres) - using permutational multivariate analysis of variance (PERMANOVA). The relevance of contemporary environmental factors in explaining the observed spatial patterns was also assessed using PERMANOVA. Results: Consistent with previous studies, species richness of coral assemblages, commonly the focus of biogeographical studies, showed little variance at large spatial scales. In contrast, species composition and relative abundance showed significant variability at regional scales. Coral, sponge and octocoral assemblages each varied independently across spatial scales. Rugosity and wave exposure were key drivers of the composition and relative abundance of coral and octocoral assemblages. Main conclusions: Caribbean reef assemblages exhibit considerable biogeographical variability at broad spatial scales (hundreds of kilometres) when more responsive community attributes were used. However, the high degree of variability within sites (kilometres) highlights the relevance of local ecological drivers such as rugosity and wave exposure in structuring assemblages. The high levels of within-site variability that is not explained by environmental variables may suggest a previously unrealized contribution of anthropogenic disturbance operating at local scales throughout the region.

Aim: Coral assemblages on Caribbean reefs have largely been considered to be biogeographically homogeneous at a regional scale. We reassess this in three taxa (corals, sponges and octocorals) using three community attributes with increasing levels of information (species richness, composition and relative abundance) across hierarchical spatial scales, and identify the key environmental drivers associated with this variation. Location: Caribbean Basin. Methods: We assessed reefs along 546 transects positioned within the same forereef habitat (Orbicella reef) in 11 countries, using a consistent methodology and surveyors. Spatial variability in richness, composition and relative abundance was assessed at four hierarchical spatial scales - transects (metres), sites (kilometres), areas (tens of kilometres) and regions (hundreds of kilometres) - using permutational multivariate analysis of variance (PERMANOVA). The relevance of contemporary environmental factors in explaining the observed spatial patterns was also assessed using PERMANOVA. Results: Consistent with previous studies, species richness of coral assemblages, commonly the focus of biogeographical studies, showed little variance at large spatial scales. In contrast, species composition and relative abundance showed significant variability at regional scales. Coral, sponge and octocoral assemblages each varied independently across spatial scales. Rugosity and wave exposure were key drivers of the composition and relative abundance of coral and octocoral assemblages. Main conclusions: Caribbean reef assemblages exhibit considerable biogeographical variability at broad spatial scales (hundreds of kilometres) when more responsive community attributes were used. However, the high degree of variability within sites (kilometres) highlights the relevance of local ecological drivers such as rugosity and wave exposure in structuring assemblages. The high levels of within-site variability that is not explained by environmental variables may suggest a previously unrealized contribution of anthropogenic disturbance operating at local scales throughout the region.

A one-dimensional wave model is combined with an analytical sediment transport model to investigate the likely influence of sea-level rise on net cross-shore sediment transport on fetch-limited barrier reef and lagoon island beaches. The modelling considers if changes in the nearshore wave height and wave period in the lagoon induced by different water levels over the reef flat are likely to lead to net offshore or onshore movement of sediment. The results indicate that the effects of SLR on net sediment movement are highly variable and controlled by the bathymetry of the reef and lagoon. A significant range of reef-lagoon bathymetry, and notably shallow and narrow reefs, appears to lead hydrodynamic conditions and beaches that are likely to be stable or even accrete under SLR. Loss of reef structural complexity, particularly on the reef flat, increases the chance of sediment transport away from beaches and offshore.

Multinational conservation initiatives that prioritize investment across a region invariably navigate trade-offs among multiple objectives. It seems logical to focus where several objectives can be achieved efficiently, but such multi-objective hotspots may be ecologically inappropriate, or politically inequitable. Here we devise a framework to facilitate a regionally cohesive set of marine-protected areas driven by national preferences and supported by quantitative conservation prioritization analyses, and illustrate it using the Coral Triangle Initiative. We identify areas important for achieving six objectives to address ecosystem representation, threatened fauna, connectivity and climate change. We expose trade-offs between areas that contribute substantially to several objectives and those meeting one or two objectives extremely well. Hence there are two strategies to guide countries choosing to implement regional goals nationally: multi-objective hotspots and complementary sets of single-objective priorities. This novel framework is applicable to any multilateral or global initiative seeking to apply quantitative information in decision making.

Well-designed and effectively managed networks of marine reserves can be effective tools for both fisheries management and biodiversity conservation. Connectivity, the demographic linking of local populations through the dispersal of individuals as larvae, juveniles or adults, is a key ecological factor to consider in marine reserve design, since it has important implications for the persistence of metapopulations and their recovery from disturbance. For marine reserves to protect biodiversity and enhance populations of species in fished areas, they must be able to sustain focal species (particularly fishery species) within their boundaries, and be spaced such that they can function as mutually replenishing networks whilst providing recruitment subsidies to fished areas. Thus the configuration (size, spacing and location) of individual reserves within a network should be informed by larval dispersal and movement patterns of the species for which protection is required. In the past, empirical data regarding larval dispersal and movement patterns of adults and juveniles of many tropical marine species have been unavailable or inaccessible to practitioners responsible for marine reserve design. Recent empirical studies using new technologies have also provided fresh insights into movement patterns of many species and redefined our understanding of connectivity among populations through larval dispersal. Our review of movement patterns of 34 families (210 species) of coral reef fishes demonstrates that movement patterns (home ranges, ontogenetic shifts and spawning migrations) vary among and within species, and are influenced by a range of factors (e.g. size, sex, behaviour, density, habitat characteristics, season, tide and time of day). Some species move

Tropical reefs are dynamic ecosystems that host diverse coral assemblages with different life-history strategies. Here, we quantified how juvenile (

Marine reserves are a promising tool for recovering overfished ecosystems. However, reserves designed to rebuild profits in the long-term may cause short-term losses-a serious issue in regions where fisheries are key for food security. We examine the tension between the long-term benefits of reserves and short-term losses, using a multispecies model of coral reef fisheries. Reserves designed to maximize long-term profits caused significant short-term losses. We model several policy solutions, where we incrementally increased either: the number of months per year that the reserve is closed to fishing; the size of the reserve; or the number species protected within the reserve. Protecting species sequentially, starting with the most valued species, provided the best outcome in the short-term with the most rapid recovery of profits. Solving the dilemma of meeting short- and long-term goals will ultimately improve the effectiveness of marine reserves for managing fisheries and conserving ecosystems.

Cumulative pressures from global climate and ocean change combined with multiple regional and local-scale stressors pose fundamental challenges to coral reef managers worldwide. Understanding how cumulative stressors affect coral reef vulnerability is critical for successful reef conservation now and in the future. In this review, we present the case that strategically managing for increased ecological resilience (capacity for stress resistance and recovery) can reduce coral reef vulnerability (risk of net decline) up to a point. Specifically, we propose an operational framework for identifying effective management levers to enhance resilience and support management decisions that reduce reef vulnerability. Building on a system understanding of biological and ecological processes that drive resilience of coral reefs in different environmental and socio-economic settings, we present an Adaptive Resilience-Based management (ARBM) framework and suggest a set of guidelines for how and where resilience can be enhanced via management interventions. We argue that press-type stressors (pollution, sedimentation, overfishing, ocean warming and acidification) are key threats to coral reef resilience by affecting processes underpinning resistance and recovery, while pulse-type (acute) stressors (e.g. storms, bleaching events, crown-of-thorns starfish outbreaks) increase the demand for resilience. We apply the framework to a set of example problems for Caribbean and Indo-Pacific reefs. A combined strategy of active risk reduction and resilience support is needed, informed by key management objectives, knowledge of reef ecosystem processes and consideration of environmental and social drivers. As climate change and ocean acidification erode the resilience and increase the vulnerability of coral reefs globally, successful adaptive management of coral reefs will become increasingly difficult. Given limited resources, on-the-ground solutions are likely to focus increasingly on actions that support resilience at finer spatial scales, and that are tightly linked to ecosystem goods and services.

Cumulative pressures from global climate and ocean change combined with multiple regional and local-scale stressors pose fundamental challenges to coral reef managers worldwide. Understanding how cumulative stressors affect coral reef vulnerability is critical for successful reef conservation now and in the future. In this review, we present the case that strategically managing for increased ecological resilience (capacity for stress resistance and recovery) can reduce coral reef vulnerability (risk of net decline) up to a point. Specifically, we propose an operational framework for identifying effective management levers to enhance resilience and support management decisions that reduce reef vulnerability. Building on a system understanding of biological and ecological processes that drive resilience of coral reefs in different environmental and socio-economic settings, we present an Adaptive Resilience-Based management (ARBM) framework and suggest a set of guidelines for how and where resilience can be enhanced via management interventions. We argue that press-type stressors (pollution, sedimentation, overfishing, ocean warming and acidification) are key threats to coral reef resilience by affecting processes underpinning resistance and recovery, while pulse-type (acute) stressors (e.g. storms, bleaching events, crown-of-thorns starfish outbreaks) increase the demand for resilience. We apply the framework to a set of example problems for Caribbean and Indo-Pacific reefs. A combined strategy of active risk reduction and resilience support is needed, informed by key management objectives, knowledge of reef ecosystem processes and consideration of environmental and social drivers. As climate change and ocean acidification erode the resilience and increase the vulnerability of coral reefs globally, successful adaptive management of coral reefs will become increasingly difficult. Given limited resources, on-the-ground solutions are likely to focus increasingly on actions that support resilience at finer spatial scales, and that are tightly linked to ecosystem goods and services.

While positive interactions have been observed to influence patterns of recruitment and succession in marine and terrestrial plant communities, the role of facilitation in macroalgal phase shifts is relatively unknown. In December 2012, typhoon Bopha caused catastrophic losses of corals on the eastern reefs of Palau. Within weeks of the typhoon, an ephemeral bloom of monospecific macroalgae (Liagora sp.) was observed, reaching a peak of 38.6 % cover in February 2013. At this peak, we observed a proliferation of a second macroalgal species, Lobophoravariegata. Lobophora was distributed non-randomly, with higher abundances occurring within the shelter of Liagora canopies than on exposed substrates. Bite rates of two common herbivorous fish (Chlorurus sordidus and Ctenochaetus striatus) were significantly higher outside canopies (2.5- and sixfold, respectively), and cage exclusion resulted in a significant increase in Lobophora cover. Experimental removal of Liagora canopies resulted in a 53.1 % decline in the surface area of Lobophora after 12 days, compared to a 51.7 % increase within canopies. Collectively, these results indicate that Liagora canopies act as ecological facilitators, providing a ‘nursery’ exclusion zone from the impact of herbivorous fish, allowing for the establishment of understory Lobophora. While the ephemeral Liagora bloom had disappeared entirely 9 months post-typhoon, the facilitated shift to Lobophora has persisted for over 18 months, dominating ~40 % of the reef substrate. While acute disturbance events such as typhoons have been suggested as a mechanism to reverse algal phase shifts, our results suggest that typhoons may also trigger, rather than just reverse, phase shifts.

While positive interactions have been observed to influence patterns of recruitment and succession in marine and terrestrial plant communities, the role of facilitation in macroalgal phase shifts is relatively unknown. In December 2012, typhoon Bopha caused catastrophic losses of corals on the eastern reefs of Palau. Within weeks of the typhoon, an ephemeral bloom of monospecific macroalgae (Liagora sp.) was observed, reaching a peak of 38.6% cover in February 2013. At this peak, we observed a proliferation of a second macroalgal species, Lobophora variegata. Lobophora was distributed non-randomly, with higher abundances occurring within the shelter of Liagora canopies than on exposed substrates. Bite rates of two common herbivorous fish (Chlorurus sordidus and Ctenochaetus striatus) were significantly higher outside canopies (2.5- and sixfold, respectively), and cage exclusion resulted in a significant increase in Lobophora cover. Experimental removal of Liagora canopies resulted in a 53.1% decline in the surface area of Lobophora after 12 days, compared to a 51.7% increase within canopies. Collectively, these results indicate that Liagora canopies act as ecological facilitators, providing a 'nursery' exclusion zone from the impact of herbivorous fish, allowing for the establishment of understory Lobophora. While the ephemeral Liagora bloom had disappeared entirely 9 months post-typhoon, the facilitated shift to Lobophora has persisted for over 18 months, dominating ~40% of the reef substrate. While acute disturbance events such as typhoons have been suggested as a mechanism to reverse algal phase shifts, our results suggest that typhoons may also trigger, rather than just reverse, phase shifts.

Burgeoning threats to coral reefs have prompted calls for management actions that can enhance ecosystem resilience, such as restoring herbivore populations whose grazing is critical to maintaining ecological function. However, lack of longitudinal datasets has hindered objective assessment of strategies aimed at recovering herbivory. Addressing this gap, we investigated the response of the Bermuda fish assemblage to a trapping ban that amounted to de facto protection of herbivorous parrotfishes (Scaridae). Hook-and-line fishing for piscivores continued during the ban, creating a natural experiment that freed scarids from both fishing mortality and adult-stage predation. Over the 9 yr study period, biomass of piscivores remained low because of the hook-and-line fishery, with the exception of trumpetfish Aulostomus maculatus whose biomass increased more than 6-fold. Although scarid post-recruit biomass increased by a factor of 3.7, there was no increase in recruits (

Many biological systems, from fragmented landscapes to host populations, can be represented as networks of connected habitat patches. Links between patches in these connectivity networks can represent equally diverse processes, from individuals moving through the landscape to pathogen transmissions or successive colonization events in metapopulations. Any of these processes can be characterized as stochastic, with functional links among patches that exist with various levels of certainty. This stochasticity then needs to be reflected in the algorithms that aim to predict the dispersal routes in these networks. Here we adapt the concept of reliability to characterize the likelihood that a specific path will be used for dispersal in a probabilistic connectivity network. The most reliable of the paths that connect two patches will then identify the most likely sequence of intermediate steps between these patches. Path reliability will be sensitive to targeted disruptions of individual links that form the path, and this can then be used to plan the interventions aimed at either preserving or disrupting the dispersal along that path. The proposed approach is general, and can be used to identify the most likely dispersal routes in various contexts, such as predicting patterns of migrations, colonizations, invasions and epidemics.

There has been ongoing flattening of Caribbean coral reefs with the loss of habitat having severe implications for these systems. Complexity and its structural components are important to fish species richness and community composition, but little is known about its role for other taxa or species-specific responses. This study reveals the importance of reef habitat complexity and structural components to different taxa of macrofauna, total species richness, and individual coral and fish species in the Caribbean. Species presence and richness of different taxa were visually quantified in one hundred 25-m2 plots in three marine reserves in the Caribbean. Sampling was evenly distributed across five levels of visually estimated reef complexity, with five structural components also recorded: the number of corals, number of large corals, slope angle, maximum sponge and maximum octocoral height. Taking advantage of natural heterogeneity in structural complexity within a particular coral reef habitat (Orbicella reefs) and discrete environmental envelope, thus minimizing other sources of variability, the relative importance of reef complexity and structural components was quantified for different taxa and individual fish and coral species on Caribbean coral reefs using boosted regression trees (BRTs). Boosted regression tree models performed very well when explaining variability in total (82·3%), coral (80·6%) and fish species richness (77·3%), for which the greatest declines in richness occurred below intermediate reef complexity levels. Complexity accounted for very little of the variability in octocorals, sponges, arthropods, annelids or anemones. BRTs revealed species-specific variability and importance for reef complexity and structural components. Coral and fish species occupancy generally declined at low complexity levels, with the exception of two coral species (Pseudodiploria strigosa and Porites divaricata) and four fish species (Halichoeres bivittatus, H. maculipinna, Malacoctenus triangulatus and Stegastes partitus) more common at lower reef complexity levels. A significant interaction between country and reef complexity revealed a non-additive decline in species richness in areas of low complexity and the reserve in Puerto Rico. Flattening of Caribbean coral reefs will result in substantial species losses, with few winners. Individual structural components have considerable value to different species, and their loss may have profound impacts on population responses of coral and fish due to identity effects of key species, which underpin population richness and resilience and may affect essential ecosystem processes and services.

There has been ongoing flattening of Caribbean coral reefs with the loss of habitat having severe implications for these systems. Complexity and its structural components are important to fish species richness and community composition, but little is known about its role for other taxa or species-specific responses. This study reveals the importance of reef habitat complexity and structural components to different taxa of macrofauna, total species richness, and individual coral and fish species in the Caribbean. Species presence and richness of different taxa were visually quantified in one hundred 25-m(2) plots in three marine reserves in the Caribbean. Sampling was evenly distributed across five levels of visually estimated reef complexity, with five structural components also recorded: the number of corals, number of large corals, slope angle, maximum sponge and maximum octocoral height. Taking advantage of natural heterogeneity in structural complexity within a particular coral reef habitat (Orbicella reefs) and discrete environmental envelope, thus minimizing other sources of variability, the relative importance of reef complexity and structural components was quantified for different taxa and individual fish and coral species on Caribbean coral reefs using boosted regression trees (BRTs). Boosted regression tree models performed very well when explaining variability in total (82·3%), coral (80·6%) and fish species richness (77·3%), for which the greatest declines in richness occurred below intermediate reef complexity levels. Complexity accounted for very little of the variability in octocorals, sponges, arthropods, annelids or anemones. BRTs revealed species-specific variability and importance for reef complexity and structural components. Coral and fish species occupancy generally declined at low complexity levels, with the exception of two coral species (Pseudodiploria strigosa and Porites divaricata) and four fish species (Halichoeres bivittatus, H. maculipinna, Malacoctenus triangulatus and Stegastes partitus) more common at lower reef complexity levels. A significant interaction between country and reef complexity revealed a non-additive decline in species richness in areas of low complexity and the reserve in Puerto Rico. Flattening of Caribbean coral reefs will result in substantial species losses, with few winners. Individual structural components have considerable value to different species, and their loss may have profound impacts on population responses of coral and fish due to identity effects of key species, which underpin population richness and resilience and may affect essential ecosystem processes and services.

Coral cover on Caribbean reefs has declined rapidly since the early 1980's. Diseases have been a major driver, decimating communities of framework building Acropora and Orbicella coral species, and reportedly leading to the emergence of novel coral assemblages often dominated by domed and plating species of the genera Agaricia, Porites and Siderastrea. These corals were not historically important Caribbean framework builders, and typically have much smaller stature and lower calcification rates, fuelling concerns over reef carbonate production and growth potential. Using data from 75 reefs from across the Caribbean we quantify: (i) the magnitude of non-framework building coral dominance throughout the region and (ii) the contribution of these corals to contemporary carbonate production. Our data show that live coral cover averages 18.2% across our sites and coral carbonate production 4.1 kg CaCO3 m-2 yr-1. However, non-framework building coral species dominate and are major carbonate producers at a high proportion of sites; they are more abundant than Acropora and Orbicella at 73% of sites; contribute an average 68% of the carbonate produced; and produce more than half the carbonate at 79% of sites. Coral cover and carbonate production rate are strongly correlated but, as relative abundance of non-framework building corals increases, average carbonate production rates decline. Consequently, the use of coral cover as a predictor of carbonate budget status, without species level production rate data, needs to be treated with caution. Our findings provide compelling evidence for the Caribbean-wide dominance of non-framework building coral taxa, and that these species are now major regional carbonate producers. However, because these species typically have lower calcification rates, continued transitions to states dominated by non-framework building coral species will further reduce carbonate production rates below 'predecline' levels, resulting in shifts towards negative carbonate budget states and reducing reef growth potential.

Coral cover on Caribbean reefs has declined rapidly since the early 1980's. Diseases have been a major driver, decimating communities of framework building Acropora and Orbicella coral species, and reportedly leading to the emergence of novel coral assemblages often dominated by domed and plating species of the genera Agaricia, Porites and Siderastrea. These corals were not historically important Caribbean framework builders, and typically have much smaller stature and lower calcification rates, fuelling concerns over reef carbonate production and growth potential. Using data from 75 reefs from across the Caribbean we quantify: (i) the magnitude of non-framework building coral dominance throughout the region and (ii) the contribution of these corals to contemporary carbonate production. Our data show that live coral cover averages 18.2% across our sites and coral carbonate production 4.1 kg CaCO3  m(-2)  yr(-1). However, non-framework building coral species dominate and are major carbonate producers at a high proportion of sites; they are more abundant than Acropora and Orbicella at 73% of sites; contribute an average 68% of the carbonate produced; and produce more than half the carbonate at 79% of sites. Coral cover and carbonate production rate are strongly correlated but, as relative abundance of non-framework building corals increases, average carbonate production rates decline. Consequently, the use of coral cover as a predictor of carbonate budget status, without species level production rate data, needs to be treated with caution. Our findings provide compelling evidence for the Caribbean-wide dominance of non-framework building coral taxa, and that these species are now major regional carbonate producers. However, because these species typically have lower calcification rates, continued transitions to states dominated by non-framework building coral species will further reduce carbonate production rates below 'predecline' levels, resulting in shifts towards negative carbonate budget states and reducing reef growth potential.

Environmental policy instruments often require that natural resource managers safeguard the resilience of ecosystems. However, 'resilience' has been a difficult concept to operationalise. Two forms of resilience are recognised in the ecological literature. 'Ecological resilience' concerns ecosystems that possess alternative equilibrial states (attractors) and has been operationalised in a few systems. 'Engineering resilience' was developed for ecosystems with a single attractor, but its use is confined to systems that gravitate towards a stable equilibrium. We present a general method to quantify engineering resilience that can be applied irrespective of an ecosystem's stability or proclivity to obey multiple attractors. The technique uses a system model to distinguish the effects of globally driven (and essentially unmanageable) stressors, such as climate change and ocean acidification, from regional- and local-scale (manageable) stressors on the ecosystem. We illustrate the technique using a simple coral reef model and find it able to calculate the impacts of managing crown-of-thorns starfish against a background of increasing stress from climate change and ocean acidification. Resilience analyses using our approach help assess the relative importance of local- or regional-scale management interventions under varying degrees of global environmental change, even if they preside over long-term ecosystem decline. Several frameworks of varying complexity are provided to guide the linkage of resilience metrics to environmental decision-making.

Summary: Environmental policy instruments often require that natural resource managers safeguard the resilience of ecosystems. However, 'resilience' has been a difficult concept to operationalise. Two forms of resilience are recognised in the ecological literature. 'Ecological resilience' concerns ecosystems that possess alternative equilibrial states (attractors) and has been operationalised in a few systems. 'Engineering resilience' was developed for ecosystems with a single attractor, but its use is confined to systems that gravitate towards a stable equilibrium. We present a general method to quantify engineering resilience that can be applied irrespective of an ecosystem's stability or proclivity to obey multiple attractors. The technique uses a system model to distinguish the effects of globally driven (and essentially unmanageable) stressors, such as climate change and ocean acidification, from regional- and local-scale (manageable) stressors on the ecosystem. We illustrate the technique using a simple coral reef model and find it able to calculate the impacts of managing crown-of-thorns starfish against a background of increasing stress from climate change and ocean acidification. Resilience analyses using our approach help assess the relative importance of local- or regional-scale management interventions under varying degrees of global environmental change, even if they preside over long-term ecosystem decline. Several frameworks of varying complexity are provided to guide the linkage of resilience metrics to environmental decision-making.

Coral reefs are subjected globally to a variety of natural and anthropogenic stressors that often act synergistically. Today, reversing ongoing and future coral reef degradation presents significant challenges and countering this negative trend will take considerable efforts and investments. Scientific knowledge can inform and guide the requisite decision-making process and offer practical solutions to the problem of protection as the effects of climate change exacerbate. However, implementation of solutions presently lags far behind the pace required to reverse global declines, and there is a need for an urgent and significant step-up in the extent and range of strategies being implemented. In this paper, we consider scientific frontiers in natural and social science research that can help build stronger support for reef management and improve the efficacy of interventions. We cover various areas including: (1) enhancing the case for reef conservation and management, (2) dealing with local stressors on reefs, (3) addressing global climate change impacts, (4) and reviewing various approaches to the governance of coral reefs. In sum, we consider scientific frontiers in natural and social science that will require further attention in coming years as managers work toward building stronger support for reef management and improve the efficacy of local interventions.

Increasing threats to natural ecosystems from local and global stressors are reinforcing the need for baseline data on the distribution and abundance of organisms. We quantified spatial and/or temporal patterns of seagrass distribution, shoot density, leaf area index, biomass, productivity, and sediment carbon content in shallow water (0-5 m) at Lizard Island, Great Barrier Reef, Australia, in field surveys conducted in December 2011 and October 2012. Seagrass meadows were mapped using satellite imagery and field validation. A total of 18.3 ha of seagrass, composed primarily of Thalassia hemprichii and Halodule uninervis, was mapped in shallow water. This was 46% less than the area of seagrass in the same region reported in 1995, although variations in mapping methods may have influenced the magnitude of change detected. There was inter-annual variability in shoot density and length, with values for both higher in 2011 than in 2012. Seagrass properties and sediment carbon content were representative of shallow-water seagrass meadows on a mid-shelf Great Barrier Reef island. The data can be used to evaluate change, to parameterize models of the impact of anthropogenic or environmental variability on seagrass distribution and abundance, and to assess the success of management actions.

Recent epizootics have removed important functional species from Caribbean coral reefs and left communities vulnerable to alternative attractors. Global warming will impact reefs further through two mechanisms. A chronic mechanism reduces coral calcification, which can result in depressed somatic growth. An acute mechanism, coral bleaching, causes extreme mortality when sea temperatures become anomalously high. We ask how these two mechanisms interact in driving future reef state (coral cover) and resilience (the probability of a reef remaining within a coral attractor). We find that acute mechanisms have the greatest impact overall, but the nature of the interaction with chronic stress depends on the metric considered. Chronic and acute stress act additively on reef state but form a strong synergy when influencing resilience by intensifying a regime shift. Chronic stress increases the size of the algal basin of attraction (at the expense of the coral basin), whereas coral bleaching pushes the system closer to the algal attractor. Resilience can change faster—and earlier—than a change in reef state. Therefore, we caution against basing management solely on measures of reef state because a loss of resilience can go unnoticed for many years and then become disproportionately more difficult to restore.

© 2015 Springer-Verlag Berlin Heidelberg Sea-level rise will change environmental conditions on coral reef flats, which comprise extensive habitats in shallow tropical seas and support a wealth of ecosystem services. Rapid relative sea-level rise of 0.6 m over a relatively pristine coral reef in Solomon Islands, caused by a subduction earthquake in April 2007, generated a unique opportunity to examine in situ coral reef response to relative sea-level rise of the magnitude (but not the rate) anticipated by 2100. Extent of live coral was measured from satellite imagery in 2003, 2006, 2009 and 2012. Ecological data were obtained from microatolls and ecological surveys in May 2013. The reef was sampled at 12 locations where dense live hard coral remained absent, remained present or changed from absent to present following subsidence. Ecological data (substratum depth, live coral canopy depth, coral canopy height, substratum suitability, recruitment, diversity and Acropora presence) were measured at each location to identify factors associated with coral response to relative sea-level rise. Vertical and horizontal proliferation of coral occurred following subsidence. Lateral expansion of live coral, accomplished primarily by branching Acropora spp. resulted in lower diversity in regions which changed composition from pavement to dense live coral following subsidence. of the ecological factors measured, biotic factors were more influential than abiotic factors; species identity was the most important factor in determining which regions of the reef responded to rapid sea-level rise. On relatively pristine reef flats under present climatic conditions, rapid relative sea-level rise generated an opportunity for hard coral to proliferate. However, the species assemblage of the existing reef was important in determining response to sea-level change, by providing previously bare substrate with a source of new coral colonies. Degraded reefs with altered species composition and slower coral growth rates may be less able to respond to climate change-induced sea-level changes.

The first public product of the Intergovernmental Platform on Biodiversity and Ecosystem Services (IPBES) is its Conceptual Framework. This conceptual and analytical tool, presented here in detail, will underpin all IPBES functions and provide structure and comparability to the syntheses that IPBES will produce at different spatial scales, on different themes, and in different regions. Salient innovative aspects of the IPBES Conceptual Framework are its transparent and participatory construction process and its explicit consideration of diverse scientific disciplines, stakeholders, and knowledge systems, including indigenous and local knowledge. Because the focus on co-construction of integrative knowledge is shared by an increasing number of initiatives worldwide, this framework should be useful beyond IPBES, for the wider research and knowledge-policy communities working on the links between nature and people, such as natural, social and engineering scientists, policy-makers at different levels, and decision-makers in different sectors of society.

One striking feature of coral reef ecosystems is the complex benthic architecture which supports diverse and abundant fauna, particularly of reef fish. Reef-building corals are in decline worldwide, with a corresponding loss of live coral cover resulting in a loss of architectural complexity. Understanding the dynamics of the reef architecture is therefore important to envision the ability of corals to maintain functional habitats in an era of climate change. Here, we develop a mechanistic model of reef topographical complexity for contemporary Caribbean reefs. The model describes the dynamics of corals and other benthic taxa under climate-driven disturbances (hurricanes and coral bleaching). Corals have a simplified shape with explicit diameter and height, allowing species-specific calculation of their colony surface and volume. Growth and the mechanical (hurricanes) and biological erosion (parrotfish) of carbonate skeletons are important in driving the pace of extension/reduction in the upper reef surface, the net outcome being quantified by a simple surface roughness index (reef rugosity). The model accurately simulated the decadal changes of coral cover observed in Cozumel (Mexico) between 1984 and 2008, and provided a realistic hindcast of coral colony-scale (1-10 m) changing rugosity over the same period. We then projected future changes of Caribbean reef rugosity in response to global warming. Under severe and frequent thermal stress, the model predicted a dramatic loss of rugosity over the next two or three decades. Critically, reefs with managed parrotfish populations were able to delay the general loss of architectural complexity, as the benefits of grazing in maintaining living coral outweighed the bioerosion of dead coral skeletons. Overall, this model provides the first explicit projections of reef rugosity in a warming climate, and highlights the need of combining local (protecting and restoring high grazing) to global (mitigation of greenhouse gas emissions) interventions for the persistence of functional reef habitats.

Coral reefs are one of the most highly productive marine ecosystems, with a strong connection between herbivores and the production of benthic algae. The epilithic algal matrix (EAM) is a major source of primary production on coral reefs, and it is one of the dominant benthic microhabitats, covering up to 80% of reef flats and back reefs and up to 70% of reef slopes on outer-shelf sites of the Great Barrier Reef, Australia. Although herbivorous surgeonfish (Acanthuridae) are dominant members of most reef fish assemblages, there is a lack of quantitative information on their grazing impact, particularly those that feed upon the EAM in the Indo-Pacific. Therefore, the aim of this study was to investigate the role of surgeonfish in maintaining algal turf biomass on coral reefs. Spatial patterns of EAM productivity, and herbivorous fish biomass and grazing intensity were quantified at different depths (deep vs. shallow) and exposures (windward vs. leeward) of reef slope environments of Heron Island, southern Great Barrier Reef. Surgeonfish were the numerically-dominant EAM grazing fish family, and to identify the daily impact of surgeonfish species on the EAM, data on their biomass (gm-2) and grazing intensity (total bitesm-2day-1) were combined with EAM productivity estimates (gCm-2day-1). EAM productivity was greatest in windward and shallow sites, and herbivorous fish biomass mirrored this pattern. Yet, there was no difference in the EAM standing crop or grazing intensity among habitats. In the most productive habitat (windward-shallow), grazer/detritivore surgeonfish species accounted for 74% of the total herbivore biomass (gm-2), took 51% of the total bites (m-2day-1), and removed an estimated 73% of daily EAM productivity (gCm-2day-1). This study quantifies the role of surgeonfish in maintaining EAM biomass, and highlights their possible contribution to preventing shifts from coral- to algal-dominance following disturbance.

Symbiodinium D, a relatively rare clade of algal endosymbiont with a global distribution, has attracted interest as some of its sub-cladal types induce increased thermal tolerance and associated trade-offs, including reduced growth rate in its coral hosts. Members of Symbiodinium D are increasingly reported to comprise low-abundance ‘cryptic’ (30 % of corals per site found to harbour the symbiont. When the same samples were analysed using the conventional screening technique, denaturing gradient gel electrophoresis, Symbiodinium D1 was only detected in 12 populations and appeared to be hosted by

In 2010, the international community, under the auspices of the Convention on Biological Diversity, agreed on 20 biodiversity-related "Aichi Targets" to be achieved within a decade. We provide a comprehensive mid-term assessment of progress toward these global targets using 55 indicator data sets. We projected indicator trends to 2020 using an adaptive statistical framework that incorporated the specific properties of individual time series. On current trajectories, results suggest that despite accelerating policy and management responses to the biodiversity crisis, the impacts of these efforts are unlikely to be reflected in improved trends in the state of biodiversity by 2020. We highlight areas of societal endeavor requiring additional efforts to achieve the Aichi Targets, and provide a baseline against which to assess future progress.

When assessing future changes in fishing, research has focused on changes in the availability of the resource. Fishers' behaviour, however, also defines fishing activity, and is susceptible not only to changes in weather but also to changes in the economy, which can be faster and more ubiquitous. Using a novel modelling approach and spatially explicit predictors we identified the current drivers of artisanal fishing activity and predicted how it is likely to change in 2025 and 2035 under two climate and two economic scenarios. The model is effective at explaining the activity of fishers (AUC = 0.84) and suggests that economic variables overwhelm the importance of climate variables in influencing the decisions of fishers in our case study area (Utila, Honduras). Although future changes in the overall incidence of fishing activity are modest, decreases in the number of accessible fishing grounds with projected increases in fuel prices will increase localised fishing effort depleting fish resources near the port. Compelling adaptation strategies in the area require the intervention of the market chain to make the sale price of fish more responsive to fuel price fluctuations and changes in fishing behaviour to improve fuel efficiency, including the revival of traditional ways of fishing. © 2014 Elsevier B.V.

Caribbean reefs have steadily declined during the past 30 years. Thermal disturbances that elicit coral bleaching have been identified as a major driver of such coral degradation. It has been suggested that either the evolution of more tolerant symbionts, or shifts in the distribution of existing, tolerant symbionts could ameliorate the effect of rising sea temperatures on Caribbean reefs. Using a spatial ecosystem model we describe the characteristics that new tolerant symbionts, 'super-symbionts', and their coral hosts, require for coral cover to be maintained. We also quantify the time necessary for such symbionts to become dominant before their potential beneficial effect is lost. Running scenarios under two levels of greenhouse gas emissions, we find that aggressive action to reduce emissions could almost triple the time available for new super-symbionts to become dominant and potentially mitigate the effect of thermal disturbances. The benefits of thermally tolerant super-symbionts depend on the life-history traits of the host, the number of coral species infected and the present coral assemblage. Corals that are strong competitors with macroalgae are likely to become dominant on future reefs if a super-symbiont appears in the next 25-60 years. In principle, super-symbionts could have ecosystem-level benefits in the Caribbean providing that they become dominant in multiple coral hosts with specific life-history traits within the next 60 years. This potential benefit would only be realized if the appearance of the super-symbiont is combined with drastic reductions of greenhouse gas emissions and maintenance of ecosystem processes such as herbivory. © 2013 Springer Science+Business Media New York.

The idea that there is an identifiable set of boundaries, beyond which anthropogenic change will put the Earth system outside a safe operating space for humanity, is attracting interest in the scientific community and gaining support in the environmental policy world. Rockstrom et al. (2009) identify nine such boundaries and highlight biodiversity loss as being the single boundary where current rates of extinction put the Earth system furthest outside the safe operating space. Here we review the evidence to support a boundary based on extinction rates and identify weaknesses with this metric and its bearing on humanity's needs. While changes to biodiversity are of undisputed importance, we show that both extinction rate and species richness are weak metrics for this purpose, and they do not scale well from local to regional or global levels. We develop alternative approaches to determine biodiversity loss boundaries and extend our analysis to consider large-scale responses in the Earth system that could affect its suitability for complex human societies which in turn are mediated by the biosphere. We suggest three facets of biodiversity on which a boundary could be based: the genetic library of life; functional type diversity; and biome condition and extent. For each of these we explore the science needed to indicate how it might be measured and how changes would affect human societies. In addition to these three facets, we show how biodiversity's role in supporting a safe operating space for humanity may lie primarily in its interactions with other boundaries, suggesting an immediate area of focus for scientists and policymakers.

Several species of coral reef herbivorous fish and groupers (Serranidae) are among the main targets of Micronesian spearfishers. Since 1994, a closed season (April-July) protects spawning aggregations of five grouper species in Palau, and, although this regulation may affect fishers targeting behaviour towards herbivores and increase their catch levels, the extent of these effects was previously unknown. This study conducted market surveys and interviews to examine if the closed grouper season in 2009 had any effect on herbivore spearfishing catches, or caused changes in the targeting behaviour of fishers. Catch volumes of the most desirable herbivores were unaffected by the grouper season, but the catch per unit effort of herbivores regularly caught opportunistically (i.e. if seen) or avoided raised by 45% during the grouper closure. The size composition of the catch of the bluespine unicornfish Naso unicornis during the grouper closure was significantly skewed to smaller sized fish due to the high proportion of immature individuals. Further investigation is required to clarify whether this pattern emerged because fishers had relaxed size selectivity during the closure or due to a paucity of adults in July. Fifty-seven per cent of the interviewed fishers indicated that while groupers would be their first choice during open season, N.unicornis would become their preferred target during the closure, and that other herbivores were also more likely to be targeted. This study took an important step in identifying a factor driving short and acute changes in the herbivore catch composition. Further efforts should be directed to quantify the ecological implications of the observed changes and determine if these are aggravated by the life-history traits or functional roles of the focal species. Relaxed species selectivity might emerge elsewhere, if inherently selective fishing methods are used and highly prized targets are temporarily or permanently banned, or overfished to critical levels. Such implications should be considered when assessing the sustainability of local fisheries. © 2013 the Zoological Society of London.

© 2014 the Author(s) Published by the Royal Society. All rights reserved.Coral cover has declined rapidly on Caribbean reefs since the early 1980s, reducing carbonate production and reef growth. Using a cross-regional dataset, we show that widespread reductions in bioerosion rates-a key carbonate cycling process-have accompanied carbonate production declines. Bioerosion by parrotfish, urchins, endolithic sponges and microendoliths collectively averages 2 G (where G = kg CaCO3 m(-2) yr(-1)) (range 0.96-3.67 G). This rate is at least 75% lower than that reported from Caribbean reefs prior to their shift towards their present degraded state. Despite chronic overfishing, parrotfish are the dominant bioeroders, but erosion rates are reduced from averages of approximately 4 to 1.6 G. Urchin erosion rates have declined further and are functionally irrelevant to bioerosion on most reefs. These changes demonstrate a fundamental shift in Caribbean reef carbonate budget dynamics. To-date, reduced bioerosion rates have partially offset carbonate production declines, limiting the extent to which more widespread transitions to negative budget states have occurred. However, given the poor prognosis for coral recovery in the Caribbean and reported shifts to coral community states dominated by slower calcifying taxa, a continued transition from production to bioerosion-controlled budget states, which will increasingly threaten reef growth, is predicted.

Coral cover has declined rapidly on Caribbean reefs since the early 1980s, reducing carbonate production and reef growth. Using a cross-regional dataset, we show that widespread reductions in bioerosion rates-a key carbonate cycling process-have accompanied carbonate production declines. Bioerosion by parrotfish, urchins, endolithic sponges and microendoliths collectively averages 2 G (where G = kg CaCO3 m(-2) yr(-1)) (range 0.96-3.67 G). This rate is at least 75% lower than that reported from Caribbean reefs prior to their shift towards their present degraded state. Despite chronic overfishing, parrotfish are the dominant bioeroders, but erosion rates are reduced from averages of approximately 4 to 1.6 G. Urchin erosion rates have declined further and are functionally irrelevant to bioerosion on most reefs. These changes demonstrate a fundamental shift in Caribbean reef carbonate budget dynamics. To-date, reduced bioerosion rates have partially offset carbonate production declines, limiting the extent to which more widespread transitions to negative budget states have occurred. However, given the poor prognosis for coral recovery in the Caribbean and reported shifts to coral community states dominated by slower calcifying taxa, a continued transition from production to bioerosion-controlled budget states, which will increasingly threaten reef growth, is predicted.

Many ecosystems suffer systemwide outbreaks of damaging species propagating from primary outbreak sites. Connectivity patterns can identify parts of the ecosystem that help turn local outbreaks into a systemwide contagion through a series of transmission events. Here, we show that patterns of larval connectivity among reefs can help explain periodic crown-of-thorns starfish (COTS) epidemics across the Great Barrier Reef (GBR). We simulated potential dispersal of COTS larvae to obtain a connectivity network of coral reefs across the entire GBR. Network analysis revealed areas of high local connectivity where any outbreaks could be amplified locally, as well as those areas with potential to cause large-scale epidemics with ecosystem-wide impacts. We find that the regions where COTS epidemics are known to originate are predictable from their high local and systemwide connectivity. Extensive larval exchanges among reef clusters in these regions can start a chain reaction of COTS population build-up. The same regions also have high potential to reach and affect other parts of the GBR, thereby maximizing the likelihood that any outbreaks would eventually propagate throughout the ecosystem. Hydrodynamic properties and geography of the GBR make it vulnerable to COTS epidemics. Using network analysis to identify regions with high-risk high-impact sources could help control these devastating events in future. Synthesis and applications. The observed centre of origin for COTS epidemics (the Cooktown-Cairns region) can be predicted from its elevated short- and long-range levels of larval connectivity. Connectivity analysis of per-reef risks provides spatially explicit targets to guide surveillance and control measures that might help curtail COTS epidemics through prioritization of highly connected reefs. The analytical approach developed here for COTS connectivity can also be applied to identify well-connected patches and regions in other interconnected ecological systems. The observed centre of origin for COTS epidemics (the Cooktown-Cairns region) can be predicted from its elevated short- and long-range levels of larval connectivity. Connectivity analysis of per-reef risks provides spatially explicit targets to guide surveillance and control measures that might help curtail COTS epidemics through prioritization of highly connected reefs. The analytical approach developed here for COTS connectivity can also be applied to identify well-connected patches and regions in other interconnected ecological systems.

Coral reefs are highly sensitive to the stress associated with greenhouse gas emissions, in particular ocean warming and acidification. While experiments show negative responses of most reef organisms to ocean warming, some autotrophs benefit from ocean acidification. Yet, we are uncertain of the response of coral reefs as systems. We begin by reviewing sources of uncertainty and complexity including the translation of physiological effects into demographic processes, indirect ecological interactions among species, the ability of coral reefs to modify their own chemistry, adaptation and trans-generational plasticity. We then incorporate these uncertainties into two simple qualitative models of a coral reef system under climate change. Some sources of uncertainty are far more problematic than others. Climate change is predicted to have an unambiguous negative effect on corals that is robust to several sources of uncertainty but sensitive to the degree of biogeochemical coupling between benthos and seawater. Macroalgal, zoanthid, and herbivorous fish populations are generally predicted to increase, but the ambiguity (confidence) of such predictions are sensitive to the source of uncertainty. For example, reversing the effect of climate-related stress on macroalgae from being positive to negative had no influence on system behaviour. By contrast, the system was highly sensitive to a change in the stress upon herbivorous fishes. Minor changes in competitive interactions had profound impacts on system behaviour, implying that the outcomes of mesocosm studies could be highly sensitive to the choice of taxa. We use our analysis to identify new hypotheses and suggest that the effects of climatic stress on coral reefs provide an exceptional opportunity to test emerging theories of ecological inheritance.

Different marine species and their larvae have characteristics that can expand or contract their potential dispersal, which can add complexity to the management of species assemblages. Here we used a multi-scale biophysical modeling framework, the Connectivity Modeling System, for the analysis of network connectivity for 5 Caribbean coral reef-associated species in order to gauge similarities and dissimilarities among species as well as among Caribbean regions. We estimated local dispersal and retention to assess regional exchanges, and our results revealed that the population structures of coral and fish are different and should thus have dissimilar management requirements in many regions, with some notable exceptions. Populations of Porites astreoides corals appear fragmented, suggesting that loss of adult colonies in any region may significantly impact regional recruitment success and connectivity. At the other end of the spectrum, populations of bluehead wrasse Thalassoma bifasciatum are highly connected, and removal of adults in any single region would not imply future recruitment failure in that region. We suggest using a 'diversity of exogenous settlement' index as a proxy of recolonization potential, which is related to the stability of regional connectivity networks. We demonstrate that resolving multispecies larval transport dynamics helps identify regions of both network stability for multi-generational connectivity (e.g. stable larval sources and corridors) pertinent to regionallevel management and network inconsistencies among species which are pertinent to the success of local management. © the authors 2014. Open Access under Creative Commons by Attribution Licence.

Corals thrive in low nutrient environments and the conservation of these globally imperiled ecosystems is largely dependent on mitigating the effects of anthropogenic nutrient enrichment. However, to better understand the implications of anthropogenic nutrients requires a heightened understanding of baseline nutrient dynamics within these ecosystems. Here, we provide a novel perspective on coral reef nutrient dynamics by examining the role of fish communities in the supply and storage of nitrogen (N) and phosphorus (P). We quantified fish-mediated nutrient storage and supply for 144 species and modeled these data onto 172 fish communities (71 729 individual fish), in four types of coral reefs, as well as seagrass and mangrove ecosystems, throughout the Northern Antilles. Fish communities supplied and stored large quantities of nutrients, with rates varying among ecosystem types. The size structure and diversity of the fish communities best predicted N and P supply and storage and N : P supply, suggesting that alterations to fish communities (e.g. overfishing) will have important implications for nutrient dynamics in these systems. The stoichiometric ratio (N : P) for storage in fish mass (~8 : 1) and supply (~20 : 1) was notably consistent across the four coral reef types (but not seagrass or mangrove ecosystems). Published nutrient enrichment studies on corals show that deviations from this N : P supply ratio may be associated with poor coral fitness, providing qualitative support for the hypothesis that corals and their symbionts may be adapted to specific ratios of nutrient supply. Consumer nutrient stoichiometry provides a baseline from which to better understand nutrient dynamics in coral reef and other coastal ecosystems, information that is greatly needed if we are to implement more effective measures to ensure the future health of the world's oceans. © 2014 John Wiley & Sons Ltd.

Corals thrive in low nutrient environments and the conservation of these globally imperiled ecosystems is largely dependent on mitigating the effects of anthropogenic nutrient enrichment. However, to better understand the implications of anthropogenic nutrients requires a heightened understanding of baseline nutrient dynamics within these ecosystems. Here, we provide a novel perspective on coral reef nutrient dynamics by examining the role of fish communities in the supply and storage of nitrogen (N) and phosphorus (P). We quantified fish-mediated nutrient storage and supply for 144 species and modeled these data onto 172 fish communities (71 729 individual fish), in four types of coral reefs, as well as seagrass and mangrove ecosystems, throughout the Northern Antilles. Fish communities supplied and stored large quantities of nutrients, with rates varying among ecosystem types. The size structure and diversity of the fish communities best predicted N and P supply and storage and N : P supply, suggesting that alterations to fish communities (e.g. overfishing) will have important implications for nutrient dynamics in these systems. The stoichiometric ratio (N : P) for storage in fish mass (~8 : 1) and supply (~20 : 1) was notably consistent across the four coral reef types (but not seagrass or mangrove ecosystems). Published nutrient enrichment studies on corals show that deviations from this N : P supply ratio may be associated with poor coral fitness, providing qualitative support for the hypothesis that corals and their symbionts may be adapted to specific ratios of nutrient supply. Consumer nutrient stoichiometry provides a baseline from which to better understand nutrient dynamics in coral reef and other coastal ecosystems, information that is greatly needed if we are to implement more effective measures to ensure the future health of the world's oceans.

Ecosystem management is beset with potentially confusing terminology over the use of resilience, robustness and vulnerability. Here, we distinguish these concepts, discuss their operationalization, and identify the objectives that each is suited to. Resilience is useful when ecosystems risk losing the ability to recover and requires system modelling. Vulnerability can either be quantitative, measuring the ability of a system to remain above a critical threshold, or qualitative and used to evaluate the exposure of a system to disturbance and attributes that confer adaptive capacity and sensitivity to disturbance. As such, vulnerability is well-suited to assessments of coupled social-ecological systems. Robustness measures the ability of a system to maintain itself within a narrow range of function and is ideally suited to problems that require careful setting of upper and lower bounds for system properties, such as optimal fisheries yield. © 2013 Elsevier B.V.

Dominance shifts in ecosystems can occur rapidly, resulting in alternative stable states. While some coral reef ecosystems shift and recover relatively quickly, others recover slowly or not at all over periods of centuries. We explore the role of large (fishing-susceptible) parrotfish in triggering algal phase shifts as alternative attractors that may lock reefs into coral-depleted alternative stable states. We designed an experiment to modestly reduce herbivory only from large parrotfish in the immediate vicinity of experimental coral settlement nursery habitats. We used vertical pegs ('parrotfish deterrents' or PDs) around coral settlement plates on 2 Belizean fore reefs. Time-lapse videos and a year's accumulation of bite-marks on plates confirmed that only herbivory from large parrotfish declined significantly due to PDs. Patches of macroalgae developed around PDs reducing coral recruitment in this treatment only. Two dominant reefdwelling coral genera (Porites and Agaricia) recruited to our settlement plates. The fast-growing, high-light requiring, reef-building coral Porites was more negatively affected by phase shifts; this coral failed to recruit at and above mid-levels of algal abundance. We illustrate the direct roles eco logical processes such as herbivory from large parrotfish play in regulating algal abundance, which in turn reduces the recruitment potential of reefs and thus the ecosystem's capacity to recover. Combining our empirical results with an individually-based ecological simulation model, we determined that these processes cascade to drive alternative states and create a 'hysteresis' effect delaying or preventing recovery of the coral reef ecosystem. © Inter-Research 2014.

Even if carbon emissions are reduced drastically in the next decade the amount of carbon already stored in the atmosphere would lead to the occurrence of extreme thermal events every three to four years between 2040 and 2080. This time lag on the effect of reducing emissions suggests that the benefits of carbon emission reduction on the health of coral reefs will be noticeable only in the long term. Here, we use a spatially explicit ecosystem model to compare the potential ecosystem benefits that Caribbean and Pacific reefs could gain from reductions in carbon emissions, and the timescale of these benefits. We found that whereas the effect of a reduction in emissions on Caribbean reefs will be modest and realized only in the long term (more than 60 years), Pacific reefs would start to show benefits within the first half of this century. Moreover, it seems that Pacific reefs have the potential to maintain their ecological integrity and ecosystem state in the mid- to long term if carbon emissions are reduced, but only if plate-like corals are present.

Marine protected areas (MPAs) are key tools for combatting the global overexploitation of endangered species. The prevailing paradigm is that MPAs are beneficial in helping to restore ecosystems to more 'natural' conditions. However, MPAs may have unintended negative effects when increasing densities of protected species exert destructive effects on their habitat. Here, we report on severe seagrass degradation in a decade-old MPA where hyper-abundant green turtles adopted a previously undescribed below-ground foraging strategy. By digging for and consuming rhizomes and roots, turtles create abundant bare gaps, thereby enhancing erosion and reducing seagrass regrowth. A fully parametrized model reveals that the ecosystem is approaching a tipping point, where consumption overwhelms regrowth, which could potentially lead to complete collapse of the seagrass habitat. Seagrass recovery will not ensue unless turtle density is reduced to nearly zero, eliminating the MPA's value as a turtle reserve. Our results reveal an unrecognized, yet imminent threat to MPAs, as sea turtle densities are increasing at major nesting sites and the decline of seagrass habitat forces turtles to concentrate on the remaining meadows inside reserves. This emphasizes the need for policy and management approaches that consider the interactions of protected species with their habitat.

Marine protected areas (MPAs) are key tools for combatting the global overexploitation of endangered species. The prevailing paradigm is that MPAs are beneficial in helping to restore ecosystems to more 'natural' conditions. However, MPAs may have unintended negative effects when increasing densities of protected species exert destructive effects on their habitat. Here, we report on severe seagrass degradation in a decade-old MPA where hyper-abundant green turtles adopted a previously undescribed below-ground foraging strategy. By digging for and consuming rhizomes and roots, turtles create abundant bare gaps, thereby enhancing erosion and reducing seagrass regrowth. A fully parametrized model reveals that the ecosystem is approaching a tipping point, where consumption overwhelms regrowth, which could potentially lead to complete collapse of the seagrass habitat. Seagrass recovery will not ensue unless turtle density is reduced to nearly zero, eliminating the MPA's value as a turtle reserve. Our results reveal an unrecognized, yet imminent threat to MPAs, as sea turtle densities are increasing at major nesting sites and the decline of seagrass habitat forces turtles to concentrate on the remaining meadows inside reserves. This emphasizes the need for policy and management approaches that consider the interactions of protected species with their habitat.

Determining how ecosystem function and services are related to diversity is necessary for predicting the consequences of diversity loss and for setting goals and priorities for marine conservation. The consequences of biodiversity loss for ecosystem functions and services depend on the level of functional redundancy - the number of species with similar ecological functional traits. Using field data on fish assemblages from 199 coral reef and lagoon sites from six islands, and on local fisheries from four islands in the Bahamas, we examined levels of functional diversity and redundancy within these assemblages and determined how fish biomass and local fisheries catches vary with local diversity. A majority of functional groups contain few species, suggesting that these assemblages have limited functional redundancy. Most also include species targeted by local fisheries, thus fishing has the potential to broadly impact food webs. Comparisons between a large marine reserve and fished reefs confirm that fishing significantly reduces functional redundancy and removes whole functional groups. Positive exponential relationships of fish biomass and fisheries catches with species and functional diversity highlight that even small declines in biodiversity may result in large reductions in secondary production and seafood provision. Taken together, these results indicate that Caribbean fish assemblages have low functional redundancy and high vulnerability of ecosystem functions and services to diversity loss, and that protection of multi-species assemblages is needed to maintain functions and services. © 2014 Elsevier Ltd.

A one-dimensional wave model was used to investigate the reef top wave dynamics across a large suite of idealized reef-lagoon profiles, representing barrier coral reef systems under different sea-level rise (SLR) scenarios. The modeling shows that the impacts of SLR vary spatially and are strongly influenced by the bathymetry of the reef and coral type. A complex response occurs for the wave orbital velocity and forces on corals, such that the changes in the wave dynamics vary reef by reef. Different wave loading regimes on massive and branching corals also leads to contrasting impacts from SLR. For many reef bathymetries, wave orbital velocities increase with SLR and cyclonic wave forces are reduced for certain coral species. These changes may be beneficial to coral health and colony resilience and imply that predicting SLR impacts on coral reefs requires careful consideration of the reef bathymetry and the mix of coral species. © 2014 Elsevier Ltd.

A one-dimensional wave model was used to investigate the reef top wave dynamics across a large suite of idealized reef-lagoon profiles, representing barrier coral reef systems under different sea-level rise (SLR) scenarios. The modeling shows that the impacts of SLR vary spatially and are strongly influenced by the bathymetry of the reef and coral type. A complex response occurs for the wave orbital velocity and forces on corals, such that the changes in the wave dynamics vary reef by reef. Different wave loading regimes on massive and branching corals also leads to contrasting impacts from SLR. For many reef bathymetries, wave orbital velocities increase with SLR and cyclonic wave forces are reduced for certain coral species. These changes may be beneficial to coral health and colony resilience and imply that predicting SLR impacts on coral reefs requires careful consideration of the reef bathymetry and the mix of coral species.

Ecosystems are linked within landscapes by the physical and biological processes they mediate. In such connected landscapes, the response of one ecosystem to climate change could have profound consequences for neighbouring systems. Here, we report the first quantitative predictions of interdependencies between ecosystems in response to climate change. In shallow tropical marine ecosystems, coral reefs shelter lagoons from incoming waves, allowing seagrass meadows to thrive. Deepening water over coral reefs from sea-level rise results in larger, more energetic waves traversing the reef into the lagoon, potentially generating hostile conditions for seagrass. However, growth of coral reef such that the relative water depth is maintained could mitigate negative effects of sea-level rise on seagrass. Parameterizing physical and biological models for Lizard Island, Great Barrier Reef, Australia, we find negative effects of sea-level rise on seagrass before the middle of this century given reasonable rates of reef growth. Rates of vertical carbonate accretion typical of modern reef flats (up to 3 mm yr ̂'1) will probably be insufficient to maintain suitable conditions for reef lagoon seagrass under moderate to high greenhouse gas emissions scenarios by 2100. Accounting for interdependencies in ecosystem responses to climate change is challenging, but failure to do so results in inaccurate predictions of habitat extent in the future. © 2014 Macmillan Publishers Limited. All rights reserved.

Identification of critical life-stage habitats is key to successful conservation efforts. Juveniles of some species show great flexibility in habitat use while other species rely heavily on a restricted number of juvenile habitats for protection and food. Considering the rapid degradation of coastal marine habitats worldwide, it is important to evaluate which species are more susceptible to loss of juvenile nursery habitats and how this differs across large biogeographic regions. Here we used a meta-analysis approach to investigate habitat use by juvenile reef fish species in tropical coastal ecosystems across the globe. Densities of juvenile fish species were compared among mangrove, seagrass and coral reef habitats. In the Caribbean, the majority of species showed significantly higher juvenile densities in mangroves as compared to seagrass beds and coral reefs, while for the Indo-Pacific region seagrass beds harbored the highest overall densities. Further analysis indicated that differences in tidal amplitude, irrespective of biogeographic region, appeared to be the major driver for this phenomenon. In addition, juvenile reef fish use of mangroves increased with increasing water salinity. In the Caribbean, species of specific families (e.g. Lutjanidae, Haemulidae) showed a higher reliance on mangroves or seagrass beds as juvenile habitats than other species, whereas in the Indo-Pacific family-specific trends of juvenile habitat utilization were less apparent. The findings of this study highlight the importance of incorporating region-specific tidal inundation regimes into marine spatial conservation planning and ecosystem based management. Furthermore, the significant role of water salinity and tidal access as drivers of mangrove fish habitat use implies that changes in seawater level and rainfall due to climate change may have important effects on how juvenile reef fish use nearshore seascapes in the future.

Rapid sea level rise over the 21st century threatens coastal settlements and populations worldwide. Significant land-use policy reform will be needed to mitigate exposure to hazards in the coastal zone. Sea-level rise maps that indicate areas that are potentially prone to future inundation are a valuable tool for policymakers and decision makers. However, errors, assumptions, and uncertainties inherent in spatial data are not often explicitly recognised or communicated. In 2011, the state of Queensland, Australia, published a series of 'state of the art' sea-level rise maps as part of its coastal planning regime. This article uses the Queensland coastal planning regime as a case study to explore how errors, uncertainties and variability in physical, geographical and biological processes in the coastal zone pose challenges for policy makers. Analysis of the case study shows that the use of spatial data in sea-level rise policy formulation is complicated by the need to: (1) acknowledge and communicate uncertainties in existing and projected rates of rise; (2) engage in site-specific mapping based upon best available scientific information; (3) incorporate probabilities of extreme weather events; (4) resolve whether coastal engineering solutions should be included in mapping; (5) ensure that mapping includes areas required for future ecosystem migration; (6) manage discretion in planning and policy decision-making processes; (7) create flexible policies which can be updated in line with scientific developments; and (8) balance the need for consistency with the ability to apply developments in science and technology. Scientists working with spatial data and governments developing and implementing coastal planning policies can recognise, communicate, and seek to overcome uncertainty by addressing these factors.

Ecosystem management frequently aims to manage resilience yet measuring resilience has proven difficult. Here, we quantify the ecological resilience of the largest reef in the Caribbean and map potential benefits of marine reserves under two scenarios of greenhouse gas emissions. Resilience is calculated using spatial ecological models and defined as the probability of a reef remaining in its coral-dominated basin of attraction such that it does not flip into an alternate, algal-dominated attractor. In practice, resilience is the probability that coral populations will maintain the ability to exhibit a recovery trend after acute disturbances such as hurricanes. The inputs required to estimate resilience are a reef's initial state, physical environment, and disturbance regime. One major driver of reef resilience is herbivory by parrotfish and recent action to protect parrotfish in Belize was found to have increased resilience 6-fold. However, the expected benefits of parrotfish protection to future coral cover were relatively modest with only a 2- to 2.6-fold improvement over a business-as-usual scenario, demonstrating how resilience and ecosystem states are decoupled. Global action to reduce greenhouse gas emissions had little impact on average coral state unless it was accompanied by local controls of fishing. However, combined global and local action reduced the rate of reef degradation threefold. Operationalizing resilience explicitly integrates available biophysical data and accommodates the complex interactions among ecological processes and multiple types of disturbance. © 2013 Wiley Periodicals, Inc.

The 1997/1998 El Niño Southern Oscillation (ENSO) was the most severe coral bleaching event in recent history, resulting in the loss of 16 % of the world's coral reefs. Mortality was particularly severe in French Polynesia, where unprecedented mortality of massive Porites was observed in lagoonal sites of Rangiroa Atoll. To assess the recovery of massive Porites 15 years later, we resurveyed the size structure and extent of partial mortality of massive Porites at Tivaru (Rangiroa). Surveys revealed an abundance of massive Porites colonies rising from the shallow lagoonal floor. Colony width averaged 2.65 m, reaching a maximum of 7.1 m (estimated age of ~391 ± 107 years old). The relative cover of recently dead skeleton within quadrats declined from 42.8 % in 1998 to zero in 2013, yet the relative cover of old dead skeleton increased only marginally from 22.1 % in 1998 to 26.1 % in 2013. At a colony level, the proportion of Porites dominated by living tissue increased from 34.9 % in 1998 to 73.9 % in 2013, indicating rapid recovery of recent dead skeleton to living tissue rather than transitioning to old dead skeleton. Such rapid post-bleaching recovery is unprecedented in massive Porites and resulted from remarkable self-regeneration termed the 'Phoenix effect', whereby remnant cryptic patches of tissue that survived the 1997/1998 ENSO event regenerated and rapidly overgrew adjacent dead skeleton. Contrary to our earlier predictions, not only are large massive Porites relatively resistant to stress, they appear to have a remarkable capacity for recovery even after severe partial mortality. © 2014 Springer-Verlag Berlin Heidelberg.

Reef managers cannot fight global warming through mitigation at local scale, but they can use information on thermal patterns to plan for reserve networks that maximize the probability of persistence of their reef system. Here we assess previous methods for the design of reserves for climate change and present a new approach to prioritize areas for conservation that leverages the most desirable properties of previous approaches. The new method moves the science of reserve design for climate change a step forwards by: (1) recognizing the role of seasonal acclimation in increasing the limits of environmental tolerance of corals and ameliorating the bleaching response; (2) using the best proxy for acclimatization currently available; (3) including information from several bleaching events, which frequency is likely to increase in the future; (4) assessing relevant variability at country scales, where most management plans are carried out. We demonstrate the method in Honduras, where a reassessment of the marine spatial plan is in progress.

Factors affecting coral recruitment are critical in influencing the scope and rate of reef recovery after disturbance. In December 2012, super-typhoon Bopha caused immense damage to the eastern reefs of Palau, resulting in near complete loss of coral cover. Within weeks following the typhoon, an ephemeral monospecific bloom of the foliose red macroalga Liagora (up to 40 % cover in February 2013) was recorded at impacted reefs with moderate wave exposure. Conversely, impacted and un-impacted reefs in areas of low wave exposure remained Liagora free. To quantify the effect of this ephemeral macroalgal bloom on coral recruitment, we installed settlement tiles during the major spawning period (March-April 2013) at forereefs with and without Liagora. Reefs (n = 3) with Liagora (13-24 % cover in April) experienced an almost complete failure of settlement, with only two individual corals recorded on settlement tiles (n = 90). This settlement failure was unexpected, as tiles were situated adjacent to, and not within Liagora canopies. In contrast, settlement was significantly higher on reefs that lacked macroalgae (n = 3), ranging from an average of 0.5-2.5 and 2.7-18.9 individuals 25 cm-2 per top- and under-sided tile, respectively. Reefs with and without Liagora were in close proximity (≤8 km), and hydrodynamic models predicted that larval supply did not limit coral settlement among sites. While some differences in the community composition on the tiles were observed among sites, settlement substrate availability also did not limit coral settlement. Generalised linear mixed effects models indicated that while no settlement substrate explained more than 10 % of the variability in coral settlement, coral cover positively accounted for 26 %, and the cover of Liagora on reefs negatively accounted for more than 50 % of the observed variation. Combined, our results indicate that the typhoon induced ephemeral macroalgal bloom resulted in a reef-scale failure of coral settlement. © 2014 Springer-Verlag Berlin Heidelberg.

Measurements of coral structural strength are coupled with a fluid dynamics-structural analysis to investigate the resilience of coral to wave loading under sea level rise and a typical Great Barrier Reef lagoon wave climate. The measured structural properties were used to determine the wave conditions and flow velocities that lead to structural failure. Hydrodynamic modelling was subsequently used to investigate the type of the bathymetry where coral is most vulnerable to breakage under cyclonic wave conditions, and how sea level rise (SLR) changes this vulnerability. Massive corals are determined not to be vulnerable to wave induced structural damage, whereas branching corals are susceptible at wave induced orbital velocities exceeding 0.5. m/s. Model results from a large suite of idealised bathymetry suggest that SLR of 1. m or a loss of skeleton strength of order 25% significantly increases the area of reef flat where branching corals are exposed to damaging wave induced flows.

Measurements of coral structural strength are coupled with a fluid dynamics-structural analysis to investigate the resilience of coral to wave loading under sea level rise and a typical Great Barrier Reef lagoon wave climate. The measured structural properties were used to determine the wave conditions and flow velocities that lead to structural failure. Hydrodynamic modelling was subsequently used to investigate the type of the bathymetry where coral is most vulnerable to breakage under cyclonic wave conditions, and how sea level rise (SLR) changes this vulnerability. Massive corals are determined not to be vulnerable to wave induced structural damage, whereas branching corals are susceptible at wave induced orbital velocities exceeding 0.5m/s. Model results from a large suite of idealised bathymetry suggest that SLR of 1m or a loss of skeleton strength of order 25% significantly increases the area of reef flat where branching corals are exposed to damaging wave induced flows.

© 2014 the Author(s) Published by the Royal Society. All rights reserved.Climate-driven changes in biotic interactions can profoundly alter ecological communities, particularly when they impact foundation species. In marine systems, changes in herbivory and the consequent loss of dominant habitat forming species can result in dramatic community phase shifts, such as from coral to macroalgal dominance when tropical fish herbivory decreases, and from algal forests to 'barrens' when temperate urchin grazing increases. Here, we propose a novel phase-shift away from macroalgal dominance caused by tropical herbivores extending their range into temperate regions. We argue that this phase shift is facilitated by poleward-flowing boundary currents that are creating ocean warming hotspots around the globe, enabling the range expansion of tropical species and increasing their grazing rates in temperate areas. Overgrazing of temperate macroalgae by tropical herbivorous fishes has already occurred in Japan and the Mediterranean. Emerging evidence suggests similar phenomena are occurring in other temperate regions, with increasing occurrence of tropical fishes on temperate reefs.

Climate-driven changes in biotic interactions can profoundly alter ecological communities, particularly when they impact foundation species. In marine systems, changes in herbivory and the consequent loss of dominant habitat forming species can result in dramatic community phase shifts, such as from coral to macroalgal dominance when tropical fish herbivory decreases, and from algal forests to 'barrens' when temperate urchin grazing increases. Here, we propose a novel phase-shift away from macroalgal dominance caused by tropical herbivores extending their range into temperate regions. We argue that this phase shift is facilitated by poleward-flowing boundary currents that are creating ocean warming hotspots around the globe, enabling the range expansion of tropical species and increasing their grazing rates in temperate areas. Overgrazing of temperate macroalgae by tropical herbivorous fishes has already occurred in Japan and the Mediterranean. Emerging evidence suggests similar phenomena are occurring in other temperate regions, with increasing occurrence of tropical fishes on temperate reefs.

Efforts to conserve marine biodiversity must move beyond conserving individual species within protected areas and seek to preserve the functional roles that species perform in ecosystems across seascapes. For instance, herbivorous and predatory (including invertebrate-feeding) fish are critical for maintaining coralreef habitat and the diversity of dependent fish assemblages. However, increasing the biomasses of fished species may come at a cost to fisheries. Using coral reefs as an example, we examined critical functional roles and model trade-offs between fishery profits and the spatial extent of functional fish communities. The nature of the trade-off depended on the management scenario: protecting functions in small areas could be achieved with marine reserves at minimal cost to fisheries, whereas reducing fishing effort was a more effective method for protecting functional communities across a seascape. An appropriate choice of management actions can alter the trade-off and, in doing so, ameliorate potential for conflict with resource users. © the Ecological Society of America.

Over 1.3 billion people live on tropical coasts, primarily in developing countries. Many depend on adjacent coastal seas for food, and livelihoods. We show how trends in demography and in several local and global anthropogenic stressors are progressively degrading capacity of coastal waters to sustain these people. Far more effective approaches to environmental management are needed if the loss in provision of ecosystem goods and services is to be stemmed. We propose expanded use of marine spatial planning as a framework for more effective, pragmatic management based on ocean zones to accommodate conflicting uses. This would force the holistic, regional-scale reconciliation of food security, livelihoods, and conservation that is needed. Transforming how countries manage coastal resources will require major change in policy and politics, implemented with sufficient flexibility to accommodate societal variations. Achieving this change is a major challenge - one that affects the lives of one fifth of humanity. © 2014 the Authors.

Over 1.3 billion people live on tropical coasts, primarily in developing countries. Many depend on adjacent coastal seas for food, and livelihoods. We show how trends in demography and in several local and global anthropogenic stressors are progressively degrading capacity of coastal waters to sustain these people. Far more effective approaches to environmental management are needed if the loss in provision of ecosystem goods and services is to be stemmed. We propose expanded use of marine spatial planning as a framework for more effective, pragmatic management based on ocean zones to accommodate conflicting uses. This would force the holistic, regional-scale reconciliation of food security, livelihoods, and conservation that is needed. Transforming how countries manage coastal resources will require major change in policy and politics, implemented with sufficient flexibility to accommodate societal variations. Achieving this change is a major challenge - one that affects the lives of one fifth of humanity.

Coral reefs face a diverse array of threats, from eutrophication and overfishing to climate change. As live corals are lost and their skeletons eroded, the structural complexity of reefs declines. This may have important consequences for the survival and growth of reef fish because complex habitats mediate predator-prey interactions [1, 2] and influence competition [3-5] through the provision of prey refugia. A positive correlation exists between structural complexity and reef fish abundance and diversity in both temperate and tropical ecosystems [6-10]. However, it is not clear how the diversity of available refugia interacts with individual predator-prey relationships to explain emergent properties at the community scale. Furthermore, we do not yet have the ability to predict how habitat loss might affect the productivity of whole reef communities and the fisheries they support. Using data from an unfished reserve in the Bahamas, we find that structural complexity is associated not only with increased fish biomass and abundance, but also with nonlinearities in the size spectra of fish, implying disproportionately high abundances of certain size classes. By developing a size spectrum food web model that links the vulnerability of prey to predation with the structural complexity of a reef, we show that these nonlinearities can be explained by size-structured prey refugia that reduce mortality rates and alter growth rates in different parts of the size spectrum. Fitting the model with data from a structurally complex habitat, we predict that a loss of complexity could cause more than a 3-fold reduction in fishery productivity. Video Abstract © 2014 Elsevier Ltd.

Coral reefs face a diverse array of threats, from eutrophication and overfishing to climate change. As live corals are lost and their skeletons eroded, the structural complexity of reefs declines. This may have important consequences for the survival and growth of reef fish because complex habitats mediate predator-prey interactions [1, 2] and influence competition [3-5] through the provision of prey refugia. A positive correlation exists between structural complexity and reef fish abundance and diversity in both temperate and tropical ecosystems [6-10]. However, it is not clear how the diversity of available refugia interacts with individual predator-prey relationships to explain emergent properties at the community scale. Furthermore, we do not yet have the ability to predict how habitat loss might affect the productivity of whole reef communities and the fisheries they support. Using data from an unfished reserve in the Bahamas, we find that structural complexity is associated not only with increased fish biomass and abundance, but also with nonlinearities in the size spectra of fish, implying disproportionately high abundances of certain size classes. By developing a size spectrum food web model that links the vulnerability of prey to predation with the structural complexity of a reef, we show that these nonlinearities can be explained by size-structured prey refugia that reduce mortality rates and alter growth rates in different parts of the size spectrum. Fitting the model with data from a structurally complex habitat, we predict that a loss of complexity could cause more than a 3-fold reduction in fishery productivity.

Earth system models (ESMs) provide high resolution simulations of variables such as sea surface temperature (SST) that are often used in off-line biological impact models. Coral reef modellers have used such model outputs extensively to project both regional and global changes to coral growth and bleaching frequency. We assess model skill at capturing sub-regional climatologies and patterns of historical warming. This study uses an established wavelet-based spatial comparison technique to assess the skill of the coupled model intercomparison project phase 5 models to capture spatial SST patterns in coral regions. We show that models typically have medium to high skill at capturing climatological spatial patterns of SSTs within key coral regions, with model skill typically improving at larger spatial scales (≥4°). However models have much lower skill at modelling historical warming patters and are shown to often perform no better than chance at regional scales (e.g. Southeast Asian) and worse than chance at finer scales (

Coral reefs face multiple anthropogenic threats, from pollution and overfishing to the dual effects of greenhouse gas emissions: rising sea temperature and ocean acidification. While the abundance of coral has declined in recent decades, the implications for humanity are difficult to quantify because they depend on ecosystem function rather than the corals themselves. Most reef functions and ecosystem services are founded on the ability of reefs to maintain their three-dimensional structure through net carbonate accumulation. Coral growth only constitutes part of a reef's carbonate budget; bioerosion processes are influential in determining the balance between net structural growth and disintegration. Here, we combine ecological models with carbonate budgets and drive the dynamics of Caribbean reefs with the latest generation of climate models. Budget reconstructions using documented ecological perturbations drive shallow (6-10 m) Caribbean forereefs toward an increasingly fragile carbonate balance. We then projected carbonate budgets toward 2080 and contrasted the benefits of local conservation and global action on climate change. Local management of fisheries (specifically, no-take marine reserves) and the watershed can delay reef loss by at least a decade under "business-as-usual" rises in greenhouse gas emissions. However, local action must be combined with a low-carbon economy to prevent degradation of reef structures and associated ecosystem services.

The detrimental effect of climate change induced bleaching on Caribbean coral reefs has been widely documented in recent decades. Several studies have suggested that increases in the abundance of thermally tolerant endosymbionts may ameliorate the effect of climate change on reefs. Symbionts that confer tolerance to temperature also reduce the growth rate of their coral host. Here, we show, using a spatial ecosystem model, that an increment in the abundance of a thermally tolerant endosymbiont (D1a) is unlikely to ensure the persistence of Caribbean reefs, or to reduce their rate of decline, due to the concomitant reduction in growth rate under current thermal stress predictive scenarios. Furthermore, our results suggest that given the documented vital rates of D1a-dominated corals, increasing dominance of D1a in coral hosts may have a detrimental effect by reducing the resilience of Caribbean reefs, and preventing their long-term recovery. This is because Caribbean ecosystems appear to be highly sensitive to changes in the somatic growth rate of corals. Alternative outcomes might be expected in systems with different community-level dynamics such as reefs in the Indo-Pacific, where the ecological costs of reduced growth rate might be far smaller. © 2012 Blackwell Publishing Ltd.

The distribution and abundance of seagrass ecosystems could change significantly over the coming century due to sea level rise (SLR). Coastal managers require mechanistic understanding of the processes affecting seagrass response to SLR to maximize their conservation and associated provision of ecosystem services. In Moreton Bay, Queensland, Australia, vast seagrass meadows supporting populations of sea turtles and dugongs are juxtaposed with the multiple stressors associated with a large and rapidly expanding human population. Here, the interactive effects of predicted SLR, changes in water clarity, and land use on future distributions of seagrass in Moreton Bay were quantified. A habitat distribution model of present day seagrass in relation to benthic irradiance and wave height was developed which correctly classified habitats in 83% of cases. Spatial predictions of seagrass and presence derived from the model and bathymetric data were used to initiate a SLR inundation model. Bathymetry was iteratively modified based on SLR and sedimentary accretion in seagrass to simulate potential seagrass habitat at 10 year time steps until 2100. The area of seagrass habitat was predicted to decline by 17% by 2100 under a scenario of SLR of 1.1 m. A scenario including the removal of impervious surfaces, such as roads and houses, from newly inundated regions, demonstrated that managed retreat of the shoreline could potentially reduce the overall decline in seagrass habitat to just 5%. The predicted reduction in area of seagrass habitat could be offset by an improvement in water clarity of 30%. Greater improvements in water clarity would be necessary for larger magnitudes of SLR. Management to improve water quality will provide present and future benefits to seagrasses under climate change and should be a priority for managers seeking to compensate for the effects of global change on these valuable habitats. © 2013 John Wiley & Sons Ltd.

The distribution and abundance of seagrass ecosystems could change significantly over the coming century due to sea level rise (SLR). Coastal managers require mechanistic understanding of the processes affecting seagrass response to SLR to maximize their conservation and associated provision of ecosystem services. In Moreton Bay, Queensland, Australia, vast seagrass meadows supporting populations of sea turtles and dugongs are juxtaposed with the multiple stressors associated with a large and rapidly expanding human population. Here, the interactive effects of predicted SLR, changes in water clarity, and land use on future distributions of seagrass in Moreton Bay were quantified. A habitat distribution model of present day seagrass in relation to benthic irradiance and wave height was developed which correctly classified habitats in 83% of cases. Spatial predictions of seagrass and presence derived from the model and bathymetric data were used to initiate a SLR inundation model. Bathymetry was iteratively modified based on SLR and sedimentary accretion in seagrass to simulate potential seagrass habitat at 10 year time steps until 2100. The area of seagrass habitat was predicted to decline by 17% by 2100 under a scenario of SLR of 1.1 m. A scenario including the removal of impervious surfaces, such as roads and houses, from newly inundated regions, demonstrated that managed retreat of the shoreline could potentially reduce the overall decline in seagrass habitat to just 5%. The predicted reduction in area of seagrass habitat could be offset by an improvement in water clarity of 30%. Greater improvements in water clarity would be necessary for larger magnitudes of SLR. Management to improve water quality will provide present and future benefits to seagrasses under climate change and should be a priority for managers seeking to compensate for the effects of global change on these valuable habitats.

Nominally herbivorous fish play a variety of functional roles that are important in maintaining coral reef resilience, yet are major targets of spear fisheries in Micronesia. Although protection is afforded to iconic species in some areas, impacts of the fishery on the ecosystem are poorly understood. The goal of this study was to locate the major potential ecological threats from the fishery by integrating catch data with species-specific metrics of ecological importance and vulnerability to fishing. Region-wide and country-specific grounds for ecological concern were identified. The heavy exploitation of Naso unicornis was the most serious regional concern-not only was it the most vulnerable species involved in the fishery, but it plays a low-redundancy functional role (i.e. macroalgal browsing) in the ecosystem. The parrotfishes Cetoscarus bicolor, Scarus rubroviolaceus and Chlorurus microrhinos were also implicated in ecological risks (most noticeable in Palau), and the large proportion of immature catch aggravated the concerns found in Pohnpei. An interview-based assessment of species desirability among fishers highlighted the challenges managers may meet locally in diverting attention away from heavily harvested species. Opportunities to alleviate the ecological risks posed by a significant sector of the Micronesian fisheries were identified. Inducing changes in fishers' targeting behaviour towards opportunis - tically-caught species may prove feasible in most countries, and if enacted, may reduce fishing pressure in low-redundancy functional roles. The effectiveness of the policy options supported by the present approach in sustaining reef function and resilience has yet to be assessed. However, we anticipate that informing fishers about the implications of their selectivity may achieve tangible progress in conservation of the species. Therefore, policies which moderate catch rates of highly desirable species, as well as efforts to promote more conscious targeting behaviours, may complement the benefits of the existing networks of marine protected areas. © Inter-Research 2013.

A process-orientated understanding of ecosystems usually starts with an exploratory analysis of empirical relationships among potential drivers and state variables. While relationships among herbivory, algal cover, and coral recruitment, have been explored in the Caribbean, the nature of such relationships in the Pacific appears to be variable or unclear. Here, we examine potential drivers structuring the benthos and herbivorous fish assemblages of outer-shelf reefs in Micronesia (Palau, Guam and Pohnpei). Surveys were stratified by wave exposure and protection from fishing. High biomass of most herbivores was favoured by high wave exposure. High abundance of large-bodied scarids was associated with low turf abundance, high coral cover, and marine reserves. The remaining herbivores were more abundant in reefs with low coral cover, possibly because space and hence food limitation occur in high-coral-cover reefs. Rugosity had no detectable effect on herbivorous fish abundance once differences in exposure and coral cover were accounted for. At identical depths, high wave exposure was associated with greater volumes (cover × canopy height) of macroalgae and algal turfs, which most likely resulted from high primary productivity driven by flow. In exposed areas, macroalgal cover declined as the acanthurid biomass increased. The volume of algal turfs was negatively associated with coral cover and herbivore biomass. In turn, high coral cover and herbivore biomass are likely to intensify grazing. The density of juvenile corals was variable where macroalgal cover was low but was confined to lower densities where macroalgal cover was high. High coral cover and density of juvenile corals were favoured in sheltered habitats. While a weak positive relationship was found between scarid biomass and juvenile coral density, we hypothesise that high scarid densities may hinder juvenile density through increased corallivory. New hypotheses emerged that will help clarify the role of acanthurids, wave exposure, and corallivory in driving the recovery of Pacific coral communities. © 2012 Springer-Verlag Berlin Heidelberg.

Synthesis Coral reefs are widely thought to exhibit multiple attractors which have profound implications for people that depend on them. If reefs become 'stuck' within a self-reinforcing state dominated by seaweed, it becomes disproportionately difficult and expensive for managers to shift the system back towards its natural, productive, coral state. The existence of multiple attractors is controversial. We assess various forms of evidence and conclude that there remains no incontrovertible proof of multiple attractors on reefs. However, the most compelling evidence, which combines ecological models and field data, is far more consistent with multiple attractors than the competing hypothesis of only a single, coral attractor. Managers should exercise caution and assume that degraded reefs can become stuck there. Testing for the existence of alternate attractors in ecosystems that possess slow dynamics and frequent pulse perturbation is exceptionally challenging. Coral reefs typify such conditions and the existence of alternate attractors is controversial. We analyse different forms of evidence and assess whether they support or challenge the existence of multiple attractors on Caribbean reefs, many of which have shown profound phase shifts in community structure from coral to algal dominance. Field studies alone provide no insight into multiple attractors because the non-equilibrial nature of reef dynamics prevents equilibria from being observed. Statistical models risk failing to sample the parameter space in which multiple attractors occur, and have failed to account for the confounding effects of heterogeneous environments, anthropogenic drivers (e.g. fishing), and major disturbances (e.g. hurricanes). Simple and complex models all find multiple attractors over some - though not all - regions of a system driver (fishing). Tests of model predictions with field data closely match theory of alternate attractors but a forward-leaning monotonic curve with only a single attractor can also be fitted to these data. Deeper consideration of the assumptions of this monotonic relationship reveal significant ecological problems which disappear under a model of multiple attractors. To date, there is no evidence against the existence of multiple attractors on Caribbean reefs and while there remains no definitive proof, the balance of evidence and ecological reasoning favours their existence. Theory predicts that Caribbean reefs do not exhibit alternate attractors in their natural state but that disease-induced loss of two key functional groups has generated bistability. Whether alternate attractors becomes a persistent element of reef dynamics or a brief moment in their geological history will depend, in part, on the ability of functional groups to recover and the impacts of climate change and ocean acidification on coral growth and mortality. © 2012 the Authors. Oikos © 2012 Nordic Society Oikos.

Summary: with ever-increasing human pressure on ecosystems, it is critically important to predict how ecosystem functions will respond to such human-induced perturbations. We define perturbations as either changes to abiotic environment (e.g. eutrophication, climate change) that indirectly affects biota, or direct changes to biota (e.g. species introductions). While two lines of research in ecology, biodiversity-ecosystem function (BDEF) and ecological resilience (ER) research, have addressed this issue, both fields of research have nontrivial shortcomings in their abilities to address a wide range of realistic scenarios. We outline how an integrated research framework may foster a deeper understanding of the functional consequences of perturbations via simultaneous application of (i) process-based mechanistic predictions using trait-based approaches and (ii) detection of empirical patterns of functional changes along real perturbation gradients. In this context, the complexities of ecological interactions and evolutionary perspectives should be integrated into future research. Synthesis and applications. Management of human-impacted ecosystems can be guided most directly by understanding the response of ecosystem functions to controllable perturbations. In particular, we need to characterize the form of a wide range of perturbation-function relationships and to draw connections between those patterns and the underlying ecological processes. We anticipate that the integrated perspectives will also be helpful for managers to derive practical implications for management from academic literature. Management of human-impacted ecosystems can be guided most directly by understanding the response of ecosystem functions to controllable perturbations. In particular, we need to characterize the form of a wide range of perturbation-function relationships and to draw connections between those patterns and the underlying ecological processes. We anticipate that the integrated perspectives will also be helpful for managers to derive practical implications for management from academic literature. © 2013 British Ecological Society.

K-selected species with low rates of sexual recruitment may utilise storage effects where low adult mortality allows a number of individuals to persist through time until a favourable recruitment period occurs. Alternative methods of recruitment may become increasingly important for such species if the availability of favourable conditions for sexual recruitment decline under rising anthropogenic disturbance and climate change. Here, we test the hypotheses that asexual dispersal is an integral life history strategy not only in branching corals, as previously reported, but also in a columnar, 'K-selected' coral species, and that its prevalence is driven by the frequency of severe hurricane disturbance. Montastraea annularis is a long-lived major frame-work builder of Caribbean coral reefs but its survival is threatened by the consequences of climate induced disturbance, such as bleaching, ocean acidification and increased prevalence of disease. 700 M. annularis samples from 18 reefs within the Caribbean were genotyped using six polymorphic microsatellite loci. We demonstrate that asexual reproduction occurs at varying frequency across the species-range and significantly contributes to the local abundance of M. annularis, with its contribution increasing in areas with greater hurricane frequency. We tested several competing hypotheses that might explain the observed pattern of genotypic diversity. 64% of the variation in genotypic diversity among the sites was explained by hurricane incidence and reef slope, demonstrating that large-scale disturbances combine with local habitat characteristics to shape the balance between sexual and asexual reproduction in populations of M. annularis.

Clionaids are important competitors and bio-eroding agents on coral reefs; however, little is known of their biology. We studied aspects of life history of Cliona tenuis, in particular its sexual reproduction and growth. Temporal variations in these traits were studied over a year, in correlation with water temperature as a proxy for seasonality. Growth and sexual reproduction occurred at separate times and followed intra-annual variations in temperature. Growth increased during the warmest months of the year, reaching an average rate of 29.9 ± 6.7 mm during 286 days. Cliona tenuis is oviparous, and the results suggest gonochorism. Gametogenesis occurred between the coldest months and the period when temperature was increasing. Recruitment was constant throughout the year, possibly associated with post-settlement processes. Juvenile-size individuals were represented in the studied population, suggesting that processes like competition and mortality may control the population, whose size structure may be sustained by high recruitment rates. © 2013 © Taylor and Francis Group.

Small grazing motile epifaunal invertebrates play an important ecosystem role on coral reefs, influencing both the abundance and composition of macroalgal communities and acting as a key food source for a range of predatory fishes. The first aim of this study was to investigate the associations between motile epifaunal communities and four common macroalgal species (Lobophora variegata, Dictyota divaricata, Microdictyon marinum and Halimeda opuntia) on fore-reef environments in the Exuma Cays (Bahamas, wider Caribbean). Secondly, we investigated the implications of the well documented rise of Caribbean macroalgal cover on invertebrate densities by surveying sites inside and outside the Exuma Cays Land and Sea Park (ECLSP), where increases in parrotfish grazing intensity inside the marine reserves have led to reductions in macroalgal cover. Therefore, surveys compared similar reefs with significantly different macrolagal cover. Comparisons between macroalgal species revealed a four to fivefold difference in motile epifaunal densities per unit volume of macroalgae. Post-hoc tests revealed that this difference was significant only for Lobophora, with no difference observed among the other species. As macroalgae provide both a refuge from predation and a food source for grazing epifauna, the higher densities of epifauna observed in Lobophora may be attributed to either refuge from visual predators through morphological features (high cover of overlapping blades close to the substrate) or lack of palatability for parrotfish grazing, providing a more stable refuge. Our results revealed no significant differences in diversity, density or community structure of motile epifauna per unit volume of macroalgae between sites inside and outside the ECLSP. Since canopy height and invertivore biomass did not vary systematically across reserve boundaries, this suggests that algal cover does not affect the density of epifaunal invertebrates. However, areal cover was consistently higher for all macroalgal species at sites outside the ECLSP than those inside the reserve. Therefore, when scaled by aerial cover of macroalgae, total abundance of epifauna was twofold higher outside the ECLSP. We suggest that the increasing abundance of macroalgae on Caribbean reefs may be having dramatic effects on epifaunal invertebrate populations and potentially their ecological functions. © 2013 Blackwell Verlag GmbH.

Growing concern about biodiversity loss underscores the need to quantify and understand temporal change. Here, we review the opportunities presented by biodiversity time series, and address three related issues: (i) recognizing the characteristics of temporal data; (ii) selecting appropriate statistical procedures for analysing temporal data; and (iii) inferring and forecasting biodiversity change. With regard to the first issue, we draw attention to defining characteristics of biodiversity time series--lack of physical boundaries, uni-dimensionality, autocorrelation and directionality--that inform the choice of analytic methods. Second, we explore methods of quantifying change in biodiversity at different timescales, noting that autocorrelation can be viewed as a feature that sheds light on the underlying structure of temporal change. Finally, we address the transition from inferring to forecasting biodiversity change, highlighting potential pitfalls associated with phase-shifts and novel conditions.

Growing concern about biodiversity loss underscores the need to quantify and understand temporal change. Here, we review the opportunities presented by biodiversity time series, and address three related issues: (i) recognizing the characteristics of temporal data; (ii) selecting appropriate statistical procedures for analysing temporal data; and (iii) inferring and forecasting biodiversity change. With regard to the first issue, we draw attention to defining characteristics of biodiversity time series--lack of physical boundaries, uni-dimensionality, autocorrelation and directionality--that inform the choice of analytic methods. Second, we explore methods of quantifying change in biodiversity at different timescales, noting that autocorrelation can be viewed as a feature that sheds light on the underlying structure of temporal change. Finally, we address the transition from inferring to forecasting biodiversity change, highlighting potential pitfalls associated with phase-shifts and novel conditions.

Ecosystem engineers that create habitats facilitate the coexistence of many interacting species. This biotic response to habitat engineering may result in non-intuitive cascading interactions, potentially including feedbacks to the engineer. Such feedback mechanisms, either positive or negative, may be especially important for the maintenance of biogenic habitats and their community-wide facilitation. Here, we describe the complex interactions and feedbacks that link marine habitat-forming engineers, the reef-building corals, and a group of herbivores, the parrotfishes; the latter preventing the overgrowth of macroalgae, a major competitor of corals. Using density data of eight parrotfish species on a Caribbean reef, we first describe the form of the response of parrotfish abundance to increasing topographic complexity generated by coral growth. Topographic complexity enhanced parrotfish abundance by promoting habitat suitability, but the shape (linear vs asymptotic) and strength of this response varied across species and size. Parrotfish grazing intensity, estimated from data on abundance and species-, size- and life phase-specific grazing rates also increased with topographic complexity despite an increase in the surface area over which parrotfish graze. Depending on fish species, this functional response was found to be linear or asymptotic. Using a simple analytical model we then explored the effects of topographic complexity and fishing pressure on coral-algal competition, with particular emphasis on the implications of non-linearities in the intensity of grazing. Simulations demonstrate that fishing and habitat degradation impair the performance of grazing, but that an asymptotic response of grazing intensity to topographic complexity increases the ecological resilience of coral reefs. Parrotfish and corals are mutually beneficial by creating a loop of positive, indirect feedbacks that maintain their own structure and function: coral growth promotes habitat suitability for parrotfish, concordantly enhancing grazing intensity, which in turn facilitates coral growth by reducing competitive exclusion by macroalgae. We conclude that the resilience of biogenic habitats is enhanced by non-linear biotic responses to engineering and by the emergence of reciprocal facilitation linking habitat engineering and response organisms. © 2012 the Authors. Oikos © 2012 Nordic Society Oikos.

Ocean temperature increase is recognised as one of the major threats to the future of coral reefs. During the past 50. years, global mean temperatures have risen by 0.13. °C/decade, but in the Caribbean warming trends are greater, and are of the order of 0.29. °C/decade. In light of this threat, some researchers have proposed that reefs may survive better in locations of naturally low thermal stress, and have hypothesised that such refugia may be located in: (1) deep areas; (2) areas of high currents; (3) upwelling; and (4) high-latitude areas. These regions have been targeted as priorities for conservation activities; however, with the exception of deep reefs, formal assessment of the efficacy of these potential refugia is lacking. Here we tested the three remaining hypotheses in the wider Caribbean region using remotely sensed data and hydrodynamic model outputs. We began by determining the location of the hypothesised refugia, and then quantified the extent to which they minimise acute and chronic thermal stress in a significant and consistent manner through time. Furthermore, recognising the increasing sea warming and the concern that high temperatures could frequently exceed lethal thresholds for many organisms in the future, we assessed the ability of these areas to slow the rates of increase of temperatures. We show that the proposed areas do not constitute meaningful refugia from acute thermal stress. However, upwelling areas in the Caribbean have conservation utility because rates of thermal warming are lower. © 2013 Elsevier Ltd.

Understanding patterns of connectivity among populations of marine organisms is essential for the development of realistic, spatially explicit models of population dynamics. Two approaches, empirical genetic patterns and oceanographic dispersal modelling, have been used to estimate levels of evolutionary connectivity among marine populations but rarely have their potentially complementary insights been combined. Here, a spatially realistic Lagrangian model of larval dispersal and a theoretical genetic model are integrated with the most extensive study of gene flow in a Caribbean marine organism. The 871 genets collected from 26 sites spread over the wider Caribbean subsampled 45.8% of the 1900 potential unique genets in the model. At a coarse scale, significant consensus between modelled estimates of genetic structure and empirical genetic data for populations of the reef-building coral Montastraea annularis is observed. However, modelled and empirical data differ in their estimates of connectivity among northern Mesoamerican reefs indicating that processes other than dispersal may dominate here. Further, the geographic location and porosity of the previously described east-west barrier to gene flow in the Caribbean is refined. A multi-prong approach, integrating genetic data and spatially realistic models of larval dispersal and genetic projection, provides complementary insights into the processes underpinning population connectivity in marine invertebrates on evolutionary timescales.

No-take marine fishery reserves sustain commercial stocks by acting as buffers against overexploitation and enhancing fishery catches in adjacent areas through spillover. Likewise, nursery habitats such as mangroves enhance populations of some species in adjacent habitats. However, there is lack of understanding of the magnitude of stock enhancement and the effects on community structure when both protection from fishing and access to nurseries concurrently act as drivers of fish population dynamics. In this study we test the separate as well as interactive effects of marine reserves and nursery habitat proximity on structure and abundance of coral reef fish communities. Reserves had no effect on fish community composition, while proximity to nursery habitat only had a significant effect on community structure of species that use mangroves or seagrass beds as nurseries. In terms of reef fish biomass, proximity to nursery habitat by far outweighed (biomass 249% higher than that in areas with no nursery access) the effects of protection from fishing in reserves (biomass 21% lower than non-reserve areas) for small nursery fish (≤ 25 cm total length). For large-bodied individuals of nursery species (>25 cm total length), an additive effect was present for these two factors, although fish benefited more from fishing protection (203% higher biomass) than from proximity to nurseries (139% higher). The magnitude of elevated biomass for small fish on coral reefs due to proximity to nurseries was such that nursery habitats seem able to overrule the usually positive effects on fish biomass by reef reserves. As a result, conservation of nursery habitats gains importance and more consideration should be given to the ecological processes that occur along nursery-reef boundaries that connect neighboring ecosystems.

A generic method was developed for analysing the capabilities of optical remote sensing of aquatic systems in terms of environmental components and imaging sensor configurations. The method was based on a component based model of the entire system in which not only benthic composition but other environmental components such as water inherent optical properties (IOPs), bathymetry, sun elevation, wind speed and sensor noise characteristics were defined by datasets with the potential to include across-image variation. The model was applied to data from Pacific Ocean reefs in an airborne sensor context to estimate the primary environmental or sensor factors confounding discrimination of benthic mixtures of key reef types: live coral, bleached coral, dead coral and macroalgae. Results indicate that spectral variation of benthic types and sub-pixel mixing is the primary limiting factor for benthic mapping objectives, whereas instrument noise levels are a minor factor. © 2012 by the authors.

The fishing down of marine food webs has been described in pelagic and demersal systems but rarely documented in coral reef environments. We recorded a rapid shift in fish community structure in Belize that accompanied a marked decline in grouper and snapper abundance and a switch towards smaller, less desirable, herbivorous parrotfishes. In a 6 to 7 yr period (2002-2008/09), observations of large-bodied grouper (Serranidae) declined significantly from an encounter probability of 21% per 200 m2 transect to just 2%. The biomass of carnivorous snappers (Lutjanidae) underwent a 7-fold decline, primarily in the species Ocyurus chrysurus. During this period, the inclusion of parrotfish in fish catches at nearby Glover's Atoll increased from a frequency of 6% in 2004 to ∼20% of speared individuals by 2008. Parrotfish biomass declined by 41% between 2002 and 2008/09, with a major decline in the large and dominant herbivore Sparisoma viride. No changes in parrotfish biomass were detectable in nearby marine reserves during this time. Several important indirect effects of fishing were observed. The biomass of mesopredators including Cephalopholis fulvus, C. cruentatus, and Epinephelus guttatus increased dramatically by 880% as compared to the 2002 levels. We putatively attribute this response to a release from predation and constraints to foraging behaviour imposed by large serranids. Further, we find that the density of adult damselfish of the species Stegastes planifrons and S. partitus decreased by ∼45%. We attribute this decline to elevated predation by the increased densities of mesopredators, which have been shown to prey upon juvenile damselfish. No change in damselfish densities was found at 2 control locations where fishing was prohibited. The decline in parrotfish in the central Mesoamerican barrier reef likely accounts for recent anecdotal observations of Halimeda tuna spreading to microhabitats that have previously been grazed intensively. While these results imply that the resilience of these reefs may be seriously impaired, the Belize Government has recently enacted new legislation to improve the management of grouper and outlaw harvesting of most herbivorous fish. © Inter-Research 2012.

The great sensitivity of coral reefs to climate change has raised concern over their resilience. An emerging body of resilience theory stems largely from research carried out in a single biogeographic region; the Caribbean. Such geographic bias raises the question of transferability of concepts among regions. In this article, we identify factors that might predispose the Caribbean to its low resilience, including faster rates of macroalgal growth, higher rates of algal recruitment, basin-wide iron-enrichment of algal growth from aeolian dust, a lack of acroporid corals, lower herbivore biomass and missing groups of herbivores. Although mechanisms of resilience are likely to be ubiquitous, our analysis suggests that Indo-Pacific reefs would have to be heavily degraded to exhibit bistability or undergo coral-macroalgal phase shifts.

Clionaids, an abundant group of bioeroding sponges, are important competitors of corals, but their interactions with other major taxa are poorly understood. This study examined the relative effect of predation and macroalgal competition on the growth of Cliona tenuis at Glover's Reef Atoll, Belize. A field experiment was designed to isolate the importance of each factor and its interactions, by means of exclusion cages to assess the effects of fish predators, and algal transplantation to assess the effects of macroalgal competition (Lobophora variegata), over 286 d. To obtain complementary data on the net outcome of predation and competition in situ, predation intensity and the competitive effects on C. tenuis of 5 different competitors were monitored in the field. Competition with macroalgae significantly reduced the size of the sponge by 38 ± 11% (SE). Despite a high predation rate (1 bite 100 cm-2 h-1), no effect of the interaction of predation with macroalgal competition was detected. The in situ observations found that L. variegata was the strongest competitor limiting the growth of C. tenuis. Overgrowth of corals by clionaids and macroalgae continues to be a matter of concern, but our results suggest that the antagonistic competition between sponges and algae might weaken their potential combined effect on corals. © Inter-Research 2012.

Newly settled recruits typically suffer high mortality from disturbances, but rapid growth reduces their mortality once size-escape thresholds are attained. Ocean acidification (OA) reduces the growth of recruiting benthic invertebrates, yet no direct effects on survivorship have been demonstrated. We tested whether the reduced growth of coral recruits caused by OA would increase their mortality by prolonging their vulnerability to an acute disturbance: fish herbivory on surrounding algal turf. After two months' growth in ambient or elevated CO2 levels, the linear extension and calcification of coral (Acropora millepora) recruits decreased as CO2 partial pressure (pCO2) increased. When recruits were subjected to incidental fish grazing, their mortality was inversely size dependent. However, we also found an additive effect of pCO2 such that recruit mortality was higher under elevated pCO2 irrespective of size. Compared to ambient conditions, coral recruits needed to double their size at the highest pCO2to escape incidental grazing mortality. This general trend was observed with three groups of predators (blenny, surgeonfish, and parrotfish), although the magnitude of the fish treatment varied among species. Our study demonstrates the importance of size-escape thresholds in early recruit survival and how OA can shift these thresholds, potentially intensifying population bottlenecks in benthic invertebrate recruitment. © 2012 by the Ecological Society of America.

Increased frequency and severity of stressors associated with climate change are drastically altering ecosystems. Caribbean coral reefs differ markedly from just 30 years ago, with much restructuring attributable to infectious disease outbreaks. Using a classic epidemiological approach, we demonstrate how density-dependent demographic rates serve as a mechanism for intrinsic coral resilience to population perturbations arising from disturbances such as disease. We explore the impact of allowing infection status to influence demographic rates and ascertain outbreak thresholds that are corroborated by epizootic patterns observed in the field. We discuss how our threshold calculations may provide metrics of coral epizootic early warning systems. Integrating our infection model with equations describing the interspecific competition for space between coral and macroalgae, we provide new mechanistic understanding of the influence that coral life history dynamism and infectious disease have on the changing face of these threatened ecosystems.©Australian Mathematical Society 2013.

While relationships between adult fish density and structural habitat features are well established, relatively little is known about the habitat associations of juvenile reef fish. In a reserve system in Palau, we quantified microhabitat association with juvenile reef fish community structure, and determined the influence of foraging space, predator size and confamilial attraction on juvenile and adult pomacentrid abundance. Habitat structure and juvenile reef fish communities differed significantly among microhabitats with one exception: no difference was found between foliose and consolidated rubble microhabitats. Overall, pomacentrids characterised the juvenile community structure of each microhabitat. The abundance of early juvenile pomacentrids is simultaneously determined by microhabitat structure and predator size, with little evidence for settlement selection near adults. The results also suggest that the influence of habitat structure become weaker with ontogeny which in part, drives large predators to negatively influence the abundance of adult pomacentrids. The results have important implications on management, specifically in prioritizing areas for protection, and in modeling the impacts of habitat loss on reef fish communities. © 2012 Springer Science+Business Media B.V.

Providing accurate maps of coral reefs where the spatial scale and labels of the mapped features correspond to map units appropriate for examining biological and geomorphic structures and processes is a major challenge for remote sensing. The objective of this work is to assess the accuracy and relevance of the process used to derive geomorphic zone and benthic community zone maps for three western Pacific coral reefs produced from multi-scale, object-based image analysis (OBIA) of high-spatial-resolution multi-spectral images, guided by field survey data. Three Quickbird-2 multi-spectral data sets from reefs in Australia, Palau and Fiji and georeferenced field photographs were used in a multi-scale segmentation and object-based image classification to map geomorphic zones and benthic community zones. A per-pixel approach was also tested for mapping benthic community zones. Validation of the maps and comparison to past approaches indicated the multi-scale OBIA process enabled field data, operator field experience and a conceptual hierarchical model of the coral reef environment to be linked to provide output maps at geomorphic zone and benthic community scales on coral reefs. The OBIA mapping accuracies were comparable with previously published work using other methods; however, the classes mapped were matched to a predetermined set of features on the reef. © 2012 Copyright Taylor and Francis Group, LLC.

Successful recruitment in shallow reef ecosystems often involves specific cues that connect planktonic invertebrate larvae with particular crustose coralline algae (CCA) during settlement. While ocean acidification (OA) can reduce larval settlement and the abundance of CCA, the impact of OA on the interactions between planktonic larvae and their preferred settlement substrate are unknown. Here, we demonstrate that CO2 concentrations (800 and 1300μatm) predicted to occur by the end of this century significantly reduce coral (Acropora millepora) settlement and CCA cover by ≥45%. The CCA important for inducing coral settlement (Titanoderma spp. Hydrolithon spp.) were the most deleteriously affected by OA. Surprisingly, the only preferred settlement substrate (Titanoderma) in the experimental controls was avoided by coral larvae as pCO2 increased, and other substrata selected. Our results suggest OA may reduce coral population recovery by reducing coral settlement rates, disrupting larval settlement behaviour, and reducing the availability of the most desirable coralline algal species for successful coral recruitment. © 2012 Blackwell Publishing Ltd/CNRS.

Ecology Letters (2012) 15: 338-346 ABSTRACT: Successful recruitment in shallow reef ecosystems often involves specific cues that connect planktonic invertebrate larvae with particular crustose coralline algae (CCA) during settlement. While ocean acidification (OA) can reduce larval settlement and the abundance of CCA, the impact of OA on the interactions between planktonic larvae and their preferred settlement substrate are unknown. Here, we demonstrate that CO2 concentrations (800 and 1300 μatm) predicted to occur by the end of this century significantly reduce coral (Acropora millepora) settlement and CCA cover by ≥ 45%. The CCA important for inducing coral settlement (Titanoderma spp. Hydrolithon spp.) were the most deleteriously affected by OA. Surprisingly, the only preferred settlement substrate (Titanoderma) in the experimental controls was avoided by coral larvae as pCO2 increased, and other substrata selected. Our results suggest OA may reduce coral population recovery by reducing coral settlement rates, disrupting larval settlement behaviour, and reducing the availability of the most desirable coralline algal species for successful coral recruitment.

In the Caribbean region, forereef habitats dominated by Montastraea spp. have the highest biodiversity and support the largest number of ecosystem processes and services. Here we show that the distribution of this species-rich habitat can be explained by one environmental predictor: wave exposure. The relationship between wave exposure and the occurrence of Montastraea reefs was modelled using logistic regression for reefs throughout the Belize Barrier Reef, one of the largest and most topographically complex systems in the region. The model was able to predict correctly the occurrence of Montastraea reefs with an accuracy of 81%. Consistent with historical qualitative patterns, the distribution of Montastraea reefs is constrained in environments of high exposure. This pattern is likely to be driven by high rates of chronic sediment scour that constrain recruitment. The wide range of wave exposure conditions used to parameterize the model in Belize suggest that it should be transferable throughout much of the Caribbean region, constituting a fast and inexpensive alternative to traditional habitat mapping and complementing global efforts to map reef extent. © 2012 Springer-Verlag.

Managing coral reefs for resilience to climate change is a popular concept but has been difficult to implement because the empirical scientific evidence has either not been evaluated or is sometimes unsupportive of theory, which leads to uncertainty when considering methods and identifying priority reefs. We asked experts and reviewed the scientific literature for guidance on the multiple physical and biological factors that affect the ability of coral reefs to resist and recover from climate disturbance. Eleven key factors to inform decisions based on scaling scientific evidence and the achievability of quantifying the factors were identified. Factors important to resistance and recovery, which are important components of resilience, were not strongly related, and should be assessed independently. The abundance of resistant (heat-tolerant) coral species and past temperature variability were perceived to provide the greatest resistance to climate change, while coral recruitment rates, and macroalgae abundance were most influential in the recovery process. Based on the 11 key factors, we tested an evidence-based framework for climate change resilience in an Indonesian marine protected area. The results suggest our evidence-weighted framework improved upon existing un-weighted methods in terms of characterizing resilience and distinguishing priority sites. The evaluation supports the concept that, despite high ecological complexity, relatively few strong variables can be important in influencing ecosystem dynamics. This is the first rigorous assessment of factors promoting coral reef resilience based on their perceived importance, empirical evidence, and feasibility of measurement. There were few differences between scientists' perceptions of factor importance and the scientific evidence found in journal publications but more before and after impact studies will be required to fully test the validity of all the factors. The methods here will increase the feasibility and defensibility of including key resilience metrics in evaluations of coral reefs, as well as reduce costs. Adaptation, marine protected areas, priority setting, resistance, recovery.

Investigating the functional role of herbivorous fish species is important for understanding reef resilience and developing targeted management plans. Among the most abundant fish species on Indo-Pacific coral reefs are the surgeonfishes Acanthurus nigrofuscus and Ctenochaetus striatus. A. nigrofuscus is an herbivorous grazer that crops filamentous algae from the epilithic algal matrix, while C. striatus is detritivorous and was thought to 'brush' detritus from the surface of filamentous algae, causing little damage to algal strands. Although the foraging mechanisms and general diet of these surgeonfishes have been established, their grazing impact on epilithic algal turfs has been unclear. This is the first study to quantify the grazing impact of A. nigrofuscus and C. striatus on algal turfs. Through aquaria trials using epilithic algal turf grown on experimental tiles, we found that both A. nigrofuscus and C. striatus consistently fed more intensively upon sparse/short algal turfs even though the yield of algae per bite was greater for dense/long algal turfs. As there was no difference in the nutritional value of sparse and dense algal turfs, we hypothesise that A. nigrofuscus avoided dense turf due to its significantly greater sediment load than sparse turf, while C. striatus likely avoided dense turf as it would become entangled in their bristle-like teeth. Unexpectedly, despite its dental morphology, C. striatus removed significantly more algal turf per hour than A. nigrofuscus, irrespective of canopy height. The capability of C. striatus to remove significant quantities of algal turf through their foraging activity implies that this abundant and widespread species may substantially affect algal turf dynamics. If this is the case, the exclusion of detritivorous Ctenochaetus species from herbivorous fish functional groups used in resilience monitoring will need to be re-evaluated. © 2012 Springer-Verlag.

Recent changes in ocean temperature have impacted marine ecosystem function globally. Nevertheless, the responses have depended upon the rate of change of temperature and the season when the changes occur, which are spatially variable. A rigorous statistical analysis of sea surface temperature observations over 25. years was used to examine spatial variability in overall and seasonal temperature trends within the wider Caribbean. The basin has experienced high spatial variability in rates of change of temperature. Most of the warming has been due to increases in summer rather than winter temperatures. However, warming was faster in winter in the Loop Current area and the south-eastern Caribbean, where the annual temperature ranges have contracted. Waters off Florida, Cuba and the Bahamas had a tendency towards cooling in winter, increasing the amplitude of annual temperature ranges. These detailed patterns can be used to elucidate ecological responses to climatic change in the region. © 2012 Elsevier Ltd.

Recent changes in ocean temperature have impacted marine ecosystem function globally. Nevertheless, the responses have depended upon the rate of change of temperature and the season when the changes occur, which are spatially variable. A rigorous statistical analysis of sea surface temperature observations over 25 years was used to examine spatial variability in overall and seasonal temperature trends within the wider Caribbean. The basin has experienced high spatial variability in rates of change of temperature. Most of the warming has been due to increases in summer rather than winter temperatures. However, warming was faster in winter in the Loop Current area and the south-eastern Caribbean, where the annual temperature ranges have contracted. Waters off Florida, Cuba and the Bahamas had a tendency towards cooling in winter, increasing the amplitude of annual temperature ranges. These detailed patterns can be used to elucidate ecological responses to climatic change in the region.

Corals and macroalgae compete for space, but the influence of species and size on the competitive outcome is poorly understood. Using a manipulative experiment, we evaluated the effect of macroalgal competition on the growth rate of corals with an emphasis on the colony size, species identity and the intensity of competition. Coral-macroalgal competition was studied among 3 Caribbean coral species (Porites astreoides, Agaricia agaricites and Colpophyllia natans) and 2 macroalgal species (Lobophora variegata and Halimeda opuntia) for 1 yr. Two coral colony sizes were used and, for the smaller size class, 2 levels of intensity for macroalgal competition (25 and 100% contact with the coral perimeter). Coral size had the greatest effect on competitive outcome; 2 species of large corals under competition grew as much as controls and a third species did not lose tissue. All small colonies lost between 18 and 22% of their original area after a year of competing with macroalgae, and the competitive outcome was insensitive to algal species. Coral colony size is a critical factor for the competitive outcome with algae and the intensity of contact between competitors is not important in smaller corals. In general, our results support the theory that algal blooms can inhibit coral population dynamics by causing a bottleneck in the survivorship of smaller size classes. © Inter-Research 2012.

Coral resilience is important for withstanding ecological disturbances as well as anthropogenic changes to the environment. However, the last several decades have demonstrated a decline in resilience that has often resulted in phase shifts to a degraded coral-depleted state with high levels of algal abundance. A major defining issue in current research is to identify when and how it is possible to reverse these phase shifts allowing for the ecosystem to escape coral depletion and maintain coral-based ecosystem services. We extend an analytic model to focus on the effects of over-harvesting of herbivorous reef fish in the Caribbean by explicitly including grazer dynamics which introduces feedbacks between habitat and grazer abundance posing constraints on management options excluded in previous studies. This allows us to develop ecosystem-based management recommendations for two distinct scenarios of coral reef recovery: the first follows significant habitat damage in response to a large disturbance and the second maintains reef structure but has suffered from events such as coral bleaching. We identify critical fishing effort levels to allow for coral recovery and demonstrate that regions exhibiting severe damage to reef structure have little resilience implying that fishing reductions should be coupled with other restoration methods. Regions that are coral-depleted but maintain reef structure allow for recovery given sufficiently small levels of fishing mortality. However, we demonstrate the difference in recovery time in response to varying levels of control efforts on fishing. © 2010 the Author(s).

Habitat structure is frequently an important variable affecting species' abundances and diversity, and identifying the key aspects and spatial scales of habitat complexity is critical for understanding the ecology and conservation of a range of communities. Many coral-reef fishes are intimately linked with benthic habitat structure, and previous research has demonstrated rugosity as an important predictive variable of assemblage parameters. However, these studies typically consider rugosity at small scales, amalgamate multiple habitat features, or are semi-quantitative. This study considers meso-scale rugosity (within 51 plots of 25 m 2 on a Belizean forereef) generated by varying coral densities, heights, and complexities. Seven rugosity metrics were calculated for each plot, and were regressed against each of 11 fish assemblage parameters. Intra-habitat variability of each fish parameter was significantly positively or curvilinearly correlated to at least one metric of mesoscale rugosity, but the metric generating the strongest correlation varied. The abundance of small fishes, and consequently most of the assemblage statistics (e.g. total fish abundance and diversity) were best predicted by the number of tall (>50 cm) corals. The abundance of damselfishes, parrotfish biomass, the abundances of medium-sized and large fishes, and total fish biomass were curvilinearly related to mean coral height. The abundances of wrasses and surgeonfishes were most strongly correlated with the number of corals within a plot. Because coral-generated mesoscale rugosity is an important factor influencing intrahabitat variation in fishes, it should be explicitly considered when investigating fish-habitat relationships and predicting the impacts of coral mortality on ecosystem processes and services. © 2011 Springer Science+Business Media B.V.

The interaction between multiple stressors on Caribbean coral reefs, namely, fishing effort and hurricane impacts, is a key element in the future sustainability of reefs. We develop an analytic model of coral-algal interactions and explicitly consider grazing by herbivorous reef fish. Further, we consider changes in structural complexity, or rugosity, in addition to the direct impacts of hurricanes, which are implemented as stochastic jump processes. The model simulations consider various levels of fishing effort corresponding to' several hurricane frequencies and impact levels dependent on geographic location. We focus on relatively short time scales so we do not explicitly include changes in ocean temperature, chemistry, or sea level rise. The general features of our approach would, however, apply to these other stressors and to the management of other systems in the face of multiple stressors. It is determined that the appropriate management policy, either local reef restoration or fisheries management, greatly depends on hurricane frequency and impact level. For sufficiently low hurricane impact and macroalgal growth rate, our results indicate that regions with lower-frequency hurricanes require stricter fishing regulations, whereas management in regions with higher-frequency hurricanes might be less concerned with enhancing grazing and instead consider whether local-scale restorative activities to increase vertical structure are cost-effective.

The influence of habitat quality on a species' demographics is critical for understanding its ecology and effective conservation. However, quantifying habitat quality is problematic because it may comprise of abiotic components at different spatial scales and also be influenced by biotic processes. This study investigated the relationship between reef-associated Caribbean fishes and habitat quality at 2 spatial scales: (1) multiple characteristics of Montastraea annularis coral colonies (

Climate change is reshaping biological communities and has already generated novel ecosystems. The functioning of novel ecosystems could depart markedly from that of existing systems and therefore obscure the impacts of climate change. We illustrate this possibility for coral reefs, which are at the forefront of climatic stress. Disease has been a principal cause of reef degradation and is expected to worsen with increased future thermal stress. However, using a field-tested epizoological model, we show that high population turnover within novel ecosystems enhances coral resistance to epizootics. Thus, disease could become a less important driver of change in the future. We emphasize the need to move away from projections based on historic trends toward predictions that account for novel behavior of ecosystems under climate change.

A thematic map of benthic habitat was produced for a coral reef in the Republic of Palau, utilizing hydroacoustic data acquired with a BioSonics DT-X echosounder and a single-beam 418 kHz digital transducer. This article describes and assesses a supervised classification scheme that used a series of three discriminant analyses (DAs) to refine training samples into end-member structural and biological elements utilizing E1′ (leading edge of first echo), E1 (trailing edge of first echo), E2 (complete second echo), fractal dimension (first echo shape) and depth as predictor variables. Hydroacoustic training samples were assigned to one of six predefined groups based on the plurality of benthic elements (sand, sparse submerged aquatic vegetation (SAV)) rubble, pavement, rugose hardbottom, branching coral) that were visually estimated from spatially co-located ground-truthing videos. Records that classified incorrectly or failed to exceed a minimum probability of group membership were removed from the training data set until only 'pure' end-member records remained. This refinement of 'mixed' training samples circumvented the dilemma typically imposed by the benthic heterogeneity of coral reefs, that is either train the acoustic ground discrimination system (AGDS) on homogeneous benthos and leave the heterogeneous benthos unclassified, or attempt to capture the many 'mixed' classes and overwhelm the discriminatory capability of the AGDS. It was made possible by a conjunction of narrow beam width (6.4°) and shallow depth (1.2 to 17.5 m), which produced a sonar footprint small enough to resolve the microscale features used to define benthic groups. Survey data classified from the third-pass training DA were found to: (i) conform to visually apparent contours of satellite imagery, (ii) agree with the structural and biological delineations of a benthic habitat map (BHM) created from visual interpretation of IKONOS imagery and (iii) yield values of benthic cover that agreed closely with independent, contemporaneous video transects. The methodology was proven on a coral reef environment for which high-quality satellite imagery existed, as an example of the potential for single-beam systems to thematically map coral reefs in deep or turbid settings where optical methods are not applicable. © 2011 Taylor & Francis.

Lionfish (Pterois volitans/miles) have invaded the majority of the Caribbean region within five years. As voracious predators of native fishes with a broad habitat distribution, lionfish are poised to cause an unprecedented disruption to coral reef diversity and function. Controls of lionfish densities within its native range are poorly understood, but they have been recorded in the stomachs of large-bodied Caribbean groupers. Whether grouper predation of lionfish is sufficient to act as a biocontrol of the invasive species is unknown, but pest biocontrol by predatory fishes has been reported in other ecosystems. Groupers were surveyed along a chain of Bahamian reefs, including one of the region's most successful marine reserves which supports the top one percentile of Caribbean grouper biomass. Lionfish biomass exhibited a 7-fold and non-linear reduction in relation to the biomass of grouper. While Caribbean grouper appear to be a biocontrol of invasive lionfish, the overexploitation of their populations by fishers, means that their median biomass on Caribbean reefs is an order of magnitude less than in our study. Thus, chronic overfishing will probably prevent natural biocontrol of lionfishes in the Caribbean.

Coral reefs have been more severely impacted by recent climate instability than any other ecosystem on Earth. Corals tolerate a narrow range of physical environmental stress, and increases in sea temperature of just 1°C over several weeks can result in mass coral mortality, often exceeding 95% of individuals over hundreds of square kilometres. Even conservative climate models predict that mass coral bleaching events could occur annually by 2050. Unfortunately, managers of coral-reef resources have few options available to meet this challenge. Here, we investigate the role that fisheries conservation tools, including the designation of marine reserves, can play in altering future trajectories of Caribbean coral reefs. We use an individual-based model of the ecological dynamics to test the influence of spatially realistic regimes of disturbance on coral populations. Two major sources of disturbance, hurricanes and coral bleaching, are simulated in contrasting regions of the Caribbean: Belize, Bonaire, and the Bahamas. Simulations are extended to 2099 using the HadGEM1 climate model. We find that coral populations can maintain themselves under all levels of hurricane disturbance providing that grazing levels are high. Regional differences in hurricane frequency are found to cause strikingly different spatial patterns of reef health with greater patchiness occurring in Belize, which has less frequent disturbance, than the Bahamas. The addition of coral bleaching led to a much more homogenous reef state over the seascape. Moreover, in the presence of bleaching, all reefs exhibited a decline in health over time, though with substantial variation among regions. Although the protection of herbivores does not prevent reef degradation it does delay rates of coral loss even under the most severe thermal and hurricane regimes. Thus, we can estimate the degree to which local conservation can help buy time for reefs with values ranging between 18 years in the Bahamas and over 50 years in Bonaire, compared with heavily fished systems. Ultimately, we demonstrate that local conservation measures can benefit reef ecosystem services but that their impact will vary spatially and temporally. Recognizing where such management interventions will either help or fail is an important step towards both achieving sustainable use of coral-reef resources and maximizing resource management investments. © 2010 Blackwell Publishing Ltd.

The effects of increasing sea temperatures extend far beyond changes in species' distributions. By altering local fish abundances, temperature changes will have profound effects on the structure, functioning and services of marine ecosystems.

Ocean warming and acidification from increasing levels of atmospheric CO2 represent major global threats to coral reefs, and are in many regions exacerbated by local-scale disturbances such as overfishing and nutrient enrichment. Our understanding of global threats and local-scale disturbances on reefs is growing, but their relative contribution to reef resilience and vulnerability in the future is unclear. Here, we analyse quantitatively how different combinations of CO2 and fishing pressure on herbivores will affect the ecological resilience of a simplified benthic reef community, as defined by its capacity to maintain and recover to coral-dominated states. We use a dynamic community model integrated with the growth and mortality responses for branching corals (Acropora) and fleshy macroalgae (Lobophora). We operationalize the resilience framework by parameterizing the response function for coral growth (calcification) by ocean acidification and warming, coral bleaching and mortality by warming, macroalgal mortality by herbivore grazing and macroalgal growth via nutrient loading. The model was run for changes in sea surface temperature and water chemistry predicted by the rise in atmospheric CO2 projected from the IPCC's fossil-fuel intensive A1FI scenario during this century. Results demonstrated that severe acidification and warming alone can lower reef resilience (via impairment of coral growth and increased coral mortality) even under high grazing intensity and low nutrients. Further, the threshold at which herbivore overfishing (reduced grazing) leads to a coral-algal phase shift was lowered by acidification and warming. These analyses support two important conclusions: Firstly, reefs already subjected to herbivore overfishing and nutrification are likely to be more vulnerable to increasing CO2. Secondly, under CO2 regimes above 450-500ppm, management of local-scale disturbances will become critical to keeping reefs within an Acropora-rich domain. © 2011 Blackwell Publishing Ltd.

Although a consensus in marine science is developing on the need to adopt ecosystem-based fishery management, few studies try to quantify the contextspecific gains from implementing it. Using a multi-species bioeconomic model for a Caribbean reef community, we determine the optimal harvesting rates for predator and prey species and ask how this more comprehensive optimization differs from traditional single-species approaches. We also identify tradeoffs when the objective of the manager includes nonfishing values. We find that the optimal solution when accounting for nonfishing values can include temporary or permanent fishing moratoriums in contrast to continuous fishing at low levels when only fishing profits are considered. We also show that the greatest gains from ecosystem-based fishery management are not from improved estimation of the trophic coupling, but from reforming the social and economic management of individual fish stocks and by explicitly incorporating a broader set of values into management decisions. © 2010 Wiley Periodicals, Inc.

This study determined whether the acoustic roughness of Caribbean reef habitats is an accurate proxy for their topographic complexity and a significant predictor of their fish abundance. Fish abundance was measured in 25 sites along the forereef of Glovers Atoll (Belize). At each site, in situ rugosity (ISR) was estimated using the "chain and tape" method, and acoustic roughness (E1) was acquired using RoxAnn. The relationships between E1 and ISR, and between both E1 and ISR and the abundance of 17 common species and the presence of 10 uncommon species were tested. E1 was a significant predictor of the topographic complexity (r2 = 0.66), the abundance of 10 common species of surgeonfishes, pomacentrids, scarids, grunts and serranids and the presence of 4 uncommon species of pomacentrids and snappers. Small differences in E1 (i. e. {increment}0.05-0.07) reflected in subtle but significant differences in fish abundance (~1 individual 200 m-2 and 116 g 200 m-2) among sites. Although we required the use of IKONOS data to obtain a large number of echoes per site, future studies will be able to utilise RoxAnn data alone to detect spatial patterns in substrate complexity and fish abundance, provided that a minimum of 50 RoxAnn echoes are collected per site. © 2010 Springer-Verlag.

Rising sea temperatures cause mass coral bleaching and threaten reefs worldwide. We show how maps of variations in thermal stress can be used to help manage reefs for climate change. We map proxies of chronic and acute thermal stress and develop evidence-based hypotheses for the future response of corals to each stress regime. We then incorporate spatially realistic predictions of larval connectivity among reefs of the Bahamas and apply novel reserve design algorithms to create reserve networks for a changing climate. We show that scales of larval dispersal are large enough to connect reefs from desirable thermal stress regimes into a reserve network. Critically, we find that reserve designs differ according to the anticipated scope for phenotypic and genetic adaptation in corals, which remains uncertain. Attempts to provide a complete reserve design that hedged against different evolutionary outcomes achieved limited success, which emphasises the importance of considering the scope for adaptation explicitly. Nonetheless, 15% of reserve locations were selected under all evolutionary scenarios, making them a high priority for early designation. Our approach allows new insights into coral holobiont adaptation to be integrated directly into an adaptive approach to management.

The past few decades have seen an increase in the frequency and intensity of disturbance on coral reefs, resulting in shifts in size and composition of coral populations. These changes have lead to a renewed focus on processes that influence demographic rates in corals, such as corallivory. While previous research indicates selective corallivory among coral taxa, the importance of coral size and the density of coral colonies in influencing corallivory are unknown. We surveyed the size, taxonomy and number of bites by parrotfish per colony of corals and the abundance of three main corallivorous parrotfish (Sparisoma viride, Sparisoma aurofrenatum, Scarus vetula) at multiple spatial scales (reefs within islands: 1-100 km, and between islands: >100 km) within the Bahamas Archipelago. We used a linear mixed model to determine the influence of coral taxa, colony size, colony density, and parrotfish abundance on the intensity of corallivory (bites per m(2) of coral tissue). While the effect of colony density was significant in determining the intensity of corallivory, we found no significant influence of colony size or parrotfish abundance (density, biomass or community structure). Parrotfish bites were most frequently observed on the dominant species of reef building corals (Montastraea annularis, Montastraea faveolata and Porites astreoides), yet our results indicate that when the confounding effects of colony density and size were removed, selective corallivory existed only for the less dominant Porites porites. As changes in disturbance regimes result in the decline of dominant frame-work building corals such as Montastraea spp. the projected success of P. porites on Caribbean reefs through high reproductive output, resistance to disease and rapid growth rates may be attenuated through selective corallivory by parrotfish.

Our view of ecosystems has evolved from one emphasizing determinism to an understanding that systems can exhibit dramatic, and often surprising, shifts in state. Perhaps the most well-known shift is the replacement of corals by macroalgae, but others occur when systems experience overwhelming bioerosion or heavy sedimentation. Preventing undesirable shifts in ecosystem state is a key goal of management, particularly given the need to stem the loss of ecosystem services. However, ecosystem shifts have proved difficult to predict because they can occur with little warning. Worse, the symptoms, such as loss of coral, and may be difficult to reverse because ecological feedback processes can constrain recovery. Thus, it is important to understand the factors that drive shifts in ecosystem state and the stability of such states. This is the study of resilience. A resilient reef is usually considered to be one that absorbs disturbances and recovers to a coral-rich state (though other states are also possible). We describe methods to quantify explicitly the resilience of a reef by combining models of a reef's equilibrial dynamics with its stochastic disturbance regime. In this case, resilience can be calculated as the probability that a reef will avoid shifting to an alternate stable state in a prescribed period of time, given its current state and anticipated disturbance regime. We then discuss the opportunities to manage for resilience. Because many acute disturbances, such as coral bleaching, cannot be mitigated directly, the emphasis for management is to enhance processes of coral recovery through the management of watersheds, nutrient-runoff, and grazers. In addition, scientists are beginning to understand spatial patterns of the response of corals to disturbance. Although such research is at an embryonic stage, it promises to play an important role in helping to stratify the interventions of managers across the seascape. © 2011 Springer Science+Business Media B.V.

Sponges constitute an abundant and functionally important component of coral reef systems. Given their demonstrated resistance to environmental stress, it might be expected that the role of sponges in reef systems under modern regimes of frequent and severe disturbance may become even more substantial. Disturbances have recently reshaped the community structure of many Caribbean coral reefs shifting them towards a state of persistent low coral cover and often a dominance of macroalgae. Using competition and growth rates recorded from Glover's Atoll in Belize, we parameterise a mathematical model used to simulate the three-way competition between sponges, macroalgae and coral. We use the model to determine the range of parameters in which each of the three species might be expected to dominate. Emergent properties arise from our simple model of this complex system, and these include a special case in which heightened competitive ability of macroalgae versus coral may counter-intuitively prove to be advantageous to the persistence of corals. Importantly, we show that even under scenarios whereby sponges fail to invade the system, inclusion of this third antagonist can qualitatively affect the likelihood of alternative stable states - generally in favour of macroalgal dominance. The interplay between multi-species competition and predation is complex, but our efforts highlight a key process that has, until now, remained unexplored: the extent to which sponges dissipate algal grazing pressure by providing generalist fish with an alternative food source. We highlight the necessity of identifying the extent by which this process takes place in tropical systems in order to improve projections of alternative stable states for Caribbean coral reefs. © 2011 Elsevier B.V.

Maps of coral reef habitats are fundamental tools for reef management, and high map accuracy is desirable to support appropriate decisions, such as the stratification of marine reserves by habitat class. While satellite sensors have been used to map different reef communities, the accuracy of these maps tends to be low (overall accuracy

Multiple anthropogenic impacts, including bleaching from climate change-related thermal stress, threaten coral reefs. Protecting coral capacity to respond to the increase in future thermal stress expected with climate change can involve (1) protecting coral reefs with characteristics indicative of greater resistance and resilience to climate change, and (2) reducing other anthropogenic impacts that are more likely to reduce coral resistance and resilience to climate change. Here, we quantitatively compare possible priorities and existing recommendations for protecting coral response capacity to climate change. Specifically, we explore the relative importance of the relevant dynamics, processes, and parameters in a size-structured model of coral and zooxanthellae ecological and evolutionary dynamics given projected future thermal stress. Model results with varying initial conditions indicate that protecting diverse coral communities is critical, and protecting communities with higher abundances of more thermally tolerant coral species and symbiont types secondary, to the long-term maintenance of coral cover. A sensitivity analysis of the coral population size in each size class and the total coral cover with respect to all parameter values suggests greater relative importance of reducing additional anthropogenic impacts that affect coral-macroalgal competition, early coral life history stages, and coral survivorship (compared with reproduction, growth, and shrinkage). Finally, model results with temperature trajectories from different locations, with and without connectivity, indicate that protection of, and connectivity to, low-thermal-stress locations may enhance the capacity for corals to respond to climate change. © 2009 Blackwell Publishing Ltd.

Conservation plans are usually developed for regions that encompass only one environmental realm (terrestrial, freshwater or marine) because of logistical, institutional and political constraints. This is inadequate because these realms often interact through processes that form, utilize and maintain interfaces or connections, which are essential for the persistence of some species and ecosystem functions. We present a conceptual framework for systematic conservation prioritization that explicitly accounts for the connectivity between the terrestrial, marine, and freshwater realms. We propose a classification of this connectivity that encompasses: (1) narrow interfaces, such as riparian strips; (2) broad interfaces, such as estuaries; (3) constrained connections, such as corridors of native vegetation used by amphibians to move between natal ponds and adult habitat; and (4) diffuse connections, such as the movements of animals between breeding and feeding habitats. We use this taxonomy of inter-realm connectivity to describe existing and new spatial conservation prioritization techniques that aim to promote the persistence of processes that operate between realms. © 2009 Elsevier Ltd. All rights reserved.

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

Recent empirical studies have demonstrated that human activities such as fishing can strongly affect the natural capital and services provided by tropical seascapes. However, policies to mitigate anthropogenic impacts can also alter food web structure and interactions, regardless of whether the regulations are aimed at single or multiple species, with possible unexpected consequences for the ecosystems and their associated services. Complex community response to management interventions have been highlighted in the Caribbean, where, contrary to predictions from linear food chain models, a reduction in fishing intensity through the establishment of a marine reserve has led to greater biomass of herbivorous fish inside the reserve, despite an increased abundance of large predatory piscivores. This positive multi-trophic response, where both predators and prey benefit from protection, highlights the need to take an integrated approach that considers how numerous factors control species coexistence in both fished and unfished systems. In order to understand these complex relationships, we developed a general model to examine the trade-offs between fishing pressure and trophic control on reef fish communities, including an exploration of top-down and bottom-up effects. We then validated the general model predictions by parameterizing the model for a reef system in the Bahamas in order to tease apart the wide range of species responses to reserves in the Caribbean. Combining the development of general theory and site-specific models parameterized with field data reveals the underlying driving forces in these communities and enables us to make better predictions about possible population and community responses to different management schemes.

Trends in the percentage cover of macroalgae are generally used as an important indicator of the health of coral reefs. While considerable data exist on patterns of macroalgal cover, the underlying patch dynamics of macroalgae are poorly understood. It is important to appreciate the dynamical processes of algae because they determine the frequency and duration of competitive interaction with other taxa, such as corals, and thereby contribute to our understanding of competitive interactions. We used transition matrices to quantify and describe the patch dynamics of 2 common macroalgae in the Caribbean, Dictyota pulchella and Lobophora variegata, over a 9 mo period. Size-based matrices were constructed for both species from forereef habitats subjected to contrasting levels of wave exposure. The dynamics of D. pulchella are highly sensitive to the physical environment, whilst those of L. variegata are far less sensitive. The patch dynamics of D. pulchella showed a higher temporal variation than L. variegata, but only on the exposed forereef. D. pulchella virtually disappeared in January at both the exposed and sheltered sites, whereas L. variegata exhibited a continuing increase in patch size irrespective of exposure. D. pulchella formed larger, more dynamic patches under high exposure. This implies that contact interactions with coral colonies and space preemption for settling planulae will occur more frequently than in sheltered environments. Our results demonstrate the need to investigate patch dynamics of macroalgae at the individual species level, whilst taking into account environmental conditions. © Inter-Research 2010.

The fisheries and biodiversity benefits of marine reserves are widely recognised but there is mounting interest in exploiting the importance of herbivorous fishes a tool to help ecosystems recover from climate change impacts. This approach might be particularly suitable for coral reefs which are acutely threatened by climate change yet the trophic cascades generated by reserves are strong enough that they might theoretically enhance the rate of coral recovery after disturbance. However, evidence for reserves facilitating coral recovery has been lacking. Here we investigate whether reductions in macroalgal cover, caused by recovery of herbivorous parrotfishes within a reserve, have resulted in a faster rate of coral recovery than in areas subject to fishing. Surveys of 10 sites inside and outside a Bahamian marine reserve over a 2.5 year period demonstrated that increases in coral cover, including adjustments for the initial size-distribution of corals, were significantly higher at reserve sites than that in non-reserve sites. Furthermore, macroalgal cover was significantly negatively correlated with the change in total coral cover over time. Recovery rates of individual species were generally consistent with small-scale manipulations on coral-macroalgal interactions, but also revealed differences that demonstrate the difficulties of translating experiments across spatial scales. Size-frequency data indicated that species which were particularly affected by high abundances of macroalgae outside the reserve had a population bottleneck restricting the supply of smaller corals to larger size classes. Importantly, because coral cover increased from a heavily degraded state, and recovery from such states has not previously been described, similar or better outcomes should be expected for many reefs in the region. Reducing herbivore exploitation as part of an ecosystem-based management strategy for coral reefs appears to be justified.

Coral reefs are one of the world's most biologically diverse and productive ecosystems. However, these valuable resources are highly threatened by human activities. Satellite remotely sensed observations enhance our understanding of coral reefs and some of the threats facing them by providing global spatial and time-series data on reef habitats and the environmental conditions influencing them in near-real time. This review highlights many of the ways in which satellites are currently used to monitor coral reefs and their threats, and provides a look toward future needs and capabilities.

Phase-shifts from one persistent assemblage of species to another have become increasingly commonplace on coral reefs and in many other ecosystems due to escalating human impacts. Coral reef science, monitoring and global assessments have focused mainly on producing detailed descriptions of reef decline, and continue to pay insufficient attention to the underlying processes causing degradation. A more productive way forward is to harness new theoretical insights and empirical information on why some reefs degrade and others do not. Learning how to avoid undesirable phase-shifts, and how to reverse them when they occur, requires an urgent reform of scientific approaches, policies, governance structures and coral reef management.

Mortality of corals is increasing due to bleaching, disease andalgal overgrowth. In the Caribbean, low rates of coral recruitment contribute to the slow or undetectable rates of recovery in reef ecosystems. Although algae have longbeen suspected to interfere with coral recruitment, the mechanisms of that interaction remain unclear. We experimentally tested the effects of turf algal abundance on 3 sequential factors important to recruitment of corals: the biophysical delivery of planktonic coral larvae, their propensity to settle, andthe availability of microhabitats where they survive. We deployed coral settlement plates inside and outside damselfish Stegastes spp. gardens and cages. Damselfish aggression reduced herbivory from fishes, and cages became fouled with turf algae, both locally increasing algal biomass surrounding the plates. This reduced flushing rates innursery microhabitats on the plate underside, limiting larvae available for settlement. Coral spat settled preferentially on an earlysuccessional crustose coralline alga Titanoderma prototypumbut also on or near other coralline algae, biofilms, and calcareous polychaete worm tubes. Post-settlement survival washighest in the fully grazed, lowest algal biomass treatment,and after 27 mo "spat" densitieswere 73% higher in this treatment. The "gauntlet"; refers to the sequence of ecological processes through which corals must survive to recruit. The highest proportion of coral spat successfully running the gauntlet did so under conditions of low algal biomass resulting from increased herbivory. If coral recruitment is heavily controlled at very local scales by this gauntlet, then coral reef managers could improve a reef's recruitment potential by managing for reduced algal biomass. © Inter-Research 2010.

Global warming is a severe threat to coral reefs. It has been proposed that upwelling could minimise the thermal stress caused by ocean warming, and therefore upwelling areas may serve as a refuge for corals. Here, using 21 yr of satellite sea surface temperature data, we analysed the degree to which the thermal stress experienced by corals is reduced in 4 seasonal upwelling areas with reef development: Colombia in the southern Caribbean, Panama in the eastern tropical Pacific, Oman in the Arabian Sea and Madagascar in the Indian Ocean. Upwelling areas do not always offer protection from thermal stress. When compared with nearby non-upwelling areas, upwelling can only provide defence against warming events if: (1) the threat and the upwelling coincide, and (2) this overlap produces a meaningful decrease in thermal stress in upwelling areas. These conditions were met in only 2 of the 4 upwelling areas analysed: Colombia and Oman. In Oman, upwelling decreased the magnitude, frequency and duration of thermal disturbances (identified when Coral Bleaching HotSpots, anomalies exceeding the average temperature of the warmest month, are larger than 1 φ C), while in Colombia upwelling only decreased their frequency. The protective role of upwelling seems to be limited geographically; therefore, further upwelling areas need to be assessed individually in order to evaluate their capacity as a refuge from thermal stress.© Inter-Research 2010.

With coral cover in decline on many Caribbean reefs, any process of coral mortality is of potential concern. While sparisomid parrotfishes are major grazers of Caribbean reefs and help control algal blooms, the fact that they also undertake corallivory has prompted some to question the rationale for their conservation. Here the weight of evidence for beneficial effects of parrotfishes, in terms of reducing algal cover and facilitating demographic processes in corals, and the deleterious effects of parrotfishes in terms of causing coral mortality and chronic stress, are reviewed. While elevated parrotfish density will likely increase the predation rate upon juvenile corals, the net effect appears to be positive in enhancing coral recruitment through removal of macroalgal competitors. Parrotfish corallivory can cause modest partial colony mortality in the most intensively grazed species of Montastraea but the generation and healing of bite scars appear to be in near equilibrium, even when coral cover is low. Whole colony mortality in adult corals can lead to complete exclusion of some delicate, lagoonal species of Porites from forereef environments but is only reported for one reef species (Porites astreoides), for one habitat (backreef), and with uncertain incidence (though likely

Macroalgae are a major benthic component of coral reefs and their dynamics influence the resilience of coral reefs to disturbance. However, the relative importance of physical and ecological processes in driving macroalgal dynamics is poorly understood. Here we develop a Bayesian belief network (BBN) model to integrate many of these processes and predict the growth of coral reef macroalgae. Bayesian belief networks use probabilistic relationships rather than deterministic rules to quantify the cause and effect assumptions. The model was developed using both new empirical data and quantified relationships elicited from previous studies. We demonstrate the efficacy of the BBN to predict the dynamics of a common Caribbean macroalgal genus Dictyota. Predictions of the model have an average accuracy of 55% (implying that 55% of the predicted categories of Dictyota cover were assigned to the correct class). Sensitivity analysis suggested that macroalgal dynamics were primarily driven by top-down processes of grazing rather than bottom-up nutrification. BBNs provide a useful framework for modelling complex systems, identifying gaps in our scientific understanding and communicating the complexities of the associated uncertainties in an explicit manner to stakeholders. We anticipate that accuracies will improve as new data are added to the model. © 2009 Elsevier B.V. All rights reserved.

Caribbean coral reefs are widely thought to exhibit two alternate stable states with one being dominated by coral and the other by macroalgae. However, the observation of linear empirical relationships among grazing, algal cover and coral recruitment has led the existence of alternate stable states to be questioned; are reefs simply exhibiting a continuous phase shift in response to grazing or are the alternate states robust to certain changes in grazing? Here, a model of a Caribbean forereef is used to reconcile the existence of two stable community states with common empirical observations. Coral-depauperate and coral-dominated reef states are predicted to be stable on equilibrial time scales of decades to centuries and their emergence depends on the presence or absence of a bottleneck in coral recruitment, which is determined by threshold levels of grazing intensity and other process variables. Under certain physical and biological conditions, corals can be persistently depleted even while increases in grazing reduce macroalgal cover and enhance coral recruitment; only once levels of recruitment becomes sufficient to overwhelm the population bottleneck will the coral-dominated state begin to emerge. Therefore, modest increases in grazing will not necessarily allow coral populations to recover, whereas large increases, such as those associated with recovery of the urchin Diadema antillarum, are likely to exceed threshold levels of grazing intensity and set a trajectory of coral recovery. The postulated existence of alternate stable states is consistent with field observations of linear relationships between grazing, algal cover and coral recruitment when coral cover is low and algal exclusion when coral cover is high. The term 'macroalgal dominated' is potentially misleading because the coral-depauperate state can be associated with various levels of macroalgal cover. The term 'coral depauperate' is preferable to 'macroalgal dominated' when describing alternate states of Caribbean reefs. © Springer-Verlag 2009.

Profound ecological changes are occurring on coral reefs throughout the tropics, with marked coral cover losses and concomitant algal increases, particularly in the Caribbean region. Historical declines in the abundance of large Caribbean reef fishes likely reflect centuries of overexploitation. However, effects of drastic recent degradation of reef habitats on reef fish assemblages have yet to be established. By using meta-analysis, we analyzed time series of reef fish density obtained from 48 studies that include 318 reefs across the Caribbean and span the time period 1955-2007. Our analyses show that overall reef fish density has been declining significantly for more than a decade, at rates that are consistent across all subregions of the Caribbean basin (2.7% to 6.0% loss per year) and in three of six trophic groups. Changes in fish density over the past half-century are modest relative to concurrent changes in benthic cover on Caribbean reefs. However, the recent significant decline in overall fish abundance and its consistency across several trophic groups and among both fished and nonfished species indicate that Caribbean fishes have begun to respond negatively to habitat degradation.

Disease has dramatically reduced populations of the herbivorous urchin Diadema antillarum Philippi on Caribbean reefs, contributing to an increased abundance of macroalgae and reduction of coral cover. Therefore, recovery of D. antillarum populations is critically important, but densities are still low on many reefs. Among the many potential factors limiting these densities, the focus of this study is on predation pressure by fishes. Marine reserves provide opportunities to examine large-scale manipulations of predator-prey interactions and, therefore, D. antillarum densities were compared inside and outside a reserve in the Bahamas (Exuma Cays Land and Sea Park; ECLSP). Urchins and their fish predators were surveyed at nine sites inside and outside the ECLSP. Because of lower fishing effort, the total biomass of urchin predators, weighted by their dietary preferences for urchins, was significantly higher inside the ECLSP. Furthermore, fish community structure was significantly different inside the Park because of the increased biomass of the majority of species. No urchins were seen inside the ECLSP and this was significantly lower than the density of 0.04 urchin m-2 outside the Park. Regression analysis indicated that the relationship between the biomass of urchin predators and the proportion of transects containing urchins was non-linear, suggesting that small increases in fish biomass dramatically reduce urchin abundances. The link between lower density of urchins and higher density of their predators inside the ECLSP is strengthened by discounting five alternative primary mechanisms (variations in macroalgal cover, larval supply, environmental setting, density of other urchin species and abundance of predators not surveyed). Caribbean marine reserves have an important conservation role, but increased fish predation appears to reduce densities of D. antillarum. Urchins currently have limited functional significance on Bahamian reefs, but any future recovery of D. antillarum is likely to be limited in reserves, with potentially important ecological consequences. © Springer-Verlag 2009.

Numerous studies have been conducted to compare the classification accuracy of coral reef maps produced from satellite and aerial imagery with different sensor characteristics such as spatial or spectral resolution, or under different environmental conditions. However, in additional to these physical environment and sensor design factors, the ecologically determined spatial complexity of the reef itself presents significant challenges for remote sensing objectives. While previous studies have considered the spatial resolution of the sensors, none have directly drawn the link from sensor spatial resolution to the scale and patterns in the heterogeneity of reef benthos. In this paper, we will study how the accuracy of a commonly used maximum likelihood classification (MLC) algorithm is affected by spatial elements typical of a Caribbean atoll system present in high spectral and spatial resolution imagery. The results indicate that the degree to which ecologically determined spatial factors influence accuracy is dependent on both the amount of coral cover on the reef and the spatial resolution of the images being classified, and may be a contributing factor to the differences in the accuracies obtained for mapping reefs in different geographical locations. Differences in accuracy are also obtained due to the methods of pixel selection for training the maximum likelihood classification algorithm. With respect to estimation of live coral cover, a method which randomly selects training samples from all samples in each class provides better estimates for lower resolution images while a method biased to select the pixels with the highest substrate purity gave better estimations for higher resolution images. © 2009 Elsevier Inc. All rights reserved.

In recent decades, a rise in coral mortality, attributed to increased frequency of massbleaching events, increased prevalence of disease, and more frequent and severe hurricanes, has contributed to a rapid proliferation of macroalgae across many Caribbean reefs. As a consequence, the frequency of coral-algal interactions has risen. Here, we document the effects of 2 dominant Caribbean macroalgae, Dictyota spp. and Lobophora variegata, and a mixed algal community on the fecundity of a massive coral. Montastraea annularis is a dominant Caribbean reef-building coral characterised by a low recruitment rate. To investigate the effects of macroalgae on coral fecundity, algal contact was experimentally manipulated around the perimeter of M. annularis patches. Fecundity was measured as the diameter of eggs (ES), the number of eggs per gonad (E#) and the number of gonads per polyp (G#). Algal contact was shown to significantly reduce the diameter of eggs at both the coral-algal boundary and at the centre of coral patches. The presence of Dictyota spp. or a mixed algal community was shown to have more detrimental effects on ES than the presence of L. variegata. Removal of algal contact immediately prior to gametogenesis increased the reproductive output of polyps directly adjacent to the cleared areas, with an increase in ES, E# and G#. Our results imply that algal competitors can reduce the fecundity of M. annularis through mechanical and/or allelochemical damage of polyps directly adjacent to the algae and by causing the reallocation of energy within the coral patch from reproduction to defence and repair. © Inter-Research 2008.

The decline of many coral reef ecosystems in recent decades surprised experienced managers and researchers. It shattered old paradigms that these diverse ecosystems are spatially uniform and temporally stable on the scale of millennia. We now see reefs as heterogeneous, fragile, globally stressed ecosystems structured by strong positive or negative feedback processes. We review the causes and consequences of reef decline and ask whether management practices are addressing the problem at appropriate scales. We conclude that both science and management are currently failing to address the comanagement of extractive activities and ecological processes that drive ecosystems (e.g. productivity and herbivory). Most reef conservation efforts are directed toward reserve implementation, but new approaches are needed to sustain ecosystem function in exploited areas.

1. No-take reserves are a common tool for fisheries management and biodiversity conservation in marine ecosystems. Despite much discussion of their benefits, data documenting many reserve effects are surprisingly scarce. Several studies have also been criticized for a lack of rigour so that changes within reserves cannot be separated from underlying natural variation and attributed unequivocally to protection. 2. We sampled both benthic (video quadrats) and associated fish communities (underwater visual censuses) in a well-enforced reserve in the Bahamas. Sampling was explicitly stratified by habitat ('Montastraea reef' and 'gorgonian plain'). To distinguish reserve effects from natural variation, we compared changes inside and outside the reserve with those seen at equivalent spatial scales in other reef systems in the Bahamian archipelago that lack reserves. Reserve-level differences in benthic or fish communities not documented in other reef systems are categorized as 'robust' effects. 3. Robust reserve effects were limited to Montastraea reefs. The reserve supported an average of ≈ 15% more fish species per site compared to outside the reserve. This pattern was particularly driven by more large-bodied grouper, damselfish, and butterflyfish species inside the reserve. Increases in fish biomass and differences in community structure inside the reserve were limited to large-bodied groupers. Increased grazing pressure by parrotfishes in the reserve has lowered macroalgal cover, and caused previously undocumented changes in benthic community structure compared to sites outside the reserve. 4. Some reserve-level differences in fish communities were categorized as 'misleading' because equivalent differences were seen in other reef systems, and are likely to be caused by natural intra-habitat variation. Separation of robust and misleading results was only possible because of archipelago-scale sampling. 5. Synthesis and applications. The Bahamas represents a relatively lightly fished system within the Caribbean. However, cessation of fishing has still increased the mean number of species, the abundance of the most highly prized fishes and, through trophic cascades, altered benthic community structure. In certain habitats, reserves are clearly important for conserving fisheries and biodiversity. However, reserve effects must be explicitly separated from confounding variables to ensure conservation benefits are accurately identified and reported, and not oversold to managers and local stakeholders. © 2008 the Authors.

1. Ontogenetic dispersal of animals has been observed among many ecosystems, but its full ecological significance is poorly understood. By modelling the consequences of ontogenetic reef fish dispersal between Caribbean mangroves and adjacent coral reefs, we quantify the broader implications of ecosystem connectivity for ecosystem function and resilience to climate-driven disturbance. 2. Mangrove-driven enrichment of parrotfish grazing on two coral reef habitats was calculated using empirical data. The consequences of increased grazing were then investigated using a spatial simulation of coral reef dynamics in shallow (depth 3-6 m) and mid-shelf forereefs (depth 7-15 m). 3. The largest increase in grazing occurred in shallow reefs, but was found to have negligible consequences for coral population dynamics. 4. In contrast, relatively weak increases in grazing on deeper reefs had profound consequences: reefs near mangroves were able to experience coral recovery under the most intense hurricane regimes of the Caribbean, whereas those lacking ecosystem connectivity had little capacity for recovery. 5. This surprising result occurs because reefs exhibit multiple stable equilibria and mangrove enrichment of grazing in mid-shelf reefs coincides with a zone of system instability. A small increase in grazing shifted the reef beyond a bifurcation point, thereby enhancing resilience massively. A relatively large increase in grazing in shallow reefs had minimal ecosystem consequence because the grazing levels concerned were more than double the levels needed to exceed the corresponding bifurcation point for this habitat. 6. Synthesis and applications. Caribbean mangroves are being deforested at a faster rate than rainforests, yet their protective role against hurricane damage extends not only shoreward to coastal environments but also seaward to increasing the resilience of offshore coral reefs. Specifically, ontogenetic mechanisms of ecosystem connectivity involving parrotfish may increase the probability that coral populations will recover from climate-induced changes in hurricane disturbance. Efforts to arrest mangrove deforestation and restore mangrove habitats are likely to increase the likelihood of recovery of corals on mid-depth (7-15 m) reefs after disturbance. In general, the ecosystem-level consequences of ontogenetic migration do not correspond necessarily to the magnitude of locally observed effects (i.e. the pattern of grazer enrichment exhibited the opposite pattern to that of its consequences for system resilience). Therefore, caution must be exercised when interpreting the functional significance of changes in species abundance for ecosystem process (e.g. grazing pressure and its implications for coral growth and survival). Impacts of shifting abundance or process are perhaps best appreciated using mechanistic ecosystem models. © 2008 the Authors.

Habitat maps are frequently invoked as surrogates of biodiversity to aid the design of networks of marine reserves. Maps are used to maximize habitat heterogeneity in reserves because this is likely to maximize the number of species protected. However, the technique's efficacy is limited by intra-habitat variability in the species present and their abundances. Although communities are expected to vary among patches of the same habitat, this variability is poorly documented and rarely incorporated into reserve planning. To examine intra-habitat variability in coral-reef fishes, we generated a data set from eight tropical coastal habitats and six islands in the Bahamian archipelago using underwater visual censuses. Firstly, we provide further support for habitat heterogeneity as a surrogate of biodiversity as each predefined habitat type supported a distinct assemblage of fishes. Intra-habitat variability in fish community structure at scales of hundreds of kilometers (among islands) was significant in at least 75% of the habitats studied, depending on whether presence/absence, density, or biomass data were used. Intra-habitat variability was positively correlated with the mean number of species in that habitat when density and biomass data were used. Such relationships provide a proxy for the assessment of intra-habitat variability when detailed quantitative data are scarce. Intra-habitat variability was examined in more detail for one habitat (forereefs visually dominated by Montastraea corals). Variability in community structure among islands was driven by small, demersal families (e.g. territorial pomacentrid and labrid fishes). Finally, we examined the ecological and economic significance of intra-habitat variability in fish assemblages on Montastraea reefs by identifying how this variability affects the composition and abundances of fishes in different functional groups, the key ecosystem process of parrotfish grazing, and the ecosystem service of value of commercially important finfish. There were significant differences in a range of functional groups and grazing, but not fisheries value. Variability at the scale of tens of kilometers (among reefs around an island) was less than that among islands. Caribbean marine reserves should be replicated at scales of hundreds of kilometers, particularly for species-rich habitats, to capture important intra-habitat variability in community structure, function, and an ecosystem process.

Many species of coral reef fish undertake ontogenetic migrations between seagrass beds, mangroves, and coral reefs. A recent study from the Caribbean found that the availability of mangrove nursery habitat had a striking impact on the community structure and biomass of reef fish in their adult, coral reef habitat. The biomass of several species more than doubled when the reefs were connected to rich mangrove resources (defined as having at least 70 km of fringing Rhizophora mangle within a region of 200 km2). Here, the results of this large-scale empirical study are translated into a series of algorithms for use in natural resource management planning. Four algorithms are described that identify (i) the relative importance of mangrove nursery sites, (ii) the connectivity of individual reefs to mangrove nurseries, (iii) areas of nursery habitat that have an unusually large importance to specific reefs, and (iv) priority sites for mangrove reforestation projects. The algorithms generate a connectivity matrix among mangroves and coral reefs that facilitates the identification of connected corridors of habitats within a dynamic planning environment (e.g. reserve selection algorithms). © 2005 Elsevier Ltd. All rights reserved.

Quantifying the beta diversity (species replacement along spatiotemporal gradients) of ecosystems is important for understanding and conserving patterns of biodiversity. However, virtually all studies of beta diversity focus on one-dimensional transects orientated along a specific environmental gradient that is defined a priori. By ignoring a second spatial dimension and the associated changes in species composition and environmental gradients, this approach may provide limited insight into the full pattern of beta diversity. Here, we use remotely sensed imagery to quantify beta diversity continuously, in two dimensions, and at multiple scales across an entire tropical marine seascape. We then show that beta diversity can be modeled (0.852 > or = r2 > or = 0.590) at spatial scales between 0.5 and 5.0 km2, using the environmental variables of mean and variance of depth and wave exposure. Beta diversity, quantified within a "window" of a given size, is positively correlated to the range of environmental conditions within that window. For example, beta diversity increases with increasing variance of depth. By analyzing such relationships across seascapes, this study provides a framework for a range of disparate coral reef literature including studies of zonation, diversity, and disturbance. Using supporting evidence from soft-bottom communities, we hypothesize that depth will be an important variable for modeling beta diversity in a range of marine systems. We discuss the implications of our results for the design of marine reserves.

Caribbean coral reef habitats, seagrass beds and mangroves provide important goods and services both individually and through functional linkages. A range of anthropogenic factors are threatening the ecological and economic importance of these habitats and it is vital to understand how ecosystem processes vary across seascapes. A greater understanding of processes will facilitate further insight into the effects of disturbances and assist with assessing management options. Despite the need to study processes across whole seascapes, few spatially explicit ecosystem-scale assessments exist. We review the empirical literature to examine the role of different habitat types for a range of processes. The importance of each of 10 generic habitats to each process is defined as its "functional value" (none, low, medium or high), quantitatively derived from published data wherever possible and summarised in a single figure. This summary represents the first time the importance of habitats across an entire Caribbean seascape has been assessed for a range of processes. Furthermore, we review the susceptibility of each habitat to disturbances to investigate spatial patterns that might affect functional values. Habitat types are considered at the scale discriminated by remotely-sensed imagery and we envisage that functional values can be combined with habitat maps to provide spatially explicit information on processes across ecosystems. We provide examples of mapping the functional values of habitats for populations of three commercially important species. The resulting data layers were then used to generate seascape-scale assessments of "hot spots" of functional value that might be considered priorities for conservation. We also provide an example of how the literature reviewed here can be used to parameterise a habitat-specific model investigating reef resilience under different scenarios of herbivory. Finally, we use multidimensional scaling to provide a basic analysis of the overall functional roles of different habitats. The resulting ordination suggests that each habitat has a unique suite of functional values and, potentially, a distinct role within the ecosystem. This review shows that further data are required for many habitat types and processes, particularly forereef and escarpment habitats on reefs and for seagrass beds and mangroves. Furthermore, many data were collected prior to the regional mass mortality of Diadema and Acropora, and subsequent changes to benthic communities have, in many cases, altered a habitat's functional value, hindering the use of these data for parameterising maps and models. Similarly, few data exist on how functional values change when environmental parameters, such as water clarity, are altered by natural or anthropogenic influences or the effects of a habitat's spatial context within the seascape. Despite these limitations, sufficient data are available to construct maps and models to better understand tropical marine ecosystem processes and assist more effective mitigation of threats that alter habitats and their functional values.

The patch dynamics (colonisation rate, growth rate, and extinction rate) are quantified for two dominant species of macroalgae on a Caribbean forereef in Belize: Lobophora variegata (Lamouroux) and Dictyota pulchella (Hörnig and Schnetter). Measurements were taken on time scales of days, weeks, months, and years during which three hurricanes occurred. All patches were followed on naturally occurring ramets of dead Montastraea annularis. The first hurricane (Mitch) caused massive coral mortality and liberated space for algal colonisation. The cover of Lobophora increased throughout the study and herbivores did not appear to limit its cover within a 4 year time frame. In contrast, the cover of D. pulchella fluctuated greatly and showed no net increase, despite an increase in parrotfish biomass and settlement space. Variation in the overall percent cover of an alga is not indicative of the underlying patch dynamics. The steady rise in the cover of Lobophora took place despite a high turnover of patches (12-60% of patches per year). The patch dynamics of Dictyota were slower (7-20%), but a greater patch density and threefold higher lateral growth rate led to greater fluctuations in total cover. The dynamics of algal patches are size-specific such that larger patches are less likely to become extinct during hurricanes. © Springer-Verlag 2005.

Specular reflection of solar radiation on non-flat water surfaces is a serious confounding factor for benthic remote sensing in shallow-water environments. This problem was recently overcome by Hochberg et al. who provided an effective method for the removal of 'sun glint' from remotely sensed images by utilization of the brightness in a near-infrared (NIR) band. Application of the technique was shown to give an increase in the accuracy of benthic habitat classification. However, as presented, the method is sensitive to outlier pixels, requires a time-consuming masking of land and cloud, and is not formulated in a manner leading to ease of implementation. We present a revised version of the method, which is more robust, does not require masking and can be implemented very simply. The practical approach described here will hopefully expedite the routine adoption of this effective and simple technique throughout the aquatic remote sensing community. © 2005 Taylor & Francis Group Ltd.

There has been a vast improvement in access to remotely sensed data in just a few recent years. This revolution of information is the result of heavy investment in new technology by governments and industry, rapid developments in computing power and storage, and easy dissemination of data over the internet. Today, remotely sensed data are available to virtually anyone with a desktop computer. Here, we review the status of one of the most popular areas of marine remote sensing research: coral reefs. Previous reviews have focused on the ability of remote sensing to map the structure and habitat composition of coral reefs, but have neglected to consider the physical environment in which reefs occur. We provide a holistic review of what can, might, and cannot be mapped using remote sensing at this time. We cover aspects of reef structure and health but also discuss the diversity of physical environmental data such as temperature, winds, solar radiation and water quality. There have been numerous recent advances in the remote sensing of reefs and we hope that this paper enhances awareness of the diverse data sources available, and helps practitioners identify realistic objectives for remote sensing in coral reef areas.

Hyperspectral remote sensing has shown promise for detailed discrimination of coral reef substratum types, but, by necessity, it samples at pixel scales larger than reef substratum patch sizes. Spectral unmixing techniques have been successful in resolving subpixel areal cover in terrestrial environments. However, the application of spectral unmixing on coral reefs is fundamentally challenging, due not only to the water column, but also to the potentially large number of spectrally similar and ecologically significant end-member (substratum) classes involved. A controlled ex-situ experiment was conducted using field-spectrometer data to assess the accuracy of spectral unmixing techniques to estimate the areal cover of small-scale (< 0.25 m2) assemblages of reef substrata (e.g. changes in cover between massive corals, branching corals, bleached corals, macroalgae, and coralline red algae). Mixture compositions were obtained precisely by analysis of digital images collected by a camera calibrated to the field of view of the spectrometer. Linear unmixing techniques were applied to derive estimates of substratum proportions using the full spectral resolution data and various transformations of it, including derivatives and down sampling (merging adjacent wavelengths into broader spectral bands). Comparison of actual and estimated substratum proportions indicate that spectral unmixing may be a practical approach for estimating subpixel-scale cover of coral reef substrata. In the most accurate treatment, coefficients of determination across all mixture sets were high for most end-member classes (37 of 52 cases with r2 > 0.64, i.e. r > 0.8). The most successful analyses were based on derivatives of down-sampled data, implying that spectral unmixing benefits more from spectral smoothing and judicious choice of band locations than from high spectral resolution per se. Although these results show that changes in coral and algal cover can be determined by unmixing their spectra, the method is not yet an operational remote sensing tool. Primary empirical research is needed before taking the next step, which is to incorporate a water column, of variable depth, above the sea bed. © Springer-Verlag 2003.

Trends in coral cover are widely used to indicate the health of coral reefs but are costly to obtain from field survey over large areas. In situ studies of reflected spectra at the coral surface show that living and recently dead colonies can be distinguished. Here, we investigate whether such spectral differences can be detected using an airborne remote sensing instrument. The Compact Airborne Spectrographic Imager (Itres Research Ltd, Canada) was flown in two configurations: 10 spectral bands with 1-m2 pixels and 6 spectral bands with 0.25-m2 pixels. First, we show that an instrument with 10 spectral bands possesses adequate spectral resolution to distinguish living Porites, living Pocillopora spp. partially dead Porites, recently dead Porites (total colony mortality within 6 months), old dead (>6 months) Porites, Halimeda spp. and coralline red algae when there is no water column to confuse spectra. All substrata were distinguished using fourth-order spectral derivatives around 538 nm and 562 nm. Then, at a shallow site (Tivaru) at Rangiroa Atoll, Tuamotu Archipelago (French Polynesia), we show that live and dead coral can be distinguished from the air to a depth of at least 4 m using first- and fourth-order spectral derivatives between 562-580 nm. However, partially dead and recently dead Poritescolonies could not be distinguished from an airborne platform. Spectral differences among substrata are then exploited to predict the cover of reef substrata in ten 25-m2 plots at nearby Motu Nuhi (max depth 8 m). The actual cover in these plots was determined in situ using quadrats with a 0.01-m2 grid. Considerable disparity occurred between field and image-based measures of substrate cover within individual 25-m2 quadrats. At this small scale, disparity, measured as the absolute difference in cover between field and remote-sensing methods, reached 25% in some substrata but was always less than 10% for living coral (99% of which consisted of Porites spp.). At the scale of the reef (all ten 25-m2 quadrats), however, disparities in percent cover between imagery and field data were less than 10% for all substrata and extremely low for some classes (e.g.

The problem of subpixel heterogeneity in cover types has been addressed in terrestrial environments by the application of linear spectral unmixing techniques. However, in aquatic systems the interceding depth of water causes the apparent reflectance of the substrate to diverge from a linear model, and if depth is unknown these methods cannot be applied. A new technique is presented in which the conventional spectral unmixing method has been modified to calculate depth at each pixel in addition to the proportions of substrate type. The technique requires knowledge of the reflectance spectra of m pure substrata in n (n > m) spectral bands at depth 0 and the water diffuse attenuation coefficients for the site in the same bands. Depth, z, can be entirely unknown. The method is comparable to "classical" spectral unmixing and proceeds by performing a Gaussian elimination for endmember quantities and then solving the remaining nonlinear function of z for f(z) = 0 by successive approximation. Computer-based models are used to test the technique with realistic water diffuse attenuation coefficients and random spectra and actual spectra of coral reef substrata. The robustness of the technique is assessed against three forms of introduced error: measurement errors on the spectra to be unmixed, differences between the true endmember spectra and those used in the analysis, and measurement error on the water diffuse attenuation coefficients. The results of these tests imply the technique is sufficiently robust for use on real data. Furthermore, spectral unmixing of aquatic systems appears to be relatively insensitive to inaccuracies in depth estimation and offers great utility for benthic mapping.

Ten IKONOS images of different coral reef sites distributed around the world were processed to assess the potential of 4-m resolution multispectral data for coral reef habitat mapping. Complexity of reef environments, established by field observation, ranged from 3 to 15 classes of benthic habitats containing various combinations of sediments, carbonate pavement, seagrass, algae, and corals in different geomorphologic zones (forereef, lagoon, patch reef, reef flats). Processing included corrections for sea surface roughness and bathymetry, unsupervised or supervised classification, and accuracy assessment based on ground-truth data. IKONOS classification results were compared with classified Landsat 7 imagery for simple to moderate complexity of reef habitats (5-11 classes). For both sensors, overall accuracies of the classifications show a general linear trend of decreasing accuracy with increasing habitat complexity. The IKONOS sensor performed better, with a 15-20% improvement in accuracy compared to Landsat. For IKONOS, overall accuracy was 77% for 4-5 classes, 71% for 7-8 classes, 65% in 9-11 classes, and 53% for more than 13 classes. The Landsat classification accuracy was systematically lower, with an average of 56% for 5-10 classes. Within this general trend, inter-site comparisons and specificities demonstrate the benefits of different approaches. Pre-segmentation of the different geomorphologic zones and depth correction provided different advantages in different environments. Our results help guide scientists and managers in applying IKONOS-class data for coral reef mapping applications. © 2003 Elsevier Inc. All rights reserved.

This paper uses the Special Issue of the International Journal of Remote Sensing on Remote Sensing of the Coastal Marine Environment to highlight recent advances in knowledge of remote sensing of the coastal zone and to define a series of priorities where future research into the application should be addressed. Advances were identified in the benefit of high spatial and spectral resolution data and complementary remote sensing techniques (e.g. optical and acoustic, optical and Synthetic Aperture Radar (SAR). Further benefits are identified in rapid and more frequent data acquisition, faster and more automated processing and a greater sampling intensity over conventional field-based techniques. Issues associated with adoption of remotely sensed data for management are discussed. Research priorities include the need for improved understanding and description of biotope classes and the functional interpretation of biotope maps and continued developments in understanding the radiative transfer properties of coastal environments. New knowledge is required on spatial and temporal variations of water column optical properties and its constituents. Methods for the best approaches to processing hyperspectral data require further investigation, as does the need for further testing of hyperspectral sensors for bottom type discrimination using data obtained at space-borne altitudes. Areas of value which continue to remain poorly investigated include the improvements to be gained from synergistic use of multi-wavelength remote sensing approaches, change detection techniques and multi-temporal comparisons and knowledge-based approaches to improve classification. The importance of specifically dedicated coastal zone sensors is discussed, as is alternative means of deployment (e.g. International) Space Station (ISS) and Un-inhabited Aerial Vehicles (UAVs)). The potential role of airborne digital photography for marine mapping is highlighted. The lack of accurate near-shore bathymetric data is identified as a key limitation in the application of geospatial data to coastal environments.

Coral reef communities face unprecedented pressures on local, regional and global scales as a consequence of climate change and anthropogenic disturbance. Optical remote sensing, from satellites or aircraft, is possibly the only means of measuring the effects of such stresses at appropriately large spatial scales (many thousands of square kilometres). To map key variables such as coral community structure, percentages of living coral or percentages of dead coral, a remote sensing instrument must be able to distinguish the reflectance spectra (i.e. "spectral signature", reflected light as a function of wavelength) of each category. For biotic classes, reflectance is a complex function of pigmentation, structure and morphology. Studies of coral "colour" fall into two disparate but potentially complementary types. Firstly, biological studies tend to investigate the structure and significance of pigmentation in reef organisms. These studies often lack details that would be useful from a remote sensing perspective such as intraspecific variation in pigment concentration or the contribution of fluorescence to reflectance. Secondly, remote sensing studies take empirical measurements of spectra and seek wavelengths that discriminate benthic categories. Benthic categories used in remote sensing sometimes consist of species groupings that are biologically or spectrally inappropriate (e.g. merging of algal phyla with distinct pigments). Here, we attempt to bridge the gap between biological and remote sensing perspectives of pigmentation in reef taxa. The aim is to assess the extent to which spectral discrimination can be given a biological foundation, to reduce the ad hoc nature of discriminatory criteria, and to understand the fundamental (biological) limitations in the spectral separability of biotic classes. Sources of pigmentation in reef biota are reviewed together with remote sensing studies where spectral discrimination has been effectively demonstrated between benthic categories. The basis of reflectance is considered as the sum of pigmented components, such as zooxanthellae, host tissues and skeletons of corals. Problems in the empirical in situ measurement of reflectance are identified, such as the differing types of reflectance which can be measured, the interaction of the light field with morphology, and depth-dependent variability of measured reflectance due to fluorescence. The latter is estimated in some cases to introduce an error of up to 20% when depth differs by 8 m. Spectral features useful in discriminating reef benthos are identified and related to pigmentation. The slope in the reflectance spectra between 650 and 690 nm is dependent on chlorophyll-a concentration and can be used to discriminate bare sand with no algal component from chlorophyll-a containing benthos (algae, corals). The slope in reflectance at various locations between 500 and 560 nm can be useful in discriminating bleached and unbleached corals, possibly due to reduced peridinin concentration. Rhodophyta may be discernible by the presence of a dip in reflectance at 570 nm, due to a phycoerythrin absorption peak. However, the utility of some discriminatory criteria in deeper waters is mitigated by the relatively poor transmission of light through water at longer wavelengths (especially >600 nm). Contrary to suggested categorizations of fluorescent pigments in coral host tissues, it is shown that these pigments form an almost continuous distribution with respect to their excitation and emission peaks. Remote sensing by induced fluorescence is a promising approach, but further details about the variation and distribution of these pigments are required. It is hoped that this review will promote cross-disciplinary collaboration between pigment biologists and the reef remote sensing community. Where possible, the discriminative criteria adopted in remote sensing should be related to biological phenomena, thus lending an intuitive, process-orientated basis for interpreting spectral data. Similarly, remote sensing may provide a novel scaling perspective to biological studies of pigmentation in reef organisms.

Coral reef communities face unprecedented pressures on local, regional and global scales as a consequence of climate change and anthropogenic disturbance. Optical remote sensing, from satellites or aircraft, is possibly the only means of measuring the effects of such stresses at appropriately large spatial scales (many thousands of square kilometres). To map key variables such as coral community structure, percentages of living coral or percentages of dead coral, a remote sensing instrument must be able to distinguish the reflectance spectra (i.e. "spectral signature", reflected light as a function of wavelength) of each category. For biotic classes, reflectance is a complex function of pigmentation, structure and morphology. Studies of coral "colour" fall into two disparate but potentially complementary types. Firstly, biological studies tend to investigate the structure and significance of pigmentation in reef organisms. These studies often lack details that would be useful from a remote sensing perspective such as intraspecific variation in pigment concentration or the contribution of fluorescence to reflectance. Secondly, remote sensing studies take empirical measurements of spectra and seek wavelengths that discriminate benthic categories. Benthic categories used in remote sensing sometimes consist of species groupings that are biologically or spectrally inappropriate (e.g. merging of algal phyla with distinct pigments). Here, we attempt to bridge the gap between biological and remote sensing perspectives of pigmentation in reef taxa. The aim is to assess the extent to which spectral discrimination can be given a biological foundation, to reduce the ad hoc nature of discriminatory criteria, and to understand the fundamental (biological) limitations in the spectral separability of biotic classes. Sources of pigmentation in reef biota are reviewed together with remote sensing studies where spectral discrimination has been effectively demonstrated between benthic categories. The basis of reflectance is considered as the sum of pigmented components, such as zooxanthellae, host tissues and skeletons of corals. Problems in the empirical in situ measurement of reflectance are identified, such as the differing types of reflectance which can be measured, the interaction of the light field with morphology, and depth-dependent variability of measured reflectance due to fluorescence. The latter is estimated in some cases to introduce an error of up to 20% when depth differs by 8 m. Spectral features useful in discriminating reef benthos are identified and related to pigmentation. The slope in the reflectance spectra between 650 and 690 nm is dependent on chlorophyll-a concentration and can be used to discriminate bare sand with no algal component from chlorophyll-a containing benthos (algae, corals). The slope in reflectance at various locations between 500 and 560 nm can be useful in discriminating bleached and unbleached corals, possibly due to reduced peridinin concentration. Rhodophyta may be discernible by the presence of a dip in reflectance at 570 nm, due to a phycoerythrin absorption peak. However, the utility of some discriminatory criteria in deeper waters is mitigated by the relatively poor transmission of light through water at longer wavelengths (especially > 600 nm). Contrary to suggested categorizations of fluorescent pigments in coral host tissues, it is shown that these pigments form an almost continuous distribution with respect to their excitation and emission peaks. Remote sensing by induced fluorescence is a promising approach, but further details about the variation and distribution of these pigments are required. It is hoped that this review will promote cross-disciplinary collaboration between pigment biologists and the reef remote sensing community. Where possible, the discriminative criteria adopted in remote sensing should be related to biological phenomena, thus lending an intuitive, process-orientated basis for interpreting spectral data. Similarly, remote sensing may provide a novel scaling perspective to biological studies of pigmentation in reef organisms.

The IKONOS 2 satellite was launched in late 1999 and carries the first commercial multispectral instrument to achieve 4 m spatial resolution. The cost and accuracy of using IKONOS imagery to map shallow-water marine environments is evaluated and compared directly to that using a suite of satellite and airborne instruments including Landsat Multispectral Scanner (MSS) and Thematic Mapper (TM), Satellite Pour l'Observation de la Terre (SPOT) High-Resolution Visible (HRV) multispectral and panchromatic, and Compact Airborne Spectrographic Imager (CASI). Evaluations were conducted in the Turks and Caicos Islands which are ideally suited to aquatic remote sensing because of the large areas of clear, shallow water containing a range of different habitats. Over 600 field sites were surveyed and used to define habitat categories, supervise image classification, and make an independent assessment of thematic map accuracy. For the high-resolution IKONOS imagery, pixel sizes were small enough to allow within-habitat textural information to be added to the classification. Making full use of this textural information in supervised classifications significantly improved (P

A large river plume generated by anomalous precipitation and oceanic circulation associated with Hurricane Mitch was detected off Honduras in October 1998 using SeaWiFS ocean color images. This event provides the background for analyzing connectivity between coral reefs and land in the Meso-American reef system. We discuss the potential implications of such short-term events for disease propagation and nutrification, and their potential significance in evolutionary processes.

Territorial behaviour is a conspicuous determinant of social organisation in many reef fishes including parrotfishes. Most parrotfish studies in the Caribbean have focused on the species Scarus iserti and Sparisoma viride over limited ranges of reef habitat. By contrast, our study has included all common parrotfishes in Belize (Sc. iserti, Sp. viride, Sparisoma aurofrenatum, Sparisoma chrysopterum, and Sparisoma rubripinne) at three sites with different physical and biotic conditions and a wide range of fish densities. Density in Sc. iserti was strongly positively correlated to substrate rugosity. In contrast, densities of Sp. chrysopterum and Sp. rubripinne were unrelated to rugosity and territories were large. Territory size was smallest in Sc. iserti (mean areas at the three sites ranged from 41 to 120m2) and largest in Sp. rubripinne (ranged from 168 to 1400m2). All species except Sp. chrysopterum exhibited significantly larger territories where density was low as suggested by territory theory. Territory size decreased rapidly with increasing density of competitors. Patterns of harem size differed between two groups of parrotfishes. (1) Sc. iserti, Sp. viride, and Sp. aurofrenatum exhibited an expected positive correlation with territory size. (2) Harem size was smaller in Sp. rubripinne and Sp. chrysopterum, and showed no spatial pattern. Aggression in Sp. viride and Sc. iserti was directed entirely towards intraspecifics and positively density dependent. Interspecific interactions accounted for only 10% of observations and were recorded exclusively whilst following Sp. chrysopterum, Sp. rubripinne, and, to a lesser extent, Sp. aurofrenatum. A meta analysis of species interactions suggested that intraspecific interactions were most common where overall fish density was greatest and conversely, interspecific interactions occurred more often at lower densities. This may suggest that the economic defensibility of territories is largely confined to intraspecifics where density is greatest. Most (62%) of the interspecific interactions comprised Sp. rubripinne chasing the smaller species Sp. chrysopterum, suggesting that territorial behaviour has at least some non-reproductive origin and may therefore be associated with either food or shelter. It is feasible that at such low population densities, it is economically feasible for Sp. rubripinne to defend against intraspecifics and Sp. chrysopterum. Social behaviour in Sp. chrysopterum and Sp. rubripinne, and to a lesser extent Sp. aurofrenatum, differs to that of Sc. iserti and Sp. viride which conform to existing theories of social behaviour in reef fish.

The importance of considering statistical power in marine pollution studies is unequivocal. However, the vast majority of ecological literature on power analysis focuses on parametric rather than non-parametric tests. This note describes a Monte Carlo simulation method for estimating the power of non-parametric tests. The method is illustrated using ordinal data.

During the 1998 El Niño-Southern Oscillation (ENSO) event, mass coral bleaching in French Polynesia was patchy at a scale of 100s of km. Bleaching was extensive in parts of the Tuamotu archipelago (creating up to 99% coral mortality) but extremely mild in the Society Islands (Tahiti, Moorea), ca 350 km to the south-west, despite sea surface temperature (SST) anomalies being of similar magnitude to previous years in which mass bleaching occurred. We examine whether environmental variables account for this unexpected paucity of bleaching using a 50 yr record of SST, a 17 yr record of daily wind and cloud cover, and a 17 yr record of monthly sun hours. Records from Tahiti reveal that exceptionally high cloud cover significantly reduced the number of sun hours during the summer of 1998. Quadratic discriminant analyses of annual bleaching occurrence based on up to 3 predictors (cumulative degree heating months, wind speed, and cloud cover during periods of elevated summer SST) only predicted the correct bleaching scenario for 1998 when cloud cover was added to the function. The results demonstrate that the interactive effect of cloud cover can reverse the bleaching predictions of such statistical models. We suggest that reduced radiative stress, resulting from high cloud cover, may have prevented large-scale coral bleaching in 1998.

Almost three-quarters of the world's coral reefs are thought to be deteriorating as a consequence of environmental stress. Until now, it has been possible to evaluate reef health only by field survey, which is labour-intensive and time-consuming. Here we map live coral cover from the air by remote imaging, a technique that will enable the state of shallow reefs to be monitored swiftly and over large areas.

In April-May 1998, mass coral bleaching was observed in the lagoon of Rangiroa Atoll, Tuamotu Archipelago, French Polynesia. Six months later, the extent of bleaching-induced coral mortality was assessed at three sites. Corals in the fast-growing genus Pocillopora had experienced > 99% mortality. Many large colonies of the slow-growing genus Porites (mean horizontal cross-sectional area 5.8 m2) had also died - a phenomenon not previously observed in French Polynesia and virtually unprecedented world-wide. At one site, 25% of colonies, or 44% of the pre-bleaching cover of living Porites, experienced whole-colony mortality. At the two other sites, recently dead Porites accounted for 41% and 82% of the pre-bleaching live cover. Mortality in Porites was negatively correlated with depth between 1.5 and 5 m. Using a 50-year dataset of mean monthly sea surface temperature (SST), derived from ship- and satellite-borne instruments, we show that bleaching occurred during a period of exceptionally high summer SST. 1998 was the first year in which mean monthly SSTs exceeded the 1961-1990 upper 95% confidence limit (29.4°C) for a period of three consecutive months. We suggest that the sustained 3-month anomaly in local summer SST was a major cause of coral mortality, but do not discount the synergistic effect of solar radiation. Recovery of the size-frequency distribution of Porites colonies to pre-bleaching levels may take at least 100 years.

Interest in mapping tropical coastal resources using remote sensing has never been so extensive. Tropical coastal resources are vital to many national economies but are threatened by development, over-fishing and large-scale climatic phenomena including the El Nino-Southern Oscillation. Remote sensing is the only practicable means of making large-scale synoptic assessments of coastal resources and we are entering an age of unprecedented access to remotely sensed data. Generally speaking, airborne sensors with high spectral and spatial resolution distinguish finer biological detail than coarser resolution satellite sensors. The current mapping capabilities for the major tropical systems of mangrove, seagrass and reefs are: mangrove boundaries, mangrove canopy height and closure, mangrove leaf area index, seagrass boundaries, seagrass density (three classes), seagrass standing crop, reef geomorphology, reef habitats (assemblages of species and associated substrata), and living/non-living coral colonies in very shallow clear water (

Although relatively easy to distinguish the spectra of bleached and living coral, once corals have died their skeletons remained bleached (white) for only a short period. Rapid colonisation by algae can give rise to pigmentation that may be similar to that of living coral. Thus, by the time remotely sensed imagery has been acquired, discrimination of live and dead corals is no longer facile. Field measurements of spectral reflectance of live and algal-colonised dead corals (arising from different mortality events) were made in French Polynesia. Derivative analysis revealed wavelengths and slope characteristics that could be used to discriminate between mortality states with an accuracy of ∼ 85%. These results encourage application of hyperspectral remote sensing to quantitatively assess the extent of coral bleaching events. © 2000 Taylor & Francis Group, LLC.

In 1998, coral populations in Belize were disturbed simultaneously by a severe coral bleaching event and Hurricane Mitch. The impact of these disturbances was assessed for naturally occurring populations of coral recruits (2 to 20 mm diameter), at a depth of 8 to 10 m on the forereef of Glovers Atoll. Bleaching took place at all 4 study sites but the hurricane only affected 2 sites, enabling the effects of bleaching to be compared to those arising from bleaching plus hurricane damage. Predisturbance recruit density, size-frequency distribution, and community structure were similar between sites (at kilometre scales). The bleaching event lasted ca 3.5 mo. From 70 to 90 % of adult colonies bleached and at least 25 % of recruits exhibited signs of bleaching. A month after adult colonies had regained usual colouration, only 1 % of recruits showed even partial bleaching. Surprisingly, coral bleaching alone had no measurable effect on either recruit density or community structure. The combination of bleaching and hurricane disturbance reduced total recruit densities to 20 % of pre-disturbance levels. Effects of bleaching/hurricane disturbance on community structure were spatially patchy, and I suggest that such patchiness may arise from variable cover of protective microhabitat and/or different storm conditions mediated by proximity to reef cuts (breaks in the reef crest).

Understanding and predicting the connectivity of coral reef organisms linked by larval dispersal is a key goal of tropical coastal ecosystem science and management. As oceanographers make advances modelling transport processes between reefs, ecologists should be prepared to embrace the population dynamics of organisms at larger metapopulation scales. A metapopulation is demographically closed but contains multiple open local populations. Metapopulation models of coral dynamics would aid the identification of larval source and sink areas and help identify the boundaries of demographically closed populations. Metapopulation models would also aid the understanding of species extinctions and help formulate transboundary management strategies to conserve ecosystem function. Existing metapopulation models are not spatially realistic or proven to represent physical and biological processes at appropriate spatial and temporal scales. Before more realistic alternatives can be established, further research is needed into (1) the larval transport between reefs (i.e. the coupling of reef-scale and oceanic models of water circulation, the pre-settlement mortality rates of larvae, and larval mobility in the water column), (2) the influence of larval supply on coral population dynamics at local (10s of kilometres) scales (i.e. processes of settlement behaviour, post-settlement mortality, and the pre-emption of space by algae), and (3) processes affecting the net fecundity of local populations (i.e. interactions of colony size, partial mortality rate, competition with algae, and the influence of habitat, physical disturbance, herbivore pressure, nutrification and sedimentation).

Although coastal habitat mapping is expensive, remote sensing is a more cost-effective technique than alternative field-survey methods (where effectiveness is defined as overall map accuracy). Satellite imagery is suitable for coarse detail habitat mapping where overall accuracies of c. 70% can be achieved but is inadequate for fine detail mapping, achieving c. 40% accuracy. Four types of cost are encountered when undertaking remote sensing: (1) set-up costs, (2) field survey costs, (3) image acquisition costs and (4) the time spent on analysis of field data and processing imagery. The largest of these are set-up costs such as the acquisition of hardware and software which may comprise 48-78% of the total cost of the project depending on specific objectives. For coarse-detail habitat mapping with satellite imagery, the second highest cost is field survey which can account for c. 20% of total costs and > 80% of total costs if a remote sensing facility already exists. Field survey is a vital component of any habitat mapping programme and may constitute c. 70% of project duration. For mapping small coastal areas (< 60 km in any direction) in coarse detail, SPOT XS is the most cost-effective satellite sensor; but for larger areas Landsat TM is the most cost-effective and accurate sensor. Detailed habitat mapping should be undertaken using digital airborne scanners or interpretation of colour aerial photography (API). The cost of commissioning the acquisition of such imagery can be high [£15,000-£27,000 (US$24,000-$43,000) even for small areas of 150 km2] and may constitute 27-40% of total costs (64-75% if set-up costs are excluded). Acquisition of digital airborne imagery is more expensive than the acquisition of colour aerial photography but is offset against the huge investment in time required to create maps from API. If habitat maps are needed urgently, API may be prohibitively time-consuming. For small areas of say 150 km2, a map could be created within 25 days using CASI but might take six times longer to create using API. We estimate that API is only cheaper if the staff costs for API are considerably less than £80 day-1. As the scope of the survey increases in size, the cost of API is likely to rise much faster than that arising from digital airborne scanners. If the costs of API and digital airborne scanners are similar, the latter instruments should be favoured because they are likely to yield more accurate results than API.

Classification accuracy of coral reefs can be increased significantly by compensation for light attenuation in the water column and contextual editing to account for generic patterns of reef distribution. Both processes are easily implemented and collectively constitute an accruement in accuracy of 22 per cent for airborne multispectral imagery (CASI) and up to 17 per cent for satellite sensor imagery, for each extra days effort using the technique (up to maximum accuracies of 89 and 73 per cent respectively). © 1998, Taylor & Francis Group, LLC. All rights reserved.

The digital airborne sensor, CASI (Compact Airborne Spectrographic Imager) has considerable potential for mapping marine habitats. Here we present an account of one of the first coral reef applications. The CASI was flown over reefs of the Turks and Caicos Islands (British West Indies) and set to view 1 m pixels in 8 spectral bands. In addition, reef habitats were sampled in situ by visual assessment of percent cover in 1 m quadrats. Seagrass standing crop was assessed using a calibrated visual scale. Benthic habitats were classified using hierarchical cluster and similarity percentage analyses of the field survey data. Two levels of habitat discrimination were assessed: a coarse level (corals, algae, sand, seagrass) and a fine level which included nine reef habitats. Overall accuracies of CASI-derived habitat maps were 89% and 81% for coarse and fine levels of habitat discrimination, respectively. Accuracies were greatest once CASI data had been processed to compensate for variations in depth and edited to take account of generic patterns of reef distribution. These overall accuracies were significantly (P < 0.001) better than those obtained from satellite imagery of the same site (Landsat MSS, Landsat TM, SPOT XS, SPOT Pan, merged Landsat TM/SPOT Pan). Results from CASI were also significantly better than those from interpretation of 1:10 000 colour aerial photographs of reefs in Anguilla (Sheppard et al. 1995). However, the studies may not have been entirely comparable due to a disparity in the areas mapped.

Different approaches to the classification of remotely sensed data of mangroves are reviewed, and five different methodologies identified. Landsat TM, SPOT XS and CASI data of mangroves from the Turks and Caicos Islands, were classified using each method. All classifications of SPOT XS data failed to discriminate satisfactorily between mangrove and non-mangrove vegetation. Classification accuracy of CASI data was higher than Landsat TM for all methods, and more mangrove classes could be discriminated. Merging Landsat TM and SPOT XP data improved visual interpretation of images, but did not enhance discrimination of different mangrove categories. The most accurate combination of sensor and image processing method for mapping the mangroves of the eastern Caribbean islands is identified. © 1998, Taylor & Francis Group, LLC. All rights reserved.

Airborne multispectral sensors combine many of the advantages inherent in both satellite systems and aerial photography. However, they have not been used in remote sensing studies of mangrove areas which have traditionally utilised the latter two approaches. High resolution (1 m) multispectral imagery of mangroves in the Turks and Caicos Islands was collected using a Compact Airborne Spectrographic Imager (CASI). Hierarchical agglomerative clustering with group-average sorting identified six mangrove classes which were used to direct a supervised classification (overall accuracy 78.2%). Normalised difference vegetation index (NDVI) was calculated from CASI data: linear regression models were used to predict leaf area index and percent canopy closure from NDVI. LAI and canopy closure data, estimated from field measurements for a set of sites different to those used to derive the regression models, were used to test the accuracy of LAI and canopy closure prediction. Accuracy was defined as the proportion of accuracy sites at which the LAI or percent canopy closure value (as estimated from field measurements) lay within the 95% confidence interval for the predicted value. Accuracy was high: 94% for LAI and 80% for canopy closure. The superior spatial and spectral resolution of CASI allows mangrove areas to be assessed to a greator level of detail and accuracy than with satellite sensors. Some logistics for planning CASI campaigns are discussed.

1. Ground-truthing techniques for measuring seagrass standing crop need to be simple, precise, non-destructive and quick. 2. Mellors (1991) designed a visual assessment technique for estimating above-ground seagrass biomass. This paper builds on Mellors' work and presents a modified method for estimating standing crop which uses a six-point ordinal scale (excluding zero). 3. Being non-destructive, this technique is ideally suited for resource assessment in environmentally sensitive areas and, being quick, is potentially useful when threats are imminent. 4. Statistical methods and data presented in this study will allow sample size/statistical power relationships to be estimated for any comparable study and therefore negate the need to conduct pilot surveys.

The capability of satellite and airborne remote-sensing methods for mapping Caribbean coral reefs is evaluated. Reef habitats were categorised into coarse, intermediate and fine detail, using hierarchical classification of field data (percent cover in 1 m quadrats and seagrass standing-crop). Habitats were defined as assemblages of benthic macro-organisms and substrata and were mapped using the satellite sensors Landsat MSS, Landsat TM, SPOT XS, SPOT Pan and merged Landsat TM/SPOT Pan. Habitats were also mapped using the high-resolution digital airborne sensor, CASI (compact airborne spectrographic imager). To map areas > 60 km in any direction with coarse detail, Landsat TM was the most accurate and cost-effective satellite sensor (SPOT XS when < 60 km). For maps with intermediate habitat detail, aerial photography (from a comparable study in Anguilla) exhibited similar accuracy to Landsat TM, SPOT XS, SPOT Pan and merged Landsat TM/SPOT Pan. Landsat MSS was consistently the least accurate sensor. Maps from CASI were significantly (p < 0.001) more accurate than satellite sensors and aerial photographs. Maps with detailed habitat information (i.e. > 9 reef classes) had a maximum accuracy of 37% when based on satellite imagery, but aerial photography and CASI achieved accuracies of 67 and 81%, respectively. Commissioning of new aerial photography does not appear to be a cost-effective option; satellites are cheaper for coarse habitat-mapping, and detailed habitat-mapping can be conducted more accurately and cheaply with CASI. The results will guide practitioners in matching survey objectives to appropriate remote-sensing methods.

The relationship between the normalised difference vegetation index (NDVI) and leaf area index (LAI) was modelled for mangroves growing on the Caicos Bank, Turks and Caicos Islands. NDVI values were used to predict LAI with this model and a thematic map of LAI produced from satellite data for the whole Bank. Mangrove LAI ranged between 0.8 and 7.0, with a mean of 3.96. LAI data, estimated from in situ measurements of canopy transmittance for a set of sites independent of those used to derive the LAI/NDVI model, were used to test the accuracy of this image. Accuracy was defined as the proportion of accuracy sites at which the LAI value (as estimated from field measurements) lay within the 95% confidence interval for the predicted value of LAI. The accuracy of this map was high (88%) and the mean difference between predicted and measured LAI was low (13%). Remote sensing is thus demonstrated as a powerful tool for estimating the spatial distribution of LAI for whole mangrove ecosystems. This information can be obtained rapidly compared to alternative methods of measuring LAI and can minimise the logistical and practical difficulties of fieldwork in inaccessible mangrove areas.

The standing crop of seagrass is highly sensitive to environmental disturbance. We evaluate 3 optical remote sensing methods for measuring standing crop in the tropical Western Atlantic. Extensive held measurements of standing crop were used to define empirical relationships with imagery from satellite sensors [Landsat Thematic Mapper and SPOT (Systeme Probatoire de l'Observation de la Terre) XS (multispectral)], and the digital airborne imager CASI (Compact Airborne Spectrographic Imager). Predictions of standing crop from processed imagery had high coefficients of determination: 0.74, 0.79 and 0.81 respectively. Using a bootstrap method to measure standard error, the 95% confidence interval of predictions was found to have a similar order of magnitude to quadrat sampling in situ at a precision (standard error/mean) of 10%. Explicit cost-benefit and monitoring considerations are discussed.

This article reviews applications of remote sensing to the assessment of tropical coastal resources. These applications are discussed in the context of specific management objectives and sensors used. Remote sensing remains the only way to obtain synoptic data for large coastal areas uniformly in time and space, repeatedly and nonintrusively. Routine applications to tropical coastal management include the mapping of littoral and shallow marine habitats, change detection, bathymetry mapping, and the study of suspended sediment plumes and coastal currents. The case studies reviewed suggest that wider use of remote sensing in tropical coastal zone management is limited by (1) factors that affect data availability, such as cloud cover and sensor specification; and (2) the problems that decision makers face in selecting a remote sensing technique suitable to their project objectives. These problems arise from the difficulty in comparing the capabilities of different sensors and the limited amount of published information available on practical considerations, such as cost-effectiveness and accuracy assessments. The latter are essential if management decisions are to be based upon the results. © 1996 Taylor & Francis.

1. This paper describes a straightforward method for introducing species weightings into the calculation of a similarity matrix using the Bray-Curtis coefficient. Weighting may be required in order to provide differential emphasis in abundances on the basis of species' size, ecological importance, abundance or in mixing different data types. The similarity matrix can then be used for a range of multivariate analytical procedures, such as cluster analysis or ordination using non-metric multi-dimensional scaling (MDS). Such techniques are widely used for the identification of species' assemblages and habitats in marine resource and conservation assessment. 2. The weighting procedure was used to examine the effect of variable accuracy in species identification by trained volunteer divers conducting baseline surveys of reefal habitats in Belize. The accuracy of identification was found to vary asymmetrically between species. 3. The modified Bray-Curtis similarity coefficient was used to incorporate individual species weightings which are proportional to the frequency at which each species is correctly identified. The results of the study demonstrate the fundamental robustness of the Bray-Curtis similarity coefficient/multivariate approach which together, are insensitive to the asymmetric accuracy levels present in the data.

The planning process for marine protected areas in Belize, Central America, adopts geographic information system (GIS) technology to integrate data from a variety of sources. This article describes the importance of GIS in assisting institutional cooperation and illustrates the many advantages of GIS over conventional approaches to mapping and data management. GIS is a powerful analytical tool that has allowed the improvement of inadequate ground control and base mapping through the incorporation of differential global positioning systems technology. Subsequent resource mapping has been carried out through the application of SPOT Panchromatic and other remotely sensed imagery, field survey, and existing GIS data. In Belize, GIS products are increasingly being used as the primary source for management plans. The technology will play a key role in the future development of management initiatives for the country's coastal zone. © 1995 Taylor and Francis.