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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.Reservas Marinas, Vedas Pesqueras y 20 Años de Cambios Positivos en un Ecosistema de Arrecife de Coral Resumen Para el año 2004, Belice estaba exhibiendo la clásica pesca de los niveles más bajos de las cadenas alimenticias marinas. Los meros (Serranidae) y los pargos (Lutjanidae) eran escasos y las pesquerías comenzaron a consumir a los peces loro (Scarinae), lo que resultó en una declinación del 41% de su biomasa. Entre el 2009 y el 2010 se promulgaron varias políticas, incluyendo una moratoria para la pesca del pez loro y un nuevo parque marino con zonas de no consumo. Mediante una serie temporal de 20 años para los peces de arrecifes y el bentos, evaluamos el impacto de estas políticas aproximadamente diez años después de su implementación. La creación de la Reserva Marina del Cayo Southwater resultó en la recuperación del pargo en dos de tres sitios, pero no hubo evidencias de la recuperación fuera de la reserva. Las poblaciones de pargos en una reserva más vieja continuaron su incremento, lo que implica que se requieren al menos nueve años para su recuperación. A pesar de la preocupación por la viabilidad de la veda para el pez loro una vez que se haya convertido en una pesquería dominante, los peces loro regresaron al sitio de pesca y excedieron los niveles de biomasa previos a la pesquería. La mayoría de estos cambios involucró un incremento en la densidad de los peces loro; la composición de especies y la talla corporal adulta generalmente exhibieron pocos cambios. La recuperación ocurrió equitativamente bien en las reservas y en las áreas abiertas a otras formas de pesca, lo que implica un estricto cumplimiento de las restricciones. Las tendencias temporales en la intensidad de pastoreo de los peces loro estuvieron fuertemente asociadas de manera negativa con la cobertura de macroalgas, la cual para el 2018 había caído a los niveles más bajos observados desde que se comenzó a medir en 1998. Las poblaciones coralinas permanecieron resilientes y continuaron exhibiendo periodos de recuperación neta después de la perturbación. Descubrimos que una moratoria para la pesca de pez loro es viable y parece ayudar a restringir las macroalgas, las cuales de otra forma pueden impedir la resiliencia del coral.至 2004 年, 伯利兹的渔业展现出典型的沿食物网向小型鱼类转移。由于石斑鱼 (Serranidae) 和笛鲷 (Lutjanidae) 已十分稀少, 渔业捕捞转向了鹦嘴鱼 (Scarinae), 导致其生物量下降了 41% 。为此, 政府在 2009-2010 年颁布了多项政策, 如暂停捕捞鹦嘴鱼, 以及新设一个包含禁捕区的海洋保护区。我们利用珊瑚礁鱼类和底栖生物 20 年的时间序列数据, 评估了这些政策实施约 10 年后的影响。我们发现, Southwater Caye 海洋保护区建立后, 三个研究地点中的两个点的笛鲷数量得到恢复, 但在保护区以外并无恢复迹象。笛鲷种群数量在一个较早建立的保护区中持续增加, 意味着其种群恢复至少需要 9 年时间。尽管人们担心鹦嘴鱼一旦成为鱼翅产业主要鱼类后对其禁捕是否可行, 鹦嘴鱼已经重回该地区且其生物量已超过捕捞前的水平。其间发生的主要变化包括鹦嘴鱼密度的增加, 而物种组成和成体体型变化不大。在保护区和开放其它形式捕捞的地区, 鹦嘴鱼的恢复情况也同样可观, 这意味着政策得到了严格遵守。此外, 鹦嘴鱼摄食强度的时间变化趋势与大型藻类覆盖表现出强烈的负相关, 到 2018 年, 大型藻类覆盖已降至 1998 年开始测量以来的最低水平。珊瑚种群在受到干扰后仍保持恢复能力, 并在一段时间内保持着净恢复。本研究表明暂停捕捞鹦嘴鱼是可行的, 且有助于抑制影响珊瑚恢复力的大型藻类。【翻译:胡怡思; 审校:聂永刚】.

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.

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.

To ensure standardized, quantitative and repeatable methodologies, marine ecologists have engineered a range of artificial units to survey benthic communities with varying designs depending on target taxa, life history stage and habitat. In tropical ecosystems, autonomous units have typically lacked microhabitat complexity (e.g. planar tiles), short-term efficacy (

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) 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.

Reef carbonate production and sediment generation are key processes for coral reef development and shoreline protection. The calcified green alga Halimeda is a major contributor of calcareous sediments, but rates of production and herbivory upon Halimeda are driven by biotic and environmental factors. Consequently, estimating rates of calcium carbonate (CaCO3) production and transformation into sediment requires the integration of Halimeda gains and losses across habitats and seasons, which is rarely considered in carbonate budgets. Using seasonal rates of recruitment, growth, senescence and herbivory derived from observations and manipulative experiments, we developed an individual-based model to quantify the annual cycle of Halimeda carbonate and sediment production at Heron Island, Great Barrier Reef. Halimeda population dynamics were simulated both within and outside branching Acropora canopies, which provide refuge from herbivory. Shelter from herbivory allowed larger Halimeda thalli to grow, leading to higher rates of carbonate accumulation (3.9 and 0.9 kg CaCO3 m-2 yr-1 within and outside Acropora canopies, respectively) and sediment production (2.5 versus 1.0 kg CaCO3 m-2 yr-1, respectively). Overall, 37% of the annual carbonate production was transformed into sediments through senescence (84%) and fish herbivory (16%), with important variations among seasons and habitats. Our model underlines that algal rates of carbonate production are likely to be underestimated if herbivory is not integrated into the carbonate budget, and reveals an important indirect pathway by which structurally complex coral habitats contribute to reef carbonate budgets, suggesting that coral losses due to climate change may lead to further declines in reef sediment production.

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.

Herbivory is a key ecosystem function that influences ecosystem trajectories. However, interactions between plants and herbivores are species-specific and change throughout the plants’ lifetime. On coral reefs, herbivorous fishes reduce competition between corals and macroalgae through their grazing activity, thereby regulating the ecosystem state. Grazing vulnerability of marine algae generally decreases with increasing algal size. Therefore, the removal of newly settled recruits by herbivorous fish is likely important in preventing macroalgal blooms and reducing competition with corals. We studied the grazing susceptibility of recruits of the brown macroalga Lobophora to multiple fish species through a combination of feeding observations and manipulative in situ and ex situ experiments. Further, we recorded short-term Lobophora growth patterns and adult survival over 9 wk. Lobophora recruits were more susceptible to herbivory than adults, likely owing to their smaller size. However, recruit mortality was driven by only 3 of the studied species: Acanthurus nigrofuscus, Scarus niger and Chlorurus spilurus, whereas other common herbivores did not remove any Lobophora recruits. Our data also suggest variable growth and recruitment among months. These findings point to a possible increase in grazing resistance with age for Lobophora. As such, a decrease in grazing pressure by key fish species controlling Lobophora recruits could permit Lobophora to establish more grazing-tolerant adult populations.

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 (

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 degrees 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 similar to 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.

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

Aim: Widespread 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. Location: The Great Barrier Reef, Australia. Methods: Contemporary biophysical larval dispersal models were used to predict long-distance multigenerational connections for two common and foundational coral species (Acropora tenuis and Acropora 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. Results: At long distances, biophysical models predicted a preponderance of north-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-south; and asymmetric eigenvectors derived from north-south connections in the biophysical models were significantly better predictors of spatial genetic patterns than eigenvectors derived from symmetric null spatial models. Main conclusions: Results are consistent with biophysical dispersal models yielding approximate summaries of past multigenerational gene flow conditioned upon directionality of connections. For A. tenuis and A. 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.

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.

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.

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 piece of Lobophora was distributed throughout a 100 cm 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.

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.

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.

International audience; 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 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, welldesigned, and rapidly executed strategy with political and social commitments at the level of other grand challenges.

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 modelling (SEM) approach, we explored the interactions between the shark abundance and teleost mesopredator and prey functional group density and biomass, whilst explicitly accounting for the potentially confounding influence of environmental variation across sites. While 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.

In recent decades, extensive mortality of reef-building corals throughout the Caribbean region has led to the erosion of reef frameworks and declines in biodiversity. Using field observations, structural models, and high-precision U–Th dating methods, we quantify changes in structural complexity in the major framework-building coral Orbicella annularis over a 20-year period at Long Caye (Belize). Despite extensive mortality following the mass coral bleaching event of 1998, the structural complexity of frameworks remained largely unchanged between 1998 (rugosity index, R, of 2.35±0.1) and 2018 (R of 2.29±0.1). Colony-scale structural complexity was maintained, as the rapid growth of surviving ramets (0.69±0.1 cm yr−1) offset the slower bioerosion of dead ramets (-0.11±0.16 cm yr−1). Despite the apparent stability of the structural complexity at colony scales, bioerosion of individual dead ramets over 2 decades led to declines in microhabitat complexity, with an overall reduction in the depth of microhabitats within frameworks. Altered microhabitat complexity appears to have negative effects on cryptic fauna, with the grazing urchin Echinometra viridis declining from 1.5±0.4 individuals m−2 in 1998 to 0.02± individuals m−2 in 2018. Changes in microhabitat complexity have the potential to alter ecological interactions that can impact recovery dynamics on coral reefs in ways that are undetectable using traditional rugosity metrics of structural complexity.

Stress-induced reductions in the world’s coral populations are, in many locations, giving way to an increase in macroalgae, for example the common brown macroalgal genus Lobophora. While many ecological studies report a single species (Lobophora variegata), DNA-based identification methods have recently shown that Lobophora is a highly diverse genus with over 100 reported species. Here, we aim to identify possible ecological differences among Lobophora species by investigating environmental drivers of Lobophora assemblages. We sampled Lobophora thalli from 12 reefs around Palau (Micronesia) at varying depths, wave exposure, and herbivore biomass. Using one mitochondrial marker (cox3) and two chloroplast markers (psbA, rbcL), we uncovered a striking cryptic diversity of 15 species, including 8 undescribed taxa. Associations between potential drivers and Lobophora assemblages varied at two spatial scales. At the larger scale of both island coastlines only a single variable—wave exposure—was found to be important. On a smaller geographic scale, confined to the east coast, all factors—wave exposure, depth and herbivory—were associated with assemblages of Lobophora. Widespread sampling indicates the presence of generalist species, which were found in most sampled habitats, and specialists, which occupy specific habitats. Such high levels of cryptic diversity have important implications for ecological studies. Given that species inhabit different environments, have a variable growth form, and have a threefold difference in thallus thickness, it seems likely that species differ in their function. If these differences manifest in competitive strengths, these results have broad implications for our understanding of coral reef recovery following perturbation.

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.

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'.

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.

Some of the fundamental drivers of reef functioning are being rewritten through progress in understanding nutrient cycling. The sponge loop, described in 2013, revealed that some cryptic sponges can convert dissolved organic carbon (DOC) into detritus. In subsequent studies, researchers proposed that sponges and seaweeds could mutually reinforce their abundance by utilizing each other's waste products, thereby helping to suppress coral recovery. We build on these ideas, including the provision of a new but related hypothesis to explain the reinforcement of coral-algal phase shifts: Detritus and DOC resulting from fleshy algae reduce light penetration and increase the stress on corals, particularly in terms of calcification. We then consider the wider ecosystem implications of nutrient cycling and arrive at some novel conclusions. In particular, we propose that the combination of higher sponge biomass, which generates detritus, with the relative paucity of detritivory should generate a surplus of detritus on Caribbean reefs compared with that of the Indo-Pacific. New studies are needed to quantify the generality of the sponge loop and to track the fate of detritus to determine whether there is a surplus in the Caribbean. Although Charles Darwin identified enigmatic aspects of the nutritional status of coral reefs, this research field continues to surprise and redefine how we view the dynamics of this complex 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.

1. Human activities have led to widespread ecological decline; however, the severity of degradation is spatially heterogeneous due to some locations resisting, escaping, or rebounding from disturbances.2. We developed a framework for identifying oases within coral reef regions using long-term monitoring data. We calculated standardised estimates of coral cover (z-scores) to distinguish sites that deviated positively from regional means. We also used the coefficient of variation (CV) of coral cover to quantify how oases varied temporally, and to distinguish among types of oases. We estimated "coral calcification capacity" (CCC), a measure of the coral community's ability to produce calcium carbonate structures and tested for an association between this metric and z-scores of coral cover.3. We illustrated our z-score approach within a modelling framework by extracting z-scores and CVs from simulated data based on four generalized trajectories of coral cover. We then applied the approach to time-series data from long-term reef monitoring programmes in four focal regions in the Pacific (the main Hawaiian Islands and Mo'orea, French Polynesia) and western Atlantic (the Florida Keys and St. John, US Virgin Islands). Among the 123 sites analysed, 38 had positive z-scores for median coral cover and were categorised as oases.4. Synthesis and applications. Our framework provides ecosystem managers with a valuable tool for conservation by identifying "oases" within degraded areas. By evaluating trajectories of change in state (e.g., coral cover) among oases, our approach may help in identifying the mechanisms responsible for spatial variability in ecosystem condition. Increased mechanistic understanding can guide whether management of a particular location should emphasise protection, mitigation or restoration. Analysis of the empirical data suggest that the majority of our coral reef oases originated by either escaping or resisting disturbances, although some sites showed a high capacity for recovery, while others were candidates for restoration. Finally, our measure of reef condition (i.e., median z-scores of coral cover) correlated positively with coral calcification capacity suggesting that our approach identified oases that are also exceptional for one critical component of ecological function.

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.

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.

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.

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.

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. This article is protected by copyright. All rights reserved.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

Coral reefs are among the world's most endangered ecosystems. Coral mortality can result from ocean warming or other climate-related events such as coral bleaching and intense hurricanes. While resilient coral reefs can recover from these impacts as has been documented in coral reefs throughout the tropical Indo-Pacific, no similar reef-wide recovery has ever been reported for the Caribbean. Climate change-related coral mortality is unavoidable, but local management actions can improve conditions for regrowth and for the establishment of juvenile corals thereby enhancing the recovery resilience of these ecosystems. Previous research has determined that coral reefs with sufficient herbivory limit macroalgae and improve conditions for coral recruitment and regrowth. Management that reduces algal abundance increases the recovery potential for both juvenile and adult corals on reefs. Every other year on the island of Bonaire, Dutch Caribbean, we quantified patterns of distribution and abundance of reef fish, coral, algae, and juvenile corals along replicate fixed transects at 10 m depth at multiple sites from 2003 to 2017. Beginning with our first exploratory study in 2002 until 2007 coral was abundant (45% cover) and macroalgae were rare (6% cover). Consecutive disturbances, beginning with Hurricane Omar in October 2008 and a coral bleaching event in October 2010, resulted in a 22% decline in coral cover and a sharp threefold increase in macroalgal cover to 18%. Juvenile coral densities declined to about half of their previous abundance. Herbivorous parrotfishes had been declining in abundance but stabilized around 2010, the year fish traps were phased out and fishing for parrotfish was banned. The average parrotfish biomass from 2010 to 2017 was more than twice that reported for coral reefs of the Eastern Caribbean. During this same period, macroalgae declined and both juvenile coral density and total adult coral cover returned to pre-hurricane and bleaching levels. To our knowledge, this is the first example of a resilient Caribbean coral reef ecosystem that fully recovered from severe climate-related mortality events.

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.

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.

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.

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.