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The ecology of many coral reefs has changed markedly over recent decades in response to various combinations of local and global stressors. These ecological changes have important implications for the abundance of taxa that regulate the production and erosion of skeletal carbonates, and thus for many of the geo‐ecological functions that coral reefs provide, including reef framework production and sediment generation, the maintenance of reef habitat complexity and reef growth potential. These functional attributes underpin many of the ecosystem goods and services that reefs provide to society. Rapidly changing conditions of reefs in the Anthropocene are likely to significantly impact the capacity of reefs to sustain these geo‐ecological functions. Although the Anthropocene footprint of disturbance will be expressed differently across ecoregions and habitats, the end point for many reefs may be broadly similar: (a) progressively shifting towards net neutral or negative carbonate budget states; (b) becoming structurally flatter; and (c) having lower vertical growth rates. It is also likely that a progressive depth‐homogenisation will occur in terms of these processes. The Anthropocene is likely to be defined by an increasing disconnect between the ecological processes that drive carbonate production on the reef surface, and the net geological outcome of that production, that is, the accumulation of the underlying reef structure. Reef structures are thus likely to become increasingly relict or senescent features, which will reduce reef habitat complexity and sediment generation rates, and limit reef potential to accrete vertically at rates that can track rising sea levels. In the absence of pervasive stressors, recovery of degraded coral communities has been observed, resulting in high net‐positive budgets being regained. However, the frequency and intensity of climate‐driven bleaching events are predicted to increase over the next decades. This would increase the spatial footprint of disturbances and exacerbate the magnitude of the changes described here, limiting the capacity of many reefs to maintain their geo‐ecological functions. The enforcement of effective marine protection or the benefits of geographic isolation or of favourable environmental conditions (“refugia” sites) may offer the hope of more optimistic futures in some locations. A >plain language summary is available for this article. Plain Language Summary Foreign Language Resumen La ecología de muchos arrecifes de coral ha cambiado notablemente en las últimas décadas en respuesta a combinaciones de factores de estrés locales y globales. Estos cambios ecológicos tienen implicaciones importantes para la abundancia de taxones que regulan la producción y la erosión de esqueletos de carbonato de calcio, y por lo tanto, para muchas de las funciones geo‐ecológicas clave que brindan los arrecifes de coral, incluida la construcción del marco arrecifal, la generación de sedimentos, el mantenimiento de la complejidad del hábitat y el potencial de crecimiento del arrecife. Estos atributos funcionales también sustentan muchos de los bienes y servicios del ecosistema que los arrecifes proporcionan a la sociedad. Es probable que las condiciones cambiantes de los arrecifes en el Antropoceno afecten significativamente la capacidad de los arrecifes de mantener estas funciones geo‐ecológicas. Si bien la huella de perturbación del Antropoceno se expresará de manera diferente en diferentes ecoregiones y hábitats, el punto final de muchos arrecifes puede ser muy similar: (a) cambiando progresivamente hacia estados con presupuesto de carbonato neutro o negativo netos; (b) reducir su complejidad estructural; o (c) tener menores tasas de crecimiento vertical. También es probable que se produzca una homogeneización de profundidad progresiva en términos de estos procesos y atributos. Es probable que el antropoceno se defina por la desconexión entre los procesos ecológicos que determinan la producción de carbonato en el arrecife y el producto geológico neto de esa producción, es decir, la acumulación de estructuras arrecifales. Es posible, por lo tanto, que las estructuras arrecifales no se renueven (se vuelvan cada vez más decrépitas), lo que perjudicará su capacidad de mantener la complejidad del hábitat, altas tasas de generación de sedimentos y en términos generales limitaría el potencial de crecimiento vertical, limitando así el potencial de alcanzar el aumento del nivel del mar. En ausencia de factores de estrés permanentes, se ha observado la recuperación de comunidades de corales degradadas, lo que resulta en la recuperación de presupuestos netos positivos. Sin embargo, se prevé que la frecuencia e intensidad de los eventos de blanqueamiento relacionados al cambio climático aumentarán en las próximas décadas, lo que aumentaría la magnitud de los cambios descritos aquí. Limitando, así la capacidad de muchos arrecifes de mantener sus funciones geo‐ecológicas. La aplicación efectiva de la protección marina, los beneficios del aislamiento geográfico o de las condiciones ambientales favorables (sitios de “refugio”) pueden ofrecer esperanza de un futuro más optimista en algunos lugares.

Marine ecosystems globally have suffered habitat, biodiversity and function loss in response to human activity. Marine Protected Areas (MPAs) can limit extractive activities and enhance ecosystem resilience, but do not directly address external stressors. We surveyed 48 sites within seven MPAs and nearby unprotected areas to evaluate drivers of coral reef condition in the Mexican Caribbean. We found that local human activity limits protection effectiveness. Coral cover was positively related to protection characteristics, but was significantly lower at sites with elevated local human activity. Furthermore, we predict ongoing coastal development will reduce coral cover despite expanded protection within a regionwide MPA if an effective integrated coastal zone management strategy is not implemented. Policy makers must acknowledge the detrimental impact of uncontrolled coastal development and apply stringent construction and wastewater regulations in addition to marine protection.

Stony coral tissue loss disease (SCTLD) is one of the most aggressive coral syndromes recorded, affecting over 30 scleractinian species and causing high mortality rates. Despite its impact, most available information is derived from assessments that estimate prevalence at a single point in time, rather than examining its temporal dynamics. This study analyzed the susceptibility of 16 coral species to SCTLD and tracked the 2018–2019 outbreak on a fringing reef in the Mexican Caribbean using epidemiological methods commonly employed in human epidemics but rarely in coral epizootics. Between June 2018 and July 2019, we monitored 990 coral colonies. For each affected colony, we estimated the progression of tissue death over time, allowing us to identify the days of lesion onset and total tissue mortality. To assess vulnerability and provide a detailed prognosis of outbreak progression, magnitude, and severity during the epizootic we employed epidemic curves, Kaplan-Meier risk and survival functions, and measures of period prevalence and mortality. Epidemiological parameters from these analyses were integrated into a multi-dimensional framework for a comprehensive assessment of coral susceptibility. Our findings revealed that species-specific susceptibility was associated with the risk, magnitude, and severity of the epizootic but not with its progression. Temporal analyses revealed community-level patterns, including secondary outbreak waves following increases in mortality. This suggests a potential feedback mechanism, where mortality may contribute to secondary transmission events, a phenomenon not previously described in the study of coral epizootics. As a contribution to the characterization of coral susceptibility to SCTLD, we outline a four-level framework based on diverse epidemiological indicators, beyond prevalence. This approach revealed a higher-than-expected susceptibility in Siderastrea siderea, Agaricia agaricites and Agaricia tenuifolia, compared to previous studies. This study underscores the importance of epidemiological approaches in investigating coral epizootics. By challenging traditional reliance on prevalence measurements, our findings offer a novel perspective on coral disease dynamics.

Sea-level rise (SLR) is predicted to elevate water depths above coral reefs and to increase coastal wave exposure as ecological degradation limits vertical reef growth, but projections lack data on interactions between local rates of reef growth and sea level rise. Here we calculate the vertical growth potential of more than 200 tropical western Atlantic and Indian Ocean reefs, and compare these against recent and projected rates of SLR under different Representative Concentration Pathway (RCP) scenarios. Although many reefs retain accretion rates close to recent SLR trends, few will have the capacity to track SLR projections under RCP4.5 scenarios without sustained ecological recovery, and under RCP8.5 scenarios most reefs are predicted to experience mean water depth increases of more than 0.5 m by 2100. Coral cover strongly predicts reef capacity to track SLR, but threshold cover levels that will be necessary to prevent submergence are well above those observed on most reefs. Urgent action is thus needed to mitigate climate, sea-level and future ecological changes in order to limit the magnitude of future reef submergence. Analyses of current coral reef growth rates in the tropical western Atlantic and Indian Ocean show that few reefs will have the capacity to track sea-level rise projections under Representative Concentration Pathway scenarios without sustained ecological recovery.

Diseases are major drivers of the deterioration of coral reefs and are linked to major declines in coral abundance, reef functionality, and reef-related ecosystems services. An outbreak of a new disease is currently rampaging through the populations of the remaining reef-building corals across the Caribbean region. The outbreak was first reported in Florida in 2014 and reached the northern Mesoamerican Reef by summer 2018, where it spread across the ~450-km reef system in only a few months. Rapid spread was generalized across all sites and mortality rates ranged from 94% to <10% among the 21 afflicted coral species. Most species of the family Meandrinadae (maze corals) and subfamily Faviinae (brain corals) sustained losses >50%. This single event further modified the coral communities across the region by increasing the relative dominance of weedy corals and reducing reef functionality, both in terms of functional diversity and calcium carbonate production. This emergent disease is likely to become the most lethal disturbance ever recorded in the Caribbean, and it will likely result in the onset of a new functional regime where key reef-building and complex branching acroporids, an apparently unaffected genus that underwent severe population declines decades ago and retained low population levels, will once again become conspicuous structural features in reef systems with yet even lower levels of physical functionality. A new deadly coral disease, known as stony coral tissue loss disease, has modified the coral communities across the Caribbean region by disproportionately affecting key reef-building corals and reducing reef functionality.

Caribbean reef corals have experienced unprecedented declines from climate change, anthropogenic stressors and infectious diseases in recent decades. Since 2014, a highly lethal, new disease, called stony coral tissue loss disease, has impacted many reef-coral species in Florida. During the summer of 2018, we noticed an anomalously high disease prevalence affecting different coral species in the northern portion of the Mexican Caribbean. We assessed the severity of this outbreak in 2018/2019 using the AGRRA coral protocol to survey 82 reef sites across the Mexican Caribbean. Then, using a subset of 14 sites, we detailed information from before the outbreak (2016/2017) to explore the consequences of the disease on the condition and composition of coral communities. Our findings show that the disease outbreak has already spread across the entire region by affecting similar species (with similar disease patterns) to those previously described for Florida. However, we observed a great variability in prevalence and tissue mortality that was not attributable to any geographical gradient. Using long-term data, we determined that there is no evidence of such high coral disease prevalence anywhere in the region before 2018, which suggests that the entire Mexican Caribbean was afflicted by the disease within a few months. The analysis of sites that contained pre-outbreak information showed that this event considerably increased coral mortality and severely changed the structure of coral communities in the region. Given the high prevalence and lethality of this disease, and the high number of susceptible species, we encourage reef researchers, managers and stakeholders across the Western Atlantic to accord it the highest priority for the near future.

Coral reefs are rich in biodiversity, in large part because their highly complex architecture provides shelter and resources for a wide range of organisms. Recent rapid declines in hard coral cover have occurred across the Caribbean region, but the concomitant consequences for reef architecture have not been quantified on a large scale to date. We provide, to our knowledge, the first region-wide analysis of changes in reef architectural complexity, using nearly 500 surveys across 200 reefs, between 1969 and 2008. The architectural complexity of Caribbean reefs has declined nonlinearly with the near disappearance of the most complex reefs over the last 40 years. The flattening of Caribbean reefs was apparent by the early 1980s, followed by a period of stasis between 1985 and 1998 and then a resumption of the decline in complexity to the present. Rates of loss are similar on shallow (<6 m), mid-water (6-20 m) and deep (>20 m) reefs and are consistent across all five subregions. The temporal pattern of declining architecture coincides with key events in recent Caribbean ecological history: the loss of structurally complex Acropora corals, the mass mortality of the grazing urchin Diadema antillarum and the 1998 El Nino Southern Oscillation-induced worldwide coral bleaching event. The consistently low estimates of current architectural complexity suggest regional-scale degradation and homogenization of reef structure. The widespread loss of architectural complexity is likely to have serious consequences for reef biodiversity, ecosystem functioning and associated environmental services.

The decline of reef‐building corals in conjunction with shifts to short‐lived opportunistic species has prompted concerns that Caribbean reef framework‐building capacity has substantially diminished. Restoring herbivore populations may be a potential driver of coral recovery; however, the impact of herbivores on coral calcification has been little studied. We performed an exclusion experiment to evaluate the impact of herbivory on Orbicella faveolata coral growth over 14 months. The experiment consisted of three treatments: full exclusion cages; half cage procedural controls; and uncaged control plates, each with small O. faveolata colonies. We found that herbivorous fish exclusion had a substantial impact on both macroalgal cover and coral growth. Fleshy macroalgae reached 50% cover within some exclusion cages, but were almost absent from uncaged control plates. Critically, O. faveolata calcification rates were suppressed by almost half within exclusion cages, with monthly coral growth negatively related to overgrowth by fleshy macroalgae. These findings highlight the importance of herbivorous fishes for coral growth and the detrimental impact of macroalgal proliferation in the Caribbean. Policy makers and local managers should consider measures to protect herbivorous fishes and reduce macroalgal proliferation to enable coral communities to continue to grow and function. We performed a herbivore exclusion experiment to evaluate the impact of herbivory on Caribbean coral growth. We found that herbivorous fish exclusion had a substantial impact on both macroalgal cover and coral growth, with calcification rates suppressed by almost half within exclusion cages. These findings highlight the importance of herbivorous fishes for coral growth and the detrimental impact of macroalgal proliferation in the Caribbean.

Phase shifts from hard coral to macroalgae have led to the formulation of a top-down herbivory paradigm, whose assumption is that a reduction in herbivory is the primary driver of these changes. Caribbean parrotfish from Scarus and Sparisoma genera are usually known as main reef herbivorous. Yet, they are a diverse group of organisms that perform multiple functions, including the bioerosion of reef structures. Generalizing functions at the group level likely explains why the direct effects of parrotfish on macroalgae regulation are not always evident. In this study, we tested the hypothesis that parrotfish potential functions are strongly linked to the habitat’s benthic characteristics. Furthermore, we expect that the parrotfish bioerosion potential will be highly sensitive to changes in benthic conditions, while herbivory will be more robust. We conducted in situ benthic and parrotfish surveys across the diverse reefscape of the remote Alacranes Reef, the most extensive system in the Gulf of Mexico. Both bioerosion and herbivory potential were highest in the most complex and structured sites, while only macroalgae removal was high in deep low-coral cover sites dominated by fleshy macroalgae. Interestingly, both functions were highly diminished in shallow and reticulated inner reefs dominated by turf algae and cyanobacteria, suggesting that even the herbivory function can be depleted under unfavorable benthic conditions. Our findings highlight the need to reconsider parrotfish management strategies to account for the specific roles of different species and consider reciprocal benthic-fish interactions.

Coral reefs in the wider Caribbean declined in hard coral cover by ~80% since the 1970s, but spatiotemporal analyses for sub-regions are lacking. Here, we explored benthic change patterns in the Mexican Caribbean reefs through meta-analysis between 1978 and 2016 including 125 coral reef sites. Findings revealed that hard coral cover decreased from ~26% in the 1970s to 16% in 2016, whereas macroalgae cover increased to ~30% in 2016. Both groups showed high spatiotemporal variability. Hard coral cover declined in total by 12% from 1978 to 2004 but increased again by 5% between 2005 and 2016 indicating some coral recovery after the 2005 mass bleaching event and hurricane impacts. In 2016, more than 80% of studied reefs were dominated by macroalgae, while only 15% were dominated by hard corals. This stands in contrast to 1978 when all reef sites surveyed were dominated by hard corals. This study is among the first within the Caribbean region that reports local recovery in coral cover in the Caribbean, while other Caribbean reefs have failed to recover. Most Mexican Caribbean coral reefs are now no longer dominated by hard corals. In order to prevent further reef degradation, viable and reliable conservation alternatives are required.