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1. Modeling the effects of selectively fishing key functional groups of herbivores on coral resilience

   https://doi.org/10.1002/ecs2.4749  

   Cook, Dana T; Schmitt, Russell J; Holbrook, Sally J; Moeller, Holly V (January 2024, Ecosphere)

   Abstract Mounting evidence suggests that fishing can be a major driver of coral‐to‐macroalgae regime shifts on tropical reefs. In many small‐scale coral reef fisheries, fishers target herbivorous fishes, which can weaken coral resilience via reduced herbivory on macroalgae that then outcompete corals. Previous models that explored the effects of harvesting herbivores revealed hysteresis in the herbivory–benthic state relationship that results in bistability of coral‐ and macroalgae‐dominated states over some levels of fishing pressure, which has been supported by empirical evidence. However, past models have not accounted for the functional differences among herbivores or how fisher selectivity for different herbivore functional groups may alter the benthic dynamics and resilience. Here, we use a dynamic model that links differential fishing on two key herbivore functional groups to the outcome of competitive dynamics between coral and macroalgae. We show that reef state depends not only on the level of fishing but also on the types of herbivores targeted by fishers. Selectively fishing browsing herbivores that are capable of consuming mature macroalgae (e.g., unicornfish) increases precariousness of the coral state by moving the system close to the coral‐to‐macroalgae tipping point. By contrast, selectively harvesting grazing herbivores that are only capable of preventing macroalgae from becoming established (e.g., parrotfishes) can increase catch yields substantially more before the tipping point is reached. However, this lower precariousness with increasing fishing effort comes at the cost of increasing the range of fishing effort over which coral and macroalgae are bistable; increasing hysteresis makes a regime shift triggered by a disturbance more difficult or impractical to reverse. Our results suggest that management strategies for small‐scale coral reef fisheries should consider how functional differences among harvested herbivores coupled with fisher selectivity influence benthic dynamics in light of the trade‐off between tipping point precariousness and coral recovery dynamics following large disturbances. 

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2. Patterns and implications of spatial covariation in herbivore functions on resilience of coral reefs

   https://doi.org/10.1038/s41598-024-83672-1  

   Cook, Dana T; Holbrook, Sally J; Schmitt, Russell J (December 2025, Scientific Reports)

   Abstract Persistent shifts to undesired ecological states, such as shifts from coral to macroalgae, are becoming more common. This highlights the need to understand processes that can help restore affected ecosystems. Herbivory on coral reefs is widely recognized as a key interaction that can keep macroalgae from outcompeting coral. Most attention has been on the role ‘grazing’ herbivores play in preventing the establishment of macroalgae, while less research has focused on the role of ‘browsers’ in extirpating macroalgae. Here we explored patterns, environmental correlates and state shift consequences of spatial co-variation in grazing and browsing functions of herbivorous fishes. Grazing and browsing rates were not highly correlated across 20 lagoon sites in Moorea, French Polynesia, but did cluster into 3 (of 4) combinations of high and low consumption rates (no site had low grazing but high browsing). Consumption rates were not correlated with grazer or browser fish biomass, but both were predicted by specific environmental variables. Experiments revealed that reversibility of a macroalgal state shift was strongly related to spatial variation in browsing intensity. Our findings provide insights and simple diagnostic tools regarding heterogeneity in top-down forcing that influences the vulnerability to and reversibility of shifts to macroalgae on coral reefs. 

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3. Host-independent persistence of the Diadema antillarum Scuticociliatosis Philaster clade in coastal environments

   https://doi.org/10.64898/2026.01.07.698123  

   Henson, Michael W; Leon-Rodriguez, Axel J; DeRito, Christopher M; Lessios, Harilaos; Quod, Jean-Pascal; Vilanova-Cuevas, Brayan; Hewson, Ian (January 2026, bioRxiv)

   Abstract The mass mortality of the keystone herbivoreDiadema antillarumin the Caribbean was caused by the pathogenic ciliate from theDiadema antillarumScuticociliatosisPhilasterclade (DaScPc). Despite its confirmed pathogenicity, the environmental distribution and persistence strategies of DaScPc outside its host remain poorly understood. We used quantitative PCR, nested PCR, and Sanger sequencing across a 16-month time series and broad geographic surveys to investigate its ecological dynamics and potential environmental reservoirs. Sequencing-confirmed detections at a Florida coastal site devoid ofD. antillarumshow that DaScPc is a natural, host-independent component of the reef environment. Molecular detection on coral and macroalgal surfaces and in the plankton fraction indicates that multiple substrates can harbor the ciliate. Temporal observations revealed emerging trends with macroalgal cover and reef productivity, though no direct correlations were observed. Geographically, DaScPc was absent from outbreak sites in Panama and Réunion. Together, this data suggests spatial patchiness and a cryptic “boom-and-bust” lifestyle in which the organism persists at low abundance between outbreaks. The co-occurrence of a related nonpathogenic ciliate (Acropora/CHN/2009) further underscores the ecological complexity of thePhilasterclade. These findings broaden understanding of DaScPc ecology, confirming environmental persistence independent of its host and suggesting that parasitism may be intermittent, triggered by changing environmental conditions. This work highlights the need for higher-resolution surveillance and long-term monitoring to link ecosystem processes with the reemergence of marine disease in vulnerable coral reef systems. ImportanceThe 2022 mass mortality of the sea urchinDiadema antillarumdevastated Caribbean coral reefs, yet little is known about how the pathogenic ciliate responsible for the event persists in nature. We show that theDiadema antillarumScuticociliatosisPhilasterclade (DaScPc) occurs in reef environments even where the host(D. antillarum) is absent, indicating that it can persist independently of its host. Our findings suggest that DaScPc occupies a cryptic ecological niche within reef microbial communities and may follow a “boom–bust” dynamic, fluctuating between rare environmental states and occasional proliferation. Although direct environmental drivers remain unresolved, emerging trends with macroalgal cover and reef productivity highlight the potential influence of ecosystem conditions on ciliate abundance. This work broadens the understanding of how marine pathogens persist between outbreaks and underscores the importance of environmental surveillance for predicting and mitigating future disease events on coral reefs. 

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4. A spatial numerical model for seagrass–herbivore interactions and the formation of reef halos

   https://doi.org/10.1007/s00338-025-02729-3  

   Llabrés, Eva; Innes-Gold, Anne A; DiFiore, Bartholomew; Sintes, Tomàs; Madin, Elizabeth (October 2025, Coral Reefs)

   Abstract Reef halos are circular patterns of bare sand surrounding patch reefs, formed by herbivorous fish grazing near their reef refuges. These formations serve as indicators of ecological processes, providing insights into interactions among herbivores, vegetation, and predators. Their size and prevalence are influenced by predator and herbivore densities, fishing pressure, and temperature, making them valuable proxies for assessing the impact of anthropogenic stressors on reef ecosystems. Halos can also be monitored using satellite imagery and artificial intelligence tools, offering a scalable method for evaluating ecosystem health. In this study, we present the first spatially explicit agent-based model to explore reef halo formation. By integrating seagrass growth models with herbivorous fish behavior, we capture the spatial complexity of halo dynamics. Our model reproduces observed field patterns, including halo size variability driven by temperature. In addition, the model uncovers new insights into the mechanisms behind the formation of sand corridors—vegetation-free pathways that link isolated halos—an aspect of halo dynamics that was previously unresolved. We propose that these corridors are shaped by limitations in rhizome growth rather than shifts in herbivore foraging behavior. These findings advance our understanding of the ecological processes driving halo formation and enhance the predictive value of halos as indicators of coral reef ecosystem health. The model offers a deeper insight into how reef systems respond to environmental pressures, providing a powerful tool for monitoring and managing reefs amid climate change and anthropogenic impacts. 

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5. Nutrient enrichment strengthens feedbacks that promote and stabilize coral‐to‐macroalgae regime shifts on tropical reefs

   https://doi.org/10.1002/ecs2.70642  

   Gallagher, Jordan P; Schmitt, Russell J; Burkepile, Deron E; Holbrook, Sally J (May 2026, Ecosphere)

   Abstract Ecosystems around the world have experienced shifts in community state as a result of anthropogenic activities that alter important ecological feedbacks. On coral reefs, transitions to a state where fleshy macroalgae are a major space holder have often been associated with the loss of top‐down control, which frequently has been attributed to overharvesting of herbivorous fishes. However, nutrients could also facilitate the proliferation of macroalgae, but evidence for the role of this mechanism in state shifts on coral reefs is inconsistent. Here, we combine a common garden nutrient enrichment experiment with surveys of algal traits to assess potential mechanisms by which nutrient subsidies could trigger and/or maintain a regime shift to abundant macroalgae on reefs. We explored how nutrients influenced individual performance at three life stages of the frondose brown algaTurbinaria ornata, which is often a dominant fleshy macroalga on coral reefs throughout the Indo‐Pacific. Our enrichment experiment revealed that nutrients greatly increased growth and survival rates of youngTurbinariarecruits during this brief life stage when they are most vulnerable to herbivory. For the juvenile stage, we found strong correlations between nutrient availability and the expression of physical defenses that deter herbivory. Additionally, reproductive investment by adults in natural populations was positively correlated with nutrient availability. Taken together, our findings provide several mechanisms by which nutrients could facilitate a persistent shift from coral to fleshy macroalgae by allowing more vulnerable recruit and juvenile life stages to escape herbivore control and by enhancing the reproductive output of adults that produce germlings that recruit locally. These results lend novel insights into bottom‐up mechanisms by which increases in nutrients can bolster the establishment and subsequent replenishment of populations of fleshy macroalgae, which can inform management strategies for conserving or restoring coral reefs. 

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