Modelling Coral Reef Futures: Exploring the role of structural complexity in sustaining ecosystem services

Environmental disturbances driven by climate change are causing unprecedented degradation of natural systems across the globe. Rapid environmental changes limit our capacity to forecast future habitat conditions based on historical benchmarks as we face scenarios unlike any observed in the past. Tropical coral reefs are experiencing widespread biodiversity and habitat loss due to increasingly frequent marine heatwaves, intense storms, pathogens, pollutants, and human exploitation. Reef flattening has been observed across the entire range of latitudes where coral reefs develop. Coral reef fauna are specialised to inhabit one of the most structurally complex habitats in the world, making them particularly vulnerable to habitat degradation. The flattening of reef habitats changes system dynamics and jeopardizes the stability of the ecosystem services we rely on reefs to provide. In this thesis, I develop and explore ecosystem models that explicitly consider the influence of habitat quality on dynamic processes. Using parameters that simulate a generic reef ecosystem, I manipulate habitat quality in several ways, revealing key aspects of the interaction between fish communities and habitat quality with a focus on the provision of ecosystem services. These models can be used as predictive tools to inform ecosystem management strategies and determine trade-offs in decision-making, allowing us to plan for a future where coral reef ecosystems are likely to be drastically different from those of the past.

To set the stage for this work, Chapter 1 begins with a comprehensive overview of coral reef ecosystems and the critical issues threatening their survival. The relationship between various ecological factors and their collective impacts on coral reefs is highlighted, focussing on trophic relationships and the consequences of disturbance. This is followed by a detailed examination of structural complexity in marine environments, emphasizing its crucial role as a structuring force in reef ecosystems. The next section dives into the functional ecology of reefs, reviewing observed impacts of habitat change on the functioning and structure of reef communities. Considering the myriad threats to reefs, current management efforts are explored, focusing on the role of ecosystem models in policy, strategic planning, and decision-making. Finally, I provide a framework for the research, detailing the primary objectives of each chapter and the work as a whole.

As ecosystem engineers on reefs, hard corals form complex, three-dimensional structures as they grow. These structures provide refuge from competitors, predators, and environmental stressors. By influencing predator-prey interactions, reef refuges promote juvenile survivorship and facilitate the transfer of energy up the food chain, allowing reefs to support abundant and diverse fish communities. In Chapter 2, I explore the impact of the refuge profile, a metric that quantifies both the abundance of predation refuges on a reef and the size range of fish that they can accommodate. Using a size-based ecosystem model, I evaluate how different sizes and distributions of refuges impact the ecosystem and affect the provision of ecosystem services. Model predictions indicate that refuges used by fish between 5 and 10 cm in length significantly increase fish biomass and fisheries yields, highlighting the importance of small-scale refuges for sustaining coral reef health. I also identify features of refuge profiles that maximise three valuable reef services: reef resilience, potential fisheries productivity, and ecotourism. These insights can inform the strategic design of artificial reefs to support ecosystem services through climate change.

Ecosystem models that capture trophic dynamics are valuable tools for predicting and managing the effects of exploitation and environmental change. Accounting for species interaction through food-web links reveals ecosystem-wide impacts of changes to dynamics processes, providing a more comprehensive view of potential outcomes of environmental change. Unfortunately, most of these frameworks require extensive data to set up, making them difficult to use for coral reefs and more difficult to generalize. Data collection, monitoring, and management enforcement are a consistent challenge for most of the world’s coral reefs, which develop along tropical coastlines, often in remote regions. Size-spectrum models offer a simpler perspective on trophic modelling, employing the assumption that predator-prey interactions are determined primarily by body size. However, there are no size-spectrum frameworks available for managers that incorporate a measure of habitat quality, a key component of reef ecosystems. Chapter 3 presents MizerReef, a novel R package that facilitates the development of dynamic, multi-species size-spectrum models specifically tailored for coral reef ecosystems. By incorporating the critical role of predation refuges, MizerReef enables users to simulate complex interactions among multiple species groups under various scenarios of habitat degradation. The chapter also presents some examples of package use and a set of steady-state parameters tuned for comparison to the size-spectrum model presented in Chapter 2. The MizerReef package offers a feasible pathway towards large-scale modelling of coral reef ecosystems to support management and maintain crucial services through climate change.

Physical traits, such as body shape and swimming ability, and behavioural traits, such as foraging strategy and activity pattern, shape the relationship between an organism and its environment. Functional structure, defined as the abundance and diversity of these traits within an environment, plays a pivotal role in how communities respond to disturbance and exploitation, influencing overall system stability. As reef habitat quality diminishes, functional structure also tends to change, and these shifts can have profound impacts on ecosystem service provision. Chapter 4 investigates how changes to the refuge profile impact ecosystem services and fish assemblage structure using a generic reef ecosystem model set up with MizerReef and several of the refuge profiles designated in Chapter 2. Predictions indicate that fish assemblage composition is dependent on the refuge profile. Profiles that supported the highest reef resilience in Chapter 2 were dominated by parrotfish, reinforcing the concept that reef resilience is supported by small-scale habitat structure. However, the productivity of the profile deemed best for fishing was also supported primarily by parrotfish, emphasizing the trade-offs involved in exploiting reefs with plentiful small predation refuges. Herbivores generally appear to benefit from habitat structure at any size while the productivity of larger piscivores is hindered by plentiful refuge. These results reveal a more resolved picture of how habitat quality affects reef communities, allowing us to fine-tune management strategies to support essential reef functions.

Coral reefs are subject to a multitude of stressors on local and global scales. Disturbances can cause rapid changes in the entire community, but also more subtle shifts that play out over decades. The process of reef flattening and recovery is continuous and dynamic and can result in a variety of stable ecosystem states. Considering the inherent limitations of steady-state dynamics in accounting for the episodic nature of disturbances and their impacts, Chapter 5 addresses the critical need to understand how coral reef ecosystems respond to acute environmental change. Using historical data, I develop a realistic timeline describing how the refuge profile changes following disturbance, with a particular focus on the consequences of mass bleaching events. This is used to create a new degradation dynamic for the MizerReef package that simulates changes to the refuge profile for three common disturbed coral reef states: coral rubble-dominated, macroalgae-dominated, and recovered. Predictions indicate that the assemblage composition of disturbed reefs is dependent on the recovery trajectory. Recovered reefs have the potential to support relatively stable fish assemblages, but macroalgal and rubble reefs become dominated by herbivores and generalist predators, respectively. This information can help managers plan for different degradation scenarios and demonstrates the potential for MizerReef to explore temporal dynamics.

This thesis encompasses a comprehensive exploration of the intricate relationships between habitat quality, community dynamics, and ecosystem service provision within a coral reef ecosystem model. Through a series of innovative modelling approaches, it sheds light on the role of structural complexity in sustaining reef biodiversity and the functionality of reef-associated communities. The findings underscore the urgent necessity for informed management strategies that prioritize habitat quality and structural complexity to mitigate the adverse effects of environmental disturbances. Ultimately, this thesis contributes to our understanding of coral reef ecosystems, providing a foundation for future efforts to preserve these critical habitats in the face of unprecedented global change.