In order to properly assess human impacts and appropriate restoration goals, baselines of pristine conditions on coral reefs are required. In Saudi Arabian waters of the central Red Sea, widespread and heavy fishing pressure has been ongoing for decades. To evaluate this influence, we surveyed the assemblage of offshore reef fishes in both this region as well as those of remote and largely unfished southern Sudan. At comparable latitudes, of similar oceanographic influence, and hosting the same array of species, the offshore reefs of southern Sudan provided an ideal location for comparison. We found that top predators (jacks, large snappers, groupers, and others) dominated the reef fish community biomass in Sudan’s deep south region, resulting in an inverted (top-heavy) biomass pyramid. In contrast, the Red Sea reefs of central Saudi Arabia exhibited the typical bottom-heavy pyramid and show evidence for trophic cascades in the form of mesopredator release. Biomass values from Sudan’s deep south are quite similar to those previously reported in the remote and uninhabited Northwest Hawaiian Islands, northern Line Islands, Pitcairn Islands, and other remote Pacific islands and atolls. The findings of this study suggest that heavy fishing pressure has significantly altered the fish community structure of Saudi Arabian Red Sea reefs. The results point towards the urgent need for enhanced regulation and enforcement of fishing practices in Saudi Arabia while simultaneously making a strong case for protection in the form of marine protected areas in the southern Sudanese Red Sea.

Herbivorous coral reef fishes play an important role in helping to structure their environment directly by consuming algae and indirectly by promoting coral health and growth. These fishes are generally separated into three broad groups: browsers, grazers, and excavators/scrapers, with these groupings often thought to have a fixed general function and all fishes within a group thought to have similar ecological roles. This categorization assumes a high level of functional redundancy within herbivorous fishes. However, recent evidence questions the use of this broad classification scheme, and posits that there may actually be more resource partitioning within these functional groupings. Here, I use a compound-specific stable isotope approach (CSIA) to show there appears to be a greater diversity of functional roles than previously assumed within broad functional groups. The δ13C signatures from essential amino acids of reef end-members (coral, macroalgae, detritus, and phytoplankton) and fish muscle were analyzed to investigate differences in resource use between fishes. Most end-members displayed clear isotopic differences, and most fishes within functional groups were dissimilar in their isotopic signature, implying differences in the resources they target. No grazers closely resembled each other isotopically, implying a much lower level of functional redundancy within this group; scraping parrotfish were also distinct from excavating parrotfish and to a lesser degree distinct between scrapers. This study highlights the potential of CSIA to help distinguish fine-scale ecological differences within other groups of reef organisms as well. These results question the utility of lumping nominally herbivorous fishes into broad groups with assumed similar roles. Given the apparent functional differences between nominally herbivorous reef fishes, it is important for managers to incorporate the diversity of functional roles these fish play.

Coral reef ecosystems are under increasing threat from ocean warming and deoxygenation. Mass coral bleaching events in recent years have been linked to marine heatwaves but reporting of hypoxia-induced bleaching has also been increasing. Oxygen availability in coral reefs is driven by community metabolism and they experience a dynamic range of oxygen concentrations throughout diel cycles, hyperoxia during the day and hypoxia during the night. It has been suggested that the highest oxygen concentrations coincide with the hottest part of the day and this may protect marine taxa from high temperatures. We evaluated experimentally whether excess oxygen availability would increase the thermal threshold of the branching coral Stylophora pistillata, from the Southern Red Sea. We did this by exposing coral fragments of this species to varying dissolved oxygen concentrations (hypoxia, normoxia and hyperoxia) and a short-term temperature ramping regime (1˚C h-1). Hyperoxia did extend the thermal tolerance of S. pistillata fragments, with an LT50 of 39.1˚C as opposed to 39.0˚C for the normoxic treatment and 38.7˚C for the hypoxic treatment. Hyperoxia also increased respiration and gross photosynthesis and had a negative effect on photochemical efficiency at high temperatures. Net photosynthesis, P:R ratio and symbiont density were not significantly affected by oxygen concentration. Corals in this experiment displayed exceedingly high thermal thresholds, which were at least 2˚C higher than previously reported for the same species in the Central Red Sea. The corals used in the experiment had previously survived mass bleaching events in 2015 and hence we may have selected for individuals adapted to thermal stress. This is the first study to investigate the role of oxygen in the thermal tolerance of hermatypic corals and the first assessment of thermal thresholds from corals in the Southern Red Sea, where previously thermal thresholds have been based on a 1-2˚C increase in maximum mean monthly temperatures and visual bleaching observations. This highlights the need for increased experimental assessments of thermal thresholds in the Southern regions of the Red Sea and the important role of oxygen in moderating thermal stress.

Long-term coral reef monitoring programs have been established and used efficiently in many parts of the world to assess the state of coral reefs under increasing anthropogenic pressures and natural disturbances, as well as to evaluate the efficiency of established marine protected areas (MPAs) or other conservation strategies. Over the past decade, Red Sea coral reefs have experienced two major bleaching events in 2010 and five years later, in 2015/2016, with severe coral loss along the central and southern Saudi Arabian coast. With this study we present the first characterization of fish community changes through time in the Red Sea. Fish abundance data from twenty-three reefs from two different regions in Saudi Arabia, central (Thuwal) and south-central (Al Lith), surveyed between 2008 and 2019 were examined. A significant decline of hard coral was observed on nearshore reefs in both regions following two bleaching events. The results revealed a persistent cross-shelf partitioning of fish communities before and following a substantial drop in coral cover. Offshore reef fish communities appeared to be more stable and homogeneous through time, whereas nearshore reef fish communities had less similar composition throughout the study period. Species-specific analyses revealed the decline in the abundance of several obligatory corallivorous species, a contrasting response from most herbivore fish species that generally experienced an increase in their abundance since 2008. These findings indicate that the bleaching events from this period had less effect on communities as a whole, but instead cause changes in abundance in several key species, mostly affected by coral loss and subsequent algal increase. While a well-structured and standardized long-term monitoring system is yet to be established for Saudi Arabian coral reefs, our findings provide a sound baseline of fish assemblages over the last decade. These findings are critical for future studies as well as effective conservation strategies in the face of ongoing coastal developments, overfishing and climate change.

Acoustic telemetry is an important tool for studying the movement patterns, behaviour, and site fidelity of marine organisms; however, its application is challenged in coral reef environments where complex topography and intense environmental noise interferes with acoustic signals, and there has been less study. Therefore, it is particularly critical in coral reef telemetry studies to first conduct a long-term range test, a tool that provides informa- tion on the variability and periodicity of the transmitter detection range and the detection probability. A one-month range test of a coded telemetric system was conducted prior to a large-scale tagging project investigating the movement of approximately 400 fishes from 30 species on offshore coral reefs in the central Red Sea. During this range test we determined the effect of the following factors on transmitter detection efficiency: distance from receiver, time of day, depth, wind, current, moon-phase and temperature. The experiment showed that biological noise is likely to be responsible for a diel pattern of -on average- twice as many detections during the day as during the night. Biological noise appears to be the most important noise source in coral reefs overwhelming the effect of wind-driven noise, which is important in other studies. Detection probability is also heavily influenced by the location of the acoustic sensor within the reef structure. Understanding the effect of environmental factors on transmitter detection probability allowed us to design a more effective receiver array for the large-scale tagging study.

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Parrotfishes (Scarinae) are dominant Caribbean herbivores that play an important role in reducing coral-algae competition by grazing algae; yet some species are also occasional coral predators (corallivores) and thereby can have direct negative impacts on coral growth and survivorship. There is concern that parrotfish corallivory may contribute to substantial long-term declines in targeted coral species, particularly in areas with a high biomass of parrotfishes and low cover of corals. However, the capacity of target coral species to heal from parrotfish predation and the ecological drivers of corallivory are poorly understood. In Chapter 1, we examined the patterns of coral healing from parrotfish predation scars on Orbicella annularis – an ecologically important framework building coral that is one of the most intensely grazed Caribbean coral species and an endangered species. While some researchers have suggested that parrotfishes may have significant long-term impacts on heavily targeted species such as O. annularis, the patterns of coral recovery from parrotfish predation scars remain poorly understood. To address this knowledge gap, we tracked the fate of parrotfish bite scars on O. annularis colonies across two Caribbean islands for up to two months. We evaluated differences in coral healing between islands in response to a number of variables including the initial scar surface area, scar abundance per coral colony, colony surface area, and water depth. We used these data to develop a predictive model of O. annularis tissue loss from recent parrotfish bite scars. We then applied this model to surveys of the distribution of bite scars at a point in time to estimate long-term tissue loss of O. annularis colonies from a standing stock of bite scars. Our findings suggest that the initial scar surface area is one of the most important predictors of coral tissue loss. The data also indicate that there are thresholds in patterns of coral tissue regeneration: we observed that small scars (≤1.25 cm2) often fully heal, while larger scars (≥8.2 cm2) had minimal tissue regeneration. The vast majority of observed scars (~87%) were 1.25 cm2 or less and our model predicted that O. annularis colonies would regenerate nearly all the corresponding scar area. In contrast, while scars greater than or equal to than 8.2 cm2 were infrequent (~6% of all observed scars), our model predicted that these larger scars would account for over 96% of the total tissue loss for grazed colonies. Overall, our results suggest that the immediate negative impacts of parrotfish predation on coral tissue loss appear to be driven primarily by a few exceptionally large bite scars. While further work is needed to understand the long-term impacts of corallivory and quantify the net impacts of parrotfish herbivory and corallivory on Caribbean coral reefs, this study is an important step in addressing factors that impact the recovery of a heavily targeted and ecologically important Caribbean coral from parrotfish predation. In Chapter 2, we examined the ecological drivers of corallivory across all coral taxa and across three regions of the Greater Caribbean – the Florida Keys, St. Croix, and Bonaire. To do so, we observed how parrotfish grazing intensity varied using both size and abundance-based metrics across multiple spatial scales. At the reef community and regional scale, we found no effect of the biomass of corallivorous parrotfishes or the percent cover of target coral species on the intensity of parrotfish corallivory. However, at the scale of individual coral colonies, we found that coral taxa and colony size were important predictors of corallivory intensity, and that predation intensity increased as colony size increased. Our findings suggest that previous assertions that conservation of corallivorous parrotfishes may have net negative impacts on coral communities, particularly as live coral cover declines, are not supported at the reef-scale. Instead, our research suggests that colony-level traits such as coral taxa and colony size may be stronger drivers of predation intensity. Additionally, our research suggests that parrotfishes do not heavily graze upon the majority of coral species, but have a higher level of grazing intensity on three taxa, Orbicella annularis, Porites astreoides and other Porites spp. across multiple regions of the Caribbean. Therefore, the direct consequences of parrotfish corallivory for coral tissue loss are likely low for the majority of coral species, but further research is needed to better understand the ultimate causes of selective predation and the long-term consequences of corallivory for heavily targeted coral taxa.

Coral reefs are threatened due to anthropogenic stressors, especially due to warming. Corals typically live in a narrow range of environmental conditions; however, some individuals are able to thrive in extreme temperatures. Such colonies could provide insight into how the coral holobiont acclimates or adapts to extreme temperatures. This study used the model coral species Stylophora pistillata (Esper, 1797) in the Saudi Arabian Red Sea, which is abundant and occurs across a range of desired microhabitats to examine the role of the environment on population structure and physiology. Specifically, this project aimed to 1) review the literature on S. pistillata used in stress studies to better understand the threats it faces, and where knowledge gaps exist, 2) conduct a demographic assessment of S. pistillata populations across different reefs and microhabitats, and 3) evaluate the physiological state of S. pistillata colonies occurring in these microhabitats with differing temperature profiles. The literature review revealed disparities in stress studies on S. pistillata, with most originating from the Gulf of Aqaba and conducted on temperature tolerance. The population assessment showed a high spatial variability in size structure, but a tendency for offshore reefs to have larger colonies and higher colony density. It also showed that purple color morphs tended to be more frequently encountered in the exposed reef flat zones. Similarly, the physiological study showed high spatial variability in chlorophyll, protein and lipid content, and skeletal and symbiont density. However, there was a clear seasonal component, with a multivariate analysis revealing the coolest sampling period as distinct. The metabolic profiles of S. pistillata indicated that offshore colonies differ from midshelf and nearshore colonies. Finally, an opportunistic study reports a case of S. pistillata bleaching due to an unusual occurrence of cold stress coupled with a low tide, supporting the notion that continued monitoring of this population on the reef flat is important for documenting rare evets and understanding their impacts on coral ecology. Taken together, this thesis establishes baseline information on the ecology of an important Red Sea coral inhabiting an extreme environment, and will be important for understanding its response to future changes.

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