Caribbean reef ecosystems have undergone major ecological changes in the last 30 – 40 years, with the result that ecological systems once dominated by structurally complex Acropora cervicornis and Montastraea annularis corals now consist mainly of flattened carbonate substrates with macroalgal overgrowth. A need for greater understanding of coral reef ecosystems is imperative if we are to attempt to conserve them. The threespot damselfish, Stegastes planifrons, is herbivorous damselfish species ubiquitous to Caribbean reefs, where it has been termed a keystone species. Aggressive in nature, S. planifrons defends territories of around 70 cm in diameter from other roving herbivorous fish and urchins, in apparent effort to maintain the algal resources therein for its own use. The predilection of Stegastes planifrons for basing its territories on the now Critically Endangered staghorn coral, Acropora cervicornis, and the Endangered boulder coral Montastraea annularis is well known, however the likely ecological implications of this fact have not been investigated. Using a combination of experimental and observational methodologies we examine the ecological implications of coral microhabitat choice and use by S. planifrons. We also assess the magnitude of the direct and indirect effects of S. planifrons’ territorial behaviour on macroalgal dynamics both within and outside of territory confines, at the reef-wide level. We find that coral microhabitat is a more important determinant of algal community structure than damselfish presence, and that this can be explained by a previously unrecognised effect of coral microhabitat on the grazing behaviour of roving herbivorous fishes - on which S. planifrons’ territorial behaviour has little effect. In a modification of the space availability hypothesis of Williams et al (2001) we suggest that Acropora cervicornis acts as a grazing fish „exclusion zone‟, and we further hypothesise that the existence of large stands of this coral prior to the Caribbean „phase shift‟ may have acted to concentrate the grazing pressure of excluded roving fish onto the remaining areas of the reef. We further hypothesise that the loss of such „exclusion zones‟ and accompanied effective dilution of grazing pressure may have been on a scale large enough to have been a significant underlying factor in the proliferation of macroalgae seen on modern day Caribbean reefs. In the absence of demonstrable direct or indirect effects on benthic algal communities we question the continued keystone status of S. planifrons, particularly since the status 6 was originally based on interference behaviour involving the important grazing urchin Diadema antillarum, which is now functionally absent from Caribbean reefs. Implications of the context-dependant nature of keystone status are also discussed. We find that the effect of S. planifrons on coral community may be more important than its effects on benthic algal community. In examining the factors involved in habitat coral choice we establish a significant preference for 100% live coral substrate over substrates with a supply of algal food. Territory selection was followed by a high rate of coral biting – a behaviour which has previously been shown to result in coral tissue death and the fast establishment of algal turf communities on which S. planifrons likes to feed (Kaufman 1977). We also demonstrate a novel and significant association between S. planifrons presence and disease incidence its primary habitat coral, the Critically Endangered staghorn coral Acropora cervicornis, and a significant correlation between areas of fish biting and the later onset of disease. Changes to the overall role of damselfish on today's Caribbean reefs are discussed in light of these insights.

Over the past 40 years, coral cover has reduced by as much as 80%. At the same time, Coral Reefs are coming under increasing threat from hurricanes, as climate change is expected to increase the intensity of hurricanes. Therefore, it has become increasingly important to understand the effect of hurricanes on a coral population. This Thesis focuses on the reef-building coral Montastraea annularis. This species once dominated Caribbean Coral Reefs, but is fast being replaced by faster growing more opportunistic species. It is important that the underlying dynamics of the decline is understood, if managers stand any chance of reversing this decline. The aim of this Thesis is to investigate the effect of hurricane activity on the dynamics of the reef-building coral Montastraea annularis. To achieve this the Integral Projection Model (IPM) method was adopted and the results compared to those produced using the more traditional method of Population Projection Matrix (PPM) method. The models were fitted using census data from June 1998 to January 2003, which described the area of individual coral patches on a sample of ramets on Glovers Reef, Belize. Glovers Reef is a marine reserve that lies 30km off the coast of Belize and 15km east of the main barrier reef. Three hurricanes struck Glovers Reef during the study: Hurricane Mitch (October 1998), Hurricane Keith (September 2000) and Hurricane Iris (October 2001). The data have been divided by two different methods in order to test two research questions, firstly if the initial trauma following a hurricane affects the long term dynamics of a population and, secondly, if the dynamics exhibited during a hurricane varied with hurricane strength. In this Thesis five main results are shown: 1. All models for all divisions of data are in long term decline. 2. As initial trauma increased, the long term growth rates decreased, conversely the short term extremes increased. 3. Fragmentation is more likely as patch size increased and more likely under stronger hurricanes. 4. Integral Projection Modelling painted a similar picture to Population Projection Matrix models and should be a preferred method of analysis.5. Interaction of the IPMs can be used to model the changing occurrence of hurricanes under climate change. It is shown that with increased intensity, the population could become extinct 6.3 years sooner. This research is the first step in modelling coral patch populations by the IPM method. It suggests possible functional forms and compares the results with the PPM method. Further research is required into the biological functions which drive fragmentation, the method by which large patches divide into groups of smaller patches. The conclusions from this Thesis add to the growing body of knowledge concerning the response of coral species to hurricanes, focusing on the importance of understanding patch dynamics, in order to understand colonial dynamics.

Coral reefs are one of the most economically important ecosystems on the planet. Despite their great contribution to the world economy, anthropogenic influence via carbon dioxide emissions is leading to unprecedented changes with concerns about subsequent negative impacts on reefs. Surface ocean pH has dropped 0.1 units in the past century; in spite of this rapid shift in oceanic chemistry, it is unclear if individual species or life stages of Caribbean stony corals will be more sensitive to ocean acidification (OA). Examined is the relationship between CO2-induced seawater acidification, net calcification, photosynthesis, and respiration in three model Caribbean coral species: Orbicella faveolata, Montastraea cavernosa, and Dichocoenia stokesi, under near ambient (465 ± 5.52 ppm), and high (1451 ± 6.51 ppm) CO2 conditions. A species specific response was observed for net calcification; D. stokesi and M. cavernosa displayed a significant reduction in CaCO3 secreted under OA conditions, while O. faveolata fragments showed no significant difference. At the cellular level, transmission electron micrographs verified that all species and treatments were actively calcifying. Skeletal crystals nucleated by O. faveolata in the high CO2 treatments were statistically longer relative to controls. These results suggest that the addition of CO2 may shift the overall energy budget, causing a modification of skeletal aragonite crystal structures, rather than inhibiting skeletal crystal formation. Consequential to this energy shift, Orbicella faveolata belongs in the category of Scleractinian corals that exhibit a lower sensitivity to ocean acidification.

Scleractinian corals are the ‘engineers’ of tropical coral reef ecosystems. Their three-dimensional structure provides habitat for thousands of fish and invertebrate species. The persistence of corals is threatened by climate change. In this study I investigated if corals may be able to increase tolerance to ocean warming through developmental acclimation, i.e. if corals that experience warmer temperatures during embryonic and larval development are better able to cope with higher temperatures later in life. Larvae of the broadcast spawning coral Montastraea cavernosa were raised at ambient (29°C) and future projected ocean warming temperatures (+2°C, 31°C). After larval settlement, coral juveniles from each treatment were split and reared for two months at either current or +2°C conditions. Larvae reared at the warmer temperature had lower survival and displayed a smaller size at settlement. Juveniles that were in the warmer conditions had faster growth rates. Individuals raised during larval and juvenile stages at 31°C had faster growth rates than individuals only in the elevated temperature treatment after settlement, thus indicating that developmental acclimation may have occurred. However, the highest mortality also occurred in this treatment, therefore the growth results could also be explained by positive selection of the most thermally tolerant individuals. My results suggest that acclimation and/or directed selection may help corals withstand future rises in ocean temperature.

Corals combine photosynthesis and calcification in an intricate and delicately balanced relationship to form large biomineralized structures that are dominant features of tropical coastlines worldwide. Coral reefs have great scientific and economic importance but have recently experienced widespread decline attributed to increasing anthropogenic pressure on reef systems. Physical damage events, such as ship groundings, when coupled with existing nutrient stress and changing global climate present a poor outlook for successful natural recovery of reef communities. The main goal of the proposed research is to better understand how environmental factors, both local and global, affect the coral holobiont and influence overall coral fitness. The target species of this research, Montastraea cavernosa and Porites astreoides, are important and widespread Caribbean reef-builders. While it has been shown that nutrient and pCO2 stress affect coral growth and calcification, study of specific effects on coral tissue and reproductive success has not received significant attention in the literature despite considerable current interest. This study addresses this data gap in quantitatively examining the effect of elevated nutrients and pCO2 on 1) P. astreoides recruit survivorship, development, early calcification, and symbiotic zooxanthellae morphology; 2) M. cavernosa and P. astreoides wound regeneration, tissue characteristics over time at the histological and ultrastructural level, and trends in symbiotic zooxanthellae morphology; and 3) survival, growth and histological/ultrastructural characteristics of M. cavernosa and P. astreoides fragments transplanted to the field and in the laboratory. Histological and ultrastructural observations from corals transplanted to the field are then compared to ex-situ laboratory experimental corals. In the fleshy and large-polyped faviid M. cavernosa, healing of a linear wound was characterized by granulation of new tissue across the wound site, facilitated by coalescent granular amoebocytes. The wound healing strategy of this species appears to progress with wound closure and re-epithelialization before calcification resumes, as actively calcifying calicodermis was generally not observed at the healing front. Tissue regeneration in the small-polyped P. astreoides was characterized by formation of multiple islands of eosinophilic healing fronts along the depth of the wound track, and an accumulation of granular amoebocyte cells in regenerating tissue. The wound healing strategy of this species appeared to result in re-epithelialization of exposed body wall without necessarily closing the wound. Elevated pCO2 significantly reduced survivorship in P. astreoides recruits, and both nutrient enrichment and elevated pCO2 significantly reduced wound regeneration rate in M. cavernosa and P. astreoides. In both species, phosphate enrichment had the greatest deleterious effect on wound repair. A significant application of this study is the identification of possible zooxanthellar morphological indices of elevated nutrients and ocean acidification. The similarity in starch, lipid and uric acid accumulation patterns in Symbiodinium sp. from P. astreoides recruits and coral fragments of both species indicate a correlation between these anthropogenic stressors and the intracellular accumulation of excess carbon and nitrogen by the symbiont. Zooxanthellar carbon accumulation, in the form of starch and/or lipid, was the greatest under elevated nitrate. Zooxanthellar nitrogen accumulation, in the form of uric acid, was the greatest under elevated CO2. Comparison of zooxanthellar metrics between the field corals (P. astreoides, and M. cavernosa) and ex-situ corals and recruits indicated that carbon accumulation in Symbiodinium from field corals was consistently significantly less than in the ex-situ experimental P. astreoides recruits and M. cavernosa fragments exposed to elevated nitrate. This indicates that the field corals were likely not exposed to elevated nitrate at the time of collection. Both M. cavernosa and P. astreoides adults in the field accumulated significantly less uric acid than their counterparts in the tissue repair experiment, indicating that the field corals were exposed to higher pH and lower CO2 than the ex-situ corals. These results suggest that the field corals were not exposed to nutrient concentration profiles similar to the experimental treatments, particularly elevated nitrate. However, histological metrics indicated that the transplanted corals were subjected to increasing sedimentation stress over time. Overall, nitrate was found to affect recruits and adults on a similar scale, while phosphate and pCO2 affected carbon and nitrogen storage more in recruits compared to adults. While nutrients and pCO2 had no mechanistic effect on regeneration at histological level, ultrastructural metrics indicate an impact on the mutualistic energy exchange between the symbiotic partners, partially decoupling symbiosis. Effects were generally found to be greater in P. astreoides compared to M. cavernosa, and the unique life history strategy of the subject species and differences in their endosymbiont physiology reveal distinct responses to elevated nutrients and pCO2. Although the laboratory findings were not necessarily applicable to field observations, they provide insight into factors that may influence fragment success in the field. Quantitative assessment of the effect of elevated nutrients and pCO2 is thus useful in management decisions involving water quality standards, and is essential in the prediction of future coral condition and resilience.