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Caribbean coral reefs are in crisis. Degradation of living coral and fish assemblages has accelerated during the past half century, with a suite of anthropogenic drivers –from local fishing pressure to unprecedented global scale climate change– implicated. Accompanying these losses is the physical disintegration of the three-dimensional calcium carbonate reef structure. Flattening of reefs, synonymous with loss of ecosystem function and provision of services, is caused by an imbalance in the carbonate budget: a trade-off between carbonate production and consolidation by calcifying organisms (principally coral-algal symbioses) and framework breakdown by bioeroding organisms and storms. This thesis focuses on expanding our understanding of two functionally critical issues that strongly influence Caribbean coral reef community composition and dynamics, and which look likely to have a key bearing on the future state of reefs in the region: coral photosynthetic endosymbionts, and carbonate budgets. The former exert an important role in the production of the coral carbonate framework, whilst the latter reflect the dynamics of reef carbonate production and erosion. In the first part of the thesis, existing information on rates of carbonate production and erosion on Caribbean reefs is utilised to construct a detailed theoretical carbonate budget model. The model is used to chart historic changes in Caribbean carbonate budgets, tracking reef flattening across time and identifying key ecological drivers of these changes. This “eco-geomorphic” model is then coupled with state-of-the-art climate and ecological models, to project reef processes to the end of the century, asking the question ‘at what point will Caribbean reefs shift to net erosional regimes?’. The models are also used to explore the efficacy of local management and climate mitigation in altering the negative trajectory of reefs under projected warming and ocean acidification. In the second part of the thesis, 632 corals from across the wider Caribbean are screened, to construct the largest recorded baseline of symbiont biogeography for the region’s key remaining reef framework builder, Montastraea annularis. Spatial patterns of symbiont diversity are explored in terms of environmental, geographic and genetic factors, contributing to the growing body of work currently in the early stages of cataloguing symbiont diversity and its ecological significance. Although carbonate budget models forecast a bleak outlook for the Caribbean, detection of widespread low-level prevalence of thermally-tolerant endosymbionts in M. annularis provides a weak ‘nugget of hope’ for potential coral acclimation. Combined local management and aggressive mitigative action on carbon emissions are pre-requisites for maintenance of functioning reefs into the next century. Coral reef conservation efforts can be improved if we fully appreciate the contributions of all reef components –not just the enigmatic ones– to healthy reef functioning.

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.

Knowledge of effective reef restoration techniques are necessary in this age of worldwide coral reef decline. Coral transplantation is a restoration technique employed after natural (i.e. hurricanes) and anthropogenic (i.e. vessel groundings) physical disturbance events. The study was conducted to compare the efficacy of propagating small colony fragments in laboratory and field conditions in terms of survival and growth. Fragment growth and survival were assessed for six scleractinian boulder corals common to Florida and Caribbean reefs: Montastraea annularis, M. cavernosa, Diploria clivosa, Siderastrea siderea, S. radians and Dichocoenia stokesii. Broken coral colonies were salvaged from vessel grounding sites and marine debris, fragmented into pucks and secured to travertine tiles. One hundred and fifty-three coral colony fragments were cultivated in an ex situ laboratory nursery and 133 coral colony fragments were cultivated in an in situ field nursery and monitored for 13 months. Survival of all colonies was 94%, with 98% survival in the laboratory treatment and 89% survival in the field treatment. Complete colony mortality was documented in three S. radians colonies, all in the laboratory treatment. All colony loss in the field treatment was due to colony pucks being detached from the tiles. Overall mean percent change in colony tissue area from initial to final monitoring events was calculated to determine growth. Across species, growth was greater in the laboratory treatment (76 ± 4 % SEM) in comparison to the field treatment (27 ± 5 % SEM). Positive growth was observed in D. clivosa, D. stokesii, M. annularis, M. cavernosa and S. siderea in the laboratory treatment. In the field treatment, D. clivosa, M. annularis and M. cavernosa were the only species that exhibited positive growth. Negative growth was observed in both the laboratory and field treatments for S. radians. In conclusion, colonies propagated in the ex situ nursery (laboratory treatment) had higher growth and survival than colonies propagated in the in situ nursery (field treatment). A critical acclimation period accomplished through the use of stable laboratory conditions will produce healthier, more secure coral colonies that may be used to repopulate disturbed reef sites.