In 1988 data on coral reef community composition were collected from two areas, Akumal and Chemuyil, Quintana Roo, Mexico, ranging from 5-35m depth. These areas were revisited in 2005 and data were collected by the same methods and at the same depths as in 1988. Data from 1988 and 2005 were compared to determine if the coral reefs had undergone significant changes, and what specific changes had occurred. Chi-square analysis determined that community composition data collected in 1988 are significantly different from data collected in 2005 at all sites and depths within the categories of corals, gorgonians, sponges, and macroalgae. Mann-Whitney U analyses were performed on abundance data for coral, gorgonians, sponges, macroalgae, crustose coralline algae, erect coralline algae/calcareous algae, filamentous/multi-species turf algae, and non-living substrate. Results from the Mann-Whitney U analysis varied between sites; however significant trends of increasing macroalgae, crustose coralline algae and filamentous/multi-species turf, and declining non-living substrate were observed at almost all sites. H' biodiversity indices J' evenness values and species number (S) were calculated for all sites over the two time periods, with no discernable trends observed. Increases in crustose coralline algae and filamentous/multi-species turf algae suggest that eutrophication and overfishing may be responsible for the trends observed on the reefs at Akumal and Chemuyil. Anecdotal accounts also suggest that eutrophication from septic water flowing through the highly porous karst limestone of the Yucatan Peninsula may be the largest malefactor causing the observed changes. The increase in filamentous/multi-species turf algae exhibited by the data suggests that eutrophication is predominantly responsible for the alternate states of the reefs. Furthermore, evidences indicative of other forms of stress on the reefs, such as bleaching, scraped or broken coral heads, disease, and sedimentation, were rarely observed.

Coral reefs are one of the most productive, diverse and complex ecosystems on Earth. They are very important ecologically, economically and socially, but are subject to increasing deleterious disturbances. To protect coral reefs and manage the sustainable use of their resources it is necessary to understand how coral communities respond to disturbances and to use this understanding to project the likely ecological trajectories of disturbed coral reefs in spatial and temporal contexts. Three powerful tools exist to address this issue: (1) in situ monitoring that describes ecological transitions of coral communities at very fine spatial scale; (2) time-series of maps derived from high spatial resolution remote sensing images that provide multi-temporal synoptic views of the reefs; and (3) spatially- and temporally-explicit models that are able to handle ecosystems complexity and represent their spatial dynamics. The combination of these three tools to map and monitor coral communities remained to be addressed. This dissertation developed an integrative approach to characterise, map and model coral communities’ responses to disturbances. This approach provides a basis for monitoring coral reefs at temporal and spatial scales matched to disturbance impacts and coral reefs patchiness. This was achieved by investigating the dynamics of three different Indo-Pacific reefs and by following four steps: - Developing and applying a method to characterise how detailed coral communities can be mapped before and after a major cyclone event from a short time-series of high spatial resolution images (IKONOS, Quickbird) on Aboré Reef (New-Caledonia); - Using the methods developed in the first step to assess whether decadal-scale coral dynamics can be retraced and monitored from time-series of aerial photographs and satellite images spanning at least 30 years on Saint-Leu (Réunion Island) and Heron (Australia) Reefs; - Developing a spatially- and temporally-explicit model of coral communities’ dynamics with cellular agent-based formalism on the western section of Heron reef flat; and - Assessing the relevance of the mapping, monitoring and modelling tools developed in this work, into an integrated approach for coral reef monitoring. For the first step, accurate monitoring requires that descriptions of the reef features are coherent with the local scale of disturbance impacts in space and time. While such a monitoring paradigm is applied in terrestrial environments, it is not the case for coral reefs. A before-after cyclone time-series of satellite images from Aboré Reef was used to test this paradigm on coral reefs. In situ data provided a new three-level hierarchical coral community typology (45 classes at the finest level). Photo-interpretation and hierarchical mapping methods were applied to an IKONOS image and a Quickbird image taken before and after cyclone Erica respectively. Application of this paradigm yielded a highly detailed multi-temporal maps of pre- and post-cyclone coral communities and recommendations to design reef-scale monitoring protocols. For the second step, the temporal scale of monitoring projects needs also to match the inherent reef dynamics. To assess the applicability of this temporal component of the paradigm at a decadal scale, the hierarchical mapping approaches developed for Aboré Reef were applied to a 33-year time-series of satellite images (two Quickbird images) and airborne photographs (five scanned images) of Saint-Leu Reef. The mapping approach overcame challenges due to different images qualities and to the lack of in situ observations in time and space before cyclone Firinga in 1989. This demonstrated the potential for further applications of the approach in reef monitoring protocols based on complementary in situ and remote sensing data to help understand the dynamics of reef-top coral reef communities and geomorphology over years to decades. In the next step, the modelling component of this work focused on a proof-of-concept for spatially-explicit modelling of coral growth by simulating maps of reef flat colonisation on a 16 686 m2 section of Heron Reef. To do this a 35-year time-series of two satellite Quickbird pan-sharpened images and five aerial photographs of Heron Reef was first used to hierarchically map and quantify the areal expansion of coral on the reef flat. The coral growth was driven by several artificially induced local sea-level rises associated with engineering works on the reef flat. Vertical and horizontal growth rates were quantified in terms of percentage of the total area colonised each year by corals. Coral community maps and coral growth rates estimated from the image time-series were used to constrain an accretive cellular growth model. Although only preliminary the model produced coral growth likelihood maps corresponding to observed fine-scale coral growth patterns. This suggested the tool had promise for further applications in reef management. This dissertation developed an integrative approach to characterise, map and model coral communities’ responses to disturbances, providing a basis for monitoring coral reefs at ecological, temporal, and spatial scales matching the patchiness of the communities’ distribution and disturbance impacts. The contributions of the work to the applied fields of coral reef mapping, modelling and monitoring were demonstrated through the results achieved and the development of protocols that do not require specialized image processing algorithms and methods. This opens perspectives for further development of the approach on other coral reefs around the world.