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Image analysis was used to measure basal areas of selected colonies of Montastraea annularis and Porites astreoides, following the colonies over a three-year period from 2002 to 2004. Existing digital images of permanently-marked quadrats in the Caye Caulker Marine Reserve, Belize, were selected based on image quality and availability of images of selected quadrats for all three years. Annual growth rates were calculated from the basal-area measurements. Mean growth rates (radial skeletal extension) for M. annularis and P. astreoides were 0.02 cm yr-1 and -0.20 cm yr-1, respectively. Basal area measurements demonstrated a large degree of variability. Increases were approximately balanced by declines giving the impression of stasis. By removing negative values and correcting by 25% to allow for comparison with vertical growth rates, mean values increased to ~0.5 cm yr-1 for M. annularis and ~0.8 cm yr-1 for P. astreoides. Basal area as a growth measure was compared to methods used in earlier studies. A new growth index based on basal area and perimeter was proposed and modeled. This growth index can be useful for reporting growth measured from basal areas and comparable other methods. The index also measures negative growth, or mortality, which conventional methods cannot do.

Reef-building corals are subject to high amounts of stress, including pollution and rising sea surface temperatures due to climate change. These factors can affect the ability of corals to produce their calcium carbonate skeletons. Evaluation of the effects of climate change may be facilitated by evaluation of records of coral skeletal growth over a long period of time. The aim of this study was to evaluate skeletal growth of the coral Orbicella faveolata in La Parguera, Puerto Rico over a 32-year period. For this, 14 Orbicella faveolata core samples were collected from corals at two reefs (1.2 km apart) in southwestern Puerto Rico. Coral cores were used to obtain skeletal growth data. Average skeletal extension, density, and calcification was determined for subannual and annual periods, and compared between sites. Time series and growth master chronologies were constructed and compared between corals at the two reef sites. In addition, sea surface temperature (SST) data was obtained and summarized into time series, and correlated with coral growth chronologies for the 32-year period. Results showed that two Orbicella faveolata, growth parameters (extension and calcification) were similar between Turrumote and Pinnacles reefs, while density was non-significantly greater on Pinnacles Reef between 1973 and 2004. SST had a weak, and non-significant correlation to growth parameters over time.

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.

The presence of annual density banding in certain long-lived reef-building corals provides a record of the coral’s growth rate over time in response to changing environmental conditions. Coral growth is best described by three parameters: linear extension, bulk density, and calcification. Coral growth is generally controlled by the combined influences of light, temperature, and water quality; however, corals are highly responsive to their surrounding conditions and thus record environmental variations through their rates and patterns of skeletal accretion. Because coral growth rates reflect environmental conditions over time, they allow testing of hypotheses regarding the effects of climate change, more specifically global warming which affects sea surface temperatures and rising atmospheric carbon dioxide which affect the aragonite saturation state of seawater. Influences on coral growth include local changes in sea surface temperature and rainfall as well as large scale climatic indices such as the Atlantic Multidecadal Oscillation (AMO), the North Atlantic Oscillation (NAO), and the Southern Oscillation Index (SOI). Chapter 1, Background, reviews the current state of knowledge in three primary areas: 1) coral biology, growth, density band formation, and measurement of extension, density, and calcification, 2) potential climate change impacts on coral growth, and 3) long-term coral growth records. This section is broadly intended to review the literature, identify possible information gaps, and recognize current debate within coral and climate change research. Chapter 2, Sample Size for Coral Sclerochronology, presents data of sample size correlations based on statistical analyses of annual extension rates. A standardized period (1970-1985) of annual extension rates from the largest number of Montastraea faveolata samples available from southeast Florida (136 corals) was used to test correlation on varying spatial scales and to determine sample size requirements for desired levels of correlation based on objective criteria. The results provide basic information on masterchronology construction for sclerochronological growth rate studies and provide a framework from which further growth rate variability can be assessed. Extension and bulk density can be measured from X-ray films of coral skeletal slabs and can be used to calculate calcification. Chapter 3, Relative Optical Densitometry, describes the techniques and associated errors through the process of coral coring, sectioning, X-raying, developing, digitizing, calibrating and analyzing. The principles of relative optical densitometry and the calculation of mass absorption coefficient ratios for aragonite and aluminum standards are explained. Calculated and measured errors are quantified to define the accuracy and precision of these techniques necessary to detect potentially subtle changes in coral growth caused by climate change. Coral cores from the Florida Key, USA, were used to construct growth records over a 60-yr period from 1973-1996. Chapter 4, Coral Growth Records and Climate Change, uses linear extension rate, bulk-density, and calcification rate from annual and sub-annual bands in order to assess: 1) growth averages, variability, and relationships between growth parameters, 2) long term trends with respect to rising carbon dioxide levels and sea surface temperature, 3) correlation with local environmental variables of temperature and rainfall, and 4) correlation with major climate indices of Atlantic Multidecadal Oscillation, North Atlantic Oscillation, and the Southern Oscillation.

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.