This thesis is composed of two articles. The first is an analysis of long-term survival among A. cervicornis outplants in the Florida Keys, from 2007 to the present. The second is a review of literature that informs coral restoration and guides both restoration practitioners and coral researchers towards greater effectiveness in outplant survival and understanding biological processes involved in restoration. In the first article, despite promising initial evidence of outplant survival and health, the long-term results, using Weibull survival analysis, are discouraging with almost all out planted corals over an 8 year long study exhibiting steep declines in percent live tissue and survival between three and five years. Not only is this 3-5 year collapse apparent in all the outplanted cohorts, but the evidence is highly significant that the length of outplant survival is decreasing with each passing year (diminished resilience). These findings suggest that some shared, likely environmental factor, is increasingly impacting all outplants. Further, no cohorts appear to adapt to the environmental conditions in which these declines are occurring (diminished adaptive capacity), a trend that would be evident if their declines slowed or reversed and Weibull beta-parameterization would show. The second article, reviews several areas of recent study which offer avenues for future research: these include, ecological history and biogeography, developmental pathways of colonial form and function, polarity and symmetry, genetics, wound healing, fecundity, reproduction, sexual maturity and community interactions. The thesis concludes with questions for further research and understanding in the field of coral restoration.

Photosensitive behaviors and circadian rhythms are well documented in reef-building corals and their larvae, yet photoreceptive structures and opsins have not been described in these organisms. Here I provide evidence for red sensitivity in several species of coral larvae. Behavioral experiments with two Caribbean corals, Porites astreoides and Acropora palmata demonstrated that larvae settle and metamorphose at a greater frequency on red substrata than on similar substrata of other colors. Attachment to red substrata was not observed when larvae were maintained in the dark, suggesting that red sensitivity was responsible for the observed behavior. Extracellular recordings confirm photosensitivity and indicate that the peak sensitivity of coral photoreceptors are shifted towards the orange-red region of the visible light spectrum, similar to the spectra (fluorescence and reflectance) of preferred artificial (plastic) and natural (crustose coralline algae) settlement substrata. Using Blast analyses and a PCRbased approach, I have identified, sequenced and cloned two full-length opsin cDNAs from A. palmata larvae. One cDNA (Acropsin 1) encodes an opsin protein that is similar to a vertebrate melanopsin; the second (Acropsin 2) encodes a protein that is most similar to cephalopod rod opsin. I have successfully developed synthetic peptide antibodies against each Acropsin 1 and Acropsin 2. Western blots of adult A. palmata and A. cervicornis protein detect a 37kDa and 40kDa band, corresponding to the predicted molecular weights of Acropsins 1 and 2, respectively. Immunohistochemistry confirms expression of both opsins in A. palmata larvae. Staining of sectioned larvae demonstrates that Acropsin 1 is localized in the larval gastroderm while Acropsin 2 is localized in solitary epithelial cells, scattered throughout the larval ectoderm but with a polarized distribution and higher concentration in the aboral epidermis. This research provides several lines of evidence to support the existence, and demonstrate one potential ecological function, of opsin-based photosensitivity in corals.

Generations of hard corals have built the complex reef ecosystems that harbour a huge diversity of sea-life in the world’s shallow tropical oceans. These undergo both sexual and clonal reproduction, and may contain signatures in their genomes which help to decipher the riddles of past population dynamics and evolutionary history. Two species of coral, Acropora austera and Platygyra daedalea, were collected from sites along the east African coastline from Kenya in the north to Maputaland, South Africa in the south, and from the Chagos Archipelago. Sequences of two different DNA regions were tested, in a preliminary study, for their potential ability to elucidate connectivity and differentiation among these coral populations. These were the nuclear ribosomal ITS region of P. daedalea populations, and a previously-unused marker, the carbonic anhydrase 3/550 nuclear intron of A. austera. These molecular markers indicated high levels of connectivity amongst populations in a preliminary study based on limited sample sizes and a subset of populations. It was decided to further explore the variability of the carbonic anhydrase 3/550 intron, which showed evidence of subdivision and structuring within Mozambique populations relative to South African populations, in a study in which both the sample size per site and the number and range of sampled sites were increased. ITS sequences, although highly variable, revealed no population differentiation in P. daedalea; STR markers were used in subsequent studies of population differentiation in this species. Populations of both A. austera and P. daedalea showed signs of high connectivity along the region of the coastline sampled in this study. However, there appeared to be a disjunction in ecological connectivity between reefs in Maputaland, South Africa and those in southern Mozambique, between Durban and Maputo where the Agulhas Current originates. This was reinforced in A. austera populations which displayed a region of genetic discontinuity between Inhaca Island and Maputaland reefs of the central reef complex, in the region of Rabbit Rock. Northern reef complexes also harboured unique haplotypes in contrast to southern reefs which shared all haplotypes with those in the north, an indication that northern reefs have seeded the southern (Maputaland) reefs. P. daedalea populations appeared evolutionarily panmictic over scales relevant to this study. Evidence for fine-scale structure indicated that populations were separated from one another over ecologically relevant time-scales. These populations were defined by both their habitats and their sampling location. There was a possibility that the Platygyra species complex included cryptic species that were not distinguishable from P. daedalea. However, the disjunction in the connectivity between northern and southern population groups was also evident in the population structure of P. daedalea. There was a net immigration of propagules of both P. daedalea and A. austera into populations north of the disjunction between groups, where the prevailing current regime is dictated by the Mozambique Channel eddies. In contrast populations to the south of the disjunction (the southern population group) which are subject to the swiftly flowing Agulhas Current, showed a net emigration of propagules from Maputaland reefs. These emigrants were likely to be lost to inhospitable habitat south of the marginal Maputaland region. Although there was evidence for migration of both Platygyra and Acropora propagules between the Bazaruto Archipelago reefs and certain Maputaland reefs, genetic exchange between Mozambique and Maputaland reefs appeared to be limited and may have occurred primarily at evolutionary rather than demographic levels. Managers may need to treat the regional Maputaland reefs as separate stocks and manage them accordingly, as the relative isolation of these corals in the central and southern reef complexes in Maputaland, South Africa, means that they are at risk to losing species to evolutionary extinction. It is also important that reef health in northern Mozambique and Tanzania is maintained as, despite evidence of a break in demographic connectivity, between reefs in these regions and those in Maputaland, there was evidence to suggest that reefs were connected at evolutionary scales, thus maintaining levels of genetic diversity on southern African reefs. / Thesis (Ph.D.)-University of KwaZulu-Natal, Westville, 2010.

Reef-building corals are cornerstones of life in the oceans. Understanding their interactions with microorganisms and their surrounding physicochemical conditions is important to comprehend reef functioning and ultimately protect coral reef ecosystems. Corals associate with a complex and specific array of microorganisms that supposedly affect their physiology and therefore can significantly determine the condition of a coral ecosystem. As environmental conditions may shape bacterial diversity and ecology in the coral symbiosis, ecosystem changes might have unfavorable consequences for the holobiont, to date poorly understood. Here, we were studying microbial community changes in A. hemprichii as a consequence of simulated eutrophication and overfishing over a period of 16 weeks by using in situ caging and slow release fertilizer treatments in an undisturbed Red Sea reef (22.18ºN, 38.57ºW). We used 16S rDNA amplicon sequencing to evaluate the individual and combined effects of overnutrification and fishing pressure, two of the most common local threats to coral reefs. With our data we hope to better understand bacterial population dynamics under anthropogenic influences and its role in coral resilience. Projecting further, this data will be useful to better predict the consequences of human activity on reef ecosystems.

Unprecedented population losses of the staghorn coral, Acropora cervicornis, since the 1970s have been attributed primarily to disease. Although a positive linear relationship between disease prevalence and increased water temperature has been described, the pathogen(s) causing disease and whether they are spread through the water or vectors is still poorly understood. Additionally, an increase in disease outbreaks and severity has provided an urgent need to identify natural genotypic resistance to disease in Caribbean acroporids. Studies to date have explored a variety of pathogen transmission methods, but prior to this study, there has been no examination of differences among common techniques. I investigated pathogen transmission and resistance to development of the disease known as rapid-tissue loss (RTL) in 11 different genotypes by comparing two common transmission methods (direct contact vs. waterborne). Additionally, I investigated changes in tissue condition over a 9-day acclimation period to determine the potential effect of acclimation on disease susceptibility. Overall, disease was significantly higher in the direct contact treatment, though resulting disease varied greatly by genotype, with only one genotype appearing resistant to developing disease. Acclimation time influenced tissue condition with a significant decline in condition occurring from day zero to day two, but significant improvements in surface body wall parameters were observed from days two to nine. These results highlight the differences between disease transmission methods and demonstrate the importance of selecting an appropriate transmission method and acclimation period for future studies.

Coral reefs are "constructional physiographic features of tropical seas consisting fundamentally of a rigid calcareous framework made up mainly of the interlocked and encrusting skeletons of reef-building (hermatypic) corals (Wells,1957). The principal organisms responsible for the construction of modern day coral reefs, the stony corals, comprise the cnidarian order Scleractinia, which is closely allied to the sea anemones (Actinaria). Individual polyps secrete a calcium carbonate skeletal cup (calyx) beneath the basal epidermis. In most coral species the polyps remain connected by living tissue forming a colony and calcium carbonate is deposited beneath the basal epidermis of the entire colony, thereby constructing a three-dimensional mass of calcium carbonate which increases in size with the passage of time. The living tissues of reef building corals are packed with unicellular symbiotic dinoflagellates termed zooxanthellae which have been shown to be of Importance in both the calcification of the skeleton and in production of organic material on the reef.

Choi Mei Mei. / Thesis submitted in: December 2002. / Thesis (M.Phil.)--Chinese University of Hong Kong, 2003. / Includes bibliographical references (leaves 214-236). / Abstracts in English and Chinese. / Abstract --- p.i / Acknowledgements --- p.vi / Table of Contents --- p.viii / List of Tables --- p.xi / List of Figures --- p.xii / Chapter Chapter One: --- General Introduction --- p.1 / Chapter 1.1 --- Introduction --- p.1 / Chapter 1.1.1 --- Coral bleaching --- p.2 / Chapter 1.1.2 --- Predation of corals by corallivorous gastropods --- p.20 / Chapter 1.2 --- Introduction of Study Sites- Tung Ping Chau --- p.33 / Chapter 1.3 --- Objectives of the Study --- p.35 / Chapter 1.4 --- Structure of this Thesis --- p.36 / Chapter Chapter Two: --- "Coral Bleaching and Predation by Corallivorous Gastropods in the Coral Communities of A Ye Wan and A Ma Wan, Tung Ping Chau" --- p.40 / Chapter 2.1 --- Introduction --- p.40 / Chapter 2.2 --- Materials and Methods --- p.45 / Chapter 2.2.1 --- Quantitative surveys --- p.45 / Chapter 2.2.2 --- "Quantifying the colour of corals, Porites lobata, in Tung Ping Chau" --- p.47 / Chapter 2.2.3 --- Physical parameters --- p.49 / Chapter 2.2.4 --- Data and statistical analysis --- p.49 / Chapter 2.3 --- Results --- p.50 / Chapter 2.3.1 --- Live coral coverage in A Ye Wan and A Ma Wan --- p.50 / Chapter 2.3.2 --- Proportion of Porites lobata paled --- p.52 / Chapter 2.3.3 --- Changes in colour intensity of Porites lobata between seasons --- p.54 / Chapter 2.3.4 --- Density of corallivorous gastropods --- p.55 / Chapter 2.3.5 --- Percentage coverage of live and dead Acropora tumida --- p.55 / Chapter 2.3.6 --- Physical parameters --- p.57 / Chapter 2.4 --- Discussion --- p.59 / Chapter 2.4.1 --- Live coral cover in A Ye Wan and A Ma Wan --- p.59 / Chapter 2.4.2 --- Bleaching of Porites lobata in summer and winter --- p.61 / Chapter 2.4.3 --- Colour intensity of Porites lobata in different seasons --- p.67 / Chapter 2.4.4 --- Predation on corals by corallivorous gastropods --- p.69 / Chapter Chapter Three: --- "Study on Coral Bleaching, Pontes bbata, in Tung Ping Chau by using Permanent Quadrats" --- p.103 / Chapter 3.1 --- Introduction --- p.103 / Chapter 3.2 --- Materials and Methods --- p.104 / Chapter 3.2.1 --- Study sites --- p.104 / Chapter 3.2.2 --- Permanent quadrat monitoring --- p.105 / Chapter 3.2.3 --- Corals sampling for zooxanthellae density and chlorophyll a concentration analysis --- p.106 / Chapter 3.2.3.1 --- Tissus collection --- p.106 / Chapter 3.2.3.2 --- Zooxanthellae counting --- p.107 / Chapter 3.2.3.3 --- Chlorophyll a determination --- p.107 / Chapter 3.2.3.4 --- Determination of coral surface area --- p.108 / Chapter 3.2.4 --- Data analysis --- p.108 / Chapter 3.3 --- Results --- p.109 / Chapter 3.3.1 --- Monitoring of bleaching of porties lobata in permanent quadrat --- p.109 / Chapter 3.3.2 --- Density of Zooxanthellae in Porites lobata --- p.111 / Chapter 3.3.3 --- Concentration of Chlorophyll a in Porites lobata --- p.112 / Chapter 3.3.4 --- Chlorophyll a per zooxanthellae --- p.113 / Chapter 3.4 --- Discussion --- p.114 / Chapter Chapter Four --- Study of Predation on coral Acropora tumida by Corallivorous Gastropods in Tung Ping Chau --- p.138 / Chapter 4.1 --- General Introduction --- p.138 / Chapter 4.2 --- Materials and Methods --- p.140 / Chapter 4.2.1 --- Study sites --- p.140 / Chapter 4.2.2 --- Preliminary evaluation of corallivorous gastropods as the coal predator --- p.141 / Chapter 4.2.3 --- Monthly monitoring of permanent quadrat --- p.142 / Chapter 4.2.4 --- Data and statistical analysis --- p.144 / Chapter 4.3 --- Results --- p.145 / Chapter 4.3.1 --- Species of corallivorous gastropods in Tung Ping Chau --- p.145 / Chapter 4.3.2 --- Feeding behavior of corallivorous gastropods in Tung Ping Chau --- p.146 / Chapter 4.3.3 --- Density of corallivorous gastropods --- p.147 / Chapter 4.3.3.1 --- Monthly change in density of corallivorous gastropods --- p.147 / Chapter 4.3.3.2 --- Correlation between gastropod density and temperature --- p.149 / Chapter 4.3.4 --- Cumulative percentage of area of feeding scar over time --- p.149 / Chapter 4.3.5 --- Monthly percentage change in the areas of feeding scar --- p.152 / Chapter 4.3.5.1 --- Monthly percentage change in the areas of feedling scar due to predation by Cronia margariticola and Drupella rugosa --- p.152 / Chapter 4.3.5.2 --- Correlation between gastropod density and monthly percentage change in area of scar --- p.153 / Chapter 4.3.5.3 --- Correlation between temperature and monthly percentage in area of the feeding scar --- p.154 / Chapter 4.3.6 --- Rate of predation --- p.154 / Chapter 4.3.6.1 --- Rate of predation by the corallivorous gastropods --- p.154 / Chapter 4.3.6.2 --- "Correlation between rate of predation, gastropod density and seawater temperature" --- p.155 / Chapter 4.3.7 --- Population size structure of the corallivorous gastropods --- p.156 / Chapter 4.3.7.1 --- Population size structure of Cronia margariticola --- p.156 / Chapter 4.3.7.2 --- Population size structure of Drupella rugosa --- p.158 / Chapter 4.4 --- Discussion --- p.159 / Chapter 4.4.1 --- Feeding behaviours of corallivorous gastropods --- p.159 / Chapter 4.4.2 --- Density of corallivorous gastropods --- p.162 / Chapter 4.4.3 --- Cumulative percentage of area of feeding scar --- p.170 / Chapter 4.4.4 --- Monthly percentage change of area of feeding scar --- p.173 / Chapter 4.4.5 --- Rate of predation --- p.175 / Chapter 4.4.6 --- Size structure of population size --- p.178 / Chapter 4.4.7 --- Predatory pressure from corallivorous gastropods in Tung Ping Chau --- p.185 / Chapter Chapter Five --- Summary and Perspectives --- p.207 / References --- p.214

This thesis is the first study to provide a detailed characterization of Acropora cervicornis transplants and donor colony survival on southeast Florida coral reefs. Since May 2006 this species has been listed as a threatened species under the Endangered Species Act. As populations continue to decline restoration efforts need to be evaluated to determine if there is an effort that could facilitate a population rebound. The overall goal of this project was to examine potential Acropora cervicornis restoration techniques along the entire Florida reef tract including Broward County, Miami Dade County, and Monroe County. For my thesis I used a portion of the data collected from the Broward County region nursery. I analyzed data on the donor colonies and the nursery fragments. The goals were to determine if fragments generated from clippings removed from donor colonies can 1) be transplanted to a nursery site, 2) have acceptable survivorship and 3) increase in complexity (branching). Beyond survival and growth, I also examined genotypic differences in fragment survival and growth rates. Twelve A. cervicornis donor colonies separated by as much as 26 km were identified, and monitored quarterly for 19 months. From each donor colony three 10 cm clippings were removed for transplantation to the nursery habitat and one 1 cm clipping was taken for genetic analysis. Prior to transplantation, each 10 cm clipping was cut into 3 cm fragments. Transplantation occurred in September, October, and December 2007, transplanting 1/3 of the fragments horizontal and 2/3 vertical in orientation. Fragments in the nursery were monitored monthly through November 2008. During each monthly monitoring, images were taken, fragments were measured, branches were counted, and condition (partial mortality, disease, predation, etc.) was assessed. Each donor colony sampled with in Broward County for this project was determined to be a unique genotype using microsatellites. Significant differences in survival, growth, and number of branches were determined among fragment genotypes. Vertically orientated fragments had higher survivorship, but horizontal fragments had higher mean growth rates and number of branches per fragment. This coral restoration project has the real possibility of providing important information on the effectiveness of utilizing the asexual, fragmentation, capacity of A. cervicornis to facilitate A. cervicornis population conservation. My effort could contribute to a quantitative comparison of Acropora genotypic variation in survivorship and growth, which will provide information on intra- and inter-regional potential for large-scale restoration within the Florida reef tract.

This thesis provides a detailed analysis of the growth and survivorship of outplanted Acropora cervicornis corals from underwater nurseries within three regions of the Florida Reef Tract. Substantial loss of stony coral cover on Florida’s coral reefs, including the branching staghorn coral, Acropora cervicornis, has occurred for decades due to disturbances such as disease, temperature induced bleaching, hurricanes, sedimentation, and pollution. This rapid population decline contributed to A. cervicornis being listed as a threatened species under the U.S. Endangered Species Act in May 2006. To aid in the recovery of the species, coral fragments were grown in underwater nurseries and outplanted to selected sites located within unique cross-shelf zones in the Upper Florida Keys, Lower Keys, and Biscayne regions. This study evaluated the regional and zonal variation in growth and survivorship of known genotypes of outplanted A. cervicornis corals to better inform future large-scale restoration projects. The zone in which corals of A. cervicornis were outplanted to had a more significant effect on growth than the coral genotype. The forereef zone within the Upper and Lower Keys regions and the mid-channel zone in the Biscayne region had significantly higher mean growth rates. When comparing growth rates of genotypes that performed best, high growth, in the Lower Keys nursery, these same genotypes did not perform the best at any of the outplant sites. Survivorship was not significantly different in any of the regions. Based on these results, future coral outplantings focused in the forereef and mid-channel zones would maximize growth. Choosing coral genotypes based on their high growth rates in the nursery does not ensure the same high growth rates when outplanted.

This thesis is the first known study to relocate Acropora cervicornis across multiple regions of the Florida Reef Tract. Since 2006, A. cervicornis has been listed as a threatened coral species under the U.S. Endangered Species Act. In response, restoration efforts utilizing coral nursery methods have been implemented throughout the Caribbean. The primary objective of this research was to determine the response of A. cervicornis colonies to being relocated between two coral nurseries separated by approximately 150km along the Florida Reef Tract. To accomplish this, a reciprocal transport was conducted between coral fragments with known genotypes from Broward County and Monroe County, Florida. A subset of coral ramets (fragments of a single genotype) was removed from the nursery of origin and relocated to the opposing coral nursery, while the remaining ramets stayed in their original nursery to serve as controls. Following transplant, both relocated and non-relocated corals were monitored for 14 months and survivorship, growth rates, branching frequency, and coral condition data were collected. In addition, tissue samples were collected twice during the monitoring period to determine zooxanthellae densities. Reaction norms were used to predict the responses of each measured variable for each genotype in response to being relocated. Relocated coral colonies from both nurseries exhibited equal or greater survivorship than the non-relocated corals from their original nursery. Growth rates, branching frequency, and zooxanthellae densities were highest in the corals that were previously in or relocated to Broward County. Within each nursery, relocated and non-relocated corals were not significantly different in any of the measured parameters. Throughout the study period, there were no signs of disease, bleaching, or predation on any of the corals. These findings demonstrate that A. cervicornis colonies can be successfully relocated across regions of the Florida Reef Tract suggesting that colonies throughout the FRT may be used for collaborative restoration efforts. Reaction norm analysis indicated phenotypically plastic responses in each growth parameter with some instances of genotype-by-environment interactions. Finally, these results suggest the need for additional research to investigate regional differences in A. cervicornis populations for proper management and restoration approaches.