Geometric morphometrics are a useful tool for studying morphological variation in scleractinian corals, extant and extinct. In the case of modern specimens, three-dimensional features of the calical surface can be measured. These features are rarely preserved in fossil corals, however, necessitating measurement of 2-D landmarks in transverse thin-sections of corallites. Unfortunately, 2-D and 3-D methods often yield differing answers to questions about interspecific, intraspecific and intracolonial variation. This issue is addressed in the present study by directly comparing results of 2-D and 3-D geometric morphometric analyses of identical colonies of extant members of the Montastraea "annularis" species complex. Ten colonies of each extant species in the complex (M. annularis s.s., M. faveolata and M. franksi), identified in the field during collection and verified by molecular data, were selected for analysis. Slabs of colony surfaces and transverse thin-sections from ~1 cm below the surface were cut from tops and edges of each colony. Six corallites from each slab were measured in 3-D using a Reflex microscope, and six measured in 2-D on digital images of each transverse thin-section. Both datasets were explored using geometric morphometric methods and analyzed statistically to address questions related to measurement error, intracolonial variation in corallite morphology between tops and edges of colonies, and interspecific morphological differences. The shape data were superimposed using Procrustes generalized least squares, and examined using principal components and canonical variates analyses. Shape differences implied by axes obtained from PCA and CVA were depicted as deformations using the thin-plate spline, to identify which morphological features are correlated with axes of greatest total variance (PCA) and greatest between-group variance (CVA). Goodall's F-test was used to detect significant morphological differences among species and colony positions. All of the data used in these analyses are available in the supplementary file that accompanies this thesis (see Appendix C for a description of the contents of this file). Measurement error analyses show significant differences among variances associated with replicate measurements of 2-D and 3-D landmarks. In many cases the variance is asymmetrical, and for 2D data especially, this asymmetry coincides with orientation of anatomical features. Significant shape differences between corallites from tops and edges of colonies of M. annularis and M. faveolata are found when 3-D data are used. These intracolonial differences are due in large part to height and shape of the septal margin. As a result, 2-D data are unable to find significant differences within colonies. Both datasets find significant interspecific differences, but different anatomical features are found to be responsible. Important interspecific differences for 2-D data are relative thickness of the corallite wall and lengths of septa and costae. When 3-D data are used, results are most influenced by height of primary and secondary septa above the calical surface, as well as length of septa from the corallite wall toward the columella. Patterns of relative morphological similarity among species also differ between datasets. 2-D data show closest similarity between M. annularis and M. faveolata, while M. faveolata and M. franksi are most similar when 3-D data are used. The former result is consistent with previous 2-D analyses, while the latter conclusion is without precedent. Neither is consistent with relationships inferred using molecular data.

No description available.

Stony coral tissue loss disease (SCTLD) has been spreading throughout Caribbean coral reefs since 2014, heavily impacting scleractinian corals. To mitigate losses, this experiment assessed the effectiveness of two SCTLD intervention treatments in situ. SCTLD-affected Montastraea cavernosa colonies offshore of Broward County were divided into three treatment groups: 1) chlorinated epoxy, 2) Base 2B plus amoxicillin, and 3) untreated controls, plus a fourth group of healthy untreated controls. These colonies were monitored over 11 months to record SCTLD status, lesion activity, colony mortality, and changes in healthy tissue area with 3D modelling. The Base 2B plus amoxicillin treatment was more effective at halting SCTLD lesions, slowing the rate of tissue loss, and decreasing the overall proportion of tissue lost as compared to chlorinated epoxy or no treatment. However, neither treatment prevented new SCTLD lesions from developing. These findings can enhance the effectiveness of Caribbean management efforts to mitigate SCTLD impacts. / Includes bibliography. / Thesis (M.S.)--Florida Atlantic University, 2020. / FAU Electronic Theses and Dissertations Collection

Coral reef ecosystems worldwide are facing increasing degradation due to disease, anthropogenic damage, and climate change, particularly in the Tropical Western Atlantic. Mesophotic coral ecosystems (MCEs) have been recently gaining attention through increased characterization as continuations of shallow reefs below traditional SCUBA depths (>30 m). As MCEs appear to be sheltered from many stressors affecting shallow reefs, MCEs may act as a coral refuge and provide larvae to nearby shallow reefs. The Deep Reef Refugia Hypothesis (DRRH) posits that shallow and mesophotic reefs may be genetically connected and that some coral species are equally compatible in both habitats. The research presented here addresses key questions that underlie this theory and advances our knowledge of coral connectivity and MCE ecology using the depth-generalist coral Montastraea cavernosa. Chapter 1 presents an overview of the DRRH, a description of MCEs in the Gulf of Mexico (GOM), and the framework of research questions within existing reef management infrastructure in the GOM. Through microsatellite genotyping, Chapter 2 identifies high connectivity among shallow and mesophotic reefs in the northwest GOM and evidence for relative isolation between depth zones in Belize and the southeast GOM. Historical migration and vertical connectivity models estimate Gulf-wide population panmixia. Chapter 3 focuses on population structure within the northwest GOM, identifying a lack of significant population structure. Dominant migration patterns estimate population panmixia, suggesting mesophotic populations currently considered for National Marine Sanctuary protection benefit the Flower Garden Banks. Chapter 4 quantifies the level of morphological variation between shallow and mesophotic M. cavernosa, revealing two distinct morphotypes possibly representing adaptive tradeoffs. Chapter 5 examines the transcriptomic mechanisms behind coral plasticity between depth zones, discovering a consistent response to mesophotic conditions across regions. Additionally, variable plasticity of mesophotic corals resulting from transplantation to shallow depths and potential differences in bleaching resilience between shallow and mesophotic corals are identified. The dissertation concludes with a synthesis of the results as they pertain to connectivity of shallow and mesophotic corals in the Gulf of Mexico and suggests future research that will aid in further understanding of MCE ecology and connectivity. / Includes bibliography. / Dissertation (Ph.D.)--Florida Atlantic University, 2018. / FAU Electronic Theses and Dissertations Collection

Coral reefs worldwide are experiencing unprecedented and rapid declines. However, deeper, mesophotic coral ecosystems (MCEs; 30–150 m) may act as refuges for coral species, providing larvae to recolonize degraded shallow reefs. This study assessed the genetic connectivity of shallow and mesophotic Montastraea cavernosa populations on the Belize Barrier Reef and the community structure of their endosymbiotic algae (Family Symbiodiniaceae) across a fine-scale depth gradient (10, 16, 25, 35 m). Evaluation of nine polymorphic microsatellite markers demonstrated that relatively shallow (10 and 16 m) M. cavernosa populations were genetically distinct from relatively deep (25 and 35 m) populations. High throughput sequencing of ribosomal coding DNA from Symbiodiniaceae communities of M. cavernosa revealed differences in community structure across depth, with shallow-specialist and depth-generalist community profiles. This research provides important information for the management of distinct deep and adds to the body of research on the understudied MCEs of the Mesoamerican Reef. / Includes bibliography. / Thesis (M.S.)--Florida Atlantic University, 2019. / FAU Electronic Theses and Dissertations Collection

Coral reefs are threatened in Florida and worldwide. Successful resource management requires rapid identification of anthropogenic sources of stress before they affect the reef community. I tested a multi-scale approach for assessing reef condition at seven reefs within the Florida Keys National Marine Sanctuary and Biscayne National Park between 2001 and 2003. I examined multiple environmental parameters to identify potential sources of stress. I utilized the Atlantic and Gulf Rapid Reef Assessment Biotic Reef Index to assess benthic community structure and an indicator species of Foraminifera (Amphistegina gibbosa) to determine if environmental conditions were suitable for calcareous organisms that host algal endosymbionts. Small tissue samples were extracted from colonies of Montastraea annularis species complex to assay a suite of cellular biomarkers to elucidate possible mechanisms of the coral stress response. I monitored regeneration rates of the resultant lesions to determine if the coral colonies were capable of recovering from damage. Multivariate data analyses indicated that corals at all study sites were experiencing stress with different degrees of response and decline. On reefs with coarse grain sediments that are adjacent to an intact mangrove shoreline, the Cellular Diagnostic System indicated that corals were responding to a xenobiotic stress but appeared to be compensating as evidenced by consistently high lesion regeneration rates, a high percentage of healed lesions, low coral mortality and high abundances of A. gibbosa. On reefs with silt-sized sediments adjacent to developed coastlines, corals also were responding to xenobiotic stresses, but were negatively affected as evidenced by low regeneration rates, a low percentage of healed lesions, high coral mortality, and low abundances of A. gibbosa. Corals at an 18 m offshore site exhibited abnormally low biomarker levels and some died during the study, indicating that sampled colonies were incapable of upregulating necessary protective proteins. Further research will be required to determine stressor sources. This study demonstrates that a multiple-indicator approach, spanning scales from cellular to community, can provide marine resource managers with data linking decline of coral populations to specific environmental conditions and events, thereby providing potential for early detection of stressors allowing for preventive management.

Submitted by Alberto Vieira (martins_vieira@ibest.com.br) on 2018-01-31T00:18:00Z No. of bitstreams: 1 414933.pdf: 15896634 bytes, checksum: 6e86128ee7096bec949c9b616f290355 (MD5) / Made available in DSpace on 2018-01-31T00:18:00Z (GMT). No. of bitstreams: 1 414933.pdf: 15896634 bytes, checksum: 6e86128ee7096bec949c9b616f290355 (MD5) Previous issue date: 2000 / CAPES / Animais clonais crescem por acréscimo de unidades funcionais (zoóides) as quais formam a colônia. A abordagem modular consiste em descrever a forma das colônias do ponto de vista do arranjo e tamanho dos módulos. A abordagem modular foi usada aqui para quantificar variações na forma de crescimento do coral Montastraea cavernosa a partir da mensuração do arranjo e áreas dos pólipos na face interna do tecido colonial. Foram coletadas 46 amostras no Parcel das Paredes (BA) e João Pessoa (PB). Os resultados mostraram que área dos pólipos é parcialmente explicada por fatores ligados ao espaçamento entre eles. Estes fatores variam com a forma da colônia e com a faixa de tamanho de pólipos considerada. Foi proposto um modelo conceitual hipotético para a relação entre a forma de crescimento colonial, o tamanho e a organização dos pólipos. São discutidas possíveis razões evolutivas para o modelo proposto e implicações deste para estudos morfométricos da espécie. / Clonal animals grow through addition of functional units (zooids), whose assemblage constitutes a colony. The modular approach consists in describing colony form from the arrangement and size of modules. The modular approach was used here to access variations in growth forms of the coral Montastraea cavernosa using the arrangement and the size of polyps in the inner face of the colonial of 46 samples collected in Parcel das Paredes (BA) and João Pessoa (PB). Results showed that area of the polyps is partially explained by factors related to the spacing among them. These factors vary with the form of the colony and with the range of polyp sizes being analyzed. A hypothetical conceptual model for the relationship among colonial growth forms, polyp sizes and organization is proposed. Possible evolutionary reasons for such a model are discussed as well as possible implications to morphometric studies of this species.

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.

Coral reefs on Florida’s Reef Tract (FRT) are susceptible to many anthropogenic influences including controlled freshwater discharges and agricultural runoff as well as high natural environmental variability from seasonal rainfall, runoff and upwelling. To better understand coral population structure and responses to sublethal stressors, populations of the scleractinian coral Montastraea cavernosa in the northern FRT were examined using a combination of genomic and transcriptomic techniques. Microsatellite genetic markers identified high local retention among sites and a slight southward gene flow. An in-situ temporal gene expression analysis utilizing a tag-based sequencing transcriptomic approach was used to analyze baseline coral health at St. Lucie Reef (SLR), off Stuart, FL. Temporal variation had the greatest influence of differential gene expression among M. cavernosa at SLR. Results will be shared with local resource managers and coupled with a complementary ex-situ experimental trial. / Includes bibliography. / Thesis (M.S.)--Florida Atlantic University, 2017. / FAU Electronic Theses and Dissertations Collection

Part I: Coral reefs are essential to coastal economies, protecting coastlines from storms, and harboring high biodiversity. However, reefs are declining due to local anthropogenic stressors and ocean warming. Sedimentation, a local stressor, aggravates the impacts of warming on corals and hinders their survival and growth. Therefore, it is important to investigate whether sedimentation and temperature have a synergistic effect on vulnerable coral species, especially during earlier stages of development. To quantify these effects, survival and growth of newly settled Acropora cervicornis corals were measured at two temperatures (29 and 31°C, representing current and predicted for 2050 Summer temperatures) and three sediment concentrations (30, 60 and 120 mg.cm-2, representing a range from natural sedimentation to dredging conditions). The intent of this study was to mix multiple genotypes to test temperature and sedimentation among genotypic unique individuals. However, only 20% of colonies spawned, and spawning was asynchronous by genotype. Therefore, individuals were produced from self-fertilization. The overall high mortality seen in this study suggests that self-fertilization in A. cervicornis does not produce viable juveniles. Although temperature did not have a significant effect on the survival of self-fertilized juveniles, sediment concentration did. The lowest sediment concentration led to the highest juvenile survival in both ambient and heated conditions. The growth of A. cervicornis selfed individuals was not significantly affected by temperature or sedimentation. These results suggest that reducing sedimentation in dredging and coastal construction areas around coral reefs facilitates the survival of Acropora cervicornis juveniles and may help to ensure their persistence in the future. Because self-fertilized larvae were used, these results need to be interpreted with caution, and this research needs to be repeated with outcrossed A. cervicornis. What is clear is that genotypic diversity is needed for A. cervicornis population growth and resilience. Part II: Chimeras occur when two or more genetically unique individuals of the same species fuse together. The presence of chimerism can aid in the survival and evolution of organisms. This study investigated whether the prevalence of chimerism differs between coral species of different reproduction modes and growth rates. To fulfill this goal, the surface area of egg and/or larvae of three coral species, Montastraea cavernosa, Acropora cervicornis, and Porites astreoides, were measured and compared with the respective surface areas of the newly settled juveniles. This comparison suggested that M. cavernosa displayed a greater tendency to form chimeras than A. cervicornis and P. astreoides. Observations during embryogenesis confirmed this prediction. Montastraea cavernosa is a slow grower and has the smallest eggs of all three study species. Chimerism during embryogenesis may increase this species’ tendency to start the sessile stage at a slightly bigger size and thus increases its competitive abilities for reef space. In contrast, A. cervicornis is a broadcast spawner, fast grower and has a relatively larger egg size, possibly explaining the reduced chimeric tendency during embryogenesis. It is possible that P. astreoides formed chimeras during embryogenesis within the polyp, but they did not form them in the swimming planulae stage. The lack of chimerism during P. astreoides planulae development may be attributed to its brooding reproductive mode, directly releasing large competent larvae that have large initial sizes at settlement. Therefore, the ability to form chimeras in an early developmental stage might provide an ecological advantage to M. cavernosa that contributes to its abundance in Broward County: the greater size at settlement caused by chimerism during embryogenesis may provide this species a competitive advantage for reef space.