Thesis (Ph. D.)--University of Hawaii at Manoa, 2003. / Includes bibliographical references.

M.Sc. / Please refer to full text to view abstract

Worldwide, coral reefs are recognized as highly valuable ecosystems offering numerous environmental and economic services. In Saudi Arabia, the primary ecosystem service derived from coral reefs is the support of reef-based fisheries, accounting for ~75% of total fisheries landing in the kingdom. Saudi Arabian reefs experienced high fishing pressure for decades due to the growing population and associated fishing pressure. Despite the importance of the provisioning service there are limited ecosystem services valuations for this region. In the wake of a 2015 mass bleaching event, we quantified the effect of habitat degradation on the potential fisheries revenue in the central southern Red Sea. We conducted in situ reef fish surveys in 2014 and 2015 before the bleaching event and in 2019, nearly four years after the bleaching event. Using species-specific prices collected from local fish markets, we calculated values per hectare from multiple reefs in this region, to assess how the reef-based fishery was impacted by the bleaching event. A loss in live hard and soft coral cover was recorded after the bleaching event with associated shifts in the dominance of commercially important fish species. Notably, prior to bleaching, a larger proportion of the high value carnivorous species (70% carnivores, 25% herbivores) dominated the fish assemblage whereas post-bleaching reefs had a higher dominance of lower-valued herbivorous species (25% carnivores, 50% herbivores). While the total revenue was not significantly different before (7,913 USD/hectare) to after the bleaching event (6,814 USD/hectare), the loss of high value species observed suggests that if reefs continue to degrade there are potential negative flow-on effects impacting fisheries provisioning with time. Overall, an increasing percentage of live hard coral cover was positively correlated with fisheries revenue per reef, further providing evidence for the potential loss of revenue in degraded reef ecosystems in the region.

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.

Monitoring the health status of coral reefs is a crucial activity in protecting the environment. One way is by conducting "Manta tow surveys." For a long time, these surveys were conducted by a diver holding a board being towed by a boat. In this thesis, we propose a new vehicle design that works as a platform to help conduct the "towboard" activities for underwater coral reef surveys. It utilizes paravane or depressor features which is a common tool used by fishermen to catch fish at a specified depth. The vehicle offers a compact size, modular design, and control surfaces to maneuver around and close to reef walls. The thesis describes the architecture of the overall system and its components, the design decisions, the mechanical interfaces, and a brief description of the dynamics. An experiment is conducted to validate the design and verify system performance, measuring pressure, speed, and orientation. The prototype is presented as a proof of concept.

Latitudinal patterns in reef fish assemblages reflect the influence of long-term environmental conditions, evolutionary processes and the recent, short-term influence of fishing. Long-term processes generate the typically common latitudinal patterns in reef fish assemblages, such as decreases in diversity and herbivory towards higher latitudes. These patterns reflect the global gradient in water temperature and the isolation of temperate regions from the tropics. Fishing also influences reef fish assemblages in that it decreases the abundance of large-bodied carnivore species on reefs, often leading to over-exploitation, depletion and in some cases the extirpation of populations. Indirectly, the removal of these large-bodied carnivores can influence the abundance of their prey, leading to an increase in non-target species. This study examines the latitudinal patterns in reef fish assemblages across a unique biogeographic region, the temperate Western Australian coast, and incorporates an investigation of the influence of fishing on the structure of these assemblages. Seven regions across seven degrees of latitude and seven degrees of longitude covering approximately 1500 km of coastline were sampled. Fish assemblages were characterised at each region using diver operated stereo-video transects. At each region, four locations, and within each location, four reefs were surveyed totalling 1344 transects. A significant gradient in water temperature exists with latitude and longitude. Along the Western Australian coast, and in contrast to other regions species diversity of reef fish increased towards higher latitudes and there was no evidence for a decrease in the biomass and abundance of herbivorous reef fish. The presence of the poleward flowing warm water Leeuwin current combined with the absence of major extinction events means the temperate Western Australian coast contrasts with global latitudinal trends in reef fish assemblage structure. The unique biogeographic history of temperate Western Australia has also generated a high degree of endemism among reef fish. Nearly 30 % of the species found along the west coast in this study are endemic to Western Australia, with the narrow range of these species playing an important role in the large scale patterns and spatial vi heterogeneity in reef fish assemblage structure. Furthermore, many of these endemic species are large-bodied carnivores and targeted by fishers. The impact of fishing on the abundance of large-bodied carnivores throughout the Western Australian temperate region is clear both spatially and temporally. The distribution of fishing effort is greatest along the west coast and decreases towards the south following the gradient in SST. Along the west coast, high levels of fishing effort have reduced the biomass and abundance of target carnivores to well below the standing biomass of the south coast where a low level of fishing effort occurs. This reduction in biomass is related to the historical declines in catch per unit effort (CPUE) of many key target species. These target species include endemic species such as Choerodon rubescens, Glaucosoma herbraicum, Epinephilides armatus Nemadactylus valenciennesi and Achoerodus gouldii.

The unique coral reef at St. Lucie Reef (Stuart, FL) persists despite environmental variability from extensive freshwater discharges, summer upwelling, and thermal instability. By examining the symbiotic zooxanthellae, or Symbiodinium, that reside in corals, we can gain insight to coral physiology impacted by local stressors. Two scleractinian corals, Montastraea cavernosa and Pseudodiploria clivosa were sampled over 1.5 years, including both wet and dry seasons. Zooxanthellae were isolated and quantitatively characterized using standard measurements and molecular techniques. Both coral species varied in zooxanthellae biomass, where Pseudodiploria clivosa had Higher cell densities and chlorophyll concentrations than Montastraea cavernosa. Over time, these parameters varied, but were not significantly altered by fresh water discharge events. Symbiodinium diversity and abundance were identified by ITS2 region amplification and next-generation sequencing .Novel associations between Symbiodinium and each coral explained the observed physiological differences. The symbioses remained stable throughout and could indicate local adaptation for St. Lucie Reef corals. / Includes bibliography. / Thesis (M.S.)--Florida Atlantic University, 2014. / FAU Electronic Theses and Dissertations Collection

Corals, the foundation species of tropical reefs, are in rapid global decline as a result of anthropogenic disturbance. On many reefs, losses of coral have coincided with the over-harvesting of reef herbivores, resulting in ecosystem phase-shifts from coral to macroalgal dominance. It is hypothesized that abundant macroalgae inhibit coral recovery and recruitment, thereby generating ecological feedback processes that reinforce phase-shifts to macroalgae and further diminish reef function. Notwithstanding, the extent to which macroalgae directly outcompete coral, the mechanisms involved, and the species-specificity of algal-coral competition remains debated. Moreover the capacity for herbivores to prevent vs. reverse ecosystem phase-shifts to macroalgae and the roles of herbivore diversity in such phenomena remain poorly understood. Here I demonstrate with a series of field experiments in the tropical Pacific and Caribbean Sea that multiple macroalgae common to degraded reefs directly outcompete coral using chemical warfare, that these interactions are mediated by hydrophobic secondary metabolites transferred from algal to coral surfaces by direct contact, and that the outcomes of these allelopathic interactions are highly species-specific. Using field observations and experiments in the tropical Pacific, I also demonstrate that the process of herbivory attenuates the competitive effects of allelopathic algae on corals by controlling succession of algal communities, and that the herbivore species responsible for macroalgal removal possess complementary tolerances to the diversity of chemical defenses deployed among algae, creating an essential role for herbivore diversity in reversing ecosystem phase-shifts to macroalgae. Lastly, I demonstrate with field experiments in the tropical Pacific that algal-coral competition simultaneously induces allelochemicals and suppresses anti-herbivore deterrents in some algae, likely due to trade-offs in the productions of defense metabolites with differing ecological functions. Together, these studies provide strong evidence that chemically mediated competitive and consumer-prey interactions play principal roles in coral reef degradation and recovery, and should provide resource managers with vital information needed for effective management of these ecologically and economically important but threatened ecosystems.

This dissertation investigates social and ecological factors that facilitate effective management of coral reefs as social-ecological systems. Meta-analytical and field-based methods were employed to examine current management challenges and identify strategies that improve management effectiveness and coral reef health. A meta-analysis was used to evaluate biological indicators of reef health in relation to the types of fishing regulations in place (no-take areas, gear restriction areas, and periodic closures) and the actor groups (community-based, co-management, state, private) involved in management efforts for coral reef fisheries throughout the world. Other than enhancement of fish biomass within no-take areas that was significantly greater than in gear restriction areas, most biological indicators benefitted similarly from management techniques of no-take areas and gear restriction areas. Community-based and co-management were the best performing management arrangements for some biological outcomes but require further case studies to verify findings. Investigation of management effects by region indicated that previously degraded reefs received fewer benefits from management implementation than did relatively healthier reefs. For field investigations, the Comoros islands in the Western Indian Ocean served as a model for tropical coral reefs with challenging socioeconomic contexts, high biodiversity, and high vulnerability to coral reef degradation. Empirical study at 21 sites was used to identify the relative effects of natural and anthropogenic threats to coral reefs of the Comoros. Most previous studies of reef health focus on primarily natural factors or a single anthropogenic threat. This study examined suites of natural factors and human activities to identify the relative importance of each on reef health. Human activities including fishing, sand extraction, and beachfront housing and development were the best predictors of reef health status. Most notably, human population and fishing predicted fish richness, abundance, and biomass with seasonal variation in the effects, while site orientation strongly predicted benthic cover. Field studies in the Comoros were also used to investigate the roles of community and state actors in co-management and compare effectiveness of comanagement across sites with varying levels of actor participation. Effective management was found to occur with community or `meta-community' (in this case, a Marine Protected Area in which the efforts of several communities were organized) participation in governance and support of state or external agents, while resilient management that overcame considerable challenges was found to occur only with strong community participation and leadership in governance. External agents were found to contribute to development of meta-community governance structure and initiation of community participation through education and capacity building. The findings from these studies reveal that coral reef management can be improved through context appropriate regulations that address detrimental human activities and through wide acceptance and participation in governance with cooperation among states, communities, and external agents.

The purpose of this thesis was to provide a revision and characterization of the species of nongeniculate coralline algae previously ascribed to the now defunct genus Porolithon / to provide a modern account of selected taxa from the genus Hydrolithon and descriptions of taxa found to conform the generic delimitation of Hydrolithon and to use a phenetic cluster analysis to determine the taxonomic relationships between the various taxa ascribed to the genera Polorithon and Hydrolithon.