Over the last decade, coral reef remote sensing research has focused on habitat map development. Advances in field methods, spatial and spectral resolution of remote sensing data, and algorithm development have led to more detailed map categories and to heightened map accuracy. Studies have provided guidance for practitioners in areas such as imagery selection, algorithm application, and class selection methods, but the product has remained relatively unchanged – a habitat map showing the spatial distribution of a range of substrate classes, classified primarily on the basis of their spectral signature. However, the application of such a product in a management context has not been elaborated by the remote sensing community. The research described in this thesis addresses the challenge that the application of remotely-sensed coral reef information in a coral reef management environment elicits. In such an environment, the coral reef manager asks: "What can the map do to help me?", while the remote sensing scientist asks: "What type of information do you need?". The research described here aims to reconcile these two points of view, by answering the research question of this thesis: How can coral reef remotely-sensed information address stakeholder-specific coral reef management objectives? This question was answered through the development of a four-stage strategy. The strategy includes: 1) developing a traditional habitat map, 2) investigating stakeholder receptivity to the habitat map, 3) linking stakeholder interests with habitat data, and 4) illustrating the linked habitat data in what we term a management map. The strategy was applied on Bunaken Island, Indonesia, and involved the collection of both qualitative and quantitative data sets. The research was relevant to the communities on Bunaken Island, as they are directly responsible for the management of the coral reef resources surrounding Bunaken Island, and they are regularly planning and implementing coral reef management projects. The effectiveness of the four-stage strategy was evaluated in a framework that compares potential and actual uses of habitat maps and management maps in coral reef management projects. It was shown that management maps are superior to habitat maps for a wide range of management purposes. This research has provided two main contributions to the field of coral reef remote sensing and management. The first is the four-stage strategy that results in the development of management maps, and the second is the framework for evaluating the effectiveness of the management maps. This research seeks to traverse the gap between producers and users of coral reef remotely-sensed information. The recommendations made from this research addresses coral reef management procedures, action research, and cross-cultural communication. Each recommendation is founded on collaboration between scientist and manager. Such collaboration is crucial for successful application of remotely-sensed information to management.

Overfishing of stock and decreasing biodiversity are grave concerns for the U.S. and the rest of the world. Understanding and applying spatial and temporal information of marine species’ reproductive ecology and critical life habitat is vital to the development of effective strategies for marine resource management. In the Caribbean, one of the critical science gaps hindering effective management is the lack of information on how environmental factors may make fish spawning aggregation (FSA) sites optimal for spawning. Understanding the patterns of seafloor characteristics of spawning aggregation sites is of great interest to managers who need a means to efficiently design marine protected areas to help rebuild regional fish stocks. The specific goals of the study were: (1) to map the seafloor at historically known grouper and snapper spawning aggregation sites in three different countries, and (2) to characterize quantitatively the geomorphology of the sites including horizontal and vertical curvature profiles of the reefs, bottom depth at spawning sites, distance between spawning sites and shelf-edges/reef promontory tips, and the shortest distance between the spawning sites and 100 m water depth. These data were field-collected with a GPS and single-beam eco-sounder that provided latitude/longitude and depth. The point data were interpolated to surfaces in GIS to determine slope, aspect, curvature, and distance from spawning sites and three-dimensional reef structures. This study revealed that all 12 known Nassau grouper spawning aggregation sites in Belize and 5 known sites in the Cayman Islands were located at convex-shaped seaward extending reefs (reef promontories) jutting into deep water, within 1 km of reef promontory tips. However, spawning aggregations did not always occur at the tips of reef promontories, though all were found along the shelf edges within 1 km of promontory tips. Sixteen sites were multi-species spawning sites. These general characteristics were used to predict an undiscovered multi-species spawning aggregation in Belize. A successful prediction in Belize, together with the compiled data from multiple sites indicate: 1) reef promontories are vital locations for transient reef fish spawning aggregations, and 2) this study provides a potential tool for prediction of unknown spawning sites in the Caribbean.

Along with advancement of human industrialization, pollution in the ocean is getting worse. Moreover, the overfishing through the years has caused catastrophic damage to the ocean eco-system. In order to avoid exhaustion of fishery resource, many concepts of planned administrative fishery has become popular, and thereamong, ocean ranch draws the most attention. Artificial reef plays a key role in an ocean ranch, which starts with incubating brood fish in the laboratory. Often, the brood fish will grow in the cage near coast till proper size, then be released to the artificial reef. If fish groups do not disperse and multiply, the artificial reef can be considered successful. The success of the artificial reef relies on the stable foundation. Consequently, the composition of seabed sediment under the planned site should be investigated thoroughly before hand. This research introduced a remote investigation method, which an active sonar, depth sounder, was used to emit and collect acoustic signals. By using the signals reflected from the seabed, the sediment composition can be analyzed. However, all acoustic signals are subjected to noise through propagation, and distorted somehow. Therefore, certain signal pre-processing should be applied to the received signal, and representative characteristics can be extracted from it. In this research, the recognition platform was built on artificial neural network (ANN) in this research. Among many network algorithm modes, this research chose the widely used backpropagation learning algorithm to be the main structure in ANN. The goal of this research was to discriminate among three seabed sediments: fine sand, medium sand, and rock. During the signal processing, characteristics were extracted by using peak value selection method. Selected major frequency peaks were fed into the network to train and learn. According to partial error relation between recognition and practical result, weights of the network were adjusted for improving successful ratio. Finally, a reliable acoustic wave signal recognition system was constructed.

An ecosystem always involves some implicit relations between habitat environment and inhabitants, whose reciprocal links can not be identified easily. Three sets of ecological monitoring data were analyzed in this study, including coral reef, algae (Thalassia hemprichii Aschers) in Kenting National Park, and Formosan landlocked salmon (Oncorhynchus masou formosanus) in the basin of Chichiawan Stream. Two data-oriented analysis techniques, which are Habitat Evaluation Procedure (HEP) and Group Method of Data Handling (GMDH), were applied to retrieve the embedded patterns from these data sets. Eventually, for each data set, a forecasting model based on the technique of combined forecasting were developed, which is to integrate the results from HEP and GMDH, for improving the overall modeling precision. The results of this study show that the data-oriented analyses, such as HEP and GMDH, are useful for finding valid information from the ecological data. Furthermore, the combined forecasting technique can really improve the performance of model prediction even for the ecological research. In order to acquire the most important habitat environmental factors affecting the inhabitants, this study also performed sensitivity analysis of the models. The contributions of this study are to identify effective knowledge for future ecological research and to provide reasonable suggestions for formulating conservation strategy.

Thesis (Ph.D.)--University of Wyoming, 2008. / Title from PDF title page (viewed on Mar. 11, 2010). Includes bibliographical references.

Thesis (Ph. D.)--University of Texas at Austin, 2001. / Vita. Includes bibliographical references (leaves 173-201). Available also in a digital version from Dissertation Abstracts.

The Along-Track Reef-Imaging System (ATRIS) is a vessel-mounted, digital camera, depth sounder and Global Positioning System (GPS) package that facilitates the rapid capture of underwater images in shallow-water benthic environments. This technology has the potential to collect ecologically significant data, particularly in benthic habitats less than 10 m in depth, with better location referencing and in less time than is required for surveys carried out by Scuba divers. In October 2004, ATRIS was tested coincidently with SCUBA-assisted video along transects on five patch reefs in Biscayne National Park. Images from both data sets were subsampled, viewed, and benthic cover under random points were identified and counted. Digital-still images of reef benthos collected by ATRIS were of higher quality than SCUBA-acquired video imagery, allowing more reliable classification of benthos. “Substrate”, which included areas of hard-ground, sand or rubble, was the most frequently identified benthic category (43%), followed by octocoral (21%), unidentifiable (19%), and macroalgae (12%). Total stony coral cover averaged less than 5%. ATRIS-acquired benthic-cover data were compared with rugosity data derived from the Experimental Advanced Airborne Research Lidar (EAARL), revealing no strong correlations, probably because much of the hard substrate patch reef topography was created by corals that have died in the past few decades. ATRIS, diver-acquired data, and EAARL provide different scales of information, all of which can be valuable tools for assessing and managing coral reefs.

Acropora cervicornis was once one of the dominant reef building corals of the Caribbean, Florida Keys, and Dry Tortugas (DRTO), but since the 1970’s populations have been decimated throughout their geographic range. Recently, a repopulation was documented through detailed benthic surveys conducted by the U.S. Geological Survey at three locations (Pulaski Shoal, East Key, and Loggerhead Key) within DRTO. Benthic surveys using the U.S Geological Survey’s Along-Track Reef Imaging System (ATRIS) revealed hundreds of previously undocumented colonies. These discoveries have provided a unique data-set, allowing a comparison between the historical (1883, 1976) and contemporary distributions (2009, 2011) of A. cervicornis. Kernel density estimates were used to analyze shifts in high density areas and non-parametric multivariate analysis of variance tests were used to analyze differences between years in location and extent of the distribution. The results from the KDEs indicated high density areas have shifted among year’s at all three study areas. The comparison of the location and extent of the historical and modern A. cervicornis distributions revealed similarities and differences among years that varied among the study areas. This information is important to the management of this species because it provides vital information on the extent and location of the current distribution relative to historical levels. This study also provides documentation of the population dynamics and ecosystem changes over large time scales within the DRTO region. The above mentioned dataset was also used in a second study to quantify 1) variations in density among factors such as location (study area), suitable habitat type, and water depth, 2) overall spatial population patterns, and 3) spatial patterns in A. cervicornis density. Results indicated population structure was significantly clustered (P = 0.001) at Pulaski Shoal and Loggerhead Key with areas containing hotspots or significantly higher density (P < 0.05). Although significant hotspots existed, density did not significantly differ among suitable habitat types. Compared to all other factors, water depth had the largest effect on the variation in mean density of A. cervicornis. These findings are vital to understanding the recovery of this species in terms of current habitat and depth associations.

An artificial oyster reef constructed in Boca Ciega Bay, off of the War Veteran's Memorial Park, St. Petersburg, Florida, in 2005, was used to compare a mined shell material to the typical oyster shell substrate used in artificial reef projects as an alternative substrate and cultch material. Half of the reef's veneer was the fresh oyster shell and the other half was mined material. Experimental trays were deployed on top of the sediment along the leeward reef base and sampled quarterly to test the hypothesis that fresh shell is the preferential cultch material of the Eastern Oyster, Crassostrea virginica, promoting more oyster and epifaunal community development than the mined material. Monthly field observations along the reef face monitored the oyster community development on both substrates. The unanticipated influence of the reef's presence on the local current flows resulted in significant sediment loading on the reef. The sediment inundated and smothered the experimental trays over the course of the study, thereby converting the trays from hard substrate to soft bottom habitats. Any influence the different substrates might have had on community development was overwhelmed by sediment burial. Monthly field observations revealed positive oyster community development on both substrates. Live oyster abundance was significantly dissimilar between June and December 2006 on the fresh shell compared to the mined material (R = 0.241, p = 0.001). Epifaunal abundance showed even greater dissimilarity over the same time period (R = 0.474, p< [or] = 0.001). Greater abundances of large oysters were found on the fresh shell substrate due to an instability and deterioration of the larger pieces of mined material. A low replicate sample size of n = 3 leaves results from between month and between quarter sampling analyses open to interpretation. Though no definitive conclusions were drawn, the data from the community analyses provides useful information on the species inhabiting and utilizing oyster reefs in the Tampa Bay area.

The tropical Indo-Pacific is the location of highest global foraminiferal biodiversity. However, the shallow-water hydrothermal system in Tutum Bay at Ambitle Island, Papua New Guinea, possesses some of the world's highest naturally-occurring [As]. Foraminifers were collected in this intriguing system in 2003 and 2005 as part of a larger project to examine the possible effects of As and other hydrothermal factors on benthic communities. Despite the high ambient [As], a diverse foraminiferal fauna was observed. Foraminferal communities were examined from surface sediment and from material adhered to rubble at locations from 1-300m from venting and from reference sites, at depths from 1-28m. From this material, 159 species were identified representing 107 genera, 55 families, 30 superfamilies, and 10 orders. Species abundances exhibit a logarithmic series distribution, with two species comprising 40%, twelve species comprising two-thirds, and 20 species comprising 80% of all identified specimens. All other species individually contributed <1% to the total community. Foraminiferal abundance and diversity were analyzed across the hydrothermal field; both increase with decreasing hydrothermal influence: decreasing sediment and pore water [As] and temperature, and increasing pH and salinity. A thorough taxonomic reference of the region was compiled, consulting appropriate original descriptions, and is herein presented, and initial steps in creating an online database of all Recent foraminifers is described. Scanning electron micrographs of the most common taxa are provided. Laboratory experiments assessed the effects of [As³?] and [As5?] on growth of Amphistegina gibbosa. Exposure to As³? and As5? at concentrations of 0- 1000µg/kg showed that As³? is approximately 2.2 times more toxic than As5?, that [As³?] of 600- 1000µg/kg is sufficient to kill or severly impair specimens on approximately two-week timescales, and that [As5?] of 1000µg/kg or [As³?] of 200µg/kg are sufficient to retard the growth of A. gibbosa on approximately four-week timescales. Over timescales of several months, cultures with extremely low [As] (2µg/kg As5? and 0µg/kg As), showed growth rates not significantly greater than high-[As] treatments, possibly due to antimicrobial/parasiticidal properties of low [As]. Foraminifers displayed an exponentially-decaying functional relationship to [As], halving their rate of growth with every 300µg/kg increase in [As³?] or 600µg/kg increase in [As5?]. Measurements of foraminiferal whole-specimen [As] via SEM-EDX, AFS, and ICP-MS revealed high [As] of ~20mg/kg for specimens near hydrothermal venting declining to background values of ~2mg/kg for distal and non-hydrothermal reference species. Laboratory-exposed specimens contain [As] of ~6mg/kg indicating an As adsorption rate of ~0.25mg/kg/wk. The major portion of foraminiferal As likely occurs in a reduced-toxicity organoarsenical form, such as arsenobetaine.