Thesis (M.S. in Engineering Acoustics)--Naval Postgraduate School, December 2008. / Thesis Advisor(s): Rice, Joseph A. "December 2008." Description based on title screen as viewed on January 29, 2009. Includes bibliographical references (p. 89-91). Also available in print.

Thesis (Ph. D.)--University of Rhode Island, 2004. / Typescript. Includes bibliographical references (leaves 118-121).

Thesis (Ph. D.)--University of Rhode Island, 2003. / Typescript. Includes bibliographical references (leaves 148-152).

Thesis (M.S. in Electrical Engineering and M.S. in Applied Physics)--Naval Postgraduate School, June 2005. / Thesis Advisor(s): Joseph Rice, Roberto Cristi. Includes bibliographical references (p. 117-119). Also available online.

Bonefish (Albula spp.) support an economically important catch-and-release recreational fishery, as well as artisanal harvesting, in The Bahamas. Little is known about the large-scale movement patterns of bonefish, yet such information is essential for proper species conservation and management. I used acoustic telemetry to determine large-scale movement patterns of bonefish around Andros, Bahamas, in conjunction with presumed spawning migrations. I conclude that bonefish travel long distances from shallow flats to pre-spawning aggregation sites in proximity to off-shore reef locations. Off-shore movement to deeper reef locations occurs around both new and full moons. This study has also confirmed anecdotal reports that the North Bight is an important spawning migration corridor for bonefish. This information is critical for the protection of bonefish and identifies important habitats (e.g. migration corridors and pre-spawning aggregations) on Andros that warrant protection from coastal degradation or fishing pressures.

Movement and behavior studies are traditional yet effective ways to understand the biology and ecology of a species. For an endangered species like the whale shark (Rhincodon typus), a comprehensive knowledge of its movement and behavior is particularly critical for successful management and conservation. For this dissertation, acoustic telemetry and biologging tagging studies were carried out at a seasonal whale shark aggregation site near Al Lith in the Saudi Arabian Red Sea. Acoustic telemetry data revealed consistent path usage in a narrow longshore area with patterns in seasonality and diel horizontal movements within a smaller scale. Some individuals specifically concentrated on this path and made non-stop back and forth movements along it. In another dimension, depth use of whale sharks derived from biologgers showed distinct diel patterns. The sharks heavily utilized shallow waters with mixed depth usage consisting of surface swimming and varied types of dives, which explained the data of previous visual surveys. Vertical velocities indicated potential energy expenditure strategies that were further investigated based on acceleration data. Energy expenditure data suggested strategies that fine-tuned foraging efforts to optimize the balance between feeding and foraging. However, while these strategies fit well in the natural habitat, local human impacts could be of great disturbance if not well managed.

Acoustic telemetry is an important tool for studying the movement patterns, behaviour, and site fidelity of marine organisms; however, its application is challenged in coral reef environments where complex topography and intense environmental noise interferes with acoustic signals, and there has been less study. Therefore, it is particularly critical in coral reef telemetry studies to first conduct a long-term range test, a tool that provides informa- tion on the variability and periodicity of the transmitter detection range and the detection probability. A one-month range test of a coded telemetric system was conducted prior to a large-scale tagging project investigating the movement of approximately 400 fishes from 30 species on offshore coral reefs in the central Red Sea. During this range test we determined the effect of the following factors on transmitter detection efficiency: distance from receiver, time of day, depth, wind, current, moon-phase and temperature. The experiment showed that biological noise is likely to be responsible for a diel pattern of -on average- twice as many detections during the day as during the night. Biological noise appears to be the most important noise source in coral reefs overwhelming the effect of wind-driven noise, which is important in other studies. Detection probability is also heavily influenced by the location of the acoustic sensor within the reef structure. Understanding the effect of environmental factors on transmitter detection probability allowed us to design a more effective receiver array for the large-scale tagging study.

International Telemetering Conference Proceedings / October 22-25, 2001 / Riviera Hotel and Convention Center, Las Vegas, Nevada / Undersea warfare (USW) was perceived as a large-area, deep-water operation in the past therefore Fleet USW training ranges were designed to meet these requirements. Currently the bigger threat is the likelihood of regional conflict throughout the world by aggressive nations in littoral waters. The U.S. Navy must stand ready to respond to these regional conflicts when national interests are threatened. Consequently, naval forces must train to operate in the littoral environments where such regional conflicts are likely to occur. The West Cost Shallow Water Undersea Warfare Training Range (WC SWUWTR) is being developed to provide this training.

Atlantic salmon Salmo salar has a complex life cycle, including long migrations and habitat shifts for both juveniles and adults. As such, salmon populations are vulnerable to habitat degradation and fragmentation along their migratory routes. This makes management and conservation a complex task requiring knowledge of salmon ecology at different temporal and spatial scales. In this thesis I highlight the use of a holistic life-history based approach in the conservation and management of wild and hatchery-reared salmon in regulated rivers and lakes. Small populations of wild-reproducing landlocked salmon and trout Salmo trutta exist in the regulated River Klarälven, Sweden. Since the 1930s, transportation of adult spawners upstream of eight dams has given the fish access to spawning grounds. The number of returning wild spawners became critically low in the 1960s, but stocking of hatchery smolts resulted in an increase in spawners that continues today. My data show that wild smolt may suffer high mortality due to multiple dam passages. To ensure viable populations of wild populations, future management should include both up- and downstream solutions that ensure connectivity in the system. The recreational and commercial salmonid fishery are maintained by compensatory stockings, yielding annual catches of about 75 tons, and a river return rate of hatchery fish of about 1%. As a large portion of the stocked smolts does not survive downstream migration to the lake, there has been discussion about the quality of the stocked smolt and about stocking strategies. Based on my studies, producing hatchery smolts more closely resembling wild-born conspecifics should result in reduced loss rates. I suggest changes in the hatchery and stocking procedures to increase the survival of stocked smolts. The results of my research should be applicable to other regulated systems, particularly those with mixed stocks of wild and hatchery salmonid populations. / Atlantic salmon Salmo salar has a complex life cycle, including long migrations and habitat shifts for both juveniles and adults. As such, salmon populations are vulnerable to habitat degradation and fragmentation along their migratory routes, which make management and conservation a complex task requiring knowledge of salmon ecology at different temporal and spatial scales. In this thesis, I highlight the use of a holistic approach in the conservation and management of wild and hatchery-reared salmon in regulated rivers and lakes. Small populations of wild-reproducing landlocked salmon and trout Salmo trutta exist in the regulated River Klarälven, Sweden. Since 1930, transportation of adult spawners upstream of eight dams has been done to give the fish access to the spawning grounds. My data indicate that a large proportion of the wild smolts are lost due to multiple dam passages, and future management should include both up- and downstream solutions, ensuring connectivity in the system. The fishery in Klarälven and Lake Vänern is maintained by compensatory stockings, yielding catches of about 75 metric tons and a river return rate of stocked fish of about 1%. I suggest changes in the hatchery and stocking procedures to increase the survival of stocked smolts.

Tracking an individual specimen can be a difficult task especially when one also has to keep track of the environmental factors that affect the tracked specimen’s behavior. The task of tracking these animals becomes impossible when they become submerged in water and their number increases to more than just one. The aquatic species that are being tracked by this project in Lake Pontchartrain and the Gulf of Mexico are: tarpon, scalloped hammerhead, whale shark, tiger shark, yellowfin tuna, spotted seatrout, redfish, and bull shark. We are tracking these fish using acoustic and satellite transmitters. The insertion of transmitters in the fish was handled by the Louisiana Department of Wildlife and Fisheries biologists. The acoustic transmitters were implanted on smaller fish that only swam in Lake Pontchartrain. Due to this, receivers were only implanted at locations across the lake on various types of attachments such as buoys, PVC pipes, and pilings. These receivers were positioned at more than ninety locations in order to maximize the acquisition of detections. These species were tracked in Lake Pontchartrain and the Gulf of Mexico. After this preliminary setup, a constant batch of data was generated on a regular basis and this data was process by the application developed in this project. A Ruby on Rails application was then setup in order to store this data and manipulate it to display an animated track. The application utilizes: Ruby, Rails, HTML, CSS, SQL, JavaScript and multiple third part libraries. Many optimizations were performed in order to ensure reliability and performance when loading a high volume of fish or if a high volume of users were to use the application.