Modern man has successfully farmed penaeid shrimp since 1904 at Kumamoto, when a Japanese farmer over-wintered kuruma prawns (Penaeus japonicus) by feeding them boiled anchovy. Within fifty years, the penaeid life cycle had been closed by Dr. Motosaku Fujinaga (Hudinaga 1935), and commercial production was accomplished by the late sixties (Hudinaga 1942; Kittaka 1967). Yet, more than thirty years later, bottlenecks and barriers to profitable commercial culture still plague this industry. Diseases due to inadequate bio-security and environmental degradation; oceanic and coastal zone pollution, and antibiotic, hormone and chemical misuse have together drained resources, profits and consumer confidence from an already struggling industry. This dissertation presents a collection of experiments that aided in the development of a production protocol for the commercial culture of Litopenaeus vannamei within a zero discharge, very low salinity, inland system. These experiments suggest that the technology exists for profitable commercial culture of this species without dependence on an oceanic nexus. Chapter 1 introduces the science of aquaculture and reviews the state of the industry, including the demand for ocean products and its attendant stresses, as well as stresses caused by aquaculture. Included in this chapter is an overview of factors that contribute to choices of species, research needs and protocol for inland culture. Chapter 2 describes the methods and materials used in experiments related to inland, low-salinity penaeid culture. These include experiments on salinity and ionic acclimation of Litopenaeus vannamei postlarvae for zero-exchange inland nurseries; density and feeding for the inland culture of L. vannamei in zero-exchange, freshwater nurseries; density and feeding for the inland culture of L. vannamei in zero-exchange, freshwater ponds; salinity and density for polyculture of both Oreochromis aureus and O. niloticus with L. vannamei within zero-exchange freshwater treatment ponds, and nitrite toxicity in low salinity waters. Chapter 3 presents the results from the experiments described in Chapter 2. Chapter 4 discusses the results found in Chapter 3 and commercial protocols developed with the use and reliance on the experiments presented. in this dissertation. The protocols presented are not proofs nor based upon any single proof but upon the work carried out over seven years.

No description available.

This study examined enhancing coral recruitment to artificial substrate by manipulating fish assemblages and the use of coral attractant substrates. One hundred sixty artificial reef modules were organized into 40 four-module replicate configurations (quads) of varying complexity to induce different fish assemblages. The deployment array consisted of the 40 quads, each in a square configuration with three to four-meter sides (approximately 1 m separation between modules) measured from the outside corners. The quads were divided into four fill treatments of differing complexity: Empty, Small, Mixed, and Large. Each quad had four potential coral attractant treatments on settlement plates: CaCO3, iron, coral transplants, and control. Each module in a quad contained a different attractant. Fish counts were conducted quarterly (January, April, July, October) for three years. During the study, fishes comprised of 166 species from 40 families were counted. Twenty-six species accounted for 90% of the fish counted with bluehead wrasse (Thalassoma bifasciatum), juvenile grunts (Haemulon spp.), and slippery dicks (Halichoeres bivitattus) making up over 55% of the fishes counted. Fish abundance and species richness were significantly less on Empty treatment quads than the other three treatments while species richness was less on the Empty and Small treatments than the Mixed and Large. Because of low coral recruitment rates, a single survey was conducted at the end of the study period to record the number and species of coral recruits. A total of 186 coral recruits were counted on a sub-sample of modules. Porites astreoides was the most abundant recruit (47.8%) followed by Agaricia agaricites (13.4%). Coral recruits were categorized by size and, based on an assumed 12 mm/yr-1 coral growth rate, separated into year classes post reef deployment. Size classes were then compared with fish abundance data. Correlations were found with Year 1 coral recruits and damselfishes (Pomacentridae), reef butterflyfish (Chaetodon sedentarius), and grunts (Haemulon spp.). Additionally, correlations were found between Year 3 recruits and all fish species combined, and between Year 4 recruits and reef butterflyfish. Thirty coral recruits were counted on the settlement plates, with P. astreoides making up over 63% of the recruits. Due to the low number, rigorous statistical analysis could not be performed on the data; however, CaCO3 plates had almost twice the number of recruits than the other attractants. Recommendations from this study include design of artificial reef with holes and shadowed refuge, placement of reef near natural hard-bottom or reef, and use of limestone aggregate to enhance coral recruitment. Additionally, coral transplantation may be an effective coral recruit attractant, but care should be taken in transplant species selection and collection methodology.

The goals of this research are to understand the dynamical processes that lead to the seasonal variation of the tropical instability waves (TIWs) in the central and eastern Pacific Oceans and to their meridional asymmetry about the equator. Two types of ocean models are used, namely, the fully nonlinear and linearized versions of the 21/2-layer model used by McCreary and Yu (1992). The nonlinear model, which is forced by climatological data, is used to simulate the TIWs and to identify differences in their character at different times of the year. The linearized model is used to investigate the effect of various background states on generating asymmetric unstable waves. Solutions to the fully nonlinear model simulate the seasonal variation and asymmetry of the TIWs reasonably well. Results from our main run show that the TIWs seen in the upper-layer temperature field share most of the features of the TIWs observed in both the Pacific and Atlantic Oceans: they have periods of 15-20 days, propagate westward, are most active in the summer and fall, and tend to be concentrated north of the equator. Various budget analyses reveal that the TIWs in the upper layer are a mixed type of barotropic and frontal instabilities, that the Reynolds-stress term associated with these waves significantly weakens the shear within the two branches of the South Equatorial Current (SEC), and that their eddy heating is as large as the surface heat flux during the wave season. The instabilities in the lower layer, which have longer periods of around 30 days, are of the Kelvin-Helmholtz type. Energetics analyses indicate that the seasonal variation of the TIWs is determined by the sharpness of the sea-surface-temperature (SST) front. The same analyses show that their asymmetry is due to the asymmetry about the equator of the two branches of the SEC and of the SST front, but not to the presence of the North Equatorial Countercurrent. These properties are confirmed by the linear instability analysis.

This is a report of an experiment designed to study the bottom boundary layer of the Florida Current at a representative site in the Straits of Florida. The objectives of the experiment were (1) to determine the bottom frictional stress τ0 and (2) to determine whether the bottom boundary layer is a turbulent Ekman layer. A typical mean value of the bottom stress τ0 was found to be ~ 0.2 dynes/cm2. A mean veering of ~10° in the correct sense was observed in the logarithmic layer. No mean veering was observed above the logarithmic layer; this is believed to be a consequence of the strong modulation of the bottom current by the diurnal tide. The implication of τ0 ~ 0.2 dynes/cm2 is considered in a simplified model of the Gulf Stream current system; this analysis suggests that, dynamically, the role of bottom friction is rather small.

The instability of density fronts is investigated as a possible generation mechanism of the small-scale, wave-like patterns observed along upwelling fronts and filaments. Solutions are obtained using three different models: a linearized 1½-layer model, a nonlinear 1½-layer model, and a linearized continuously stratified model confined to the surface layer of the ocean. The front is specified in two different ways: vertically oriented isopycnals along with slab-like current in the layer model, and nearly vertical isopycnals associated with vertical shear in the continuously stratified model. The prescribed state used for both the linearized and nonlinear models consists of either a uniform or zonally sheared current in a layer of constant thickness that is geostrophically balanced by the horizontal temperature gradient within the layer. In the layer model, an analytical solution is obtained to the linearized system. When the background current is balanced by the horizontal temperature gradient alone, this solution is unconditionally unstable. Energetic analyses of numerical solutions for both uniform and zonally sheared, background currents indicate that frontal instability, which utilizes the available potential energy associated with the horizontal temperature gradient within the layer, is responsible for the growth of the unstable waves. Interestingly, the unstable waves have negative energy due to the presence of the non-positive definite terms in the definition of the wave energy. A nonlinear solution for a zonally sheared, initial current simulates the observed wave-like patterns. In the continuously stratified model, the unstable waves have positive energy and are generated by baroclinic instability. For a uniform background current, they are essentially the ageostrophic extensions of the Eady's baroclinic waves. For a zonally sheared current, they resemble the observed wave-like patterns, suggesting that the observed features are generated by ageostrophic baroclinic instability. Although there are some differences between solutions in the layer and continuously stratified models, the layer system including vertically oriented isopycnals provides a reasonable alternative of the continuously stratified system. Moreover, the difference in wave energetics between the layer and continuously stratified models is likely an artifact of the different model formulations.

I conducted a multifactorial field study examining the relative importance of and interactions between reef-based and recruitment processes on small model reefs off the southeast coast of South Florida. Four manipulative experiments were completed using 40, 1m3 model reefs. Reefs were deployed at a depth of seven meters on sandy substrate in a grid pattern 30 meters from each other and a minimum of 30 meters from any natural reef. Ten reefs were permanently assigned within the grid as count-only (CO) reefs and were not manipulated during the study. The remaining 30 reefs were evenly assigned and rotated monthly between three additional treatments. Fishes on each of the these reef treatments were removed monthly with an ichthyocide. Reefs assigned to the clean (CL) treatment were manipulated only by removing all fishes each month. The remaining 20 reefs were assigned to treatments that were designed to add prey refugia and exclude predators. Partially caged (PC) treatment reefs had cage material placed on two sides of the reef while the fully caged (CG) reefs had cage material placed on all four sides of the reef totally excluding predators. Divers using SCUBA recorded fish abundance, size distribution, species richness, and species composition for each reef monthly from April 1995 through October 1996. Experiment I examined the importance of competition for limited reef-based resources on reefs with identical structural refugia (CO and CL reefs). The removal of resident fishes from the CL reefs did not provide evidence for reef-based resource limitation. Recruit abundance (fishes less than five cm total length (TL)) was not affected by the additional resources available on the CL reefs. Recruit species richness and composition were also not affected by the removal of resident fishes. Experiment 2 examined the importance of post-settlement predation and refuge availability. When prey refugia were added to the reefs excluding predators (CG and PC reefs), the abundance of recruits was significantly increased. Recruit abundance was greatest on the CG reefs followed by the PC reefs, both of which supported significantly greater recruit abundance than the non-caged reefs (CO and CL). Predation did not appear to affect recruit species composition. The eight most abundant recruit species were common on all treatments. Temporal variations in recruit species abundance and composition was identified. This variable recruitment affected the importance of post-settlement predation and refuge limitation. The relationship between predation and refuge availability was shown to be density-dependant. During times of high recruitment, higher peaks in recruit abundance were seen on the CG and PC reefs than on the CO and CL reefs. When recruitment was low, differences in mean recruit abundance between the treatments were reduced. Recruitment variability appears to be very important in determining species composition on the reefs. Recruit species richness nearly always paralleled recruit abundance. This study illustrates the importance of the interactions among multiple processes in structuring reef fish assemblages. Recruitment variability and the coupling of postsettlement predation and refuge limitation influenced the structure of fish assemblages on small model reefs off South Florida. In addition to providing specific information on the processes important in this area, this study provides clear evidence that reef fish assemblages are not structured by any single process but by interactions between reef-based and recruitment processes.

Chapter 1 The mating systems of two annually-reproducing hammerhead sharks (scalloped hammerhead Sphyrna lewini, bonnethead Sphyrna tiburo) were investigated by genetically-profiling 82 litters (902 embryos). Unlike three biennially-reproducing shark species previously studied that are polygynandrous, genetic monogamy was common in females of both of these hammerheads (S. lewini [70.6 % of litters], S.tiburo [85.4-62.5%]), suggesting a polygynous mating system overall. These mating system characteristics suggest that hammerheads may have lower ratios of effective to census population sizes than polygynandrous sharks, adding to conservation concerns for these species. Results suggest that female mating behavior may play a more limited role in determining the population-level of multiple paternity than currently envisioned in sharks, with the interplay between male mating tactics and female reproductive periodicity (biennial or annual) perhaps being more influential. Two lines of evidence infer that multiple paternity is associated with larger females in S. tiburo: mothers of multi-sired litters are significantly larger than mothers of single paternity litters in West Florida and the frequency of multiple paternity is significantly higher in South Carolina, where females are larger. Large females may therefore produce larger, more genetically-diverse litters in some shark species and could contribute disproportionately to recruitment and population genetic diversity, increasing their importance from a conservation perspective. Chapter 2 Although most shark species have relatively small body-sizes as adults (<100 cm total length), little is known about the genetic population structure and lineage diversification of small sharks. Mitochondrial control region and nuclear internal transcribed spacer 2 sequences combined with three independent microsatellite loci all concordantly show that the diminutive hammerhead shark Sphyrna tiburo (bonnethead) consists of two highly divergent lineages from South Carolina, U.S.A. to Belize, a coastal distance of less than 6000 km. One lineage was restricted to Belize, while the other was almost completely restricted to five North American sampling sites (pairwise CR ΦST = 0.891-0.915, microsatellite Fst=0.277-0.319). This represents the highest degree of population structure recorded concordantly at both mitochondrial and nuclear loci in a shark along a continuous coastline. Regional measures of population structure and genetic divergence in this diminutive hammerhead shark mirror but exceed values obtained for larger shark species over the same sampling range and are comparable to those observed in a larger congener on a global scale. Direct evidence of interbreeding between these lineages indicates that speciation has not yet occurred. Gene-flow was generally high among North American populations, but there was evidence that female-mediated gene flow is moderately restricted between subtropical Florida Bay and higher latitude populations, suggesting that changes in latitude and climate regime may help drive population genetic differentiation in this species. This study is the second to reveal unexpectedly high lineage diversification within Atlantic hammerhead sharks, which suggests that further genetic surveys are required to fully understand and conserve hammerhead shark biodiversity in this region. Chapter 3 Dried fins from the scalloped hammerhead shark (Sphyrna lewini) are highly-valued for utilization in the Asian delicacy shark-fin soup. While global landings of this species annually measure in the millions to supply this market, Western Atlantic populations have collapsed and are now considered to be endangered. This study reveals that Western Atlantic S. lewini comprise at least three distinct management units that will be reliant on intrinsic reproduction rather than immigration for rebuilding (MU’s: U.S.A., Central American Caribbean and Brazil; overall ΦST=0.64). These MU’s are sufficiently differentiated from each other, eastern Atlantic and Indo-Pacific stocks to use mixed-stock analysis (MSA) to better understand the impact of the fin trade on sharks of this region. Stock of origin was determined for 57 Hong Kong market-derived S. lewini dried fins, revealing that contemporary trade is globally-sourced with a substantial presence of fins from imperiled Western Atlantic stocks. Results are used to formulate regional management recommendations and to develop monitoring strategies for the Asian fin trade that could dramatically improve global conservation of S. lewini and serve as a template for other sharks impacted by this trade. Chapter 4 Longline sampling (83 sets) supplemented with 6 pop-off archival tag (PAT) deployments were used to characterize vertical habitat use by Caribbean reef sharks, Carcharhinus perezi, at Glover’s reef atoll, Belize. Longline CPUE in two shallow reef habitats (lagoon < 18m depth, fore-reef < 40 m depth) underwent significant nocturnal increases for sharks larger than 110 cm total length (TL) but not for smaller sharks. Nocturnal CPUE of small sharks increased in the lagoon and decreased on the fore-reef, suggesting movements to avoid larger conspecifics. PAT deployments (7-20 days) indicate that large C. perezi generally increased the amount of time they spent in the upper 40 m of the water column during the night and have a much wider depth and temperature range than previously thought (0 to 356 m, 31-12.4oC). The wide vertical range of this top-predator reveals ecological coupling of deep and shallow reef habitats and has implications for place-based conservation. Chapter 5 Marine Protected Areas (MPAs) are increasingly advocated for the restoration and conservation of coral reef ecosystems, yet given the typically small size of most no-take MPAs it remains unknown how effective this strategy will be for roving, top-level predators such as sharks. Movement patterns of Caribbean reef sharks, Carcharhinus perezi, tagged with coded acoustic transmitters were monitored with an array of up to 22 underwater receivers from May 2004 to October 2006 at Glover’s Reef Marine Reserve, a zoned MPA in Belize. Thirty one tagged sharks ranged in size from 80-215 cm total length [TL], spanning young-of-the-year to mature specimens of both genders. Twenty five of these sharks provided data for more than one week after tagging. Individual sharks were detected within the array on from 5 to 464 days and all but four were predominantly detected on the receiver(s) nearest their original capture. Although daily movements of up to 20-50 km were documented by large sharks (>110 cm TL), most individuals were detected at Glover’s Reef on an almost daily basis throughout the year and appear to be residents of this reef system. Small sharks were documented to be residents for at least six months. The daily dispersal ranges and distribution of sharks tracked in this study suggest that typically small-sized no-take zones will be of limited value for reef shark conservation. However, the long-term residency and site-fidelity of large and small C. perezi to this reef system in its entirety indicates that nesting this no-take zone within a broader ocean zoning plan tailored to protect large roving predators achieves the scale necessary to provide meaningful protection for these ecologically important, threatened predators.

No description available.

This thesis examines the generalization of the classical quasigeostrophic baroclinic linear-stability model to include the effects of cross-stream sloping topography. Both approximate analytical and precise numerical approaches are examined and compared. The modifications due to topography of the Eady-type instabilities are obtained. Most interesting is the emergence of a new type of instability consisting of hybridized primary Eady modes which would otherwise be individually stable. The second-order dynamics of these two types of instability are examined. The eddy Reynolds stress and the eddy heat flux are of the same magnitude for the hybrid instabilities, whereas for the modified Eady instabilities the Reynolds stress/heat flux ratio is O(ε), where ε is a bottom-curvature parameter. This result may have important consequences in the energetics of the instabilities, particularly if horizontal shear were present.