Upwelling, atmospheric nitrogen (N2) fixation by cyanobacteria, and freshwater inputs from the Mississippi River system have been shown to stimulate new production by alleviating nitrogen (N) limitation in the northern Gulf of Mexico (GoM). Stable carbon (delta13C) and nitrogen (delta15N) isotopes were used to investigate whether these sources are utilized differentially by coastal and marine pelagic food webs. Particulate organic matter (POM), Trichodesmium, and zooplankton were collected from the Mississippi River plume and Loop Current (LC) which were detected using remote sensing data. Stable isotope values were used to separate coastal and marine water masses and environmental data (salinity, nutrient and pigment concentrations) allowed me to relate variability to the degree of freshwater influence. Published food web data from these two environments were then assessed to establish whether isotopic baseline shifts observed in our data occur at an ecosystem level. Isotope values of the POM and zooplankton were found to be significantly different between coastal and marine water masses. This was not the case for Trichodesmium whose isotope values were not significantly different between the two water masses. We found that marine water masses (sal > 35) exhibited silicate concentrations, cyanobacterial pigments and DIN: P that suggest an increased abundance of diazotrophs. In contrast, coastal water masses (sal < 35) exhibited increased diatom pigments and molar C:N indicating terrestrial sources fuel phytoplankton production. When published food web data were compared, we found producer and consumer delta15N values were enriched in the coastal compared to the marine environments. This work suggests that differences in delta15N values within my data set and published data reflect a shift in the use of biologically available N where higher trophic levels are sustained by diazotrophic activity in marine environments versus those supported by terrestrial sources in coastal ones. Food webs that have been constructed without considering Trichodesmium as a significant source of organic matter in the GoM should be reconsidered. By re-evaluating published data, this research gives insight into the early life ecology of larval fishes and works to help answer questions about the structure and function of pelagic food webs.

Little is known about the population structure and genetic variability of blackfin tuna despite catch increases over the past 25 years. In this thesis, levels of genetic variation contained in 323bp of the mitochondrial DNA (mtDNA) control region-I (CR-I) and in six microsatellite loci were characterized for two regions: the Gulf of Mexico (GoM) and the Northwest Atlantic. Large amounts of mtDNA diversity (h>0.99; =0.047) were observed in both regions. Mismatch distribution analysis of the CR-I sequence data, using a mutation rate of 1.6% Ma-1for scombroid fishes, indicate blackfin tuna underwent population expansion about 1.4 Ma, a timeline concordant with the expansion of other tunas and billfishes. Estimates of female effective population size were very large at 7.8 million and 12.8 million individuals for the NW Atlantic and the GoM, respectively. Both mtDNA and six microsatellite loci were used to determine blackfin tuna population structure. Microsatellite and mtDNA AMOVAs revealed significant differentiation (msat st=0.01, p=0.006 and mtDNA st=0.01, p=0.049) between the GoM and the NW Atlantic samples. Migration estimates using mtDNA data indicate that twice as many females enter the NW Atlantic from the GoM (346 individuals/generation) than the opposite direction (150 individuals/generation). Migration estimates using microsatellite data were substantially smaller, with the Gulf receiving 7 individuals/generation and the NW Atlantic 4 individuals/generation. Finally, low levels of genetic differentiation using microsatellite data have been reported in other highly abundant marine fishes, which have been attributed to homoplasy in allele size. To test this hypothesis, the allele frequency distributions of blackfin and yellowfin tuna at six microsatellite loci were compared. The distances between species were surprisingly small (Da=4.0%, (delta mu)squared=1.08), with a large degree of similarity in frequency distributions at four loci. The comparison of bigeye tuna at two microsatellite loci revealed additional inter-specific similarities. A mutation rate for these loci was estimated by modifying an equation used to estimate time since divergence. Microsatellites in tunas appear to evolve at a rate (4.3x10-7 Ma-1) that is two orders of magnitude slower than other fishes (1x10-5 Ma-1). Accordingly, microsatellite allele size similarities are plesiomorphic and not due to homoplasy.

This dissertation provides a thorough analysis of the costs associated with, and efficacy of, sequential license buyback auctions. I use data from the Texas Shrimp License Buyback Program - a sequential license buyback auction - to estimate the effects of a repeated game set-up on bidding behavior. I develop a dynamic econometric model to estimate parameters of the fisherman's optimal bidding function in this auction. The model incorporates the learning that occurs when an agent is able to submit bids for the same asset in multiple rounds and is capable of distinguishing between the fisherman's underlying valuation of the license and the speculative premium induced by the sequential auction. I show that bidders in the sequential auction do in fact inflate bids above their true license valuation in response to the sequential auction format. The results from our econometric model are used to simulate a hypothetical buyback program for capacity reduction in the offshore shrimp fishery in the Gulf of Mexico using two competing auction formats: the sequential auction and the one-time auction. I use this simulation analysis to compare the cost and effectiveness of sequential license buyback program relative to one-time license buyback programs. I find that one-time auctions, although they impose a greater up-front cost on the management agency - are capable of retiring more fishing effort per dollar spent then sequential license buyback programs. In particular, I find one-time license buyback auctions to be more cost effective than sequential ones because they remove the possibility for fishermen to learn about the agency's willingness to pay function and use this information to extract sale prices in excess of the true license value.

Microbial community interactions within many ecosystems are still relatively unknown. Investigating links between environmental dynamics and shifting pelagic bacterial community structures on the Texas-Louisiana shelf, Eubacterial community profiles of Operational Taxonomic Units (OTUs) were generated using Automated Ribosomal Intergenic Spacer Analysis (ARISA) of the 16S rDNA and 23S rDNA intergenic spacer region. This ITS region is highly variable in both length and sequence. Community diversity was assessed by the comparison of ARISA-generated community fingerprints of samples collected from four distinct regions along the Texas-Louisiana shelf in a cross-shelf pattern on 10m, 20m, and 40m isobaths. Incubations of samples with a thymidine analog, 5-Bromodeoxyuridine (BrdU), allowed for the isolation and analysis of the actively growing subset within the total bacterial population. Community composition was determined through the construction of clone libraries for sequencing and putative phyla affiliation of community 16 rRNA genes. Hydrographic data were also collected for analysis of shifts in microbial community diversity correlated with a variety of influential environmental factors. ARISA profiles of Eubacterial species richness suggest strong distinction between the two communities found within Zones A and C along the Texas-Louisiana Shelf. Further analysis of salinity gradients originating from the two main fluvial sources, the Mississippi and the Atchafalaya Rivers, identified possible sources of variation between the individual communities. Whereas composition of these communities remains discrete between regions, the active subset of the population becomes more similar across the shelf through the summer. Possibly due to undersampling of hypoxic sites, no relationship could be determined between hypoxia formation and the Eubacterial community dynamics. Several OTUs within the communities were identifiable as α - and β - Proteobacteria, Actinobacteria, Synechococcus, Prochlorococcus, and Cytophaga/Flavobacterium/Bacteroides. Through validation studies of 5-Bromodeoxyuridine field sampling, this study indicates the power of BrdU incorporation and ARISA analysis to study a dynamic environmental system and explore the factors that determine the structure of the pelagic community on the Texas-Louisiana Shelf.

A combination of in situ sampling and numerical modeling was used to investigate the effects of mesoscale (<50 km) circulation patterns and stratification on the evolution of hypoxia on the Louisiana Shelf. Temperature, salinity, and dissolved oxygen concentrations records reveal the presence of an alongshelf meander, which is manifested vertically and horizontally as a wave-like distribution of the properties in the water column. The observations suggest the meander is a ubiquitous characteristic of the shelf with alongshore spatial scale approximately 50 km and less, which is consistent with the locations of sandy shoals along the coast and the local deformation radius. Twelve numerical experiments using an idealized three-dimensional shelf circulation model were performed to evaluate the relative importance of the variable bottom topography and freshwater forcing on the development, evolution, and scales of the dynamic instabilities. The inclusion of the shoals into the bottom topography showed the development of the dynamic instabilities as the flow passed over the shoals and downstream. Introduction of fresh water onto the shelf resulted in greater salinity differences, and, as a consequence in the formation of the dynamically unstable salinity fronts along the plume edge. The combination of the freshwater forcing and shoaling topography produced competing and complex interactions. Six numerical experiments were analyzed in order to investigate the effect of dynamic instabilities on spatial and temporal patterns of dissolved oxygen concentrations along the shelf. Although a linear relationship between Brunt-Väisälä frequency and dissolved oxygen deficit was expected, a nonlinear loop-like relationship was discovered that reflects the response of biochemical properties to the alongshelf variability of the density field. Comparison of the numerical modeling runs to observations of density and dissolved oxygen concentrations on the Louisiana Shelf reinforces the importance of physical processes such as topographic steering and/or freshwater forcing on the alongshore distribution of physical and biochemical properties. It suggests that the time scales of respiration (~3 days) and buoyancy transfer processes (~5-7 days), associated with the physical processes that are responsible for water column stability and ventilation, are similar to the time scales associated with the benthic respiration rates.

Using a high-resolution deep-towed seismic system, we have discovered a series of contour-current bedforms at the base of the Sigsbee Escarpment in the Bryant Canyon region of the northern Gulf of Mexico. We identify a continuum of bedforms that include furrows, meandering furrows, flutes and fully eroded seafloor. These contourcurrent bedforms are linked to current velocities ranging from 20 to upwards of 60 cm/s based on nearby current meter measurements and similar flume generated bedforms (Allen, 1969). We identify erosion and non-deposition of up to 25 meters of surface sediment at the base of Sigsbee Escarpment. Using 3-D and high-resolution seismic data, sediment samples, and submersible observations from the Green Knoll area, we further define contour-current bedforms along the Sigsbee Escarpment. The study area is divided into eleven zones based on bedform morphology, distribution, and formation processes. We identify a contourcurrent bedform continuum similar to that of the Bryant Canyon region, while the data reveals additional features that result from the interaction between topography and contour-currents. Three regional seismic marker horizons are identified, and we establish an age of ~19 kyr on the deepest horizon. The seismic horizons are correlated with very subtle changes in sediment properties, which in turn define the maximum depth of erosion for each of the individual bedforms. Finally, we show for the first time that furrowed horizons can be acoustically imaged in three dimensions below seafloor. Analysis of imagery of several horizons obtained from 3-D seismic data from the Green Knoll region establishes the existence of multiple paleo-furrow events. The contour current pattern preserved by the paleofurrows is similar to the presently active seafloor furrows. And, based on the morphology and development that we establish for the active seafloor furrows, we show that paleo-furrows are likely formed by currents that are in the same range as those measured today (20-60 cm/s), that erode into sediments with similar physical properties to the fine-grained hemipelagic sediments of the present-day seafloor. We further suggest the possibility that furrows are formed during inter-glacial highstands and buried during glacial lowstands.

The Gulf of Mexico hypoxic zone is created by strong persistent water stratification and nutrient loading from the Mississippi River which fuels primary production and bacterial decomposition. The Texas-Louisiana shelf becomes seasonally oxygen depleted and hypoxia (O2 less than or equal to 1.4 ml l-1) occurs. Low oxygen environments are conducive for the microbial production of nitrous oxide (N2O), a powerful greenhouse gas found in the atmosphere in trace amounts (319 ppbv). Highly productive coastal areas contribute 61% of the total oceanic N2O production and currently global sources exceed sinks. This study is the first characterization of N2O produced in the Gulf of Mexico hypoxic zone. Because of enhanced microbial activity and oxygen deficiency, it is hypothesized that the Gulf of Mexico hypoxic zone is a source of N2O to the atmosphere. Seasonal measurements of N2O were made during three research cruises in the Northern Gulf of Mexico (Sept. 2007, April 2008, and July 2008). Water column N2O profiles were constructed from stations sampled over time, and bottom and surface samples were collected from several sites in the hypoxic zone. These measurements were used to calculate atmospheric flux of N2O. The Gulf of Mexico hypoxic zone was a source of N2O to the atmosphere, and N2O production was highest during times of seasonal hypoxia. N2O was positively correlated with temperature and salinity, and negatively correlated with oxygen concentration. Atmospheric fluxes ranged from -11.27 to 153.22 umol m-2 d-1. High accumulations of N2O in the water column (up to 2878 % saturated) were associated with remineralization of organic matter at the base of the pycnocline and oxycline. Seasonal hypoxia created a source of N2O to the atmosphere (up to 2.66 x 10-3 Tg N2O for the month of September 2007), but there was a slight sink during April 2008 when hypoxia did not occur. Large fluxes of N2O during the 3 to 5 month hypoxic period may not be counterbalanced by a 7 to 9 month sink period indicating the Gulf of Mexico hypoxic zone may be a net source of N2O to the atmosphere.

Recent hurricanes in the Gulf of Mexico (e.g., Ivan, Dennis, Katrina, Rita and Ike) were observed to develop wave conditions that were near or exceeded the predicted 100-year conditions. As a result, many offshore facilities, as well as coastal infrastructure, which were designed to withstand the 100-year condition, were damaged. New estimates of extreme conditions, which incorporate recently observed maxima, are needed to provide better guidelines for design of coastal and offshore structures. Berek et al. (2007) have used modeled data to develop new criteria, but these estimates can be very sensitive to the data and to the statistical methods used in the development. Berek's estimates also do not cover the entire Gulf of Mexico. We have developed updated estimates of the 100-year extreme wave conditions for the entire Gulf of Mexico using a more comprehensive approach. First, the applicability of standard parametric wind models was examined and appropriate adjustments to the Rankine vortex model were developed to reduce the wind field errors during hurricane conditions. The adjusted winds reduced the error by up to 25 percent compared to the original Rankine vortex model. To obtain reliable wave data, merged wind fields were generated using the NCEP/NCAR Reanalysis 1 project modeled wind data for background wind and the parametric wind model for hurricane conditions. Next, the SWAN wave model was used for the 51-year period from 1958 to 2008 along with multiple statistical methods (Gumbel, Weibull and GEV-Generalized Extreme Value distribution). The effect of the recent hurricane season (2004-2008) shows that maximum 100-year wave height values and their distribution changes. A resampling technique (bootstrap) is used to evaluate and select the optimum statistical method to estimate more appropriate extreme wave conditions.

Total mercury (Hg) levels were determined in the tissues of ten taxa of pelagic fishes, with a special emphasis on apex predators (large vertebrates). Highest Hg levels were observed in blue marlin (Makaira nigricans), carcharhinid sharks (Genus Carcharhinus) and little tunny (Euthynnus alletteratus), ranging from 1.08 to 10.52 ppm. Moderate to low concentrations (<1.0 ppm) were observed in blackfin tuna (Thunnus atlanticus), cobia (Rachycentron canadum), dolphinfish (Coryphaena hippurus), greater amberjack (Seriola dumerili), king mackerel (Scomberomorus cavalla), wahoo (Acanthocybium solandri) and yellowfin tuna (Thunnus albacares). For the majority of species examined, Hg level did not vary significantly between locations (Texas and Louisiana) and years (2002 and 2003). The relationship between Hg level and fish size/weight was also explored and six taxa (blackfin tuna, carcharhinid sharks, dolphinfish, king mackerel, wahoo, yellowfin tuna) showed significant positive relationships between Hg level and body size and/or weight. Natural dietary tracers, stable isotopes (15N, 13C) and fatty acids were used to evaluate the relationship between Hg and trophic position and the relationship between Hg and dietary history. Stable nitrogen isotope analysis showed that Hg levels in fish tissues were positively associated with trophic position. Based on the 13C and 15N values of pelagic consumers examined in this study, three natural groups were identified with cluster analysis, and the same groupings were detected based on fatty acid profiles. This not only confirmed the existence of these natural groupings, but also indicated that the distinguishing factors for the grouping was likely connected with the dietary history of these fishes. The classification tree based on the fatty acid profiles of pelagic fishes readily separated fishes from different regions, suggesting that diets of pelagic taxa within the same region are similar or these consumers share a common source of organic matter in their food web. Findings from this study complement other Hg investigations conducted in the Gulf and also furthered our understanding of the link between feeding ecology and Hg accumulation. Moreover, the combined use of stable isotope and fatty acid techniques provided new insights on the dietary history of pelagic fishes in the Gulf of Mexico.

Hydrocarbon exploration involves drilling into or near salt deposits in the Gulf of Mexico, Brazil, Egypt, and the Middle East. Drilling these systems has proven to be quite dangerous, challenging, and expensive due to the pressure and stress perturbations that exist around the salt. My study focuses on characterizing the pressure and stress distribution at the Mad Dog field, which is a large oil field below an allochthonous salt body in the deepwater Gulf of Mexico. The Mad Dog field lies beneath the Sigsbee Escarpment, which represents the surface and seaward-most indicator of a mobile salt in Green Canyon blocks 781, 782, 825, and 826, 190 miles southwest of New Orleans in 4,500-6,500 feet of water. I characterize the pressure distribution within the Lower Miocene sandstone reservoir which has produced over 100 million barrels to date. I map the reservoir horizon using 3D seismic data and that the reservoir is a complex regional anticlinal structure that is separated by numerous normal faults that cause it to be segmented into compartments. The in-situ pore pressures show that the compartments are not in pressure communication across the field and that multiple aquifer phase pressures are present. The in-situ pore pressure measurements are used to characterize the pressure distribution in the Miocene sediments below the salt body and in front of the mobile salt body. These measurements show that between the upper Miocene to middle Miocene there is an absolute pressure decrease and between the middle to lower Miocene there is a large pressure increase. This pressure distribution is seen both within the Miocene sediments below salt and in front of salt. A porosity and effective stress relationship from shallow Pleistocene sediments was developed to predict the pressure behavior observed within the Miocene and compare the predicted pressure with in-situ pore pressure measurements. The mudstone pressure prediction overestimates the in-situ sand pore pressure. The mudstones bounding regional sandstone have a constant porosity throughout the field, suggesting that the vertical effective stress is constant. These observations can be used to estimate the mudstone pore pressure in a new well location. If the vertical effective stress in an offset well is known and given knowledge of the total vertical stress in the new well location, the mudstone pore pressure can be estimated. / text