The aim of paleoenvironmental studies is to reconstruct characteristics of the past environment from fossil assemblages preserved in sedimentary strata. Thus, studies of modern surface assemblages, quantitatively correlated to the environmental parameters, are required before reliable interpretations can be made. For this dissertation, two different techniques were applied in two case studies: a reconstruction making use of a benthic foraminiferal transfer function from the intertidal marshes in the eastern Mississippi Sound, Alabama/Mississippi, and a qualitative reconstruction of ocean current activity on the Western Australian shelf. Modern salt-marsh foraminifera were collected from Grand Bay, Pascagoula, Fowl River, and Dauphin Island across several elevation transects and different salinity regimes. Cluster analysis yielded nine dead biofacies and five live assemblages from Open Estuarine to Upland Transition. Canonical correspondence analysis indicated a strong relationship between distributions of dead biofacies and elevation. Both dissolution of calcareous species in the organic marsh sediment and the long-term accumulative nature of the dead assemblage favored the use of non-estuarine dead assemblages. A Weighted Average-Partial Least Squared transfer function was applied to the surface data and yielded a Root Mean Squared Error of Prediction (RMSEP) of 0.14 m, which represents 33% Mean Range of Tide at Grand Bay and 39% at Dauphin Island. The transfer function was applied to two sedimentary cores from Grand Bay and two from Dauphin Island, which revealed disparate developments between the regions during the last 1,900 years. While both Dauphin Island cores indicated relative sea-level trends aligned with other Gulf of Mexico studies, Grand Bay was likely impacted by a river avulsion event disconnecting Grand Bay from fluvial sediment influx, and by the erosion of a protective headland, Grand Batture Island. Sediments spanning the last ~100 years contained increased abundances of low marsh foraminifera likely associated with coastline erosion, which was most prominently displayed by a lithology shift towards grey silt in the Dauphin Island cores. Surface carbonate sediments from Western Australia’s Northwestern Shelf and Carnarvon Ramp were collected from 127–264 m water depth. Foraminiferal assemblages changed between 127 m and 145–264 m due to rapidly decreasing water temperature in the thermocline, and loss of sufficient light for support of “larger” benthic foraminifera. Latitudinal differences were likely caused by three factors: (1) limited influence of the warm Leeuwin Current to support tropical taxa at the sampled depths, (2) reduced habitat diversity on the narrow Carnarvon Ramp compared to surrounding shelves, and (3) differing water-mass characteristics. The gathered information was used to interpret the assemblages from a Carnarvon Ramp core (total depth 300 m), providing insight into the activity of the warm, surficial Leeuwin Current for the last 3.54 My (Pliocene). Abundant infaunal taxa were inferred to indicate low oxygenation, increased supply of organic matter, and high sea-surface productivity during the absence of the Leeuwin Current above the coring site. Dominance of epifaunal species signified higher oxygenation at the sediment-water interface when upwelling of nutrient-rich waters was effectively suppressed by the Leeuwin Current. Around 1.14 Ma, waning of hypoxic conditions was initiated until a more substantial change was marked at 0.91 Ma. Suspension-feeding sponges became common sediment constituents during a Leeuwin Current flow optimum at ~0.6 Ma. The epifaunal taxa dominance persisted on the modern shelf, yet short episodes of infaunal peaks were likely caused by lateral shifts and fluctuating influence of the Leeuwin Current during more intense glacial cycles.

Density, species diversity, species richness, and evenness of bivalve mollusks were measured in the deep (0.2km to 3.7km) northern Gulf of Mexico to describe the community structure of benthic bivalve mollusks. Density decreased gradually from shallow continental slope depths, with remarkably high values in the Mississippi canyon, to the deepest sites. Diversity of bivalve mollusks increased from shallow continental slope depths, with low values in the Mississippi canyon, to a maximum at intermediate depths (1-2km), followed by a decrease down to the deepest locations (3.7km). Nine distinct groups were formed on the basis of the similarity in species composition. The pattern varied more abruptly on the slope compared to the deeper depths, possibly due to steeper gradients in physical variables. ANOVA indicated that the density of bivalve mollusks was not significantly different at different depths, was not significantly different on different transects, was not significantly different between basin and non-basin, but was significantly different in canyon and non-canyon locations. Similar distinctions were observed in diversity, except that basins were lower than non-basins. The patterns observed reflect the intense elevated input of terrigenous sediments accompanied by high surface-water plankton production from the Mississippi River to the north central gulf.

The hypoxic area in the Gulf of Mexico is the second largest in the world, which has received extensive scientific study and management interest. Previous modeling studies have concluded that the increased hypoxic area in the Gulf of Mexico was caused by the increased anthropogenic nitrogen loading of the Mississippi River; however, the nitrogen-area relationship is complicated by many other factors, such as wind, river discharge, and the ratio of Mississippi to Atchafalaya River flow. These factors are related to large-scale climate variability, and thus will not be affected by regional nitrogen reduction efforts. In the research presented here, both statistical (regression) and numerical models are used to study the influence of anthropogenic and climate factors on the hypoxic area variability in the Gulf of Mexico. The numerical model is a three-dimensional, coupled hydrological-biogeochemical model (ROMS-Fennel). Results include: (1) the west wind duration during the summer explain 55% of the hypoxic area variability since 1993. Combined wind duration and nitrogen loading explain over 70% of the variability, and combined wind duration and river discharge explain over 85% of the variability. (2) The numerical model captures the temporal variability, but overestimates the bottom oxygen concentrations. The model shows that the simulated hypoxic area is in agreement with the observations from the year 1991, as long as hypoxia is defined as oxygen concentrations below 3 mg/L rather than below 2 mg/L. (3) The first three modes from an Empirical Orthogonal Function (EOF) analysis of the numerical model output results explain 62%, 8.1% and 4.9% of the variability of the hypoxic area. The Principle Component time series is cross-correlated with wind, dissolved inorganic nitrogen concentration and river discharge. (4) Scenario experiments with the same nitrogen loading, but different duration of upwelling favorable wind, indicate that the upwelling favorable wind is important for hypoxic area development. However, a long duration of upwelling wind decreases the area. (5) Scenario experiments with the same nitrogen loading, but different discharges, indicate that increasing river discharge by 50% increases the area by 42%. Additionally, scenario experiments with the same river discharge, but different nitrogen concentrations, indicate that reducing the nitrogen concentration by 50% decreases the area by 75%. (6) Scenario experiments with the same nitrogen loading, but different flow diver- sions, indicate that if the Atchafalaya River discharges increased to 66.7%, the total hypoxic area increases the hypoxic area by 30%, and most of the hypoxic area moved from east to west Louisiana shelf. Additionally, if the Atchafalaya River discharge decreased to zero, the total hypoxic area increases by 13%. (7) Scenario experiments with the same nitrogen loading, but different nitrogen forms, indicate that if all the nitrogen was in the inorganic forms, the hypoxic area increases by 15%. These results have multiple implications for understanding the mechanisms that control the oxygen dynamics, reevaluating management strategies, and improving the observational methods.

The Gulf of Mexico is home to two of the world?s ten busiest ports by cargo volume, the Port of New Orleans and the Port of Houston; and in 2008, these ports hosted a combined 14,000 ships, a number which is likely only to increase. Past research shows that this increase in shipping worldwide has historically lead to an increase in ambient noise level of 3-5dB per decade. Sperm whales in the Gulf of Mexico are considered a genetically distinct, resident population. They have a preference for the Louisiana-Mississippi Shelf region which directly overlaps with the entrance to the Mississippi and the Port of New Orleans. Disruptions from vessel noise could influence feeding and breeding patterns essential to the health of the stock. Data used in this analysis were collected continuously over 36 days in the summer of 2001 from bottom moored Navy Environmental Acoustic Recording System (EARS) buoys. Results showed a significant difference (P<0.05) in noise level between hours with ships passing and hours without. Metrics for 56 ship passages were analyzed to compare duration of ship passage with duration of maximum received level (MRL) during ship passage. Results of that analysis showed an average ship passage of 29 minutes with average MRL lasting 23% of the ship passage and an average increase of 40dB. Lastly, click counts were made with the Pamguard. Click counts for ship passages were completed for 35 min and 17.5 min before and after the estimated closest point of approach (CPA) for each ship. Results showed a 36% decrease in the number of detectable clicks as a ship approaches when comparing clicks detected at intervals of both 35 minutes before and 17 minutes before the CPA; additionally, 22% fewer clicks were counted 30 min after the ship than 30 min before (results significant at the P=0.01 level). These results indicate a potential change in sperm whale behavior when exposed to large class size vessel traffic (e.g. tankers and container ships) from major shipping lanes. Recommendations for addressing this issue are discussed.

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.