Recent advances in statistical understanding have focused fisheries research attention on addressing the theoretical and statistical issues encountered in standardizing catch-rate data. Similarly, the present study evaluates the performance of boosted regression trees (BRT), the product of recent progress in machine learning technology, as a potential tool for catch-rate standardization. The BRT method provides a number of advantages over the traditional GLM and GAM approaches including, but not limited to: robust parameter estimates as a result of the integrated stochastic gradient boosting algorithm; model structure learned from data and not determined a priori, thereby avoiding assumptions required for model specification; and easy implementation of complex and/or multi-way interactions. Performance of the BRT method was evaluated comparatively, where GLM, GAM and BRT main-effects models, and a BRT two-way model, were trained using zero-truncated, lognormal catch-rate data, with identical predictors and dataset. Data used were observer-collected records of yellowfin tuna catch from the Gulf of Mexico longline fishery, 1998-2005. Model comparisons were based, primarily, on percent deviance explained by the trained models and prediction error using a test dataset, measured as root mean squared error (RMSE). Secondarily, the relative influence of model predictors and handling of spatially correlated error structures by each of the four models were examined. Fitted GLM, GAM, BRT and BRT two-way models accounted for 19.56%, 25.10%, 26.10% and 37.3% of total model deviance, respectively. RMSE values for the GLM (0.3552), GAM (0.3554), BRT (0.3546) and BRT two-way (0.3509) models indicate that the BRT-based models performed marginally better than the traditional GLM and GAM methods, with lower prediction error. Indices of predictor influence and spatial analysis of model residuals, for the main-effects models, suggest GAM and BRT models perform comparably in the partitioning of variance amongst predictors and handling of autocorrelated variance structures. Overall, results of the main-effects models indicate that the BRT method is as equally adept as GAMs in fitting non-linear responses, however unlike the GAM, the BRT avoided overfitting the data, thereby providing more robust estimates. The BRT two-way interaction model further demonstrates: the ability of the BRT method in fitting complex models, while avoiding overfitting; the ease with which interactions can be incorporated and specific terms extracted, such as the year term; and the potential role of complex interactions in accounting for non-stationary processes. Although the results presented here are not definitive, for every measure of performance examined the BRT-based models performed as equally well or better than the traditional GLM/GAM standardization methods, thereby confirming the utility of the BRT method for catch standardization purposes.

This dissertation evaluates the hypothesis that hurricane activity levels in the North Atlantic during the late Holocene have been driven by latitudinal movements of the North Atlantic circulation system. Multi-millennial sedimentary proxy records, based on the occurrence of overwash clastic layers, provide clear evidence of abruptly alternating periods of hurricane landfall frequency for Nicaragua and Belize. Three Belizean transects exhibit an Active period (hyperactivity) occurring from ~2000-6000 cal yr BP, although dating is inconsistent across the transects. An Active period covering the last 500 years is found at one location. The Nicaraguan record, derived from three transects covering >90 km of coastline, consistently displays an Active period covering the last 800 years, preceded by a Quiet period that lasts until at least ~2800 years BP, before which time environmental factors render the sites insensitive. For both coastlines the calculated strike frequency increased by a factor of 3-12 during Active periods. The Barbados depositional record is characterized by sudden shifts from organic to clay, attributed to increased aridity, with the arid periods being roughly contemporaneous with the Active periods occurring in Belize and Nicaragua, as well as periods of southern residency of the Intertropical Convergence Zone. Latitudinal movements of a unified North Atlantic circulation system were probably the driver of these changes, with southern migration increasing both landfall frequency and aridity regionally. When correlated with published records, the timing of activity regime changes identified from our sites indicates that periods of increased hurricane activity proceed across the North Atlantic in a time-transgressive manner, with the Caribbean hyperactive period preceding that of the Gulf of Mexico. The Active period for Nicaragua beginning ~850 years BP is anti-phase with a recently published model, predicated upon basin-wide synchroneity in activity patterns. This discrepancy possibly results from differences in spatial coverage, as correlations between hurricane landfall and track patterns indicate three distinct groupings resulting from atmospheric conditions. The basin-wide pattern is derived from locations contained within a single (Atlantic coast) track set, while our time-transgressive model is derived from sites within both the Caribbean and Gulf of Mexico track sets.

Tropical cyclone impacts on wetland, terrestrial, and shelf systems have been previously studied and reasonably delineated, but little is known about the response of coastal lakes to storm events. For the first time, tropical cyclone impacts on a shallow coastal lake in the Louisiana coastal plain have been studied using direct lines of evidence and numerical modeling. Using side-scan sonar, CHIRP subbottom and echo sounder bathymetric profiles, the lake bottom and shallow subsurface of Sister Lake was imaged pre- and post-Hurricanes Katrina and Rita to provide a geologic framework for assessing the effects of these storms. Box cores were collected to provide site-specific ground truth data to further evaluate the accretion or erosion of sediment over the short storm period between synoptic geophysical surveys. Coupled hydrodynamic models MIKE 21 and MIKE 3 were used to hindcast Hurricane Rita conditions, and clarified sediment transport and deposition patterns in the geologically complex Sister Lake region. X-ray radiographs of box cores showed clear increments of recent event sedimentation (1 - 10 cm in thickness), corroborated with radionuclide dating as being products of the storm period. High percentages of approximately 40% fine sand in the storm layer and its thickness relative to an average long-term sedimentation rate of 2.0 mm/yr suggest that storm-related deposition is a large factor in Sister Lake sedimentation. Modeling results from Hurricane Rita forcing conditions hindcast maximum water elevations of approximately 1 m and wave heights of 1 m in Sister Lake. Bed shear stresses across almost the entire model domain prior to Hurricane Ritas landfall were above the critical value causing erosion of fine bottom sediments, and quickly decreased in the western portion during Ritas landfall, indicating significant deposition in this western portion of the lake. The ideal event sedimentation unit that would result from the storm conditions hindcast from the numerical model was corroborated with stratigraphy identified in box cores; units with an erosional base overlain by recently deposited silty material topped by clays. This study provides a framework and fundamental understanding of lake bottom characteristics and impacts of storm-related physical processes on erosion and deposition.

active compounds (PhACs) have been detected in the aquatic environment as a result of loading from various sources. In Louisiana, USA, many municipalities treat wastewater using natural systems, such as lagoons and wetlands, rather than using conventional wastewater treatment technologies and may discharge PhACs into the environment. These treatment systems are not designed to remove PhACs from wastewater, nor is it currently a regulatory requirement. Research on the fate of PhACs in the environment is needed to understand impacts on Louisianas important coastal system. Wastewater sampling for PhACs at the Mandeville, LA wastewater treatment plant (WWTP) determined that this system significantly reduces the concentrations of PhACs prior to discharge into the environment. Most of the concentration reduction occurred in the first phase of treatment, where research suggests sorption may have been the major removal pathway. A wetland soil similar to the forested wetland at the Mandeville WWTP was tested for sorption and desorption of ciprofloxacin, ofloxacin and norfloxacin. Two HPLC methods were developed for compound analyses in this experiment. It was determined that sorption to wetland soil is a major and potentially long-term removal pathway for these pharmaceutical compounds from wastewater. The presence of antibiotics in the environment may have the ability to alter the microbial community in soils. We observed the greatest effect of antibiotics on soil microbial respiration followed this trend: sulfamethoxazole>ciprofloxacin>tetracycline. Most antibiotic effects were seen in the mineral, not the peat soil. Suppression of microbial respiration was observed, at low or high concentrations, depending on the antibiotic and soil examined. This result indicates that antibiotics can have negative impacts on microbial functions in treatment wetlands at environmentally relevant concentrations. Based on the findings of these studies, WWTPs systems similar to the Mandeville plant are effective at reducing the concentrations of many PhACs discharged into surface waters. Furthermore, sorption appears to be a major pathway for this concentration reduction. However, antibiotics showed the potential to exhibit a negative influence on microbial activity in wetland soil. These natural treatment systems appear to be ideal for effectively treating PhACs in surface waters.

A current method to restore Louisianas estuaries includes reintroducing freshwater and sediments to wetlands that are hydrologically isolated from the Mississippi River due to the construction of levees. In this dissertation, I examined effects of the second largest freshwater diversion in Louisiana, the Caernarvon Freshwater Diversion (CFD), on estuarine nekton in Breton Sound. Before focusing on Breton Sound, I examined the status of nekton communities in the northern Gulf of Mexico (GOM), and Louisiana wetlands in particular, using the mean trophic level index (MTLI). I demonstrated that commercial targeting caused the previously reported low and declining MTLI from the GOM. Evaluation of Breton Sound alone showed an increasing MTLI, which is possibly a positive effect of hydrological restoration. With a Before-After-Control-Impact study, I demonstrated that nekton species biomass distributions (SBD) changed significantly after the opening of the CFD in 1991. The biomass of selected economically or ecologically important species showed an increase relative to the control (Micropterus salmoides, Micropogonias undulatus, Brevoortia patronus, Farfantepenaeus aztecus and Litopenaeus setiferus), one was not affected (Cynoscion nebulosus). In addition, nekton species richness, abundance and the proportion of smaller individuals increased, indicating increased nursery function. I identified salinity as the main environmental variable separating SBDs among study sites due to freshwater inflow, although seasonal variation had the greatest effect on SBD. The CFD did not change dissolved oxygen or turbidity to the extent that it had an effect on nekton in the areas examined. Applying stable isotope techniques, I identified a positive effect of freshwater inflow on trophic diversity and niche breath of the consumer community, and on the relative contribution of particulate organic matter in the food web, resulting in energy density increases in nekton species. Finally, I created an ecosystem model of Breton Sound, which I used to simulate changes in SBD under different salinity scenarios. This model can be used to evaluate future restoration projects. These various analyses, including the model predictions, revealed only neutral or positive effects of the CFD as currently operated on nekton communities in Breton Sound.

With the expansion of the human population and associated industries there is a concomitant increase in both resource utilization and the production of waste and deleterious by-products. Mercury is a naturally-occurring toxic metal with a complicated and unique biogeochemical cycle, and is often a contaminant of ecotoxicological concern in unindustrialized aquatic habitats. The research described herein was designed to elucidate multiple aspects regarding the behavior of mercury in oligohaline wetland habitats, particularly with respect to edaphic and vegetative effects, through a monitoring and characterization study as well as a series of manipulative experiments. The observational study, conducted in the wetlands surrounding Lake Maurepas, Louisiana, indicated that during the time of the study, little reduction of sulfate to sulfide was occurring, and thus soil methyl mercury concentrations were quite minimal. Further, the total mercury concentrations in local vegetation were found to be typical of uncontaminated environments in the United States. The first experimental study was a hydroponic greenhouse study that evaluated the capacity of several species of local wetland plants to function as phytoremediation agents for aqueous mercury contamination. Several of the species tested demonstrated the ability to reduce aquatic inorganic mercury concentration, but generally not to a greater extent than has been shown for other plant species. The second experimental study assessed vegetative response and partitioning of elevated surface water inorganic mercury into the soils and vegetation in a wetland mesocosm. The concentration of mercury in the surficial soil became elevated, but mostly occurred in biologically unavailable forms, while substantial mercury uptake by plants occurred only in belowground tissues. The final experimental study investigated the potential stimulation of soil methyl mercury concentration via elevated surface water nutrients in a benchtop soil core incubation study. No evidence of significantly increased soil methyl mercury concentration was found.

Wetlands in the coastal zone are slowly becoming more saline under rising sea level over the long-term. However, there are a number of events in the coastal environment which lead to quick and temporary changes in the salinity of coastal marshes. Seawater driven inland from storm surge can significantly increase salinity in oligohaline wetlands over the short-term (weeks). Recent large-scale efforts to restore coastal wetlands in Louisiana have utilized Mississippi River surface water diversions to re-introduce freshwater into coastal marshes, decreasing the salinity of coastal marshes. We examined the effect of salinity changes on two important nitrogen cycling processes, potential denitrification and N-mineralization, in fresh and salt marsh soils/sediments in the Breton Sound estuary, LA. All soils/sediments were subjected to freshwater and saline treatments (0-35 ppt) simulating conditions within the soil that are caused by instantaneous flux of seawater due to storm surge events or high rates of freshwater flow directed by a surface water diversion. At 0 ppt potential denitrification in fresh and salt marsh soils reached 373 ± 22.2 and 9.18 ± 3.27 mg N2O-N kg-1 d-1, respectively. At 35 ppt, the rates were 615 ± 182 in salt marsh and 99.7 ± 21.1 mg N2O-N kg-1 d-1 in fresh marsh soils. Potentially mineralizable N rates in fresh marsh soils at 0 and 35 ppt averaged 28.6 ± 3.71 and 38.2 ± 4.31 mg-N kg-1 d-1, respectively. In salt marsh soils at 0 and 35 ppt, PMN rates were 12.3 ± 0.4 and 8.70 ± 0.32 mg-N kg-1 d-1, respectively. The effects of changing salinity on N-mineralization and potential denitrification will allow us to begin to discern the mechanisms of salinity-driven influences on overall nitrogen cycling and marsh biogeochemical function. Significance of these findings are applicable to large surface water diversion projects in the coastal Florida Everglades and Mississippi River Delta, where more saline sediments are exposed to freshwater and nitrogen pulses as well as impacts of increased salinity driven into the fresh-brackish marsh from hurricanes. Sudden fluxes in salinity had short-term effects on N mineralization, while denitrification showed significant effects with sudden salinity changes in wetlands soils.

The need to characterize offshore resources as borrow areas for beach restoration has initiated interest of the impact of storms to the inner continental shelf. While numerous studies have investigated the response of coastal systems to major storms, very little is known about the geological response of inner shelves to frequent and intense storms. This approach integrated a geological study with modeling of hydrodynamics during recent storms, in order to relate trends in the geological signature to physical forcing mechanisms during storms. First, waves and hydrodynamic conditions were modeled during two major recent storms that made landfall in the northeastern Gulf of Mexico. Results of the models were used in calculations of bottom shear stress and potential for resuspension of sediments. These results were further corroborated with satellite images of suspended particles. Second, vibracores, seismic and bathymetry data were collected to characterize the geologic history and recent changes to the geology of the inner shelf. These data were analyzed through physical interpretations, granulometric and radiocarbon analyses, and erosion/accretion calculations. The results indicate that storms have the potential to have a tremendous impact on the continental shelf, and can resuspend sediments in depths of 80 m or more, and last for several hours to a few days. A substantial offshore movement and downwelling component is also evident, with implications for a southwest moving geostrophic flow. The results of the geological analysis indicate that the stratigraphy of the inner shelf is a derivative of the last glacial to interglacial changes in sea level, with a highly modified Holocene reworked section. These modifications include winnowed sediments that coarsen to the inner shelf seafloor, the maintenance and migration of shelf shoals, and the development of numerous shelf ridges and troughs. These modifications are the direct result of frequent and intense hurricanes impacting the northeastern Gulf of Mexico. The modifications observed can be directly correlated to different phases of a storms impact on the shelf. From this, a conceptual model was developed that summarizes these modifications and the phases from which they formed.

Spatial and temporal patterns of mangrove vegetation in the Florida Coastal Everglades (FCE) reflect a major interplay of resources, regulators and hydroperiod gradients. I investigated landscape patterns of community structure, biomass and NPP of mangroves along two FCE estuaries: Shark River and Taylor River. I also evaluated whether pulsing events such as Hurricane Wilma are significant to soil nutrient inventories and vertical accretion of mangroves in FCE. There was a higher forest structural complexity of mangroves in Shark River relative to Taylor River. The biomass root:shoot ratio was 17 times higher in Taylor River relative to Shark River, indicating that scrub mangroves allocate a larger proportion of their total biomass to belowground. Root turnover rates consistently decreased as the root size classes increased from fine to coarse roots, indicating differences in longevity. Fine root biomass was negatively correlated with soil P density and frequency of inundation. Average total NPP was twice in Shark River compared to Taylor River. Aboveground production accounted for 68% (Shark River) and 42% (Taylor River) of the total NPP. Total root production contributed 32% (Shark River) and 58% (Taylor River) of the total. Sediment deposition from Wilma decreased with distance inland at each site. Vertical accretion resulting from this hurricane was one order of magnitude greater than the long-term accretion rate. Total P inputs from hurricane sediments were equivalent to twice the average soil P density (0.19 mg cm-3). Results from this study indicate that scrub mangroves of Taylor River have adapted to P limitation and flooded hydroperiods by allocating more biomass and production belowground relative to aboveground. Allochthonous mineral inputs from Hurricane Wilma represent a significant source of sediment to vertical accretion rates and nutrient resources in mangroves of southwestern Everglades. This source of P is significant to forest development due to the P-limited condition of this carbonate ecosystem. This information on how mangrove biomass and NPP are distinctly allocated between above- and belowground in response to environmental gradients across the FCE will be used to develop carbon budgets before and after hurricanes and to improve our understanding of carbon dynamics in neotropical mangrove forests.

River water entering estuaries affects the physical and chemical environment at irregular intervals creating a highly dynamic aquatic habitat. Phytoplankton are important primary producers in estuaries that respond quickly to their changing environment. Since 1991, Breton Sound estuary in southeast Louisiana has been directly influenced by Mississippi River water through the Caernarvon Freshwater Diversion structure. Over a 12 month period, the phytoplankton response was examined, in terms of biomass, abundance, community composition and potential phycotoxin production to seasonal changes in river input into the estuary. Within this 12 month period, a short pulse study was also carried out to examine the immediate response of phytoplankton to pulsed river input. Chlorophyll a (chl a) measurements estimated phytoplankton biomass and light microscopy identified phytoplankton abundance and community composition. Phycotoxins were measured using ultra-sensitive ELISA. During the seasonal study, chl a and cell abundance concentrations exhibited an inverse relationship with river input rates. Mean chl a concentrations were 79.1+38.7 and 55.2+48.5 µg chl a l-1 for low and high river input, respectively. Phytoplankton cell abundance concentrations averaged 7.5x105+6.7x105 cells l-1 and 1.2x105+2.5x105 cells l-1 during low and high river input, respectively. The community was dominated by cyanobacteria for most of the year, corresponding to higher temperatures. For the rest of the year, cyanobacteria decreased while chlorophytes and centric diatoms increased to approximately equal contributions. Chlorophytes dominated during the entire pulse study, however, cyanobacteria increased during high river input. Over both studies, the phytoplankton community composition was most commonly moderated by salinity and nutrient availability. Salinity, temperature and nutrient availability primarily influenced phytoplankton biomass and abundance during the seasonal study. The distance from the diversion and phosphate availability were the most important factors influencing phytoplankton biomass and abundance during the pulse study. Microcystins (MCs) were detected throughout the seasonal and pulse studies, ranged from below detection to 2.92 µg MCs l-1 and were highest during low river input and toward the outer estuary. The detection of MCs in Breton Sound estuary illustrates a potential risk to human health and economically important estuarine food webs.