College of Science Theses and Dissertations
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Item DISCARD MORTALITY, RECRUITMENT, AND CONNECTIVITY OF RED SNAPPER (LUTJANUS CAMPECHANUS) IN THE NORTHERN GULF OF MEXICO(11/10/2014) Curtis, Judson MatthewRed Snapper (Lutjanus campechanus) is the most economically important reef fish species in the Gulf of Mexico. Despite being intensively managed, stocks have been slow to recover from overharvest and the population is still rebuilding. One possible reason is that Red Snapper experience high discard mortality after catch-and-release. Additionally, there is a decoupling of the stock-recruit relationship in the fishery with high levels of recruitment despite low spawning stock biomass. This dissertation addressed these gaps in knowledge in three principal chapters. In Chapter II, I evaluated if certain release methods reduced discard mortality of Red Snapper at different depths and temperatures. I used acoustic telemetry to determine the best-release practices for enhancing survival and to estimate the extent of delayed mortality. Venting and rapid recompression release methods were more beneficial for enhancing survival, and delayed mortality events occurred within a 72-hour time period. In Chapter III, I used novel acoustic transmitters to analyze the post-release behavior and activity patterns of Red Snapper that survived catch-and-release. Red Snapper had different acceleration and depth activity over diel time periods, and increases in acceleration were correlated with higher depth in the water column. Release treatments did not affect long-term behavior and activity. In Chapter IV, I examined the stock-recruit relationship for the Red Snapper fishery by assessing whether localized cryptic spawning stock biomass is responsible for maintaining high recruitment levels. Acoustic telemetry and catch data were used to show that large, sow Red Snapper have high site fidelity and residency patterns in the western Gulf of Mexico, suggesting high recruitment observed in the stock may be originating locally from non-targeted sites. By identifying the source of the high spawning stock biomass, protection measures and regulations can be implemented to ensure that the current high recruitment to the fishery is sustained. Determining the best-release practices to enhance survival of discarded fish will result in larger stock sizes. Ultimately, implementation of findings from this dissertation into the management process will further assist and expedite the rebuilding of Red Snapper stocks and promote the recovery towards sustainability in this historically important Gulf of Mexico fishery.Item INTERACTIONS BETWEEN SUSPENDED SEDIMENTS, NUTRIENTS AND(11/10/2014) Paudel, BhanuThe objectives of the present study were to identify the effects of freshwater inflow (FWI) on sediment transport and nutrients supply to estuaries, and the effects of sediments on nutrient supply at sediment-water interface. The Nueces River and its estuary, the Guadalupe River and its estuary, and the Lavaca-Colorado Estuary were selected for field studies. Laboratory experiments were conducted to test the study hypotheses, and data was analyzed using multivariate modeling and statistical approaches. In the Guadalupe Estuary, variability of suspended solids and nutrients were correlated with FWI, whereas in the Nueces and Lavaca-Colorado Estuary they were related with seasonal differences. Suspended solids in the estuaries increased during frontal events and during windy days. In some of the field samplings, stations closer to the Gulf of Mexico had higher suspended sediments than the stations closer to the river. The increase in suspended sediments increased ammonia concentration in the Guadalupe Estuary, phosphorus and silicate concentrations in the Nueces Estuary, and silicate concentration in the Lavaca-Colorado Estuary. The presence of silicate minerals in the estuaries maintains silicate concentration as well. Organic matter and calcium carbonate shells in sediments of the estuaries can bind phosphate, thus, may have played role in decreasing phosphate concentration in the water. Guadalupe River sediments, when transported to the estuary, can release ammonia at higher concentrations the river water concentration. Salinity in the estuary, thus, has a significant role in controlling nutrient concentrations. The release of ammonia by organic matter decomposition was lower in the Guadalupe Estuary than in the Nueces Estuary. The high inflow volumes in the Guadalupe Estuary may have washed away organic matter from the sediments and may have disturbed bacterial community resulting in the lower release of ammonia from Guadalupe Estuary sediments. The research performed here demonstrates the importance of sediments, organic matter, and inflow in maintaining nutrient concentrations in estuaries. Fluctuation of these nutrients can affect water quality, and hence, may influence the ecology of the estuary.Item DISTRIBUTION AND DIVERSITY OF OCTOCORALS IN THE GULF OF MEXICO(11/11/2014) Etnoyer, Peter; T. C. ShirleyOctocorals are broadly distributed throughout the world’s oceans, from the shallow intertidal zone to deeper than 5800 meters. Fishermen refer to large colonies as ‘trees’. This is appropriate because colonies provide complex structural habitat for associated species, they are broadly distributed, and they are threatened by industrial practices, such as bottom trawling. Below the warm water layer (50 – 70 m deep), octocorals are presumed to be cosmopolitan in the West Atlantic, with a broadly homogenous distribution. This creates a problem for conservation and management because it is difficult to justify conservation of one place, if all others are the same. This dissertation tested the null hypothesis of no difference in octocoral assemblages at the three spatial scales (referred to as basin, region, and site scale) through meta-analysis of two large, original datasets. The first was 1881 records of octocoral occurrences in the Gulf of Mexico from cruise reports and museums. The second was 8495 seafloor images from six outer continental shelf banks, and one site between banks, in the northwestern Gulf region. Univariate, multivariate, and spatial analysis techniques were used to compare genera, depth zones, regions, and banks within a Geographic Information System framework.Octocoral assemblages in the Gulf of Mexico differed significantly between depth zones and regions, but there was no difference in diversity between depth zones less than 800 m, due to species replacement. Composition of octocoral assemblages varied significantly between sites, and hotspots for richness and abundance were evident within sites. Null hypotheses of no difference between banks, depth zones, and regions were rejected with confidence. The findings support the broad distribution of octocorals in the Gulf of Mexico, but not homogeneity of octocoral assemblages. Based on these results, place-based conservation of deep octocoral habitat is justified, because some sites have higher diversity and abundance of octocorals than others.Item Biological productivity associated with the serpulid reefs of Baffin Bay, Texas(1997-08) Hardegree, Beau; McKee, David A.; Prouty, Jennifer S.; Tunnell, John W.; Dunton, Kenneth H.The upper Laguna Madre and Baffin Bay-complex has long been noted for its abundant finfish populations despite its generally persistent hypersaline condition. The purpose of this present study was to determine the contribution of the serpulid worm reefs to the productivity of Baffin Bay. The primary focus of this thesis was to test the hypothesis that fish were larger and found in higher concentrations near the serpulid worm reefs in Baffin Bay, and to quantify the abundances of potential prey items associated with the reefs. In addition, I measured the productivity (by O2 evolution) of the epiphytic algae growing on the reefs and compared it to published seagrass studies in the upper Laguna Madre. Lastly, I examined the dependence of consumers on carbon fixed by these primary producers using stable carbon isotope ratios as tracers. A total of 5,396 individuals representing 35 fish species, were collected by trammel net during the study. Seven fish species (Mugil cephalus = 27.3 o/q Pogonias cromis = 20.2 %, Cynoscion nebulosus = 15.2 %, Leiostomus xanthurus = 12.1 %, Arius felis = 10.7 %, Lagodon rhomboides = 2.3 %, and Sciaenops ocel/atus = 1.1 %) comprised 89.0 % of the total catch. The overall ichythyofaunal catch rate was not significantly different between reef and non-reef sites and only a seasonal effect in the catch rate data was observed. Seasonal differences can be explained by the recruitment of fish into the bay in Spring and Summer. These seasonal peaks can be attributed to three species: Arius felis, Pogonias cromis, and Leiostomus xanthurus. No strong evidence was found to support the hypothesis that larger fish congregate around the serpulid worm reefs.Item Geoid determination in the coastal areas of the Gulf of Mexico(2/24/2014) Song, HongzhiCoastal areas of the Gulf of Mexico are important for many reasons. This part of the United States provides vital coastal habitats for many marine species; the area has seen-ever increasing human settlement along the coast, ever increasing infrastructure for marine transportation of the nation's imports and exports through Gulf ports, and ever increasing recreational users of coastal resources. These important uses associated with the Gulf coast are subject to dynamic environmental and physical changes including: coastal erosion (Gulf-wide rates of 25 square miles per year), tropical storm surges, coastal subsidence, and global sea level rise. Coastal land subsidence is a major component of relative sea level rise along the coast of the Gulf of Mexico. These dynamic coastal changes should be evident in changes to the geoid along the coast. The geoid is the equipotential gravity surface of the earth, which the best fits the global mean sea level. The geoid is not only been seen as the most natural shape of the Earth, but also it serves as the reference surface for most of the height systems. By using satellites (GRACE mission) scientists have been able to measure the large scale geoid for the Earth. A small scale geoid model is required to monitor local events such as flooding, for example, flooding created by storm surges from hurricanes such as Katrina (2005), Rita (2005), and Ike (2008). The overall purpose of this study is to evaluate the accuracy of the local coastal geoid. The more precise geoid will enable to improve coastal flooding predictions, and will enable more cost effective and accurate measurement of coastal topography using global navigation satellite systems (GNSS). The main objective of this study is to devise mathematical models and computational methods to achieve the best possible precision for evaluation of the geoid in the coastal areas of the Gulf of Mexico. More specifically, the numerical objectives of this study are 1) to obtain a continuous map of gravity anomalies and a continuous map of gravity by using spatial interpolation methods and to evaluate errors; 2) to solve the Laplace boundary value problem and evaluate errors; 3) to evaluate precision of the local geoid by using geospatial statistical tools and numerical techniques. This dissertation investigates modeling of the geoid, especially the gravimetric equipotential surface that approximates mean sea level, in the coastal areas of the Gulf of Mexico as well as errors in the geoid determination. The document begins with Chapter 1 which introduces the study of this dissertation. Different models of kriging are used to determine the precision of the geoid based on the free-air gravity anomalies data supplied by United States Naval Research Laboratory and the airborne gravity data provided by the U.S. National Geodetic Survey, which can be found in Chapters 2 and 3. Research in Chapters 2 shows that more precise evaluation of errors in gravity anomalies can be achieved by using different models of kriging. Results from Chapters 2 and 3 show that ordinary kriging with the stable semivariogram model provide better predictions. Research results from Chapter 3 provide estimation of maximum possible errors in the calculation of the geoid undulation. The dissertation also investigates behavior of gravity equipotential surfaces around coastal lines and its impact on the geoid evaluation. Chapters 4 and 5 are about evaluation of errors in the Dirichlet problem for calculation of gravity potential with uncertain boundary and boundary values has been achieved by solving the Laplace equation by means of separation of variables. Research has provided a theoretical model in Chapter 4 to estimate very small changes in gravimetric potential relative to the coast. Maximum possible error in the solution of Direchlet problem is determined in Chapter 5. Maximum possible error depends on the errors of boundary values and the precision of the boundary itself. Chapter 6 describes a novel approach to sea level rise modeling. Factor analysis is used to analyze local and global sea level rise and relationships between changing sea levels, currents, and the shape of the Earth. Results of factor analysis from Chapter 6 show that the elevation of sea level relates to the geoid and ocean circulation. Chapter 7 describes the relationship between the geoid and wetlands modeling. Research in Chapter 7 shows that the predicted continuous elevation map obtained through the ordinary stable kriging was sufficiently precise and fairly reliable. Chapter 7 is an exploratory chapter, and the ideas of this chapter will help the future research.Item Estimated increase in inundation probability with confidence intervals for the Gulf of Mexico(2/25/2014) Warner, Natalya N.The main objective of this research is to study the impact of sea level rise on the relative increase in frequency of inundation for the low-lying coastal zones of the Gulf of Mexico caused by storms of different sizes. The research is based on locations around the Gulf of Mexico that benefit from existing long term sea level records and are located near population centers: Galveston Pier 21, Galveston Pleasure Pier, Port Isabel, Rockport, Texas, Grand Isle, La, and Pensacola, Key West, and St Petersburg, Florida stations. The stations' long-term water level records are divided into a long term sea level trend, a tidal component and a stationary surge component. Several extreme value distributions, such as three and four parameters Burr, Dagum, log-logistic, and generalized extreme value distribution (GEV), are compared using multiple statistical measures for the modeling of maximum annual storm surges. While differences are small the GEV and log logistic distributions are selected for this work based on performance, sensitivity to the series outliers and ease of implementation. Increases in inundation frequencies are computed by combining the stations' respective annual maximum surge models with two possible sea level rise scenarios, a conservative linear continuation of the past century trend and a scenario based on the upper limit of the sea level range in the IPCC (Intergovernmental Panel on Climate Change) AR4 report (Assessment Report 4), i.e. the A1FI scenario. Differences in oceanographic setting are discussed and affect vulnerability to sea level rise. To compare vulnerability to sea level rise, the ratios of future and present exceedance probabilities are computed for a range of water levels. The locations' respective vulnerabilities to sea level rise are assessed by comparing the maximum ratios of future to present water level exceedance probabilities and the corresponding water levels. Water levels at maximum ratios have a strong correlation with most common moment- and quantile - based statistics of surges, except the maximum annual surges. This indicates that the results of this study are not overly sensitive to the most extreme values or largest surge on the record provided that the record includes at least one large surge. Statistical bootstrap methods are used to estimate 90% and 95% confidence intervals for increases in inundation probability. For most cases the confidence intervals show a substantial decrease in interval width for stations with lengths of datasets of 50 years or longer indicating a preferred data length provided that a large surge event is included. For all locations the lower bounds of the confidence intervals imply significant increase in exceedance probabilities for both sea level rise scenarios. While expected increases in inundation frequencies are substantial for all stations, the results show considerable variation depending on the sizes of the surges, the station locations and the sea level rise scenarios. Annual maximum water levels resulting from small storms/surges will have higher frequencies, typically by a factor of 3 or more, than the historical frequency of water levels resulting from large hurricanes. As a result more frequent, smaller storm surges may have a larger impact on coastal communities than the effects of the less frequent, larger storm surges. Ratios of the exceedance probabilities depend mostly on sea level trends and the shape of the curves of the exceedance probabilities. The relative importance of these parameters depends on the sea level rise scenario. For a continued linear sea level rise maximum ratios are strongly correlated to the sea level trends or vertical land motion. For the conservative sea level rise scenario the study's highest increase in water level exceedance probability of 17 times is computed for a water level of 1.23m above present mean sea level for Grande Isle, Louisiana. For higher rates of global sea level rise local subsidence becomes less important and the dominant factor becomes the range of the locations' surges. For the study's A1FI based sea level rise scenario, the highest increase in water level exceedance probability is over 100 times for a water level of 0.83m above present mean sea level for Key West, Florida. The results of this research provide coastal decision makers quantitative estimates of future inundation risks for two sea level rise scenarios and a calibrated method to compute such risks for more sea level rise scenarios. This research is relevant for engineers, planners, insurance executives, and others to take into account the increasing impacts of storm surges of various sizes as sea level rises. The results will help develop better insurance rates, plan structures, land-use zoning, and others as the century progresses. The models, methodology and estimates developed as part of this research may be used to estimate the time before specific locations may become economically uninhabitable due to surge inflicted damages as sea level rises. Particularly, it is expected that this work will allow better to quantify coastal vulnerability to sea level rise along the Gulf of Mexico.Item Trinational governance to protect ecological connectivity: support for establishing an international Gulf of Mexico marine protected area network(2/25/2014) Nash, Harriet LouiseThe Gulf of Mexico is a semi-enclosed, international sea that is bordered by the United States, Mexico, and Cuba. The three nations share transboundary living marine resources that move freely across political borders. Each nation has a vested interest in protecting the sustainability of living marine resources and the state of the large marine ecosystem. Uncommon, hard-bottom, high-biodiversity habitats occur on the continental shelf within United States, Mexican, and Cuban waters. An existing ecological network connects these hard-bottom habitats via migratory patterns and passive transportation of pelagic organisms through oceanic currents. Regional marine policy is needed to protect transboundary connectivity and ensure sustainability of shared living marine resources. An international network of marine protected areas throughout the Gulf of Mexico would conserve high-biodiversity habitats and ecological connectivity, which preserves the ecosystem's natural resiliency to natural and anthropogenic threats. Legal systems, laws, and governance regimes of the United States, Mexico, Cuba, and the international arena vary. Although the regulatory frameworks differ among the nations, each has marine policy and governance objectives that support ecosystem-based management. Analysis of marine policy was conducted to propose a trinational policy approach to establish and administer the International Gulf of Mexico Marine Protected Area Network under existing law. Domestically, the three nations each have one or more agencies that regulate marine protected areas, and such agencies would likely administer a transboundary marine protected area network. Internationally, several treaties are in place to protect living marine resources in the Gulf of Mexico. The Cartagena Convention was identified as the treaty to best support creation of the International Gulf of Mexico Marine Protected Area Network based on the treaty's scope and ratification by all three Gulf-facing nations. Collaboration and negotiation under the treaty could support an international memorandum of understanding and creation of a trinational commission to establish and oversee the network. The marine protected area network would connect sites that share features or biota. Coral reef ecosystems are important sites in the Gulf of Mexico. Four well-studied coral reefs--Florida Keys, Flower Garden Banks, Veracruz Reef System, and Alacranes Reef--are cornerstones of connectivity. Selected coral and fish species that occur at the four cornerstone sites were explored as examples of stepping-stone connectivity among several sites on the continental shelf throughout the Gulf. The selected species exemplify biological connectivity and provide justification for regional connectivity in the human dimension also. Marine protected area practitioners from the United States, Mexico, and Cuba gathered at a workshop in July 2012 to create the International Gulf of Mexico Marine Protected Area Network. Trinational collaborators identified design parameters and candidate sites that demonstrate biophysical connectivity and can be linked through standardized governance methods for sustaining human and environmental health and well-being. Of the candidate sites identified, several are collections of sites that are unprotected or not comprehensively protected. One example is the South Texas Banks; a case study for site selection was performed for the group of sites. Few biological data are available for the South Texas Banks. Multivariate statistical tests were performed on geomorphic variables that collectively acted as an abiotic surrogate for biodiversity patterns for 12 outer-shelf South Texas Banks. The analysis culminated with a ranking tool to guide prioritization of future biological explorations and site selection for designation of marine protected areas. A minimum of five outer-shelf South Texas Banks was proposed for place-based protection and inclusion in the International Gulf of Mexico Marine Protected Area Network. Similar methodology can be applied to other multi-site candidates to refine the spatial design of the network. Analyses of marine policy, ecological connectivity, and biodiversity hotspots yielded results that serve as a foundation for the International Gulf of Mexico Marine Protected Area Network. The network's objectives are to preserve natural resiliency to adverse anthropogenic and natural disasters and phenomena, to protect ecological connectivity, and to conserve biodiversity through shared resources and management tools. Continued trinational communication and collaboration are critical for successful ecosystem-based management at the regional scale. Proper trilateral administration of the International Gulf of Mexico Marine Protected Area Network could mitigate adverse effects of chronic and episodic stressors and increase protection of the ecosystem's natural resiliency, connectivity, and biodiversity.Item Turbidity and wave energy affect community composition and trophic interactions(2014-08) Lunt, Jessica; Smee, Delbert LeeAbiotic variables are well known community regulators and can strongly influence species distributions when they are outside of a species physiological tolerance limits. However, environmental variables within tolerance limits may also alter species distributions, morphology, predator-prey interactions, and influence the structure and function of communities. The purpose of this study was to determine how abiotic variables (notably turbidity) alter diversity, species distributions and abundances, predation rates on and species morphology. Texas Parks and Wildlife Department Fisheries Independent Survey Data from 1991-2008 were used in addition to field surveys of St. Charles Bay to determine the effects of turbidity on fish and crab diversity and abundance. Feeding assays were conducted in the field using groups of 5 mud crabs and 10 juvenile oysters to assess feeding rates in high and low turbidity. Juvenile oysters were also allowed to grow in the field to test the effects of turbidity on oyster growth. In addition, the effects of wave energy on oyster reef species composition and size were assessed using field surveys. I found that turbidity affects top-down control and biodiversity in estuaries and has similar effects to salinity and temperature. Elevated turbidity reduced fish diversity and abundance (p < 0.01), while increasing the diversity and abundance of crabs (p < 0.01). Predation by visual fish predators was also reduced in elevated turbidity (p = 0.02), which leads to an increase in the abundance of crabs and increased predation on mud crabs in high turbidities (p = 0.03). Juvenile oysters respond to increased crab abundance by growing heavier shells, which may lower fecundity. In laboratory assays, increased turbidity decreased the predation efficiency of visual predators (fish) but not of chemosensory predators (crabs). Differences were found between wave exposed and wave protected areas. Areas with higher wave energy had fewer species (p < 0.001) and the average size of species was smaller. This research identifies turbidity as an important variable within estuarine systems and extends the effects of wave energy from rocky intertidal systems to oyster reef communities. Both of these variables should be considered for effective management and restoration of estuarine communities.Item Identifying habitat conservation needs for the endangered whooping crane along the Central Texas Coast(2014-11) Lumb, Luz; Dr. James GibeautThe Aransas-Wood Buffalo whooping cranes (Grus americana) make up the only natural self-sustaining population of these endangered migratory wading birds in the world. Human and natural pressures threaten habitat quantity, quality, and integrity on their wintering grounds along the central Texas coast. This project developed tools for habitat conservation planning to support the endangered species downlisting goal of 1,000 cranes in the Aransas-Wood Buffalo population. First, a Comprehensive Habitat Type Database (CHTD) of benthic, wetland, and upland environments was developed from best available land cover information and bathymetric data. Then, habitat preference was determined using the CHTD and a spatially explicit dataset of whooping crane sightings from 2004 to 2010. About 1,000 km2 of preferred habitat were mapped across the 7,000 km2 study area. Projected losses and gains of preferred habitat as a result of sea level rise were then identified using results from the Sea Level Affecting Marshes Model (SLAMM) for various sea level rise scenarios up to the year 2100. Under 1 m of sea level rise, about 33% of preferred habitat is expected to be lost by 2100. Results showed that to reach the International Recovery Plan downlisting goal of 1,000 cranes, habitat conservation efforts must extend beyond the central Texas coast.Item Modeling Nutrient Dynamics in Coastal Lagoons(2014-12) Turner, Evan L.; Montagna, Paul A.; Sadovski, AlexeyThe declining health of estuary waters from nutrient pollution is a concern globally as human populations increase. The objective of this dissertation is to understand how nutrient inputs to estuary waters affect the estuary ecosystem. Field samplings (Chapter II), computational simulation code (Chapter III), and comprehensive model testing (Chapter IV) were used to accomplish the dissertation objectives. Inorganic nutrient concentrations were measured in Corpus Christi Bay, Texas for a continuous year to determine patterns of annual nutrient dynamics. Nutrient loading from runoff caused by precipitation affects estuary water quality along the shoreline. Corpus Christi Bay was found to have spatially dependent and seasonally driven nutrient dynamics. A robust computational programming toolkit was written to aid in the development and implementation of mathematical models. The toolkit, called EasyModel, contains a graphical utility to simulate a series of differential equations. The system is extendable for advanced users to calibrate mathematical models to ecological observation data. Five different models of nutrient dynamics were used to simulate nutrient dynamics of Copano Bay and San Antonio Bay, Texas. The complexity of the model equations was not related to how well measurements in the study area compared to simulated results. Including benthic components to the model design had the most positive affect on model performance. This research demonstrates that each estuary has a unique combination of biogeochemical characteristics that affect nutrient dynamics both spatially and temporally. Estuary responses to nutrient input were found to be non-linear, but predicable with the appropriate modeling techniques. Ensemble models can improve the accuracy of these predictions.Item Patterns of evolution in gobies (Teleostei: Gobiidae): a multi-scale phylogenetic investigation(2014-12) Tornabene, Luke M.; Frank L PezoldThe family of fishes commonly known as gobies (Teleostei: Gobiidae) is one of the most diverse lineages of vertebrates in the world. With more than 1700 species of gobies spread among more than 200 genera, gobies are the most species-rich family of marine fishes. Gobies can be found in nearly every aquatic habitat on earth, and are often the most diverse and numerically abundant fishes in tropical and subtropical habitats, especially coral reefs. Their remarkable taxonomic, morphological and ecological diversity make them an ideal model group for studying the processes driving taxonomic and phenotypic diversification in aquatic vertebrates. Unfortunately the phylogenetic relationships of many groups of gobies are poorly resolved, obscuring our understanding of the evolution of their ecological diversity. This dissertation is a multi-scale phylogenetic study that aims to clarify phylogenetic relationships across the Gobiidae and demonstrate the utility of this family for studies of macroevolution and speciation at multiple evolutionary timescales. In the first chapter, I present a DNA sequence matrix derived from two nuclear genes to help resolve intergeneric level phylogenetic relationships with the Gobiidae. My study is the first to use data from conserved nuclear loci to infer relationships across the Gobioidei, and the results provide strong support for the monophyly of, and interrelationships between, several ecologically divergent clades. Specifically, I show that gobies are asymmetrically divided into two clades, one of which contains primarily marine species and the other comprises mostly estuarine or freshwater taxa. In the second chapter, I focus on the evolution of microhabitat association and morphology in one of the most diverse lineages of gobies, the reef-associated genus Eviota. Eviota species have invaded novel microhabitats multiple times throughout their evolutionary history, often occurring independently of diagnostic morphological changes in pectoral-fin ray branching and arrangement of sensory cephalic lateralis pores. The combination of historical ecological flexibility coupled with resilience to local extinction events may explain the elevated extant biodiversity in Eviota. Lastly, in my third chapter, I use Eviota as a model for studying fine-scale speciation in the Coral Triangle, a marine biodiversity hotspot in the Western Pacific Ocean. A phylogeographic analysis of two species complexes that have diverged within the Coral Triangle provides strong support for the hypothesis that the Coral Triangle serves as a `center of origin' or cradle of new species. Specifically, I demonstrate that a combination of biotic and abiotic factors may be contributing to rapid speciation both in allopatry and sympatry within the last 1.5 million years. The presence of recently diverged cryptic species in the Coral Triangle implies that our current estimates of biodiversity in this marine hotspot are severely underestimated. Ultimately, this dissertation demonstrates that gobies and other ecologically diverse clades of fishes serve as excellent model groups for studying the processes driving taxonomic and phenotypic diversification in marine species at a variety of spatial and temporal scales. This project will serve as a foundation for future studies that aim to use more comprehensive genomic datasets to address questions regarding drivers of speciation and ecological diversification in gobiid fishes.Item Population genetic structure of the crashed snook fishery (Centropomus spp.)(2015-05) González, AlinSnook (Centropomus spp.) are an important game fish in the warmer coastal regions of the West Atlantic and East Pacific Oceans. In Texas, the snook fishery crashed >80 years ago and has exhibited weak signs of recovery. Here, we investigated the patterns of population genetic structure of snook in Texas with 16S mtDNA and 9 microsatellite markers. Three species of snook were identified: C. undecimalis, C. poeyi, and C. parallelus. The mtDNA of Texan C. parallelus form a monophyletic lineage that is 0.8% divergent from C. parallelus in Florida and Costa Rica. Centropomus poeyi and C. parallelus exhibited a pattern consistent with rampant hybridization and introgression and were so intertwined that we analyzed them as a single stock. Both C. undecimalis and C. poeyi - C. parallelus exhibited elevated homozygosity consistent with inbreeding. Mild chaotic genetic patchiness in C. undecimalis and C. poeyi - C. parallelus was mostly explained by elevated levels of kinship that are also associated with inbreeding. There was one instance where a sample of juveniles shared higher kinship coefficients with adults from another location than each other, suggesting that the juveniles originated near the sample of adults, in Texas. Overall, these results suggest that the recovery of the Texas snook populations has been slow due to low amounts of migration from other locations in the Gulf of Mexico.Item Mathematical results for slipping flows past a cylinder or a sphere embedded in a porous medium(2015-07) Alshehri, NadaFlow past a circular cylinder or a sphere embedded in a porous medium is investigated mathematically by treating porous matrix as an incompressible fluid. Closed form analytic solutions for the fourth order scalar boundary-value problems for Ψ (r, θ) - known as the Stokes stream function - are obtained by using Navier-slip conditions. Our exact results for Ψ (r, θ) capture flow fields prevailing in the vicinity of a cylinder/sphere suspended in a uniform or a shear flow field. All the physical quantities computed from our solutions depend on two key parameters, namely, δ (the effective permeability) and ζ (slip coefficient). Flow separation and velocity overshoot behavior are found for certain values of δ and ζ. The force acting on the cylinder/sphere is calculated in each case. It is observed that the presence of slip decreases the force on the boundary. Our results show that in the limit δ -> 0, there is no solution to the two-dimensional boundary-value problem, confirming the familiar Stokes paradoxItem Network television dynamics: a conceptual mathematical model(2015-07) Maceyko, Aimee EIn this thesis we will be expanding on modifications we previously made relating to Edwards and Buckmire’s model of box office dynamics to network television. We will introduce the number of viewers with a negative reaction to the product as a function with respect to time. The interaction of the main parameters of the box office dynamics as they translate to the network television problem: viewership, revenue, and audience perception for television programming will be presented as a conceptual model of a system of three 1st order differential equations. The eigenvalue method, Routh-Hurwitz stability criterion, and control theory will be used to solve the problem and the stability of the solution will be checked. Finally, based on the numerical solution and its stability, recommendations will be presented.Item Investigation of the cytotoxicity, anti-oxidant, and anti-inflammatory effects of Ligusticum porteri (Osha) on human peripheral lymphocytes and promyelocytic leukemia cells(2015-08) Nguyen, Khanh T.P.Ligusticum porteri is a traditional Native American herb. The roots of L. porteri have been used in treatments for many kinds of diseases as well as for boosting the immune system. Even though L. porteri has been widely used in traditional remedies, its acclaimed medicinal effects have been barely validated. This study is the first investigation into the medicinal effects of L. porteri on the cytotoxicity, anti-oxidative, and anti-inflammatory activity in human peripheral blood lymphocytes (PBLs) and promyelocytic leukemia (HL-60). This study also investigated the attenuating effects of L. porteri on the cytotoxicity of hydrogen peroxide induced oxidative damage in these cell cultures. Methods: Vacuum-dried ethanolic root extract of L. porteri was dissolved in dimethyl sulphoxide (DMSO) to prepare a stock solution. Appropriate volumes of stock solution of the root extract were added to cultured PBLs and HL-60 cells (1:10 v/v) so that the final concentrations of L. porteri root extract in each batch of cell culture were respectively 0 μg/ml (control), 50 μg/ml, 100 μg/ml, 200 μg/ml, and 400μg/ml. Additionally, to investigate the attenuating effects of L. porteri in oxidative-damaged cell cultures, PBLs and HL-60 cells were challenged with 50 μM of hydrogen peroxide. The cell suspensions were incubated at 37°C humidified with 5% C02. After each day during the incubation period, cell pellets and supernatants were harvested for the investigation of the cytotoxicity, anti-oxidation, and antiinflammation induced by the cell cultures treated with L. porteri root extract. Results: Treatments with L. porteri at concentrations as high as 400 μg/ml could enhance the viability and proliferation of human PBLs and HL-60 cells. After 2 days incubation with 200 μg/ml and 400 μg/ml of root extract, the viability of PBLs was 2 and 2.5 fold higher than the control. The PBLs treated with L. porteri at 200 μg/ml and 400 μg/ml proliferated until day 3 while the untreated and those treated with lower concentrations {50 μg/ml and 100 μg/ml) of the root extract did not survive. After 7 days of incubation with 200 μg/ml and 400 μg/ml of L. porteri root extract, the proliferation of HL-60 cells was two-fold higher than the control {P < 0.05). This study also found that the oxidative stress induced by hydrogen peroxide {H202) reduced the viability of PBLs and HL-60 cells. Data showed that the percentage viability of stress-induced PBLs and HL-60 cells was reduced by 54% and 42%, respectively {P < 0.05). The anti-proliferative effect of H202 was ameliorated by 400 μg/ml L. porteri treatment. This effective dose helped maintain the PBLs' viability at 1.5 times higher than the control after 2 days of incubation while this dose increased the proliferation of stressed HL-60 cells by 42% {P < 0.05). Treatments at lower concentrations did not have a significant proliferative effect which ultimately resulted in growth decline due to H202-exposure. Lipid peroxidation was measured in terms of malondialdehyde {MDA) formed during the stress. Data showed that the root extracts reduced the MDA accumulation in stressed PBLs and HL-60 cells {P < 0.05). The addition of 400 μg/ml L. porteri significantly decreased the lipid peroxidation in stressed PBLs by 94% {P < 0.05). Treatment of stressed HL-60 cells with the root extract concentration equal or higher than 100 μg/ml reduced the lipid peroxidation by 12-13% {P < 0.05). Treatment with 400 μg/ml of the root extract resulted in 26.4% and 29.4% increase of glutathione levels {GSH) in stressed PBLs and HL-60 cells respectively as compared to stressed cell cultures without the root extract {P < 0.05). Studies on the superoxide dismutase {SOD) and catalase {CAT) activities in H202-challenged PBLs and HL-60 cells showed increased activities in response to oxidative stress. Positive modulatory effects of L. porteri to the activities of these enzymes in stressed cells were noted at concentrations as low as 100 μg/ml (P < 0.05). The activities of SOD and CAT increased significantly, by 17.5% and 55.2% respectively, when stressed PBLs were treated with 400 μg/ml L. porteri for 2 days. Treatment with root extract at 100 μg/ml significantly {P < 0.05) increased the activity of SOD in H202-challenged HL-60 cells. This study found that CAT activity in stressed HL-60 cells showed a 2- to 2.5-fold increase after treatment with more than 50 μg/ml L. porteri. Treatment with 400 μg/ml L. porteri significantly {P < 0.05) increased IFN-y and IL-2 in H202- challenged cells. Addition of the root extract did not cause a significant difference in IL-10 levels between stressed PBLs with and without 400 μg/ml L. porteri (P > 0.05). However, treatment with ·400 μg/ml L. porteri diminished the effect of H202-induced decrease in IL-10 in stressed HL-60 cell cultures {P < 0.05). Conclusion: The use of ethanolic root extract of L. porteri at high concentration {400 μg/ml) enhanced the viability of human PBLs and HL-60 cells. Treatment with L. porteri may protect the cells against H202-induced oxidative stress by reducing lipid peroxidation and oxidation of GSH, as well as by elevating the activities of SOD and CAT. Treatment with the L. porteri root extract further enhanced the production of IFN-y and IL-2. Along with the mild enhancement of secretion of IL-10, cytokine stimulation by the addition of L. porteri suggested that the root extract may be a potential immune-modulating agent involving protective effects against oxidative damage.Item Suspended Sediment Dynamics of Texas Estuaries(2015-08) Reisinger, Anthony Sherman; Gibeaut, James C.Suspended sediments are an integral part of estuarine systems in that they impact water quality and form habitats; their flux is driven by the interplay between freshwater inflow, tidal currents, wind-wave resuspension, commercial fishing, and dredging operations. The objective of this dissertation is to investigate the relative importance of the aforementioned drivers of suspended sediment in the three largest Texas estuaries (Galveston, Matagorda, and Corpus Christi Bays) using a variety of analysis methods. Analyses of suspended sediment drivers using a Texas State water quality database of in situ samples (Chapter II), development of an algorithm to transform satellite imagery into suspended sediment concentrations (Chapter III), and analysis of a 12-year time series of satellite-derived suspended sediment concentrations (Chapter IV) were used to accomplish the dissertation objectives. The relative importance of freshwater inflow, tidal currents, and wind-wave resuspension was determined by statistical analyses of in situ point measurements of total suspended solids (TSS) and environmental forcings for the period of 2000-2010. The findings from these analyses show that wind-wave resuspension is the most dominant forcing of TSS in Corpus Christi, Matagorda, and Galveston Bays. The analyses further indicated that freshwater inflow in Galveston Bay and astronomical tides in Matagorda Bay also influence the variability of TSS. An algorithm to transform satellite reflectance data into TSS was created Analyses determined the best model was an exponential fit of a red-green band ratio. The algorithm was then used to create synoptic time series of TSS for the period of 2002-2014 for the estuaries. Analysis of the satellite-derived time series shows how freshwater inflow, tidal currents, wind-wave resuspension, commercial fishing, and dredging operations influence the long-term variability of TSS in Galveston, Matagorda, and Corpus Christi Bays. Median and interquartile range composites of suspended sediments were generated for seasonal wind and inflow regimes in each estuary. TSS patterns show that the Galveston Bay system is dominated by riverine inflow with some influence from frontal passages. Surprisingly, the influence of oyster harvesting causing locally high TSS values in Galveston Bay is the most salient pattern within the estuary. Matagorda Bay’s patterns indicate that the system is mostly controlled by wind-wave resuspension with patterns changing between northern frontal passages and southeasterlies dominated seasons. Corpus Christi Bay is similarly influenced by wind-wave resuspension with different patterns during the predominant northerlies and prevalent southeasterlies seasons. The impact of dredging is also apparent in long-term patterns of Corpus Christi Bay as concentrations of suspended sediments over dredge spoil disposal sites are higher and more variable than surrounding areas, which is most likely due to less consolidated sediments and shallower depths requiring less wave energy for sediment resuspension. For Corpus Christi and Matagorda Bays, this research (Chapters II & IV) showed that wind-wave resuspension is the dominant forcing of TSS. Satellite data allowed the identification of patterns characteristic of different wind regimes. Additionally the point data analysis (Chapter II) showed that tidal forcing has an influence on TSS in Matagorda Bay. Both analyses (Chapters II & IV) show that wind forcing is less influential in Galveston Bay as compared to the other estuaries, and that freshwater inflow are important in Galveston Bay. A major highlight of this research is the advantage provided by long synoptic time series of satellite-derived TSS that elucidated the major drivers of suspended sediments in estuaries as well as their seasonal variability. With usage of satellite data, this research identified oyster harvesting to be a significant source of suspended sediment in Galveston Bay.Item Evolution of the genus Sicydium (Gobiidae:sicydiinae)(2015-08) Chabarria, Ryan Earl; Pezold, FrankGobies are one of the most speciose groups of fishes on the planet. Despite their prominence little is known about their evolution and diversity. Gobies of the genus Sicydium are abundant inhabitants of tropical streams in the Atlantic and eastern Pacific basins. The amphidromous life history of Sicydium presents challenges in understanding their diversity and the evolutionary relationships among species. With this life history, the adults live and breed in freshwater streams. Newly hatched larvae are carried out to the marine environment where they live as ichthyoplankton for a period of time. Upon completion of the marine larval phase juveniles will re-enter the freshwater environment. Additionally, poor species descriptions, parochial studies, and highly variable morphological characters have resulted in taxonomic uncertainty within the genus. This dissertation presents separate phylogenetic hypotheses of the relationships between species of Sicydium based upon morphology and DNA data. In the first chapter, I present a phylogenetic hypothesis of the relationships among the species of Sicydium based upon morphological characters. This chapter shows that changes in jaw morphology are important in the evolution of Sicydium. Three clades of Sicydium were recovered, however the relationship among these clades was unresolved. Different oral morphology characters were important in determining the relationships between species. This includes morphology of the premaxillary teeth, which has been used as a diagnostic character for species of Sicydium. This study presents the first phylogenetic hypothesis based on morphology for the species of Sicydium. The second chapter presents a molecular assessment of species diversity and a molecular phylogenetic hypothesis of Sicydium based upon two nuclear and two mtDNA genes. Previous molecular studies that have included Sicydium were at the population or subfamily level. Here I present the first molecular hypothesis of the evolutionary relationships among the species of Sicydium. The analysis recovered two clades of a monophyletic Sicydium, one less than morphological data, with most relationships among species well resolved. The species recovered in these two clades were similar to those recovered with the morphological data. However some species were not recovered as monophyletic in the molecular analysis, most likely due to incomplete lineage sorting. In the third chapter, I present a population level study of an eastern Pacific species, Sicydium salvini, Ogilvie-Grant, 1884. This chapter explores the diversity of a species recovered by the previous chapters. This study showed that S. salvini inhabits a wide geographic range including areas previously considered to be occupied by Sicydium multipunctatum. DNA samples from across the range of this species were used to test for population structure and population expansion. A lack of structure between river populations was found which is most easily explained by the amphidromous life history. The dispersion capabilities of the marine larvae allow free exchange of genes between distant populations. I also show that tectonic activity may explain a historic population expansion for Sicydium salvini. In this dissertation I present different views on the evolution of Sicydium. In the first two chapters, I present phylogenetic hypotheses of the species of Sicydium. The third chapter shows a population level view of Sicydium salvini. These data can be used as a stepping-stone for future work involving the evolution of sicydiine gobies as well as providing new characters for a much needed taxonomic revision of Sicydium. It also clarifies population level dynamics and historical environmental influences on those dynamics.Item Associations between chlorophyll and wind forcing in the Gulf of Mexico derived from satellite observations(2015-08) Trnka, Maureen C.The Gulf of Mexico supports many industries that rely on its natural resources. Primary production is required to sustain fish populations and contributes to ocean carbon exchange. Ocean color satellites make it possible to observe large geographic areas; however, an individual sensor has limited coverage. The GlobColour project merges observations from multiple satellites into a single product. The purpose of this study is to use GlobColour and QuikSCAT to investigate the seasonal and non-seasonal associations between chlorophyll and wind from 2000-2008 in the Gulf of Mexico. An overview of the Gulf of Mexico’s physical setting, circulation, and main features is presented. The Gulf is divided into: Interior Basin, West Florida Shelf, Louisiana-Texas Shelf, Tamaulipas-Veracruz Shelf, Bay of Campeche, and Campeche Bank. Phytoplankton biomass is discussed in the context of nutrient-transport mechanisms including coastal upwelling, Ekman pumping, horizontal advection, and vertical turbulent mixing. Seasonal associations are evaluated between chlorophyll and wind using Empirical Orthogonal Functions and Singular Value Decomposition. Chlorophyll has strong seasonal variability over the shelves. The interior variability of chlorophyll and wind speed is in-phase with annual periodicity, increasing in winter and decreasing in summer. Strong winter winds increase the upward turbulent transport of nutrients into the mixed layer. The northern chlorophyll variability has a dipole with increased anomalies over the Western Shelf and decreased anomalies around the Mississippi mouth; associated with intensified easterly winds. Non-seasonal anomalies of chlorophyll and wind are similarly investigated. Increases in wind speed are associated with chlorophyll increases over the Campeche Bank, Bay of Campeche, and West Florida Shelf; the mechanism is upward entrainment of nutrients by turbulent mixing. Northerly winds are associated with coastal upwelling in the Bay of Campeche, offshore advection in the west, and a chlorophyll dipole across the Mississippi mouth. The non-seasonal coupled patterns are predominantly intraseasonal and spatially coherent with interannual modulations. This study is the first to apply a merged ocean color product to research in the Gulf of Mexico. Overall, this project provides baseline information on the seasonal and non-seasonal variability of chlorophyll and winds, identifies statistical associations, and proposes dynamical mechanisms.Item Fuzzy ranking from fuzzy pairwise comparisons with applications(2015-08) Wang, YunfengOne method of ranking items is to score all of them against a standard scale. Sometimes it is difficult to create or use such a scale. As an alternative, it is possible to make side-by-side comparisons of some or all of the pairs of items. Then the problem is to convert the collective pairwise comparisons into a ranking. This problem has been studied previously in many contexts. This thesis addresses several methods, including where fuzzy comparisons are made for some, but not all, of the pairs. The Colley method and PageRank algorithm both use pairwise comparisons for some pairs to rank all items in a set. This thesis shows how those pairwise comparisons can be fuzzy. It also shows how Saaty's method for ranking alternatives can be completed when not all comparisons are used.Item Assessing short-term sediment accretion rates and hydrological influences on a microtidal estuarine wetland: Mustang Island, TX(2015-12) Martinez, MelindaAs sea level rises there has been a growing concern whether salt marsh wetlands can withstand an accelerated rise in sea level by vertically accreting. Sediment accretion is a natural process that changes the elevation of the marsh surface relative to sea level. For a wetland to persist in the long-term, its accretion rate must at least match the rate of relative sea level rise. This study describes sedimentation rates in the estuarine wetlands located on Mustang Island, TX, a sandy barrier island. Sedimentation rates were measured bi-weekly from June 2014 to July 2015 using sediment plates and erosion pins, and over periods of 2.4 to 3.3 years (2012- 2014/2015) using horizon marker techniques. Water level loggers were used to assess hydrological controls on bi-weekly sedimentation patterns. Shallow cores (~15 cm) were collected from the horizon marker plots in August 2014 and July 2015. Vertical accretion rates were compared across different timescales including decadal rates determined using 137Cs from a previous study on Mustang Island, TX. Results indicated sediment accretion across the study area was not significantly influenced by hydrological patterns, with the exception of low marsh environments near tidal creeks (r2=0.52, p < 0.1). The most important factor in determining sediment deposition on sediment plates located near the main tidal creek was the number of flooding events, suggesting that deposition increases as frequency of flooding events increases. The total accumulation deposited on plates was dominated by inorganic sediments, suggesting there is a limit of detrital organic matter contribution for this area. Average vertical accretion using horizon markers was 8.15 ± 5.21 mm yr-1 in upland environments; 4.51 ± 5.21 mm yr-1 in high marsh environments; 3.36 ± 3.57 mm yr-1 in high flat environments; 11.92 ± 9.73 mm yr-1 in low marsh environments; and 1.88 ± 2.54 mm yr-1 in low flat environments. There was a significant difference in vertical accretion rates between both horizon markers and erosion pins, which provide annual-scale accretion rates, when compared to 137Cs, which provide decadal-scale accretion rates (p < 0.1). On average annual vertical accretion rates were 2.8 times higher than decadal rates. Differences between annual and decadal accretion rates are mostly attributed to shallow sediment compaction within the top 3 cm of the wetland surface. Variation in wetland vertical accretion rates increased significantly going from decadal (± 0.41 mm) to annual (± 2.87 mm) to annualized biweekly rates (± 9.60 mm). Annual-scale accretion rates measured using horizon markers in low marsh and upland environments appear to be keeping up with relative sea level rise (RSLR), which is 5.27 ± 0.48 mm yr-1 as measured since the 1950’s at a nearby tide gauge. However horizon marker vertical accretion rates in tidal flats and high marsh environments are not sufficient to overcome sea level rise. Vertical accretion rates were positively correlated with organic and inorganic accretion for all horizon markers (p < 0.1); however, the relative contribution of organic matter decreases as inorganic matter increases. Our findings anticipate environmental shifts in habitats with accretion rates below RSLR. Furthermore, vertical accretion was dominated by inorganic matter, making the wetlands reliant on constant wind and episodic storms to transport sediment to the area. Importantly, these data suggest that storm-induced sedimentation acts to stabilize coastal wetlands and helps certain environments cope with RSLR, but is not sufficient to prevent shifts in the relative composition of the wetland.