College of Science Theses and Dissertations
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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 The relative roles of salinity stratification and nutrient loading in seasonal hypoxia in Corpus Christi Bay, Texas(2012-10-09) Nelson, Kevin K.; Montagna, Paul A.Hypoxia (low dissolved oxygen concentration) is known to occur in the southeast corner of Corpus Christi Bay, Texas, USA each summer since its discovery in 1988. In 2006, ongoing field research discovered that the hypoxia area has a greater extent spatially and temporally than previously thought. Although it was known that hypoxia was associated with salinity stratification, it was not until 2007 that it was discovered that salty water from both Oso Bay and Laguna Madre were contributing to this stratification. This is interesting because there are three wastewater treatment plants that empty into Oso Creek and to Oso Bay, so there is a source of nutrients as well as salt. The purpose of the current study was to determine the spatial and temporal extent of hypoxia, to explore the role of nutrients and bay currents in the formation and frequency of hypoxia, to determine what, if any role small rain events play in the formation of hypoxia, and to test the feasibility of disseminating the data collected in this study and others to the public via the use of a standardized database schema and web services. Hypoxia was found to begin as early as the first week of June, and occur as late as the last week of August, i.e. stops when wind stops. Hypoxic conditions can extend from Ward Island to Shamrock Island, and area estimated to cover 80 km2. Nutrient concentrations are not at high levels however, ammonium levels are higher in the hypoxic zone, likely due to anaerobic remineralization of organic matter. Even small-scale rain events appear to flush nutrients from Oso Bay however, this does not appear to affect hypoxia in Corpus Christi Bay. Differences in acoustic opacity, current velocity, and current direction, and salinity between the bottom waters and those above may all be contributing to stratification, known to cause hypoxia. Hypoxia also appears to be influenced by the fortnightly lunar cycle, bathymetry, and bottom composition. Attempts to transform data from this project into a standard database schema were successful. However, not all of the complexities of biological nomenclature, multivariate data structures, and laboratory information requirements could be met with the system under study.Item Hyperspectral analysis of seagrass in Redfish Bay, Texas(2012-11-07) Wood, John S.; James Gibeaut; John W. TunnellRemote sensing using multi- and hyperspectral imaging and analysis has been used in resource management for quite some time, and for a variety of purposes. In the studies to follow, hyperspectral imagery of Redfish Bay is used to discriminate between species of seagrasses found below the water surface. Water attenuates and reflects light and energy from the electromagnetic spectrum, and as a result, subsurface analysis can be more complex than that performed in the terrestrial world. In the following studies, an iterative process is developed, using ENVI image processing software and ArcGIS software. Band selection was based on recommendations developed empirically in conjunction with ongoing research into depth corrections, which were applied to the imagery bands (a default depth of 65 cm was used). Polygons generated, classified and aggregated within ENVI are reclassified in ArcGIS using field site data that was randomly selected for that purpose. After the first iteration, polygons that remain classified as `Mixed' are subjected to another iteration of classification in ENVI, then brought into ArcGIS and reclassified. Finally, when that classification scheme is exhausted, a supervised classification is performed, using a `Maximum Likelihood' classification technique, which assigned the remaining polygons to the classification that was most like the training polygons, by digital number value. Producer's Accuracy by classification ranged from 23.33 % for the `MixedMono' class to 66.67% for the `Bare' class; User's Accuracy by classification ranged from 22.58% for the `MixedMono' class to 69.57% for the `Bare' classification. An overall accuracy of 37.93% was achieved. Producers and Users Accuracies for Halodule were 29% and 39%, respectively; for Thalassia, they were 46% and 40%. Cohen's Kappa Coefficient was calculated at .2988. We then returned to the field and collected spectral signatures of monotypic stands of seagrass at varying depths and at three sensor levels: above the water surface, just below the air/water interface, and at the canopy position, when it differed from the subsurface position. Analysis of plots of these spectral curves, after applying depth corrections and Multiplicative Scatter Correction, indicates that there are detectable spectral differences between Halodule and Thalassia species at all three positions. Further analysis indicated that only above-surface spectral signals could reliably be used to discriminate between species, because there was an overlap of the standard deviations in the other two positions. A recommendation for wavelengths that would produce increased accuracy in hyperspectral image analysis was made, based on areas where there is a significant amount of difference between the mean spectral signatures, and no overlap of the standard deviations in our samples. The original hyperspectral imagery was reprocessed, using the bands recommended from the research above (approximately 535, 600, 620, 638, and 656 nm). A depth raster was developed from various available sources, which was resampled and reclassified to reflect values for water absorption and water scattering, which were then applied to each band using the depth correction algorithm. Processing followed the iterative classification methods described above. Accuracy for this round of processing improved; overall accuracy increased from 38% to 57%. Improvements were noted in Producer's Accuracy, with the `Bare' vi classification increasing from 67% to 73%, Halodule increasing from 29% to 63%, Thalassia increasing slightly, from 46% to 50%, and `MixedMono' improving from 23% to 42%. User's Accuracy also improved, with the `Bare' class increasing from 69% to 70%, Halodule increasing from 39% to 67%, Thalassia increasing from 40% to 7%, and `MixedMono' increasing from 22.5% to 35%. A very recent report shows the mean percent cover of seagrasses in Redfish Bay and Corpus Christi Bay combined for all species at 68.6%, and individually by species: Halodule 39.8%, Thalassia 23.7%, Syringodium 4%, Ruppia 1% and Halophila 0.1%. Our study classifies 15% as `Bare', 23% Halodule, 18% Thalassia, and 2% Ruppia. In addition, we classify 5% as `Mixed', 22% as `MixedMono', 12% as `Bare/Halodule Mix', and 3% `Bare/Thalassia Mix'. Aggregating the `Bare' and `Bare/species' classes would equate to approximately 30%, very close to what this new study produces. Other classes are quite similar, when considering that their study includes no `Mixed' classifications. This series of research studies illustrates the application and utility of hyperspectral imagery and associated processing to mapping shallow benthic habitats. It also demonstrates that the technology is rapidly changing and adapting, which will lead to even further increases in accuracy. Future studies with hyperspectral imaging should include extensive spectral field collection, and the application of a depth correction.Item Linking ecological function and ecosystem service values of estuarine habitat types associated with a barrier island system(2012-11-15) Francis, Jeffrey M.; Fox, Joe M.; David W. YoskowitzEcosystem services are benefits humans receive as a function of natural processes. Many current studies seek to express these benefits as an economic value per unit of habitat type without quantifying the ecological functions that allow for the provision of ecosystem services. This study is designed to model each habitat type in an effort to explicitly link the major estuarine habitat types of Mustang Island (oyster reefs, seagrass meadows, and intertidal salt marsh) to their contribution to Nitrogen cycling services. First, a dynamic biomass model of each foundational species was created using Simile, a declarative modeling framework. Second, a monthly snapshot of Nitrogen captured in living biomass was used to quantify the contribution of each species to the Nitrogen cycling services. Finally, the amount of Nitrogen captured in living biomass was valued using a replacement cost approach. An effort was also made to link the provision of recreational fishing services provided by each aforementioned habitat type by partitioning travel costs and license sales weighted by the density of fish found in each habitat type. It was found that oyster reefs of Mustang Island contribute $173,000 yr-1, seagrass meadows contribute $12,054,095 yr-1, and intertidal salt marshes contribute $5,242,755 yr-1 in potential Nitrogen cycling services. The total value of recreational fishing services within the study site was calculated to be $83.8 million dollars yr-1. A portion of the total value was then attributed to each habitat type: Marsh edge: $2 million; Seagrass meadows: $81 million; and Oyster: $81,000 thousand. These efforts have been made to translate ecological function into economic benefit to improve communication among a wide variety of stakeholders that are more likely to understand economic value. Further refinement of both the models and the economic data necessary to support them, will have the potential to improve the applicability and results of these tools. These results, and the modeling framework through which they are calculated, provide a platform to evaluate management relevant scenarios in a simple, flexible manner that may be adjusted and transferred to other study sites given appropriate local data.Item Estimated increase in inundation probability with confidence intervals for the Gulf of Mexico(2013-04-15) 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 Geoid determination in the coastal areas of the Gulf of Mexico(2013-07-01) 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 Trinational governance to protect ecological connectivity: support for establishing an international Gulf of Mexico marine protected area network(2013-07-03) 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 Biodiversity, ecology, and natural history of polychaetous annelids from the Gulf of Mexico(2013-11-15) Reuscher, Michael Gerhard; Shirley, Thomas C.; Tunnell Jr., John W.; Pezold, Frank L.; Schulze, Anja; Withers, Kim; Cifuentes, Lauren; Canales, JoAnnPolychaetes are abundant and ecologically important benthic organisms, yet their diversity and phylogenetic relationships are far from being resolved. The purpose of my dissertation was to measure their diversity in the Gulf of Mexico and to compare polychaete assemblages of different regions, depths, and sampling periods. Furthermore, I studied the natural history of the diverse polychaete family Paraonidae. The polychaete diversity of the Gulf of Mexico was examined using a comprehensive species database. Species were assigned to ecological, morphological, and biogeographical categories and each category's contribution was examined throughout different depths and regions. Spatial and temporal comparisons of polychaete assemblages were conducted at three transects on the northern Gulf of Mexico continental slope. Phylogenetic relationships within the family Paraonidae were studied based on the examination of type material. Polychaete diversity changed with depth. The shelf break was accompanied by a steep change in the species composition. The southeastern Gulf had the most distinct polychaete fauna. Endemism was at 10%; in the deep-sea more than 30% of the species were endemic and the relative contribution of carnivorous species doubled. At the continental slope, abundance did not continuously decrease with depth between 350 and 1500 m, but dropped between 1500 and 2100 m. Abundance in the spring was approximately twice as high as in the fall, in depths up to 1500 m. Polychaete assemblages changed continuously with increasing depth. Short-term temporal changes of polychaete assemblages had reversed in the long run. In the cladistic analyses, monophyly of Paraonidae was supported. Its synapomorphies are the complete fusion of prostomium and peristomium and the dorsal location of the anus. Cirrophorus and Paradoneis should be considered synonyms. The prostomial antenna, which was used to distinguish both genera, is a homoplastic character. Two species of Paradoneis are being moved to a new genus. Spatial and temporal patterns of polychaete diversity in the Gulf of Mexico were discovered. Additional sampling efforts are needed for a more complete picture of the diverse polychaete fauna. The phylogenetic analyses based on morphology resolved important issues. However, additional genetic markers are needed to uncover sister species relationships.Item Evaluation of dietary feeding stimulants for the sea urchin Lytechinus variegatus(2014-04-08) Bandolon, AdrianSea urchins shape their environment primarily through their feeding behavior. For Lytechinus variegatus this behavior is largely guided by the detection and response to chemical stimulus. The extent of which compounds and how these specific chemicals influence behavior in sea urchins has received only cursory investigation. The purpose of this study is to characterize the role of several amino acids in the feeding behavior of the sea urchin Lytechinus variegatus. Specimens of L. variegatus were collected from Cape San Blas within the Port St. Joseph Peninsula State Park, FL, USA (30 °N, 85.5 °W). Sea urchins were maintained in a semi-recirculating system and fed a standard reference diet (SRD) at ad libitum levels. This diet is used routinely in all sea urchin research at the Shrimp Mariculture Project. To standardize conditions for testing olfactory and gustatory response, a series of experiments were performed to evaluate the effects of water flow rate and hunger on the chemical response of L. variegatus. To characterize the effects of flow rate, feed consumption rate and travel speed was measured while the sea urchins were subjected to different current velocities. Lytechinus variegatus was subjected to different lengths of food deprivation to assess the effects of hunger on their feeding behavior. Finally, olfactory and gustatory response was evaluated by exposing L. variegatus to one of eight concentrations of six individual amino acids (L-alanine, L-arginine, DL-glutamate, glycine, L-leucine and L-tyrosine). Results from these studies suggest that Lytechinus variegatus is positively rheotactic and under the conditions of the study, increases feed consumption rate with increased flow rate. Also, during periods of prolonged food limitation, L. variegatus decreases physical activity but consumes larger amounts of food when it becomes available. Lytechinus variegatus also employ food-sourced amino acids to identify food sources and evaluate food palatability. These findings help expose components of scantily studied mechanisms that drive sea urchin navigation, foraging, distribution, food choice and interactions. These findings could also impact sea urchin aquaculture, affecting both feed formulation and sea urchin husbandry techniques.Item Increasing resilience of urban development on Texas barrier islands(2014-04-18) Taylor, Eleonor BarrazaThe purpose of the dissertation was to develop information, at a local scale, that can be incorporated into a spatial planning process to increase the resilience of urban development on Mustang and North Padre Islands, Texas. About 12% of U.S. barrier islands are completely urbanized, and 36% are heavily developed. This development trend is exposing more people, property, and infrastructure to coastal hazards. Therefore, coastal communities must plan for resiliency to remain functional and prosperous after a storm strikes or environmental conditions change. Each chapter presents an element of the spatial planning process, including the following: a geohazards map, an ecosystem services valuation, and a land-use policy analysis. The geohazards map describes the effect of ongoing geologic processes and future evolution of a barrier island as a geomorphic system in response to relative sea-level rise (RSLR). The assessment and monetary valuation of the storm protection provided by beaches and foredunes informs decision-making regarding beach-dune management alternatives and supports their preservation. Land-use policies are analyzed and recommendations made to preserve current and future critical environments and guide future urban growth towards safer and more stable areas. Results of the study show that RSLR could cause 50% of the study area to change by 2072. About 55% of the assessed beach-foredune areas provide overwash protection against at least a 100-year storm. Beaches and foredunes cover 6.9 sq. km; however, they save an estimated $141.4 million/year (2013 USD) in storm protection expenditures. It was found that 26% of the study area can accommodate higher density development, 23% should be left undeveloped or planned for lower density development, and 51% includes public spaces and preservation areas. Current state and federal regulations offer only limited protection to present and future locations of critical environments, with beaches and dunes receiving the most protection compared to bay-margin wetlands. A transfer of development rights program may be a sensible land-use policy for addressing the realities of a dynamic coastal environment and balancing private and public interests. While coastal vulnerability continues to increase, this dissertation provides actionable information and a process to follow for increasing the resilience of human activities on barrier islands.Item INTERACTIONS BETWEEN SUSPENDED SEDIMENTS, NUTRIENTS AND(2014-07-01) 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 Turbidity and wave energy affect community composition and trophic interactions(2014-07-07) 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 Discard mortality, recruitment, and connectivity of red snapper (Lutjanus Campechanus) in the Northern Gulf of Mexico(2014-07-10) 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 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 Patterns of evolution in gobies (Teleostei: Gobiidae): a multi-scale phylogenetic investigation(2014-11-14) 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 Modeling Nutrient Dynamics in Coastal Lagoons(2014-12) Turner, Evan Lee; 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 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.