ItemDynamics of ocean circulation and air-sea interaction in the Southeast Indian Ocean and their impact on Ningaloo Niño(2022-08) Feng, XueExtreme ocean warmings associated with the Ningaloo Niño have had significant impacts on regional climate and the health of the marine ecosystem in the Southeast Indian Ocean. The generation and development of the Ningaloo Niño are caused by a combination of atmospheric forcing and oceanic processes, including air-sea heat fluxes and the heat transport associated with the Leeuwin Current (LC). In addition, the large-scale climate variability in the tropics can also affect the Ningaloo Niño via atmosphere and ocean teleconnections. In this dissertation, the variability of the Southeast Indian Ocean, including the air-sea flux and LC variability, is investigated systematically using observations, reanalysis, and numerical model experiments to advance our understanding of the driving mechanism of the Ningaloo Niño. Firstly, the air-sea heat flux variability during the Ningaloo Niño is analyzed using six major air-sea heat flux datasets. One of the major sources of uncertainties in the latent heat flux climatology is the bulk flux algorithm. Over the life cycle of Ningaloo Niño, the anomalous latent heat flux is dominant in the net surface heat flux variations, and the uncertainties in latent heat flux anomaly largely depend on the phase of the Ningaloo Niño. During the developing and peak phase, the contribution of air-sea heat flux to the surface warming has large uncertainties, which are primarily caused by the differences in the sea surface temperature. However, during the decay phase, large negative latent heat flux anomalies (cooling the ocean) are found in all datasets, indicating the important role of latent heat flux in damping anomalous warming during the recovery phase. Secondly, the sensitivity of model resolution on the climatology and variability of the LC is evaluated in an eddy-permitting and eddy-resolving Ocean General Circulation Model (OGCM). The magnitude and structure of the mean LC are more realistic in the high-resolution (eddy-resolving, 1/12°) OGCM experiment. During the 2010-2011 Ningaloo Niño, the high-resolution experiment simulates a stronger LC, which leads to a warmer ocean temperature off the west coast of Australia. Lastly, the effect of the continental shelf and slope on the LC and Ningaloo Niño are investigated using a series of high-resolution Indo-Pacific OGCM experiments. The “control” experiment uses a realistic bottom topography along the west coast of Australia, whereas the sensitivity (“no-shelf”) experiment uses a modified topography with no continental shelf and slope near the coast. The LC in the no-shelf experiment is located closer to the coast, and the strength is decreased by about 28% compared to the control experiment. During the 2010-2011 Ningaloo Niño, stronger enhancements of the LC are detected in the control experiment, which lead to a 26% increase in the upper 50 m ocean temperature. The analysis of ocean dynamical processes indicates that the shelf-slope topography can effectively trap the positive sea level anomaly at the coast and suppress the Rossby wave radiation from the coast, thereby maintaining a stronger LC. ItemInfluence of Colorado River discharge variability on phytoplankton communities in Matagorda Bay, Texas(2022-06-27) McBride, Molly Rose; Wetz, Michael; Turner, Jeffrey; Hardison, RancePhytoplankton are important primary producers in estuaries and are also indicators of environmental changes, such as freshwater inflow or nutrient loadings. Some phytoplankton are also harmful algal bloom (HAB) species, negatively impacting estuaries with toxin production or by generating hypoxia during bloom termination. Blooms of the HAB Dinophysis sp. have negatively affected the Matagorda Bay (Texas) ecosystem on multiple occasions since 2008. Estuaries of the Texas coast, such as Matagorda Bay, are vulnerable to long-term decreases in freshwater inflow due to increasing human freshwater needs as well as climate change. It is critical to understand how phytoplankton communities, including HABs, respond to freshwater inflow variability to estuaries in order to project how future inflow changes may affect estuaries. Over a 24-month period, a suite of environmental parameters along with phytoplankton community composition and biovolume was measured to determine the influence of freshwater inflow from the Colorado River on these parameters in Matagorda Bay. Spatiotemporal distribution of nutrients, chlorophyll and phytoplankton were influenced by riverine inflow. In particular, all of these factors decreased moving away from the river mouth, indicating a strong influence of the river on their distributions. Dinophysis sp. was observed in January, February and April 2020 during a period of cool temperatures and higher salinities, and its biovolume was positively correlated with nitrate+nitrite and the ratio of silicate to dissolved inorganic nitrogen. Other non-HAB phytoplankton taxa had distinct responses to environmental variability. Future work should consider HAB taxa on an individual basis, as well as consider more frequent sampling and toxin analysis. The unique environment, as well as phytoplankton communities and responses of Matagorda Bay underscore the necessity of investigating changes over time on an individual estuary basis, and for potential blooms, on a species-specific basis. ItemSalt marsh and mangrove regime shifts: The effects of disturbance and mangrove seedling survival and morphology(2022-07-21) Doty, Jacob Kavanaugh; Proffitt, Ed; Devlin, Donna; Armitage, AnnaAnthropomorphic climate change has driven changes in the distribution of tropical species worldwide. Along the Texas Gulf coast, Avicennia germinans has progressed in a poleward expansion leading to a shift in species dominance from salt marsh flora to mangrove forest. Shifts from salt marsh dominance to mangrove dominance can lead to changes in species diversity, sediment chemistry, shoreline stabilization, and many more ecological functions. However, disturbance events (such as low temperature freeze events) can cause a mass mortality of tropical mangroves and drive shifts in dominance back to salt marsh flora. Directly following mass mortality inducing freeze events, population recovery will be largely dependent on the success and growth to reproductive age of black mangrove seedlings. Our study assessed the response of black mangrove young-of-the-year seedlings (green cotyledons attached) to an extreme low temperature disturbance event (Winter Storm Uri, Feb. 2021). We also quantified plant community structure following the mass mortality of black mangrove shrubs and its impacts on the ongoing regime shift along the Texas coast. Freeze disturbance affected shrub and seedling survival. In the Lower Laguna Madre (Boca Chica site) where freeze effects were minimal propagules recruiting any time that fall and winter survived and grew. At higher latitudes (Corpus Christi Bay & Matagorda Bay) where freeze effects were more severe, rooted seedlings died along with most adult shrubs and new colonization appeared to be by seedlings recruiting from propagules likely floating in the water at the time of the freeze. Growth of seedlings recruited prior (southernmost Boca Chica site) and after Uri (CC Bay and Matagorda Bay) were not significantly different. At freeze-disturbed sites 10-53% of new seedlings flowered within 16 months of the freeze event, while 0 % flowered at the non-disturbed southernmost location. As age of first reproduction is an important component of population growth, these results suggest that reproduction of 1 year old seedlings may be an important aspect of mangrove recovery and will contribute to the regime shift, barring additional hard freezes. ItemA novel di-iron ligand complex for water oxidation catalysis and the development of bis-bipyridinium-based gemini surfactants for template-directed self-assembly(2022-07-22) Tran, Ha Hoang; Olson, Mark; Billiot, Fereshteh; Holubowitch, NicolasThis thesis reports the designs and synthetic routes for a variety of organic molecules that served as the starting materials for the construction of supramolecular complexes via non-covalent interactions. The first project involved the development of a rationally designed dinucleating ligand that would form various stable diiron complexes as potential water oxidation catalysts (WOCs). The WOCs can promote the clean production of hydrogen gas, a green and potential fuel to replace traditional carbon-based fuels, by lowering its cost and increasing its efficiency. The second research project focused on synthesizing novel bis-bipyridinium-based gemini amphiphiles that were capable of self-assembling or co-assembling with a template molecule (the neurotransmitter melatonin) to form ?-? donor-acceptor charge-transfer complexes. This research provided fundamental insights into the structure-property relationships between the amphiphiles and their self-assembly processes which are important for developing methodology that uses self-assembly to construct complex stimuli-responsive functional molecular architectures. The target compounds, which include the ligand and gemini amphiphiles were synthesized using a two-step SN2 route. Supramolecular complexes were formed from the combination of two species (1st: the ligand and an iron salt, and 2nd: the amphiphile and the template). The obtained compounds were characterized by various techniques including 1H-NMR, 13C-NMR, 2D-COSY, 2D-HSQC, and TOF-ESI-MS. The synthesis of the ligand was achieved with a yield of 86% for the 1st step and 45% for the second step. The ligand was later used to form diiron complexes which can be great WOCs due to their ability to form high valent intermediates for O-O bond formation. The synthesis of the gemini amphiphiles had a yield of 62% for 1st step and 62 – 79% for the 2nd step. The formation of ?-? donor acceptor charge transfer complexes were verified by UV-Vis, 1H-NMR, 2D-ROESY NMR, and 2D-DOSY NMR. Melatonin demonstrated its ability to serve as “molecular glue” that can minimize the Coulombic repulsion among positive charged tetracationic gemini amphiphiles as they underwent self-assembly. This resulted in 1) the formation of larger aggregates; 2) a more thermodynamically favorable self-assembly process; and 3) an overall increase in the efficiency of the amphiphiles to self-assemble into micellar superstructures at lower concentrations. ItemAssessing embryonic toxicity and end fates of nanoplastics in freshwater environments using gastropod Biomphalaria Glabrata(2022-07-22) Merrill, MacKenzie Leigh; Xu, Wei; Bahr, Keisha; Wagner, Daniel; Mozzachiodi, RiccardoThe wide use of plastics has resulted in not only the accumulation of macroplastic pollution in the aquatic environment but also plastic particles at micro and nano levels (MPs and NPs). Accumulation of these MPs and NPs have numerous adverse effects on the morphology, behavior, and reproduction of living organisms. In this study, we investigated the effects of NPs on the embryonic development of Biomphalaria glabrata, a commonly used gastropod in toxicology studies. This study identified the adsorption of NPs by the embryos of B. glabrata and showed evidence of NP absorption by the hatched juveniles. NP bioaccumulation subsequently triggered the alteration in the expression of several stress response genes, including heat shock protein-70 (HSP70), cytochrome P450 (CYP450), and macrophage migration inhibitory factor (MIF). With the influence of NPs, the hatching rates of B. glabrata embryos varied depending on the sizes of NPs. In addition, the NPs with mean diameters of 1.0 µm or 0.03 µm led to higher embryo mortality rates than 0.5 µm NPs. This preliminary study demonstrated the impact of NPs on the development of B. glabrata embryos. Further studies on the mechanism of NP toxic effects are desired. ItemEffect of freshwater inflow on mollusk community and population dynamics in Texas estuaries(2022-07-18) Rener, Lauren Melissa; Montagna, Paul; Pollack, Jennifer; Hu, XinpingMollusks are an abundant species rich phylum within the animal kingdom. Over 130,00 species have been documented, and the Texas Gulf Coast is home to a large portion of these species. Many of these species reside within Texas Estuaries that experience differing freshwater inflow patterns. Freshwater inflow changes can alter estuarine dynamics such as salinity, nutrients, and some biological communities. Many mollusks species’ survival and growth rely on freshwater inflow for nutrients for reproduction and survival and are thus suitable bioindicators of freshwater inflow effects within estuaries. Existing mollusk and salinity data from 1987 - 2019 were used, and estuaries compared include Lavaca-Colorado, Guadalupe, Mission-Aransas, Nueces, and Baffin Bay-Upper Laguna Madre. Current environmental inflow standards were determined using Rangia cuneata, a brackish water clam found only in Guadalupe Estuary, as a bioindicator. In addition to Rangia cuneata, other dominant species with the highest frequency along all estuaries such as Mulinia lateralis, Nuculana acuta, Mysella planulata, and Macoma mitchelli were examined. were also examined as bioindicators. There were distinct differences in community structure along the salinity gradient on The Texas Coast. Laguna Madre was greatly different compared to other estuarine systems because of being seagrass habitat in comparison to other systems that were bay-bottom mud habitat. Laguna Madre also has the highest salinity leading to a diverse community of mollusks. High inflow systems, such as Guadalupe and Lavaca-Colorado, resulted in high abundance of opportunistic species such as Mulinia lateralis, and in contrast there was a higher mollusk diversity found in estuarine systems with higher salinity. All the dominant species responded to freshwater inflow with reproductive events, that often resulted in a population size decrease after lengths reached ~ 3 mm in size due to predation by bottom feeding species, competition, or inadequate hydrologic conditions such as salinity. Although Rangia cuneata indicates when there is a major inflow event, this species is only found in Guadalupe estuary, and requires a salinity between 5 - 12. Due to the infrequency of these conditions, additional species such as Mulinia lateralis who is an opportunist species that can reproduce and grow in a wide range of salinity conditions, would be a reliable bioindicator of estuarine health. ItemAssessing the influence of genotypic diversity on sulfur dynamics in the seagrass halodule wrightii using stable isotope analysis(2022-07-19) Girard, Allyson; Larkin, Patrick; Adbulla, Hussain; Felix, JosephCoastal development and other mounting anthropogenic pressures are threatening valuable seagrass habitats. The greatest risks posed to seagrasses are the effects of coastal eutrophication, which stimulates primary productivity and ultimately supplies abundant organic matter to marine sediments. The decomposition of this material is initially facilitated by aerobic microorganisms, depleting dissolved oxygen and generating anoxic conditions. Under these conditions, anaerobic microorganisms such as sulfate-reducing bacteria begin to dominate the degradation process, which reduce sulfate (SO42-) to sulfide (H2S) for energy production. The accumulation of H2S in marine sediments is problematic for seagrasses, as this molecule can be highly toxic. Yet, seagrasses can withstand relatively high concentrations of H2S in their environments. Stable isotope analyses have been used to investigate sulfide intrusion in seagrass meadows, as the unique isotopic signature of sediment-derived sulfur can be used to trace the uptake of H2S and its distribution throughout the plant. This technique has allowed the study of factors that may influence sulfide production and intrusion, such as reduced light availability, organic matter enrichment, and high temperatures. However, few studies have examined the biological or biochemical features that enable seagrasses to withstand relatively high sedimentary sulfide levels. One biological feature that may help confer resistance is population genetic diversity, which has been identified as an important trait in the survival and performance of seagrass meadows under environmental stress. In general, genetic diversity is thought to play an important role in population resistance to environmental disturbance, as a wider assortment of functional traits encoded at the molecular level results in a variety of phenotypes likely to possess morphological and physiological differences that are complementary. This genotypic complementarity may extend to biochemical strategies associated with tolerance to, or detoxification of, H2S. The purpose of this study was to determine whether sulfide intrusion differs between genotypes of the seagrass Halodule wrightii, a prominent species in the Gulf of Mexico. Further, as the sulfur isotopic composition of marine sediments and seagrass vegetation is known to exhibit high spatial variability, this study also sought to assess sulfide intrusion between populations from distinct sites along the Texas Gulf Coast. Stable isotope data was used to infer the proportion of sulfur in H. wrightii tissues that was derived from sedimentary sulfide, while total sulfur (TS) data was also considered to understand the extent of sulfur accumulation within the plant. H. wrightii genotypes were determined by screening each sample at a series of microsatellite loci previously identified for this species. Although no difference in sulfide intrusion was observed between genotypes, sulfide uptake and distribution was significantly different between the three study sites. The results offer important insight to the effect of local conditions on sulfide intrusion in seagrass meadows and may guide future investigations concerned with the influence of genotypic diversity on H2S metabolism in seagrasses. ItemAssessing the acute toxicity of photodegraded anthracene with in vitro and in vivo skin models(2022-07-20) Brzezinski, Molly; Xu, Wei; Seemann, Frauke; Conkle, Jeremy; Zhu, LinThe Gulf Coast of Texas is heavily inundated with petroleum refineries that release Polycyclic Aromatic Hydrocarbons (PAHs) into nearby waters, and these chemicals may pose a threat to human health when they interact with environmental conditions. PAHs are a group of hundreds of different chemicals, and the Environmental Protection Agency has identified 16 priority PAHs. Many of these chemicals are acute skin irritants and can cause skin, lung, bladder, and liver cancer with chronic exposure. Humans can be exposed when they interact with contaminated air, soil, and water. Recent studies have demonstrated that abiotic factors such as UV light, salinity, and pH can modify PAH structure, however, it is unknown how these modifications affect acute toxicity to the human skin barrier. The objectives of this study were to characterize the phototoxic effects of a priority PAH, anthracene by testing photodegradation treatments on cell culture and animal models. Gas chromatography and mass-spectroscopy confirmed the presence of 1,9-anthraquinone and phthalic acid, both known skin irritants, in photodegradation products. Keratinocyte cell culture was used to assess the impacts of photodegraded anthracene on cell migration, viability, and stratification development. We found that longer photodegradation times resulted in decreased cell viability and increased migration. A unique three-dimensional stratification assay demonstrated that photodegraded anthracene reduces differentiation in apical keratinocytes. Relative gene expression analysis suggests that keratinocytes bypass TLR-4 activation and utilize IL-1?, IL-1?, and TNF-? to produce an inflammatory response. Mus musculus studies indicate that extracellular matrix remodeling may be induced by 4, 8, and 24-hour photodegraded intermediates by keratinocyte-derived Il-1?, S100a9, Mmp1, and Connexin43. The results of this study indicate that photodegradation can produce intermediates that may elicit dermal inflammation, and the presence of these intermediates should be evaluated in bays with high foot-traffic. ItemLivelihoods in transition across the Gulf of Mexico: A three case study approach(2022-07-07) Lozada, Coral; Yoskowitz, David; McLaughlin, Richard; Maresh-Fuehrer, Michelle; Stunz, GregLivelihood transitions within coastal communities can result from biophysical changes to the environment that people make a living from, or from policies that affect an individual’s or community’s way of life. Using the socio-ecological framework, these transitions, and the adaptions that fishers in coastal communities have employed were analyzed for adaptive co-management potential. The hypothesis is that coastal communities that have policies that allow for adaptive co-management to occur have an increased capacity to positively adapt to a transitioning livelihood. A mixed methods convergent design was created for three case studies, where semi-structured interviews were conducted in select communities, followed by content analysis of relevant fishing policies. The Yucatan Case Study studied small-scale fishers across two coastal towns, Sisal and San Felipe. The Texas Case Study examined the Gulf shrimp fishery fleet in Palacios and Port Isabel/Port Brownsville. The last case study focused on content analysis of Cuban fishing and tourism policies. In each case study themes emerged from inductive coding of interviews that created typologies that were then paired with the findings of the content analysis, or policies from each case study. The convergence and divergence analysis were then used to produce adaptive co-management recommendations within the communities. This approach allowed a deeper synthesis and thus an understanding of the dissonance that exists when livelihood change occurs. ItemImproving assessments of water resources characterization and relationships to climate variabilities(2022-07-07) Gyawali, Bimal; Murgulet, Dorina; Ahmed, Mohamed; Liu, Chuntao; Tissot, PhilippeWith the increasing vulnerability of water resources due to climate change and the associated more frequent and intensive extreme events, there is a growing need to monitor the spatial and temporal variability in water resources. Coastal aquifers are a major source of freshwater for almost 40% of the world’s population living in coastal regions. Changes in groundwater level impact groundwater discharge to surface waters, which in turn affects the amount of streamflow resulting in variability in freshwater inflow to estuaries. However, lack of continuous spatial and temporal coverage of groundwater elevation data hinders direct measurements of groundwater storage (GWS). The first objective of this dissertation is to quantify the spatial and temporal variation in coastal GWS using uninterrupted monthly Gravity Recovery and Climate Experiment (GRACE) derived terrestrial water storage (TWSGRACE) utilizing the Texas Gulf Coast Aquifer as a benchmark. To accomplish this, the data gap in TWSGRACE was filled with reconstructed values from multi-linear regression (MLR) and artificial neural network (ANN) models. The reconstructed TWSGRACE was integrated with land surface model products and ground-based measurements to examine the long- and short-term trends in GWS in response to changing climate conditions. This study found a significant decline (0.35 ± 0.078 km3·yr?1, p-value: < 0.01) in GWS during the study period 2002-2019 and was able to capture extreme climate events (i.e., drought and flood). The second objective provides an innovative approach to deriving a continuous TWSGRACE record for improved evaluation of GWS at a global scale. The approach integrates three machine learning techniques (deep-learning neural networks [DNN], generalized linear model [GLM], and gradient boosting machine [GBM]) and eight climatic and hydrological input variables to fill GRACE record gaps and reconstruct the TWSGRACE data record at both global grid and basin scales. This study’s models’ performances were found to be superior to those from 61% of previous similar studies and comparable to 21%. The reconstructed TWSGRACE data captured the occurrences of extreme hydro-climatic events over the investigated basins and grid cells. In addition, the third objective evaluates the impact of individual and coupled ocean-atmospheric phenomena (El Niño Southern Oscillation [ENSO], Pacific Decadal Oscillation [PDO], and Atlantic multidecadal oscillation [AMO]) on hydrological variables (i.e., precipitation, streamflow, and freshwater inflow) across several major estuaries located along the northwestern Gulf of Mexico (nGOM), which span a significant climatic gradient. Results show that the individual and coupled climate variability phenomena have a significant impact on all three hydrological variables and the magnitude of impact varies seasonally and spatially, with the strongest modulation on cold seasons and in the wet region (of Texas). The severity of droughts increases significantly when the La Niña phase of ENSO is coupled with the PDO/AMO cold/warm. This dissertation 1) offers a reliable approach to examine the long- and short-term trends in GWS, 2) provides a robust and effective approach to fill the data gaps in TWSGRACE that can serve as a reference tool to fill the data gaps in any hydrological system across the globe, and 3) improves the understanding of the relationship between estuarine hydrology and climate variability. The results from these studies serve as valuable tools for water management strategies and benefit water resources planning and disaster management in coastal areas. ItemThe role of artificial reefs and natural banks in the distribution and abundance of economically important fishes(2022-07-09) Martin, Kelsey; Stunz, Gregory; Campbell, Matthew; Curtis, Judson; Pollack, Jennifer; Wells, R. J. DavidIn the northern Gulf of Mexico, artificial reefs have become an important resource enhancement tool. These structures, along with natural banks, act as fish aggregation sites on a relatively barren continental shelf region that contains little to no vertical structure for fishes to seek refuge. Generally, a lack of fishery-independent studies comparing artificial reefs to their natural counterparts has led to uncertainty surrounding the role of artificial reefs. Furthermore, with increasing legislative regulations on the types of materials permitted for artificial reefs, it is important to examine which materials provide the most benefit. Thus, the goal of this dissertation was to present stakeholders and managers with the tools to understand how artificial reef design, placement, and proximity to other reefs, which are difficult to ascertain, affect population dynamics to guide future reefing projects. In Chapter 2, I used a combination of remotely operated vehicle and hydroacoustic surveys to characterize fish communities at artificial reefs and natural banks and provide absolute abundance estimates of four economically important fish species: Red Snapper, Greater Amberjack, Gray Triggerfish, and Vermilion Snapper. My results show high abundance of reef fish, particularly Red Snapper, Vermilion Snapper, and Greater Amberjack. Additionally, age 2+ Greater Amberjack extrapolated estimates were 221% of the most recent stock assessment for this species and identify a need for reevaluation of the habitat use and abundance estimates for this species. In Chapter 3, I conducted surveys using stereo-remote underwater video surveys to address the effect of prefabricated pyramid reefing location and orientation on fish community structure. Although reefing location nor orientation had a significant effect on species richness, diversity, and evenness, I identified differing communities between both variables (reefing location and orientation) with Red Snapper, Greater Amberjack and Gray Triggerfish among the main contributing species to these differences. Fish measurements identified primarily juvenile individuals which emphasizes the importance of lower relief reefs as habitat for younger cohorts. Absolute abundance estimates were derived from combining the video surveys and hydroacoustic surveys and were used to calculate two types of cost-benefit ratios based on overall fish density and the densities of economically important species such as Red Snapper, Greater Amberjack, Gray Triggerfish, Vermilion Snapper, and Almaco Jack. Port O’Connor nearshore reef was considered the least cost-effective reefing location in terms of overall fish density, but not for economically important species density. Port O’Connor was configured with science in mind and produced the most consistent results compared to the other reefing locations, which highlights the importance of developing a reef with science in mind to evaluate reef benefits more competently. In Chapter 4, I used the same methods from Chapter 2 to address the effect of artificial reefing material (prefabricated pyramids and railroad ties) on fish community structure and cost-benefit. Species richness was found to increase with increasing tonnage of railroad ties and is likely due to differences in structural complexity. In contrast, evaluation of the two different types of cost-benefit ratios identified a massive 4000-ton railroad tie pile as the least cost-effective in terms of overall fish density and economically important species density. As a result, I do not recommend considerably large piles of reefing material if the goal of the reef is to provide habitat for economically important species, but rather to spread this material in smaller and widely dispersed groupings. Importantly, this study identifies the need for specifying clear objectives when designing artificial reefs to maximize efficiency. In Chapter 5, I developed an individual-based model to evaluate Red Snapper, Greater Amberjack, and four competing species, population responses to changing artificial reefs in more complex, but realistic, habitat scenarios like those observed on the Texas continental shelf. My results identify the importance of artificial reefs in the growth and overall biomass of Red Snapper and Greater Amberjack, particularly in areas, like the Gulf of Mexico, where structured habitats are limited. This model also validated age- or size-based transitions in habitat for Red Snapper that have been observed in other studies, suggesting a transition from habitat-centric to forage-centric movement for this species. This model presents resource managers and stakeholders with a tool to guide future reefing projects to discern the impact of placement and density of artificial reefs on population dynamics of economically important fish species. Collectively, my findings suggest that artificial reefs in the western Gulf of Mexico play an important role in shaping fish communities and in the population dynamics of economically important species. Furthermore, I developed a unique approach to quantifying the efficacy of artificial reefs and revealed two types of reefs that were significantly less cost-effective than the others explored in this study. Future artificial reefing projects should avoid large, highly dense reefs and should consider proximity to other artificial or natural habitats. I also present a tool for resource managers and stakeholders to guide future reefing projects to discern the impact of differing artificial reef designs on populations of economically important species. This dissertation improves the scientific understanding of the role of natural and artificial habitat in fish communities and provides fisheries managers with key abundance estimates needed for stock assessment models for several economically important species on the Texas coast. ItemDistribution of pesticides in groundwater and surface water flood-impacted unconnected communities in South Texas following Hurricane Hanna(2022-08) Matarrita Rodríguez, Jessie; Abdulla, Hussain; Conkle, Jeremy L.; Murgulet, DorinaPesticides are a vital farming input as they help protect crops from pests and diseases for quality yields and high productivity. However, pesticides' high production, extensive use, and persistence are a potential risk for human health and ecosystems due to their leaching or runoff into the surface water (SW) and groundwater (GW). Over the years, there has been an increasing concern regarding the water quality of SW and GW next to farming areas, specifically after spills or industrial discharges, heavy rainfall, and intense storms. In the case of hurricanes, these cause deposition of contaminants from the atmosphere, disturbance and transport of the sediments in surface water bodies, surface run-off, and penetration of floodwaters to GW. In addition, pesticide degradation in the environment due to different biotic and abiotic transformation processes produces transformation products (TPs), sometimes even more toxic than the original compound. In July 2020, Hurricane Hanna severely damaged infrastructure and agriculture in many counties across the Rio Grande Valley. This area has the largest colonias in South Texas, predominantly Hispanic low-income semirural communities near the Texas-Mexico border that mainly rely on GW as a drinking water source. As part of this study, surface water and groundwater samples were collected from colonias in South Texas communities after hurricane Hanna for one year. The analytical approach involved solid-phase extraction (SPE) followed by suspect and target screening of pesticides using ultrahigh-pressure liquid chromatography (UPLC) coupled to a high-resolution Orbitrap Fusion Tribrid mass spectrometer system (OT-FTMS). The advantages of the state-of-the-art high resolution mass spectrometry allowed the accurate identification and quantification of pesticides using an in-house compound database of 308 pesticides for target screening. This is one of the most extensive studies that has screened and quantified over 200 pesticides in a single sample in the United States and, to my knowledge, is one of the largest in Texas. The results of eight monitoring sampling campaigns revealed the occurrence of 21 pesticides with minimum instrumental limit of detection (LOD) of 0.05 ng/mL and limit of quantification (LOQ) of 0.10 ng/mL. Six herbicides were the most detected compounds, followed by insecticides (5), fungicides (4), TPs (3), and a plant growth regulator (1). The most frequently detected compounds were atrazine, clothianidin, cycluron, DEA, dinotefuran, and norflurazon and those with the highest concentrations were clothianidin (211 ng/L), DEET (13,885 ng/L), and norflurazon (952 ng/L). In general, more compounds were detected in GW than in SW, except for atrazine and DEA. Atrazine in SW showed higher detections frequency (67%) than GW (15%) as well as DEA (GW = 6%, SW = 8%). DEET was the compound detected at the highest frequency in GW (74%) while atrazine was detected at the highest frequency in SW (67%). The leaching of pesticides to GW is a complex process and depends on the pesticide's chemical properties, characteristics of the soil, volatilization, climatic conditions of the site, plant uptake, and pesticide management practices. Mainly, pesticides with high leaching potential are more likely to be transported in groundwater beyond application area. In this study, clothianidin and norflurazon with high leaching potential showed significant concentrations in GW. This is one of the few studies able to survey more than 200 pesticides in the United States in general and in Texas specifically, using high resolution mass spectrometry. This work provides a baseline of the water quality for those communities that rely on GW as the primary source of drinking water supply. The occurrence of pesticides in GW demonstrates the vulnerability of the area and the need to continue monitoring the water quality in this region. ItemSpatial-Temporal variability in phytoplankton biomass and community composition in Texas residential canals(2022-08) Cutajar, Jordana; Wetz, Michael; Morton, Steve; Turner, Jeffrey W.Harmful algal blooms (HABs) are a natural phenomenon that appear to be increasing worldwide alongside the spread of urbanization and cultural eutrophication. As urbanization increases, many regions around the globe, including Texas, are seeing a significant increase in the number of residential canal systems along their coastlines. These canals pose unique attributes that may enhance conditions for HABs, namely shallow depths, high susceptibility to urban runoff, reduced mixing, and long residence times. Despite this, there has been little research on the water quality and phytoplankton composition of these systems. In this study, water quality and phytoplankton biomass/composition were analyzed in three sites along a mouth-interior gradient of a canal system on Padre Island (Corpus Christi, Texas). It was hypothesized that sites toward the interior of the canal system would experience increased nutrient availability, stratification, phytoplankton biomass/HAB occurrence, and reduced flow. The site at the mouth of the canal system exhibited lower nutrient concentrations and was less susceptible to temporal changes like storm events and stratification than the interior canal sites. Total biovolume did not vary among the three sites; however, phytoplankton composition did. The mouth site was diatom dominant, whereas the interior canals had higher picoplankton biovolumes. Ultimately, this research will (1) assess the water quality along the gradient of the canal system and (2) determine baseline conditions for future monitoring to evaluate shifts in phytoplankton composition and water quality. ItemMultiple linear regression models for the estimation of PH and Aragonite saturation state in the Northwestern Gulf of Mexico(2022-08) Jundt, EvaLynn; Hu, Xinping; Liu, C.; Jin, LeiThe ocean plays a vital role in making up 70% of the Earth’s surface, producing over half of oxygen globally, and absorbing approximately 30% of anthropogenic CO2 since the industrial revolution. Ocean acidification (OA) is a direct threat to many organisms living in the oceans across the globe, yet the state of carbonate chemistry and the rate of OA vary in different parts of the world’s oceans. Although current data suggest that the open Gulf of Mexico (GOM) surface waters have relatively high pH (> 8) and aragonite saturation state (ΩArag > 3), the GOM could still experience ecological impacts of OA. In addition, the combination of increasing atmospheric CO2, upwelling, and increasing terrestrial nutrient export may acidify the coastal waters even further. Acidifying ocean waters have decreasing ΩArag, posing serious threats to calcifying organisms, affecting their populations, growth patterns, and shell or skeletal density. The GOM is home to the northernmost tropical coral reefs around the contiguous United States as well as prominent shellfish industry. Historical water column carbonate measurements are scarce, so the progression of OA in the GOM is poorly understood. Research regarding OA in the GOM is needed to manage and protect these resources. In the literature, multiple linear regression (MLR) models have been created to fill data gaps in different ocean regions such as the Gulf of Alaska, the Southern Ocean, the Sea of Japan, and coasts of the northeastern and northwestern United States. Prior to this study, no statistical model existed for carbonate chemistry parameters (i.e., pH and ΩArag) in the GOM. By creating models built upon the relationships between commonly measured hydrographic properties (salinity, temperature, pressure, and dissolved oxygen (DO)) and pH as well as ΩArag, data gaps can be filled in areas that do not have sufficient sampling coverage. In this study, I created statistical models for the estimation of ΩArag and pH in the northwestern GOM (NWGOM) from latitudes 27.1-29.0˚N and longitudes 91.5-95.0˚W. The calibration data used in the models include depth, salinity, temperature, pressure, and DO collected from four cruises that took place in July 2007, July 2017, and April and August of 2021. The models predict ΩArag with R2≥0.98, RMSE ≤ 0.14 and pH with R2 ≥ 0.93, RMSE ≤ 0.02 for four different subsets of the data depending on depth (with and without removal of upper 20 m) and geographic location (with and without removal of stations to the east). The data used to create the models are also used to create contour plots that show variation of ΩArag and pH over the timeframe of the study from 2007 to 2021. Relatively low ΩArag (ΩArag ≤ 2) values are present in the depths ≥ 180 m. The depth range of the water column between ΩArag = 2-1.5 decreased over this period. The depths for ΩArag = 2 and ΩArag = 1.1 vary ±20 and ±50 m respectively, while the depth for ΩArag = 1.5 decreased 50 m from 2007 to 2021. Depth profiles for pH revealed consistent patterns over all four cruises with highest values over the shelf and upper 125 m, and minimum values around 500 m. The pH = 7.9 isopleth remained around 265 m for all cruises, while the pH = 8 isopleth showed fluctuation of ±10 m (from 2007 to 2021). On the shelf, the maximum and minimum pH values were 0.0356 and 0.0133 units lower in 2021 than in 2007, respectively. This resulted in the range of pH values experienced narrowing by 0.0223 and transitioning to lower pH values overall. These MLR models are valuable tools for reconstructing ΩArag and pH data where direct chemical observations are absent but hydrographic information is available. These models can be applied to the NWGOM within ±10 years of 2014, although observations of potential shifts in circulation, water mass composition, and anthropogenic CO2 should be monitored to improve or revise these models in the future. ItemThe role of artificial reefs and natural banks in the distribution and abundance of economically important fishes(2022-08) Martin, Kelsey; Stunz, Gregory W.; Campbell, Matthew; Curtis, Judson M.; Pollack, Jennifer Beseres; Wells, R. J. David; Jin, LeiIn the northern Gulf of Mexico, artificial reefs have become an important resource enhancement tool. These structures, along with natural banks, act as fish aggregation sites on a relatively barren continental shelf region that contains little to no vertical structure for fishes to seek refuge. Generally, a lack of fishery-independent studies comparing artificial reefs to their natural counterparts has led to uncertainty surrounding the role of artificial reefs. Furthermore, with increasing legislative regulations on the types of materials permitted for artificial reefs, it is important to examine which materials provide the most benefit. Thus, the goal of this dissertation was to present stakeholders and managers with the tools to understand how artificial reef design, placement, and proximity to other reefs, which are difficult to ascertain, affect population dynamics to guide future reefing projects. In Chapter 2, I used a combination of remotely operated vehicle and hydroacoustic surveys to characterize fish communities at artificial reefs and natural banks and provide absolute abundance estimates of four economically important fish species: Red Snapper, Greater Amberjack, Gray Triggerfish, and Vermilion Snapper. My results show high abundance of reef fish, particularly Red Snapper, Vermilion Snapper, and Greater Amberjack. Additionally, age 2+ Greater Amberjack extrapolated estimates were 221% of the most recent stock assessment for this species and identify a need for reevaluation of the habitat use and abundance estimates for this species. In Chapter 3, I conducted surveys using stereo-remote underwater video surveys to address the effect of prefabricated pyramid reefing location and orientation on fish community structure. Although reefing location nor orientation had a significant effect on species richness, diversity, and evenness, I identified differing communities between both variables (reefing location and orientation) with Red Snapper, Greater Amberjack and Gray Triggerfish among the main contributing species to these differences. Fish measurements identified primarily juvenile individuals which emphasizes the importance of lower relief reefs as habitat for younger cohorts. Absolute abundance estimates were derived from combining the video surveys and hydroacoustic surveys and were used to calculate two types of cost-benefit ratios based on overall fish density and the densities of economically important species such as Red Snapper, Greater Amberjack, Gray Triggerfish, Vermilion Snapper, and Almaco Jack. Port O’Connor nearshore reef was considered the least cost-effective reefing location in terms of overall fish density, but not for economically important species density. Port O’Connor was configured with science in mind and produced the most consistent results compared to the other reefing locations, which highlights the importance of developing a reef with science in mind to evaluate reef benefits more competently. In Chapter 4, I used the same methods from Chapter 2 to address the effect of artificial reefing material (prefabricated pyramids and railroad ties) on fish community structure and cost benefit. Species richness was found to increase with increasing tonnage of railroad ties and is likely due to differences in structural complexity. In contrast, evaluation of the two different types of cost-benefit ratios identified a massive 4000-ton railroad tie pile as the least cost effective in terms of overall fish density and economically important species density. As a result, I do not recommend considerably large piles of reefing material if the goal of the reef is to provide habitat for economically important species, but rather to spread this material in smaller and widely dispersed groupings. Importantly, this study identifies the need for specifying clear objectives when designing artificial reefs to maximize efficiency. In Chapter 5, I developed an individual-based model to evaluate Red Snapper, Greater Amberjack, and four competing species, population responses to changing artificial reefs in more complex, but realistic, habitat scenarios like those observed on the Texas continental shelf. My results identify the importance of artificial reefs in the growth and overall biomass of Red Snapper and Greater Amberjack, particularly in areas, like the Gulf of Mexico, where structured habitats are limited. This model also validated age- or size-based transitions in habitat for Red Snapper that have been observed in other studies, suggesting a transition from habitat-centric to forage-centric movement for this species. This model presents resource managers and stakeholders with a tool to guide future reefing projects to discern the impact of placement and density of artificial reefs on population dynamics of economically important fish species. Collectively, my findings suggest that artificial reefs in the western Gulf of Mexico play an important role in shaping fish communities and in the population dynamics of economically important species. Furthermore, I developed a unique approach to quantifying the efficacy of artificial reefs and revealed two types of reefs that were significantly less cost-effective than the others explored in this study. Future artificial reefing projects should avoid large, highly dense reefs and should consider proximity to other artificial or natural habitats. I also present a tool for resource managers and stakeholders to guide future reefing projects to discern the impact of differing artificial reef designs on populations of economically important species. This dissertation improves the scientific understanding of the role of natural and artificial habitat in fish communities and provides fisheries managers with key abundance estimates needed for stock assessment models for several economically important species on the Texas coast. ItemPlanetary boundary layer profiling with spaceborne GNSS radio occultation and advances in radio occultation from aerial platforms(2022-08) Nelson, Kevin; Xie, Feiqin; Liu, Chuntao; Shinoda, Toshiaki; Tissot, Philippe; Zawislak, Jonathan; Tintera, GeorgeThe Global Navigation Satellite System (GNSS) radio occultation (RO) is an effective tool for Earth atmosphere measurements that provide spatially quasi-random, temporally constant sampling of atmospheric thermodynamic profiles. The RO technique precisely measures GNSS signal bending and refraction when passing through stratified layers of the atmosphere, which can be related to vertical profiles of atmospheric pressure, temperature, and moisture content. The thermodynamic vertical structure of the atmosphere can easily be observed using GNSS RO from stratosphere down to the planetary boundary layer (PBL). The most widely used GNSS RO datasets are the Constellation Observing System for Meteorology, Ionosphere, and Climate (COSMIC-1) and COSMIC-2. The PBL height (PBLH), a key parameter in weather and climate system, is affected by numerous physical processes within the boundary layer. Specifically, the PBLH over land exhibits large spatial and temporal variation across different geographical regions. However, regular observations of the PBL and PBLH are typically limited to sparse radiosonde profiles and low-resolution infrared/microwave sounders. The Atmospheric Radiation Measurement (ARM) Southern Great Plains (SGP) research site provides a unique terrestrial location with 6-hourly radiosondes to examine the terrestrial PBL. COSMIC-1 RO can observe diurnal and seasonal variations in the terrestrial PBLH over the SGP region. Annual mean diurnal amplitude of approximately 250 m in the terrestrial PBLH was observed by COMSIC-1, with maxima occurring at around 15:00 local solar time, which is consistent with the colocated radiosonde profiles. Seasonal changes in the PBLH diurnal cycles ranging from approximately 100 m to 400 m were also observed. While the investigation of the terrestrial PBL and the PBLH using GNSS RO is difficult because of topography, GNSS RO observations in tropical cyclones (TCs) are less understood. GNSS RO profiles have not been adequately compared against in-situ observations (dropsondes), and therefore, the quality of RO profiles from both GNSS RO is not well documented, despite studies using GNSS RO for analyses in the TC environment. Clear vertical gradients in dropsonde water vapor pressure, absolute temperature, and refractivity are present in the lowest regions of theTC troposphere that indicate existence of thermodynamic boundary layers in TCs. Overall median refractivity difference between GNSS RO (COSMIC-1 and COSMIC-2) and colocated dropsondes is less than 0.1% with median absolute deviation (MAD) of 0.2%. Near-surface (2 km and below) overall negative refractivity biases of -1.60% (MAD: 0.44%) for COSMIC-1 and -1.24% (MAD: 0.27%) for COSMIC-2 are detected, which are mostly unaffected by colocation criteria. GNSS RO fractional refractivity difference also shows negative correlation with moisture content below 1.5 km and implies that water vapor pressure impacts the magnitude of N-bias in the lowest 1.5 km of TCs. Tropical cyclone boundary layer heights (TCBLHs) are also derived from GNSS RO, dropsonde, and model reanalysis profiles with the simple gradient method. TCBLH derived from refractivity matches the TCBLH derived from water vapor pressure in dropsondes, indicating consistency between the variables used to retrieve the TCBLH. However, the gradient method for determining TCBLH works best in the presence of strong vertical gradients in water vapor pressure but requires additional refinement for complicated multi-gradient-layer environments near TCs. Traditional spaceborne RO receiver satellites are custom-built and are expensive to launch but can provide high-vertical resolution global sampling. Airborne RO (ARO) platforms, on the other hand, can provide high-frequency local sampling of ROs around weather events with comparable data quality. Balloon-borne RO (BRO) has not been thoroughly explored but has the potential to minimize costs by using commercially available off-the-shelf (COTS) components and by removing fuel costs and the need for custom components. Additionally, a controlled balloon platform can potentially remain aloft much longer (e.g., weeks), resulting in thousands of ROs. Atmospheric refractivity retrievals from BRO payloads developed by Night Crew Labs, LLC (NCL) obtained during two flight campaigns (World View and ZPM-1) are presented. Modifications to traditional spaceborne retrieval methods for in-atmosphere receivers are also discussed, including the derivation of the partial bending angle designed to emulate retrieved bending angle from spaceborne platforms. COTS payloads show promise for high-quality refractivity profiles in the troposphere from both geometric optics (GO) and full spectrum inversion (FSI) retrieval methods. World View results show near-zero overall median refractivity retrieval difference compared to colocated ERA5 reanalysis refractivity profiles (MAD: 2.28%). ZPM-1 median refractivity difference is positively biased (~2.5%, MAD: 2.61%) due to multiple reasons, such as decreased platform control resulting from power failures during flight. We conclude that COTS RO payloads on balloon platforms are worth further investigation for use to obtain large quantities of RO profiles due to their comparatively low-cost and the extended flight times. Additionally, balloon RO platforms with advanced RO receivers have the potential to observe the lower troposphere including the planetary boundary layer (PBL) phenomena with high-density observations. ItemMolecular ecology and evolution of elasmobranch reproductive strategies(2022-08) Swift, Dominic; Portnoy, David S.; Grubbs, R. Dean; Bird, Christopher E.; Hogan, J. Derek; Szczerbinska, BarbaraElasmobranchs are a diverse group of cartilaginous fishes consisting of sharks and batoids that exhibit a variety of reproductive strategies. Elasmobranch reproductive biology has been studied in the wild for many decades but molecular techniques have been used more recently to broaden understanding. Though polyandry has been demonstrated to be widespread, the benefits to females are unclear. Similarly, multiple species have been shown to re-use nurseries – which may increase juvenile survival – yet the impacts of this behavior on population structure require further study. Molecular studies using high-throughput sequencing can help to address knowledge gaps; however, the application of these techniques to study elasmobranchs is limited. Therefore, this dissertation examined elasmobranch reproductive strategies using high throughput approaches. The first chapter reviewed research on elasmobranch reproductive strategies and outlined how high-throughput data can help to address knowledge gaps. For the three other chapters, the blacktip shark (Carcharhinus limbatus) was studied to advance understanding of mate choice and nursery use and inform management. Chapter two assessed for MHC-associated mate choice. Evidence of assortative choice for mhc1a was observed in four of six litters but further study is needed to validate this observation. Chapter three examined the influence of philopatry on the genetic population structure of blacktip sharks using young-of-the-year sampled in United States waters. Regional philopatry by males and females has contributed to the formation of three genetically distinct units that closely align with fishing stocks. Furthermore, philopatry by females to environmentally heterogenous estuaries where offspring are born appears to have resulted in fine-scale adaptive structure within management units. Chapter four assessed the genetic stock structure and movement of blacktip sharks sampled across the western North Atlantic Ocean to evaluate the potential for multinational fisheries management. The blacktip shark stock in the western Gulf of Mexico might straddle U.S. and Mexican waters, and stocks in Cuba and The Bahamas are much more genetically diverged compared with other stocks. Moreover, five blacktip sharks were determined to have moved across stock boundaries, but the majority of individuals were sampled in the region of their natal stock. The research provides novel insights into elasmobranch reproductive strategies and is a basis for additional studies of mate choice and nursery use. There is preliminary evidence that MHC is involved in mate choice by blacktip sharks; however, additional research is necessary to examine the benefits and mechanisms associated with MHC-mediated choice. Further, there is evidence that female natal philopatry facilitates local adaptation to nursery conditions, but more research is required to provide direct evidence of this behavior and determine the distribution of putatively adaptive loci across the genome. Future studies should examine how mating systems and patterns of habitat use can generate, maintain, and disperse adaptive variation because this is vital for resilience to environmental change. Understanding disparities in abundance and dispersal potential between continental and insular populations would be particularly informative for management. ItemThe relationship between macrofauna diversity, functional diversity, and secondary production(2022-08) Trevino, Karin; Montagna, Paul A.; Murgulet, Dorina; Proffitt, C. EdwardThe relationship between functional diversity and secondary production are known to influence ecosystem stability and can be used to measure the functioning of an ecosystem. Functional diversity is a component of biodiversity that classifies organisms by what they do (i.e., functional types) in a community or ecosystem, or more specifically by how certain traits effect the functioning of the environment. Secondary production occurs when biomass is generated by heterotrophic organisms when they consume organic material or primary producers. The research objective is to determine the relationship between secondary production and the connection between functional diversity and species diversity in estuary systems. The goal is to test the hypothesis that there is a positive relationship between functional diversity and secondary benthic productivity among bays within four mid-coastal Texas estuaries: Nueces Estuary, Laguna Madre Estuary, Guadalupe Estuary, and Lavaca-Colorado Estuary. Freshwater inflow differences among these estuaries can affect biodiversity, productivity, and habitat. Thus, changes of freshwater inflow could lead to variability in functional diversity and secondary productivity. Functional diversity was calculated based on seven classifiers: feeding strategy, habitat, mobility, lifespan, reproduction, sediment depth, and body size. There was a positive correlation between benthic production and diversity for species richness, species diversity, and species evenness and secondary production. Most functional diversity indices did not show any significance; however, functional dispersion was shown to explain >77% of variation for secondary production. Apart from functional originality, there did not appear to be a significant relationship between indicators of freshwater inflow influence (i.e., increase in nutrients and decrease in salinity) and the diversity metrics. In general, the response in primary and secondary bays is different, except for the lower part of San Antonio Bay. Overall, classical measures of macrofauna species diversity have a strong relationship with secondary production, while functional diversity does not appear to have any relationship. Thus, for Texas estuaries, it appears that functional diversity metrics do not explain or drive benthic ecosystem processes. ItemTimescales and magnitude of water quality changes in three Texas estuaries induced by the passage of Hurricane Harvey(2022-05) Walker, Lily; Wetz, Michael; Bricker, Suzanne; Hu, Xinping; Sterba-Boatwright, BlairTropical cyclones represent a substantial disturbance to water quality in coastal ecosystems via storm surge, winds, and flooding. However, evidence to date suggests that the impacts of tropical cyclones on water quality are generally short-lived (days-months) and that the magnitude of the disturbance is related to proximity to storm track. Discrete and continuous water samples were collected in three Texas estuaries (the Lavaca-Colorado, the Guadalupe, and the Nueces-Corpus) on the Gulf of Mexico coast before and after Hurricane Harvey made landfall in 2017. Of the three estuaries, the Guadalupe Estuary and its watershed received the highest rainfall totals and wind speeds. An ephemeral increase in salinity was observed (mean of 9.8 on 24 August 2017 to a peak of 32.1 on 26 August 2017) due to storm surge and was followed by a rapid decrease to < 1 as floodwaters reached the estuary. Salinity returned to pre-storm levels within one month. During the low salinity period, bottom water hypoxia developed and lasted for nine days. In all three estuaries, there was an increase in inorganic nutrients post-Harvey, but the nutrients largely returned to pre-storm baseline levels by winter. The lack of long-term water quality impacts from Harvey despite its severity corroborates previous findings that estuarine water quality tends to return to baseline conditions within days to a few months after storm passage. ItemRegression analysis of UAV collected cotton crop data for yield prediction(2022-05) Lopez, Bianca; Sadovski, Alexey; Zimmer, Beate; Davis, NothaboPrediction of cotton yield can enable farmers to make more beneficial planning, budgeting, and intervention decisions. The objective of this thesis was to assess the performance of principal component regression (PCR), partial least squares regression (PLSR), Ridge regression, and least absolute shrinkage and selection operator (LASSO) regression for predicting cotton yield. During the 2016 growing season, excess greenness index (ExG), normalized difference vegetation index (NDVI), canopy height (CH), and canopy volume (CV) were calculated weekly from UAS (unmanned aerial systems) collected RGB (red, green, blue) and multispectral images of an experimental cotton field located at the Texas A&M AgriLife Research Center in Corpus Christi, Texas, USA ( 27◦ 46’ 57.08” N, 97◦ 33’ 40.94” W). Irrigation was taken as a categorical variable, with the field split into two approximately equal sections of dry and irrigated plots. Data were split into 80 percent training data and 20 percent testing data for all models and a 10-fold cross validation was performed to find the optimal number of principal components for the PCR, latent variables for PLSR, and the hyperparameters of the LASSO and Ridge regressions. All models were trained with the weekly time series variables ExG, NDVI, CH, and CV and the categorical variable irrigation. Each model was also trained with the same time series variables up to 67 days after planting and irrigation. The set of models trained on the entire season resulted in the following test set mean squared error values and R-squared scores, respectively; PCR with ∼2.83 and ∼0.48, PLSR with ∼1.00 and ∼0.80, LASSO regression with ∼0.94 and ∼0.81, and Ridge regression with ∼1.32 and ∼0.73. The models trained on the first 67 days subset obtained the following mean squared error values and R-squared scores, respectively; PCR with ∼2.88 and ∼0.47, PLSR with ∼1.54 and ∼0.70, LASSO regression with ∼1.60 and ∼0.67, and Ridge regression with ∼1.61 and ∼0.67. LASSO regression fit best out of the four regressions used to model the entire season’s data with the highest R-squared value and lowest MSE score. This model could be useful for decision-making in preparation for future growing seasons. The PLSR model trained on the first 67 days after planting subset resulted in the lowest MSE and the highest R-squared of ∼0.70. Decisions for intervention could be made with reasonable accuracy at 67 days after planting based on the PLSR model.