The Northern Gulf of Mexico and coastal Louisiana are experiencing accelerated relative sea level rise rates; therefore, the region is ideal for modeling the global affects of sea level rise (SLR) on estuarine dynamics in a transgressive barrier island setting. The field methods and numerical modeling in this study show that as barrier islands are converted to inner shoals, tidal exchange increases between the estuary and coastal ocean. If marshes are unable to accrete at a pace comparable to SLR, wetlands will deteriorate and the tidal exchange and tidal prism will further increase. Secondary to hurricanes, winter storms are a primary driver in coastal morphology in this region, and this study shows that wind direction and magnitude, as well as atmospheric pressure change greatly affect estuarine exchange. Significant wetland loss and winter storm events produce changes in local and regional circulation patterns, thereby affecting the hydrodynamic exchange and resulting transport.

Evolution occurs and can be conceptualized along a spectrum, bounded on one extreme by the relationships between deep lineages – such as phyla, classes, and orders – and on the other by the molecular dynamics of operational taxonomic units within a species, defined as population genetics. The purpose of this dissertation was to better understand the evolutionary and population dynamics of crustaceans within the Gulf of Mexico. In the second chapter of my dissertation, I provide a guide to best phylogenetic practice while reviewing infraordinal relationships within Decapoda, including the promise held by next-generation sequencing (NGS) approaches such as Anchored Hybrid Enrichment. Chapter III is a phylogenetic study of species relationships within the economically important shrimp genus, Farfantepenaeus, targeting three mitochondrial genes and uncovering an intriguing pattern of latitudinal speciation. As the first inclusive molecular phylogeny of the genus, we find support for the newly described species F. isabelae, but a lack of support for the species status of F. notialis. Additionally, our results suggest the existence of two distinct subspecies of F. brasiliensis. Chapter IV investigates the relative impacts of habitat heterogeneity and the presence of a possible glacial refugium in determining population dynamics of the Giant Deep-Sea Isopod, Bathynomus giganteus in the northern Gulf of Mexico. Through hybrid population genetics/genomics analyses and Bayesian testing of population models, we find strong evidence for habitat heterogeneity determining population dynamics for this charismatic deep-sea invertebrate. Chapter V further investigates the role of environment in determining and maintaining genetic diversity and population connectivity, specifically focused on establishing biological baselines with which we can diagnose health and resilience of the Gulf of Mexico. This was accomplished through a comparative NGS population genomics study of three species of mesopelagic crustaceans: Acanthephyra purpurea, Systellaspis debilis, and Robustosergia robusta. While diversity and connectivity differs in each species, the comparative results bespeak the importance of access to the Gulf Loop Current in determining and maintaining population dynamics. Overall, my work significantly contributes to our knowledge of Crustacea at the phylogenetic- and population genetic-level.

Nearly all deep-sea cephalopod life history studies have been completed by examination of specimens collected in the wild. Much of this work is like piecing together a puzzle; knowledge of the life history of many species remains fragmented and hence, taxonomically and phylogenetically confused. Molecular approaches and sequencing technologies are powerful tools for deciphering wild-type cephalopod life history and population dynamics. Use of molecular markers offers additional certainty for identifying specimens damaged during deep-sea collections and can elucidate often cryptic, intra- and interspecific diversity. The research presented in this study assessed broad genetic patterns of biodiversity in deep-sea cephalopods from the Gulf of Mexico and northwestern Atlantic Ocean. This study has two key objectives: [1] to examine intraspecies variation among regionally disjunct subpopulations, comparing collections separated by the Florida Peninsula, and [2] to examine intraspecies variation within deep-sea cephalopods in the Gulf of Mexico. Through Sanger sequencing marker genes COI, 16S rRNA, and 28S rRNA, this study has generated a genetic baseline characterization of deep-sea cephalopods in the Gulf of Mexico, assessed intraspecies genetic variation, and linked morphological identification with DNA barcodes, testing morphological hypotheses of species identification and naming. Results of investigating intraspecies variation within regionally disjunct subpopulations reveal there is no regional distinction between the Gulf of Mexico subpopulations of Vampyroteuthis infernalis, Pyroteuthis margaritifera, and Cranchia scabra, and the Bear Seamount subpopulations in the northwestern Atlantic Ocean. Results of investigating intraspecies variation within the Gulf of Mexico displayed potential for cryptic species, novel sequence records, and large expansions to sequence records for species known to inhabit the Gulf of Mexico. Analysis of intraspecies variation within the Gulf of Mexico facilitated identification of damaged specimens used for this study, but also revealed GenBank database issues of misidentified records, and outdated nomenclature in accession records. Because cephalopods play a central role in most oceanic ecosystems, characteristics like a short average life span and a rapid growth rate mean that cephalopod populations have the potential to serve as an invaluable reflection of ecosystem change.

Previous studies showed that sea surface salinity (SSS) in the Florida Straits as well as Florida Current transport covaried with changes in North Atlantic climate over the past two millennia. However, little is known about earlier Holocene variability in the Florida Straits. Here, we combine Mg/Ca-paleothermometry and stable oxygen isotope measurements on the planktonic foraminifera Globigerinoides ruber (white variety) from Florida Straits sediment core KNR166-2 JPC 51 (24 degrees 24.70? N, 83 degrees 13.14?W, 198m deep) to reconstruct a high-resolution (~30 yr/sample) early to mid Holocene record of sea surface temperature and delta18OSW (a proxy for SSS) variability. We also measured Ba/Ca ratios in the same shell material as a proxy for riverine input into the Gulf of Mexico over the same time interval. After removing the influence of global delta18OSW change due to continental ice volume variability, we propose that early Holocene SSS enrichments were caused by increased evaporation/precipitation ratios in the Florida Straits associated with periods of reduced solar output, increased ice rafted debris in the North Atlantic and the development of more permanent El Nino-like conditions in the eastern equatorial Pacific. When considered with previous high-resolution reconstructions of early Holocene tropical atmospheric circulation changes, our results provide evidence that solar output variability over the Holocene had a significant impact on the global tropical hydrologic cycle over the last 10,000 years.

The numerous benefits that wetlands provide make them essential to ecosystem services and ecological functions. Historically, wetland losses have been caused by natural and anthropogenic changes. In Texas, nearly 50% of coastal wetland habitat has been lost since the 1930s and losses in the Lower Neches watershed have been some of the most extensive. Restoration is a way to mitigate these losses and can be accomplished in many ways. Each restoration design creates different aquatic habitats that can influence both submerged aquatic vegetation (SAV) and faunal communities. The restoration of the Lower Neches Wildlife Management Area (LNWMA) has created the conditions for the growth of the invasive submerged macrophyte, Myriophyllum spicatum (Eurasian watermilfoil) which may be competing with the native aquatic grass, Ruppia maritima (widgeongrass) for essential nutrients. In this study, an attempt was made to link restoration design with both SAV and aquatic fauna community structures by using a throw trap to characterize assemblages observed in three different types of restored marshes. We also performed two controlled mesocosm experiments in 0.5 gal aquariums to determine growth inhibition by M. spicatum on R. maritima. Analyses using Kruskal-Wallis non-parametric test determined that temporal variations in fauna and SAV community composition was greater than any restoration effect. Discriminant Function Analyses (DFAs) determined two to three key faunal species that best predicted association among restoration designs, but linear regressions could not determine any consistent relationship between individual species density and biomass of the dominant SAV species, M. spicatum. For the mesocosm experiments, M. spicatum inhibited the biomass production and branch count of R. maritima when the two species are grown together (ANOVA, p = 0.004 and 0.003, respectively). Changes in SAV assemblages due to competition and habitat characteristics could play a major role in determining faunal community. In order to minimize the temporal effect observed and better determine any habitat pattern that may be present, a much longer study is necessary.

Includes vita. / Title from PDF of title page. / Document formatted into pages; contains 329 pages. / Thesis (Ph.D.)--University of South Florida, 2003. / Includes bibliographical references. / Text (Electronic thesis) in PDF format. / ABSTRACT: River discharge leads to extensive phytoplankton blooms often observed in ocean color satellite images to extend far into the open ocean as high chlorophyll plumes. We investigated diversity, distribution and ecology of phytoplankton populations in the Mississippi River plume, both spatially and in the water column using molecular tools. A method was developed for the quantification of diatom/pelagophyte rbcL (large subunit of Ribulose-1,5-bisphosphate Carboxylase/Oxygenase) mRNA using quantitative PCR and applied to cultures and in the plume. The vertical structure of phytoplankton species in the Mississippi River plume was described by flow cytometry, pigments, rbcL mRNA and rbcL cDNA libraries. High productivity in the plume was associated with a large population of Synechococcus and elevated levels of cellular form IA rbcL mRNA. / ABSTRACT: rbcL cDNA libraries indicated two vertically separated clades of Prochlorococcus (high-light and low-light adapted) in addition to a diverse group of prymnesiophytes and a microdiverse clade of prasinophytes, which may have dominated the SCM (Subsurface Chlorophyll Maximum). In situ sampling and satellite image analysis were used to estimate that the plume accounted for 41% and 13% of all surface water column ix productivity in the oligotrophic Gulf of Mexico, while covering less than 3% of its area. Coastally the plume is dominated by diatoms, which are replaced by a bloom of Synechococcus as the plume moves offshore. Diatoms as indicated by pigments and rbcL clone libraries again dominated the offshore, least productive plume. 15N uptake measurements indicated that rapid recycling of ammonium despite higher levels of nitrate primarily drives production in the offshore plume. / ABSTRACT: rbcL mRNA levels and photosynthetic capacity displayed strong diel patters in three out of four time series sampled during the GRIST (Geochemical Rate/mRNA Integrated Study). In addition it was demonstrated that transcriptional regulation of the global nitrogen regulatory protein NtcA in Synechococcus WH7803 may involve a small cis-encoded anti-sense mRNA. Methods for the generation of large insert BAC (Bacterial Artificial Chromosome) from cultures and the environment were refined. Partial sequencing and genomic comparison of an ntcA containing BAC clone obtained from Synechococcus WH7803 indicated that ntcA is not part of a larger nitrogen assimilation operon in cyanobacteria. / System requirements: World Wide Web browser and PDF reader. / Mode of access: World Wide Web.

Submarine landslides retrogressively fail from intact material at the headwall and then become fluidized by strain weakening; the final deposits of these flows have low porosity, which controls their character in seismic reflection data. Submarine landslides occur on the open slope and also localized areas including margins of turbidite channel-levee systems. I develop and quantify this model with 3-D seismic reflection data, core and log data from Integrated Ocean Drilling Program Expedition 308 (Ursa Basin, Gulf of Mexico), flume experiments, and numerical modeling. At Ursa, multiple submarine slides over the last 60 ky are preserved as mass transport deposits (MTDs). Retrogression proceeded from an initial slope failure that created an excavated headwall, which reduced the horizontal stress behind the headwall and resulted in normal faults. Fault blocks progressively weakened until the gravitational driving stress imposed by the bed slope exceeded soil strength, which allowed the soil to flow for more than 10 km away from the source area. The resulting MTDs have lower porosity (higher bulk density) relative to non-failed sediments, which ultimately produces high amplitude reflections at the base and top of MTDs. In the laboratory, I made weak (low yield strength) and strong flows (high yield strength) from mixtures of clay, silt, and water. Weak flows generate turbidity currents while moving rapidly away from the source area. They create thin and long deposits with sinuous flow features, and leave behind a relatively smooth and featureless source area. In contrast, strong flows move slowly, do not generate a turbidity current, and create blocky, highly fractured source areas and short, thick depositional lobes. In Pleistocene turbidite channels of the Mississippi Fan, deep-seated rotational failures occurred in the flanking levees. The rotational failures displaced material into the channel from below where it became eroded by turbidity flows. This system achieved a delicate steady state where levee deposition and displacement along the fault into the channel was balanced by erosion rate of turbidity flows. This work enhances our understanding of geohazards and margin evolution by illuminating coupled processes of sedimentation, fluid flow, and deformation on passive continental margins. / text

The Gulf of Mexico Basin Opening project (GUMBO) is a study of the lithological composition and structural evolution of the Gulf of Mexico (GoM) that uses Ocean Bottom Seismometer (OBS) data from four transects in the Northern GoM. I examine 39 OBS shot records in the easternmost transect for shear wave arrivals and pick shear wave travel times from the 11 usable records. I then carry out a tomographic inversion of seismic refraction travel times. I use the resulting shear-wave velocity model in conjunction with a previously constructed P-wave model to examine the relationship between Vp and Vs. I compare velocities in the sediment and basement with empirical velocities from previous studies for the purpose of constraining lithological composition below the transect and make an interpretation of the structural evolution of the eastern GoM. The seismic velocities for crust landward of the Florida Escarpment are consistent with normal continental crust. Seaward of the Escarpment, velocities in the upper oceanic crust are anomalously high (Vp = 6.5 – 7 km/sec; Vs = 4.0 – 4.6 km/sec). A possible explanation for this observation is that GoM basalt formation consisted of basaltic sheet flows, forming oceanic crust that does not contain the vesicularity and lower seismic velocities found in typical pillow basalts. Increased magnesium and iron content could also account for these high velocities. Seismic refraction and reflection data provide a means of investigating the nature of the Moho in the northeastern GoM. I use a finite difference method to generate synthetic record sections for data from eight instruments that are part of the two easternmost GUMBO seismic lines (lines 3 & 4). I then vary the thickness of the Moho in these synthetic models and compare the results with the original receiver gather to examine the effects this variability has on amplitudes. The data from the instruments chosen for these two lines are representative of continental and transitional crust. The finite difference models indicate that the Moho beneath GUMBO 3 is ~1500 m thick based on the onset and amplitudes of PmP arrivals. All five instruments display consistent results. The instruments along GUMBO 4 suggest a Moho almost twice as thick as GUMBO 3 on the landward end of the transect that grades into a Moho of similar thickness (1750 m) in the deep water GoM. The three instruments used to model the Moho in this area show that the Moho ranges from ~1750 to 3500 m in thickness. The sharper boundary beneath continental crust in GUMBO Line 3 supports other evidence that suggests magmatic underplating and volcanism in the northern GoM during the mid-Jurassic. The thicker Moho seen on the landward end of GUMBO Line 4 that is overlain by continental crust was likely unaffected by GoM rifting. Therefore, the Moho beneath the Florida Platform might be as old as the Suwannee Terrane, and complex Moho structure is not uncommon for ancient continental crust. / text

In the late spring of 2008, the Chevron-led Gulf of Mexico Gas Hydrate Joint Industry Project (JIP) expects to conduct an exploratory drilling and logging campaign to better understand gas hydrate-bearing sands in the deepwater Gulf of Mexico. The JIP Site Selection team selected three areas to test alternative geological models and geophysical interpretations supporting the existence of potential high gas hydrate saturations in reservoir-quality sands. The three sites are near existing drill holes which provide geological and geophysical constraints in Alaminos Canyon (AC) lease block 818, Green Canyon (GC) 955, and Walker Ridge (WR) 313. At the AC818 site, gas hydrate is interpreted to occur within the Oligocene Frio volcaniclastic sand at the crest of a fold that is shallow enough to be in the hydrate stability zone. Drilling at GC955 will sample a faulted, buried Pleistocene channel-levee system in an area characterized by seafloor fluid expulsion features, structural closure associated with uplifted salt, and abundant seismic evidence for upward migration of fluids and gas into the sand-rich parts of the sedimentary section. Drilling at WR313 targets ponded sheet sands and associated channel/levee deposits within a minibasin, making this a non-structural play. The potential for gas hydrate occurrence at WR313 is supported by shingled phase reversals consistent with the transition from gas-charged sand to overlying gas-hydrate saturated sand. Drilling locations have been selected at each site to 1) test geological methods and models used to infer the occurrence of gas hydrate in sand reservoirs in different settings in the northern Gulf of Mexico; 2) calibrate geophysical models used to detect gas hydrate sands, map reservoir thicknesses, and estimate the degree of gas hydrate saturation; and 3) delineate potential locations for subsequent JIP drilling and coring operations that will collect samples for comprehensive physical property, geochemical and other analyses

Recent observations have identified a new species of leucothoid amphipod, Leucothoe “sp. F,” associated with the sponge Cliona varians. This project examined the relationship between this amphipod and its sponge host at three sites in the Florida Keys with differing hydrodynamic regimes. Ninety-eight sponge samples with a total of 2,030 amphipods were collected between December 2011 and September 2012. Leucothoe “sp. F” is currently a common species in the Florida Keys strongly associated with C. varians; its distribution strongly coincides with open tidal currents from the Gulf of Mexico. Seasonality, depth, and tidal regimes not only influence population dynamics and sexual characteristics of Leucothoe “sp. F,” but also the abundance and volume of its host.