Fibropapillomatosis (FP) is a tumor-forming sea turtle disease that mainly affects juvenile green turtles (Chelonia mydas) in coastal foraging sites. The cause of FP is unclear, but likely involves the putative pathogen chelonid herpesvirus 5 (ChHV5). The overall dynamics of this disease are poorly understood, in part due to the difficulty of inferring disease and infection statuses of turtles without evidence of FP. In this study, I investigated the FP disease system in juvenile green turtles of the Indian River Lagoon (IRL), Florida, USA, to better understand disease and pathogen dynamics. First, I developed a hierarchical model for predicting FP development and disease state progression. The results of the hierarchical model estimated > 99% of juvenile green turtles in the IRL developed FP, indicating that nearly every individual in the IRL is affected by this disease. The model also suggested that turtles quickly developed FP upon recruitment to the IRL and then recovered at different rates, with most completely recovering before emigrating from the IRL as they mature. Second, I assessed the viability of using qPCR of blood and skin samples to assess ChHV5 infection dynamics. I found very low prevalence of ChHV5 infections in blood (1.4% positive) and skin (6.5% positive) samples, and high prevalence in tumor samples (89.7% positive). Considering the high prevalence of FP in the IRL, and the high detection prevalence of ChHV5 from tumor samples, qPCR testing of blood and skin samples was ineffective for identifying ChHV5 infection status of individual turtles.

Ecological disturbances alter biotic communities and ecosystems. In many coastal zones disturbances are increasing, including algal blooms, storms, hypoxic events, and fish kills. These disturbances are often related, for example blooms releasing toxins or depleting dissolved oxygen, ultimately killing fish. Depending on the intensity, duration, and geographic extent of a disturbance, the fish community can take days to years to recover from disturbances. To explore the relationships among environmental disturbances, sport fish, and forage fish communities, this thesis examined two Florida estuaries with differing disturbance regimes. Using an ensemble modelling approach combining generalized linear models (GLM), Bayesian modelling, and Bayesian structural equation modeling (SEM), this complementary framework helped elucidate complex relationships among environmental variables and the fish community following a disturbance. In Banana River, both sport fish and forage fish abundances decreased following an algal bloom, but the decrease in abundance of forage fish was more rapid. Forage fish community dynamics were more closely associated with water quality metrics than sport fish communities during non-disturbed periods (December- March). However, during the algal bloom, sport fish community dynamics were more closely associated with water quality metrics than forage fish community dynamics. In the three months following the kill, the forage and sport fish communities were less strongly linked than in non-disturbed years. In the chronically stressed St Lucie Estuary, fish community dynamics and water quality were weakly linked from 2015 - 2019. These shifts in community dynamics and relationships following a disturbance suggest forage and sport fish communities, food webs, and trophic dynamics may be at increased risk of surpassing an ecological threshold as algal blooms become more common. Furthermore, the decoupling documented in fish communities and abiotic environment in the chronically stressed St. Lucie Estuary suggest this region may have already passed an ecological tipping point.

Over the last century, millions of hectares of wetlands have been lost due to urban development and agricultural activities throughout the world. In the U.S., efforts have been made by federal and state legislation to restore wetland habitat in exchange for development on wetlands. To restore ecosystem function by reestablishing hydrological metrics (e.g., groundwater level fluctuations), wetland restoration aims to facilitate the growth of wetland vegetation to approximate the original conditions as a proxy for ecological integrity. In 1992, the first landscape-scale off-site mitigation project, the Disney Wilderness Preserve (DWP) was funded by the Walt Disney Company in Poinciana, Florida. My objective was to use digitized land cover categories based on aerial photography (1941-2019) and 35 years of Landsat satellite imagery (1985-2019) to analyze landscape and spectral properties of DWP to better understand the trajectories of bayhead, cypress, and marsh wetland types before and after the eco-hydrological enhancement. After the enhancement, the areal extent of cypress and mixed hardwood swamps and marsh lands slightly increased, while the area of the bayhead swamps slightly decreased. From the spectral trajectory analyses, the initial responses to the enhancement varied among wetland communities and more overall variability among patches was observed through the post-enhancement periods compared to pre-enhancement periods. Post-enhancement trajectories returned to similar levels to pre-enhancement for the majority of the wetlands. This study illustrates the opportunities and challenges associated with monitoring complex wetlands systems for future planning and adaptive management by conservation managers and scientists.

Maintenance of genetic diversity at ecologically-relevant loci may be important for allowing invasive populations to become established despite decreases in genomic diversity due to founder effects. To evaluate this prediction, we compared genetic diversity at an expressed MHC class IIß gene fragment to a 909 bp region of the neutral cytochrome b (cytb) locus from 20 populations of the American bullfrog (Rana catesbeiana) across its North American invasive and native ranges and quantified the presence of Batrachochytrium dendrobatidis (Bd), a pathogen, for which R. catesbeiana is a vector species. We recovered 28 unique MHC alleles and found that invasive populations had significantly higher Bd prevalence and intensity and significantly higher pairwise FST than native populations, but maintained similar levels of MHC diversity, contrasted by lower neutral cytb diversity. Across all populations the two most common alleles (LiCA_B & Rapi_33) were associated with a significant decreased risk of Bd infection, and we detected positive selection acting on three MHC peptide binding residues, indicating that positive selection drives MHC evolution, likely in part due to disease pressure. A cytb phylogenetic analysis indicated that invasive populations likely arose from a single founding population from somewhere in the American Midwest with a possible subsequent invasion. In contrast, MHC phylogenetic analyses revealed widespread allele sharing across native and invasive ranges, but limited trans-species polymorphism, indicating a unique MHC evolutionary history in R. catesbeiana that may play a key role in the species' high Bd tolerance. Overall, our data indicate that balancing selection maintains MHC diversity in invasive R. catesbeiana despite founder effects evident from the cytb dataset. This study suggests that maintenance of diversity at ecologically-relevant loci contribute to the successful establishment of invasive populations and highlights the importance of quantifying diversity at functional loci to assess the evolutionary potential of invasive populations.

The Integrate-Transfer-Launch (ITL) complex impoundments located within the Kennedy Space Center security zone are known spawning sites for red drum (Sciaenops ocellatus). However, recent construction of manatee exclusion bollards around culverts leading into these impoundments may impede movement to and from this critical habitat. The goals of this study were to: 1) utilize passive acoustic telemetry to document patterns of red drum movement and habitat use within and around the ITL impoundments to assess how manatee exclusion bollards and environmental conditions may impact movement of red drum; and 2) explore red drum movement in response to environmental disturbance, specifically a severe hypoxia-induced fish kill event. Manatee exclusion devices were shown to impede the movement of relatively large red drum with head widths greater than the mean distance between bollards of 16.0 (± 3.4) cm. Additionally, the growth of biofouling organisms further reduced the spacing between bollards by an additional 0.5 (± 0.3) cm per month and thus impacted the movement of a greater size range of fish from moving successfully through the barriers. Red drum home range area and daily distance traveled were related to dissolved oxygen concentrations within the water. As dissolved oxygen levels decreased within the ITL impoundments, fish habitat use area also decreased. Episodic exposure to hypoxic conditions caused increased daily movement for fish, increasing from 2745.3 (± 1721.3) m during normoxic conditions to 3304.7 (± 1154.3) m in periods of hypoxia. However, during prolonged exposure to anoxic waters, fish distance and rate of movement was significantly reduced (normoxic: 2572.1 (± 1105.5) m / 2.5 (± 0.9) m/s; anoxic: 714.9 (± 395.4) m / 2.1 (± 1.1) m/s). The results of this study suggest manatee exclusion devices act as barriers to fish movement and decrease habitat connectivity; using this knowledge ecosystem-based management strategies are recommended that simultaneously benefit sportfish and marine mammals inhabiting Florida's estuaries.

Globally, coastal habitats are experiencing degradation due to the increase of human population growth, development along coastlines, and a constantly changing climate. This threatens the future production of critical ecosystem services such as shoreline stabilization, water filtration, nursery grounds for marine fauna, and many more. To combat these losses, resource managers are actively restoring coastal habitat. Past research suggests restoring habitats has mixed results; numerous factors influence restoration success. This study is among the first to assess the nekton community in the Matanzas River estuary and uses a BACI experimental design to quantify the effect of habitat restoration on the nekton community. Restoration sites are impacted wetlands with high elevation spoil piles that are leveled to increase intertidal habitat, enabling recruitment of intertidal flora and use by fauna. Fyke nets and seines were used to sample nekton. Over the course of 203 sampling efforts, a total of 39,857 specimens representing 62 unique taxa were collected. We compared samples collected from non-restored sites, sites recently restored in 2019, and sites restored in 2011. To quantify restoration success, nekton abundance, biomass, diversity, and indicator species were quantified. Sites restored in 2011 had greater abundances compared to the non-restored sites. No statistically significant differences in nekton community composition or nekton biomass between treatment types were detected. Common Snook, Clown Gobies, Silversides, juvenile Mullet, and Gulf Killifishes were indicator species demonstrating restoration success. Salinity, site type, and secchi depth played important roles in predicting abundances and diversity. These findings are consistent with recent restoration studies suggesting it can take years to see quantifiable differences in nekton communities following habitat restoration. Additionally, our work provides new insight on the positive ecological effects on nekton communities in restored coastal estuaries by manipulating wetland elevation to promote recruitment of intertidal flora.

Abstract Hydrologic Alteration and Sedimentation in the Upper Henry’s Fork Watershed Amelie Jeanne Charnaux The Henry’s Fork of the Snake River is venerated by the global recreational community as one of the finest trout fishing streams on the planet. Furthermore, this remarkable waterway flows within the bounds of one of the most important ecological corridors in the equally world-renowned Greater Yellowstone Ecosystem. While the recreational and biological features of this corner of Idaho may capture the interest of the broader public, the waterway is equally significant to the livelihoods of local interests, such as the ranching and farming communities. With the stakes running high for all interest groups, a case study of the Henry’s Fork watershed provides a valuable baseline narrative for understanding decision-making related to water resources not only in Idaho, but also in other Western states. Environmental impacts of the Henry’s Lake Dam and management of the stream below the structure were evaluated by literature review and GIS mapping, with research emphasis placed on the ecological integrity and fisheries of the Upper Henry’s Fork Subbasin. The literature review focused on natural processes in stream ecosystems and anthropogenic impacts, with the goal of providing information for the development of management policies that minimize the negative impacts of current flow management and land use. Literature sources overwhelmingly agree that the alteration of natural hydrologic regimes is the most serious and continuing threat to the sustainability of river ecosystems. In recent decades, downstream recreational fishing declined on the upper Henry’s Fork due to increased sedimentation, inciting investigation as to the source. Three major anthropogenic factors targeting one section of the river, the Henry’s Lake Outlet, set the stage for excess sedimentation. First, the Henry’s Lake Dam was constructed in 1923, impacting the Outlet’s hydrology through changes in the timing, magnitude, and frequency of low and high flows. Second, an artificial stream channel was constructed in the 1920s to bypass the meandering Outlet in order to increase conveyance capacity of irrigation water from Henry’s Lake to downstream water users. Third, long-term livestock grazing along this section of river dramatically reduced riparian and upland vegetation, triggering the loss of stream-bank stability and increasing erosion and sedimentation. These management practices have resulted in significant loss of biodiversity in the stream ecosystem and an increased rate of erosion in the Outlet. The Henry’s Lake Outlet restoration project, led by the Henry’s Fork Foundation, provides the opportunity to predict potential effects of large-scale restoration in the Henry’s Fork watershed. The project seeks to reduce sediment delivery downstream from the Outlet by rerouting flow from the straightened channel into the historic channel. The project tests the hypothesis that, by restoring the meandering stream channel, and thereby adding a half-mile to the Outlet, bank erosion and channel instability will decrease, the interaction between stream and riparian habitats will improve, and overall ecosystem health will benefit. In spite of the proactive intentions of the project, it will not change the current management of stream flow. In order to restore the Henry’s Lake Outlet to a state of dynamic equilibrium in terms of erosion and sediment load, the flows from Henry’s Lake Dam must more closely reflect the natural hydrologic regime. However, the ability to implement full restoration of the Outlet is complicated by the conflict between the requirements for ecosystem health and economic and socio-political pressures, a story common to many water systems throughout the West. Ultimately, it is hoped that this research may be integrated into policy and conservation strategy to mitigate streambank erosion and sedimentation in the Henry’s Fork Subbasin.

Ecologists try to understand how changing habitats alter the populations of organisms living within them, and how, in turn, these changing populations alter the environment. By linking individual or cellular (physiological) processes to system level responses, mechanistic models can help describe the feedback loops between organisms and the environment. Aquatic systems have long used mechanistic models, but increasing model complexity over the last 50 years has led to difficulty in parameterization. In fact, it is often unclear how researchers are choosing parameters at all, even though small changes in parameters can change qualitative predictions. I explore the challenges in parameter estimation present in even an ideal situation. Specifically, I conduct individual experiments for all of the needed parameters to describe a simple lab-based, aquatic system; estimate those parameters using the results from these experiments supplemented with literature data; and run a large experiment designed to test how well the lab-estimated parameters predict actual zooplankton populations and nutrient changes over time. I document best practices for finding and reporting parameter choices and show whole ecosystem level consequences of a variety of decisions. To get the best predictions I find that a mix of parameter estimation methods are necessary. Trait-based approaches are another method to understand species-environment interactions. Trait-based methods aggregate species into functional traits, perhaps making qualitative predictions easier. Theory suggests that more functionally diverse systems will be more resilient. I test this prediction in a simple aquatic system but am unable to find consistent support for this hypothesis, and instead finding that results are highly dependent on what measures of ecosystem recovery are used. Overall, more species-specific information is critical to building better models for both mechanistic and trait-based approaches. I expand species-specific data by providing new information, and collating information from literature on a small, tropical Cladocera. / Thesis / Doctor of Philosophy (PhD) / Predicting what will happen to a habitat after a disturbance is critical for conservation and management. Species specific information is useful for building a mechanistic understanding of ecology. Predictions that include underlying processes (mechanisms) may be more robust to a changing environment than predictions based on correlations. Eutrophication, the addition of excess nutrients, is a common problem in freshwater habitats. Being able to predict the effects of nutrient addition is critical for ensuring the health of freshwater ecosystems. By using species-specific life history and morphological information and a simple lab system, I test different methods of predicting and understanding the consequences of eutrophication. I find that the ramifications of eutrophication are not easily predicted by species' categorizations or with a more detailed mechanistic model.

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