Turtles are important components of ecosystems around the world, with diverse ecological niches and adaptations. However, there are few detailed studies of how turtle community structure reflects local environments. This project applied techniques of community structure analysis to sites across the United States to infer past ecosystem and environmental conditions of the early Pliocene Gray Fossil Site (GFS) in northeastern Tennessee based on the ancient turtle community. Results indicate extant turtle community structure closely reflects environmental conditions, and that ancient turtle communities can be used to infer climate and habitat conditions of past ecosystems. Application to the GFS turtle community shows similarity to modern communities of the southern Gulf Coast and subtropical southeastern United States. These findings are consistent with previous interpretations of the GFS environment as warmer and wetter than the southern Appalachian climate of today, and demonstrate the utility of fossil turtle assemblage data in determining past environmental conditions.

Freshwater ecosystems are among the most threatened ecosystems on the planet. In recent years there has been increasing concerns over precipitous declines in population sizes and increasing rates of extinction of native freshwater fauna across North America. Nearly 50% of the mussel species and 25% of the fish species in North America are imperiled. Stream habitat degradation has been cited as the principal cause for declines, with anthropogenic land uses being the leading causes of stream degradation. Species distribution models (SDMs) have become an integral tool in ecological research and conservation planning. SDMs are reliant upon occurrence datasets for the taxa of concern and museum-based information has become a popular source for such data. In the first stage of my research, I developed a centralized database for Kentucky fishes based on museum-based information. Over the course of three years, the SIUC Ichthyology Lab built an occurrence dataset of Kentucky fishes consisting of more than 50,000 records dating back to the 1890s. Each record contains three pieces of information (1) species identification, (2) georeferenced locality, and (3) date of collection. In the second stage of my research, I investigated the use of multiscale landscape data in aquatic species distribution models using a case study of a freshwater mussel. The distribution of Rabbitsfoot (Quadrula cylindrica) in the upper Green River system (Ohio River drainage) was modeled with environmental variables from multiple spatial scales. Four types of landscape environment metrics were used, including: land use/land cover (LULC) pattern, LULC composition, soil composition, and geology composition. The study showed that LULC pattern metrics are very useful in modeling the distribution of Rabbitsfoot. Together with LULC compositional metrics, pattern metrics permitted a more detailed analysis of functional linkages between aquatic species distributions and landscape structure. Moreover, the inclusion of multiple spatial scales was necessary to accurately model the hierarchical processes in stream systems. Geomorphic features played an important role in regulating species distributions at intermediate and large scales while LULC variables appeared more influential at proximal scales. I then further tested the landscape-level approach to aquatic species distribution modeling using a case study of six narrow-range endemic fishes with contrasting biogeographies. Species biogeography did not appear to affect predictive performance and all models performed well statistically. Predictive maps showed accurate estimations of ranges for five of six species based on historical collections. The relative influence of each type of environmental feature and spatial scale varied markedly with between species. A hierarchical effect was detected for narrowly distributed species which were highly influenced by soil composition at larger spatial scales and land use/land cover (LULC) patterns at more proximal scales. Conversely, LULC pattern was the most influential feature for widely distributed at all spatial scales. Lastly, I developed a hierarchical approach to the selection and management of freshwater protected areas in the upper Green River system. By aligning the spatial scales and environmental variables analyzed at each stage in the conservation planning process, from species distribution modeling to reserve selection, I present a more robust methodology to conservation planning compared to traditional approaches. Using models of species richness fitted to landscape attributes, I also provided suggestions for landscape management strategies for each conservation unit. My research comprises the core conservation plan for the focal species in the upper Green River system.

Phytoplankton account for at least half of all primary production in estuarine waters and are at the center of biogeochemical cycles and material budgets. Environmental managers use water column chlorophyll-a (chl-a) concentrations as a basic water quality indictor, as the problems of eutrophication and hypoxia are intrinsically linked to excessive phytoplankton growth. Evidence suggests that the distribution and frequency of harmful algal blooms may be increasing worldwide. For the most part, phytoplankton communities follow a standard seasonal pattern, with specific groups dominating the assemblage during the time of year when environmental conditions correspond to their requisites for growth. However, climate change will result in incremental but consistent shifts in some environmental factors known to affect phytoplankton production and biomass accumulation. Mean surface temperatures in North American mid-Atlantic coastal and estuarine regions are steadily rising, and the frequency and severity of drought and storm events are projected to fluctuate, potentially increasing the severity of extreme weather events. Anthropogenically-induced nutrient loading, especially from non-point sources, is one of the largest consistent contributors to coastal marine eutrophication. The consequences of changes in these environmental factors to estuarine ecosystems and phytoplankton community dynamics are unclear. Because different phytoplankton groups respond to environmental changes in distinctive ways, some classes thrive during periods of environmental stability and others at times of temporary or sustained disturbance. to predict how phytoplankton and therefore water quality might respond to changes in climate and land use, we built mathematical phytoplankton kinetics sub-models that differentiate phytoplankton groups using taxonomic classes with well-defined functional characteristics. Then we integrated them into a reduced-complexity estuarine ecosystem model. The sub-models were designed to simulate daily biomass of diatoms, dinoflagellates, cyanobacteria, and raphidophytes in the New River Estuary, NC. We calibrated and validated the model using data collected from 2007 – 2012 through the Aquatic Estuarine monitoring module of the Defense Coastal/Estuarine Research Program. The model was a relatively good predictor of total chl-a and primary production, and a fair predictor of group dynamics. The model was employed in heuristic simulations of changes in temperature, nutrient loading, and freshwater delivery to predict their effects on overall phytoplankton biomass, productivity, and community composition. Increases in temperature had a modest effect on mean daily simulated phytoplankton production and chl-a, but considerably decreased the relative abundance of diatoms and simultaneously increased the relative abundance of cyanobacteria. The seasonal phenology of phytoplankton abundance also shifted in response to increased temperatures: chl-a concentrations were larger in the winter and spring and smaller in the summer and fall. The model was most sensitive to changes in the watershed nutrient load. Nutrient influx had a dramatic effect on the temporal and spatial extent of phytoplankton blooms. The relative abundance of dinoflagellates and raphidophytes increased in response to elevated nutrient loading, regardless of whether load was increased directly as in nutrient simulations or indirectly as in freshwater simulations. Initially, greater freshwater discharge increased total chl-a, productivity, and the frequency of phytoplankton blooms. However, these relationships leveled off or were reversed as flow continued to increase due to greater rates of flushing and light attenuation. Results demonstrated how models like this can be important tools for both heuristic understanding and environmental management. A benefit of this model is how easy it is to update to other estuarine systems through the re-parameterization of the phytoplankton groups.

Habitats of Chesapeake Bay have been altered due to anthropogenic impacts and climate change. Due to these human disturbances, seagrasses have been extirpated from many areas in lower Chesapeake Bay and persisting beds face future losses as water temperatures continue to rise. Further loss of seagrass habitat will negatively impact juvenile blue crabs (Callinectes sapidus) that use seagrass beds as nursery grounds. Habitat degradation allows for more successful introductions of exotic species, and the communities formed from the mixing of native and exotic species are known as emerging ecosystems. Gracilaria vermiculophylla, an exotic macroalga, may be an emerging nursery habitat for juvenile blue crabs in Chesapeake Bay; however the extent to which the alga is present and used as a nursery by juvenile blue crabs are largely unknown. I investigated algal distribution in the shallow littoral areas of the York River, a subestuary of Chesapeake Bay, over two years (2013 – 2014) and found that G. vermiculophylla presence correlated with salinity and that algal presence and biomass increased with seagrass presence, although biomass was generally low. The alga was present in areas where seagrasses have been lost, and is therefore likely providing nursery habitat in these areas of high megalopal recruitment. Benthic epifaunal communities had lower species richness and were less abundant in G. vermiculophylla relative to seagrass, while benthic infaunal communities had lower species richness but similar abundance in the alga relative to seagrass. Juvenile blue crab densities were similar in the alga and seagrass, although seagrass supported about 3 times as many first and second instar crabs than G. vermiculophylla. Young juvenile blue crabs preferred seagrass, which may be due to epifaunal prey preference, and G. vermiculophylla likely represents a secondary nursery habitat. Juvenile blue crab growth rates of crabs 15 – 50 mm carapace width were similar in the alga, native seagrass, and unvegetated habitat, indicating that growth does not drive ontogenetic shifts in habitat use by larger (20 – 30 mm carapace width) juveniles. Similar growth rates also suggest that G. vermiculophylla performs similarly to seagrass as a nursery habitat in terms of providing resources for growth. Simulations of density-dependent migration of young juvenile blue crabs between habitat types suggest that G. vermiculophylla may mediate continued seagrass loss, at least in part. Together, these results increase our understanding of an emerging Chesapeake Bay ecosystem and the impacts that changes to nursery habitats have on the juvenile component of the blue crab population.

The finfish communities using the intertidal surfaces of a bay-exposed marsh and a sheltered, channel marsh of the Goodwin Islands, York River, Virginia were studied from May to November 1994. Samples were taken approximately twice monthly using a flume weir at three stations in each marsh. Species composition, abundance and biomass were estimated, and growth patterns and production rates were described for the dominant species. A total of 3001 fish were collected from 11 species and 8 families. Fundulus heteroclitus dominated both marshes and accounted for 83.07% of the total number of fish caught, and 84.83% of the total biomass collected. Menidia menidia was the second most abundant species at 9.00% of the total number of fish, but F. majalis was second in the total biomass at 7.51 % of the total. Abundance first peaked in June, and a second peak occurred in November. Biomass had a small peak in the beginning of August, and a large peak in late September. Analysis of variance showed the number of species captured did not differ significantly between the marshes. However, both the number of individuals and biomass were significantly higher in the protected marsh. Correspondence analysis showed that species composition in the protected marsh was mostly cyprinodontids, but in the open marsh species composition varied more throughout the sampling season. Species densities were highest at 9.8 ± 3.3 fish/m2 for F. heteroclitus in the protected marsh. Production for F. heteroclitus over the summer in the protected marsh was high at 10.1 g dry wt.fm2 due to the large number of rapidly growing larval and juvenile fish.

Marine turtles are distributed in temperate, sub-tropical and tropical waters and beaches worldwide, often in areas heavily impacted by humans. Although there are many threats to marine turtle populations, the growing threats of nutrient pollution and harmful algal blooms are relatively understudied despite their widespread impacts on coastal marine ecosystems that marine turtles depend on. By studying juvenile green turtles (Chelonia mydas) in the Indian River Lagoon, Florida, where nutrient pollution and HABs are a widespread and longstanding issue, I aimed to conduct a case study of how these threats may affect this federally Threatened species. In Chapter 2, I used four concurrent, 18-year data sets to characterize and assess the interrelatedness of long-term trends in seagrass cover, macroalgae occurrence, juvenile green turtle abundance, and juvenile green turtle growth rates. From 2000 to 2018, IRL seagrass cover declined precipitously, macroalgae rose slowly through 2011 then declined during two severe HABs, juvenile green turtle abundance declined slowly, and growth rates declined through 2011 then rose through 2018. In Chapter 3, I conducted a 9-year study of juvenile green turtle foraging ecology using a comparative stable isotope approach. I found that carbon and nitrogen stable isotopic variance declined during and after two severe HABs in the IRL. In Chapter 4, I used two complementary methods to assess the diet of juvenile green turtles after two severe algal blooms in order to assess changes compared to previous diet studies. Visual identification of forage items showed that juvenile green turtle diet remained dominated by nutrient-tolerant red macroalgae with smaller components of seagrass and green algae; metabarcoding techniques largely failed to resolve their diet. My results highlight the web of complex effects and responses that factor in to determining the effects of nutrient pollution and HABs on juvenile green turtles. Future studies of habitat selection, foraging ecology, and the effects of these on juvenile green turtle growth and survival are needed to fully assess the threat of nutrient pollution.

Through genome wide association of nonvolatile metabolites and leaf ecophysiological traits, historic breeding practices were found to have led to germplasm divergence within the cultivated sunflower Helianthus annuus. In genome-wide analyses of single nucleotide polymorphisms (SNPs) in relation to flower petal carotenoid content across the cultivated H. annuus germplasm, alternative methods of analysis proposed differing genetic architectures, which suggests that these methods can be used as complementary approach in prioritizing SNPs for function analysis. Leaf hyperspectral reflectance was leveraged in a machine learning framework to predict herbivore- and volatile induction across the genus with 95% accuracy, while characterizing changes in volatile metabolites. The body of work in this dissertation represents the first characterization of the standing genetic variation for nonvolatile specialized metabolite diversity in cultivated sunflower in the context of modern breeding practices, and the first assessment of hyperspectral reflectance and volatile metabolite diversity across the genus Helianthus.

Coastal habitats provide crucial nursery habitat for predatory fishes, but they are in decline worldwide, impacting economically important fisheries. Habitat restoration can simultaneously mitigate the effects of habitat loss and benefit predators (e.g., sportfish), although this relationship is understudied. Here, the response of juvenile sportfish to oyster reef and living shoreline restoration is compared to controls in the Indian River Lagoon, Florida prior to and following restoration for up to three years through examination of community (diversity, assemblage), population (abundance), biometric (size, body condition), ontogenetic, and trophic (gut contents, stable isotopes) dynamics. Stable isotopes were used to quantify dietary history, beyond the temporary record of gut content, using carbon (δ13C) and nitrogen (δ15N). This study found juvenile sportfish abundance and richness was higher at restored reefs compared to natural and degraded reefs and was comparable between stabilized and natural living shorelines. Biomass was higher at oyster reefs compared to living shorelines, which was likely driven by an ontogenetic shift of larger mangrove snapper Lutjanus griseus toward oyster habitat. Snappers and prey at live reefs were carbon (δ13C) enriched, with a smaller isotopic niche area compared to dead reefs, while restored reefs were intermediate and contracted over time. Therefore, sportfish at higher quality reefs likely exhibit greater site fidelity, particularly among less-mobile juveniles. Moreover, stabilized shorelines can achieve trophic equivalence to natural shorelines, as shown through their similar isotopic signatures and niche area. These responses were best predicted by benthic habitat (e.g., oyster density), prey abundances, and site location, demonstrating the connection between habitat quality and setting to provide prey that support sportfish populations. This study validates the benefits of habitat restoration to economically important fisheries, by augmenting various attributes of juvenile sportfish life history, which can improve their survival and recruitment into the adult population, and thus extend restoration outcomes.

Research provides biological and ecological information on Hydrilla Verticillata (L. f.) Royle in Gatun Lake, Panama for an ongoing management program of aquatic weeds in the Panama Canal. Morphological and genetic variation, standing crop and life cycle were determined.

Insect pests are the most widespread disturbance in Canadian forests, but resulting impacts of forest defoliation on stream ecosystem functions are poorly understood. This study investigated the effects of a spruce budworm outbreak on water quality and the structure and function of microbial communities in streams of 12 catchments across a gradient of cumulative defoliation severity in the Gaspésie Peninsula, Québec, Canada. Bi-weekly stream habitat sampling was conducted spring to fall 2019-2021, with stream flow rates measured and water samples collected and analyzed for water chemistry parameters, nutrients, and dissolved organic matter (DOM) structure and quality. Algal communities were assessed at the same time by measuring in-situ biomass. Bacteria and fungi communities on leaf packs were assessed by incubating six leaf packs for five weeks (mid-August- late September) in one stream reach per watershed. Microbial community composition of leaf packs was determined using metabarcoding of 16S and ITS rRNA genes, and functions were examined using extracellular enzyme assays, leaf litter decomposition rates, and taxonomic functional assignments. This study determined that cumulative defoliation increased stream temperatures, flow rates, and SUVA (DOM aromaticity), but not nutrients. It increased algal biomass and altered microbial community composition, with a stronger influence on bacteria than fungi. The observed increases in SUVA and algal biomass corresponded with changes to bacteria carbon cycling functions, which indicated that microbes were preferentially selecting carbohydrates produced by algae rather than the aromatic compounds from increased terrestrial inputs. There were no changes to other bacteria or fungi functions and no changes to taxonomic or functional diversity. Overall, results indicate that forest pest outbreaks alter carbon inputs to streams and the structure and function of stream microbial communities associated with carbon cycling. / Thesis / Master of Science (MSc) / Terrestrial and aquatic landscapes are tightly linked, and forest disturbances can influence stream ecosystems. Insect pests defoliate millions of hectares of forests each year, but the resulting impacts on stream ecosystems are poorly understood. This study investigated the effects of a spruce budworm outbreak on water quality and microbial communities in streams in Gaspésie, QC, Canada. Microbial communities are critical to the functioning of stream ecosystems as they convert energy (e.g., carbon) into useable forms for other organisms. Results indicate that defoliation altered stream flow rates, temperatures, and carbon composition, as well as the microbial communities involved in carbon cycling processes. Carbon is essential to aquatic food webs and this improved understanding of how carbon flow is altered by a widespread forest disturbance can inform pest management decisions for spruce budworm outbreaks.