This project investigated the feasibility of using the brackish water clam Rangia cuneata as a heavy metal pollution indicator, and further investigated the state of heavy metal pollution in the James River. Rangia cuneata were sampled in the fall of 1972 from the Rappahannock and James Rivers , and meats were analyzed by atomic absorption spectrophotometry for wet weight concentrations of copper, zinc, cadmium and lead. Levels of copper and zinc in Rangia cuneata were shown to be unaffected by clam size, spawning differences, salinity or distance upriver, and substrate grain size. Heavy metal concentrations in the oxidized channel sediments, determined from other studies conducted at the same time, were compared to levels in Rangia cuneata, but no relationships were found. Lead was below detection limits (0.2 ppm) in Rangia cuneata at all stations, and cadmium levels appeared to be consistent in both rivers. Copper was found to increase upriver in the James, indicating an upstream source, and zinc concentrations were found to peak at the mouth of the Chickahominy River. A number of possible causes were cited. This dissertation is from the Joint Program Degree from the College of William & Mary and University of Virginia and awarded by the University of Virginia.

A study of the biogeography of Peromyscus maniculatus was undertaken in order to ascertain a few of the environmental parameters important in defining the distribution of this species and how the species in turn has adapted to these parameters. The Columbia Gorge was chosen as it presents a climatic gradient from maritime to continental with very little elevation gain. Changes along this gradient in topography, soils and vegetation community structure are discussed.

Benthic communities in the estuarine portion of the James River are controlled mainly by salinity. Pollution effects are localized and difficult to assess because of the rigorous physical environment. Mesohaline and oligohaline communities were very similar to those in other east coast estuaries. except for the dominance of Rangia cuneata in the oligohaline zone. Communities of the tidal freshwater zone are most affected by pollution. In the areas of Richmond and Hopewell, where the major portion of the pollution load enters the river, communities are most severely depressed. Separate multivariate analyses of species distributional patterns, and pollution and physical parameters produced similar results dividing the river into mesohaline, oligohaline, and upper and lower tidal freshwater zones. Further analysis of only the tidal freshwater portion, to eliminate the effect of salinity, indicated that the distribution of benthic communities reflected the location and concentration of pollution sources along the river. The communities were dominated·by the introduced Asiatic clam, Corbicula manilensis, tubificids of the genus Limnodrilus and the chironomid larva Coelotanypus scapularis. The fauna of the freshwater zones was very eurytopic and adapted to the silty habitats that characterize the tidal freshwater James River and had great resemblance to the fauna of eutrophic lakes. The classical concept that a sharp increase in the number species occurs from the oligohaline to freshwater zones was found to be misleading. The increase does not occur until nontidal freshwater areas of greater habitat diversity are reached. Various aspects of the ecology of the poorly known tidal freshwater habitat are also discussed. This dissertation is from the Joint Program Degree from the College of William & Mary and University of Virginia and awarded by the University of Virginia.

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.

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.

<p>In 2016, chestnut oak (<em>Quercus prinus</em>) trees across southern Indiana began displaying symptoms of decline disease. In the years following, widespread patches of mortality appeared on slopes and along ridges, prompting the Indiana Department of Natural Resources (IDNR) to investigate. The IDNR noted the presence of <em>Phytophthora cinnamomi </em>on one diseased chestnut oak, leading to the initiation of this study. Our goals were to (1) determine if <em>P. cinnamomi </em>contributed to the widespread decline, (2) determine what site or stand variables were associated with higher rates decline, (3) examine the growth of declining trees prior to the onset of symptoms to determine if drought contributed to decline, and (4) use Forest Service Forest Inventory and Analysis (FIA) data to examine trends in regional chestnut oak mortality.</p> <p>From 2021-2022, we collected thirty fine root and soil samples from declining chestnut oak trees within Morgan-Monroe State Forest, Yellowwood State Forest, and the Hoosier National Forest. Throughout these forests, we established sampling plots within declining and healthy chestnut oak stands. In each plot we recorded site, stand, and tree level variables, then collected tree cores from two or three chestnut oak trees. Fine root samples were tested for the presence of <em>P. cinnamomi </em>at the Purdue Pathogen and Pest Diagnostic Laboratory (PPDL) in West Lafayette, Indiana.</p> <p>We used binomial linear regression to test for significant (α = 0.05) relationships between site and stand variables and decline, where a binary decline or no decline was used as the response variable. Both basal area increment (BAI) and ring width index (RWI) chronologies were built separately for healthy, declining, and dead chestnut oak trees. We used a paired t-test (α = 0.05) to test for significant differences in 10-year segments of BAI between the three chronologies. Finally, we used linear regression to test for significant (α = 0.05) effects of the standardized precipitation-evapotranspiration index (SPEI) in current and previous year growing seasons on RWI. Chestnut oak mortality volume across the eastern United States was calculated using the EVALIdator tool provided by USDA-FS FIA. Associations between chestnut oak mortality recorded by FIA and several climate and topographical variables were examined using a random forest classification.</p> <p>Out of thirty fine root samples, only one tested positive for the presence of <em>P. cinnamomi</em>, indicating that this decline was not associated with the pathogen. The analysis of site and stand variables revealed a greater chance of decline on east and northeastern facing slopes, with a slight increase in decline likelihood with increasing stand density. There was significantly lower BAI in dead and declining trees long before decline symptoms began, a pattern consistent with previous drought induced declines. We observed a significant relationship between RWI and SPEI in the early growing season (June and 3-month June SPEI) and throughout almost all of the prior year’s growing season (May, June, 3-month June, 3-month July, and 3-month August SPEI). Chestnut oak mortality volume across the eastern US steadily increased from 2006-2020, indicating a region-wide increase in mortality. Our random forest classification indicated the importance of increased precipitation and precipitation timing on chestnut oak mortality.</p> <p>Chestnut oak decline observed in southern Indiana was induced by a series of droughts in 2005, 2007, and 2012. The greater early life BAI of chestnut oak which were impacted by decline revealed that individuals which likely prioritized stem growth over root growth were predisposed to decline and mortality from these droughts. This prioritization could be brought on by genetic differences, favoring rapid height growth in developing even-aged stands, or by an abundance of moisture availability. Our FIA analysis of mortality revealed increased mortality volume across many states from 2006-2020, and that chestnut oak mortality may be related to greater precipitation compared to historic levels. Considering these results, we suspect that chestnut oak which have recently died or are currently declining are likely individuals which lack the root system to endure repeated drought.</p>