<p dir="ltr">Small populations often fail to thrive, as the low levels of variation that are frequently present in small populations hinder the ability to acclimate and adapt to future environmental challenges. Despite this well-known phenomenon, many small populations persist but the factors that mediate the success of these populations are often poorly understood. In this dissertation, I conduct three studies that vary in scope and scale to better contextualize the ecological and evolutionary contexts that may lead to small population persistence. The first chapter synthesizes the theoretical and empirical evidence that allelic dominance can exert a strong influence on genetic diversity after a sharp population reduction. My findings demonstrate that dominance of one allele over another can increase additive genetic variation after a population reduction. However, maintaining the maximum amount of additive variation possible with allelic dominance may require more individuals than if two alleles have only additive effects. The second chapter focuses on elucidating the patterns of establishment and spread of three invasive anuran species that underwent sharp population declines upon their introduction to novel environments. The results from my study highlight different introduction and establishment histories that have all led to the success of each invasive species. The third and final chapter evaluates the maintenance of genomic variation in a small population with strong sexual selection, a process expected to erode variation. I tested the fit of empirical genomic and phenotypic variability data to theoretical models and found little support for the hypothesis of genic capture to maintain genetic variation. I thus discuss alternative mechanisms that may be responsible for maintaining diversity in this system. The maintenance of variation in small populations involves a complex interplay of ecological, environmental, and evolutionary forces but understanding how variation is sustained in small and imperiled populations is crucial for addressing challenges in conservation biology and the management of invasive species.</p>

As the global population rises, the demand for food increases which underscores a need for improvement in food security. Disease pressures are a major concern surrounding sustainable agriculture. Static crop populations, containing little to no genetic diversity, are vulnerable to diverse pathogen populations. Wild relatives of crop plants are a reservoir for new disease resistance traits that can be introgressed into cultivated crops. The identification of novel disease resistance is of paramount importance because pathogen co-evolution is not only defeating current resistance genes (R genes) but chemical controls as well. Phytophthora sojae (P. sojae), the causal agent of Phytophthora root and stem rot disease, reduces soybean harvests worldwide. We developed an approach to screen for new R genes that recognize core effectors from P. sojae. We expect R genes identified by these screens to be durable because P. sojae requires core effectors for virulence. We utilized effector-based screening to probe Glycine soja germplasm with core RXLR effectors from P. sojae to search for novel R genes. We developed segregating populations from crosses of P. sojae resistant G. soja germplasm with susceptible G. max cultivar Williams to determine inheritance of potential R genes in germplasm that responded to core effectors. We are using marker assisted breeding to map disease resistance traits in recombinant inbred (RI) lines. To better understand pathosystems, we examined host resistance and susceptibility using bioinformatics. We analyzed the interaction between Arabidopsis thaliana ecotype Col-0 and Hyaloperonospora arabidopsidis isolate Emwa1 using a publicly available RNA time-course experiment. We describe a new algorithm to sort genes into time-point specific clusters using activation and repression parameters. Gene ontology annotations were used to identify defense genes with unique expression profiles, and A. thaliana null mutants for these genes were significantly more susceptible to Emwa1 than wild-type. We plan to use these tools to rapidly identify and guide introgression of durable disease resistance into crop species. / Ph. D.

Artificial shelters show great promise as novel, non-invasive tools for studying hellbenders, but their use thus far has faced several challenges. During initial trials in multiple river networks, artificial shelters routinely became blocked by sediment and dislodged during high stream discharge events, and were rarely used by hellbenders. We sought to determine whether these complications could be overcome via alternative shelter design, placement, and maintenance. Between 2013 and 2018, we deployed 438 artificial shelters of two different designs across ten stream reaches and three rivers in the upper Tennessee River Basin. We assessed evidence for several hypotheses, postulating broadly that the availability, stability, and use of artificial shelters by hellbenders would depend on how shelters were constructed, deployed, and/or maintained. We found that maintaining shelters at least once every 40 days limited sediment blockage, and building ~ 40 kg shelters with 3-4 cm thick walls and recessed lids improved their stability during high discharge events. Additionally, we found that hellbenders most frequently occupied and nested in artificial shelters when they were deployed in deeper (~50+ cm) portions of reaches with high adult hellbender densities. Our results suggest that artificial shelters can serve as effective tools for studying hellbenders when designed, deployed, and maintained with these advancements, but also highlight some limitations of their use. / Master of Science / Hellbenders are large, fully-aquatic salamanders that live primarily in cool, rocky, swift-flowing streams in portions of Appalachia and the lower Midwest. They are imperiled across most of their native range due to human-caused habitat degradation, but their declines, conservation needs, and population status have historically been difficult to study due to the fact that they spend the majority of their lives beneath large, often inaccessible boulders. While these boulders are sometimes possible to lift, doing so can disturb critical hellbender habitat. Therefore, alternate, less invasive hellbender sampling methods are necessary in order to improve knowledge about their conservation status and needs. Artificial shelters, which are large, hollow, concrete structures that mimic natural boulder crevices and feature removable lids, show promise as a novel, innovative tool for non-invasively studying hellbenders. However, initial trials of these shelters have yielded mixed results, with shelters often becoming swept away and destroyed during floods, becoming blocked by sand and sediment and thus inaccessible to hellbenders, or simply not being used by hellbenders when accessible. We sought to determine whether these complications could be overcome by optimizing the way that shelters were constructed, deployed, and maintained in streams inhabited by hellbenders. Between 2013 and 2018, we deployed 438 artificial shelters of two different designs across ten stream reaches and three rivers in the upper Tennessee River Basin. Using multiple analyses, we tested one broad overall hypothesis: that the efficacy of using artificial shelters to study hellbenders would depend on how they were constructed, how frequently they were maintained, and where they were placed in the stream. We found that maintaining shelters at least once every 40 days limited sediment blockage, and building ~ 40 kg shelters with 3-4 cm thick walls and recessed lids improved their stability during flood events. Additionally, we found that hellbenders most frequently occupied and nested in artificial shelters when they were deployed in deeper (~50+ cm) portions of reaches with high adult hellbender densities. Our results suggest that artificial shelters are effective tools for studying hellbenders when designed optimally, maintained frequently enough, and placed in appropriate locations. However, exceptions to these findings may exist in certain heavily degraded stream reaches.

The red imported fire ant, Solenopsis invicta, is an abundant and aggressive component of early-successional communities in the southeastern United States. After disturbance, it rapidly invades new habitats, and once there, it has strong competitive and predatory effects on the existing arthropod community. In upland coastal plain pine forests at the Savannah River Site in South Carolina, I conducted two studies of fire ant ecology. In my first study (chapter 1), I investigated the way in which fire ants colonize early-successional road and powerline cuts through forests, and I tested whether some of these linear habitats provided better fire ant habitat than others. I found that fire ant mound density (#/ha) was similar in narrow dirt roads and in wider roads with the same intermediate level of mowing disturbance, and that density was lower in wide powerline cuts where the vegetation is only removed every five years. Furthermore, mound density was greatest near the edges of cleared roads and powerline cuts and was also greater on the northern sides of roads and powerline cuts where there was less shading from the adjacent forest. Results from this study suggest that allowing increased shading from adjacent forest vegetation, especially along northern roadside edges, would limit the suitability of road and powerline cuts as fire ant habitat, thereby slowing invasion. In my second study (chapter 2), I examined the impact of fire ants on arthropod and plant species in early-successional forest gaps. In a tritrophic system, I tested whether the top-down effect of insect herbivore consumption by fire ants was strong enough to cascade through two trophic levels and improve plant growth and fitness. I compared this potential effect to that of other arthropod predators in the community. I found that fire ants controlled the level of tissue damage to plant leaves by herbivores, but that the damage was not severe enough to influence plant growth or fitness. Fire ants had stronger negative interactions with insect herbivores than other predators in the community, and for this reason, fire ants can be considered keystone predators. This project provides further evidence that fire ants successfully invade even small patches of early-successional habitat that exist within larger matrices of uninhabitable, late-successional forest, and that once there, they have a dramatic effect on the arthropod community. Restricting the amount of early-successional habitat within southeastern forests, either as permanent road and powerline cuts or as temporary gaps, would limit the potential for strong and detrimental effects by the invasive fire ant. / Master of Science

Iron corrosion is an extremely complicated process because numerous factors such as pH, DO, temperature, inhibitor, and other various constituents in water can exert a controlling influence. The economic importance of problems that are caused by corrosion has been recognized. Therefore, the necessity of better understanding corrosion phenomenon is apparent. The effect of phosphorus, especially in oxidation states different than phosphate (+V) (e.g., PO3-3, PO2-3 and PH3 gas), on anaerobic iron corrosion was examined. Tests were conducted at pH 3, 7, and 10- 11 in a solution of 10-3 M NaCl. There was not a significant catalytic effect of phosphorus species on anaerobic iron corrosion. Higher levels of PH3 did markedly increase H2 evolution, consistent with observations of other researchers, but it is possibly due to oxidation of PH3 by iron surfaces with production of H2. Various constituents were also tested for iron corrosion in anaerobic solution [Al3+ (soluble), Al(OH)3, Cu2+, Si(OH)4, Boron, NOM, and sulfide] at pH pH 3, 7, and 10-11. None of these appeared to inhibit corrosion compared to a control. At pH 7, soluble Al3+ and Cu2+ in solution led to much higher production of H2 relative to a control. Phosphorus species had little impact on iron corrosion rates in the presence of sulfides (198 mg/L as S2-). In much of the research, recovery of H2 in the headspace was much lower than was predicated based on classic equations. This implies that some other, and as yet unappreciated, reactions are occurring in this system. However, in other instances the recovery of hydrogen was consistent with classical theory. Future work should examine the circumstances in which agreements and disagreements with classic theory occur. / Master of Science

Invasive species are reported as one of the top current and future concerns for the health and functioning of native ecosystems. In response, identification of invasive plant impacts are one of the top most studied aspects of plant invasions. Yet we still know very little about invasive plant impacts, and many land managers remove invasive plants not because of known negative impacts, but because of the general negative connotation associated with invasions. Here, I develop and utilize integrative methods to more holistically measure the ecological impacts of invasive plants. I develop a meta-analysis of current invasive plant impact literature, I integrate independent ecosystem metrics into holistic measures of total ecological impact, I examine the potential for legacy and temporal effects in newly established and recently managed invasions, and I measure ecological impact of co-invaded ecosystems. Through these studies, I find that magnitude, and not direction, of impact better represents actual ecosystem changes when evaluating invasions holistically. I also find invasive plant management may not only fail to remove long term legacy effects, but may in some cases further negatively impact the plant community. Finally, I find that co-invaded systems are not intrinsically worse off than single invaded systems. Collectively, these studies help to better our understanding of the impacts of invasive plants and their implications for management, and show that simple attempts at eradication may not always be desirable. / Ph. D.

All species on Earth occupy limited geographic space. More than a century of observational, experimental, and theoretical work investigating the factors that drive species distributions have demonstrated the importance of the interactions between abiotic, biotic, and demographic factors in determining why species are found where they are. However, it is still unclear when and where these factors interact to set species range limits. Filling the existing knowledge gaps is imperative for the accurate predictions of how species will respond to global change, and particularly for invasive species, many of which are expected to benefit from global change. Here, I sought to investigate the mechanisms that enable, as well as limit, the range expansion of the globally invasive plant Sorghum halepense (L.) Pers. (Johnsongrass). I performed a series of field and laboratory experiments to study population and range dynamics throughout Johnsongrass's North American distribution, and test for the effects of climate, local habitat, and competition on multiple functional traits. I found Johnsongrass consistently demonstrated impressive performance across varying environments, often growing more than 3 m tall, producing hundreds of flowering culms within a single growing season, and maintaining positive population growth rates, even under intense competition with resident weeds. I also found evidence that seed germination has adapted to varying climates encountered during Johnsongrass's range expansion resulting in a shift in the germination temperature niche from warmer to cooler as Johnsongrass spread from warmer climates in the south to more temperate climates in higher latitudes. This shift in the germination temperature niche may have been an important contributing factor in the range expansion of Johnsongrass by enabling the optimization of seed germination in varying climates. On the other hand, results from a field study suggested a possible trade-off between flowering time and growth in populations originating from the range periphery (i.e., range boundary) which may be limiting, or slowing, continued range expansion of Johnsongrass. Together, the outcomes of this work contribute to our understanding of the factors involved in the distribution of species, which is a fundamental goal of Ecology, and essential to accurately predict how invasive species will respond to global change. / Doctor of Philosophy / Invasive species threaten our natural ecosystems, our agricultural systems, and even our infrastructure, and we spend billions of dollars each year attempting to control them and reduce their negative impacts. Climate change, habitat destruction, and other forms of global change, will benefit many of these species, magnifying their impacts and promoting their invasion into new territories. Because of the damaging effects of invasive species, and the costs to control them, it is imperative that we are able to predict how they will respond to global change so that we can improve plans to reduce their impact and spread. First, we need to understand the processes that promote their invasion across large swaths of land. Just as importantly, we must study the processes that prevent their invasion of certain areas. Here, I investigated some of the processes that have facilitated, as well as hampered, the spread of the invasive plant Johnsongrass. For this work, I used Johnsongrass plants originating from different habitats, including regions where Johnsongrass is highly invasive and those where Johnsongrass is very rare. I found Johnsongrass originating from regions where it is highly invasive were able to grow very large and produce thousands of seeds that were able to germinate under a range of conditions. These traits may have contributed to the invasion success of this species. However, I found a different pattern for plants that originated from regions where Johnsongrass is rare. These plants reached reproductive age earlier and grew smaller across all environmental conditions, potentially due to the less hospitable climates of these range edges. These findings allow us to project into future climate change scenarios, because it is likely that, as temperatures warm, invasive species will be able to invade new regions, where they will impact the work of conservationists, natural resource professionals, agricultural produces, and other land managers.

The study of shock-waves in supersonic plasma jets is essential to understanding the complex dynamics involved in many physical systems. Specifically, ion-species separation caused by a shock wave propagating through a plasma is an important but not yet well understood phenomenon. In inertial confinement fusion implosions, a shock wave precedes the rapid compression of a fuel pellet to ignition conditions that theory and computational studies suggest may be separating the fuel and reducing the neutron yield. In astrophysics, the shock wave produced when a supernovae explodes has been shown to have an effect on nucleosynthesis as a result of shock heating. In both these cases the time and length scales make them difficult to study experimentally, but experiments on more reasonable scales can shed light on these phenomena. This body of work provides the basis for doing just that. The work begins by describing the development of a small, linear, plasma-armature railgun designed to accelerate plasma jets in vacuum to high-Mach-number. This is followed by discussion of an experimental campaign to establish a plasma parameter space for the jets, in order to predict how effectively the accelerator can be used to study centimeter-scale shock structures in jet collisions. The final section presents an experimental campaign in which jet collisions are induced, and the resultant structures that appear during the collision are diagnosed to assess how conducive the experiment is to the future study of shock-wave induced species separation in laboratory plasmas. This work is a foundation for future experimental studies of ion-separation mechanisms in a multi-ion-species plasma. This research was supported in part by the National Science Foundation under grant number PHY-1903442. / Doctor of Philosophy / Plasma, the so-called fourth state of matter, is an ionized gas that often behaves like a fluid but can also become magnetized and carry an electric current. This combination leads to a lot of interesting yet often un-intuitive physics, the study of which is very important for understanding a wide array of topics. One subset of this field is the study of shock-wave induced species separation. Just like the shock-wave a jet aircraft produces when it moves through the air at a speed greater than the speed of sound, a plasma shock is characterized by a large change in parameters like density, temperature, and pressure across a very small region. A shock-wave propagating through a plasma can cause different ion species present to separate out, a phenomenon that is driven by the gradients that are present across a shock front. Understanding how these mechanisms work is important to a number of applications, including fusion energy research and astrophysical events. The first section of this work discusses the design and development of a plasma-armature railgun, a device that can produce and accelerate jets of plasma to high-Mach-number within a vacuum chamber. The next and most substantive section of the work presents results from experimental campaigns to characterize the accelerated plasma jets and then to induce plasma-jet collisions with the hope of producing shock-waves that exist on time and spatial scales that can be readily measured in a laboratory setting. This work is a foundation for future experimental attempts to measure separation induced by a shock-wave in order to better understand these complex phenomena.

Neurons have an extremely high rate of energy consumption and use mitochondrial-derived ATP as the primary energy source to drive biochemical processes involved in various functions. Consequently, neurons produce reactive oxygen species (ROS) as 'by-products' of oxidative phosphorylation. Excessive levels of ROS are highly detrimental to neurons as ROS can directly oxidize and induce damage to cellular macromolecules including lipids, DNA and proteins. Hence, the high-energy demands of neurons, together with their high levels of ROS production, place them at risk during conditions of stress, which occur during aging and in neurodegenerative disorders including Alzheimer's and Huntington's disease. Uncoupling proteins (UCPs) belong to a family of inner mitochondrial membrane proteins initially identified as regulators of thermogenesis in fat cells wherein they uncouple energy-substrate oxidation from mitochondrial ATP production, resulting in the production of heat. UCPs also regulate ROS production from mitochondria by physiologically lowering the mitochondrial membrane potential below the critical level for ROS production. Because of their important role in co-regulating energy metabolism and ROS production, there has been considerable interest in the functions of UCPs. Neurons express at least three UCPs including the widely expressed UCP2 and the brain- specific UCP4 and UCP5. Despite a great deal of interest, to date neither the molecular mechanism nor the biochemical and physiological functions of brain UCPs are well understood. Our previous studies showed that UCP4 is highly expressed in subpopulations of neurons with high energy demands. Knockdown ofUCP4 expression in cultured primary neurons markedly enhances neuronal death suggesting that endogenous UCP4 is critical for neuronal survival. Expression of UCP4 shifts cellular ATP synthesis from oxidative phosphorylation to anaerobic glycolysis, which might be beneficial to cell survival. In this study, we investigated the underlying mechanism of UCP4-mediated metabolic adaptation in response to mitochondrial inhibition. We found that UCP4 enhances glucose uptake and glycolysis which may compensate for the reduced supply of ATP from compromised mitochondria. In addition, the activation of mitogen activated protein kinases (MAPKs) and several transcription factors play a role in augmenting nonoxidative synthesis of ATP in response to metabolic stress possibly by acting downstream of UCP4. Elucidating the underlying mechanism(s) whereby this brain UCP mediates metabolic adaptation in response to mitochondrial inhibition will likely lead to the development of novel preventative and therapeutic strategies for neurodegenerative disorders.

The Caretta caretta, or Loggerhead sea turtle, is a protected species found across all temperate and subtropical oceans. Previous research has identified that the Caretta caretta has preferences for nesting sites based on beach width, beach slope, and vegetation coverage, which facilitated the development of a nesting site suitability index. In this thesis, these indices were integrated with standard coastal geomorphology metrics in the ESRI Suitability Modeler to pinpoint potential nesting locations for the C. caretta on various beach reaches. The results were then validated against observed nesting site data. The results of this study can inform critical decisions regarding beach use and maintenance as it pertains to sea turtle conservation. Overall, this study demonstrates the utility of geospatial analysis and suitability models in understanding and safeguarding sea turtle nesting habitats.