“Captorhinikos” chozaensis is a multiple-tooth-rowed captorhinid reptile from the Lower Permian Clear Fork Group, undivided formation. Upon re-examination of the materials associated with the species from both the Chicago Field Museum of Natural History, and the Smithsonian United States National Museum, I reaffirm their affinity and collective identity as a valid taxon. “Captorhinikos” chozaensis does not, however, belong with either of the two members of its genus, C. valensis or “C.” parvus, instead occupying its own branch on the phylogenetic tree of the Captorhinidae. This conclusion is based in strong results from a combined phylogenetic parsimony analysis combined with an analytical apomorphy analysis. I then conclude the current designation “Captorhinikos” chozaensis to be a nomen ambiguum.

‘Aigarchaeota’, a deeply branching lineage in the domain Archaea with no cultivated representatives, includes both thermophilic and hyperthermophilic microorganisms that reside in terrestrial and marine geothermal environments. The ‘Aigarchaeota’ consists of at least nine proposed genus-level groups that have been confirmed via 16S rRNA sequencing, with ‘Aigarchaeota’ Group 1 (AigG1) being the focus of this study. Based on cultivation-independent genomic data available from several AigG1 members in Great Boiling Spring (GBS), NV, and Yellowstone National Park, 22 different types of growth media were designed and tested for their ability to support growth of AigG1. One of these cultures, G1-10, was found to contain AigG1 at ~5% abundance, as well as other novel thermophilic microbial groups including a new species of the genus Pyrobaculum, members of the candidate phyla ‘Calescamentes’ and ‘Fervidibacteria’, and the novel archaeal lineage NAG1 (‘Geoarchaeota’). To attempt to obtain pure cultures of AigG1 and other novel thermophiles, a single-cell sorting system using an optical trap and a microfluidic device was constructed. The system was validated by sorting E. coli cells, which demonstrated that single, viable cells could be reliably obtained. Using this single cell sorting device on the G1-10 culture, a pure culture of a member of the genus Pyrobaculum was obtained, which was shown to represent a distinct species in this phylum by whole genome sequencing and in silico DNA-DNA hybridization. Additionally, a pure culture of the first representative of the candidate phylum ‘Fervidibacteria’ from an enrichment culture derived from G1-10. Additionally, to aid in morphology-based sorting of AigG1 and stable isotope labeling studies, fluorescence in situ hybridization (FISH) based on catalyzed reporter deposition (CARD-FISH) were developed and an AigG1-specific probe was tested. CARD-FISH was successfully used to detect AigG1 in both the G1-10 culture and in natural sediment samples from GBS. Stable isotope labeling incubations were performed with a variety of 13C-labeled substrates (bicarbonate, amino acids, sugars, and short chain fatty acids) on GBS sediments and G1-10 culture samples, and CARD-FISH was used to specifically detect AigG1 in the fixed samples. Nanometer-scale secondary-ion mass spectrometry (nano-SIMS) will then be used to determine whether AigG1 was capable of taking up the different carbon substrates tested. Overall, the results and accomplishments from this project and follow up nano-SIMS analysis will allow a better understanding of the metabolic potential of AigG1 and will aid future efforts to attempt to obtain pure cultures of this novel lineage.

Sediment accumulated in lakes stores valuable information about past environments and paleoclimatological conditions. Cores previously obtained from Saint Albans Bay, located in the Northeast Arm of Lake Champlain, VT record the transition from the Champlain Sea to Lake Champlain. Belrose (2015) documented the presence of a peat horizon separating the sediments of the Champlain Sea from those of Lake Champlain. Initially, this layer was thought to comprise the transition from the marine environment of the Champlain Sea to a freshwater wetland. However, based on the results from this study, the transition between marine and freshwater conditions is thought to be represented by an erosional unconformity, indicative of a lowstand at the end of the Champlain Sea period. For this study, five additional cores were collected from Saint Albans Bay along a transect following the long axis of the bay moving into progressively deeper water. These cores better constrain the spatial extent, thickness and age variability of the peat layer within the bay and allow us to better understand the environmental conditions that preceded the period of peat deposition. In each of the cores there is evidence of sediment reworking in the uppermost Champlain Sea sediments, indicated by the presence of coarse-grained sediment, which is suggestive of a lowstand at the end of the Champlain Sea period before the inception of Lake Champlain. This coarse-grained layer is immediately overlain by a thick peat horizon. The widespread occurrence of the peat layer points to a large wetland that occupied the entire inner portion of Saint Albans Bay, and lake level ~ 9 m lower than at present during the Early Holocene. Based on radiocarbon dating, this paleo-wetland existed in Saint Albans Bay from ~ 9,600-8,400 yr BP. The development of this wetland complex is time transgressive, reflecting rapidly increasing lake level during the Early Holocene. This hypothesis is supported by the basal peat radiocarbon dates, as well as by the composition of plant macrofossils recovered from the peat horizons. The shift from peat deposition to fine-grained, low organic content lacustrine sedimentation is believed to have occurred at ~8.6-8.4 ka and is likely the result of continued isostatically driven lake level rise coupled with a changing climate. Although it was not its primary focus, this study also seeks to address the variations in sediment composition in the Lake Champlain sections of the cores. Evidence from the Lake Champlain record in Saint Albans Bay indicates that there were notable fluctuations in sedimentation, which were likely linked to both climatic variations and a change in the morphology of the bay. The rebound in productivity from ~8-5 ka is likely the result of warmer conditions during the Hypsithermal period. An increase in terrigenous sedimentation during this same time suggests a change in the morphology of the bay in which the Mill River delta migrated towards the inner bay. Initially, the cooler conditions of the Neoglacial are reflected in Saint Albans Bay by a decrease in organic matter content from ~5-3 ka. During the latter part of the Neoglacial (~3-1 ka), increases in organic matter content and detrital input point to enhanced productivity in response to increased precipitation and runoff from the watershed. The most recently deposited sediments in Saint Albans Bay bear out the legacy of anthropogenic nutrient enrichment of the bay in the form of increased algal productivity.

Parasitic wasps are highly diverse and play a major role in suppression of herbivorous pest populations, but relatively little is known of the mechanisms driving their diversity. Molecular studies indicate that cryptic species complexes resulting from adaptations to specific hosts or host-foodplants may be common. The gregarious endoparasitoid, Cotesia congregata (Braconidae), is a model system for understanding parasitic wasp biology. It is reported to attack at least 15 species of sphingid caterpillars, most of which are plant family specialists. Molecular studies have demonstrated genetic differentiation of two host-foodplant complex sources originating from Manduca sexta on tobacco (MsT) and Ceratomia catalpae on catalpa (CcC). Response to female pheromone and elements of their courtship songs differ. Wasps from both sources mated and produced F1 hybrid offspring in the laboratory; however, 90% of hybrid females resulting from one of the reciprocal crosses failed to produce offspring. I built on this previous work by evaluating an ecological barrier, the evolution of courtship songs within the genus, and patterns of hybrid sterility among four additional host-foodplant complexes, as well as differentiation of their symbiotic bracovirus. Tests of developmental tolerance to nicotine demonstrate that MsT wasps are highly adapted to hosts feeding on tobacco, whereas CcC wasps experience high mortality. Acoustic analysis of courtship songs among host-foodplant sources of C. congregata and eleven additional species of Cotesia demonstrates that songs are species specific and appear to be correlated with genetic relatedness. Cotesia congregata from all sources mated and produced F1 hybrid offspring in the laboratory; however, hybrid females resulting from specific reciprocal crosses failed to produce progeny. Dissections of hybrid females revealed that sterile wasps lacked mature ovaries and functional bracovirus, a symbiotic virus integrated into the wasp genome and necessary to suppress the host immune system. Relative in vivo expression of wasp bracovirus genes differs between MsT and CcC host-foodplant complexes. Cumulatively, these behavioral, ecological, and genetic barriers to reproduction indicate that C. congregata is diverged into two incipient species with limited gene flow, and provides insight into the role of varied reproductive barriers in speciation of parasitic wasps.

Native bees are only recently gaining attention for the extent to which they aid in pollination and ecosystem services. These services are threatened by predictions of warming temperatures if bees are not able to respond. Voltinism - the number of generations produced annually- can strongly influence thermal conditions experienced by both developing and adult bees based on emergence strategies for each voltinism type. Differences in experienced thermal conditions brought on by climate change could therefore affect upper thermal limits (UTL) in bees. This study observes UTLs across a foraging season within and among native bee species vi to elucidate the potential response by bees to a warming climate. Bees were collected across the field season in Central Virginia and subjected to dynamic ramping trials to determine the fatal knockdown point (FKP). Results show in both univoltine and multivoltine bees an increase in upper thermal tolerance as the foraging season progresses (in quadratic and linear fashions respectively). Within multivoltine bees, FKP was related to nest type; with stem-nesting bees having the highest FKP. All average FKPs were higher than historic air temperatures of the study region, but within several degrees of the highest recorded maximum temperature. The diversity of responses in native bees provides evidence for both genetic and plastic responses to extreme temperature. While bees still face a potential myriad of other issues brought on by climate change, the observed increases in FKP across warming temperatures offer tentatively hopeful predictions for limited physiological responses in native bees to a warming climate

Wildlife in captivity has a long history of benefiting global conservation goals. Captive animals can raise awareness and appreciation for the conservation of endangered species. Additionally, captive animals can be used as source populations to reintroduce animals back to the wild or to supplement existing wild populations. The rapid increase in amphibian species threatened with imminent extinction has necessitated the creation of dozens of captive-breeding programs. The focus of this dissertation has integrated topics across the spectrum of animals in captivity and the wild, and the results provide useful recommendations for conservation action. First, I describe how market pressures over a 28-year period are causing meteoric increases in the prices of amphibians sold in the pet trade, indicating a high risk of overexploitation. Pet amphibians may facilitate greater understanding and appreciation of amphibians, but the pet trade must be sustainable. Improving amphibian husbandry will increase the number of captive-bred animals available in the pet trade, and it will allow greater production of threatened species for reintroductions. Secondly, by performing a systematic review of husbandry for 289 amphibian species native to the US, I identified a critical lack in taxon-specific husbandry and developed husbandry research prioritizations. Next, I used a combination of laboratory and field studies to examine domestication processes in amphibians by comparing defensive behaviors in two species of captive-bred and wild poison frog. Captive-bred amphibians had significantly reduced defensive behaviors compared to wild conspecifics, likely resulting from habitation processes related to their husbandry. Finally, I performed three reintroductions of the critically endangered Wyoming Toad (Anaxyrus baxteri) in Wyoming, US. I demonstrated how providing a transitionary period, called a soft-release, to captive-bred toads moving to a novel, wild environment can improve reintroduction success. My work illustrates how improving our understanding of the nexus between captivity and the wild can improve conservation action for endangered species.

Herbivory is thought to be nutritionally inefficient relative to carnivory and omnivory. But, herbivory evolved from carnivory in many lineages, suggesting that there are advantages to eating plants. To understand the adaptive significance of the transition from carnivory to herbivory, I proposed five hypotheses for the adaptive evolution of herbivory and reviewed the current freshwater literature to identify conditions where eating plants might be adaptive over eating animals. I tested three of these ideas (Suboptimal Habitat, Heterotroph Facilitation, and Lipid Allocation) using the herbivorous Sailfin Molly (Poecilia latipinna)and identified each as a potential mechanism for the evolution of herbivory. To understand the origins of herbivory in Sailfin Mollies, I reconstructed ancestral habitats and dietsacross a phylogeny of the genus Poeciliaand then used phylogenetically independent contrasts to identify patterns of diet evolution. I found that the degree of herbivory increases with increasing salinity affiliation, suggesting that in this genus, herbivory evolved as an adaptation for invading less productive saline habitats from freshwaters. This result is consistent with the Suboptimal Habitat hypothesis, which states that herbivory allows organisms to invade and persist in ‘suboptimal’ habitats. To understand how herbivory is maintained in extant populations, I raised juvenile Sailfin Mollies in mesocosms and enclosure cages placed in the Everglades to document that dietary autotrophic lipids play a role in early life history by supporting rapid growth (Lipid Allocation). However, dietary bacterial fatty acids promoted fish survival, consistent with the Heterotroph Facilitation hypothesis, which states that indirect detritivory supplements the herbivorous diet. Finally, I quantified periphyton quality/availability and consumer density across the Everglades landscape to examine the correlates of trophic dynamics in nature. Results revealed that herbivores can persist in diverse habitats and survive on varying resources when habitats are unfavorable, supporting the Suboptimal Habitat hypothesis.

Urban landscapes are quickly replacing native habitat around the world. As wildlife and people increasingly overlap in their shared space and resources, so does the potential for human-wildlife conflict, especially with predators. Bobcats (Lynx rufus) are a top predator in several urban areas across the United States and a potential contributor to human-carnivore conflicts. This study evaluated the movements and habitat use of bobcats in the Dallas-Fort Worth (DFW), Texas metroplex. Spatial data were collected from 10 bobcats via Global Positioning Satellite (GPS) for approximately one year. Average home range size was 4.60 km2 (n=9, SE=0.99 km2) for all resident bobcats, 3.48 km2 (n=5, SE=1.13 km2) for resident females, and 6.00 km2 (n=4, SE=1.61 km2) for resident males. Resource selection function (RSF) models show that bobcats avoid areas close to and far from grasslands and low-medium development, while selecting for these areas at intermediate distances. Bobcats also selected areas closer to developed open space, agricultural areas, and railroads. In addition, camera trap data analyzed with spatially explicit capture-recapture (SECR) models informed by the RSF results estimated a population density of 0.64 bobcats/km2 (SE = 0.22). Bobcats in DFW have significantly smaller home ranges and occur at higher densities compared to rural bobcat populations. Home ranges were also slightly smaller and densities higher than the most closely similar peri-urban bobcat studies. These differences likely arise due to the abundant urban prey species the DFW landscape provides despite limited space and habitat for bobcats. The dense urban development surrounding this population of bobcats may also discourage dispersing from the area, and contributing to higher densities. These results provide information to facilitate management of urban bobcats by providing new insight into how bobcats live amidst people in urban areas.

World-wide amphibian declines sparked concern and encouraged investigation into potential causes beginning in the 1980’s. Infectious disease has been identified as one of the major potential contributors to amphibian declines. For example, Ranavirus has caused amphibian die-offs throughout the United States. Investigators isolated Ranavirus from dead or moribund amphibians during large-scale die-offs of amphibians in the Cades Cove area of Great Smoky Mountains National Park in 1999-2001. In 2009, after nearly a decade without follow-up monitoring, I undertook an investigation to determine if the virus persisted in the area, and if so, to assess spatial, temporal, and taxonomic patterns in prevalence. Three amphibian breeding ponds, including Gourley Pond, the site of these earlier mortality events, were monitored for Ranavirus during the 2009 amphibian breeding season. A peak in prevalence occurred at Gourley Pond corresponding to a massive amphibian die-off. Prevalence varied among three different taxonomic groups during this mortality event with the highest prevalence, 84%, detected in larval Ambystomatids, 44.4% prevalence in adult Newts, and no virus detected in adult Plethodontids. I did not detect virus at either of the other two breeding ponds despite equivalent sampling effort, similar community composition, and close proximity to Gourley Pond. These results suggest that the severity and spatial extent of Ranavirus in Cades Cove remains unchanged since its initial detection a decade ago. Also, despite the observed massive die-offs there is no evidence of local amphibian extinction at Gourley Pond.

Hardwood bottomland ecosystems provide critical habitat for various wildlife among numerous ecosystem services. Since the 1800s, these forested wetlands have been logged and drained for agriculture. The federal government passed a series of legislative acts that protected wetlands and provided monetary support for restoration. The Wetlands Reserve Program (WRP) was established in 1990 with the goal of restoring ecological function in wetlands. Although several studies have measured plant and wildlife responses to WRP restorations, no standard protocol has been developed to monitor the state of ecological restoration at sites. Index of biotic integrity (IBI) models are commonly used to evaluate ecological function by assigning scores derived from biological characteristics measured at disturbed sites and comparing them with reference sites. Therefore, the objectives of my study were to: (1) characterize vegetation, amphibian and bird communities among 17 WRP restoration and 4 reference bottomland sites, and (2) develop IBI models for these communities to use in monitoring ecological restoration. My study was conducted across 10 counties in western Tennessee from March – August 2008, and communities were measured using standard sampling techniques. I detected 15 amphibian and 95 bird species at bottomland WRP sites, which ranged 2 – 21 years old. Anurans were common among sites, but salamanders were only detected at reference sites containing mature forests. The bird community changed predictably in response to succession, with grassland birds dominating young restoration sites and scrub-shrub and forest birds dominating older restoration and reference sites. Vegetation structure was related to site age, and a good predictor of bird community composition. Variables retained in the vegetation IBI model included density of snags, logs and overstory trees, basal area, and percent vertical cover measured using a profile board. The bird IBI model contained relative abundance of bark feeding, branch nesting, and twig nesting guilds. Presence of salamanders was the only variable in the amphibian IBI model. My results indicate that the WRP is contributing to the regional biodiversity of western Tennessee. The IBI models that I developed can be used for monitoring ecological restoration in Tennessee hardwood bottomlands; however, their applicability outside this region should be validated.