The occurrence and ecology of the apicomplexan parasite Toxoplasma gondii in arctic wildlife is not well understood. Transmission cycles, especially in terrestrial systems, are enigmatic because environmentally resistant oocysts, shed by felid definitive hosts, might be less responsible for transmission in the Arctic than in more southern latitudes. Toxoplasma gondii can also be transmitted through the food web by carnivory, and by transmission from mother to fetus during gestation, and these routes are thought to play a large role in the ecology of T. gondii in the Arctic. In this thesis, I examine T. gondii in a well-described part of the food web at Karrak Lake, Nunavut, in the central Canadian Arctic and through experimental infections of domestic waterfowl. In the field over 3 years, I sampled generalist carnovires (arctic foxes), migratory herbivores (Ross’s Geese and Lesser Snow Geese), and resident herbivores (lemmings). Using an occupancy modeling approach that accounted for imperfect detection, I compared commonly used serological assays to estimate prevalence of T. gondii antibodies in sera from arctic foxes and eluted blood on filter paper from Ross’s geese and Lesser Snow Geese and compared commonly used serological assays. I also used a naïve estimator to determine prevalence of T. gondii antibodies in sera from Ross’s Geese and Lesser Snow Geese, and blood on filter paper from lemmings. I detected antibodies against T. gondii in sera from arctic foxes (47-60%, depending on age category), Ross’s Geese (32%) and Lesser Snow Geese (28%). I also detected antibodies in blood on filter paper from Ross’s Geese (39% seropositive) and Lesser Snow Geese (36% seropositive) but not in lemmings. These findings suggest that light geese might introduce T. gondii to the Karrak Lake ecosystem with the annual spring migration and that oocyst transmission might not occur in the terrestrial system, because the parasite was not detected in resident rodents. For the in vivo experimental infections, we used a novel application of a multi-scale occupancy framework to determine within-host detection probability of T. gondii in experimentally inoculated domestic geese and then used those results to guide tissue sampling in wild Ross’s Geese and Lesser Snow Geese. In the experimental inoculation trial, the heart and brain had the highest detection probability for T. gondii through a real-time PCR with melt-curve analysis. Toxoplasma gondii DNA was not detected in tissues from wild geese, suggesting that the parasite was either not present, or methodological difficulties prevented its detection. The research presented in this thesis forms the groundwork for further T. gondii studies in this region.

Master of Science / Department of Biology / Craig Paukert / The North American river otter (Lontra canadensis) was extirpated throughout much of its range but is now recovering in many areas. Consequently, there is a need to determine river otter occupancy and habitat associations. We conducted sign surveys from January to April 2008 and 2009 in eastern Kansas to assess how local- and landscape-scale habitat affects river otter occupancy and how survey methods and habitat affect the detectability of river otter sign. Multiple observers surveyed 3-9 400-m stretches of stream and reservoir shorelines for 110 randomly-selected sites and measured local-scale (within a 100 m buffer of site) habitat variables (e.g., stream order, sinuosity, proportion of land cover types) and landscape-scale (Hydrological Unit Code 14 watershed) habitat variables (e.g., road density, shoreline diversity, proportion of land cover types). We then modeled occupancy and detection probability as a function of these covariates using Program PRESENCE. The overall probability of occupancy accounting for detection probability was 0.329. The best-fitting model indicated river otter occupancy increased with the proportion of woodland cover and decreased with the proportion of cropland and grassland cover at the local scale. The best-fitting model also indicated occupancy increased with decreased shoreline diversity, waterbody density, and stream density at the landscape scale, possibly because of the influence of large reservoirs in the watershed. Occupancy was not affected by land cover or human disturbance at the landscape scale, perhaps due to our relatively homogeneous study area or because river otters are habitat generalists. Detection probability for 400-m surveys was highest in mud substrates (p = 0.600) and lowest in snow (p = 0.180) and litter substrates (p = 0.267). Detection probability for scat was more than double that for tracks, and detection probabilities were 17-64% lower for novice observers than experienced observers. Detection probability also increased with survey length. Sign surveys are a useful technique for monitoring many species, including river otters, and accounting for detection probability will improve estimation of occupancy. Furthermore, understanding the ecological factors and the scale important to river otter occurrence will be useful in identifying areas for restoration and management efforts.

The extensive clearing and modification of natural systems from anthropogenic activities is a pressing global concern. Forest habitats and animal communities within forests are among the most highly impacted, globally. Forest destruction has been repeatedly documented as a driver of biodiversity loss. However, little is known about how animal communities respond when altered landscapes are abandoned and left to regenerate into secondary forests. It is thought that the regrowth of secondary forests may help reverse biodiversity loss by restoring habitats to similar conditions as prior to land conversion. Of the forest cover that remains, over half is secondary forest, and in many countries secondary forest cover has been steadily increasing. Therefore, it is important to understand how and if faunal communities recover during secondary forest regeneration. I combined meta-analytic, field-survey-based, and lab-based experimental techniques to determine how amphibians and reptiles respond to habitat change in general, and secondary forest regeneration on landscapes previously cleared for use as pasture. I addressed five specific questions: 1) what are the effects of habitat alteration on amphibians and reptiles?, 2) what are the effects of secondary forest succession on amphibians and reptiles?, 3) what is the relative importance of stochastic and deterministic effects on community assembly during secondary forest succession?, 4) how do amphibian and reptile species composition, probability of occurrence, and species richness change over the course of secondary forest succession?, and 5) is thermal quality of habitat an important mechanism of species response to secondary forest succession? I found that secondary forest has high conservation value for many amphibian and reptile species, environmental changes associated with secondary forest succession have a significant effect on shaping amphibian and reptile community composition, thermal quality is an important mechanism for species response and that strength of response is mediated by species-specific thermal biology. I also highlight the importance of riparian corridors in maintaining species diversity in modified habitats.

The marsh rice rat (Oryzomys palustris) is a semi-aquatic rodent classified as state-threatened in Illinois due to historical wetland loss coupled with being on the northern periphery of its range. The most recent survey for this species in Illinois occurred in 1988, and this study reassessed its status and distribution. From 2007 to 2009, I used live traps to sample for rice rats at previously occupied and random wetland-dominated sites in 5 southern Illinois watersheds. I captured 132 individual rice rats 192 times in 13,248 trap nights. Capture success was 15.10 captures/1,000 trap nights. I detected rice rats within 3 of 5 watersheds, 16 of 48 sites, and 5 new locations. Most rice rats were captured in permanent or semi-permanent emergent wetlands and rice rat occurrence was strongly related with coal mine-associated wetlands. I collected microhabitat measurements at 10% of trap locations and recorded landcover types within and around sites. I analyzed data using t-tests, logistic regression, and occupancy modeling. Percent herbaceous cover and percent visual obstruction (0.0-0.5m) positively influenced rice rat occurrence and were among the most important microhabitat models. The best model in the candidate set of landcover variables included proportion of upland grass in areas surrounding wetlands as a predictor of rice rat occurrence. I believe insufficient evidence exists to warrant removal of the threatened status of the marsh rice rat. However, current management practices, such as wetland restoration, grassland restoration, and mowing of roadside ditches, likely benefit rice rat populations. Slight modification of these management activities may facilitate the eventual delisting of marsh rice rats.

Although Panamá is an important global hotspot for biodiversity, basic information on large carnivore and prey distributions as well as habitat needs is largely unknown. Wildlife studies in Panamá have been limited to populations located in protected areas along the Panamanian Atlantic Mesoamerican Biological Corridor (PAMBC) and have not considered potentially important refuge habitats located outside the PAMBC. Further, research on human attitudes and perceptions associated with large carnivores, such as jaguars (Panthera onca), is limited in Panamá. My study was conducted in 2 disparate study areas: Cerro Hoya National Park (CHNP), an isolated remnant of tropical rainforest habitat 125 km from the PAMBC that straddles the Veraguas and Los Santos provinces on the Azuero Peninsula; and Serranía de Pirre (SP), a comparative study area in the PAMBC located in Darién National Park (DNP). I used remote cameras to investigate patterns of site occupancy and detection probabilities, as affected by habitat and anthropogenic influences, for 3 species of felids (jaguars, pumas [Puma concolor], and ocelots [Leopardus pardalis]) and 2 species of peccaries (white-lipped [Tayassu pecari] and collared [Pecari tajacu]). In addition, I assessed attitudes and perceptions of rural Panamanians about jaguars and the conservation of CHNP and DNP via oral surveys. Site occupancy did not appear to differ between study areas for any felid or peccary, but detection frequencies and detection probabilities of focal species were overall higher in SP than CHNP. For collared peccaries, probability of detection was a function of survey year, study area, and Julian date, and estimated occupancy was higher in CHNP than SP. For ocelots, probability of detection was significantly higher in SP than CHNP when an ocelot was detected in a previous occasion. For pumas, detection increased with Julian date in CHNP but was seasonally unaffected in SP. Puma occupancy was higher closer to river systems. For jaguars, detection probability decreased with Julian date, increased with number of camera days per occasion, and was higher in SP than CHNP. Jaguars were more likely to use habitat at higher elevations in both study areas. White-lipped peccaries were never detected in CHNP, which may indicate their local extirpation in this region of Panamá. Regarding surveys measuring perceptions of rural people, factors such as gender, level of education, land ownership, and number of cattle affected knowledge and attitudes towards jaguars and criticism towards park management. Additionally, there was a higher frequency of human-jaguar conflict in SP than CHNP and coyotes (Canis latrans) were the most commonly reported threat to livestock in CHNP. My research elucidates previously unknown distribution limits of jaguars and coyotes in the Azuero Peninsula, as well as providing evidence for the potential local extirpation of white lipped peccaries in CHNP. I provide wildlife managers with improvements for survey design of future occupancy studies in the Neotropics. Further, my research provides targeted areas to prioritize for future wildlife conservation efforts and mitigation efforts concerning human-jaguar conflict.

The greenhouse frog, Eleutherodactylus planirostris, native to Cuba and the Bahamas, was recently introduced to Hawaii. Studies from other invaded habitats suggest that it may impact Hawaiian ecosystems by consuming and potentially reducing endemic invertebrates. However, there have been no studies on the greenhouse frog in Hawaii. The first component of this study was to conduct a diet analysis. We conducted a stomach content analysis of 427 frogs from 10 study sites on the island of Hawaii. At each site, we also collected invertebrates using two different sampling methods: leaf litter collection and sticky traps to characterize available resources. Greenhouse frogs consumed predominantly leaf litter invertebrates. Dominant prey items consisted of Hymenoptera: Formicidae (32.4%), Acari (19.2%), and Collembola (17.4%). Greenhouse frogs consumed more Formicidae than was measured in the environment. At one study site, we estimated there were 12,500 frogs ha-1 using mark-recapture methods and greenhouse frogs consumed 129,000 invertebrates ha-1 night-1 at this site. The second component of this study was to determine the distribution of the greenhouse frog on the island of Hawaii, with a male breeding call presence/absence survey at 446 points along the major road network. The greenhouse frog was detected at 61 sites (14%), and found mostly in lowland areas, in habitats of native shrublands and forests, nonnative forests, agricultural lands, and pastures on the southwestern and eastern sides of the island. We determined detection probabilities of the greenhouse frog and the invasive coqui frog, E. coqui. Detection probability of the greenhouse frog was low on the first two surveys and improved by the third survey. Detection probability of the coqui was higher than the greenhouse frog, but overall site occupancy estimates were similar for both species. Because the greenhouse frog appears to be as widespread as the coqui, we recommend that research be conducted to investigate its impacts ecologically to determine whether control efforts should also be aimed at this species.

Within managed pine forest systems, a plethora of bird species exist throughout the lifecycle of a stand akin to what may be experienced through post-disturbance regeneration in a natural forest system. I sought to address how breeding avian communities shift across time in response to stand aging and forest management, evaluate species-specific responses to stand conditions, investigate the responses of at-risk avian species to forest management, and determine avian non-breeding, over-wintering presence in a managed loblolly pine (Pinus taeda) forest. I conducted breeding bird point count and vegetation surveys within five stands of privately owned and managed pine forest in Mississippi, each of which was split into quadrants with different management strategies implemented. I designed and executed night surveys for Chuck-will’s-widow (Antrostomus carolinensis). Lastly, I conducted winter bird banding to explore over-wintering diversity, dietary isotope assimilation, and parasite prevalence. I found evidence that the avian community shifted in response to forest stage and structure, with differences created by management practices and forest succession. Switchgrass (Panicum virgatum) intercropping allowed some grassland and early successional species to remain in forest stands with closing canopies longer than in plots with standard management, with few diversity differences between treatments. Abundance of Chuck-will’s-widow was found to relate positively with the percent cover of early successional forest stands, those which were recently harvested and replanted and were in a pine-grassland state. Over-wintering bird species richness remained relatively low, and capture rates were consistently greatest in a young open canopy stand, which contained a higher level of vegetation structure and plant abundance when compared to three older stands. This represents a limited number of studies where investigations into bird community responses to forest management took place in the same forest stands across a long temporal period. Managers in forest systems should consider the implications of management undertaken at different stages in the rotational lifetime of a forest stand. To focus on conservation of priority bird species, managers should increase heterogeneity by maintaining or creating pine-grassland and early successional forest conditions within forest stands while also ensuring stands of various ages exist concurrently within the forest ecosystem.

Urbanization offers unique challenges for wildlife. The urban landscape is fragmented and changes available resources for wildlife. Human-dominated landscapes can provide food, shelter, or cover through human-subsidized resources. However, to thrive in human-dominated landscapes, wildlife must adapt or disperse, otherwise they will die. In this study, I investigated how the urban landscape and human behavior influence urban wildlife occurrence. I established 35 camera sites during April 2020. I surveyed residential property dwellers around each camera site to determine what behavior they performed that could increase species occurrence. Gray fox and coyote site use decreased with increased isolation while no species responded to patch area. Almost all species investigated responded to attractants but not all showed a positive response. Although number of survey participants was small, site use by wildlife tended to increase with owning a bird feeder and putting out trash the day before pickup.

Understanding how habitat amount and configuration affect species richness, occurrence or abundance has been one of the major foci of research in ecology and biogeography, given its central importance for conservation planning and landscape management. We conducted bird point counts within clearcuts and mature pine stands of different sizes and configuration in working pine forest in north-central Mississippi to determine species associations. Early-successional and mature pine focal species showed varying response to the proportion and proximity of vegetation conditions in the landscape. While elements of configuration exhibited a greater influence on predicted avian abundance in this landscape, meaning many species require a mosaic of habitat conditions that come from both early-successional and mature vegetation types. Efforts to combine management of timber and conservation of songbirds must consider both species’ habitat requirements and the distribution of these requirements in the landscape.

Freshwater turtles are among the most threatened groups of taxa globally, and the bog turtle, Glyptemys muhlenbergii is among the most imperiled in North America. In Virginia, USA, bog turtles are restricted to occupying Appalachian Mountain fens. Fens are naturally small and fragmented wetlands characterized by elevated water tables and an open canopy. Although there is a strong need to document and monitor populations of bog turtles, efforts to do so are often limited by the low detection of the species. The first objective of this thesis was to assess proposed methodologies for locating populations of turtles on the landscape. My first chapter assessed a previously-developed habitat distribution model for bog turtles using an occupancy modeling approach. I conducted 216 surveys of 49 discretely predicted patches of habitat, recording conditions such as weather, size of wetland and time of year, hypothesized to affect detection during each survey. In addition, I assessed factors including stream entrenchment, grazing presence and surrounding impervious surfaces for each surveyed patch to identify data sources that could improve future models or better assess sites. I found that sites with larger total wetland area had higher detection per survey, possibly due to larger sites having higher densities of turtles (among other explanations), and that sites with higher amounts of impervious surfaces within their drainage were less likely to be occupied. In addition to the bog turtle, several plant species also occur in mountain fens. These species usually have a locally rare distribution or are disjuncts from a more northern latitude. Because of these traits, a high diversity of specialist plants may be indicative of a fen with a robust hydrology that has historically been less disturbed. Past site quality analyses have proposed using indicator diversity to assess sites, but no study has found if these species to tend to co-occur. My second chapter examines this hypothesis. I first chose a list of plant species that would most likely have habitat requirements similar to those of turtles. Then, at 12 sites, 6 with turtles and 6 without, I conducted a complete floral inventory. I first tested community-wide differences between the floral communities of these sites and found no difference, but when I narrowed my analysis to examining occurrence patterns of plant species determined a priori to be fen specialists and Glyptemys muhlenbergii, a pattern of co-occurrence was found. This lends support to the idea that indicator plants could be used as a tool to better evaluate sites that may have bog turtles. My last chapter investigated movement of bog turtles in a landscape impacted by anthropogenic development. Movement of turtles between adjacent sites is critical to maintaining genetic diversity and maintaining metapopulation integrity. Despite this importance, records of long distances movements among wetlands are scarce in the literature, likely due to the lack of long-term studies for areas with multiple adjacent sites. In Virginia, mark recapture monitoring has been done intermittently in a cluster of sites for over 32 years. To determine the prevalence of movement among sites for bog turtles, I examined the dataset for all instances of turtles found at sites different from their last capture. I calculated the straight-line distance for each recorded movement. I also examined the sex of the turtle to test whether sex influences movement the frequency and distance of movements. For a subset of movements, I calculated least-cost pathways to identify possible barriers to movement using a previously published resistance model. I found 21 instances where a turtle was caught at a different site than its last capture over 32 years of monitoring. Neither sex was more likely to move farther than the other. Although the study's observed rate of movement may appear low, it is likely an underestimate when detection and asymmetric sampling are taken into account. The least cost pathways analysis suggested that roads or driveways were likely crossed for a significant portion of movement events. Finally, to examine how movement may be affecting the current distribution of bog turtles, I described a method to test whether adjacency to known populations influences the probability of a new site being occupied by turtles. I prove the utility of the method by applying it to a map of bog turtle occurrences collected over this study and show that it can account for habitat differences and barriers to movement between sites as well. In spite of plausibility of the method, limitations in how occurrence data are currently collected prevent its immediate application. Together, this thesis will help managers not only find and assess wetlands on the landscape, it will also provide information about the network of connected patches on the landscape. Knowing where bog turtles are and what wetlands or sub-populations are potentially connected will allowed for a more directed and informed regional management strategy. / Master of Science / Freshwater turtles are facing population declines worldwide, and the bog turtle Glyptemys muhlenbergii is among the most imperiled in North America. Bog turtles occupy naturally small, specialized wetlands called Appalachian Mountain fens. The prevalence of fens on the landscape has declined over recent decades due to agricultural practices. Although there is a strong need to document and monitor bog turtle populations due to their threatened status, bog turtles are difficult to find due to their small size and ability to burrow completely into substrate. Thus, considerable effort must be expended to find populations and track their status. The first overall objective of this thesis was to assess methods for locating populations of bog turtles. My first chapter tests a habitat distribution model that uses publicly available landscape data such as topopgraphy and land cover to predict areas likely to contain turtles. To do this, I systematically surveyed 49 predicted sites multiple times each over 2 years. Simultaneously, I recorded variables such as the time of year, size of the wetland and the weather to determine whether any factor significantly explained the ability to find turtles on any given survey. In addition, I was able to record several variables relating to wetland quality and isolation that were not in the initial model. I found that larger wetlands were easier to search than smaller wetlands, possibly due to larger sites having more turtles, and that wetlands near more impermeable surfaces (such as roads and buildings) were less likely to have bog turtles. As another potential method to find bog turtles and assess sites, we tested the use of 'pristine indicator' plants as a metric for potential wetlands. Mountain fens have specific attributes, such as high groundwater influence and exposure to a large amount of sunlight. Several species, including the bog turtle, are specialized to these factors and are rarely found in the surrounding landscape. Because a distinct community exists for mountain fens in this region, sites with a higher diversity of fen specialist plants may be indicative of a higher quality site which can support more specialists, including the bog turtle. My second chapter tests this hypothesis. I first chose a list of species that would most likely have habitat requirements similar to those of bog turtles. Then, at 12 sites I documented every plant species I encountered within the wetland. I compared the plant community as a whole between bog turtle-occupied and unoccupied sites and found no significant difference between the two. When I narrowed my analysis to focus on plants I previously identified as sharing habitat requirements with the bog turtle, I found a strong pattern of their co-occurrence with bog turtles. This lends support to the idea that these 'pristine indicator' plants could be used as a tool to better evaluate sites that may have bog turtles. My last chapter investigates movement of bog turtles in a landscape impacted by human development. Movement of turtles between adjacent wetlands is critical to maintaining long term regional viability of the species, as it lets turtles colonize new sites and exchange genes. Despite the importance of these movements, records of turtles moving long distances between two wetlands is scarce in the literature, likely due to the lack of long-term studies for areas with multiple adjacent wetlands. One method of recording movements is by marking turtles with a unique ID and recording where it was encountered as wetlands are surveyed on the landscape. In Virginia, this procedure has been conducted at multiple sites over 32 years. To understand the prevalence of movement between sites for this species, I examined this dataset and examined all instances of a turtle being found at a site different from its last capture. I recorded the straight-line distance moved for each recorded movement as well as the sex of the turtle, to test if either sex was more or less likely to undertake these movements. Then, for a subset of movements, I calculated least-cost pathways, a metric that accounts for landscape features and plots the easiest route for turtles to move. This way, I could evaluate the prevalence of barriers to movement, such as roads or development, on the landscape. I found 21 documented movements among sites over 32 years of monitoring. Neither sex was more likely to move further than the other. Compared to studies looking at other freshwater turtles, the observed rate of movement appeared low, but this was likely an underestimate due to the difficulty of capturing specific individuals. I also found evidence of significant barriers to movement in 13 out of 17 evaluated least-costs paths, usually roads or driveways. Finally, to examine how movement affects bog turtle distribution, I describe a methodology of testing if adjacency to known populations influences the probability of a new site being occupied by turtles. I demonstrate the plausibility of the method by applying it to a map of occurrences collected over this study and show that it can account for habitat differences and barriers to movement between sites as well. However, limitations in my sampling scheme limit conclusions from my dataset. Together, these findings will help future managers find where turtles are and which sites may be connected. These results will help managers make more informed decisions for managing bog turtles at a statewide level.