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The effects of aquaculture decline on piscivorous birds in the Mississippi Delta concern catfish farmers with possible increases in fish loss and disease transmission. My study was aimed to (1) develop a new harassment method using unmanned aerial vehicles (UAVs) to effectively control piscivorous birds at fish farms; (2) determine change in spatial distribution of American white pelicans (Pelecanus erythrorhynchos) in the Mississippi Delta since aquaculture decline; and (3) determine third-order habitat selection by the pelicans in the wintering grounds. The UAV harassment did not reduce piscivorous bird abundance more than human harassment in a 2-year field experiment. Aerial surveys demonstrate that the pelicans used natural water bodies to find food more frequently in 2015–2017 than in 1997–1999. Average pelican flock size decreased following the aquaculture decline. Lastly, land cover and land use did not predict fine-scale habitat selection by the pelican.

Human activity affects white-tailed deer (Odocoileus virginianus) movement and habitat selection during all times of the year, but knowledge is limited regarding how human risk affects white-tailed deer during the summer and winter. During spring and summer, variation in patch selection varied. Natural vegetation was selected for early in the year, with anthropogenic forages being important for deer use during the summer. During the winter, deer responded to different levels of risk. As hunter risk increased on the landscape, deer altered selection of the landscape. Deer avoided areas that were heavily used by hunters, using areas containing less hunter risk. Use of land cover classifications varied temporally, with cover selected for during the day and forage selected for at night. I have demonstrated that deer respond to human activity on the landscape, by selecting for anthropogenic foraging sources during the spring and summer and avoiding patches that contain risk.

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Predators play a critical role in regulating the structure and function of ecosystems by exhibiting top-down forces on lower trophic levels. Despite their important contributions in maintaining ecosystem health, lethal predator control remains a global wildlife management strategy to reduce predation on livestock, culturally and/or economically important species, and species at risk, as well as to reduce conflict with humans. Predator control has received criticism due in part to a paucity of rigorous research on the community-level impacts of this practice, beyond the target prey species. Specifically, there is a lack of understanding of the behavioural consequences of predator control on the wider ecological community. In this thesis, I used a multi-year camera trap dataset to evaluate how government-mandated grey wolf (Canis lupus) population reduction to conserve boreal woodland caribou (Rangifer tarandus caribou) could impact the resource selection of the carnivore community in northeast Alberta, Canada. In my second chapter, I investigated whether perceived persecution risk due to predator control may alter wolf habitat selection. I found that wolves switched from positively associating with roads before predator control to avoiding anthropogenic linear features and selecting for block features after predator control. These results suggest that lethal control may prompt wolves to prioritize local prey acquisition near block features over movement on linear features. In my third chapter, I examined whether coyote, lynx, and black bear exhibited shifts in co-occurrence with habitat features, competitors, and prey consistent with a release from top-down suppression in response to predator control. I found that predator control triggered unexpected behavioural changes among coyote and lynx consistent with a release from top-down suppression, but not among black bears. Non-apex predator response to predator control may depend on the strength of competition between the apex and non-apex predator, emphasizing the need to consider bottom-up processes when trying to understand the indirect effects of predator control. This research demonstrates that predator control can have trickle-down effects within the larger ecological community, specifically affecting how species utilize resources. As predator control continues to be a recommended wildlife management strategy, it is imperative to continue investigating its unintended consequences throughout the ecological community. / Graduate

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Modeling the complex relationships between habitat characteristics and a species' habitat preferences pose many difficult problems for ecological researchers. These problems are complicated further when information is collected over a range of time or space. Additionally, the variety of factors affecting these choices is difficult to understand and even more difficult to accurately collect information about. In light of these concerns, we evaluate the performance of current standard habitat preference models that are based on Bayesian methods and then present some extensions and supplements to those methods that prove to be very useful. More specifically, we demonstrate the value of extending the standard Bayesian hierarchical model using finite mixture model methods. Additionally, we demonstrate that an extension of the Bayesian hierarchical changepoint model to allow for estimating multiple changepoints simultaneously can be very informative when applied to data about multiple habitat locations or species. These models allow the researcher to compare the sites or species with respect to a very specific ecological question and consequently provide definitive answers that are often not available with more commonly used models containing many explanatory factors. Throughout our work we use a complex data set containing information about horseshoe crab spawning habitat preferences in the Delaware Bay over a five-year period. These data epitomize some of the difficult issues inherent to studying habitat preferences. The data are collected over time at many sites, have missing observations, and include explanatory variables that, at best, only provide surrogate information for what researchers feel is important in explaining spawning preferences throughout the bay. We also looked at a smaller data set of freshwater mussel habitat selection preferences in relation to bridge construction on the Kennerdell River in Western Pennsylvania. Together, these two data sets provided us with insight in developing and refining the methods we present. They also help illustrate the strengths and weaknesses of the methods we discuss by assessing their performance in real situations where data are inevitably complex and relationships are difficult to discern. / Ph. D.

The purpose of this research was to evaluate current management strategies for the New River, Virginia, muskellunge Esox masquinongy fishery, which is the premier muskellunge fishery in the state. The primary objectives were to evaluate potential benefits and angler support for more restrictive harvest regulations and to quantify habitat selection at multiple spatial scales. A secondary objective was to develop an alternative procedure for testing differences in muskellunge condition from relative weight Wr data that incorporates uncertainty regarding the accuracy of the standard weight equation and that is based on derived statistical properties of the Wr index. Abundance of memorable-length (³1,070 mm) muskellunge was predicted to increase with minimum length limits of 914, 1,016, and 1,143 mm. Although yield per recruit would decline under a 1,143-mm minimum length limit, it was predicted to remain fairly stable at length limits of 914 and 1,016 mm due to fast growth rates of young fish. Even though most anglers defined trophy muskellunge to be in excess of 1,016 mm, angler support for length limits in excess of 1,000 mm was low. Habitat variables that were most strongly related to muskellunge habitat selection were measures of patch shape complexity and water depth. Increased river discharge was found to significantly affect muskellunge habitat use and selection, with fish abandoning deeper open-water habitats and moving to shallower areas closer to the shoreline during periods of high discharge. As for the secondary objective, a new statistical test (R-test) was developed that can be used to test for differences in Wr between and within fish stocks. Comparison with other statistical tests indicated that the R test provides more conservative results than traditional statistic procedures, and that substantial variability in standard weight equations will make it more difficult to detect statistical differences. Management recommendations for the New River muskellunge fishery include increasing the minimum length limit to approximately 965 to 1,067 mm and limiting the stocking of muskellunge only to those areas with sufficient juxtaposition of shallow- and deep-water habitat patches. / Ph. D.

Red foxes (Vulpes vulpes) have been identified as a key predator of the threatened piping plover (Charadrius melodus) along the U.S. Atlantic coast. However, little is known about coastal red fox ecology, making it difficult to create effective red fox management strategies in these settings. Here, we quantify aspects of red fox population, spatial, and dietary ecology and interactions with threatened piping plovers on Fire Island, New York. We conducted remote camera surveys, scat and sign surveys, den monitoring, and GPS tracking of red foxes on the island in 2015–2018. We used these data to estimate red fox occupancy, reproduction, survival, and population density. We used GPS data to investigate red fox space use, habitat selection, and responses to piping plover nest exclosure setup, pre-hatch pipping, and hatching. We used fecal dietary analyses and data from den prey item surveys to quantify the frequency of piping plover predation and to identify major prey items of red foxes on the island. Red fox occupancy remained high even after substantial decreases in abundance, population density, annual reproduction, and seasonal survival following 2 sarcoptic mange outbreaks. Within their home ranges, red foxes selected areas that were closer to vegetation during the daytime and twilight hours, but farther from vegetation at night. We did not find clear evidence that red foxes in our study area keyed in on piping plover nest exclosure setup, pipping, or hatching at the spatial scales considered in our comparisons, although fox penetration of and digging at exclosures was an issue in 2015 at Smith Point County Park. Items from Orders Rodentia (rodents, 43% of scats), Coleoptera (beetles, 38%), and Decapoda (crabs and other crustaceans, 29%) were most frequently found in 293 red fox scats examined. Skates (Family Rajidae, 89% of dens with food items) and Atlantic surf clams (Spisula solidissima, 67%) were found most frequently outside of dens. We did not find any identifiable piping plover remains in red fox scats or outside of dens. Our results suggest that direct interactions between red foxes and piping plovers during our study period and in our study area were less frequent than expected, but concurrent work by collaborators documented that the trap success of red foxes was negatively related to piping plover reproductive output during our study period. Lethal removal of red foxes is unlikely to eliminate them from shorebird nesting areas unless complete eradication of foxes from the island can be achieved. We recommend strategic vegetation management in and around piping plover nesting areas to reduce daytime resting areas and hunting cover for red foxes, and continued use of nest exclosures. We also recommend further investigation into indirect impacts of red foxes on piping plover populations, and into the possibility that anthropogenic food resources could be subsidizing the island's red fox population. / Doctor of Philosophy / Red foxes have been identified as a key predator of the piping plover, a small migratory shorebird that breeds along the U.S. Atlantic coast and is considered 'threatened' (at risk of becoming endangered and eventually disappearing) within the United States. The lack of information about red fox ecology in coastal settings has been a challenge for wildlife biologists tasked with reducing predation on piping plovers. We investigated red fox ecology, behavior, and interactions with piping plovers on Fire Island, New York. We used trail cameras, collected scat (feces), monitored dens, and tracked red foxes on the island with global positioning system (GPS) collars in 2015–2018. We used these data to estimate red fox distribution, litter sizes, survival rates, and population sizes. We used GPS data to estimate red fox territory sizes, describe habitat selection, and investigate responses to piping plover nest exclosure setup, pipping (a period before hatching during which chicks vocalize inside the eggs), and hatching. We dissected red fox scats and recorded prey items found outside of dens to determine what red foxes on the island were eating. The proportion of each study area used by red foxes remained high even after substantial decreases in abundance, population density, annual reproduction, and seasonal survival following 2 parasitic disease (sarcoptic mange) outbreaks. Within their territories, red foxes selected areas that were closer to vegetation during the daytime and twilight hours but farther from vegetation at night. We did not find clear evidence that red foxes in our study area keyed in on piping plover nest exclosure setup, pipping, or hatching, although fox penetration of and digging at exclosures was an issue in some years at a site not included in those comparisons. Rodents, beetles, and crustacean remains were found most frequently in red fox scats. Skates and surf clams were found most frequently outside of dens. We did not find any identifiable piping plover remains in red fox scats or outside of dens. Our results suggest that that direct interactions between red foxes and piping plovers may be less frequent than previously believed, but concurrent work by collaborators documented that the trap success of red foxes was negatively related to piping plover reproductive output during our study period. Lethal removal of red foxes is unlikely to eliminate red foxes from shorebird nesting areas unless all foxes on the island are removed. We recommend strategic vegetation removal in and around piping plover nesting areas to reduce daytime resting spots and hunting cover for red foxes, and continued use of nest exclosures. We also recommend further investigation into indirect impacts of red foxes on piping plover populations, and into the possibility that anthropogenic food resources could be subsidizing the island's red fox population.

The southwestern willow flycatcher (Empidonax traillii extimus) is a federally-endangered neotropical migrant that breeds in the southwestern United States. The population of southwestern willow flycatchers on the South Fork Kern River in California was once thought to be one of the largest E. t. extimus populations. It declined from 38 pairs in 1997 to 12 pairs in 2000. My goals were to examine E. t. extimus habitat selection on the South Fork Kern River, to determine how habitat characteristics and food availability affect E. t. extimus demographics, and to make inferences about possible reasons for the decline. My first objective was to determine southwestern willow flycatcher habitat selection on the Kern on two spatial scales: territory and nest site. Southwestern willow flycathers selected habitat characteristics that appeared to be related to food availability, foraging ecology, or nest cover. Territories within the riparian forest were closer to water and the edge of forest and had fewer cottonwoods than unused areas. Nest sites had denser and more uniform canopy cover and a denser understory than randomly selected sites within territories. My second objective was to determine a relationship between measures of fitness (reproductive success and occupancy frequency) and territory categories (occupied 2 years, occupied 1 year, abandoned). Also, I examined the relationship between indirect measures of fitness, habitat characteristics and food availability, and territory categories. Compared to other territories, territories occupied more frequently had higher reproductive success, higher insect abundance indices, greater habitat heterogeneity, denser understories, and more stems 30-50 cm dbh. All of the habitat characteristics important in habitat selection and habitat quality on the South Fork Kern River were similar to other recent studies on E. t. extimus habitat selection and reproductive success. On the Kern, both suitable and optimal habitat appear to be limited and this limitation appears to be contributing to the population decline. Habitat quality may affect E. t. extimus demographics, particularly when the number of high quality territories in a population is limited as in site-dependent population regulation. Since the amount of suitable habitat is likely to continue to decline across the range of southwestern willow flycatchers, managers should consider manipulating habitat for high quality E. t. extimus habitat to aid conservation of this endangered species. / Master of Science