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Oyster reef restoration may enhance the production of ecologically or economically important fish species, an ecosystem service, by providing refuge and foraging habitat. Predicting the effects of oyster habitat restoration on fisheries production in Chesapeake Bay requires a better understanding of fish habitat use, trophic dynamics, and the processes leading to production on a habitat-scale. The objective of this thesis was to evaluate the influence of restored subtidal oyster reefs on the abundance and foraging patterns of mobile estuarine fishes. Specifically, I compared the 1) abundance, 2) stomach fullness, 3) diet composition, and 4) daily consumption rate of fishes collected from restored oyster reef habitat and from unstructured (control) habitat in the Lynnhaven River System (LRS), Virginia, a tributary of Chesapeake Bay. I sampled fishes from April – October 2016 to assess seasonal abundance and diet trends using multi-panel gill nets, and conducted 24-hour sampling events in July and September 2016 to assess daily foraging patterns and estimate habitat-specific consumption rates. The most abundant non-filter feeding fishes collected all came from the Sciaenid (drum) family: spot (Leiostomus xanthurus), silver perch (Bairdiella chrysoura), and Atlantic croaker (Micropogonias undulatus). Overall catch in oyster reef habitat was reduced relative to unstructured bottom, but species-level responses to habitat type varied. Stomach fullness trends varied by species but were associated with habitat type. Benthic prey dominated the diet of all three species, and evidence of habitat-related shifts in diet composition were apparent. Reef-affiliated prey contributed most prominently to silver perch, comprising nearly 30 – 50 % by weight. The daily consumption rate and total daily caloric intake of silver perch foraging in oyster reef habitat were nearly double the estimates from control habitat. The results suggest restored oyster reefs influence habitat use and foraging behavior in species-specific manners, likely a result of differences in functional morphology and prey preference. Restored oyster reefs in the LRS likely act as valuable forage habitat for silver perch, an important trophic link in coastal and estuarine systems. Developing realistic estimates of fisheries production on a habitat-scale requires studying species-specific trophic dynamics. Empirical estimates of the processes contributing to production are necessary to better understand the functional role of restored oyster reefs in shallow estuarine and coastal systems, and the ecosystem services these reefs may provide.

Amphibians suffer from large-scale population declines globally, and emerging infectious diseases contribute heavily to these declines. Amphibian Perkinsea (hereafter Pr) is a worldwide anuran pathogen associated with mortality events, yet little is known about its overall impact on amphibian populations and species. Thus, we sought to determine the epidemiological patterns of Pr across individual hosts, populations, communities, and the overall landscape. To accomplish this, we conducted two field-based and one experimentally-based study to identify specific factors that contribute to pathogen prevalence, infection intensity, and overall disease outcomes for Pr in individuals and populations. We collected 1973 total anurans across the two field chapters of this dissertation with 32% of individuals infected with Pr in more "natural" habitats while 8.8% of individuals were infected with Pr in the urban Xenopus tropicalis invasion range. We identified that co-variates including co-infection status, host species, host life stage, sampling month, and sampling site explained much of the variability of infection status within individuals and sites. In the experimental infection studies, we identified that host susceptibility to Pr varied significantly by species, but sub-lethal impacts may still occur in tolerant species. This study is the first to establish epidemiological patterns of Pr across space, time, and host species and fills knowledge gaps in our understanding of how invasive species alter pathogen dynamics. Ultimately, this work highlights the need for ongoing monitoring, experimental studies, and mitigation efforts to address the challenges pathogens pose to amphibian biodiversity.

Hybridization, the process of interbreeding between individuals of different species, is one method by which plants and animals adapt to a changing environment. One example of such adaptation through hybridization may be occurring on the California Channel Islands with two species of Castilleja. While United State Geological Survey (USGS) researchers have been studying the populations of Castilleja affinis and Castilleja mollis to determine if hybridization is occurring on Santa Rosa Island since the early 1990s, up until this point primarily overt phenotypic characteristics have been used to differentiate between the two species. Genetic methods of differentiation were adopted to confirm that hybridization is in fact occurring on the island, possibly in response to climate change. Hybrids may be expanding into areas once occupied by pure C. mollis, because they might carry some of C. affinis’ traits like an ability to survive warmer, drier climates as parts of the island are starting to become warmer and drier. In this study, I have developed a cleaved amplified polymorphic sequences (CAPS) marker based on internal transcribed spacer (ITS) regions to differentiate between the two species and hybrids and have applied these CAPS markers to genotype DNA samples isolated from 132 individuals. This protocol was used to determine the extent of hybridization on Santa Rosa Island in conjunction with ongoing surveys conducted by the USGS. Work focused on genotyping previously collected samples from two main sites on the island, which allowed confirmation that patterns observed based on phenotype in the field are supported by genetic data. In the future, findings will link genetic type with survivorship and growth data, to test whether hybrids perform differently than pure C. mollis. Broadly, this will determine if the two species are in fact hybridizing as a method for adapting to climate change, the most severe threat to Channel Island biodiversity.

Climate change coupled with land-use change will likely alter habitats and affect state parameters of the animal populations that dwell in them. Affected parameters are anticipated to include site occupancy and abundance, population range, and phenophase cycles (e.g., arrival dates on breeding grounds for migrant bird species). Detecting these changes will require monitoring many sites for many years, a process that is well suited for an automated system. We developed and tested monitoR, an R package that is designed for long-term, multi-taxa automated passive acoustic monitoring programs. monitoR correctly identified presence for black-throated green warbler and ovenbird in 64% and 72% of the 52 surveys using binary point matching, respectively, and 73% and 72% of the 52 surveys using spectrogram cross-correlation, respectively. Of individual black-throated green warbler song events, 73% of 166 black-throated green warbler songs and 69% of 502 ovenbird songs were identified by binary point matching. Spectrogram cross correlation identified 64% of 166 black-throated green warbler songs and 64% of 502 ovenbird songs. False positive rates were We describe a method to identify the probability of survey presence in a template-based automated detection system using known false positive rates for each template. True and false positive detection rates were observed in 146 training surveys. These probabilities were used in a Bayesian approach that discriminates between detections in occupied surveys and unoccupied surveys. We evaluated this approach in 146 test surveys. A total of 1142 Black-throated green warbler (Setophaga virens) songs were observed in the training surveys and test surveys, which we attempted to locate with 3 different binary point matching templates. When only posterior probabilities greater than 0.5 were considered detections, the average ratio of accurate identifications of survey presence to false positive identifications in 500 bootstrapped samples improved from 1.2:1 using a standard score cutoff approach to 2.8:1 using all 3 templates and a likelihood-based discriminator. With the selected score cutoffs the average true positive and false positive rates for the combined three templates were 0.18 and 0.002, respectively. Automated detection methods are increasingly being used for identification and monitoring of landscape-scale responses to climate change and land-use change. Skepticism of automated acoustic monitoring software is largely due to higher false positive and negative error rates than those in traditional human surveys, but the false positive multiple method occupancy model is capable of estimating detection parameters and occupancy state when one method has occasional false positive detections. We test the accuracy of the model when automated detection of black-throated green warbler is mixed with human detection in 4 recorded surveys at 60 sites. Precision and accuracy are evaluated by simulation, and we use the results to optimize future sampling. In simulation, parameter estimates by the multiple method occupancy model are close to those we computed manually when two surveys are manually analyzed. Our results support the use of the multiple method false positive occupancy model to track detection rates in automated monitoring programs.

Maintaining desired numbers of wildlife species requires an understanding of species-specific population dynamics. For ungulate species such as the white-tailed deer (Odocoileus virginianus), understanding the neonatal survival rate of a population and factors that influence that survival rate, may be two of the most important factors to successful deer management. We examined neonatal survival in an eastern Kentucky population of deer living in relatively low densities (/ km2), with adequate habitat and supposedly poor population growth. Neonates (102) were captured in the summer birth periods of 2014 - 2016 and radio-monitored until the beginning of the fall archery deer season. We found moderate-to-low survival estimates to four months of 43% (95% CI: 29 – 57%) that are consistent with many areas in the Midwest and southeastern United States. Predation, including suspected predation events, from bobcats (Lynx rufus) and coyotes (Canis latrans) accounted for 80% of all neonate mortalities. A thorough examination of the survival and mortality in the neonate component of this population is discussed herein.

ABSTRACT Spiny softshell turtles (Apalone spinifera) occur at the northwest limit of their range in Lake Champlain. This species, although widespread across North America, is listed as threatened in Vermont due to habitat destruction and disturbances of anthropogenic origin. The population of spiny softshell turtles in Lake Champlain is isolated from other North American populations and is considered as an independent management unit. Efforts to obtain information on the biology of spiny softshell turtles in Lake Champlain precede 1936 with conservation measures being initiated in 1987. Methods of studying spiny softshell turtles in Lake Champlain have included direct observation, mark-recapture, nest beach monitoring, winter diving, and radio telemetry. Each of these approaches has provided some information to the sum of what is known about A. spinifera in Lake Champlain. For example major nesting beaches, hibernacula, and home range size have been determined. Currently spiny softshell turtles primarily inhabit two areas within Lake Champlain, Missisquoi Bay and the mouth of the Lamoille River. However, the population structure and gene flow between spiny softshell turtles inhabiting the Lamoille and Missisquoi regions remained unknown. A GIS model was created and tested in order to identify additional nesting beaches used by spiny softshell turtles along the Vermont shores of Lake Champlain. Although some additional small potential nesting beaches were found, no additional major nesting sites were found. The GIS model identified the mouth of the Winooski River (the site of a historical population) as potentially suitable nesting habitat; however, no evidence of spiny softshell turtle nesting was found at this site. A series of methods developed for collecting molecular and population genetic data about spiny softshell turtles in Lake Champlain are described, including techniques for DNA extraction of various tissue types and the design of new primers for PCR amplification and sequencing of the mitochondrial control region (mtD-loop). Techniques for circumventing problems associated with DNA sequence alignment in regions of a variable numbers of tandem repeats (VNTRs) and the presence of heteroplasmy within some individuals are also described. The mtD-loop was found to be a suitable marker to assess the genetic structure of the Lake Champlain population of spiny softshell turtles. No significant genetic sub-structuring was found (FST=0.082, p=0.223) and an indirect estimate of the migration rate between Lamoille and Missisquoi regions of Lake Champlain was high (Nm>5.576). In addition to consideration of A. spinifera in Lake Champlain, the mtD-loop was modeled across 46 species in 14 families of extant turtles. The primary structure was obtained from DNA sequences accessed from GenBank and secondary structures of the mtD-loop were inferred, (from thermal stabilities) using the program Mfold, for each superfamiliy of turtles. Both primary and secondary structures were found to be highly variable across the order of turtles; however, the inclusion of an AT-rich fold (secondary structure) near the 3' terminus of the mtD-loop was common across all turtle families considered. The Cryptodira showed conservation in the primary structure at regular conserved sequence blocks (CSBs), but the Pluerodira displayed little conservation in the primary structure of the mtD-loop. Overall, greater conservation in secondary structure than primary structure was observed in turtle mtD-loop. The AT-rich secondary structural element near the 3' terminus of the mtD-loop may be conserved across turtles due to it serving a functional role during mtDNA transcription.

Landscape change affects the distribution of wildlife and represents a conservation concern, especially in Asia, which is experiencing rapid development. In Mongolia, mining, livestock grazing, infrastructure development and climate change represent major drivers of change that will impact habitats and few tools exist to predict how wildlife will respond. I examined the impacts of landscape change on the corsac fox (Vulpes corsac) in a steppe region of Mongolia. The corsac fox occurs widely throughout northern Asia, but has experienced declines in many regions and remains one the least studied canids. I addressed two questions: 1) how do common features of a landscape, such as habitats, topography, herder camps, and roads, shape the distribution of the species? and 2) how will changes in those features affect distribution in the future? I collected locations of foxes from radio-collared animals, scat surveys, and opportunistic sightings in Ikh Nart Nature Reserve, then used maximum likelihood methods and model selection techniques to develop a model that predicts occupancy probability. I then applied the model to simulations of landscape change. I collected 1,965 locations and examined 19 candidate models. The model with the most support indicated that occupancy is best described by the additive combination of shrublands, open plains, tall grasslands, and rocky habitat. Models with other covariates (camps, roads, and ruggedness) had little support. A Receiver-Operator-Characteristic plot of model performance had an Area Under the Curve of 77%, indicating that the model predicted occupancy better than expected by chance. Average occupancy across the reserve was 22% under current conditions. Incremental reductions in shrubland, open plains, and tall vegetation resulted in occupancy declines with average occupancy being 7%, 13%, and 14%, respectively, when these habitats were completely absent. The loss of all three habitats due to the desertification of the landscape through climate change resulted in an average occupancy of 7%. The results provide the first model of corsac fox occupancy, which can be used to quantitatively examine distribution and impacts of change in other parts of the species' range. In Ikh Nart, results suggest that climate change poses the greatest threat to the species as it is expected to reduce high quality habitats and confine corsac foxes to areas with high competition from red foxes.

Stonecats (Noturus flavus, Rafinesque 1818) are designated as a Vermont state-listed endangered species because their known distribution is limited to two systems, the LaPlatte and Missisquoi rivers. The restricted distribution and lack of knowledge on abundance in either river is cause for concern in the continued survival of these populations. Based on the capture numbers and large size range of individuals, we predicted that the population in the LaPlatte River, which provides quality benthic habitat, is stable. However, the Missisquoi River population has the potential for increased intermittent mortalities from two sources, lampricide (3-trifluoromethyl-4-nitrophenol) treatment every four years and dewatering during drought conditions. In 2012, 2013, and 2014 we captured, PIT tagged (> 90 mm total length), and VIE marked all Stonecats collected using backpack electrofishing and minnow traps in the LaPlatte and Missisquoi rivers. A total of 1252 were PIT tagged in the LaPlatte River and 125 in the Missisquoi River. First we estimated survival and seniority of Stonecats in the LaPlatte River, using the Pradel model in Program Mark, and derived an average annual lambda of 0.9826. The population estimates from the LaPlatte River were modeled in a population viability analysis (PVA). Few Stonecats were captured in the Missisquoi River, so we used the PVA model to estimate the extinction rates with increased intermittent mortalities on 4-, 6-, and 8-year cycles to predict the long-term viability of the population. With an initial number of 2000 individuals, the population became extinct 100% of the time with an increase in mortality of 0.1 on a 4-year cycle. Our results indicate that the LaPlatte River population is stable, but the Missisquoi River population, in the area affected by lampricide, is not. These results are informative for developing future management scenarios, however, our approach has uncertainty that can only be addressed through obtaining more data on the Missisquoi River population.