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Human development continues to use up more physical space in the natural world, threatening the natural habitats of many organisms. To combat the loss of biodiversity science needs to explore what landscape features are important for different organisms so that we can incorporate these into the modern environment. As bats play an important role in many ecosystems and can reflect changes through trophic levels, analyzing their preferred habitats can help planners improve biological diversity of the urban habitat. Using acoustically identified bat sightings from Artportalen.se for the years 2017-2018, this paper studied the habitats of bats in Sweden. Through multiple regression analysis we examine the response in abundance and/or diversity of bats to physical and socio-cultural attributes of the urban habitat. We examined a total of 10160 bats from 18 species in 418 land cover locales and 306 demographical statistical areas with varying degrees of urbanization. Our results indicate that bat abundance and diversity decrease significantly with higher urbanization while deciduous forests are the most important land cover type for all bats. The results also indicate that wealthier areas have less abundance and diversity even when factoring in population density. Species specific analysis suggested that bat species who are better adapted at foraging in open vegetated landscapes and over water were less susceptible to the negative impacts of the urban habitat. We conclude that diverse habitats with a mixture of open vegetated areas, watercourses and broadleaf forests are the most important land features for a diverse bat fauna along with high connectivity via tree cover and linear landscape elements. If urban planning could incorporate these features into the urban habitat, some of the negative impacts of urbanization could be prevented.

<p>This thesis aims to elucidate the mechanisms and response characteristics of neural circuits in the vertebrate brain capable of responding selectively to stimulus duration. The research within focused on, but is not limited to, auditory neurons; however, most of the results extend to other sensory modalities. These neurons are known, appropriately, as duration-tuned neurons (DTNs). Duration-tuned neurons tend to prefer stimulus durations similar to the duration of species-specific vocalizations and have preferred durations ranging from 1 ms up to over 100 ms across species.</p> <p>To study the mechanisms underlying DTNs, biologically inspired computational models were produced to explore previously hypothesized mechanisms of duration tuning. These models support the mechanisms by reproducing the responses of <em>in vivo</em> DTNs and predicting additional <em>in vivo</em> response characteristics. The models demonstrate an inherent flexibility in the mechanisms to extend across a wide range of durations and also reveal subtleties in response profiles that arise from particular model parameters.</p> <p>To quantify the encoding efficiency of <em>in vivo</em> DTNs, information theoretic measures were applied to the responses of 97 DTNs recorded from the auditory midbrain (inferior colliculus) of the big brown bat. Stimulus duration encoding robustness, as measured by stimulus-specific information, tended to align with the stimulus durations that produce the largest responses. In contrast, stimulus durations with the most sensitivity to changes in stimulus duration, as measured with an approximation of the observed Fisher information, tended to be stimulus durations shorter or longer than the duration evoking the largest response. Remarkably, both optimal and non-optional Bayesian decoding methods were able to accurately recover stimulus duration from population responses, including durations that lacked neurons dedicated to best representing that duration. These results suggest that DTNs are excellent at encoding stimulus duration, a feature that has been generally assumed but not previously quantified.</p> / Doctor of Philosophy (PhD)

Bats are crucial to ecological function and provide key ecosystem services to people but face a variety of significant threats. One current threat to North American bats is white-nose syndrome (WNS), a disease caused by the invasive fungal pathogen Pseudogymnoascus destructans (Pd) that has killed millions of hibernating bats across the continent. Remnant populations of affected bat species persist but are so depleted that they may now be highly vulnerable to new threats, or to the synergistic effects of multiple existing threats. The emergence of novel or opportunistic pathogens in bat hosts is a particular concern for the survival of these small, isolated colonies. Apart from studies of WNS and zoonotic pathogens of humans, however, bat diseases remain poorly understood. In this paper, I describe the pathology of a new, highly aggressive bat disease affecting hibernating little brown myotis (Myotis lucifugus) and identify candidate microbes as possible causative agents. The pathological signs that were observed diverged from those of WNS, and included blue fluorescence in the wings when trans-illuminated with ultraviolet light, and the rapid development of wing necroses and mortality within weeks of the onset of hibernation. Pathology, wing swab cultures, post-mortem analyses, and hemolysis testing identified an array of candidate species, but suggest that a possible cause is a polymicrobial infection involving two etiological agents – Trichosporon yeast and Serratia bacteria. Both species have been documented as part of the mycobiota and microbiota of healthy bats, and cave environments. They are also opportunistic pathogens, known to cause infection in other wild animals and immunocompromised humans. Opportunistic pathogens have been increasingly implicated as a cause of mass mortality events in wildlife. The disease identified here has, to my knowledge, not previously been described, and could represent a new threat to North American bats, compounding concerns for populations facing an already precarious situation. / Biology

Pollinator-friendly wildflower and native grass plantings are increasingly incentivized by state and federal agencies to improve ecosystem services provided by pollinating insects on farmland. However, the potential ecosystem service benefits, or even disservices, of pollinator-friendly plantings relative to wildlife, such as resident, migratory, and nesting birds (e.g., wild turkey (Meleagris gallopavo)), resident and migratory bats, and white-tailed deer (Odocoileus virginianus) are of interest to both landowners and conservation managers. First, we studied bird species diversity, presence, density, and nesting on farms planted with and without pollinator-friendly plantings to evaluate the potential value of these plantings to bird-related values, such as cultural, recreational, and pest-regulating ecosystem services. Second, we quantified bat relative activity through recorded echolocation calls and explored how relative nightly activity varied across common cover types on a farm, by survey year, and by maternity (May-August) versus non-maternity season (September-April). Third, we determined whether white-tailed deer and wild turkey camera trap success and occupancy differed between farms with and without pollinator-friendly farmscaped plots, evaluated along with their relationships to percent cover of natural, developed, crop, and water habitats within 1 km of surveyed farms. We conducted bird point counts across 20 farms on the Eastern Shore of Virginia and Maryland and the city of Virginia Beach, VA during the Spring and Fall of 2017 and 2018. We searched for bird nests in pollinator-friendly plots during the summers of 2017 and 2018. There were no differences in alpha diversity, defined as the number of species per farm per survey period, between control and pollinator farms in either Spring or Fall. We did find differences in species evenness on farms during Spring surveys, as measured by Simpson's index, with pollinator farms having a higher mean Simpson's index. When examining factors relating to presence/absence of our 15 modeled bird species out of 110 species detected on farms, landscape-level cover types were influential in 14 species and presence of pollinator plots was influential for 5 species. After stratification of density estimates by control and pollinator farm study sites, we found that during Spring surveys, the blue jay (Cyanocitta cristata) and Carolina wren (Thryothorus ludovicianus) had lower density on pollinator farms. In the Fall, the blue grosbeak (Passerina caerulea) had higher density on pollinator farms. We found nesting in the pollinator-friendly plots by red-winged blackbirds (Agelaius phoeniceus; n=7). These nests were placed in locations within the pollinator plots with higher forb coverage than random points in the same plots without nests. We estimated the presence and relative activity of bats in 4 cover types, including forest trail, a forested pond edge, a crop field on forest edge, and a farmscaped wildflower plot, on the Eastern Shore Agricultural Research Extension Center in Painter, Virginia, from April 2017- November 2019 using acoustic detectors. Of total detections, 20.11% were identified as big brown bat (Eptesicus fuscus), 17.97% evening bat (Nycticeius humeralis), 15.35% silver-haired bat (Lasionycteris noctivagans), 7.11% eastern red bats (Lasiurus borealis), 3.66% hoary bats (Lasiurus cinereus), 3.1% little brown bat (Myotis lucifugus), and 1.38% tricolored bat (Perimyotis subflavus). Relative activity measured by calls per night varied by cover type, with relative activity highest for all 7 species in the crop field-forest edge and water-forest edge cover types as compared to pollinator plot and forest trail cover types during the maternity season (May-August). All 7 bat species were recorded in the pollinator plot cover type; of the 8,877 calls in pollinator plots, 26.07% were silver-haired bat, 25.21% eastern red bats, 23.78% evening bat, 9.32% hoary bats, 9.11% little brown bat, 5.42% big brown bat, and 1.09% tricolored bat. We used camera trap surveys to measure white-tailed deer and wild turkey occupancy across 20 farms on the Eastern Shore of Virginia and in the city of Virginia Beach, Virginia during the Spring and Fall of 2017 and 2018. Of all wild species photographed, white-tailed deer were most abundant (TS, # captures/100 nights) each survey season, however this varied season to season (Spring 2017 = 98.44 TS, Fall 2017 = 106.01 TS, Spring 2018 = 80.52 TS, Fall 2018 = 99.71 TS). Wild turkey total survey camera trap success was low compared to deer and other wildlife (4.51 TS), and also varied seasonally (Spring 2017 = 1.73 TS, Fall 2017 = 1.50 TS, Spring 2018 = 7.63 TS, Fall 2018 = 5.95 TS). White-tailed deer were detected at all survey locations at least once, and the occupancy of deer decreased as the percentage of developed land within 1km of a farm increased in each survey season. The factors relating to wild turkey occupancy varied by season. In Spring 2017, wild turkey occupancy increased as the percent of natural cover within 1 km of a farm increased. In Spring 2018, wild turkey occupancy decreased as the percent of developed land within 1 km increased. However, landscape variables did not influence wild turkey occupancy in the Fall seasons; rather in Fall 2018 we found that wild turkey occupancy decreased as camera trap success of farm machinery being used increased. Overall, wild turkey had a fairly low presence on all survey sites with an occupancy ranging from 0.18-0.53%, and no clear relationship to explain the change in survey season to season or year to year. Based on these results, pollinator plot presence or absence was not found to influence detection or occupancy of either of these target game species. Rather, other factors, mainly landscape-scale features, were found to have the largest influence on both species' occupancy and presence. Our study is one of just a few in North America to demonstrate some potential benefits of pollinator-friendly plantings to multiple different wildlife species with cultural, recreational, and insect-regulating ecosystem service benefits to landowners. Generally, birds, bats, and our focal game species' presence relied on surrounding landscape variables and forest-edge configurations more than the presence of pollinator friendly plantings. This is probably in part due to the small size of our pollinator plots. We recommend that future work explore potentially increasing the size of pollinator plot plantings or placing pollinator plantings in locations on the landscape with the most surrounding natural area, and least development, to maximize the benefits of this resource to diverse wildlife species with home ranges that are often larger than any one farm. / Master of Science / Pollinator-friendly wildflower and native grass plantings are increasingly used by state and federal agencies to improve benefits from biodiversity such as increases in crop pollinating insects, but the potential benefits of such plantings for vertebrate wildlife are not well studied. We evaluated potential ecosystem services, or even disservices, of pollinator-friendly plantings related to vertebrate wildlife, such as resident, migratory, and nesting birds (e.g., wild turkey), resident and migratory bats, and white-tailed deer. Bird point counts were conducted across 20 farms on the Eastern Shore of Virginia and Maryland and the city of Virginia Beach, VA during the Spring and Fall of 2017 and 2018, and we searched for bird nests in pollinator-friendly plots during the summers of 2017 and 2018. Over the entire project, we saw 110 different species; 96 were identified as insectivorous, indicating the potential for insect regulating services from birds. The total number of bird species observed on farms with pollinator plots were higher than farms without (100 > 90). After division of density estimates between control and pollinator farm study sites, we found that during Spring surveys, the Carolina wren had lower density on pollinator farms while in the Fall the blue grosbeak had higher density on pollinator farms. We found 7 nests of red-winged blackbirds (n=7) in the pollinator-friendly plots and birds preferred nesting in locations within the pollinator plots with more dense flowering plants without woody stem coverage than random points without nests in the same plots. We examined the presence and relative activity of bats in 4 cover types, including forest trail, a forested pond edge, a crop field on forest edge, and a farmscaped wildflower plot on one of our farm sites at the Eastern Shore Agricultural Research Extension Center in Painter, Virginia, from April 2017- November 2019 using acoustic detectors that record bat echolocation. All 7 bat species were recorded in the pollinator plot cover type and of total farm detections, 20.11% were identified as big brown bat, 17.97% evening bat, 15.35% silver-haired bat, 7.11% eastern red bats, 3.66% hoary bats, 3.1% little brown bat, and 1.38% tricolored bat. As expected, relative activity varied by cover type, with relative activity highest for all 7 species in the crop field-forest edge and water-forest edge cover types as compared to pollinator plot and forest trail cover types during the maternity season (May-August). We used camera trap surveys to measure white-tailed deer and wild turkey camera trap success and occupancy across 20 farms on the Eastern Shore of Virginia and in the city of Virginia Beach, Virginia during the Spring and Fall of 2017 and 2018. Of all wild species photographed, white-tailed deer had the highest observations. Wild turkey detections were low compared to deer and other wildlife. White-tailed deer and wild turkey presence were not influenced by the presence of pollinator plots, but rather by other factors, mainly landscape features within 1 km. Our study is one of the first in North America to demonstrate some potential benefits of pollinator-friendly plantings to multiple different wildlife with cultural, recreational, and insect-regulating ecosystem service benefits to landowners. Generally, birds, bats, and our focal game specie's presence relied on surrounding landscape variables and forest-edge configurations than the presence of pollinator friendly plantings. This is probably in part due to the small size of our pollinator plots. We recommend that future work explore potentially increasing the size of pollinator plot plantings or placing pollinator plantings in locations on the landscape with the most surrounding natural area, and least development, to maximize the benefits of this resource to diverse wildlife species with home ranges that are often larger than any one farm.

Fire occurrence was widespread in the central Appalachians pre-European settlement due to Native American ignition and occasional lightning strikes, and continued through European settlement. During this time, low to mixed severity burns supported a suite of ecological communities that were fire adapted. In the mid-20th century, the frequency and intensity of fire decreased regionally, resulting in profound forest composition shifts. Land managers now are prioritizing prescribed fire as a restoration tool in current and transitioning fire dependent communities. However, it is unclear how the re-introduction of fire will affect bat community assemblages, particularly after the severe White-nose Syndrome related population declines of many cave-hibernating bat species. To address this concern we used acoustic detectors to sample bat activity levels in burned and unburned environments to examine habitat and temporal effects of fire on bat species in a repeatedly burned landscape. We found evidence for weak positive fire effects on the northern long-eared bat, Indiana bat, little brown bat, big brown bat/silver-haired bat group, high frequency phonic group, and total bat activity. Temporal effects of fire were only apparent for the big brown bat, where we observed a negative relationship between activity and time since fire. Additionally, historic wildfires may offer a suitable surrogate to assess long-term burn impacts on bats, which in turn can be used to better inform bat and prescribed fire relationships. To examine effects of historic fire on bats, we assessed bat presence using acoustic detections at 16 paired burned and unburned forest stands in Shenandoah National Park. Overall, we found few or mostly equivocal relationships of bat occupancy across species relative to burn condition or time since fire at SNP, indicating there is little evidence to support the concept that fire has a significant ecological effect on bats in this portion of the central Appalachians. Riparian areas are particularly important for bats, and serve as foraging and drinking areas, roost sites, and travel corridors. Because fire impacts dry upland and mesic riparian areas differently, is possible that fire will impact bats differently in burned and riparian habitats. To examine fire effects on bats in riparian and upland habitats, we used paired sampling to monitor bat activity in burned, unburned, riparian, and non-riparian areas. Burn and riparian variables had empirical support to explain activity of all bat species. However, coefficients for these species were small and confidence intervals overlapped zero indicating that differences between habitat configurations were marginal. Our results suggest bats have somewhat species-specific responses to fire that differ between upland and riparian habitats, but that large landscape level prescribed fire has a slightly positive to neutral impact on all bats species identified in at our study site post-fire suppression. / Master of Science / Fire occurrence was widespread in the central Appalachians pre-European settlement from to Native American ignition and occasional lightning strikes, and anthropogenic burning continued through European settlement. During this time, burns supported many ecological communities that were fire adapted, i.e., oak (Quercus spp) and pine (Pinus spp)-dominated types. In the mid-20th century, fire decreased regionally, resulting in changes to forest composition. Land managers now are prioritizing prescribed fire as a tool to restore or re-establish fire dependent communities. However, it is unclear how the re-introduction of fire will affect bats, particularly after the severe White-nose Syndrome related population declines of many bat species. To address this concern, I used acoustic detectors to measure bat activity levels in burned and unburned landscapes to examine habitat and temporal effects of fire on bat species in a repeatedly burned landscape on the northwestern portion of the George Washington National Forest. I found evidence for weak positive fire effects on the northern long-eared bat, Indiana bat, little brown bat, big brown bat/silver-haired bat group, high frequency phonic group, and total bat activity. Temporal effects of fire were only apparent for the big brown bat, where we observed decreasing activity as time since fire increased. Because riparian areas are particularly important for bats in the region as foraging and drinking areas, roost sites, and travel corridors, I also focally compared burned and unburned riparian areas. Burn and riparian variables had support to explain activity of all bat species, however differences between habitat types were marginal. My results suggest bats have somewhat species-specific responses to fire that differ between upland and riparian habitats, but that large landscape level prescribed fire has a slightly positive to neutral impact on all bats species identified at our study site post-fire suppression. Lastly, examining effects of historic wildfires may allow managers to infer long-term burn impacts not yet observable with current prescribed burning. To examine effects of historic fire on bats, I assessed bat presence using acoustic detections at paired burned and unburned forest stands in Shenandoah National Park. Overall, I found few relationships of bat occupancy across species relative to burn condition or time since fire, indicating that fire likely does not have a significant ecological effect on bats in this portion of the central Appalachians.

Two threats to bats are especially pervasive in the central Appalachian Mountains of the eastern United States: a fungal disease called White-nose Syndrome (WNS) and wind energy development. White-nose Syndrome has caused the death of millions of bats in North America, and multiple hibernating bat species are affected in the central Appalachians. Wind energy is one of the most rapidly-growing energy sources in eastern United States, and bats are often killed when they fly near wind turbines. Fatality rates at wind turbines is highest in bat species that migrate instead of hibernate. There is limited data on bats during the autumn and spring seasons in the central Appalachian Mountains, and the impacts of WNS and wind energy development may be exacerbated during these seasons. Therefore, I sought to determine patterns and drivers of activity for hibernating bat species during autumn and spring around hibernacula. Similarly, I set out to determine patterns and drivers of activity for migratory bat species during autumn and spring along mountain ridgelines in the central Appalachians. Lastly, I searched for evidence of potential WNS-induced changes in the summer ecology of the once common northern long eared bat. This study can help elucidate patterns of bat activity during largely understudied seasons. Furthermore, it can provide useful information needed by land managers to implement actions that could help alleviate and/or avoid potential additive negative impacts on bat species with existing conservation concerns. / MS / Two threats to bats are especially pervasive in the central Appalachian Mountains of the eastern United States: a fungal disease called White-nose Syndrome (WNS) and wind energy development. White-nose Syndrome has caused the death of millions of bats in North America, and multiple hibernating bat species are affected in the central Appalachians. Wind energy is one of the most rapidly-growing energy sources in eastern United States, and bats are often killed when they fly near wind turbines. Fatality rates at wind turbines is highest in bat species that migrate instead of hibernate. There is limited data on bats during the autumn and spring seasons in the central Appalachian Mountains, and the impacts of WNS and wind energy development may be exacerbated during these seasons. Therefore, I sought to determine patterns and drivers of activity for hibernating bat species during autumn and spring around hibernacula. Similarly, I set out to determine patterns and drivers of activity for migratory bat species during autumn and spring along mountain ridgelines in the central Appalachians. Lastly, I searched for evidence of potential WNS-induced changes in the summer ecology of the once common northern long eared bat. This study can help elucidate patterns of bat activity during largely understudied seasons. Furthermore, it can provide useful information needed by land managers to implement actions that could help alleviate and/or avoid potential additive negative impacts on bat species with existing conservation concerns.

Many animal species are known for their unparalleled abilities to encode sensory information that supports fast, reliable action in complex environments, but the mechanisms remain often unclear. Through fast ear motions, bats can encode information on target direction into time-frequency Doppler signatures. These species were thought to be evolutionarily tuned to Doppler shifts generated by a prey's wing beat. Self-generated Doppler shifts from the bat's own flight motion were for the most part considered a nuisance that the bats compensate for. My findings indicate that these Doppler-based biosonar systems may be more complicated than previously thought because the animals can actively inject Doppler shifts into their input signals. The work in this dissertation presents a novel nonlinear principle for sensory information encoding in bats. Up to now, sound-direction finding has required either multiple signal frequencies or multiple pressure receivers. Inspired by bat species that add Doppler shifts to their biosonar echoes through fast ear motions, I present a source-direction finding paradigm based on a single frequency and a single pressure receiver. Non-rigid ear motions produce complex Doppler signatures that depend on source direction but are difficult to interpret. To demonstrate that deep learning can solve this problem, I have combined a soft-robotic microphone baffle that mimics a deforming bat ear with a CNN for regression. With this integrated cyber-physical setup, I have able to achieve a direction-finding accuracy of 1 degree based on a single baffle motion. / Doctor of Philosophy / Bats are well-known for their intricate biosonar system that allow the animals to navigate even the most complex natural environments. While the mechanism behind most of these abilities remains unknown, an interesting observation is that some bat species produce fast movements of their ears when actively exploring their surroundings. By moving their pinna, the bats create a time-variant reception characteristic and very little research has been directed at exploring the potential benefits of such behavior so far. One hypothesis is that the speed of the pinna motions modulates the received biosonar echoes with Doppler-shift patterns that could convey sensory information that is useful for navigation. This dissertation intends to explore this hypothetical dynamic sensing mechanism by building a soft-robotic biomimetic receiver to replicate the dynamics of the bat pinna. The experiments with this biomimetic pinna robot demonstrate that the non-rigid ear motions produce Doppler signatures that contain information about the direction of a sound source. However, these patterns are difficult to interpret because of their complexity. By combining the soft-robotic pinna with a convolutional neural network for processing the Doppler signatures in the time-frequency domain, I have been able to accurately estimate the source direction with an error margin of less than one degree. This working system, composed of a soft-robotic biomimetic ear integrated with a deep neural net, demonstrates that the use of Doppler signatures as a source of sensory information is a viable hypothesis for explaining the sensory skills of bats.