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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

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.

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

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

Emerging infectious diseases (EID) pose significant threats to biodiversity. Human influence over the environment has increased opportunities for the introduction of novel pathogens to naïve hosts, potentially leading to host extinction. Understanding mechanisms of host persistence is critical for effectively conserving species affected by EIDs. Our study investigated the disease dynamics of white-nose syndrome (WNS), caused by the fungal pathogen Pseudogymnoascus destructans (Pd), in little brown bats (Myotis lucifugus) across a spatiotemporal gradient. We explored the relationship between bat roosting temperatures and Pd growth rates across three phases of pathogen invasion comprising years since WNS has been present at sites: invasion (0-3), established (4-8), and endemic (9+ years). Data used by this study comes from a combination of field-based data collection in New York where WNS has been present the longest and data from a long-running project which includes from other locations in the Northeast and Midwest regions of the United States. Our results reveal a weakening interaction between temperature and fungal growth rates time with WNS progresses. We additionally observed a decrease in early hibernation fungal loads and variation in infection prevalence over time, suggesting the onset of a coevolutionary relationship between bats and Pd. This study highlights the importance of investigating changing disease dynamics when understanding the reasonings for host persistence. / Master of Science / Emerging infectious diseases threaten species with the risk of extinction. Human activities have altered habitats which has increased the spread of new pathogens to vulnerable host populations. This research focuses on white-nose syndrome (WNS), an emerging disease caused by the fungal pathogen Pseudogymnoascus destructans (Pd). The arrival of Pd to North America resulted in widespread declines in little brown bat (Myotis lucifugus) populations, however, some populations persist at stable or growing rates. This study aims to investigate how the relationship between the growth rate of Pd and bat hibernation temperature may have changed over time. We used a combination of contemporary data collected in New York and a long-running dataset that documents the invasion and establishment of Pd across the Northeast and Midwestern regions of the United States to investigate fungal growth rates during different phases of Pd invasion: invasion, established, and endemic phases. Our results indicate the relationship between temperature and pathogen growth rate has weakened over time, suggesting potential changes in the host-pathogen relationship. Additionally, we found changes in fungal loads and infection prevalence throughout hibernation, suggesting the foundation of a coevolutionary relationship between bats and Pd. This research highlights the importance of understanding changes in disease dynamics to help understand how other species at risk of emerging infectious diseases may be able to persist.