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Bat deterrents, such as radar and acoustic methods have been suggested as potential mitigation for when bats are at risk of harm from human activities and/or structures. To date, no study has compared bat responses to these methods, for use in a European context. In this thesis, I aimed to (i) test acoustic and radar as potential deterrent devices, at foraging sites in the UK, (ii) determine the effect of an acoustic deterrent device with increasing distance and (iii) explore bat responses to an acoustic deterrent device and potential mechanisms for deterrence. I found that acoustic but not radar deterrents were effective at reducing bat activity at foraging sites and therefore I focussed on acoustic deterrents for the rest of the thesis. I developed a 2-dimensional (2D) thermal bat tracking system and used it in combination with acoustic and visual bat pass counting methods to examine bat responses to an acoustic deterrent with increasing distance. Results from a fine-scale study indicated an 80% reduction in bat activity at 15 m from the acoustic deterrent, reducing to 25% reduction at 30 m, but a larger scale experiment found no deterrent effect beyond 40 m. I then developed the thermal tracking method further and examined bat responses in 3D to deterrent broadcast and also examined the deterrent’s effect on echolocation call parameters. Bats increased their flight speed, decreased the tortuosity of their flight paths and focussed the signal of their echolocation calls into a reduced bandwidth, in line with a decrease in foraging behaviour and in support of the hypothesis that a masking effect of the deterrent sound affects echolocation behaviour. I conclude that acoustic deterrence shows great promise in the management and conservation of bat populations but warn that these methods should always be used with careful consideration and on a case-by-case basis.

Natterer's bats (Myotis nattereri) are typical of many Bat species in that they participate in a variety of distinct seasonal communities and behaviours. In summer adult females are thought to be largely philopatric to their natal community/landscape where they rear their young and form largely matrilineal communities. Bat foraging behaviour and social participation is largely unquantified, as is our understanding of how age/maturity and sex may mediate their social behaviour. Crucially, the rate of female dispersal between communities is completely unquantified. A much better understanding of bat spatial and social dynamics is necessary to inform statutory functions, effective conservation and epidemiological modelling. We have mapped and quantified the spatial and social dynamics of three communities of Natterer's bats. Uniquely our roost switching data comes from a community roosting entirely in natural roosts. Radio-tracking, ringing and DNA evidence can be combined at one site, whilst ringing and DNA can be combined at two others. In addition, DNA samples from a further two sites could be included to complete the comparison of 183 Natterer's bats from 5 sites. Microsatellite data (based on 15 markers) was used to describe relatedness at two functional scales (between roosts within a community and between communities). Relatedness and population structure was also compared to home range analysis and roost use to determine if related individuals forage close to each other or share a roosts more frequently than unrelated individuals. Novel descriptions of demographic and epidemiological rates for this species were determined, which has been incorporated into predictive models of how both the community may respond to changes in the environment, or diseases may spread within the community which will help improve bat Conservation.

How populations diverge and form new species in the face of gene flow is a key question in evolutionary biology. Recent research suggests this may be possible where the same traits affect the ecological niche and are involved in assortative mating, and that a small number of genes could be involved in driving speciation in these cases. Echolocation call frequency in bats has roles in ecology and social communication. Bats using HDC echolocation have hearing tuned to specific frequencies, with frequency shifts impacting ecological niche and mate recognition, meaning this is a good candidate trait to drive speciation. HDC echolocation has evolved independently in two highly divergent groups of bats, providing a unique opportunity to study the molecular basis of a trait potentially driving speciation. I have combined selection testing of specific loci with genomewide divergence scans to test hypotheses concerning the evolution of HDC echolocation. Members of the yangochiropteran genus Pteronotus use low duty-cycle echolocation, except for the subgenus Phyllodia. Selection tests on coding sequence data revealed loci associated with hearing under positive selection in Phyllodia and in Pteronotus, including eleven shared with a yinpterochiropteran HDC echolocator, Rhinolophus sinicus. Three size and acoustic morphs of Rhinolophus philippinensis exist in sympatry on Buton Island. Phylogenetic reconstructions revealed population structure between the morphs, though with conflicting topologies based on mitochondrial and nuclear data. Species delimitation identified at least two separate taxa. Genomewide scans of divergence indicated low background FST between the morphs, punctuated with highly diverged islands featuring an overrepresentation of genes associated with body size and hearing. 3 This thesis represents the first genome-wide investigation of HDC echolocation, highlighting candidate genes related to this trait. It additionally describes a rarely observed mammalian ecological speciation, providing support for the claim that species designated R. philippinensis represent a complex across their range.

Bats represent a quarter of all mammalian species and play vital roles in many ecosystems. They are also are the only mammals capable of powered flight and have large, light, thin wings to enable flight. However, bats face many threats, including collisions with man-made structures, fungal infections and predator attacks, all of which can cause severe wing injuries. Hundreds of bats are admitted annually for care to treat torn and injured wings. This thesis aims to investigate the causes and effects of bat wing tears. In a series of studies, this thesis will: i) characterise wing tears in P. pipistrellus and other bat species in the UK; ii) explore the anatomy of the wing in P. pipistrellus, and see if knowledge of the anatomy is sufficient to understand wing tear placement and healing rates; iii) present a novel method for analysing flight from high-speed video data to assess the effect of tears on flight; and iv) develop a systematic forensic method to identify the presence of cat DNA on wing tears. Results from Chapter 2 indicate that most tears occurred in the Plagiopatagium wing section (section P), which is closest to the body. Tears in that section also might take longer to heal. Chapter 3 suggested that knowledge of wing anatomy is not sufficient to explain tear position and orientation. Indeed, while material testing did not identify section P as being significantly weaker than the chiropatagium (the distal sections of the wing), section P tended to have the most tears. The position of the tears, close to the body and towards the trailing edge, may suggest that they were caused by predator attacks, such as from a cat, rather than collisions. Consistent with this, 38% of P. pipistrellus individuals had confirmed wing tears caused by cats, with an additional 38% identified by rehabilitators as due to suspected cat attacks. Results from high-speed video footage collected in the fourth chapter revealed that tears on both wings significantly affected wing movements, and the body orientation tended to lean towards the healthier wing. The fifth chapter developed techniques to identify cat DNA from swabs of wing tears, and found cat DNA on 66.67% of the swab samples. Results from this thesis reveal that cat attacks on bats may be far more common than first thought. In addition, future work should focus on the seasonal timings of wing tear injuries to structure recommendations for cat owners and model the implications of cat attacks on bat populations. In addition, while the tear injuries do heal, post-release monitoring is important to ensure bats survive in the long-term following rehabilitation. Recommendations for bat carers and cat owners formulated in this thesis are the first steps in addressing the prevalent and significant problem of bat wing tears.

Microbial communities play important roles in organismal and ecosystem health. High throughput sequencing has revolutionized our understanding of host-associated microbial communities, but the viral component of these communities remains poorly characterized relative to microbes such as bacteria, particularly in non-human hosts. This knowledge gap has implications for global health, as viruses originating in wildlife are responsible for recent disease outbreaks in humans and domestic animals. Although studies have identified factors differentiating viral communities between species, we have little understanding of the variability of viral communities within species. Comparative studies of viral communities are therefore necessary to characterize novel taxa and to evaluate the ecological factors influencing intraspecific viral diversity and distribution. Bats are recognized as “special” reservoirs for viruses because they are associated with diverse viral communities and display deep evolutionary relationships with individual viral taxa. Common vampire bats (Desmodus rotundus) represent a particularly interesting system in which to investigate viral communities, as they are obligate blood feeders that interact ecologically with many different host species, providing opportunities for the acquisition of diverse viruses. The overall objective of this thesis was to advance our understanding of intraspecific wildlife-associated viral communities using an established field network of common vampire bat colonies across Peru. Specifically, I developed a novel method for comparative viral community studies, characterized the viral communities of vampire bats, and examined the ecological correlates of vampire bat viral diversity across Peru. Metagenomic sequencing is a promising technique for comparative studies of viral communities in wildlife, but there is a need to first develop standardized methods that can be applied to samples collected in the field. In Chapter 2 I developed a shotgun metagenomic sequencing approach to characterizing viral communities from non-invasive samples. Specifically, I optimized extraction and sequencing protocols using fecal and oropharyngeal swabs collected from common vampire bats in Peru. Two preliminary sequencing runs were performed, the results of which motivated four pilot studies in which I tested how different storage media, nucleic acid extraction procedures, and enrichment steps affect the viral community detected. Metagenomic sequencing revealed viral contamination of fetal bovine serum, a component of viral transport medium, suggesting that swabs should be stored in RNALater or another non-biological medium. Extraction and qPCR tests were performed on swabs inoculated with known concentrations of virus, which revealed that nucleic acid should be directly extracted from swabs rather than from supernatant or pelleted material. Metagenomic sequencing of paired samples was used to test enrichment by ribosomal RNA depletion and light DNAse treatment, which both reduced host and bacterial nucleic acid in samples and improved virus detection. A bioinformatic pipeline was developed specifically for processing vampire bat shotgun viral metagenomic data. Finally, the optimized protocol was applied to twelve pooled samples from seven localities in Peru, and read subsampling demonstrated that the viral communities detected were consistent at commonly attained depths of sequencing. The protocol developed in this chapter enables minimally biased comparative viral community studies in non-invasive samples collected from wildlife. Having a detailed understanding of viral diversity in key wildlife hosts is an important first step in evaluating the risk of zoonotic disease emergence, but we still lack a holistic view of viral communities in many species including vampire bats. In Chapter 3, I used the metagenomic sequencing protocol developed in Chapter 2 to thoroughly characterize viral communities in the saliva and feces of vampire bats captured across Peru. Viruses were detected from a range of natural host groups including vertebrate-associated taxa that were potentially infecting vampire bats, bacteriophages associated with gut bacteria, and plant- or insect-infecting viruses potentially acquired from the environment. There were broad differences between fecal and saliva viral communities, showing evidence of body habitat compartmentalization. Overall, results established that vampire bat viral communities differ between body habitats and suggested that, for the vertebrate-infecting families analyzed, novel viruses mostly fall within bat-specific clades, without evidence of livestock or humans acting as a major source of viral diversity in vampire bats. Interspecific differences in ecological and life history traits are known to impact viral richness in bats, but the factors structuring viral communities within bat species are less well understood. In Chapter 4, I examined the spatial, demographic and environmental correlates of intraspecific viral diversity in vampire bats. Three measures of viral diversity were calculated at the colony level: richness, a novel measure of taxonomic diversity, and community composition. Generalized linear models were then used to test the effects of broad scale and local ecological variables on saliva and fecal viral diversity. The results showed for the first time that ecological variables can influence intraspecific viral diversity. In summary, the work presented in this thesis advances our understanding of wildlife-associated viral communities in an ecologically important bat host. Future directions in comparative wildlife viral metagenomics, as discussed in Chapter 5, will include exploring the determinants of viral communities across host species, environments and time.

Bats are unique mammals since they are able to fly and due to their crucial ecosystem roles, they are designated as keystone species. However, in many parts of the world, it is difficult to study bats due to the existence of protective legislation caused by their threatened status. Consequently, bat endoparasite studies are limited and even less is known about the bat immune system. To address this paucity of knowledge, this study was conducted using 99 pipistrelle bats (Pipistrellus pipistrellus, n=93 and P. pygmaeus, n=6 bats) that were obtained opportunistically from the Greater Manchester and Lancashire region between September 2005 and September 2008. These bats were infected with several species of helminths and protozoan parasites as previously described (Lord, 2010; Dodd et al., 2014). The data within this thesis describes further characterisation of the protozoan infections in this pipistrelle population through development of PCR-based molecular typing tools. This approach has allowed the molecular differentiation between Trypanosoma dionisii and T. vespertilionis infections, confirmed that all eimerian infections were caused by Eimeria rioarribaensis and also confirmed that Bartonella sp. infection is most likely to be non-zoonotic. In addition, Cryptosporidium sp. and Borrelia sp. infection data is presented; the former being the first report in a UK bat. Analysis of the infection profiles with respect to bat genotyping data (Dodd et al., 2014) shows that the parasites are randomly distributed with the exception of the E. rioarribaensis infections which appear to cluster in a sub-population of pipistrelles that are genetically more homogeneous. Since Toll-like receptors (TLRs) are an important element of the mammalian innate immune system, a PCR strategy was developed to isolate TLR4 and TLR2 genes from the pipistrelle bats (n=59). The TLR4 sequences were highly variable at the amino acid level (haplotypes, n=42), and a phylogenetic analysis of the protein sequences showed that they clustered into 7 major groups. Analysis of infection profiles in these bats showed that two TLR4 clusters appeared to correlate with susceptibility to trypanosomes (cluster 6) and Toxoplasma gondii (cluster 3). In addition, bats in TLR4 cluster 6 had a significantly reduced helminth burden. The TLR2 sequences were more conserved at the amino acid level (haplotypes, n=5); however, 7 bats were heterozygous at the TLR2 locus and interestingly, these correlated with a significantly reduced helminth burden. Overall, this thesis highlights the difficulty of studying bat endoparasites and this is often confounded by the lack, or absence, of parasitic material to assist developing molecular-based tools. Despite this difficulty, interesting data have been generated with respect to the pipistrelle genetics, including Toll-like receptor variations, and eimerian, trypanosome, T. gondii and helminth infection profiles, and this is worthy of further detailed investigations.

Bats are vital to Great British biodiversity; they are the primary consumers of nocturnal insects, disperse nutrients across landscapes, and are excellent bioindicators of an ecosystem’s health. The diversity of bat species in the UK is thought to be as a result of extensive resource partitioning. There are numerous methods used for studying bat diets, each with benefits and drawbacks. Past research has compared small numbers of species at a time, making inter-species comparisons difficult. Our large repository of bat guano samples, collected from around the UK, has allowed us to study the bat species under one methodological ‘umbrella’. This thesis is divided into 7 chapters. This first chapter gives a broad overview of the project, framing this research and provides an overview of the technologies available, and how their development has enabled environmental research on a scale, which, until recently, would have been unimaginable. The second chapter is a meta-analysis of the literature that pertains to bat diets. These data will be used to inform the design of primers in the barcoding stages of the project. Next is a shotgun metagenomic analysis of a selection of guano samples from across the range of the UK species. This method provides information, not only about diet species, but also about the bat, viral, and bacterial DNA. Analyses of this data show that there are several dietary forms seen between the species. The fourth chapter is a targeted amplicons metagenome study of the mitochondrial COI barcode region from the arthropod species identified in the literature review, and from metagenomic data-set. This provides a greater resolution picture of the diet species present. Analyses of these data use phylogenetic intersection analysis to ensure the robustness of the taxonomic assignments in the face of the patchy databases available. In the fifth chapter, I draw together the data gathered using the different approaches and presented in the previous chapters. I discuss the efficacy of the methods, and assess the role of resource partitioning in bat species co-existence. The sixth section will look at the appropriateness of using guano morphology as a diagnostic of species presence. Finally, in chapter seven, I summarise these data in the wider context of bat ecology, comment on the implications of the research for conservation, and discuss potential directions for the field in the light of this research.

Global efforts to address climate change have recently introduced a new source of fatality risk to bats, from wind turbines. Bat fatalities have now been confirmed in varying magnitudes at wind energy facilities around the world. Research at large turbines and wind farms has started to produce a knowledge base regarding impacts upon bats, though many questions remain. Little, however, is known about risk levels at small and medium scale wind turbines. Equally, research regarding the impacts of turbines in the UK is limited. This thesis examines the impacts of small and medium scale wind turbines upon bats. Planning records of wind turbines in Wales and south west (SW) England were reviewed. Approved planning applications for single and double turbine sites were found to greatly outnumber those for larger scale wind farms. The large majority of single and double turbine approvals were also for small turbines. The potential impacts of turbine presence and density on current bat roost populations and population changes were analysed, finding no impact. An estimate of bat fatality rates at small and medium turbines was calculated, using a trained search dog to locate carcasses. An average fatality rate between 0.81 and 15.15 turbine-1 year-1 was estimated. The higher rate accounted for uncertainty in the monitoring protocol. Only 3 bat carcasses were however observed across all monitored turbines, suggesting more stringent monitoring would likely confirm a lower maximum annual fatality rate. Bat activity levels were also compared between the turbine location and differing habitat types. A disturbance effect was consequently identified in proximity to turbines during high wind speeds. Finally moderating influences of environmental weather and habitat conditions upon bat activity were confirmed. Social Network Analysis (SNA) methods were used to analyse bat movement networks within a small grid of bat detectors centred on each turbine. Associations were identified between bats’ movement routes and habitat structures present at sites, highlighting vulnerabilities to disruption. Furthermore bats actively used the turbine area, potentially for foraging purposes. Finally by assessing bats’ activity levels in response to a turbine noise playback experiment, small turbine noise was found to have no impact upon bat activity. Planning guidance regarding bats and small and medium turbines is highlighted as a priority for policy development.

The presence of bats inside church buildings can result in negative impacts, requests for advice and disagreements about what management approaches are appropriate. Despite the suspected importance of churches for bats, there has been little research focusing on the ecology and behaviour of bats in church buildings, and current gaps in knowledge sometimes restricts the quality of advice that can be given. This study makes use of several approaches (examination of existing records, a regional field survey, temperature and acoustic monitoring and radio-tracking) to improve understanding of the ecology of bats roosting in churches, with a focus on Pipistrellus pygmaeus (which can cause some of the most severe problems) in eastern England. The study focused on this region because it had the highest number of requests for advice about bats from church representatives in England. Inside churches, roof or ceiling crevices in the south sides of churches were preferentially selected as roost sites, and were also warmer than equivalent crevices in the north sides of churches. Roost crevices were characterised by fluctuating temperatures which warmed dramatically during the day and cooled at night, whereas church interior temperatures were stable. Within the highly modified, fragmented arable landscapes of eastern England, a modelling approach showed that P. pygmaeus selects church roosts with more wetland habitat cover within typical commuting distance, and which are closer to broad-leaved woodland, than churches in general. Radio-tagged female P. pygmaeus typically select wetland and woodland habitats for foraging, with arable land consistently the least selected, but most available habitat. I found substantial differences among colonies in home range and commuting distances, with bats from one colony commuting up to 15.9 km to reach foraging resources. Mobility may be important for the persistence of P. pygmaeus in fragmented landscapes by allowing bats to exploit multiple distant and dispersed foraging patches. Radio-tracked P. pygmaeus bats from three colonies collectively made use of multiple alternative day roosts in a range of structures across large areas, but bats at two colonies mostly day roosted in their respective church roosts. Using automatic, continuous acoustic monitoring, I found that P. pygmaeus bats were present and active inside three medieval churches throughout the year, with activity peaking in July. P. pygmaeus activity inside churches was positively correlated with night-time temperatures and negatively correlated with wind speed. Recommendations for conservation management are made along with possible future directions for applied research.

Approximately 25% of bats globally are threatened, but limited data on African bats, which account for 20% of bat species, hinders our understanding of their conservation status across this ecologically diverse continent. This study combined: modelling techniques, to predict current species distributions for 58 southern African bat species and project past, current and future distributions of 22 endemic and near-endemic species; bat acoustic surveys, to assess landscape features influencing bat activity in arid and semi-arid regions; and conservation planning software to design a large-scale monitoring network for bats across this subcontinent. Species distribution models were employed using a robust and well established presence-only modelling technique (Maximum Entropy – Maxent) to model the current distributions of 58 species in southern Africa. Although the important eco-geographical variables were species- or in some cases family-specific, overall water availability (both temporary and permanent), seasonal precipitation, vegetation and karst (caves/limestone) areas were the most important factors associated with distribution patterns. These species distributions were then used to identify range-restricted and narrow niche breadth species, alongside other life-history strategies considered to put species at risk, such as Old World pteropodids and cave-dwelling bats to identify species most at risk. Nine of the 58 species in this study were identified as ‘at risk’. Considering range-restriction and endemism separately, the results showed that range-restricted species were a higher proportion (50%) of ‘at risk’ species than endemics (41%) but six of the nine identified species were endemic and range restricted (67%). If only areas of high species richness are prioritised, important areas with low species richness but rare, ‘at risk’ or endemic species would be excluded. Species distributions are not fixed but may shift due to changes in environmental conditions. Accurately predicting changes in species’ distributions due to anthropogenic climate change remains a fundamental challenge for conservation biologists, and this is amplified when dealing with taxa such as bats that are inherently difficult to study and in areas, such as Africa, with sparse ecological data. To better understand endemic bat species risk to climate change in southern Africa and to highlight historical and future likely refugia, Maxent was employed to forecast range-shifts for 22 southern African endemic or near-endemic species. Species distributions were projected during the Last Glacial Maximum (LGM ~22,000 BP), present (1950-2000) and future (2070: averaged 2061-2080, using IPCC5 scenarios) climatic conditions. Climate change was predicted to change species composition extensively within a relatively short timescale (within 60 years). By 2070, 86% of species modelled are predicted to have range contractions and six species were highlighted to be most at risk, with range contractions of more than 20%. The majority of southern Africa is composed or arid or semi-arid regions. Generally arid and semi-arid areas are overlooked and understudied due to low species richness, yet these areas are known to have a high proportion of endemic species. As part of this study, driven transects were carried out across arid and semi-arid areas to assess bat activity in these areas. Bat activity was recorded at 94% of the acoustic surveys, demonstrating that driven transects are an effective method of surveying bats in southern Africa. Bat activity increased at lower altitudes and higher latitudes, which characteristically have more rainfall, permanent water and vegetation. Although water has been shown in other studies to be important for bats, temporary water was not shown to influence bat activity and permanent water was positively correlated with bat activity for hipposiderids and rhinolophids and FM bats, which may reflect the fact that water features important for bats at smaller scale. The same two vegetation types that were consistently negatively correlated with bat activity were drier vegetation types (Karoo-Namib shrubland) and high salinity halophytic vegetation. Finally, a systematic conservation planning software tool (Marxan) was used to design multi-species monitoring networks that incorporated all 58 target species across the 11 ecoregions found in southern Africa. To ensure rare, endemic and range-restricted species were monitored at the same level as widespread species, species distributions (mapped using Maxent) were extracted by ecoregion. Monitoring targets (i.e. a percentage of species distribution across ecoregions) were standardised to ensure the same percentage of predicted distribution was included across all species (rare and widespread). To account for different resources and capacity, three optimal monitoring networks (minimum monitoring stations to achieve the monitoring targets) were proposed to survey 1, 5 or 10% of all species distributions within each ecoregion. The optimal solution for monitoring 1% of species distributions within ecoregions was found by monitoring 1,699 stations (survey sites), or for 5% 8,486 stations and finally for 10% 17,867 stations would be needed. In conclusion, the findings presented in this thesis have important conservation implications and have the potential to inform the practical steps required towards the introduction of a bat monitoring programme in southern Africa. While this study has highlighted challenges to African bat conservation, it has also demonstrated that an integrated and multi-disciplinary approach, using emerging techniques and conservation tools (e.g. conservation planning and automated call analysis software) can be used to fill knowledge gaps and inform conservation priorities in the absence of systematically collected data.

Urbanisation is a key driver in the loss, fragmentation and modification of natural habitats resulting in the global loss of biodiversity. As the human population, and consequently the rate of urbanisation, continues to increase exponentially it is important to understand how to sustain and enhance biodiversity within the built environment. Cities comprise a complex assortment of habitat types yet relatively little is known of how its composition and spatial configuration can influence species presence or foraging activities. It is therefore necessary to examine habitat use and biodiversity patterns at multiple spatial scales to fully understand how species are responding to the urban matrix. There are few other orders of animals that are as strongly associated with people as bats (Chiroptera); for some bat species human habitations provide roosts and adaptations of the environment provide food sources. However bat species richness generally declines with increasing urbanisation indicating that many species are not able to persist in highly urbanised areas. In this thesis, I show that the behaviour, habitat preferences, and distribution of bats are strongly influenced by the built environment at both a local and landscape scale. Although many animal species are known to exhibit sex differences in habitat use, adaptability to the urban landscape is commonly examined at the species level without consideration of potential intraspecific differences. I found that female Pipistrellus pygmaeus show greater selectivity in foraging locations within urban woodland in comparison to males at both a local and landscape scale. There was a lower probability of finding females within woodlands which were poorly connected, highly cluttered, with a high edge: interior ratio and fewer mature trees. The results have important implications for our understanding of how to manage areas for breeding females and highlight the need to supplement acoustic monitoring with trapping data to assess sex differences in habitat use. Determining how morphological or behavioural traits can influence species adaptability to the built environment may enable us to improve the effectiveness of conservation efforts. The morphological similarities between P. pygmaeus and P. pipistrellus suggest that both species should respond similarly to the urban matrix, however I found differential habitat use occurring within a variety of urban habitats (e.g. woodland and waterways) and at a landscape scale. In urban woodland there was a higher probability of P. pygmaeus activity relative to P. pipistrellus in woodlands with low clutter and understory cover which were surrounded by low levels of built environment. Many bat species are strongly associated with aquatic or adjacent riparian habitats yet we know little about the utilisation of urban waterways by bats. After surveying urban waterways throughout the UK, I was able to show that the built environment can negatively affect a variety of bat species from the riparian zone up to 3km from a waterway. This indicates that beneficial urban waterway rehabilitation schemes for bats require management at multiple spatial scales, from retaining a vegetated riparian zone at the local scale to highlighting the necessity for conservation funding to be spent on the implementation of landscape scale environmental improvement schemes that encompass the entire urban matrix. Undertaking surveys to confirm species presence or to estimate population sizes can be difficult, particularly for elusive species such as bats. I was able to demonstrate a variety of ways to increase surveying efficiency (e.g. the use of an acoustic lure to increase bat-capture rate) and a significant relationship between bat activity and the relative abundance of certain species of bat which can maximise the knowledge of diversity in an area whilst minimising wildlife disturbances. Urbanisation has also had strong negative effects on many insect groups, such as moths, which are important components of the diets of many bat species. I found that woodland vegetation characteristics were more important than the surrounding landscapes in determining the abundance, species richness, and species diversity of moth assemblages within urban woodland. This indicates that management at a local scale to ensure provision of good quality habitat may be more beneficial for moth populations than improving habitat connectivity across the urban matrix. The findings presented in this thesis have important implications for our understanding of the adaptability of species to the built environment and for the management and monitoring of bat populations. It also highlights that even common bat species are negatively affected by urbanisation and much greater attention should be paid to securing their future within the urban landscape.

The increase in wind energy production has been relatively rapid and is expected to continue at a global scale. However, numbers of bat carcasses found at wind turbines in North America in the early 21st century raised concern about the plight of this taxon with the growth in wind-energy generation. This led to carcass searches for bats becoming commonplace at wind farms globally. However, few large scale systematic studies have assessed the effects of wind turbines on bats, especially for species considered potentially at higher risk in Europe. In this thesis the number and species of bats killed from wind farms were estimated across Britain, and the important predictors (i.e. activity, turbine characteristics and habitat) of fatality were determined. Insect abundance, biomass and bat activity was also quantified at turbine and control locations, to assess if insects and hence bats were attracted to turbines. In addition, assessments were made of the effects of increasing temporal and spatial replication of acoustic monitoring on estimates of species composition and bat activity. This was assessed for activity monitored at ground and at the centre of the rotor sweep area (the nacelle). Carcass searches were conducted using trained search dogs and concurrently bats were surveyed acoustically at three randomly selected turbines at ground and from the nacelle at 48 wind farms throughout Britain. Bats were also monitored acoustically at paired controls (with a randomly selected turbine) at 20 of the wind farms sites. In addition, nocturnal Diptera were sampled at 18 of the sites using a paired turbine and control design. Across 139 wind turbines, 188,335 bat passes were recorded and 2,973 carcass searches performed. Edge and open aerial foraging species, in particular Pipistrellus pipistrellus and P. pygmaeus were most at risk of fatality 4 at wind farms in Britain. The number of Pipistrellus pipistrellus killed annually in Britain between mid-July and mid-October was estimated at 2,373 95% CI 513 to 4,233 and the number of P. pygmaeus at 3,082 95% CI 1,270 to 4,894. When compared to population estimates, the number of Pipistrellus pygmaeus killed was 57% higher than the number of P. pipistrellus killed (0.19% of the population versus 0.43%, respectively). This may be due to Pipistrellus pygmaeus flying more often within the rotor sweep area compared to P. pipistrellus. Activity measured at the nacelle, which is generally assumed to be a better predictor of fatalities, was not a significant predictor of the probability of a fatality for all species combined, Pipistrellus pipistrellus, or P. pygmaeus. Pipistrellus pipistrellus activity and P. pygmaeus activity, measured at ground level were not good predictors of their respective fatalities. Whilst there was some evidence that Pipistrellus pipistrellus and P. pygmaeus activity monitored at ground level, was a significant predictor of the probability of their respective fatalities occurring, across wide ranging turbine types, fatality estimates were large. This is presumably due to the importance of turbine characterises (the wind speed that turbines become operational (cut-in speeds) turbine and the distance between the ground and blade tip at the bottom of the rotor sweep area) both being important negative predictors of fatalities for Pipistrellus pipistrellus. Predicting from models, if the cut-in speed is increased from 3.5 to 5 m s-1 the number of Pipistrellus pipistrellus fatalities would be reduced by 76% (0.23 fatalities per turbine per month to 0.06). These findings have important implications for guidance, since activity is the ubiquitous measure used to assess fatality risk for all species. Since, Pipistrellus pipistrellus and P. pygmaeus were detected at 98% and 92% of sites respectively; it could be 5 assumed that these species would be detected at the majority of wind farms within their range. Therefore, in a British context, curtailing wind turbines below 5 m s-1 could be an effective mitigation strategy without the costly requirement to monitor activity. Pipistrellus pipistrellus and P. pygmaeus activity was 46% (6.3 ± 1.3 SE mean passes per night c.f. 3.4 ± 1.3 SE) and 34% (4.0 ± 1.4 SE c.f. 2.7 ± 1.4 SE) higher at turbines compared to controls, respectively. Given that habitat and elevation were consistent between paired turbines and controls and monitoring was conducted on the same nights, higher activity at turbines compared to controls provides evidence that these two species are attracted to wind turbines. Furthermore, since the biomass of nocturnal Diptera, the main insect prey for Pipistrellus spp., was higher at controls compared to turbines, and bat foraging at turbines was not predicted by insect abundance or biomass, attraction is unlikely to be due to insects. Evidence presented here shows that bats are attracted to turbines, and therefore measuring activity at pre-construction sites for environmental impact assessments is unlikely to be effective. In conclusion, these results provide further evidence that common species are killed but generally in relatively low numbers, they also support the view that monitoring activity for assessing fatality risk at wind farms is ineffective. It is imperative that wind energy is developed using an evidence based approach. However, it also important that wind energy continues to contribute to an increasing renewable energy sector. In conclusion, results presented here, support that wind turbines are likely to be having a small impact on bat populations in Britain.

Rivers and their associated floodplains are natural wildlife corridors used by a wide range of animal species. Most British rivers in both rural and urban areas have been significantly affected as a result of drainage, flood defence structures, urban development and direct habitat loss. This has, in some cases, fragmented the river corridor and affected the structure and function of the riparian zone. As landscape-scale conservation schemes aim to restore the ecology of rivers, I consider what affect the quality of the riparian zone (an area where the river channel, bank and flood plain interact) has on the foraging and activity of important riparian users, British bats, and assess their relevance as bioindicators of ecosystem health. A matched pairs design was used to test the effect of 'undisturbed' (high quality) and 'disturbed' (lower quality) riparian zones based on riparian width, habitat complexity, connectivity, and surrounding land use, on bat activity. In general, wider and more complex riparian zones did not show sign ificantly more bat activity overall, though exhibited significantly greater foraging activity expressed by the number of feeding buzzes recorded. However, species-specific responses showed that Pipistrellus pygmaeus and Myotis spp. (probably mainly Myotis daubentonil) were influenced by the quality of the riparian zone more so than known habitat generalists, such as P. pipistrellus. Small differences in the complexity and width of the riparian zone positively affected the foraging and activity of P. pygmaeus, whereas the presence of wider stands of wet woodland positively affected the foraging and activity of Myotis spp. Broader landscape features and the availability of insect prey also affected the activity of two sympatric species, P. pipistrellus and P. pygmaeus. Both species were positively associated with the presence of urban habitat within a 2 km radius of survey sites and aquatic invertebrates, and showed niche differences related to known dietary preferences. The association with invertebrate abundance may make Pipistrellus bats potential bioindicators of riverine health. Pipistrellus bats select riverine habitats that are associated with urban areas, which may indicate a dependency on rivers in urbanised areas. The composition of the riparian zone and floodplain habitat affects the foraging and activity of riparian specialist British bats and should be considered when designing landscape-scale conservation schemes that include British rivers.

The maintenance and restoration of tropical forest biodiversity is a global priority. Madagascar, a biodiversity 'hots pot', is unique, yet highly threatened due to ongoing deforestation. In this thesis I focus on the Madagascar flying fox (Pteropus rufus), the largest Malagasy fruit bat, and its role in forest regeneration and maintenance. I use ecological niche modelling to indicate the most suitable roosting habitat for the species and predict changes in distribution based on future climate change scenarios. Future predictions suggested that by 2080 there will be significant shifts in the distribution of P. rufus towards the central, more upland part of the island. To evaluate the role of these bats in forest regeneration, I compare germination rates of bat-processed and unprocessed seeds. Furthermore, I conduct high-resolution Global Positioning System (GPS) tracking of P. rufus to document their home ranges, movement, foraging patterns and habitat preferences. The results indicate that passage through the gut of bats increased the germination rate of defecated fig seeds and bats were able to disperse seeds over large areas and into areas cleared of trees. The bats were recorded to fly up to 66.5 km per night at a maximum speed of 17.04 m/s and the home range of all of the 15 tagged bats was over 58,000 ha. Additionally, the bats preferred feeding in forest remnants hence increasing the chances of seed deposition in such habitats, and ultimately their regeneration. Pteropus rufus bats have short gut retention times (GRTs) (estimated at 12 min) but are sometimes able to retain seeds for over 20 h. Through feeding observations in the wild, captive feeding trials and GPS tracking, seed shadow maps were created. The maps indicated that bats produced extensive seed shadow webs when feeding on figs within their large forging areas. Although P. rufus plays an important role in the early succession of tropical forest in Madagascar, it is threatened by hunting and by roost disturbance. This study provides new insights into the ecology and behaviour of the Madagascar flying fox.

Hibernation occurs in a diverse range of animal species including amphibians, reptiles, insects, mammals and birds. The adaptations that hibernators have evolved to survive winter are of great interest to conservation ecologists. The discovery that hibernators frequently arouse during winter has instigated much research on physiology and behaviour. Hibernation also provides an opportunity to better understand biological rhythms and entrainment to environmental cues. Using an integrative biological approach this study explores some questions important for a better understanding of mammalian hibernation. My aim was to gain insight into how hibernators use torpor during winter in a location with a mild maritime climate and to better understand some of the behavioural adaptations that have evolved to exploit opportunities that arise during winter. The primary study site was Greywell Tunnel, a disused canal tunnel situated on the Basingstoke Canal in Hampshire, England. The tunnel is an important hibernation site for Natterer's bat Myotis nattereri, four other bat species have also been recorded. The bat population using Greywell Tunnel has been monitored since the tunnel's designation as a Site of Special Scientific Interest in 1985. Long-term surveillance of bats at hibernation sites is a useful technique for assessing population trends. Findings from winter surveillance surveys conducted at Greywell Tunnel showed that numbers of M nattereri counted appeared to dip then rise over the survey period, while numbers of M daubentonii, M mystacinus and M brandtii appear to have declined significantly at this site. In locations where winter foraging opportunities exist, two strategies (which may not be mutually exclusive) may enable bats to balance winter survival with the ability to exploit foraging or possible mating opportunities.

The evolutionary history of echolocation in bats is poorly understood, as fossils provide little direct evidence, and most studies into echolocation have taken an ecological approach. Bats use a wide variety of echolocation call structures despite facing similar sensory challenges, and it is not clear how and why these echolocation call types evolved, or what impact they have on other aspects of the evolution of bats. Here, I use phylogenetic comparative methods and newly-collated echolocation call data from 410 species in 120 genera and all 19 families to investigate the origination and evolution of echolocation in bats (Chiroptera). I construct an updated phylogenetic supertree of the bats using source phylogenies from the literature between 1970 and 2009. I ask three main questions: (1) Are echolocation call structures really a product of present-day ecological conditions, or are they much more constrained by evolutionary history than is currently thought? (2) What did the first echolocation calls sound like? (3) Are echolocation calls ‘key innovations’ that promote diversification? I found that early divergences and subsequent constraints in evolutionary history have resulted in a greater variety of bat call structures than appear to be functionally necessary. The structure of the first echolocation calls was predicted to be short duration, multi-harmonic, and narrowband, suggesting that the proto-bat was a slow and manoeuvrable flier with an opportunistic and omnivorous diet, and may have used a perch-hunting foraging strategy. Finally, some echolocation call types were found to correlate with higher diversification rates such that they may be considered key innovations, but, unexpectedly, the most rapidly diversifying clades were those in which species either did not use echolocation at all (Pteropodidae), or where less sensory reliance was placed on echolocation (Stenodermatinae: Phyllostomidae).

Acoustic bat detectors are an extraordinarily valuable tool in bat research as they enable researchers to listen in on the otherwise secretive world of bats, providing the means to nqn-invasively survey and monitor bats in their natural habitats. Technological advances facilitate unprecedented data collection, considerably expanding the scope of field studies. However, the burden of manual analysis, and difficulty in identifying some species reliably from their calls, hampers the development of systematic survey and long- term monitoring methods. We developed a series of algorithms for the automated analysis of bat detector recordings, used to detect and extract calls from continuous recordings, and measure temporal and spectral call variables. By hand-labelling the .location of calls in field recordings, we were able to evaluate the accuracy of the automated method at detecting calls. Comparison on the same dataset with two conventional bioacoustic signal detectors revealed our algorithm was more accurate and robust. Using machine learning (ML) classification algorithms that learn to identify calls following training using a reference library, we developed a fully automated species identification system. Evaluation of the system was carried out by cross-validation of our reference call library, containing recordings of >5000 calls from known British species, comparing classifier predictions to ground- truth labels. The ML approach outperformed conventional statistical analysis using discriminant function analysis (DFA). We applied our novel system to two field studies that highlight its utility. Firstly, monitoring multi- species bat activity at a remote cave system over a period of three months, analysing >20,000 audio files to investigate temporal patterns in activity. Secondly, separating acoustically cryptic Myotis species from data collected in the Lake District National Park, to generate presence data for species distribution modelling, facilitatinq the creation of species-specific habitat suitability maps projected over the entire Park (ea, 3,300 km").

The lineage that gave rise to mammals split from other basal amniotes, approximately 300 million years ago. Since then, mammals have evolved many sensory novelties, including high-frequency hearing and echolocation. Sensitivity to high frequencies is particularly well developed in many echolocating mammals; for example, the upper hearing limit of several laryngeal echolocating bat species are estimated to be approximately ten times that of humans. In order to process the high frequency sounds produced during echolocation, the inner ears of laryngeal echolocating bats have undergone substantial modifications. Despite the evolutionary significance of laryngeal echolocation, it is unknown how many times it evolved within bats. Its occurrence on most, but not all, bat lineages suggests it either evolved once with secondary loss, or independently on multiple lineages. Distinguishing between these possibilities is complicated by morphological diversity and convergence. Furthermore, the genetic basis underpinning echolocation remains largely unknown. To elucidate the evolutionary history of this key trait in bats, a combined molecular and morphological approach was taken. Firstly, for two mammalian ‘hearing genes’ sequence convergence, phylogenetic signal and selection pressures were examined across echolocating and non-echolocating mammal species. Secondly, substitution rates of Conserved Non-coding Elements associated with genes regulating ear development were compared across mammals. Finally, as mammalian inner ear development is controlled by many genes, the gross structure of the bony labyrinth was studied in order to examine the combined genetic effect. Structural variation of bat cochleae and vestibular systems was examined using micro-computed tomography reconstructions, and related to ecological data. Subsequent analyses found evidence of convergence at the molecular level, in terms of amino acid substitutions, and also the morphological level, in terms of inner ear morphology. No evidence of degeneration, supporting loss-of-function in Old World fruit bats was found. Conversely, evidence of differential evolution pressures acting on the two echolocating bat lineages was found, which supports multiple origins of laryngeal echolocation in bats.

Past climate change and recent human activity have had major impacts on the distribution of habitats as well as the community and population genetic structure of the species occupying these habitats. In temperate zones, glaciation forced many taxa into southern refugia. In contrast, little is understood about the extent to which tropical taxa and habitats were affected by colder periods. In Southeast Asia, some argue that the tropical forest was replaced by savannah at the Last Glacial Maximum (LGM), whereas others suggest that the forest persisted. Studying population genetic and community structure of forest-dependent species in this region may shed light on which of these scenarios is most likely, as well as provide crucial information on the effects of recent habitat loss. To address these issues, I studied the genetic and community structure of forest-dependent insectivorous bat species in Peninsular Malaysia. Data collected at 22 sites indicated that species richness declined with latitude, consistent with post-glacial expansion of forest. To test this further, I undertook mitochondrial DNA sequencing of a widespread species, Rhinolophus affinis, and found high haplotype diversity, little phylogeographic structure and no demographic growth. These all suggest a long population history in the region with no post-LGM range expansion. Subsequent microsatellite analyses of R. affinis and the congeneric R. lepidus showed that genetic distance followed an isolation-by-distance model, and that allelic diversity was unexpectedly higher in the northern populations. Taken together, my results from the community and genetic analyses disagree with each other. These conflicts are perhaps best explained if observed clines in species richness pre-date the LGM. I conclude that there is little evidence of forest contraction in the LGM. The fact that the highest species diversity was detected in the south, which is experiencing the most forest loss due to human activity, has important conservation consequences.

Bats are one of the most numerous and diverse orders of mammals. This diversity is reflected in the wide range of bat morphologies. The relationship between bat foraging behaviours, flight styles and wing shapes has been well studied. Little research, however, has focused on other features of bat morphology, such as ear and tail membrane size, and how variations in these affect a bat’s locomotion. Indeed, knowledge on this topic has at best been speculative. In this thesis, I provide insight into the trade-offs and relationships that exist between less studied aspects of bat morphology, and their foraging and locomotion, with focus on the group of bats referred to as gleaners. In this thesis I use a model bat in wind tunnel tests to demonstrate that the long ears of some bat species have profound implications for their aerodynamic performance, and their energetics. A trade-off, however, is likely to exist, since the long ears provide a foraging benefit, which may balance the additional flight cost of the large ears. Additionally, bats may be able to minimise the flight cost of their ears through appropriate ear positioning. Using data collected from museum specimens I also demonstrate that other features of bat morphology, particularly the tail membrane, are good indicators of foraging strategy. Gleaning bats are identified as the group with the largest ears, whilst commuting bats have the shortest tail membranes. The energetic implications of these variations in morphology were then investigated using a theoretical model. The theoretical model suggested that tail morphology, as well as ear morphology, was likely to have a profound effect on flight performance in bats In contrast to bird tails the aerodynamic function of bat tail membranes is not well understood. Accordingly, I investigated bat tail membrane aerodynamics empirically using a model suspended in a wind-tunnel and from this was able to present the first evidence that bat tail membranes fulfil an important flight control function. Although bats primarily fly, certain species, such as the gleaning bats, spend a significant proportion of their foraging time on or near the ground and vegetation, landing to capture prey. Several gleaning species are also documented as frequently jumping from the ground back into flight. Research, however, on bat jumping had previously concentrated on the unusual vampire bats. I, therefore, present further data on bat jump performance and show that no ecological trend is present, with body mass being the best indicator of performance. No correlation between foraging habit and take-off performance suggested that flight so dominates bat morphology and locomotor performance that other modes of locomotion tend to be derivative. The findings of the thesis presented here, provide important insights into the relationships that exist between gleaning bat morphology, locomotor performance and foraging strategy. Areas for future research are also identified.

This thesis describes the numerical modelling of bioacoustic structures, the focus being the outer ear or pinnae of the Rufous Horseshoe bat (Rhinolophus rouxii). There have been several novel developments derived from this work including: • A method of calculating directionality based on the sphere with a distribution of measuring points such that each lies in an equal area segment. • Performance estimation of the pinna by considering the directionality of an equivalent radiating aperture. • A simple synthetic geometry that appears to give similar performance to a bat pinna. The outcome of applying the methods have yielded results that agree with measurements, indeed, this work is the first time TLM has been applied to a structure of this kind. It paves the way towards a greater understanding of bioacoustics and ultimately towards generating synthetic structures that can perform as well as those found in the natural world.