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Bats play an important role in the ecosystem of the British Isles, but are vulnerable to population decline due to human activities and thus are the subject of much scientific research. Non-invasive DNA sampling is commonly used in scientific studies of wild mammal species, but is still used in relatively few genetic studies of bat species. The overall aim of this thesis is to develop molecular techniques for application to the bat species of the British Isles. Species-specific real-time PCR primers, targeting the cytochrome b mitochondrial DNA gene, were designed for the identification of eighteen resident bat species in the British Isles. These primers were applied to a field survey of bat roosts in Ireland, in Counties Galway, Kildare, Waterford and Wexford, from which non-invasively collected faecal DNA samples were obtained. The lesser horseshoe bat (Rhinolophus hipposideros) is one of Ireland’s rarest bat species, and its population is monitored nationally each summer by emergence counts of at known summer roosts. The sex ratio of adult bats present in these roosts is an important part of calculating national population estimates, but no empirical data on this sex ratio are available from Ireland. Real-time PCR sex typing assays for the lesser horseshoe bat were designed, targeting the ZFX, SRY and DBY genes. Using these sex typing assays and previously published microsatellite DNA markers, the sex ratio of adult bats was examined at six lesser horseshoe bat summer roosts across the species’ range in Ireland using faecal DNA samples. The lesser horseshoe bat’s range in Ireland is limited to geographically isolated parts of the counties of the west coast. The population genetics of the species was examined using microsatellite genotyping of faecal DNA samples from 21 colonies from across its range, to assess the level of interbreeding and possible risk of inbreeding within this population.

HTS statistics. (A) Sample name, total number of reads, percent of reads mapping, read depth (# mapped reads/Drosophila transcriptome size (30.1 Mba)), percent unique and percent non-unique reads are shown for technical triplicates of each sample. A Studentâ s T-test was used to determine if the observed differences in percentages of non-uniquely mapping reads between samples was statistically significant. Corresponding p values are shown in the last column. (B) Total number of reads and percent or reads mapping when zero mismatches are allowed (left) and one mismatch is allowed (right) for three technical triplicates and one biological replicate (BR) of each sample. (PDF 54 kb)

Taqman assays and primers. Taqman assay ID #s and targets are shown in the top table. Targets of hp and Tn primers are shown in the middle table together with their sequences, position targeted within the Tn and references to their original use. Control GAPDH primers and primers used to assess sop RNA misprocessing are shown in the bottom table. (PDF 67 kb)

Esi1/2 precursors are polyadenylated. Polyadenylation status of CG44774 (Esi1) and CR18854 (Esi2) were assessed as described in [17]. These RNAs are more enriched in the Poly(A)â +â fraction than the polyadenylated Actin mRNA. Non-polyadenylated 18S rRNA is enriched in the poly(A)- fraction. (PDF 29 kb)

Work flow for high throughput sequencing and small RNA analysis (SMACR). (A) Drosophila cells were individually depleted of Dcr2, CPSF73, Symplekin, and GFP (or LacZ). An additional fifth sample was untreated. The untreated and GFP samples represent controls. RNA was isolated from each sample and fractionated into RNAs > than 200 nts and RNAs

Physical characteristics of miRNAs, Tn- and hp-derived esiRNAs in Symplekin, CPSF73, Dcr2 knockdown and control samples. Mapped siRNAs were sorted by type and filtered by size (21-24 nts) (A), 3â base (B), and 5â base (C) for each sample. The abundance of normalized read counts in each category was then summed and the percentage of each individual category was calculated for all samples. Percentages for each category were then plotted. (PDF 208 kb)