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The native Eurasian red squirrel is considered endangered in the UK and is under strict legal protection. Long-term management of its habitat is a key goal of the UK conservation strategy. Current selection criteria of reserves and subsequent management mainly consider species composition and food availability. However, there exists a critical gap in understanding and quantifying the relationship between squirrel abundance, their habitat use and forest structural characteristics. This has partly resulted from the limited availability of structural data along with cost-efficient data collection methods. This study investigated the relationship between squirrel feeding activity and structural characteristics of Scots pine forests. Field data were collected from two study areas: Abernethy and Aberfoyle Forests. Canopy closure, diameter at breast height, height and number of trees were measured in 56 plots. Abundance of squirrel feeding signs was used as an index of habitat use. A GLM was used to model the response of cones stripped by squirrels in relation to the field collected structural variables. Results show that forest structural characteristics are significant predictors of feeding sign presence, with canopy closure, number of trees and tree height explaining 43% of the variation in stripped cones. The GLM was also implemented using LiDAR data to assess at wider scales the number of cones stripped by squirrels. The use of remote sensing -in particular Light Detection and Ranging (LiDAR) - enables cost efficient assessments of forest structure at large scales and can be used to retrieve the three variables explored in this study; canopy cover, tree height and number of trees, that relate to red squirrel feeding behaviour. Correlation between field-predicted and LiDAR-predicted number of stripped cones was performed to assess LiDAR-based model performance. LiDAR data acquired at Aberfoyle and Abernethy Forests had different characteristics (in particular pulse density), which influences the accuracy of LiDAR derived metrics. Therefore correlations between field predicted and LiDAR predicted number of cones (LSC) were assessed for each study area separately. Strong correlations (rs=0.59 for Abernethy and 0.54 for Aberfoyle) suggest that LiDAR-based model performed relatively well over the study areas. The LiDAR-based model was not expected to provide absolute numbers of cones stripped by squirrels but a relative measure of habitat use. This can be interpreted as different levels of habitat suitability for red squirrels. LiDAR-based GLM maps were classified into three levels of suitability: unsuitable (LSC = 0), Low (LSC < 10) and Medium to High Suitability (LSC >=10). These thresholds were defined based on expert knowledge. Such a classification of habitat suitability allows for further differentiation of habitat quality for red squirrels and therefore for a refined estimation of the carrying capacity that was used to inform population viability analysis (PVA) at Abernethy Forest. PVA assists the evaluation of the probability of a species population to become extinct over a specified period of time, given a set of data on environmental conditions and species characteristics. In this study, two scenarios were modelled in a PVA package (VORTEX). For the first scenario (Basic) carrying capacity was calculated for the whole forest, while for the second scenario (LiDAR) only Medium-to-High suitable patches were considered. Results suggest a higher probability of extinction for the LiDAR scenario (74%) than for the Basic scenario (55%). Overall the findings of this study highlight 1) the importance of considering forest structure when managing habitat for squirrel conservation and 2) the usefulness of LiDAR remote sensing as a tool to assist red squirrel, and potentially other species, habitat management.

The red squirrel (Sciurus vulgaris) is native to Eurasia, but in the UK its survival is being threatened by the non-native grey squirrel (Sciurus carolinensis). Since its introduction to the UK from the USA the grey squirrel has increased its range at the expense of the red squirrel. Although competition for resources clearly plays a role in this replacement, an infectious viral disease, caused by squirrelpox virus (SQPV) and hosted apparently asymptomatically by the grey squirrels, has now been recognised as a major contributing factor. Little is known about the pathogenesis of infection in grey squirrels in comparison to red squirrels, but understanding this is essential to determining how the virus spreads within and between the red and grey squirrels. The aims of this thesis were to investigate the course of SQPV infection in red and grey squirrels and possible routes of virus transmission. Specifically, for the first time, a novel Real Time PCR (qPCR) assay and immunohistochemistry were used to investigate the presence of SQPV in various tissues from naturally infected red squirrels and experimentally infected grey squirrels. In diseased red squirrels SQPV DNA was found in several tissues with the highest amounts being found in skin samples. This reflects the multiple lesions that were easily visible on the red squirrel carcasses. There was no indication of systemic disease although the viral DNA was detected, at lower levels, in other internal organs. Grey squirrels were experimentally infected with SQPV isolated from naturally-infected red squirrels with fatal clinical disease. In contrast to SQPV-infected red squirrels no clinical lesions, other than mild scab formation at the site of inoculation, were found in the grey squirrels post-infection. No gross pathological changes indicative of systemic infection were observed and these findings were reflected in the qPCR and histopathology results. Viral DNA was only detected by qPCR in samples from the site of inoculation (scarified skin) and at lower concentrations in other skin tissues such as digital and eyelid skin. In addition, histopathology and immunohistochemistry examination revealed evidence of infection characterized by ballooning degeneration of keratinocytes, and acanthosis and spongiosis of the epidermis. These skin lesions were self limiting and minor compared to the infected red squirrel skin samples. The molecular variation in the virus isolated over time from different parts of the UK was also investigated. Seven SQPV isolates (4 from Scotland and 3 from England) were tested and results indicated that there are no significant changes in the amino acid sequence of any of the three genes examined apart from one amino acid change (one base change) in one gene. All Scottish isolates examined showed this change in comparison to English isolates. The results in this thesis show that there is a mild pathology associated with SQPV infection in grey squirrels. Scabs form at the site of infection but are less proliferative than in infected red squirrels, though they may still serve to contaminate the environment with virus leading to further outbreaks of disease. In contrast it seems likely that the proliferative lesions suffered by red squirrels and the greater amounts of virus that this leads to are likely to be more significant to the epidemiology of disease in localised outbreaks.