The herd-level incidence of Mycobacterium bovis has been increasing in the United Kingdom (UK) and Republic or Ireland (RoI) for the past thirty years, resulting in substantial economic and animal welfare issues. Failure to control this pathogen in cattle is in part due to European badgers (Meles meles), a wildlife reservoir that are responsible for a proportion of transmission of M. bovis to cattle. Monitoring infection in badger populations is currently limited due to the need to trap badgers, which requires highly trained field staff and is expensive. In addition, although contact with infected badger faeces is a potential transmission route to cattle, very little is known about the extent and variability of the environmental pool of M. bovis shed by badgers. In this project we evaluated the suitability of using environmental badger faeces and a quantitative PCR (qPCR) assay to diagnose and monitor M. bovis in badger populations and described the extent of this environmental pool of potential infection. The first study identified that intensive environmental faecal sampling and analysis with qPCR is at least, if not more, sensitive at diagnosing M. bovis in badger populations than the currently used immunoassays. This study also identified that even within a high prevalence population, the levels of shedding of M. bovis in faeces are highly variable between groups and between seasons, suggesting that there may be heterogeneity in transmission risk throughout the year. Using this non-invasive qPCR method to monitor the first field trial of oral BCG vaccination identified a trend of decreasing levels of M. bovis in faeces with increasing vaccination levels however, these results failed to reach statistical significance, highlighting the importance of adequate sample sizes when implementing this method. Finally, characterisation of the gut and faecal microbiota from animals shedding M. bovis in faeces confirmed that the source of faecal M. bovis is most likely sputum that has been expelled from the lungs, and not from colonisation of the gut. The work presented here suggests that this non-invasive monitoring method can be applied to examine the variable pool of M. bovis over periods of time and large areas, providing an epidemiological tool which has the potential to be implemented to monitor infection in badger populations and disease intervention strategies.

The neuropeptide hormone oxytocin plays an integral role in mammalian reproductive endocrinology and behaviour. It has been utilised to study the physiological factors driving maternal behaviour in both laboratory and domestic mammals, but few studies have successfully detected oxytocin in wild individuals, or linked detected concentrations to the behaviours they exhibit. Phocid seals present an excellent system in which to study oxytocin's effects on maternal behaviour in the wild. The energetic constraints placed on a phocid mother during the dependant period should cause strong selection pressure for behaviour that maximises reproductive success with the least cost to the mother. However in many phocid species, substantial variations in maternal behaviour persist. In order to investigate whether oxytocin plays a role in driving this variation, behavioural and hormonal datasets were collected from grey seal mothers and pups on two breeding colonies in Scotland. A protocol for the detection of plasma oxytocin in phocid seals was successfully developed, along with the methodology to manipulate peripheral oxytocin concentrations to directly test the hormone's impact on behaviour. Both correlatory studies on natural oxytocin concentrations and behaviour in wild mother-pup pairs and manipulation experiments on newly weaned pups show that plasma oxytocin concentrations influence behaviours that makes mother – pup separation less likely. These include increasing the time spent in close proximity to each other, increasing the number of checks performed on the pup and reducing the aggressive behaviour directed towards the other individual. Additionally, plasma oxytocin could be used as an indicator of weak maternal bonds between mother and pup, which resulted in behaviours such as abandonment and fostering. This study highlights the potential of oxytocin for studying variations in behaviours critical to an individual's reproductive success and provides the methodological framework for studies on other wild species to be conducted in the future.

Conflict within and between social groups is a conspicuous feature of cooperative animal societies. Theoretical and empirical research aims to understand the role of within- and between-group conflict in the evolution of cooperative behaviour, but these forms of conflict are rarely studied together. Eviction as a means of within-group conflict resolution can have important implications for the individuals involved, and the wider population through effects on dispersal, gene flow, and population structure. Intergroup conflict, although prevalent in many social species, is relatively understudied outside of humans and chimpanzees, but could play an important role in the evolution of cooperative behaviours. However, currently there is a lack of understanding of the causes and consequences of within- and between-group conflict to be able to draw conclusions on theoretical links to their role in social evolution. In this thesis, I use a wild population of banded mongooses, Mungos mungo, to investigate the causes and consequences of eviction and intergroup conflict in a highly cooperative species. First, I show that eviction in banded mongooses is triggered by reproductive competition in both sexes (Chapter 2). Second, I find that, once the decision to evict has been made, younger females and those older, more closely related females are preferentially evicted (Chapter 3). This surprising result is explained by a theoretical model which shows that, where individuals are capable of resisting eviction, the usual prediction of positive kin discrimination can be reversed. Third, I show that eviction has demographic effects, with consequences for group size and recruitment (Chapter 4). Finally, I show that intergroup conflict is stimulated by intensified resource competition, and that the consequences of intergroup conflict can have measureable costs to both individuals and groups in the long- and short-term (Chapter 5). This work shows that the means of resolving within-group conflict at an individual level can resonate to affect demography and dynamics at higher levels, and that the nature and intensity of intergroup conflict has the potential to influence patterns of cooperation and conflict within groups. I suggest that within- and between-group conflict may often be intimately linked, and that recognising this link could help to advance our conceptual understanding of their role in the evolution of cooperative behaviour.

Baseline data on a species' distribution and abundance are essential for developing practical conservation management plans. Such data are difficult to obtain for many low density cryptic carnivores. The Scottish wildcat, Felis silvestris silvestris, is no exception with <400 individuals thought to remain. Its conservation has been further complicated by extensive hybridisation and introgression with the domestic cat (F.s.catus). Hybridisation has also resulted in difficulties in discriminating between wildcats, wildcat x domestic hybrids (hybrids) and tabby coloured feral domestic cats. This has inhibited survey efforts, leading to a lack of general ecological information. Using the most recent identification tools available, extensive surveys using various methods including camera trapping were carried out across Northern Scotland in order to examine the current status of the Scottish wildcat. Current distribution indicates a more restricted range than recent studies. Wildcats are at risk of hybridisation from feral domestic cats and in particular, hybrids, throughout their current probable range. The distribution of hybrids overlaps with both feral domestic cats and wildcats, pointing to a significant threat from hybrids acting as a bridge between wildcats and feral cats. Mean density estimates of 3.5 (SD=0.7) wildcats/100 km² were comparable with those from other studies in Scotland using different survey methods. Total population size estimates ranged between 115-314 individuals depending on local densities and home range size. Population viability analysis (PVA) indicated the current population is not viable unless management actions are undertaken in the near future (Mean time to extinction = 48.2 years (SD = 9.39), probability of extinction=1, SE = 0), and that reducing mortality rates and/or supplementing populations from captive bred cats are likely to be necessary to achieve viability. Based on these data, the Scottish wildcat may be more endangered than many other species classified as Endangered and the current status of the Scottish wildcat should be reviewed.