Consistent individual differences (CIDs) in behaviour have been shown to occur in a large number of species. However, few studies have attempted to quantify CIDs in the behaviour of wild animals in their natural environment. Yet, in order to understand the ecological and evolutionary relevance of CIDs in behaviour, it is fundamentally important that we attempt to quantify them in wild animals, in situ. In order to address this question, a three-step analytical approach was applied to data that were collected on wild postpartum female grey seals, which were part of a ‘hands-off’ observational study. Aspects of behaviour were highly repeatable across breeding seasons. The ‘alert’ behaviour in particular, remained highly repeatable irrespective of which individuals were included in the analyses. Furthermore, these robust repeatability estimates for the ‘alert’ behaviour persisted, despite controlling for social and environmental factors that are known to influence maternal behaviour. Subsequently, the three-step analytical approach was applied to an independent dataset collected on postpartum female grey seals that are part of a long-term longitudinal study on reproductive variation. Similar patterns were observed in the results across the three steps, and once again, the ‘alert’ behaviour was one of the more repeatable behaviours. However, these highly repeatable behaviours did not explain any of the variation in commonly used proxies for short-term fitness. As a result, these preliminary findings add to the debate on whether or not CIDs in behaviour are adaptive or are a product of phenotypic and/or genotypic constraints. Consequently, the potential influence of CIDs in behaviour on fitness trade-offs, population dynamics and conservation and management practices shall be discussed. The application of the three-step analytical approach to the independent dataset did raise some important methodological considerations, which shall be discussed in relation to developing guidelines for applying this approach to other datasets.

Bovine TB in cattle is a major economic problem in the UK, costing the government approximately £100m a year. Badgers are a wildlife host of the infection that causes bovine TB, and there is strong evidence that they transmit the infection to cattle. Understanding the ecology and epidemiology of infected badger populations is therefore crucial for implementing disease management strategies relating to badgers. Genetic and phenotypic data of badgers captured during a large-scale field trial of repeated, widespread badger culls were used to assess the importance of parental roles on the impacts of badger culling. Further ecological and epidemiological dynamics were investigated through developing a stochastic simulation model of an infected badger population. An estimated 72.8% of badgers were captured during initial culls of the trial, and an estimated 57.8% during follow-up culls, based on badger parentage assignments. Further analyses of these parentage assignments revealed evidence of a genetic predisposition in infection susceptibility from parents to cubs, but no evidence of a significant infection transmission route from mothers to their young, dependent cubs. There was also no evidence that badger welfare was compromised during the trial through not capturing dependent cubs of culled mothers. Analysis of a simulation model found that moderate levels of disease-induced mortality in an infected badger population could significantly reduce the size of badger social groups with a higher prevalence of infection. The impact of these findings relating to potential disease management strategies is discussed, together with suggested directions for future research.

The main aim of this study was to estimate phylogeographic patterns from mitochondrial DNA diversity and relate them with evolutionary structure in two species complexes of genets, <italic>Genetta genetta</italic> and <italic> Genetta "rubiginosa",</italic> which have fluid morphological variation. Both are widely distributed in sub-Saharan Africa but whereas <italic>G. "rubiginosa" </italic> appears in both closed and open habitats, <italic>G. genetta</italic> is absent from the rainforest and occurs also in the Maghreb, southwest Europe, and Arabia. DNA sequence data, mainly acquired from museum skin samples (about 75% of the total number of samples), was analysed using methods from the fields of phylogenetics and population genetics. The results for <italic>G. genetta </italic> are compatible with a scenario of allopatric fragmentation in grassland refuges during the Pleistocene climatic cycles as the main factor responsible for geographic genetic structure within Africa. The Arabian isolate showed significant genetic divergence, species-level compatible, and is probably the result of a long-distance dispersal from North Africa. Genetic diversity in Europe is a subset of that found in North Africa and shallow genetic distance is concordant with their anthropogenic introduction into Europe. North Africa seems to be cyclically connected to West and Central Africa during interglacial periods in which the Sahara recedes substantially. For <italic>G. "rubiginosa", </italic> isolated biogeographic relicts in the eastern African coast, possibly unsuspected species, were uncovered. However, the dominant pattern in the evolution of this species complex seems to be ecological differentiation in parapatry after invasion of open habitats from the rainforest ancestral habitat. Three general conclusions may be extracted from this study. Firstly, the use of mitochondrial DNA is clearly informative, but both gene flow among parapatric populations and introgression are confounding factors. Secondly, the Pleistocene in Africa has had variable biogeographical and evolutionary consequences for different taxa, depending on their ecological breadth. Lastly, large-scale utilisation of museum samples in phylogeographies of cryptic taxa has been rarely attempted but should become a standard approach.

This thesis examines the role played by den use in socio-ecology, especially in leveraging group formation (i.e., the Fossorial Benefits Hypothesis; FBH), using badgers as a model species. In particular, I benefit from recent technological developments, facilitating detailed measurements of activity, energetic expenditure, ranging behaviour, and underground localisation, enabling the examination of hitherto intractable facets of badger socio-ecology, allowing a comprehensive investigation. Group-living is theorised to evolve when the benefits of living with conspecifics outweigh the costs. While pack hunting, and allo-parenting play a specific role in fostering communal living, I demonstrate in Part I that continued cohabitation at natal dens can often acts as a precursive mechanism initiating cohabitation, that can persists into adulthood among small, omnivorous/insectivorous, den-using carnivores. In this context, I then consider the implications of delayed dispersal and reproductive suppression. This provides an evolutionary basis linking fossoriality and group-living in the Carnivora, where sociality is, in part, explained by burrow-dwelling. Part II establishes that the energetic benefits of using fossorial dens as refugia from adverse weather provide a functional basis for persistent co-occupation of a common den by conspecifics. Badgers use setts strategically, with reference to their body-condition and their imperative to forage, to reduce energy expenditure and optimise their capacity for achieving minimal food security. This section also considers how badgers may compensate for ongoing rapid climate change. Part III demonstrates that cohabitation at dens does not infer group collaboration or social structure; individuals may still act independently. Nevertheless, burrow use patterns were coordinated between badger group members, evidencing that dens act as social foci. Collectively these lines of evidence support the FBH as a playing a causal role promoting spatial group formation and a complementary role driving persistent benefits of group-living in suitable resource-scapes; resulting in 'spatial' though not necessarily 'social' -groups.

Global biodiversity is declining at an unprecedented rate, principally as a consequence of increasing human population. Effects of this expansion are exemplified by the extent to which many carnivores are now in conflict with humans, particularly in unprotected rangelands. One such species is the brown hyaena (Parahyaena brunnea), classified as 'Near Threatened' (Wiesel et al., 2008). The IUCN SSC hyaenid specialist group identified that brown hyaena are under threat due to human persecution and noted that greater understanding of their distribution and abundance is needed. With the principal aim of assessing the distribution and abundance of brown hyaena in South Africa, this study responds to that challenge. Five specific objectives were established: to utilise local knowledge to map the distribution of carnivores across South Africa; to determine the factors driving attitudes and perceptions of South African farmers to carnivores; to determine differences in relative abundance of carnivores in protected areas compared to unprotected in the North West and Limpopo Provinces; to compare home range estimates and movement patterns of free living brown hyaena inside and outside protected areas in the same provinces; to determine what variables influence brown hyaena home range size. Distribution of brown hyaena and other carnivores, and attitudes to them, were determined using a web-based questionnaire involving multiple stakeholder groups. The results confirmed current knowledge on carnivore distributions but, critically, revealed wider distribution of brown hyaena and other key species than are currently known by IUCN (2013). Responses demonstrated that cultural group and land use type significantly affected attitudes towards all carnivores, with Afrikaans livestock farmers demonstrating the most overtly negative attitudes to all carnivore species. An encouraging finding was that 25% of land owner respondents had positive attitudes to brown hyaenas and were therefore likely to be well disposed to engaging in conservation activities. Further information on the abundance and movement ecology of brown hyaena was gained through an intensive field study in the North West and Limpopo Provinces, which are under-researched. The study was conducted in protected and unprotected areas since brown hyaenas are found in both but are subject to different pressures. The use of remote camera traps demonstrated that the relative abundance of brown hyaena was four times lower in unprotected areas than in the protected areas. A significant finding was that mesopredators showed higher relative abundances in the unprotected areas. This suggests probable further human-wildlife conflict if mesopredator release continues to occur. Low levels of abundance in the unprotected areas, in conjunction with persecution, led to the conclusion that conservation efforts should be focused here. GPS collars were used to determine differences between brown hyaena home range across the protected and unprotected areas, to gain insights into their habitat use, and to establish their movement patterns through the fragmented landscape. The study demonstrated that home range sizes in the unprotected areas were not only significantly smaller than in the protected areas but also substantially smaller than those found across the entire hyaena’s range. Reasons for the variation are suspected to be higher levels of persecution and greater biomass availability outside the protected areas in conjunction with the relatively high density of apex predators inside the protected areas. In conclusion, large carnivore research is critically required outside protected areas where carnivores are currently involved in the most conflict and are at the greatest risk.

Aggressive interactions arise as a means of resolving access to resources such as food, habitat or mates, but these interactions are often costly in time, energy, or physical damage. Therefore, natural selection favours social systems, spatial organisations and behavioural mechanisms which can balance the trade-offs between conflict and increasing fitness. The diversity of behaviours associated with animal conflict has been investigated in a variety of species; however, rarely are these investigations done in wild systems or with consideration of geographic and intra-seasonal variation in environmental factors, resource availability or social dynamics. Therefore, the aim of this thesis was to examine the behavioural mechanisms underpinning population and individual conflict and conflict reduction at a variety of temporal and spatial scales. I focused my investigation on a particular form of animal contest, male-male breeding aggression, and used the colonial, wild grey seal (Halichoerus grypus) as my model. Specifically, I studied males at Donna Nook, an atypical breeding colony, in order to: (1) update our current knowledge of grey seal breeding systems by comparing the behavioural patterns at recently expanding mainland colony to previously examined, offshore colonies, (2) investigate the information present in a geographically isolated behaviour used in male grey seal conflict, (3) identify the variation in assessment strategies used by individuals in grey seal conflict and conflict reduction, (4) examine how environmental, anthropogenic, and social environments shape individual variation in aggression, and (5) assess the individual variation in decision-making processes such as mating strategies within- and across seasons. Draws were identified as a common conflict outcome for male grey seals, and the acceptance of draws represented a behavioural mechanism which can promote conflict reduction. Assessment strategies relied on individual energetics when costs of conflict were high, but mutual assessment was used in low-cost contexts. Activity budgets were relatively conserved across colonies, and social stability played a key role in mediating conflict. These findings all demonstrate the trade-offs between conserving energy for reproductive activities and expending energy to ensure exploitation of resources. Methodological approaches which accounted for variation in individual partitioning of aggression and reproductive effort within- and between-seasons revealed that the relative importance of dominance as a driver of conflict, the use of specific aggressive behaviours, and broad assessment and mating strategies were all context-dependent at a variety of temporal and spatial scales. Overall, these findings have provided new insights into the evolution of conflict and conflict reduction within polygynous mating systems. This work highlights the importance of incorporating the natural environmental variation and social dynamics into models of individual behaviours. Such approaches not only reveal the plasticity or consistency in how individuals deal with tradeoffs, but they also allow for observing the importance of behavioural mechanisms such as draws, which might have been ‘artificially selected out’ in controlled, laboratory settings. Finally, by using the grey seal breeding system as a model, this work has contributed to our knowledge of this species’ behavioural repertoire, and the role of topography in the evolution of polygyny and aggression in pinnipeds.

Medfly (Ceratitis capitata) is an invasive Tephritid fruit fly that severely disrupts global agricultural productivity. Pesticides are the primary control method despite genetic resistance, questionable efficacy, and negative effects upon the environment. The sterile insect technique (SIT) is an ecofriendly alternative, that suppresses the reproduction of wild Medfly by the mass release of sterilised males. Currently, males are sterilised by irradiation, which frequently reduces the ability of males to court females and thereby suppress reproduction. To address these undesirable effects, we developed a novel sterilisation strategy, based on the tetracycline-repressible expression of a nuclease effector in the male germline. Strains expressing these effectors were 99-100% sterile in the absence of tetracycline, but fertile in the presence of tetracycline. Male mating competitiveness was not detectably reduced in one strain expressing the effector, indicating that these expression systems are suitable for field use. Subsequently, a fluorescent marking system to label sperm was developed, which provided a useful tool to assess the mating competitiveness of sterile males: it was possible to accurately differentiate whether females had mated wild or transgenic males, under field-simulated conditions. These components may be merged with a tetracycline-repressible genetic switch to remove females from the rearing population, to improve the efficacy of the strategy by releasing sterile males alone. Thereafter, a full assessment of the life history traits of the strain and its mating competitiveness under field-like conditions will be performed, to confirm that the release of these sterile males is capable of suppressing wild populations of Medfly. Finally, an efficient expression system for CRISPR effectors in the germline was developed. This will facilitate the characterisation of novel transgenic systems for the reproductive control of Medfly, and expedite the development of commercial products, by the targeted integration of transgenic effectors.

Carrion represents an important energy resource in the natural world, yet its ecological significance has often been overlooked. It also plays a crucial role facilitating energy transfer across trophic levels and between ecosystems. The aim of this thesis was to evaluate the role of marine mammal carrion in the ecology of coastal systems, investigating one of the most commonly occurring sources of marine mammal carrion in the UK, the grey seal (Halichoerus grypus). This was addressed by providing first a detailed documentation of the fate of a grey seal pup carcass with insights on the scavenging ecology existing in both terrestrial and marine ecosystems. On the shore, great black-backed gulls (Larus marinus), juvenile gulls and ravens (Corvus corax) fed on the carcass showing a distinct temporal succession using the food resource. The underwater carcass was initially dominated by Echinodermata (starfish), whose abundance dropped lately, while Malacostraca (crabs) were present in similar number during the whole monitoring. Bacterial activity was evident in both experiments. Predictability of seal carrion was then defined during the pupping season at one of the largest colonies in the UK, the Isle of May (Scotland). Data collected by aerial survey (11 years) and ground visual census (3 years) were used to estimate the inter-annual variability of carrion, from placentae and dead seals, according to its timing, biomass and energy released and spatial distribution on the island. For all measures considered, variability was below 34%, similarly to other resources, such as salmon runs, which appear to be predicted by consumers. Twenty one percent of the total biomass from dead seals was consumed at the end of the pupping season suggesting a clear response from the scavenging community to the presence of the resource carrion. The predictable nature of seal carrion was then tested exploring the spatial and temporal distribution of scavenging gulls at three geographical scales (regional, local and patch scales). The great black-backed gull was affected by carrion availability occurring on the Isle of May, while the herring gull (Larus argentatus) was not. In particular, the number of adult and juvenile great black-backed gulls feeding was directly correlated with carrion abundance, while searching behaviour was greatest after the mean seal pupping date and at the peak in mortality. The behavioural dynamics of scavengers were finally explored monitoring the feeding activity on pup carcasses and placentae of adult and juvenile great black-backed gulls. It was predicted that under conditions of predictable and abundant carrion an equal scavenging effort would be found for the two age classes when consuming carcasses. Hierarchical dominance was, instead, expected during scavenging activity on placenta as it represents a preferred energy-rich food item. Temporal trends of scavenging activity and time spent feeding on carcasses were in fact similar between the two, while young individuals spent more time feeding on placenta, highlighting the importance of this food source for juvenile gulls during winter. The house mouse was also found to scavenge on seal carrion, which until now has been undocumented. This study demonstrates the importance of marine mammal carrion as a resource for multiple facultative scavenger species in both the marine and terrestrial environment.

Cooperative species have long been the focus of much research due to the ‘special difficulty’ cooperation poses to the theory of evolution via natural selection. Despite this long history of scientific interest we actually know relatively little about the evolutionary genetics of cooperative mammalian species, especially in the wild. In this study I use long-term data from the Kalahari Meerkat Project to investigate some aspects of the evolutionary genetics of meerkats (Suricata suricatta). First, I reconstructed a genetically-validated pedigree of the Kalahari meerkat population. 1,494 meerkats (83% of the total known population) were genotyped at a panel of 18 highly variable microsatellite markers. This genetic data, in combination with phenotypic information and two different programs, COLONY2 and MASTERBAYES, was used to infer familial relationships. The resulting pedigree spanned seven generations and included 1,614 individuals of which 1,076 had both parents known. I conclude by discussing the particular merits of using COLONY2 to infer familial relationships for social animals such as meerkats. Second, I investigated the extent of inbreeding and inbreeding depression in early life traits in the Kalahari meerkat population. In the pedigree, 44% of individuals have non-zero (F>0) inbreeding coefficients. Although I found more inbreeding in meerkats than initially expected, there were few cases of inbreeding between very close relatives. Nonetheless, even low to moderate inbreeding appeared to result in inbreeding depression for pup mass at emergence, hind-foot length, growth until independence, and juvenile survival. I also found some tentative evidence for a positive effect of the social environment in ameliorating the effects of inbreeding depression. Third, I conducted a quantitative genetic analysis on mass, skull length, skull width, forearm length, and hind-foot length in up to five key meerkat life stage periods, while accounting for a number of fixed effects, including inbreeding coefficient. By attempting to apportion variance in these traits to a variety of sources I found that birth litter identity often explained much of the variance in morphological traits, although the magnitude of this effect appeared to decline with age. Furthermore, when birth litter was removed from models, the amount of variance explained by additive genetic effects tended to increase. Finally, I conducted a quantitative genetic analysis on two measures of cooperative care and on adult mass. Fixed effects, including inbreeding and relatedness coefficients, were also examined, which revealed that inbred individuals contribute more to pup-feeding, and that helper-recipient relatedness was negatively associated with baby-sitting. I found low heritable variation for baby-sitting (h2 = 0.10) and pup-feeding (h2 = 0.08), and higher heritable variation for adult body mass (h2 = 0.19). I also estimated the magnitude of non-genetic sources of variation in these traits and provide evidence for positive genetic correlations between baby-sitting and pup-feeding, and baby-sitting and adult mass.

Communication can be crucial to the profitability of reproduction by allowing individuals to attract and select an appropriate mate. Across mammals, successful reproduction can depend on the ability of individuals to gain information such as relatedness, health parameters and breeding status from potential mates. Although visual and auditory signals are utilised, scent is a crucial and ancient form of communication yet, with the exception of certain model systems, we understand little of how it functions in wild mammals. This thesis will focus on the mechanistic role of odour signals: what information they contain and how they may facilitate reproductive decision-making in the banded mongoose (Mungos mungo). I use a wild but habituated population to conduct experimental odour presentations showing these mammals are capable of discriminating scents based on sex, familiarity, relatedness and female reproductive state. The ability of odours to encode such multi-modal information suggests they may facilitate key behavioural processes such as kin recognition, mate-choice and competitive interactions. However, the discrimination of pregnancy specifically implies scent cues function within reproductive decision-making, attracting males to receptive mates. The gastro-intestinal parasite community of this banded mongoose population was also screened, allowing the ability of odour cues to advertise parasitic infection to be tested. Observations show highly parasitised individuals scent-mark less frequently, suggesting marking behaviour indicates quality in terms of parasite burdens. Furthermore, experimental odour presentations show that banded mongooses exhibit behavioural aversions toward odours of heavily infected individuals. Scent cues, in the banded mongoose system, thus appear to encode a multitude of information relevant to reproduction.