Understanding the conditions that favour the evolution and maintenance of spiteful bacteriocin production combines two important questions from the fields of social evolution and microbiology. Spiteful behaviours, though, initially thought to be rare represent an important class of interactions between bacteria through the production of bacteriocins. Bacteriocins can be considered spiteful as they are costly to produce (in many cases requiring lysis) and are costly to sensitive bacteria (i.e. they are lethal). However, much about the ecology of spiteful behaviours and bacteriocin production remains unclear. Mathematical models have given us important insights into some conditions that should favour bacteriocin production, but few empirical studies exist supporting these results. In this thesis I use the bacterium Pseudomonas aeruginosa (a prolific producer of bacteriocins), to examine conditions that favour bacteriocin production. I also investigate more specific elements about this system and toxin production in general. I find that bacteriocin production in P. aeruginosa closely follows predictions made from mathematical models under a range of different conditions (e.g. frequency, scale of competition, multiple social traits). I also find that resistance can evolve to bacteriocins and biological mechanisms such as the neutralisation of one’s own toxin can have important consequences. Finally, I consider bacteriocin as a policing trait testing predictions about the role that linkage plays in policing. This work represents a comprehensive study into the importance of bacteriocin production in bacteria.

The trophy hunting of African leopards Panthera pardus pardus may generate revenue to help foster their conservation. However, leopards are sensitive to hunting and populations decline if overharvested. The practice therefore requires careful management grounded in robust estimates of population density/status. Camera-trap surveys are commonly used to establish leopard numbers, and may guide harvest quotas. However, such surveys are limited over wide spatial scales and many African governments lack resources to implement them. In this thesis I explore the potential use of a harvest composition scheme applied to puma Puma concolor in North America, to monitor leopards. The method hinges on the susceptibility of different leopard cohorts to hunting and if this varies, then predictions can be made about harvest composition. Susceptibility is likely to be governed by space use, encounter rates with bait lures (a common method used to attract leopards to hunting hides) and hunter selectivity. Thus in this thesis I explore leopard susceptibility to these factors using a protected leopard population in northern Zululand, South Africa. In my first chapter I examine using scent lures in camera-trapping. Against a backdrop of a passive survey I show adult males, females and sub-adults are captured at similar rates compared to a passive survey using lures. The use of lures does not appear to violate closure assumptions or affect spatio-temporal patterning, but their use appears limited as density estimate precision is not improved. My second chapter examines ecological (likelihood of encountering a hunter) and anthropogenic (attractiveness to hunters) susceptibility of leopards to trophy hunting. I show that adult males are the most susceptible cohort to hunting (sub-adults least susceptible). I then take the incident rates from ecological and anthropogenic models and create a theoretical harvest composition using population parameters of protected leopards. My third data chapter departs from hunting susceptibility and examines determinants of leopard trophy package price across Africa. I show that factors such as trophy quality, outfitter leopard hunting reputation and hunt success have little impact on price determination. Instead, overall outfitter reputation and the number of charismatic species in a package are positively correlated with price. These results have important consequences on several sustainable leopard hunting schemes proposed in the literature.

This thesis addresses the methodological challenges of determining the variability of large herbivore populations through time and their impact on European vegetation. Large herbivores are at the heart of conservation policy. However, opinions widely diverge on whether we should aim for fewer herbivores and managed populations or, on the contrary as advocated by the rewilding movement, more herbivores and self-regulating populations acting as ecosystem engineers. This controversy has roots in a debate regarding the nature of ecosystems before the prevalence of human activities. Baseline ecosystems are either described as continuous forest cover with passive large herbivores, or, in contrast, as mosaics with patchy forest cover driven <i>inter alia</i> by bison, aurochs and horses, now rare or extinct in Europe. The main obstacle in moving this debate forward is a poor understanding of large-herbivore densities in the past. I analysed modern pollen and spore assemblages from known environmental settings to improve palaeoecological interpretation of fossil assemblages dating from the pre-human (baseline) period. The sites investigated are the rewilded grasslands of the Oostvaardersplassen (The Netherlands), the mosaic habitats of The New Forest (UK) and the old-growth closedcanopy forest of Białowieża (Poland). I demonstrate that the common practice of interpreting pollen percentages fails to estimate past forest cover in situations with natural grazing. As an explanation, I suggest that pollen productivity fluctuates with biotic factors such as herbivory and canopy shading. As a result, new insights into the baseline debate require additional lines of evidence. In this thesis, I develop an existing methodology to reconstruct past herbivore presence using fossil dung fungal spores. I synthesise current knowledge of this method with an emphasis on spore identification and, finally, I demonstrate that dung fungal spore abundance in lake sediments can be translated into large herbivore numbers. The evidence presented in this thesis contributes to the debate on re-wilding and addresses a fundamental challenge of nature conservation in the human-dominated landscapes of Europe.

An Allee effect is a density-dependent process that can be responsible for the extinction of small populations. This thesis focuses on the detection of Allee effects, along with other density-dependent processes, and their influence on population synchrony. In chapter 2 I investigate the spatial variation in influential density-dependent processes and density-independent weather factors for the large skipper butterfly Ochlodes sylvanus across its British range. I find both qualitative and quantitative spatial variation in these processes and factors driving population dynamics. In chapter 3, I develop and test a Bayesian methodology, that I then use in chapter 4 to analyse local population level dynamics for 38 British butterfly species. For 35 of these species I found population level Allee effects and also found that phylogeny significant influenced a species’ susceptibility to Allee effects. Finally, in chapter 5 I examine the influence Allee effects have on network population synchrony in a theoretical framework.

Spatial prioritization and systematic conservation planning methods are designed to improve land use decisions and conservation outcomes, yet remain underutilized in many biologically-rich places that need them most. This thesis applies the theory and methods developed in the discipline of spatial prioritization to conservation and land use decisions in the Central African country of Gabon. Creating a spatial information base of priority species, habitats and land uses in a region that is notoriously data-poor, I reveal that many features important for both conservation and natural resource production are highly localized; their coincidence has important implications for management. Setting conservation targets for species and habitats, I find that representation in existing protected areas is relatively low, and identify a number of near-optimal solutions that meet all targets, with minimal impact on land used for local livelihoods. I distill these solutions down to a handful of critical biodiversity sites that are top priority to protect, and make management actions explicit for the species and habitats they contain. To make the work more widely applicable, I also develop a novel method to identify where field surveys are most likely to improve decisions about protected area expansion, providing decision-makers with more options of places that could be protected to achieve conservation goals. This study contributes to the research, development and practice of conservation prioritization and spatial planning, particularly in data-poor contexts like Gabon, which still have a wealth of biodiversity, and need to carefully plan for its conservation alongside development.

Recent bio-logging technology and associated techniques have uncovered the distribution, behaviour, and phenology of marine predators at remote locations, providing us with insights of not only scientific merit, but also in terms of conservation and management. This thesis explores the at-sea behaviour of marine birds using field studies and ethoinformatic approaches by using multiple data loggers, focusing on four species of free-ranging seabirds breeding in the UK. Key findings and conclusions are: Extending travel distance in central place foragers in the wild is associated with higher prey quality as estimated by an indirect method based on dive profiles. This result is consistent with a prediction of optimal foraging theory, but my results show empirically that seabirds are able to increase reward with distance at the extended scale of the marine environment. Razorbills Alca torda are capable of adjusting their foraging behaviour in response to proximate environmental conditions. The potential mechanisms underlying this adaptive behaviour are independent of breeding stage, but the magnitude of flight orientation is scale-dependent. These results suggest that Razorbills are capable of optimising their foraging adaptively, possibly reading cues from the environment or conspecifics. Diving behaviour in sympatric Atlantic Puffins Fratercula arctica and Razorbills is very similar, in contrast to the predictions of the competitive exclusion principle. They are likely to be near carrying capacity for the location and this may explain why Skomer’s Razorbill population is declining while its puffin population is stable. Differences in foraging trip duration of chick-rearing Manx Shearwaters Puffinus puffinus reflect differences in resource allocation between provisioning offspring and self-feeding. I developed a model based on patch quality and travel time to show that birds should use bimodal foraging trip durations to optimise feeding rates for their offspring. Individual reproductive performance in Manx Shearwaters can be predicted from previous breeding phenology and is linked to differences in overwintering behaviour patterns. This carry-over effect reveals the existence of a trade-off between current parental investment and future reproductive performance.

Understanding dispersal is a central aim of evolutionary ecology. Theoretical analyses of dispersal have been crucial in identifying key variables which contribute to its evolution and maintenance, but the supporting empirical data remains elusive. Microbes offer a powerful model system on which ecological and evolutionary theory can be experimentally tested with controlled and replicated experiments, and with the convenient malleability of selective pressures and bacterial genomics. Pseudomonas aeruginosa is an ubiquitous, opportunistic pathogen that is able to induce acute or chronic infections in a broad array of hosts. As well as in vivo environments, P. aeruginosa can be found in a range of ecological habitats, from solid to aqueous, and as such requires a variety of dispersal mechanisms (including swimming, gliding on a surfactant and ‘crawling’) for effective colonisation and infectivity. In this thesis, I present a collection of papers which outline empirical ecological and evolutionary experiments to identify the abiotic and biotic forces that shape the evolution of these different dispersal mechanisms, with particular focus on the theoretically important role of kin competition and the structure of the abiotic environment.

In this thesis, I explore four different ways in which relatedness affects sexual interactions in the red junglefowl Gallus gallus ssp., and the fruit fly Drosophila melanogaster. First, I show that in both species, inbreeding depression is sex-specific and modulated by parental age and gametic age. However, the sex that suffers higher inbreeding depression was trait- and species-dependent. Second, I examined patterns of inbreeding avoidance. I found no evidence of inbreeding avoidance in the fruit fly, but in the red junglefowl both males and females avoided mating with relatives, independently from sex-ratio of the social group. Third, I investigated whether relatedness amongst members of one sex affects mate choice in members of the opposite sex. Male fruit flies preferentially courted females unrelated to females with whom they had previously mated, while female flies displayed a weak preference for males related to their previous mates. In the red junglefowl, females exposed to male trios of two males related to each other and one unrelated male, displayed a marked preference for mating with the male unrelated to the other two males, and might also bias postcopulatory sperm utilization in favour of the unrelated male. Fourth, I explored the implications of male relatedness on the intensity of male-male competition. Male red junglefowl were less aggressive towards related competitors, but invested more sperm in females that had previously mated with a related male rather than with an unrelated male. In fruit flies, male relatedness had a strong impact on female life-history and offspring viability, although I found no evidence that these effects were modulated by changes in male-male competition. Collectively, the findings of these studies demonstrate the complex relationship between relatedness and other important biological phenomena as such senescence and sexual conflict.

A crucial question in the debate about reintroducing elephant culling is whether the long-term effects of elephants and mesobrowsers on woodlands are similar. Sufficiently high biomass-densities of mesobrowsers may, following reduction or removal of elephants, continue to heavily impact earlier life-history stages of a similar suite of woody plants that elephant impacted, preventing these species from maturing. Thus a similar end-point for woodland structure and composition is achieved. No study exists in the literature where woody plant and habitat utilisation of the savanna browser guild has been determined in the same locality over the same period. A review of 49 years of literature implied that the two groups impact the same core woody-species in the same habitats. Dietary and habitat utilisation of guild members was determined in Hluhluwe-iMfolozi Park, South Africa. A small suite (n = 8) of woody species formed the core diet of all guild members. Herbivores’ densities were determined using a novel GIS approach; all members of the guild showed extensive overlap in habitat use. GPS collars and a GIS were then used to detect zones of different density of impala in the landscape, thus defining, for the first time, a natural fine-grain browsing gradient. Densities of woody seedlings were significantly less (average 48% reduction) in areas of high versus low impala density. A simple browse-browser model, incorporating, in a novel approach, functional groups of plant species, was parameterised from these results and an extensive review of the literature. Outputs suggest that over the long-term (100 years), impala will have a similar impact on woodland structure as elephant. An apparently strong synergistic effect between impala and elephant impact, suggests that reduction or removal of either impala or elephant will radically reduce long-term destruction of woodlands. In smaller or medium sized reserves, where control of mesobrowser populations is practical, profitable and more acceptable than elephant culling, these findings imply a re-direction of management efforts. Management should consider the biomass-density of both groups, rather than just focus on the system’s perceived ‘keystone’ species. Such principles may also apply to temperate and other systems.

The destruction and fragmentation of natural habitat is the leading driver of the current extinction crisis. As a result, a research area has emerged focused on studying ecology in islands of natural habitat surrounded by a sea of anthropogenic land uses, so called ‘habitat islands’. However, this research has largely been undertaken on small-medium scales, generally in single systems. Furthermore, many habitat island studies have used previous results and theory derived in the context of oceanic island research. Thus, this thesis aims to examine a variety of macroecological and biogeographical patterns using a large number of purely habitat datasets sourced from both the literature and my own sampling, with the objective of teasing out any general statistical patterns. The various macroecological and biogeographical patterns can be grouped under four broad headings: 1) species–area relationships (SAR), 2) nestedness, 3) species abundance distributions (SADs), and 4) species incidence functions (function of area). Overall, it was found that there were few hard macroecological generalities that hold in all cases across habitat island systems. This is because most habitat island systems are highly disturbed environments, with a variety of confounding variables and undesirable species (e.g. species associated with human land uses) acting to modulate the patterns of interest. Nonetheless, some clear patterns did emerge. In particular, it was found that the power model was by the far the best general SAR model for habitat islands. The slope of the island species–area relationship (ISAR) was related to the matrix type surrounding archipelagos, such that habitat island ISARs were shallower than true island ISARs. Significant compositional and functional nestedness was rare in habitat island datasets, although island area was seemingly responsible for what nestedness was observed. Species abundance distribution models were found to provide useful information for conservation in fragmented landscape, but the presence of undesirable species substantially affected the shape of the SAD. Species incidence function curves were found to vary across space for a given species, but not in any systematic manner. In conclusion, this thesis finds that the application of standard island biogeography theory to habitat islands is too simplistic. It is hoped that the results of this thesis will act as a catalyst for a more macroecological approach to habitat island research, and a starting point for the development of an integrated theory of habitat islands.