Tanzania’s Ruaha landscape is an international priority area for large carnivore conservation, harbouring roughly 10% of the world’s lions, and important populations of leopards and spotted hyaenas. However, these large carnivore populations are threatened by intense retaliatory killing due to human-carnivore conflict on village land around Ruaha National Park (RNP), mostly as a result of livestock predation by lions, leopards and spotted hyaenas. Moreover, a current lack of ecological data on the distribution of these carnivores hinders the development of effective strategies for conservation and targeted conflict mitigation in this landscape. This study aimed to identify the most significant ecogeographical variables (EGVs) influencing the distribution of lions, leopards and spotted hyaenas across the Ruaha landscape, and to map areas of conservation importance for these species. In addition, the study assessed the influence of EGVs on livestock predation risk by these carnivores in the village land around RNP, and generated a predictive map of predation risk. The relative importance of livestock husbandry practices and EGVs in terms of influencing predation risk within enclosures was also investigated. Proximity to rivers was the most important variable influencing the distribution of large carnivores in Ruaha, and contributed to predation risk of grazing livestock. The traditional livestock husbandry adopted in bomas appeared insufficient to alleviate the inherent risk of predation by large carnivores. The study produced the first detailed maps of lion, leopard and spotted hyaena distribution in the critically important Ruaha landscape, and identified likely livestock depredation hotspots. These results will target conflict mitigation approaches around Ruaha, by identifying particularly high-risk areas for livestock enclosures and grazing stock. Improving husbandry in these areas could help reduce livestock depredation and retaliatory carnivore killing, therefore reducing one of the most significant conservation threats in this critically important landscape.

This thesis examines the evolutionary biology of the RNA viruses, a diverse group of pathogens that cause significant diseases. The focus of this work is the relationship between the processes driving the evolution of virus populations within individual hosts and at the epidemic level. First, Chapter One reviews the basic biology of RNA viruses, the current state of knowledge in relevant topics of evolutionary virology, and the principles that underlie the most commonly used methods in this thesis. In Chapter Two, I develop and test a novel framework to estimate the significance of phylogeny-trait association in viral phylogenies. The method incorporates phylogenetic uncertainty through the use of posterior sets of trees (PST) produced in Bayesian MCMC analyses. In Chapter Three, I conduct a comprehensive analysis of the substitution rate of hepatitis C virus (HCV) in within- and between-host data sets using a relaxed molecular clock. I find that within-host substitution rates are more rapid than previously appreciated, that heterotachy is rife in within-host data sets, and that selection is likely to be a primary driver. In Chapter Four I apply the techniques developed in Chapter Two to successfully detect compartmentalization between peripheral blood and cervical tissues in a large data set of human immunodeficiency virus (HIV) patients. I propose that compartmentalization in the cervix is maintained by selection. I extend the framework developed in Chapter Two in Chapter Five and explore the Type II error of the statistics used. In Chapter Six I review the findings of this thesis and conclude with a general discussion of the relationship between within- and among-host evolution in viruses, and some of the limitations of current techniques.

Biologists have long used demographic approaches to answer questions in ecology and evolution. The utility of these approaches has meant a constant development and refinement of methods. A key milestone has been the development of phenotype structured population models that link ecology and evolution. Moreover, biostatistical research steadily improves methods to coax demographic information from scarce data. In this thesis, I build upon some of the recent advances in the field. My first three studies focus on the consequences of sex differences in life history for population dynamics. Firstly, I test whether males matter for the dynamics of African lion (Panthera leo) populations via a previously unquantified mechanism: the inheritance of phenotype from father to offspring. Secondly, I develop a method to estimate age-specific mortality rates for both sexes in species where one of the sexes disperses around the age of maturity. Thirdly, I apply this method to study variation in mortality between the sexes and between two populations of African lions. After these three chapters, which make contributions to the field of sex-structured population dynamics, I focus on the integration of phenotype structured modelling and quantitative genetics. I illustrate how heritability of a quantitative character that develops with age depends on (i) viability selection, (ii) fertility selection, (iii) the development of the phenotype with age, and (iv) phenotype inheritance from parents to offspring. Our results question the adequacy of quantitative genetics methods to obtain unbiased estimates of heritability for wild populations. This thesis advances our understanding of population development over ecological time scales. This knowledge has applications in conservation and population management, but also contributes to untangling evolutionary processes in wild animals.

Sex chromosomes experience distinct evolutionary environments, due to their unusual pattern of inheritance, and studies of sex chromosome evolution can shed light on the fundamental evolutionary forces acting across the genome as a whole. Here, I combine genomic and transcriptomic data across a wide range of avian species to explore the evolutionary processes governing sex chromosome evolution. Birds are female heterogametic and therefore it is possible, via comparisons with male heterogametic species, to identify the fundamental factors driving sex chromosome evolution, versus those associated with sex. In this thesis, I uncover a complex mosaic of recombination suppression between the Z and W chromosomes, characterized by repeated and independent divergence of gametologs, together with ongoing genetic exchange. Additionally, I highlight the role of mating system, and interplay between evolutionary forces, in driving coding and expression evolution on the Z and W chromosomes. My findings indicate that although the Z chromosome is masculinized for male-specific effects, the magnitude of genetic drift acting on Z-linked genes is elevated in promiscuous relative to monogamous mating systems. In contrast, evolution of the female-limited W chromosome is governed predominately by purifying selection. Together, my results suggest that the role of the Z chromosome in encoding sexual dimorphisms may be limited, but that W-linked genes play a significant role in female-specific fitness. In conclusion, my findings reveal the power of mating system in shaping broad patterns of genome evolution.

American zoological parks have been sites of intense consumer and scholar interest since their origination in the 20th century. Today, zoos reside at a tenacious hub of ideologies, practices, and priorities contributed to by various stakeholder groups. I propose that the foundational cause of this tension is zoological multiplicity: the theory that through human practices and perceptions, animals can embody multiple identities. Via an exploration of zoological multiplicity in American zoos with specific focus on zoo management, zoogoer, and animal activist stakeholder groups, this project proposes the widespread acknowledgment and understanding of zoological multiplicity as a method to improve animal care and global wildlife conservation projects.

Semi-aquatic mammals have evolved to forage in both aquatic and terrestrial environments, and they generally lack locomotor specialisation for either. Having relatively unspecialised adaptations, some semi-aquatic species are generalist foragers, and their activity and diving patterns provide insight into constraints on their foraging behaviour. The recent miniaturisation and improved accuracy of logging devices allow remote data collection from small (<1kg), shallow-diving species. The development of analytical methods has lagged behind technological advances (and techniques developed for fully aquatic animals do not account for the variability of behaviour typical of semi-aquatic animals and their switching between terrestrial and aquatic environments). I applied and developed novel analytical techniques to identify activities and diving patterns of a semi-aquatic mustelid, the American mink (Neovison vison), fitted with Time-Depth Recorders (TDRs). Using a hidden Markov model (HMM) algorithm allowed me to classify dives into three states to identify clustering, and describe sequential diving patterns by mink. TDRs were used to determine active/inactive periods on the basis of rapid TDR temperature changes, and this method was validated empirically. Having developed this methodology, I applied it to 18 datasets collected from 14 mink in lowland England. Terrestrial activity of mink was positively related to ambient temperature (across both sexes), however aquatic activity, especially diving, appeared to be more influenced by daylight than by temperature. Mink showed intersexual differences, with males being more nocturnal and more active on land, and females more diurnal, and more persistent in diving. There was considerable variability between sexes and individuals. This is the first study to use HMM to classify the dives of a semi-aquatic animal, and the first to use TDR temperature records to identify mammalian activity patterns. These methods will be generally applicable to animals that make rapid transitions between environments and have thus far been difficult to study.

Insects are often infected with facultative endosymbiotic bacteria, which can have a range of important ecological effects. The grain aphid, Sitobion avenae, harbours diverse facultative symbionts, which suggests their importance in grain aphid biology. This thesis attempts to explain the ecological roles of the facultative endosymbionts in S. avenae. It also examines the question of whether the horizontal transmission of symbionts between aphid clones and species can be important for shaping the ecology and evolution of multi-species aphid communities. Novel techniques developed for research with the grain aphid study system are presented. Grain aphid clones vary in their tolerance to low temperatures, but this trait is not affected by their facultative endosymbionts. Strains of a symbiont Hamiltonella defensa do not protect grain aphids from hymenopterous parasitoids, regardless of the host genotype. However, experienced parasitoid females preferentially oviposit in aphids which do not harbour symbionts. Comparison of the fitness consequences of infection with the same Hamiltonella strains in their original and in novel grain aphid host clones reveal no consistent differences. Symbiont strains establish easily following artificial transfer between clones of the grain aphid, but the symbionts transferred from other aphid species form less stable infections. Hamiltonella strains do not affect the fecundity of their grain aphid host clones regardless of their host species of origin, but also do not generally confer protection against parasitoids. There are no clear patterns in the distribution of parasitoid-resistant phenotypes across phylogenetic trees of Hamiltonella and its bacteriophage APSE. Strains of four unrelated species of endosymbionts, Rickettsia, Spiroplasma, Rickettsiella and Regiella, confer the same pathogen-resistant phenotype to a single pea aphid clone. The same symbiont strains can confer resistance to clones of two different aphid species. Some strains in multiple infections may compensate for the costs of infections with other symbionts. The importance of these results for understanding the ecological and evolutionary role of facultative endosymbionts in aphids and other insects are discussed, and directions for further research are proposed.

This thesis centres around two genera of large peltospirid gastropods (Mollusca: Neomphalina: Peltospiridae) endemic to hydrothermal vent ecosystems. One is the 'scaly-foot gastropod', an emblematic species of the Indian Ocean vents with unique dermal sclerites covering the foot like roof tiles. The other was recently discovered from expeditions to the Southern and Indian oceans, lacks sclerites and possesses large opercula. As both genera and their assigned species remained undescribed, they were formally described herein which forms a basis to understanding their biology. The 'scaly-foot gastropod' from both the Central Indian Ridge (CIR) and the Southwest Indian Ridge (SWIR) were confirmed to represent a single species and is formally named as Chrysomallon squamiferum. Through molecular genetic analyses using the COI gene, genetic differentiation between SWIR and CIR populations was detected for the 'scaly-foot gastropod'. In contrast, the peltospirids with large opercula from the East Scotia Ridge (ESR) and the SWIR proved to be two distinct species within an undescribed genus. The ESR species was formally described as Gigantopelta chessoia and the SWIR species as G. aegis. The molecular genetic analyses of the COI gene, confirmed the genetic isolation of the two and consolidated their status as separate species. A 3D tomographic model of Chrysomallon squamiferum was generated to characterise the soft anatomy and morphology as well as to understand its internal anatomy and adaptation which remained little-studied. Further to the enlarged esophageal gland already known to house chemosynthetic endosymbionts, C. squamiferum was discovered to have a hypertrophied circulatory system with a gigantic, muscular heart and large ctenidium to adapt to life in a hypoxic environment and to supply the endosymbionts with necessary chemicals. Histological examinations of the sclerites and operculum showed that it was unlikely that the sclerites originated from operculum duplication. Comparisons with polyplacophoran scales revealed starkly different secretion mechanisms despite the superficial similarity, which has implications on the placement of sclerite-bearing Cambrian taxa. Overall, the results from this thesis ascertained the systematic positions of these large-sized, enigmatic peltospirids, and led to improved understanding of their ecology and evolution. The important role of larval dispersal in maintaining metapopulations across the distribution of a vent-endemic taxa is highlighted. The adaptations of vent-endemic taxa remains little-known even in well-studied species, warranting future studies on these and other species.

In the light of increasing pesticides resistance in agricultural pests and in insect vectors of human diseases, leading to the rise in occurrence of mosquito-borne diseases, new, efficient and environmentally friendly methods of pest control are needed. Sterile Insect Technique (SIT), relying on mass releases of radiation sterilised males to reduce reproductive potential of target pest populations, although not new, offers an alternative to the use of pesticides and is an environmentally non-polluting method of insect control. Many insect species, however, are not very amenable to classical SIT, due to detrimental side-effects of radiation treatment. We propose a new method, a genetically engineered modification of classical SIT, replacing radiation with genetically induced sterility. Based on conditional expression of male-germline targeted nucleases which introduce double strand breaks into the male germline DNA to render males sterile, this method emulates SIT mechanism, at the same time eliminating radiation and associated detrimental side-effects. Different variants of such a system were investigated in this project, eventually leading to the creation of functional conditional male-sterility systems in two model organisms – the Yellow fever mosquito, Aedes aegypti and the Mediterranean fruit fly, Ceratitis capitata. Both systems utilise chimeric nuclease composed of protamine and FokI cleavage domain fusion. The sperm-specificity and the conditionality of the sterile phenotype have been achieved through the use of tetracycline repressible expression system driven by the &beta;2-tubulin promoter in Ceratitis capitata and by the Topi promoter in Aedes aegypti.

A combination of habitat loss, degradation and fragmentation are causing declines in butterfly species across Europe, with habitat specialists more vulnerable than generalists. The influence of climate change is serving to complicate matters, particularly at the edge of geographic ranges. Improving the quality of habitats is a key tool for the conservation of threatened species at both a local and landscape scale and this requires a thorough understanding of the ecology and habitat requirements of species. From this perspective this thesis examines and compares the ecology of two closely butterfly species, Polyommatus bellargus (the Adonis Blue) and Polyommatus coridon (the Chalkhill Blue) in southern England; calcareous grassland specialists, found in a highly fragmented ecosystem at the northern most edge of their geographic range. Chapter 2 explores whether there has been an expansion in the larval niche of P. bellargus due to a warming climate in recent decades, and finds no indication of change once concurrent local habitat change has been accounted for. Chapter 3 examines the role that differences in microhabitat requirements play in differentiating the larval niche of P. bellargus and P. coridon, showing P. coridon has broader microhabitat requirements. Chapter 4 experimentally examines the specificity of mutualistic interactions between the larvae of each butterfly species with the ants Myrmica sabuleti and Lasius niger. Chapter 5 uses microsatellites to explore the genetic structure of both P. bellargus and P. coridon, showing (as predicted) that P. coridon has a less fragmented population structure than P. bellargus, but both species have high levels of inbreeding.