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Neopterygian fishes represent over half of vertebrate richness in the Recent and display staggering phenotypic variety, yet little is known about the first 150 million years of their evolution. Furthermore, neopterygian richness and disparity is highly unevenly partitioned between teleost fishes, with ~29,000 species expressing a plethora of phenotypes, and holostean fishes, with 8 species and just two morphological styles. Fossil phenotypes have the unique ability to illuminate the assembly of neopterygian disparity, and can reveal the pattern by which the uneven partitioning of disparity arose. Morphology and function were quantified with landmarks and six functional traits, respectively, for 356 neopterygian species known globally throughout the first 150 million years of their history. The main axes of morphological and functional variation were derived and used to examine a series of evolutionary questions. Pertinently, they revealed how disparity was accumulated for 60% of the neopterygian radiation; morphological disparity increased through time, whereas functional disparity remained stable. The morphological dataset was expanded to include shape data for 398 species and size data for 471 species. Time scaled supertrees containing 671 mostly Mesozoic, but also living neopterygian species, were created. Together, the trees and traits were used to quantify evolutionary rates and innovation and test the predictions of genome duplication enhanced morphological diversification in teleosts, and the presence of 'living fossil' characteristics in holosteans. The analyses revealed higher rates and greater innovation in teleosts guaranteed to possess duplicated genomes, consistent with the predictions of genome duplication enhanced diversification. The only 'living fossil' characteristic of holosteans is their poor capacity for size innovation, yet they possess relatively high rates of shape evolution. However, estimates of rates and innovation are heavily influenced by timescale choice, emphasising the need for workers to perform their analyses on a variety of plausible timescales to determine the limits of their conclusions.

The development of behavioural resistance in Anopheles mosquitoes is an important threat to the sustainability of current vector interventions, which selectively target mosquitoes that are found indoors. Changes in the following behaviour have been reported in several Anopheles vectors: biting time, host preference, biting and resting behaviour. However, a critical review of the published literature reveals that behavioural resistance has not been demonstrated clearly in Anopheles, highlighting important limitations in using entomological data to investigate the evolution of behaviour. The availability of next generation sequencing and low-cost custom genotyping technologies makes it possible to investigate behavioural resistance using genetic information as an alternative approach. Using such technologies, this thesis aims to investigate whether Anopheles vectors are evolving towards outdoor-biting behaviour ('exophagy') by examining the genetic difference between the indoor- and -outdoor population of the main African malaria vectors, An. coluzzii and An. gambiae from The Gambia and Uganda, respectively. We also investigated the role of olfactory-related genes in driving the potential genetic difference between the two populations. We found limited divergence between the two populations overall, however close inspection identified SNPs potentially associated with outdoor-biting behaviour as well as genomic regions displaying elevated levels of differentiation between the two populations. Most notably, gustatory receptors, Gr11 and Gr12 and the odour receptor, OR1 were identified as well as, genes related to transcription, signal transduction and catalysis. We discuss the potential role of these genes in determining biting behaviour and suggest that further investigation of these genomic regions is required to confirm the early-stage divergence of indoor- and outdoor-biting Anopheles populations.

We investigate the biological constraints determined by the complex relationships between ecological and immunological processes of host-pathogen interactions, with emphasis on influenza viruses in human, which are responsible for a number of pandemics in the last 150 years. We begin by discussing prolegomenous reviews of historical perspectives on the use of theoretical modelling as a complementary tool in public health and epidemiology, current biological background motivating the objective of the thesis, and derivations of mathematical models of multi-locus-allele systems for infectious diseases with co-circulating serotypes. We provide detailed analysis of the multi-locus-allele model and its age-specific extension. In particular, we establish the necessary conditions for the local asymptotic stability of the steady states and the existence of oscillatory behaviours. For the age-structured model, results on the existence of a mild solution and stability conditions are presented. Numerical studies of various strain spaces show that the dynamic features are preserved. Specifically, we demonstrate that discrete antigenic forms of pathogens can exhibit three distinct dynamic features, where antigenic variants (i) fully self-organize and co-exist with no strain structure (NSS), (ii) sort themselves into discrete strain structure (DSS) with non-overlapping or minimally overlapping clusters under the principle of competitive exclusion, or (iii) exhibit cyclical strain structure (CSS) where dominant antigenic types are cyclically replaced with sharp epidemics dominated by (1) a single strain dominance with irregular emergence and re-emergence of certain pathogenic forms, (2) ordered alternating appearance of a single antigenic type in periodic or quasi-periodic form similar to periodic travelling waves, (3) erratic appearance and disappearance of synchrony between discrete antigenic types, and (4) phase-synchronization with uncorrelated amplitudes. These analyses allow us to gain insight into the age-specific immunological profile in order to untangle the effects of strain structures as captured by the clustering behaviours, and to provide public health implications. The age-structured model can be used to investigate the effect of age-specific targeting for public health purposes.

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.

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.

The natural world consists of a vast array of forms, some more plentiful than others, yet our understanding of the processes responsible the production of biological diversity remains surprisingly limited. Here I combine novel datasets with powerful phylogenetic modeling techniques and computer simulations to test the effects of both biotic and abiotic factors on the dynamics of species radiations and the evolution of organism traits in birds. In the first part of this thesis, I develop our understanding of the importance of abiotic factors for diversification by showing that in the early stages of lineage diversification at least, rapid adaptation to novel climatic conditions is likely to represent a prominent driver of avian diversification. In the second part I concentrate on the role of biotic factors, in particular that of sexual selection. I show that not only is sexual selection associated with accelerated rates of speciation and secondary sympatry—as well as faster rates of net diversification across the entire avian tree of life—but also that across-species variation in rates of phenotypic evolution is best understood with reference to the focus and intensity of sexual selection. Finally, given that the relative importance of such processes appears to vary predictably across latitudes, in the final part of the thesis I argue that latitudinal differences in the speciation process offers a potentially powerful explanation for conflicting viewpoints regarding the contribution of speciation to high tropical diversity. Overall, this work provides fresh insight into the processes governing broad-scale patterns in biodiversity.

Species diversity varies dramatically across the surface of the Earth. A key step in the accumulation of species diversity is the ability of species to coexist in biological communities. Thus, identifying the mechanisms underlying community assembly is a major challenge for ecologists seeking to explain patterns in species diversity and composition. Recently some consensus has been reached on the set of processes that influence community assembly: speciation, demographic stochasticity, niche-based fitness trade-offs among species and dispersal. However, it is unclear how the importance of a particular process changes with spatial scale, which interactions exist among processes at large spatial scales and the extent to which niche-based resource partitioning among species explains differences in diversity among communities. Neotropical birds offer an ideal opportunity to address these uncertainties because of their high diversity and the existence of detailed information on their evolutionary history and ecology. In this thesis, I first use trait and phylogenetic metrics of community structure to show that both habitat filtering and interspecific competition shape community composition at the scale of individual bird territories (~1-2 ha). Second, I use simulations of community assembly to show that trait-based metrics of community structure outperform phylogenetic metrics for detecting niche-based community assembly, and that both sets of metrics often have low power when multiple processes influence community composition. Third, taking a trait-based, species-level approach, I show that both habitat filtering and interspecific competition influence species occurrence at regional scales (~75000 km2), and interact with dispersal ability so that their effect on species occurrence is increased for species with greater dispersal ability. Finally, using a combination of trait- and isotope-based methods to quantify resource partitioning, I show that species' niche widths do not change and niche overlap is reduced at high compared to low species richness. Taken together, these results suggest that both habitat filtering and interspecific competition (i.e. niche-based processes) influence community assembly from local to regional scales. However, at least at regional scales, the degree to which these processes are important for determining the occurrence of any given species depends on that species's dispersal ability. They also suggest, based on niche-based interspecific competition influencing community composition, that differences in species richness among communities are in part explained by differences among sites in the breadth of available niche space, not by increased ecological specialisation or niche overlap.

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.

This thesis investigates antigenic variation and its evolution in Plasmodium falciparum, the cause of the most deadly form of human malaria. Antigenic variation is a strategy for evading immunity by switching between antigenic variants during infection. In P. falciparum, such variable antigens confer different binding phenotypes that may affect parasite survival and have also been linked to pathology. Here, a new statistical method is described for determining the switching patterns that underlie antigenic variation. This method is then applied to experimental data to yield a full description of an antigenic switching network in P. falciparum. In light of the findings, theoretical modelling is used to show how immune selection and binding phenotypes may have contributed to the evolution of antigenic repertoire structure, expression order and virulence. Related models are also used to investigate parasite population diversity, providing possible explanations for observations reported here and elsewhere, with implications for vaccine design. Together, these chapters advance understanding of P. falciparum immune evasion and how it relates to pathology. This work further reinforces the role of host immunity in shaping pathogen population diversity at multiple levels.

Antibiotic resistance in bacteria is acquired through spontaneous chromosomal mutations or horizontal gene transfer. In the absence of antibiotics, resistant mutants generally show reduced fitness due to compromised growth rate, competitive ability and virulence compared to their antibiotic-sensitive ancestors. The focus of my research is to dissect the molecular underpinnings of the variations in the fitness cost of chromosomal antibiotic resistance using a systems-level approach. From an evolutionary perspective, my research aims are to understand how the fitness cost influences adaptation in resistant populations in an antibiotic-free environment. Using rifampicin resistance in Pseudomonas aeruginosa as a model, my work shows that most of the variation in the fitness cost of rifampicin resistance can be attributed to the direct effect of rifampicin resistance mutations on transcriptional efficiency. Through RNA-Seq transcriptome profiling, I demonstrate that global changes in gene expression levels associated with resistance mutations are surprisingly subtle, suggesting that the transcriptional regulatory network of P. aeruginosa is robust against compromised transcriptional efficiency. Using experimental evolution and whole-genome sequencing, my work reveals a systematic difference in the genetic basis of adaptation in mutants that were propagated in the absence of antibiotics. During compensatory adaptation, resistant mutants can recover the fitness cost of resistance by fixing second-site mutations that directly offset the deleterious effects of resistance mutations. Amongst resistant mutant populations with low fitness costs, general adaptation limits compensatory adaptation, which is most likely to be due to the rarity of compensatory mutations and clonal interference. Far from being the most ubiquitous mechanism in the evolution of resistance, compensatory adaptation is the exception that is more likely to be observed in resistant mutants with high fitness costs. In addition, I applied key elements of the integrative experimental approach developed in this work to dissect the molecular basis of the fitness cost associated with carriage of the pNUK73 small plasmid in P. aeruginosa, which carries the rep gene encoding a plasmid replication protein. My results confirmed that rep expression generates a significant fitness cost in P. aeruginosa and demonstrate how the molecular origins of the fitness cost of resistance can be dissected in a different biological context.

Inclusive fitness theory concerns the study of social traits. Often, individuals differ in their phenotype (e.g. size, weight, nutritional state) independently of their genetic make up, that is, individuals differ in their quality. Individuals can then be classified into different “classes” according to their quality, which enable us to understand social evolution in class-structured populations. This is important because individuals in natural populations often differ in quality, either because of intrinsic factors (e.g. size), or extrinsic factors (e.g. resource availability). My thesis concerns the evolution of social traits in class-structured populations. In chapter 1, I make a brief introduction to my thesis, providing the abstract of each chapter. In chapter 2, I outline a general theory of individual quality, where I show how individual quality impacts social evolution in two fundamental ways. In chapter 3, I show that resource heterogeneity greatly influences the evolution of conditional social behaviour. In chapter 4, I show that temporal group-size heterogeneity promotes the evolution of both conditional helping and harming. In chapter 5, I analyse the effect of individual quality on kin selection. I find that individual quality has an important impact in kin selection, which can lead to extreme forms of social behaviour. In chapter 6, I show that stable environments promote the evolution of negative density-dependent dispersal, while unstable environments promote the evolution of positive density-dependent dispersal. In chapter 7, I show that budding and low local quality promote the evolution of dispersal and cooperation.

A major challenge in biology is to identify how different species arose and acquired distinct phenotypic traits. High-throughput sequencing is transforming our understanding of biology by allowing us to study genomes and cellular processes at genome-wide levels. Only a decade subsequent to the publication of the first human genome draft, genome assemblies of hundreds of organisms have been produced. Yet, genome analysis remains challenging and advances have lagged far behind our sequencing abilities and other technological advances. The next generation of comparative genomicists must therefore understand, invent and apply a wide number of computational tools in order to study biology in the most efficient manner and in order to pose the most interesting questions. This thesis spans areas covering evolutionary genomics, gene regulation, and computational methods development. A major aim was to understand how genetic variation contributes to variation in phenotypic traits. This was approached using a large variety of evolutionary and comparative genomics tools. In particular, high-throughput sequencing datasets were analysed to study single-cell transcriptomics, gene duplications, gene architecture evolution, and alternative splicing. Additionally, in cases where off-the-shelf analysis tools were inexistent, novel pipelines and programs were designed and implemented to solve algorithmic problems such as scaffolding genome assemblies and short-read mapping onto small exons.

Vertebrate genomes exhibit global methylation of cytosine residues where they occur in a cytosine-guanine dinucleotide (CpG) context and this epigenetic mark is generally thought to be repressive to transcription. Punctuating this pervasive DNA methylation landscape are short, contiguous regions of non-methylated DNA which are found at two thirds of mammalian gene promoters. These non-methylated regions exhibit CpG content close to expected levels as they escape the depletion of CpGs observed across the methylated fraction of the genome. The unique nucleotide properties of these CpG island (CGI) regions enable their identification by computational prediction in mammalian genomes. Owing to a lack of high-resolution genome-wide DNA methylation profiles in non-mammalian species, these CGI predictions have often been used as a proxy for non-methylated DNA in these organisms. In contrast to mammals, CGI predictions in cold-blooded vertebrates rarely coincide with gene promoters, leading to the belief that CGls are significantly divergent between vertebrate species, and that unique promoter-associated features may have been acquired during warmblooded vertebrate evolution. This thesis is primarily concerned with the location, establishment and biological function of non-methylated islands of DNA in vertebrate genomes. To experimentally determine genome-wide profiles of non-methylated DNA, a novel biochemical technique was established called biotinylated ZF-CxxC affinity purification (Bio-CAP), and development of this method is discussed in Chapter 3. Experimental analysis of non-methylated DNA profiles in this thesis initially addresses two main questions: (1) 'How does the non-methylated DNA landscape compare genome-wide for seven vertebrates considering distinct tissue types and developmental stages?' (2) 'How are vertebrate non-methylated regions of DNA defined and interpreted in the nuclear environment?' To address the first question, non-methylated DNA was profiled by Bio-CAP sequencing across the genomes of seven diverse vertebrate species, representing all major branch points of vertebrate evolution, and the results are discussed in Chapters 4 and S. Contrary to previously held dogma, experimentally determined nonmethylated islands of DNA (NMls) constitute an ancient epigenetic feature of vertebrate gene regulatory elements. However, despite having numerous high-resolution maps of vertebrate non-methylated DNA, the means by which NMls are identified and maintained in the nuclear environment remains poorly understood. To address the second question and identify features which determine the methylation state of DNA, exogenous DNA sequences were introduced into mouse embryonic stem (ES) c~.II~. Non-methylated DNA was profiled by Bio-CAP sequencing to investigate how different features, such as sequence-specific binding motifs, chromatin architecture and nucleotide composition of a given DNA sequence impact local DNA methylation patterns. Interestingly, the majority of exogenous promoters were appropriately non-methylated in mouse ES cells, germline and somatic cells suggesting that gene promoters have retained strong signals for the nonmethylated state across millions of years of evolution (discussed in Chapter 6). During mouse embryogenesis, genome-scale DNA demethylation and remethylation events occur to remodel the epigenetic landscape and loss of DNA methylation during this time leads to embryonic lethality. To investigate the biological function of non-methylated DNA, the third question addressed in this thesis is (3) 'What is the developmental importance of non-methylated islands of DNA during vertebrate embryogenesis?' To investigate this, members of the ZF-CxxC domain-containing family of chromatin modifiers were ablated in zebrafish embryos to perturb the chromatin landscape at NMls, and therefore interfere with their function during early development (Chapter 7). Early embryonic development and patterning was disrupted in knockdown embryos, suggesting that interpretation of non-methylated DNA and placement of chromatin modifications at NMls is essential for normal zebrafish embryogenesis. Together this work sheds light on the evolutionary origins of NMls, the mechanisms involved in the recognition and establishment of nonmethylated loci and provides an insight into the function of non-methylated DNA during early embryonic development.

In this thesis I set out to further our understanding of two broad questions, 1) why it is that sexual selection favours the evolution of particular traits and 2) why do the patterns of sexual selection on such traits differ between groups and populations? Specifically, I focused on the role that variation in intrasexual competitive structure, the non-random distribution of socio-competitive environments across individuals, plays in shaping variation in the operation of sexual selection both within and across populations. I explore the roles of three main determinants of competitive structure, namely; population structure, polyandry and non-random variation in the distribution of the intensity of competition. To achieve this, I used a combination of empirical and theoretical tools, using the model system Red junglefowl, Gallus gallus. Throughout this thesis I both develop and employ network quantitative tools as a framework to describe variation in intrasexual competitive structure. Overall, this thesis demonstrates a complex relationship between competitive structure and the operation of sexual selection. This structure can modify the strength and direction of sexual selection operating on phenotypic traits, obscure the operation of selection at the population level and influence the relative roles of pre- and post-copulatory sexual selection. Furthermore, this thesis explores how differences in local ecology can shape competitive structure itself and in turn shape sexual selection. In doing so, this thesis sheds some light on the role that variation in competitive structure may play in shaping the operation of sexual selection both within and between populations and generating the great diversity in sexually-selected traits and behaviours between populations.

The drivers of fidelity and divorce of pair-bonded individuals, along with their fitness consequences, are of great interest as they influence mating systems, population structure and productivity, and gene flow. Socially monogamous birds offer an ideal opportunity to study divorce since they show great variability in the extent to which pair bonds are maintained. However, there has been little consensus as to whether divorce is a behavioural adaptation to improve a mating situation, or a consequence of other processes. Moreover, the biological and ecological correlates of fidelity are difficult to address because previous work has been based on indirect and potentially biased methods. Finally, in terms of process, the link between the process of mate choice and subsequent mating decisions has been largely inaccessible to study. My doctoral thesis addressed these significant gaps in our understanding of cause, process and consequence in the formation and dissolution of pair bonds in socially monogamous birds. I accomplished this in three principal ways. First, I conducted a robust phylogenetic meta-analysis on 84 studies across 64 species to assess the existing empirical evidence that divorce in socially monogamous birds is adaptive (in terms of breeding success). This analysis revealed that divorce is, in general, adaptive as it is both triggered by relatively low breeding success and leads to improvement in success. Next, I developed a novel probabilistic multievent capture–mark–recapture framework that provides joint estimates of survival and fidelity while explicitly accounting for imperfect detection, capture heterogeneity, and uncertainty in pair status. By applying this model to breeding data on a wild great tit population I showed that birds that remain faithful to their partner exhibit higher survival rates and are more likely to remain faithful in the next breeding season than do birds that change partners. Subsequently, I confirmed the generality of a survival benefit by applying the model to breeding data on other tit populations. Then, by applying the model to data from a population of mute swans, I showed that fidelity decreases the likelihood of skipping breeding and mortality in this long-lived species, and that these effects depended on age, individual quality, and immigration status. Finally, I investigated how the timing of pair formation influences breeding success and divorce probability using five years of data on the over-winter social behaviour of great tits. I showed that early pair formation had a positive effect on fitness components, influencing the likelihood of divorce only indirectly, through breeding success. Further, my work revealed that males, but not females, with higher numbers of the female associates in winter, and males whose future breeding partners were ranked low amongst these, divorced more often. My research makes a significant contribution to our understanding of divorce and fidelity, and generates a number of important implications for future studies. First, my work establishes that divorce is adaptive for breeding success. Second, my results highlight that survival is an important (and likely, widespread) fitness consequence of pairing decisions. Third, I provide a novel statistically rigorous modelling framework for estimating fidelity-rates and testing hypothesis about fidelity that overcomes many of the inherent biases in traditional estimates. Fourth, it provides the first evidence for a selective advantage of early pair formation in wild, thus highlighting that there are benefits to pair familiarity that manifest via social associations of individuals prior to breeding. Finally, my work reveals the selective pressures operating via the social environment can ultimately influence the mating strategies individuals adopt.

The study of social evolution and virulence in parasites is concerned with fitness consequences of trade-offs between parasite life history traits and interactions between parasite species and/or genotypes with their hosts. I develop our understanding of social evolution and virulence in parasites in several ways. (1) I review empirical evidence for the fundamental predictions of virulence-transmission trade-off theory and demonstrate that the fit between theory and data is primarily qualitative rather than quantitative; that parasites differ in their degree of host generalism, and this is likely to impact virulence in four ways. (2) I take a comparative approach to examine the underlying causes of an observed statistical variation in the size of parasite infectious doses across taxa, revealing that mechanisms used by parasites to infect hosts are able to explain variation in both infectious dose and virulence. (3) I formally compare data on human pathogens to explain variation in virulence across taxa, revealing that immune subversion and not growth rate, explains variation in virulence. This allows me to predict that immune subverters and not fast growing parasites are likely to cause the most virulent clinical infections. (4) Using bacteria and their naturally infecting viruses (bacteriophage), I take an experimental approach to investigate the consequences of coinfection for parasite life history traits, and find that viruses cultured under a mix of single infections and coinfections evolved plasticity; they killed hosts more rapidly when coinfecting, and this resulted in high fitness under both single infection and coinfection conditions. (5) I experimentally investigate how selection within and between hosts and patches of hosts affects the fitness and virulence of populations of these viruses. I find that limited host availability favours virulent, faster killing parasites with reduced transmission; suggesting high, rather than low, virulence may be common in spatially structured host-parasite communities.

Studies of the evolution of the major histocompatibility complex (MHC) have been central to the understanding sexual selection and pathogen-mediated selection. The European badger Meles meles is well suited for exploring such questions because of its life history characteristics, reproductive biology and mating system. In this thesis, I examined both MHC class I and class II genes. Seven putatively functional sequences were found for class I genes and four for class II DRB genes. Evidence of past balancing selection of both genes was demonstrated by the dNdS ratio, by positive selection at the antigen-binding site (ABS) and by trans-species polymorphism of alleles within other mustelids and carnivores. MHC class I genes also showed evidence of concerted evolution, but domains showed different evolutionary histories. MHC genes may influence microbiota and odour of an individual and influence mating preferences. I examined the bacterial community of the subcaudal gland secretion and demonstrated a high number of bacterial species (56 operational taxonomic units), which cubs exhibited a higher diversity than adults. The microbiota may lead to an individual-specific odour as a cue signaling the MHC genotype of potential mating partners. I report the first evidence for a MHC- based mating preference in carnivores. Female badgers showed a MHC-assortative mate choice towards breeding with males that had functionally similar MHC genes, for MHC class II DRB genes. This applied to neighbouring-group matings. I also found considerable annual fluctuation in the occurrence of MHC-based mate choice. Based on genome-wide background in the same mating randomizations I found no evidence of inbreeding, which indicated that MHC similarity was apparently the actual target of mate choice. In line with MHC-assortative mate choice, MHC heterozygosity had no influence on the co-infection status. Individual MHC alleles did, however, associate with resistance and susceptibility to specific pathogens, suggesting that MHC diversity may be driven and maintained by pathogen-mediated selection through rare-allele advantages and/or fluctuating selection. My study of genetic characteristics, mate choice and pathogen pressures in a wild population revealed past and contemporary evolutionary process of the MHC genes. This increases knowledge of how the MHC may affect mating behaviour and sexual selection, ultimately influencing population processes.

Our bodies contain a vast number and diversity of microbes. These microbes interact, and these interactions can define how microbes affect us. Microbial ecology and evolution, therefore, are important for both microbiology and human health. However, our understanding of microbial communities remains limited. There is a need for theory that dissects the complexity and identifies the key factors and processes affecting microbial groups. Here I develop realistic computer simulations and population models of microbial communities. My first project seeks to explain microbial communication (quorum sensing) and argues that quorum sensing is a way to infer when competing genotypes are no longer a threat. The second project proposes an evolutionary explanation for another major microbial trait: adhesion. I argue that adhesion is a weapon allowing cells to compete within microbial groups and push competitors out, particularly when growing on a host epithelium. The third project moves from microbes to the host and asks whether a host can control which microbes grow and persist inside it. I develop a model of the human gut epithelium and show that the gut architecture amplifies the ability of hosts to select helpful microbes over harmful ones using nutrient secretion. In addition to selecting particular microbial strains, a host will also benefit from stable symbiotic communities that behave in a predictable manner. But what determines whether host-associated communities are ecologically stable? My final project uses ecological network theory to show that ecological stability is likely to be a problem for gut communities that are diverse and contain species that cooperate with each other. However, I argue that the host should function as an ecosystem engineer that increases ecological stability by weakening the strong dependence of cooperating species upon one another. While host-associated communities are complex ecological systems, my thesis identifies key factors that affect their form and function.

Many bacteria, viruses and other parasites cause severe morbidity or mortality in their host populations, creating strong selection for physiological or behavioural mechanisms to avoid disease. Likewise, changes in host susceptibility and contact patterns can dramatically influence the spread of infectious diseases, and hence selection for traits such as virulence and infectivity range in parasites. Understanding how ecological and evolutionary changes in one population affect selection in another represents a key challenge for theoreticians and empiricists alike, and is essential for gaining further insights into host-parasite relationships. This thesis contains theoretical models that explore how genetic and environmental factors shape the evolutionary and coevolutionary dynamics of hosts and parasites. In particular, the roles of genetic specificity (i.e. genotype-by-genotype interactions) and population mixing patterns are investigated, using both mathematical models and computer simulations. A broad range of scenarios are covered, including the coevolution of broad resistance and infectivity ranges (generalism), the persistence of coevolutionary cycling and the maintenance of sex, the effects of mating behaviour on disease prevalence and evolution, and the evolution of sexual and social behaviour. The models presented herein develop our understanding of host-parasite relationships and highlight the importance of genetic interactions and ecological feedbacks.

Natural selection favours those individuals that respond best to novel features of their selective environment. For many, a critical challenge is responding to evolutionary change in mutualistic species. These responses create complex feedbacks, so only coevolutionary approaches are able to fully answer key questions about the maintenance or disruption of mutualistic behaviour, and explain the range of mechanisms that allow individuals to benefit from these associations. I first consider the hypothesis that economic models studying multiple classes of traders, where each trader seeks to optimise its own payoffs will yield insights into mutualistic systems. I show that individuals can be favoured to discriminate amongst potential partners based on the price for which they provide resources. Then, I show that market mechanisms can maintain cooperation and drive specialisation in mutualistic systems. I extend this market model to allow individuals to restrict a mutualistic partner's access to resources, and show that this strategy can stabilise cooperation and increase the fitness of both partners. I also explicitly incorporate relatedness in my market model. I show that high relatedness sometimes increases cooperativeness in members of a mutualistic species, but sometimes decreases cooperativeness as it narrow the scope for partner choice to maintain cooperation. Having studied market mechanisms, I consider indiscriminate costly help to members of another species. I discover that this trait can be favoured by natural selection and can be classified as either altruism between or altruism within species. Finally, I consider a framework for analysing coevolved phenotypic responses to a partner's cooperativeness, a challenging process to model. I demonstrate that this framework can yield firm predictions about behaviour whenever partners hold private information about their costs and benefits.

Termites are important ecosystem engineers in tropical and sub-tropical terrestrial regions where they influence ecosystem processes by altering the physical and chemical structure of the habitat. Termites affect nutrient availability by decomposition and comminution (shredding) of organic matter and act as agents of bioturbation as they re-work substrates during the construction of nests, tunnels and runways. At present we have a relatively good understanding of termite diversity patterns in the tropics through the extensive use of the standardised transect sampling protocol by Eggleton et al. (1995). These diversity data suggest that there is a functional difference in termite assemblage structure, and potentially in termite abundance and biomass, among comparable habitats across continents. However due to the lack of comparable abundance and biomass data from South America this has not previously been confirmed. In this thesis I, therefore, collected extensive data on termite taxonomic and functional assemblage structure in a South American site in Peru. The data were used to compare termite abundance and biomass from two comparable sites in Africa (Cameroon) and south east Asia (Malaysia) in order to gain better understanding of the role termites play in ecosystem processes. I found that there was an intercontinental difference in the abundance and biomass of termite feeding-groups mainly due to the dominance of soil-feeding termites in Cameroon and the absence of fungus-growing termites from Peru. The impact of certain lineages on the intercontinental differences suggests that the differences may be due to biogeographical evolution. Moreover, Eggleton et al. (1998) show that larger-bodied soil-feeding termites in Cameroon process more energy per unit area than predicted by their body size. Due to the need for an examination of the allometric relationships in termite assemblages outside Africa and the development of a more sophisticated feeding-group classification I explore the findings in Eggleton et al. (1998) further using population density - body mass relationships in three termite feeding-groups among the three continental sites in Cameroon, Peru and Malaysia. I found that large-bodied soil-feeding termites in Cameroon and large-bodied wood-feeding termites in Peru had higher population densities than expected by their body masses. As the population density - body mass relationship is inverse to that of the energy - body mass relationship the results suggest that the two feeding-groups also use more energy than expected by their body masses. Further, we have a relatively good understanding of the role termites play as ecosystem engineers e.g. in nutrient cycling and distribution, however, compared with our understanding of wood and litter decomposition in tropical forests quantitative data on the impact of termites in soil processes is poorly understood. In this thesis I conducted, to our knowledge, the first in situ soil macrofauna exclusion experiment using translocated soil in Peru to examine the impact of termites on soil C and N loss. I found that termites promote soil C and N loss which may be linked to the increase in microbial activity due to the passage of soil through the termite gut as well as the affect termites have on bioturbation and nutrient distribution. To conclude, in this thesis I present the first intercontinental comparison of abundance and biomass as well as the first in situ soil macrofauna exclusion experiment to date. The link between termite ecology, biogeography and evolution is discussed as well as the contribution of this thesis to the field of termite ecology.

During human immunodeficiency virus 1 (HIV-1) infection, the viral population is in constant battle with the host immune system. The cytotoxic T-lymphocyte (CTL) response, a branch of the adaptive immune response, is implicated in viral control and can drive viral evolution in the infected host population. Endogenous viral peptides, or ‘epitopes’, are presented to CTLs by human leukocyte antigen (HLA) class I molecules on the surface of infected cells where they may be identified as non-self. Mutations in or proximal to a viral epitope can result in ‘escape’ from CTLs targeting that epitope. The repertoire of epitopes which may be presented is dependent upon host class I HLA types. As such, reversion may occur after transmission due to changes in viral fitness and selection in the context of a new HLA background. Thus, parameters describing the dynamics of CTL escape and reversion are key to understanding how CTL responses within individuals relate to HIV-1 sequence evolution in the infected host population. Escape and reversion can be studied directly using biological assays and longitudinal viral sequence data, or indirectly by considering viral sequences across multiple hosts. Indirect approaches include tree based methods which detect associations between host HLA and viral sequence but do not estimate rates of escape and reversion, and ordinary differential equation (ODE) models which estimate these rates but do not consider the dependency structure inherent in viral sequence data. We introduce two models which estimate escape and reversion rates whilst accounting for the shared ancestry of viral sequence data. For our first model, we lay out an integrated Bayesian approach which combines genealogical inference and an existing epidemiological model to inform escape and reversion rate estimates. Using this model, we find evidence for correlation between escape rate estimates across widely separated geographical regions. We also observe a non-linear negative correlation between in vitro replicative capacity and escape rate. Both findings suggest that epistasis does not play a strong role in the escape process. Although our first model worked well, it had some key limitations which we address in our second method. Notably, by making a series of approximations, we are able account for recombination and analyse very large datasets which would be computationally infeasible under the first model. We verify our second approach through extensive simulations, and use the method to estimate both drug and HLA associated selection along portions of the HIV-1 genome. We test the results of the model using existing knowledge, and determine a collection of putative selected sites which warrant further investigation. Finally, we find evidence to support the notion that the CTL response played a role in HIV-1 subtype diversification.

Left/right (L/R) asymmetries, differences in morphology between the otherwise mirrored left- and right-hand sides of the body, are found in animals across the Bilateria. For many years it was thought that the mechanisms for establishment of these asymmetries had evolved separately in the three superphyla that constitute the Bilateria, but the discovery in 2009 that the TGF-beta ligand Nodal shares a conserved role in the Deuterostomia and Lophotrochozoa has re-ignited debate and interest in this field. In this thesis, work examining the establishment and maintenance of L/R asymmetries in the lophotrochozoan superphylum is presented, aimed at uncovering the wider conservation of these pathways across the Bilateria. Illumina sequencing and a range of de novo assembly techniques were used to derive genomic and transcriptomic data respectively for two primary model organisms, the limpet Patella vulgata and the serpulid annelid Pomatoceros lamarckii. Additionally, collaborative work lead to the derivation of transcriptomes for two other mollusc species and the genome of the monogont rotifer Brachionus plicatilis. A range of analysis was performed on these novel resources and is detailed here, with particular reference to the transcription factor cassettes contained in these datasets. These sequence resources formed the basis for examination of the breaking of initial symmetry in these model organisms. Known read-outs of correct establishment of L/R asymmetry, the expression of genes Nodal and Pitx on the right of the body, were codified in the course of normal development in P. vulgata. Pharmacological inhibitors of genes implicated in the establishment of L/R asymmetry, particularly ATPase ion channels, were then applied to embryos. After development, markers of normal development were assayed for signs of bilateral inversion. Although radialised phenotypes were observed, it is unclear whether these are specifically the result of L/R asymmetry defects. The localisation of ATPase mRNA and serotonin, often posited as a small molecule potential morphogen, were also assayed, although no conclusions could be drawn as to a role in the establishment of L/R asymmetry for these molecules, counter to some evidence from vertebrates. Once symmetry is broken, the TGF-beta pathway is responsible for the communication, specification and maintenance of tissue identity across the L/R axis. The novel sequence resources described in this thesis provided a comprehensive window into this signalling cassette, and detailed here is a treatment of the TGF-beta pathway within the Lophotrochozoa. Ligand diversity has increased markedly in some clades, while signal transduction and regulatory steps are relatively unchanged. This work has increased our knowledge of lophotrochozoan biology and particularly the mechanisms underpinning the establishment of asymmetry in this under-researched clade, however, much remains to be discovered about the ultimate origin of asymmetry itself.

Fundamental to the complexity of the nervous system is the precise regulation in space and time of the production, maturation, and migration of neurons in the developing embryo. This is eloquently seen in the forming cranial sensory ganglia (CSG) of the peripheral nervous system. Placodes, which are transient pseudostratified neuroepithelia in the surface ectoderm of the embryo, are responsible for generating most of the neurons of the CSG. Placodal progenitors commit to the neuronal fate and delaminate from the epithelium as immature, multipolar neuroblasts. These neuroblasts reside in a staging area immediately outside the placode. Differentiation of the neuroblasts is intimately coupled to their adoption of a bipolar morphology and migration away from the staging area to the future site of the CSG. Thus the forming CSG is a highly tractable model to anatomically separate the three phases of a neuroblast’s lifetime: from neuroepithelial progenitor (in the placode), to immature neuroblast (in the staging area), to mature neuron (in the migratory stream). In this thesis, I used the forming CSG as a model to investigate the role of Regulator of G protein Signalling 3 (RGS3) in neuroblast commitment and differentiation. Promoters within introns of the RGS3 locus generate isoforms in which N-terminal sequences are sequentially truncated, but C-terminal sequences are preserved. Intriguingly, I found that expression of these isoforms in the forming CSG is temporally co-linear with their genomic orientation: longer isoforms are exclusively expressed in the progenitor placode; a medium isoform is expressed exclusively in the neuroblast staging area; and the shortest isoforms are expressed in the neuronal migratory stream. Furthermore, through loss- and gain-of-function experiments, I demonstrated that each of these isoforms plays a specific role in the differentiation state in which it is expressed: placode-expressed isoforms negatively regulate neurogenesis; the neuroblast-expressed isoform negatively regulates differentiation; and the neuron-expressed isoforms negatively regulate neuronal migration. The negative regulatory role which all isoforms play in different cell-biological contexts is intriguing in light of the fact that they all share a C-terminal RGS domain, which canonically negatively regulates G protein signalling. Through domain mutation and deletion, I showed that the RGS and N-terminal domains are important for the function of each isoform. Thus temporally co-linear expression within the RGS3 locus generates later-expressed isoforms which lack the regulatory N-terminal domains of the earlier-expressed isoforms, giving them new license to perform different biochemical functions. Lastly, I investigated the conservation and evolution of RGS3 and its isoforms. RGS3 was found to be present in all extant metazoans, and results from this thesis implicate it as the founding member of the R4 subfamily of RGS proteins. Furthermore, in the early vertebrate lineage, a critical domain was lost. This is intriguing in light of the fact that placodes in their stereotypic forms also emerged early in the vertebrate lineage. Ectopic overexpression of the full-length invertebrate RGS3 protein prevented pseudostratification of the vertebrate placode, suggesting that the domain loss in the early vertebrate lineage was important for the evolution of pseudostratified placodes and the expansion of the vertebrate nervous system. In summary, the work in this thesis has uncovered a previously unseen model of transcriptional regulation of a single locus: intragenic temporal co-linearity. Furthermore, the demonstrated functions of this regulation have profound implications on the generation and differentiation of vertebrate neurons, as well as the evolution of the vertebrate nervous system.

Antibiotic resistance is generally associated with a cost in terms of reduced competitive fitness in the absence of antibiotics. Despite this 'cost of resistance', the cessation of antibiotic treatment does not result in significant reductions in the prevalence of resistance. The maintenance of resistance, in spite of the costs, has been attributed to the rarity of reversion mutations, relative to compensatory mutations at other loci in the genome. However, the large size of bacteria populations, and the potential for migration, suggest that reversion mutations should occasionally be introduced to resistant populations. In this thesis, I show that additional mechanisms can prevent fixation of reversion mutations even if they do occur. Using an experimental evolution approach, with rifampicin resistance in Pseudomonas aeruginosa as a model system, I measured the costs of resistance in several environments and followed the adaptive dynamics of resistant populations where a sensitive lineage had invaded by migration. The results suggest that several additional mechanisms contribute to the maintenance of antibiotic resistance. Most rifampicin resistance mutations are not unconditionally costly in all environments, suggesting that migration between environments could maintain a resistant reservoir population. In environments where resistance is initially costly, the fixation of a revertant is not guaranteed, even if introduced through migration. Revertant fixation was impeded or prevented by clonal interference from adaptation in the resistant strain. Revertants that did successfully replace the resistant strain were forced to adapt to do so. Contrary to assumptions in the existing literature, fitness in the resistant strains was not recovered by general compensatory mutations, but instead by adaptive mutations specific to the environment. The data challenge several assumptions about the maintenance of antibiotic resistance: that resistance mutations are always costly, that the rarity of back mutations prevents the reversion of resistance, and that resistant strains recover fitness by compensatory mutations.

The first draft sequence of the human genome was published over a decade ago, yet interpreting the functional importance of nucleotides in genomes is still an ongoing challenge. I took a comparative genomic approach to identify functional sequence using signatures of natural selection in DNA sequences. Mutations that are purged or propagated by selection mark sequences of significance for biological fitness. I developed and refined methods for estimating the quantity of sequence constrained with respect to insertions and deletions (indels) between two genome sequences, a quantity I termed αselIndel. This sequence is evolving more slowly than surrounding neutral sequence due to the purging of deleterious indel variants, and thus this sequence is likely to be functional. I estimated αselIndel between diverse mammalian and avian species pairs, and found a strong negative correlation between αselIndel and the divergence between the species’ genome sequences. This implies that functional sequence turns over rapidly as it is lost and gained over time. I quantified the variable levels of sequence constraint, and rates of sequence turnover, for different types of human biochemically annotated element. Furthermore, I found that similar rates of functional turnover have occurred across mammalian and avian evolution. Finally, I identified positively selected amino acid residues that may be important for Darwin’s finch beak development, and found evidence of adaptively evolving reproductive proteins in the ancestral songbird lineage. Collectively these results demonstrate the wide-spread nature of lineage-specific functional sequence with implications for understanding species traits and the use of model organisms to inform human biology.

DNA methylation is an epigenetic modification that plays an important role in development and differentiation. The patterns of DNA methylation are largely established in early embryogenesis and maintained during development. Abnormal DNA methylation patterns have been associated with many human diseases, including cancer. Despite its importance, little is currently known about the mechanisms that determine DNA methylation patterns throughout the genome. To shed light on the molecular mechanisms that regulate DNA methylation, this study investigates whether DNA methylation patterns are established and maintained normally when human DNA is placed into a heterologous murine environment as opposed to its natural, endogenous chromosomal environment. Here, a previously generated transgenic mouse model, containing 117 kb of human DNA bearing the human α-globin cluster and all of its known regulatory elements, was analysed. The pattern of DNA methylation of the endogenous human α-globin cluster was compared with that of the transgenic cluster in the background of mouse embryonic stem cells (ESCs) and tissues. It was found that, although the normal human DNA methylation pattern was largely established and maintained in a mouse background, the region immediately around the human α-globin genes themselves is generally less methylated in mouse compared to human ESCs. It was found that regions adjacent and up to 2kb from the CpG islands (CGIs), so-called CGI shores, were unusually hypomethylated: this seems to be the result of an extension of CGIs in humanised mouse (hm) ESCs compared to human (h) ESCs. Furthermore, this hypomethylation appeared to increase during development in both erythroid and non-erythoid cells. To identify any cis-regulatory sequences responsible for the hypomethylated state of human CGI shores in the mouse, 2-4 kb human test sequences containing the CGI associated with the human α-globin 2 (α2) gene and its adjacent hypomethylated shore were re-integrated into the mouse α-globin locus via recombination-mediated cassette exchange (RMCE). Human CGI shores became hypomethylated in the context of the re-integrated test sequences, indicating that the appearance of hypomethylation is determined by the underlying human DNA sequence in the test fragments. In summary, the data presented here reveal that human CGIs become extended when placed in a mouse background leading to hypomethylation of human CGI shores in the mouse compared to the pattern of methylation at the normal endogenous human locus. These findings suggest that species-specific factors determine DNA methylation near CGIs. The transgenic mouse model provides an excellent system to dissect out species-specific regulation of CGI shore methylation. Furthermore, this study lays the foundation for future experiments addressing the role of DNA methylation in regulating human gene expression in the murine context, and examining the validity of transgenic mouse models for the study of human gene regulation.

From a Darwinian perspective, both history and environment are causal factors for change in animal social behaviour. Because behaviour leaves no fossil evidence researchers have focused on how social systems help animals and humans adapt to their current environments and have only been able to make tentative suggestions about how such systems may have evolved. However, a new theoretical framework, based on Darwin’s insights, allows phylogenetic relatedness to be incorporated into comparative analyses to discover the ancestral states of social behaviour and the ultimate drivers of change in human and primate societies. This thesis uses these new methods to investigate the history and drivers of change in human and primate sociality and proposes a new model of primate social evolution. Analyses of mating systems suggest that social monogamy in humans and other primates is the result of infanticide risk brought about by life history changes. These methods were also able to reveal how changes in inheritance rules to matriliny among Bantu-speaking societies, contributed to a switch to matrilocal residence, which in turn contributed to a change from polygynous marriage to monogamy. Cultural history effects change in both descent and residence patterns, while geographical proximity also affects descent, but residence and environmental factors drive changes in marriage. This approach may provide a way for the various schools for the study of human and primate social behaviour to collaborate more closely and provide ultimate answers to the drivers of change in human society.

A critical mechanism underpinning current biological diversity is the extent to which one species mates with, or avoids mating with, another. However, little is known about the factors that mediate hybridisation, especially during the initial and rarely observed stages of secondary contact when interspecific interactions have not responded to selection. In particular, whilst hybridisation is ultimately a behavioural phenomenon, the role of behaviour in mediating hybridisation and how it is influenced by environmental and circumstantial factors is rarely investigated. Recently introduced species provide us with unequalled opportunities to study these factors. In this thesis I examine the role of behavioural mechanisms, in particular male-male competition and mate choice, in mediating mating patterns between two genetically and phenotypically distinct lineages of European wall lizard (Podarcis muralis) that have come into recent secondary contact through human introductions. In Chapter Two, I investigated how sexual selection during allopatry is responsible for creating stark differences in phenotypic traits such as body size and weapon performance evident in the two lineages today, ultimately explaining the strong biases in dominance during territorial disputes between males. However, I also show that even given this asymmetry in male competitive ability, the extent to which it extrapolates into greater access to females in naturalistic, outdoor enclosures depends strongly on the spatial clustering of basking sites, a critically important resource for many ectotherms. In contrast to initial predictions suggested by asymmetries in male competition outlined in the previous chapter, in Chapter Three I show that both paternity and courtship behaviour was strongly assortative in the outdoor enclosures. Further investigation through staged experiments on olfactory mate choice, mating trials and analyses on specific behavioural data obtained in an enclosure experiment, I show that lineage based dominance actually contributes to assortative mating patterns in conjunction with weak conspecific male choice. In contrast, female choice seems to play no role in mediating the mating patterns observed between the two lineages. In Chapter Four I had the rare opportunity to examine the morphological and behavioural factors that predict why animals should hybridise in the first place, using the data obtained in the enclosure experiment above. I found that hybridisation was particularly common between small individuals of the larger lineage and large individuals of the smaller lineage; a result that corroborates the mechanisms determining the assortative patterns uncovered in Chapter Three. Additionally, hybridisation rates were particularly high in less dominant individuals, which I suggest is due to subordinate males having reduced opportunities for courting conspecific females due to male-male competition, requiring them to become less ‘choosy’ and therefore more likely to mate with heterospecifics. Finally, secondary contact cannot occur without at least one lineage coming into a new environment, and yet relatively little attention is paid to how this environmental change can affect the signals involved in intraspecific communication and mate choice. In Chapter Five I show that a change in the amount of time male lizards spend thermoregulating (a likely consequence of arriving in a new environment) significantly changes the chemical composition of their scent marks. However, whilst female lizards were able to detect these effects, they did not seem to base their mating decisions on them. Nevertheless, this result raises interesting questions about the potential function and consequences of this plasticity, and highlights the importance of considering plasticity in chemical communication in heterogeneous environments. Overall, this thesis shows the critically important role of behaviour in mediating intra- and interspecific mating patterns during recent secondary contact. In particular, it highlights how the direction and extent of hybridisation and competition are influenced by the degree to which differing morphological and behavioural phenotypes interact over a heterogeneous environment, particularly during the initial stage of secondary contact when mate choice has not had the chance to respond to the selective pressures of hybridisation.

This project used a variety of genetic markers to investigate the evolution and population genetics of hydrothermal vent fauna that were recovered from the Scotia Sea, in the Atlantic sector of the Southern Ocean. The origins of one of these species, an undescribed species of Kiwa sp. found on the East Scotia Ridge (ESR) and its constituent family Kiwaidae, a group of vent and seep-associated decapod squat lobsters (infraorder Anomura) was investigated using a concatenated nine-gene dataset and key divergences were dated using fossil calibrations. These results confirm earlier research showing Kiwaidae reside in the superfamily Chirostyloidea, but form a monophyletic clade with the non-chemosynthetic family Chirostylidae and not Eumunididae. Chirostyloid families diverged in the Cretaceous, although extant Kiwaidae radiated in the Eocene, consistent with many other chemosynthetic taxa that appear recently derived. The basal tree position of Pacific species (and the Alaska location of a likely stem-lineage kiwaid fossil) suggests kiwaids originated in the East Pacific. Within a Southern Hemisphere clade, the divergence between the southeastern Pacific K. hirsuta and a non-Pacific lineage (Kiwa sp. ESR and Southwest Indian Ridge kiwaids) is no earlier than 25.9 Ma, consistent with a spread from the Pacific into the Scotia Sea and beyond via now-extinct active ridge connections or mediated by a Miocene onset of the Antarctic Circumpolar Current (ACC) through a newly-opened Drake Passage. This project also investigated the population genetics of three undescribed species found at two vent fields ~ 440 km apart at either end of the ESR: Kiwa sp., a peltospirid gastropod and Lepetodrilus sp. limpets. Lepetodrilus sp. was also found at the Kemp Caldera, a submerged part of the South Sandwich Islands (SSI). Analyses of cytochrome c oxidase subunit 1 (COI) as well as microsatellite loci developed from Roche 454 sequence libraries revealed no differentiation along the ESR for all three species consistent with panmixia, or the dominance of non-equilibrium processes between vent field colonies within a metapopulation, possibly enhanced further by cold-induced arrested larval development. Despite apparent connectivity along the ESR, both COI and microsatellites revealed differentiation between ESR limpets and Kemp Caldera limpets ~ 95 km to the east, possibly owing to the hydrographic isolation of the caldera. Both COI and microsatellite diversity patterns were consistent with recent (< 1 Ma) demographic expansions for all three species (although the influence of selection sweeps on COI cannot be discounted); a pattern observed worldwide at vent communities and may reflect demographic instability over time as a consequence of the stochastic birth and death of vent colonies within a metapopulation. Different COI bottleneck ages between the three species (excluding the influence of possible selection) as well as the absence of kiwaids and peltospirids at Kemp, have been attributed to differences in life history, in particular larval morphology and presumed dispersal strategy. These results highlight the role of larval dispersal of vent fauna along active spreading ridges, both in maintaining vent metapopulations across vent colonies prone to stochastic birth and extinction in the short term, but also in the spread of taxa globally and the formation of biogeographic provinces. The likelihood that the three species presented here exist at vents east of the ESR and SSI, prompts further exploration along ridges in the South Atlantic, in order to investigate the effect of the ACC in enhancing gene flow and delineating biogeographic provinces.

Social behaviour is shaped by complex relationships between evolutionary and ecological processes interacting at different scales. Benefits gained from social associations can range from predator dilution to collective sensing, but little is known about how these can be influenced by social structure and phenotypic composition. In this thesis, I investigated how individual decision-making affects phenotypic social structure, and how this mediates social behaviour through emergent properties of collective group behaviour. First, using mixed-species flocks as a model system, I showed individual tits (Paridae, chapter 2) and thornbills (Acanthizae, chapter 3) varied significantly in their social positions. Within-species variation in network position was as large as between-species variation, sug- gesting that prescribing functional roles at the species level may not sufficiently account for potential differences in fitness operating at the individual level. Rather, this suggested that structure may be driven by phenotypic traits, underpinning network structure (chapter 4). Next, I used an extensive data set of foraging records to explore factors determining the composition, of flocks of great tits (Parus major, chapter 5). For example, assortment by dispersal phenotype (immigration status) was the result of spatial disaggregation, and I showed that this may facilitate social selection for breeding territories (chapter 6). Finally, I investigated how decision-making shaped mixed-species social structure. I found that tits used a common strategy for managing pressures of predation and starvation by shifting from exploration to exploitation at different times of the day (chapter 7). I then found that a very simple interaction rule successfully replicated mixed-species group structure (chapter 8). Strikingly, the same rule was applied to both conspecifics and het- erospecifics, potentially playing an important role in the maintenance of flock structure. Through experimental manipulation of ecological conditions, I found that heightened per- ceived predation resulted in stronger social attraction overall, whereas increased competition led to a reduction in attraction to conspecifics (chapter 9). Simulations suggested this could be one potential mechanism underpinning fission-fusion dynamics in these species. Together, the results in this thesis form a framework linking social behaviour to individ- ual fitness where natural selection is shaped by the social environment. This approach may prove useful for testing whether following common social rules reduces variance in benefits accrued by individuals, and how within-species variation in social behaviour can impact emergent properties of groups.

Understanding the transmission dynamics of infectious diseases is important to well-informed public health policy, responsive infection control and individual patient management. The on-going revolution in whole-genome sequencing provides unprecedented resolution for detecting evidence of recent transmission and characterising population-level transmission dynamics. In this thesis, I develop and apply evolutionary approaches to investigating transmission, focusing on three globally important pathogens. Hepatitis C virus (HCV) is a major cause of liver disease affecting 150 million people and killing 350,000 annually. I conducted a meta-analysis of twentieth-century HCV epidemics, finding that the age of the epidemic can be predicted by genetic diversity. Using the coalescent, I fitted classic susceptible-infected (SI), susceptible-infected-susceptible (SIS) and susceptible-infected-recovered (SIR) epidemiological models. Most epidemics showed signatures of SI dynamics, but three, from Argentina, Hong Kong and Thailand, revealed complex SIR dynamics. Norovirus is the leading viral cause of diarrhoea, estimated to cost the NHS around £115 million annually. I analysed whole norovirus genomes via a stochastic transmission model, finding that up to 86% of hospital infection was attributable to transmission from another patient in the hospital. In contrast, the rate of new introductions to hospital by infected patients was extremely low (<0.0001%), underlining the importance of ward management during outbreaks. Campylobacter is the most commonly identified cause of bacterial gastroenteritis worldwide. I developed a zoonotic transmission model based on phylogeography approaches to test whether three strains previously associated with multiple host species were in fact aggregates of strongly host-restricted sub-strains, or genuine generalists. Members of the same strain isolated from different host species were often more closely related than those isolated from the same host species. I estimated 419, 389 and 31 zoonotic transmissions in ST-21, ST-45 and ST-828 respectively, strongly supporting the hypothesis that these strains are adapted to a generalist lifestyle.

Transcription factors of the helix-loop-helix (HLH) gene family are widespread in the animal kingdom. Among them, members of HLH subfamilies such as ASCL, Neurogenin, NeuroD, COE, Atonal, Oligo, NSCL, Hairy/E(spl) and Hey (here referred to as neural HLH genes) have been shown to be fundamental for the development of the nervous system. They are expressed at different time periods of neuronal differentiation, from the specification of ectoderm towards a neural lineage, to the ultimate differentiation of neurons. Few HLH genes have been identified in the lamprey; however, considering the wide diversity of HLH gene subfamilies in metazoans, including vertebrates, it is very likely that lampreys possess a large repertoire of HLH genes in their genome. In the present study, the identification of several HLH genes in the lamprey genome, as well as the isolation and expression of different lamprey neural HLH genes is reported. As expected, a wide repertoire of HLH genes was identified in the sea lamprey (Petromyzon marinus) genome. On the other hand, the identification and expression analysis of different neural HLH genes of the ASCL, Neurogenin, COE and Hairy/E(spl) in the brook lamprey Lampetra planeri showed an overall conservation with other vertebrates, both at the sequence and expression pattern levels. In addition, novel features of the lamprey nervous system are revealed, such as the identification of possible new sensory cranial placodes in pharyngeal arches. Furthermore, these genes can serve as molecular markers for different cranial placodes and dorsal root ganglia (DRG), and their expression also highlights the presence of a ventricular zone in the brain and spinal cord, along with a complementary marginal zone. Finally, with the use of a Notch pathway inhibitor in developing L. planeri embryos, the regulation of expression of the isolated genes by the Notch signaling pathway was shown to be generally conserved between lampreys and gnathostomes in the spinal cord. This functional study also revealed that the lamprey spinal cord likely presents an independent developmental programme from the brain. All together, the present study shows that the analysis of neural HLH genes represents an excellent tool to understand the lamprey nervous system.

In under 6 decades dengue has emerged from South East Asia to become the most widespread arbovirus affecting human populations. Recent dramatic increases in epidemic dengue fever have mainly been attributed to factors such as vector expansion and ongoing ecological, climate and socio-demographic changes. The failure to control the virus in endemic regions and prevent global spread of its mosquito vectors and genetic variants, underlines the urgency to reassess previous research methods, hypotheses and empirical observations. This thesis comprises a set of studies that integrate currently neglected and emerging epidemiological, ecological and evolutionary factors into unified mathematical frameworks, in order to better understand the contemporary population biology of the dengue virus. The observed epidemiological dynamics of dengue are believed to be driven by selective forces emerging from within-host cross-immune reactions during sequential, heterologous infections. However, this hypothesis is mainly supported by modelling approaches that presume all hosts to contribute equally and significantly to the selective effects of cross-immunity both in time and space. In the research presented in this thesis it is shown that the previously proposed effects of cross-immunological reactions are weakened in agent-based modelling approaches, which relax the common deterministic and homogeneous mixing assumptions in host-host and host-pathogen interactions. Crucially, it is shown that within these more detailed models, previously reported universal signatures of dengue's epidemiology and population genetics can be reproduced by demographic and natural stochastic processes alone. While this contrasts with the proposed role of cross-immunity, it presents demographic stochasticity as a parsimonious mechanism that integrates, for the first time, multi-scale features of dengue's population biology. The implications of this research are applicable to many other pathogens, involving challenging new ways of determining the underlying causes of the complex phylodynamics of antigenically diverse pathogens.

Centrioles and basal bodies with their characteristic 9&plus;2 structure are found in all major eukaryotic lineages. The correlation between the occurrence of centrioles and the presence of cilia/flagella, but not centrosome-like structures, suggests that the ciliogenesis function of centrioles is ancestral. Here, it is demonstrated that the centriole domain of centrosomes emerged within the Metazoa from an ancestral state of possessing a centriole with basal body function but no functional association with a centrosome. Centrosome structures involving a centriole are metazoan innovations. When an axoneme is still present but no longer fully functional, such as the sensory cilia of Caenorhabditis elegans or, as depicted here, the flagellum of the intracellular amastigote stage of the Leishmania mexicana parasite, the basal body structure is less constrained and can depart from the canonical structure. A general view has emerged that classifies axonemes into canonical motile 9&plus;2 and noncanonical, sensory 9&plus;0 structures. This study reveals this view to be overly simplistic, and additional axonemal architectures associated with potential sensory structures should be incorporated into prevailing models. Here, a striking similarity between the axoneme structure of Leishmania amastigotes and vertebrate primary cilia is revealed. This striking conservation of ciliary structure, despite the evolutionary distance between Leishmania and mammalian cells, suggests a sensory function for the amastigote flagellum. Adding weight to a sensory hypothesis, close examination of Leishmania positioning inside the parasitophorous vacuole revealed frequent contact between the flagellum tip and the vacuole membrane. A sensory function could also explain the retention of a flagellum in Trypanosoma cruzi amastigotes, an intracellular stage that, as shown in this study, emerged independently to the Leishmania amastigote. Basal body appendages, such as pro-basal bodies and microtubule rootlets, also vary widely in their structure. Choanoflagellates, a sister group to the Metazoa, posses an extensive microtubule rootlet system that provides support for their characteristic collar tentacles. This atypical structure is reflected in the underlying molecular components of the choanoflagellate basal body. The importance of choanoflagellates as the closest known relative of metazoans was first revealed by their similarity to choanocytes, the feeding cells of sponges. Although phylogenetic analyses leave little doubt that choanoflagellates are a sister group of animals, comparisons of molecular and structural components of appendages associated with the collar tentacles highlight significant differences and questions the extent to which the collar structures of choanoflagellates and choanocytes can be assumed to be homologous. Finally, the confinement of a centriole-based centrosome to the Metazoa provides little support for the flagellar synthesis constraint as an explanation for the origin of multicellularity. There is, indeed, an apparent constraint; no flagellated or ciliated metazoan cell ever divides. This constraint, however, did not arise until after the incorporation of centrioles into the centrosome in the metazoan lineage and the co-option of centrioles as a structural and functional component of the centrosome. The flagellar synthesis constraint is therefore not an explanation for the origin of multicellularity but a consequence of it.

Understanding the unequal distribution of life on earth is a fundamental goal of ecology and evolutionary biology. Past efforts to explain large-scale patterns in diversity have tended to focus on two broad classes of explanation, one invoking the importance of abiotic factors (i.e. climate and vegetation) and the other biotic (i.e. competition); but neither has proven entirely adequate. Parasites are a major but poorly understood component of life that may offer some answers. Yet despite widespread theoretical support and some empirical evidence, the role of parasites in explaining patterns in the diversity, distribution, and abundance of species remains largely untested in natural communities. In this thesis I use a mega-diverse elevation gradient of birds as a model system to study the role of avian malaria in explaining these macroecological patterns. In the first data chapter I tested the extent to which patterns of infection across species is predictable. I found that the effects of host ecology and environment were weakly related to infection prevalence and were not consistent across different malaria lineages. Instead, I show that hosts coexisting with many close phylogenetic relatives consistently experience higher infection than evolutionarily distinct host species. In the second chapter I tested if parasite sharing may help explain these observed relationships and show that parasite sharing among host pairs declines with the time since divergence. Spatial contiguity between host pairs was also positively associated with parasite sharing. In the third chapter I tested how infection prevalence varies across species ranges in accordance with expected variation in host abundance. I show that birds are more likely to be infected at the centre of their elevation range, where host abundance is expected to be highest. Intriguingly, I also found that the incidence of host infection is unrelated to the position within the geographic range of the parasite. In the fourth data chapter, I tested whether parasites may regulate diversity by limiting geographic ranges of their hosts through ‘apparent competition’ in which a non-lethal parasite in a primary host, may be lethal in a secondary host. In support of this, I found that more observed bird ranges end at parasite infection zones than would be expected by chance. Taken together, my results suggest that parasites may play a major role in shaping patterns in the distribution and diversity of species, over both ecological and evolutionary scales. This is likely to arise and be maintained by host parasite interactions in which distantly related hosts are less likely to be infected by local parasites than close relatives, thus promoting the build up of diversity locally. On the basis of my analyses, I conclude that across montane elevation gradients in birds, and across diversity gradients more generally, parasites are likely to play a crucial role in the origin and maintenance of high biological diversity.

This thesis focuses on the population dynamics of three antigenically diverse RNA viruses: dengue, influenza and HIV-1. It comprises a set of studies highlighting the roles of structural constraints on critical antigenic determinants, interactions between immune responses to different antigenic types, host lifespan, and the degree of mixing between different host populations in determining the epidemiology and within-host dynamics of these pathogen systems. Dengue exists in humans as a collection of four antigenically related serotypes. Although infection by one serotype appears to convey life-long protection to homologous infection, it is believed to be a risk factor for severe disease manifestations upon secondary, heterologous infection due to the phenomenon of Antibody-Dependent Enhancement (ADE). It is not clear if third or fourth infections are possible, and if so, how they contribute to dengue epidemiology. In this thesis, I investigate the effect of third and fourth infections on the transmission dynamics of dengue. By contrast with dengue, human influenza viruses are known to be in rapid antigenic flux, manifesting in the sequential replacement of antigenic types. This pattern of evolution does not appear to be the same in shorter-lived hosts such as swine and birds. In this thesis, I have used a simple multi-locus model to explore the relationship between host lifespan and viral evolution, as well as to elucidate the effects of transmission between hosts of different lifespan in effort to capture the cross-species element of influenza transmission. My final chapter concerns the within-host evolution of HIV-1. I propose a new model for the pathogenesis of HIV-1 where the transition to AIDS is primarily linked to the gradual loss of the ability to make new antibody responses as the CD4+ population declines. Together these studies emphasise that it is the changing profile of immune responses – either at the population level or within the host – that is the principal determinant of the dynamics of the pathogen, rather than the mode and tempo of antigenic innovation.

Characterising and understanding factors that affect the rate of molecular evolution in proteins has played a major part in the development of evolutionary theory. The early analyses of amino acid substitutions stimulated the development of the neutral theory of molecular evolution, which later evolved into the nearly neutral theory. More recent work has lead to a better understanding of the role selection plays at the molecular level, but there is still limited understanding of how higher levels of protein organisation affect the way natural selection acts. The investigation of this question is the central aim of this thesis, which is addressed via the analysis of selective pressures in secondary protein structures in insects, mammals and fungi. The analyses for the first two groups were conducted using publically available datasets. To conduct the analyses in fungi, genome sequence data from the fungal genus Microbotryum (sequenced in our laboratory) was assembled and annotated, resulting in the development of a number of bioinformatics tools which are described here. The fungal, insect and mammalian datasets were interrogated with regard to a number of structural features, such as protein secondary structure, position of a site with regard to adaptively evolving sites, hydropathy and solvent-accessibility. These features were correlated with the signals of positive and purifying selection detected using phylogenetic maximum likelihood and Bayesian approaches. I conclude that all of the factors examined can have an effect on the rate of molecular evolution. In particular, disordered and hydrophilic regions of the protein are found to experience fewer physiochemical constraints and contain a higher proportion of adaptively evolving sites. It is also revealed that positively selected residues are ‘clustered’ together spatially, and these trends persist in the three taxa. Finally, I show that this variation in adaptive evolution is a result of both selective events and physiochemical constraint.

This work aimed to investigate the evolutionary origin of the involvement of the HIF Prolyl Hydroxylases (PHDs) in oxygen sensing. The α/β-heterodimer HIF (Hypoxia Inducible Factor) is a master regulator of oxygen homoeostasis in metazoans. In the nucleus, HIF binds to the Hypoxia Responsive Elements and forms a transcriptional complex that activates the transcription of a multitude of downstream genes. Under normoxic conditions, the Fe(II)- and oxygen-dependent PHDs catalyse 4R-prolyl-hydroxylation of the HIF α-subunit, which subsequently leads to its degradation. It had previously been proposed that the evolution of the HIF-pathway, shared by all metazoans but not found in other organisms, is linked to the rapid diversification of multicellular life during the Cambrian Explosion. This work investigates the structural and biochemical properties of a PHD of the basal metazoan Trichoplax adhaerens (taPHD), and a PHD-like enzyme of the protist Monosiga brevicollis (mbP4H). Two crystal structures of taPHD were obtained (1.2-1.3 Å), one containing a Trichoplax adhaerens HIFα subunit peptide (taODD). Comparison with crystal structures of human PHD2 showed a high degree of conservation of structural features and enzyme-substrate interactions. The prolyl-residue of taODD, shown to be hydroxylated by taPHD, is occupying the C4-endo conformation in the crystal structure, supporting the previously proposed mechanism of HIFα hydroxylation by PHD2 in humans. A conservation of biochemical properties with human PHD2, such as the formation of a stable enzyme-Fe(II)-2OG complex, was observed and could therefore be key to oxygen sensing by the PHDs. mbP4H was shown to catalyse 4R-prolyl-hydroxylation of taODD. It was proposed that the native substrate of mbP4H is a protein containing a prolyl-hydroxylation site similar to taODD, possibly with a YXXLAP motif. The study of biochemical properties and substrate selectivity of mbP4H suggests that the precursor of PHDs may have had similar properties to mbP4H. Further work on mbP4H could therefore yield clues about the evolutionary origin of HIF-prolyl hydroxylases in oxygen sensing and probe the previously proposed connection between metazoan life and HIF–mediated oxygen sensing.

Following their dispersal out of Africa, humans colonised all continents of the world save one, Antarctica. Whilst Europe was initially peopled soon after this exodus, paleoclimatic, archaeological, and historical evidence suggest that successive waves and migrations of people have contributed to the population resident in Europe today. I therefore examined the impact of past events on the European population through the analysis of DNA sampled both from contemporary Europeans, and from worldwide populations pertinent to its history. I genotyped and analysed data from the Y chromosomes of over 2,000 haplogroup R-M269 European men from over 30 different populations and, in combination with comparable datasets gathered from the literature, show that there it is not possible to assign a date to the origin of this lineage in Europe, and thus that any conclusion as to the ancient or recent spread of this lineage in Europe is unfounded. I also show that commonly used Y chromosome lineage dating techniques based on STR variation are biased by the markers used and conclusions based on such dates should be viewed with a large amount of caution. I next use genome-wide SNP data from 1,550 individuals from 95 worldwide populations to explore the population structure of Europe and present an analysis of the detailed structure of Europe in a novel analytical framework using ChromoPainter and fineSTRUCTURE. Admixture analysis based this data reveals distinct genomic inputs to peripheral European populations, from North Africa, Sub-Saharan Africa, the Middle East, and East Asia, and provides dates for this admixture within the last 1,000 years that correspond to the emergence and decline of empires and kingdoms in these regions of Europe. This novel analysis highlights the importance of recent historical events on European population structure, but also suggests a degree of ancient structure across European populations. Taken together, these analyses demonstrate the substantial effects of both ancient and recent migrations and mixture on the contemporary genetic structure of Europe.

The study of sex allocation is one of the most successful areas in evolutionary biology: its theoretical predictions have been supported by experimental, observational and comparative approaches. Here, I develop sex allocation theory as follows: (1) I use fertility insurance theory to predict the sex ratio strategy of the malaria parasite, in response to human medical interventions that increase mortality and decrease fertility of the parasite’s various sexual stages; (2) Haplodiploidy has been suggested as a driver of the evolution of eusociality, as under this genetic system a female may be more related to her sister than to her own offspring. I examine a model considering queen versus worker control over the sex ratio of the colony and show that haplodiploidy alone does not explain the evolution of helping; (3) I follow up this study of the haplodiploidy hypothesis by examining the idea that split-sex ratios may favour the evolution of eusociality in haplodiploid species. I study the two mechanisms of split sex ratios, that are found in natural populations and may have been important in the transition to eusociality: queen virginity and queen replacement. I focus on the impact of worker reproduction by considering the effect of woker producing a fraction of the colony offspring and by considering variation in the workers’ offspring sex ratio. My analysis shows that worker reproduction does not promote the evolution of helping in haplodiploid species; (4) I examine the evolution and function of a sterile soldier caste in parasitoid wasps from the genus Encyrtidae. Two main functions have been hypothesized for the emergence of soldiers: spiteful mediation of a sex ratio conflict in mixed-sex broods, and altruistic protection and 7 facilitation of the development of relatives. I develop a model considering variation in the oviposition behaviour of females, that may produce single-sex or mixed-sex broods. I show that, in accordance with previous theory, females are expected to produce more soldiers than males, under the sex ratio conflict hypothesis. I also show that one of the consequences of this costly conflict is that females are favoured to produce single-sex broods over mixed-sex broods.

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.

Brood parasitic birds lay eggs amongst the clutches of other species, which then assume all costs of parental care on their behalf. This thesis addresses several puzzles of avian brood parasitism, using field studies and theoretical modelling of the generalist parasite, the shiny cowbird (Molothrus bonariensis) and select hosts in Argentina. Key findings and conclusions were: • High parasitism intensity in a host population can result in a cost to hosts of removing parasite eggs from their clutches, and so help to maintain host’s acceptance of parasite eggs in evolutionary equilibrium. The cost is to host egg survival: hosts that remove parasite eggs from the clutch increase the risk that their eggs are destroyed by subsequent parasites that visit the nest. • The principal benefit of mobbing as a front-line defence of hosts may be to reduce egg loss due to parasite attack, rather than prevent parasitism itself. • Differences in the acoustic structure of begging calls between parasites and their host’s young can be to the parasite’s advantage. Parents provisioned unparasitized broods more during broadcast at the nest of shiny cowbird calls than calls of their own species’ chicks, in both a common host and a non-host. The long tremulous quality of a cowbird’s call functions analogously to a rapid call rate, thereby exploiting a common provisioning rule of avian parents. • A trade-off for maximum growth in parasite nestlings will variously favour or not favour the evolution of nestmate-killing behaviour, depending on a parasite’s abilities, relative to host young, to solicit and attain provisions from host parents. Generalist parasites can encounter both sides of the trade-off in different hosts. Meanwhile, indirect fitness costs are unlikely to constrain the evolution of nestmate-killing in shiny cowbirds, as they rarely, if ever, share the nest with siblings.

Novel infectious diseases in humans are of great concern to public health authorities and researchers in epidemiology. Zoonotic pathogens in particular have the potential to cause epidemics without any or little warning. In this thesis, I investigate evolutionary and environmental conditions, and the interactions between both, which facilitate the zoonotic emergence of novel pathogens. I start with a list of the mechanisms and processes which might influence a zoonotic emergence, and identify some unsolved problems. I address these with multiple, theoretical models. First, I use a village-city model with different adaptation scenarios to examine the influence of spatial heterogeneity on the emergence process. I derive general analytical results for the statistical properties of emergence events, including the probability distribution of outbreak sizes. My results suggest that, for typical connection strengths between communities, spatial heterogeneity has only a weak effect on outbreak size distributions, and on the risk of emergence per introduction. Next, I extend the research on environmental conditions by looking at pathogen specialisation in multi-host systems. I derive threshold connectivities for which generalist pathogens, which infect multiple species and might therefore be more dangerous to cross into the human species, can sustain transmission and are not dominated by specialists, which can only cause sustained transmission chains in a single host species, but are able to cause emergences with little warning. My third research chapter is interested in the effect of the loss of biodiversity. I analytically derive expected prevalences for fast growing and slow growing species. If fast growing species tend to perform better in degraded environments, my analytical results suggest that the overall prevalence level of infectious diseases will rise as environments degrade, which facilitates the chance of zoonotic jumps. In my last research chapter, I examine the actual impact of a novel, emerging infectious disease. I use data from the recent `Swine flu' epidemic in England to estimate epidemiological parameters of the infectious agent. My results suggest that the majority of infected cases showed no or only mild symptoms. This reveals that more data than just the estimated number of cases are necessary to fully evaluate the danger of a possible zoonotic, emerging infectious disease. I conclude by discussing my results and the implications which these might have.

Streptococcus pneumoniae (the pneumococcus) is a bacterial pathogen responsible for >1.6 million annual deaths globally. Pneumococcal penicillin-resistance is conferred by acquisition of ‘altered’ penicillin-binding protein (pbp) genes. The first penicillin-nonsusceptible pneumococci were identified in the late 1960s. Global pneumococcal penicillin-nonsusceptibility rates rapidly increased in the 1980s/90s. Since 2000, protein-conjugate vaccines, targeting 7, 10 or 13 of the ≥94 different pneumococcal capsule types (serotypes), have been introduced in many countries. Following vaccine implementation there has been a decline in vaccine-type pneumococcal disease and an increase in non-vaccine-type disease. These epidemiological changes result from “serotype replacement” and/or “serotype switching”. The former describes the expansion of non-vaccine-type clones in the absence of vaccine-type pneumococci. The latter describes serotype change following recombination at the capsule polysaccharide synthesis (cps) locus. To fully understand how pneumococci respond to vaccine- and antibiotic-induced selective pressures, we must better understand the evolutionary history of this pathogen. This thesis describes the study of a global collection of 426 pneumococci, dated 1937 - 2007. Serotype, genotype and penicillin-susceptibility data were collected. Nucleotide sequences of three pbp genes (for 389 isolates) and whole-genome sequences (for 96 isolates) were also generated. The data demonstrated the long-term persistence of certain clones within pneumococcal populations, and that pbp and large-fragment (>30 kb) cps ± pbp recombination was occurring prior to both widespread antibiotic use and vaccine implementation. The data highlighted the promiscuous nature of the globally-distributed PMEN1 clone and its contribution to the spread of pneumococcal penicillin-resistance. PMEN1 also donated multiple, large regions (1.7 - 32.3 kb) of its genome to at least two un-related clones. Finally, six “Tn916-like” genetic elements, conferring resistance to non-penicillin antibiotics, were newly identified. These included two of the oldest ever described. These results provided a unique insight into the history of pneumococcal evolution and the importance of genetic recombination.

Human populations in Africa have high levels of genetic, cultural and linguistic diversity. Despite this, only a small proportion of African populations have been studied from a genetics perspective. There is a particular dearth of information for Southern Africa, even though this region is one of the few places where hunter-gatherer, pastoralist and farmer populations remain, and where interaction between these groups can be studied. This thesis analyses novel populations from Lesotho, Namibia and South Africa, for both maternal and paternal markers, in order to provide a more accurate understanding of the history of this region. Analysis of biodemographic data for these populations highlights signatures of specific cultural traits. Interestingly, contrary to expectations, results indicate that in the patrilocal Basotho there are no differences in within and between area mtDNA and NRY variation, despite observations of a higher female than male migration rate. Females move preferentially at shorter distances than males, minimising the impact of the higher female migration rate. Further analysis of the Southern African samples indicates that the genetic composition of these populations is different to previously studied populations from Sub-Saharan Africa. Notably, there is a significantly higher maternal hunter-gatherer component, potentially as a result of an archeologically defined static frontier which existed along the Maloti/Drakensberg escarpment. Analysis of Namibian samples provides additional information about the history of populations with different lifestyles in the region, with support for a link between Southern Africa pastoralists and East Africa, while other Namibian populations appear genetically different from previously studied populations. Overall, this work demonstrates the diversity of populations in Southern Africa, improves understanding of the history of this region, and also emphasises the value of having access to geographically and ethnically well-defined samples.

Understanding the genetic basis of fitness differences has been a major goal for evolutionary biologists over the last two decades. Although there are many studies investigating how natural selection can promote local adaptation, few have succeeded to find the link between genotype and fitness of the phenotype. Polymorphic genes of the major histocompatibility complex (Mhc) are excellent candidates for such associations as they are a central component of the vertebrate immune system, playing an important role in parasite resistance, and hence can have direct effects on survival of their bearers. Although associations between Mhc and disease resistance are frequently documented, the epidemiological basis of the host-parasite interaction is often lacking and few studies have investigated the role that Mhc genes play in individual variation in fitness; thus comparatively little is known about the fitness consequences of Mhc in wild populations. Furthermore, the majority of work to date has involved testing associations between Mhc genotypes and disease. However, the mechanism by which any direct selection on the Mhc acts, depends on how genotypes map to the functional properties of Mhc molecules. The aim of this thesis was to characterize Mhc alleles in terms of their predicted functional properties and to investigate whether and how selection operates on Mhc class I functional variation using the great tit (Parus major) population at Wytham Woods as a model host species. Through a comprehensive characterization effort and the use of 454 pyrosequencing platform, I performed a detailed analysis of genetic variation at Mhc class I exon 3 and grouped alleles with similar antigen-binding affinities into supertypes to classify functionally distinct Mhc types. There was extreme complexity at the Mhc class I of the great tit both in terms of allelic diversity and gene number. A total of 862 alleles were detected from 857 individuals; the highest number yet characterized in a wild bird species. The functional alleles were clustered into 17 supertypes; there was clear evidence that functional alleles were under strong balancing selection. To understand the role of Mhc in disease resistance, I examined the linkage between Mhc supertypes, Plasmodium infection and great tit survival, and showed that certain functional variants of Mhc confer resistance to two divergent Plasmodium parasite species that are common in the environment. I further investigated the fitness consequences of functional variation at Mhc, using mark-recapture methods and long-term breeding data; and tested the hypotheses that selection: (i) maximizes Mhc diversity; (ii) optimizes Mhc diversity, or (iii) favours specific functional variants. I found that the presence of three different supertypes was associated with three different components of individual fitness: adult survival, annual recruitment probabilities and lifetime reproductive success. In contrast, there was no evidence for a selective advantage of Mhc functional diversity, either in terms of maximal or optimal supertype diversity. Finally, I explored the role that Mhc plays in female mate choice decisions and examined the reproductive fitness consequences of Mhc-dependent mating patterns. There was little evidence to suggest that functional dissimilarity at Mhc has any influence on female mate choice decisions or that dissimilarity at Mhc affects the reproductive output of the social pair. Overall, this thesis provides strong support for the suggestion that selection favours specific functional variants of Mhc, possibly as a result of supertype-specific resistance or susceptibility to parasites that exert strong selective pressures on their hosts; whereas there is no support for selection favouring maximal or optimal Mhc diversity. More importantly it demonstrates that functional variants of Mhc class I loci are an important determinant of individual fitness in natural populations.

In this thesis I apply new sequencing technologies and analytical methods derived from genomics and computer science to the neuroanatomy of gene expression. The first project explores characteristics of gene expression across adult neocortical layers in a representative mammal – the mouse. Amongst the thousands of genes and transcripts differentially expressed across layers, I found common functional characteristics of genes that define certain layers, candidate cases of isoform switching, and over a thousand apparent long intergenic non-coding RNA transcripts. The second project compares patterns of gene expression in the structurally diverged adult derivatives of the pallium in mice and chickens. Overall, gene expression levels were moderately correlated between the two species. While expression patterns of ‘marker’ genes were only poorly conserved in these regions, there nevertheless was significant conservation of cross-species marker genes for homologous structures, cell types and functionally analogous regions. Many aspects of these data from both projects can now be easily browsed and searched from custom-built web interfaces. In addition to generating unprecedented genome-wide resources for the neuroscience community to explore the functional and structural dimensions of gene expression amongst different pallial regions in mammals and birds, this work also provides new insights into the widespread evolutionary shuffling of adult marker gene expression.

Not all transcribed DNA encodes protein, and some of these noncoding RNAs (ncRNAs), such as roX1 and roX2, may play important roles in the cell. The functional roles of the majority of these, however, remain largely unknown. In this thesis, I first used EST and mRNA evidence to define 2,788 lincRNA loci within the Drosophila melanogaster genome. I suggest that up to 1,652 of these are functional, as 1,411 show evidence for significant evolutionary constraint while 241 fast-evolving loci are enriched in short RNA species. A distinct set of 1,119 lincRNA loci were defined by RNA-seq, the vast majority of which show clear primary sequence constraint. Their expression profiles and enrichment in particular chromatin domains indicate that these lincRNAs are likely involved in developmental regulation. I also identified 42 potential analogous lincRNAs with shared genomic locations between Drosophila and mouse. Constrained, non-embryonic lincRNAs defined by ESTs are transcribed preferentially in the vicinity of protein-coding genes encoding transcription factors and I demonstrated that one of these, which I name dEvf-2, positively regulates the expression of its genomically adjacent transcription factor, Dll, in cell culture. Finally, I used a reverse genetics approach to search for lincRNA promoter mutations and examined the effect of these on lincRNA expression. My findings suggest that many, previously unknown, functional lincRNAs exist within the Drosophila genome and are worthy of further in-depth experimental investigation.

I develop social evolution theory to study the evolution of cooperation as follows: (1) Many organisms undergo a dispersal phase prior to breeding; I demonstrate that knowing ones dispersal status aids the evolution of helping (by non-dispersers) and harming (by dispersers). (2) Policing driven by group-benefits may be selected to enforce cooperation in human and animal societies. I extend existing theory to show that policing may be harder to evolve that previously thought, but that it is maintained more readily than it evolves. (3) Archeological and anthropological evidence suggests that warfare was prevalent during our evolution. I show that, contrary to previous suggestions, between-group competition can favour any social behaviour (pro-social or anti-social) so long as it helps the group compete, and that such traits can be altruistic or mutually beneficial. (4) Reproductive leveling is analogous to policing; in the human literature there is doubt as to whether it can evolve. I extend my previous work to consider the coevolution of culturally and genetically inherited traits for reproductive leveling and selfishness. I find that cooperation can evolve between non-kin if they share the same culture. (5) Monogamy is thought to favour the evolution of cooperative breeding. I show that in the simplest case, because of the cost of competition between non-dispersing siblings, the level of promiscuity has little or no effect on the evolution of cooperation. (6) Spatial structure (limited dispersal) is thought to favour the evolution of inter-specific mutualisms as it aligns the partners’ interests. I consider the case of plant-fungi mutualisms and show that spatial structure can disfavour cooperation if it limits the potential fungal partners available to the plant.