This thesis is concerned with the study of dynamical models in evolution for which some provide epidemiological insight. Two approaches are taken; one adopts the perspective of community dynamics, the other of adaptive dynamics. Community dynamics studies evolution via the dynamics of a fixed large number of strains, whilst adaptive dynamics begins by considering how one resident strain may be replaced by an advantageous mutant. The work begins by considering a baseline multi-strain host-pathogen model, and analysing it via a community dynamics approach. The baseline nature of the model allows exact information to be deduced. Obtaining such exact information is rare. Investigations into equilibrium co-existence states consisting of particular allowed numbers of host and pathogen strains are completed. The possibility of stable cycles occurring in these states is investigated. Analyses into the occurrence of contingencies (outcome dependent on initial conditions) between different states whether the equilibria are both point stable or point and sustained oscillations are completed. Investigations into invasion criteria for host and pathogen strains are presented.

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The first comprehensive genetic study of North East Atlantic and Mediterranean sea stars, Asterina gibbosa and Asterina phylactica, is presented here, based on mitochondrial DNA (mtDNA) and Amplified Fragment Length Polymorphism (AFLP) data. MtDNA analysis revealed that the two putative species are distinct however there is incomplete lineage sorting, with the two most common haplotypes being shared across both species. MtDNA revealed low divergence between populations especially among most Atlantic populations, with no significant differentiation between the two basins. Although, both species possessed private haplotypes within both basins, the most common haplotype within both species is found throughout the entire geographical range of both species. Two mitchondrial haplogroups were identified, both of which showed evidence for a population expansion, occurring during the Pleistocene epoch. Haplogroup 1 was dominated by A. gibbosa (88%) whereas haplogroup 2 was dominated by A. phylactica (84%). The mtDNA results tentatively suggest that one Asterina population may descend from a population that survived the last glacial maximum (LGM) in one or more northern refugium. The AFLP data showed that A. gibbosa and A. phylactica are genetically distinct, with no apparent hybridization between species, with the possible exception of a single individual found at Rovinj, Croatia which was identified as being an A. phylactica individual at the time of sampling, but the allocation test assigned it to the Naples, Italy, A. gibbosa population. This could be the result of introgression or the individual could have been incorrectly classified as A. phylactica at the time of sampling. The AFLP data showed that there is gene flow occurring but it appears to be restricted, particularly within the Mediterranean basin, with no apparent gene flow occurring between the Atlantic and Mediterranean basins. There was no evidence with either marker to conclude that the brooding behaviour of A. phylactica provides a different pattern of genetic diversity within populations or differentiation between populations to the crawl away behaviour of A. gibbosa. The analysis suggests that gene flow is slightly more restricted for A. phylactica than A. gibbosa and, for A. gibbosa, it is more restricted in the Mediterranean than the Atlantic. The study identifies both A. phylactica and A. gibbosa populations that would be suitable to receive conservation status, based upon their unique genetic characteristics.

As one of the five evolutionary forces, recombination fulfills both a cleansing role, as well as a role in generating genetic diversity. Recombination cleanses by separating deleterious mutations from their genomic background, increasing the efficacy of purifying selection and curtailing the continuous accumulation of deleterious mutations. Recombination also plays a fundamental role in the repair of damaged DNA, and it can be a creative force, resulting in the formation of novel genotypes, haplotypes and alleles, thereby playing a key role in adaptive evolution. By uniting beneficial mutations that exist at different loci in separate lineages, meiotic recombination during sex accelerates adaptive evolution. Although recombination leaves a distinct signature or footprint in the genome of organisms, identifying this force can be difficult; subsequent recombination events tend to wipe out their past genomic footprints. This thesis presents the development of a novel software package called HybridCheck, for the detection of genomic regions affected by recombination in Next Generation Sequence data, and the rapid molecular dating of recombination events. Hybrid-Check was used to analyze recombination signal in different races of the plant pathogen Albugo candida, a generalist obligate biotroph that infects Brassica plants. I show that recombination facilitated occasional introgression and gene flow between host-specialized races. This may have accelerated the rate of adaptive evolution, and possibly broadened v the pathogen’s host-range. Finally, the genome of the polar diatom Fragilar- iopsis cylindrus contains diverged alleles that are differentially expressed in different environmental conditions. The hypothesis that ancient asexuality explains how the diverged alleles evolved is challenged, but not rejected, based on evidence of recombination presented in this thesis. An alternative hypothesis is proposed: allelic divergence might have evolved despite the homogenizing effect of meiotic recombination as a result of very large effective population sizes and strong diversifying selection on F. cylindrus in the polar environment.

There are major gaps in our understanding of the evolution of microRNA (miRNA) genes and how this relates to evolutionary changes in metazoan development. miRNAs function as trans-acting post-transcriptional modulators of gene expression. They are implicated in the canalization of development and the consequent provision of evolvability. Here I present data and analyses on miRNA evolution in insects and mammals, both on a phylogenetic scale as well as at the level of individual miRNA genes. I also perform case studies cross-comparing the expression and functions of intronic miRNAs to those of their host genes, and compare tissue-specific enrichment of miRNAs in a specific tissue (butterfly ovary) relative to the whole body. A broad overview of miRNA evolution across a clade is presented for the Lepidoptera using a combination of small RNA sequencing in two lepidopteran species coupled with bioinformatic analysis of available genomic and miRNA data across the clade. This analysis reveals a burst of rapid miRNA gain on the stem lineage of the Lepidoptera prior to the radiation of the diverse butterfly and moth lineages. I also propose that the uneven distribution of miRNA gain across the lepidopteran phylogeny, coupled with observations of high numbers of newly-emergent miRNAs on terminal branches, is evidence for a model of miRNA evolution comprising high rates of turnover for newly-acquired miRNAs with variable rates of stable miRNA retention. In depth examination is carried out on two miRNA genes, both of which occur within homeobox gene introns - eutherian-specific mir-615 and lepidopteran-specific mir-2768. Phylogenetic distribution and theories for the acquisition of mir-615 in Eutheria are considered. A combination of publicly available expression data and epigenetic modification data is used to demonstrate the existence of transcriptional regulation for mir-615 independent from that of its host gene. The study of mir-2768 reveals the first experimental evidence for an intronic miRNA performing a complementary function to that of its host gene. I also present the first miRNA transcriptome from a butterfly ovary and compare this to whole-body miRNA expression in the same species. This provides insights into the roles performed by miRNAs in the butterfly ovary, including conserved functions, and enables comparison of ovarian miRNA tissue specificity relative to time of origin. Overall, this work provides a multi-faceted analysis of miRNA evolution in animals and presents an integrated approach to our understanding of the roles of miRNAs in evo-devo.

A network of interactions between transcription factors and cis-regulatory sequences controls the expression of developmental genes. Changes in either the cis- or trans acting components of a developmental interaction can have consequences for both the output of the interaction and for the greater network of interactions. Thus, the evolution of regulation is considered to be a major force in the evolution of morphological diversity. To investigate the evolution of an interaction, this thesis has compared the Bicoid-dependent regulation of hunchback and orthodenticle expression in the Dipterans, Drosophila melanogaster, Musca domestica, Calliphora vicina, Lucilia sericata and Megaselia abdita. hb genes were isolated from Calliphora and Lucilia and these encode a number of domains that are conserved in hb from other species such as Drosophila, Musca and Tribolium. In contrast to the coding sequences, the hb promoters from Calliphora and Lucilia differ from each other and from the Drosophila and Musca hb promoters in terms of the number, sequence, orientation and spacing of Bed-binding sites that they contain. Analysis of intra-specific variation in the M. domestica hb gene demonstrated that both coding and non-coding sequences are subject to slippage generated turnover of simple motifs and that the extent of this turnover is dependent upon region specific constraints. This suggests that mechanisms of turnover are responsible for the different hb promoter configurations observed in the Dipterans. To investigate any functional consequences of the differences in both bed and hb between Drosophila, Musca and Megaselia, transcription assays were carried out using homogeneous and heterogeneous combinations of these two components in yeast. The results of these assays suggest that differences in Bed and the hb promoters between these species may have co-evolved to maintain the interaction. Therefore, to investigate how other Bed-regulated genes have evolved in Musca, the expression patterns and coding sequences of the otd gene were characterized in Musca and compared to those of Drosophila otd.

Changes in the rate at which biological evolution proceeds are widespread and common. Advancements in methodology make it possible to characterize such historical evolution more accurately and reveal complex scenarios where rates vary among organismic groups and even between individual lineages. The work presented here embraces such complexity, seeking to exploit phenotypic rate variation to reconstruct patterns and processes of evolution deep in time with unprecedented accuracy. Chapters 1 and 2 demonstrate for the first time that it is possible to reveal historical, directional trends in morphology that played out over millions and millions of years using only data from living species. These trends arose as a consequence of rapid and repeated instances of directional evolutionary change and the approach employed to detect them may be the only way to study historical adaptive trends in morphology that cannot otherwise be observed in the fossil record. Where evolution is fastest, natural selection has acted more strongly; this idea is developed further in Chapter 3 which presents a novel way to characterize an exceptional subclass of rates of morphological evolution that can be defined as positive phenotypic selection. In both Chapters 3 and 4 it is shown that such intense episodes of natural selection have punctuated the evolution of diverse groups including plants, dinosaurs and hominins. Chapter 5 demonstrates that it is possible to uncover explicit underlying causes of positive phenotypic selection and takes us one step closer to being able to truly understand the drivers of natural diversity. As a complete work, this thesis harnesses and exploits phenotypic rate heterogeneity to inform inferences about patterns and processes of evolution deep in time and to understand how natural selection has acted to sculpt morphology, giving rise to the diversity we observe today both in living species and the fossil record.

The action of natural selection in establishing barriers to gene flow between populations, or reproductive isolation, is increasingly understood to be a primary driver of speciation and thus biodiversity. ‘Ecological speciation’ is now supported by evidence from numerous studies in a range of natural populations. However, experimental tests of the role of divergent natural selection in the establishment of reproductive isolation are still scant. To address this omission, the role of larval diet in imposing divergent selection and causing ecological adaptation and reproductive isolation was tested. These tests were conducted on the Mediterranean fruit fly (Ceratitis capitata, Wiedemann) (medfly) model system, which has been relatively under-utilised in the experimental study of speciation. Using manipulative experiments and experimental evolution, the three major components of ecological speciation were examined. Firstly a source of divergent selection was established through quantification of the consequences of alteration in specific dietary nutrients during the development of medfly larvae. Following this, similar selective pressures were used as the basis of experimental evolution of medfly populations reared on divergent developmental diets. Divergence between these populations was assayed at several time points during evolution, in real time, using tests for sexual isolation. After 60 generations of experimental evolution a form of reproductive isolation between populations had evolved. The mechanism that may have led to the evolution of this isolation was also explored, through further mating tests, and also the quantification of male courtship behaviour. The genetic basis of the phenotypes associated with adaptation and sexual isolation was explored using transcriptomic sequencing and differential expression analysis of genes expressed in males from the two experimental regimes. A range of candidate genes was identified as differentially expressed, including genes associated with oxidative phosphorylation and chemosensation. Taken together, the results of this research present a novel example of how divergent ecological selection pressure can lead to the evolution of sexual isolation in experimental populations.

Phylogenetics is the study of evolutionary relationships between species. Phylogenetic trees have long been the standard object used in evolutionary biology to illustrate how a given set of species are related. There are some groups (including certain plant and fish species) for which the ancestral history contains reticulation events, caused by processes that include hybridization, lateral gene transfer, and recombination. For such groups of species, it is appropriate to represent their ancestral history by phylogenetic networks: rooted acyclic digraphs, where arcs represent lines of genetic inheritance and vertices of in-degree at least two represent reticulation events. This thesis is concerned with the efficiency, accuracy, and tractability of mathematical models for phylogenetic network methods. Three important and related measures for summarizing the dissimilarity in phylogenetic trees are the minimum number of hybridization events required to fit two phylogenetic trees onto a single phylogenetic network (the hybridization number), the (rooted) subtree prune and regraft distance (the rSPR distance) and the tree bisection and reconnection distance (the TBR distance) between two phylogenetic trees. The respective problems of computing these measures are known to be NP-hard, but also fixed-parameter tractable in their respective natural parameters. This means that, while they are hard to compute in general, for cases in which a parameter (here the hybridization number and rSPR/TBR distance, respectively) is small, the problem can be solved efficiently even for large input trees. Here, we present new analyses showing that the use of the “cluster reduction” rule – already defined for the hybridization number and the rSPR distance and introduced here for the TBR distance – can transform any O(f(p) · n)-time algorithm for any of these problems into an O(f(k) · n)-time one, where n is the number of leaves of the phylogenetic trees, p is the natural parameter and k is a much stronger (that is, smaller) parameter: the minimum level of a phylogenetic network displaying both trees. These results appear in [9]. Traditional “distance based methods” reconstruct a phylogenetic tree from a matrix of pairwise distances between taxa. A phylogenetic network is a generalization of a phylogenetic tree that can describe evolutionary events such as reticulation and hybridization that are not tree-like. Although evolution has been known to be more accurately modelled by a network than a tree for some time, only recently have efforts been made to directly reconstruct a phylogenetic network from sequence data, as opposed to reconstructing several trees first and then trying to combine them into a single coherent network. In this work, we present a generalisation of the UPGMA algorithm for ultrametric tree reconstruction which can accurately reconstruct ultrametric tree-child networks from the set of distinct distances between each pair of taxa. This result will also appear in [15]. Moreover, we analyse the safety radius of the NETWORKUPGMA algorithm and show that it has safety radius 1/2. This means that if we can obtain accurate estimates of the set of distances between each pair of taxa in an ultrametric tree-child network, then NETWORKUPGMA correctly reconstructs the true network.

This thesis is concerned with the major transitions view of evolution; the idea that general principles operate in the evolution of each new level of the biological hierarchy (Bourke, 2011). We discuss the theoretical background of this field, focussing on inclusive fitness theory and multi-level selection theory, different approaches to analysing the selection of traits. Many of the commonalities between different transitions are dependent on whether they occur within or between species, and whether relatedness is absent (`egalitarian') or present (`fraternal') (Queller, 1997). Altruism underpins fraternal transitions, and mutually beneficial behaviour underpins egalitarian transitions (Bourke, 2011). We focus on several different models relating to this four-way decomposition. Firstly, we focus on arguments that between-species donation may amount to between-species altruism; this has been a point of contention within the literature (Fletcher and Doebeli, 2009; Gardner et al., 2011; Wyatt et al., 2013). We discuss both deterministic (resting on an assumption of quasi-linkage equilibrium) and stochastic approaches to a simple model of between-species donation, finding that stable donation behaviour can evolve in the presence of assortment across all loci, but is vulnerable to unassorted modifiers. We argue that this behaviour can be interpreted as within-species altruism, using the other species as a vector for altruism, and, further, consider our models in relation to the current literature on greenbeards. Our second model concerns maternally-transmitted sex-distorting endosymbionts. Many species, particularly insect populations, are infected by sex-distorting parasites such as the bacteria Wolbachia, which are maternally-transmitted; thus, distortion of sex ratios towards the production of females may be beneficial to the symbiont. We investigate the potential for a reproductive parasite to transition towards mutualism, laying the foundation for an egalitarian transition between species; in particular, we find that population structure is key to this transition. Finally, we discuss several potential avenues for future research; in particular, we note that the social group transformation phase of a major transition involves a number of open questions, or ideas open to further investigation.