The whitefly Bemisia tabaci (Hempitera: Aleyrodidae), is one of most destructive insect pests of agriculture and horticulture worldwide. B. tabaci has an extensive host-plant range, transmits several plant viruses and is a highly invasive species. Managing B. tabaci is therefore extremely problematic and expensive, with a heavy burden placed upon insecticides. Despite a broad spectrum of insecticidal chemistry available for whitefly control, resistance is widespread and insecticide resistance management (IRM) programmes have been introduced to prolong the longevity and efficacy of these compounds. In particular, resistance is commonly associated with two morphologically indistinguishable and invasive populations, known as the B and Q biotypes. The identification of these biotypes using molecular-based diagnostics has become a key feature of IRM programmes. The development of a highthroughput real-time PCR assay which was able to discriminate between B and Q biotypes is described in Chapter 3 of this project. Two major mechanisms of resistance, target-site modification (i. e. pyrethroids and the sodium channel) and enzyme detoxification (i. e. P450-based metabolism of neonicotinoids) have been widely studied in resistant B and Q biotypes of B. tabaci. The evolutionary origins of two 'knockdown resistance' mutations associated with pyrethroid resistance are described in Chapter 4. Furthermore, the neonicotinoid, imidacloprid, is one of the most successful Insecticides registered for B. tabaci; however, reports of resistance are rapidly increasing. The molecular characterisation of imidacloprid resistance in B. tabaci, and in particular, the association of a P450-enzyme (CYP6CM1) with agespecific resistance, is reported in Chapter S. The advancement in our understanding of the molecular mechanisms underlying insecticide resistance is essential to improve management strategies Implemented against this pest.

Within vertebrates the primordial germ cells (PGCs) can either be induced by embryonic signals (known as epigenesis), or predetermined by maternally deposited germ plasm (preformation). Epigenesis is known to be the ancestral mechanism, while preformation has evolved multiple times. Epigenesis has been proposed to enforce a developmental constraint on the evolution of somatic structures that is released in species which acquired preformation. In accordance with this hypothesis, the mesoderm gene regulatory network is conserved between urodeles and mammals, which have retained epigenesis, but has diverged in anurans (preformation). An increase in speciation has also been shown in vertebrates which have acquired preformation. Our aims were to investigate whether the mode of PGC specification associates with the molecular evolution of protein-coding genes. We downloaded all publicly available vertebrate sequences. These were combined with our three novel transcriptomes from axolotl, sturgeon and lungfish. In line with previous analyses, we built 4-taxon trees to investigate the extent of phylogenetic incongruence. This revealed a bias associated with the mode of PGC specification, caused by a significant difference in the rate of evolution. Many genes in species that have acquired preformation are evolving significantly faster than in their sister taxa undergoing epigenesis. These sequences are typically expressed in early development, and are ancient genes with known orthologs at the base of Eukaryotes. Additionally, we show that Oct4 and Nanog, which are crucial for pluripotency, have been lost in taxa using preformation. Therefore our results are consistent with the proposal that developmental constraint, imposed by epigenesis, is released in species undergoing preformation.

In this thesis analytical and simulation techniques are applied to problems in biological evolution. The thesis is divided into four parts. Firstly, chapter two investigates anomalies that occur in the Penna bit-string model of ageing, an influential model of mutation accumulation and selection. These anomalies result in unusual demographic distributions and can lead to the so-called Eve effect. The anomalies are characterised along with their associated demographic distributions. It is argued that the anomalies are similar in nature to the well known first-passage problem. Secondly, chapter three uses evolutionary game theory to investigate the evolution of harmful mating tactics in hermaphrodites. These tactics benefit the function of the sperm donor at the expense of sperm recipient. The model predicts evolutionary stable values of resource allocation between sexual functions, and the level of harm. The analysis provides support for empirical observations and makes predictions about the effects of harmful mating tactics on population evolution. Thirdly, chapter four considers the sustainability of the two main types of sexual reproduction; hermaphroditism and dioecy (male and female individuals). By use of stochastic spatial simulations it is demonstrated that hermaphroditism can have an even greater advantage over dioecy than predicted by mean-field analysis. This result provides support for the observation that hermaphroditism is associated with sedentary species. Finally, chapter five considers the evolution of gynodioecy, a breeding system of plants in which populations consist of hermaphrodite and female individuals. It is both a common and widespread polymorphism, and has been identified in many species of ecological and economic interest. Mean-field calculations and stochastic spatial simulations are used to identify the conditions necessary for gynodioecy to evolve.

Placing our understanding of the function of the immune system into a more natural setting remains a fundamental challenge in biology, particularly how natural variation shapes the immune response and what the evolutionary consequences of such variation are. In this thesis, I use the three-spined stickleback as a model system for wild immunological studies. First, I developed a set of markers to measure the expression levels of key immune system genes using quantitative real-time PCR, representing the innate and adaptive immune response, and then used them to address a number of questions. I demonstrated that there are underlying differences in innate and adaptive gene expression levels between populations, as well as in innate immune response potential, which may reflect the contrasting challenges faced in these populations. By sampling individuals from multiple wild populations, I was able to demonstrate how a range of factors contribute to shaping immune system function, including sex, reproductive status, and infection with the common parasites Schistocephalus solidus and Gyrodactylus arcuatus. Next, I exposed laboratory raised fish to natural conditions and examined their response. Again, a range of factors where identified which appear to shape immune expression levels, particularly reproductive investment and infection with G. arcuatus. I also used this approach to demonstrate that immune system variation can be linked to Eda genotype, the gene which controls lateral plate phenotypic divergence during adaptive radiations. Finally, I performed a controlled infection experiment in the laboratory to show that both the innate and adaptive systems respond to Gyrodactylus infection. This thesis provides the basis for further immunological studies in stickleback, and adds to our growing understanding of the relevance of natural variation in shaping the immune response.