I have analysed data from nuclear and mitochondrial DNA sequence data in gallwasps and reviewed rare large-scale mutational changes in animals, in an attempt to understand their utility for phylogenetic analysis. Analysis of the sequence data led to the identification of fast and slow-evolving loci for insect phylogenetics. Review of published data on rare large-scale mutations (or Rare Genomic Changes - RGCs for short) suggested that RGCs are likely to be useful and low-homoplasy phylogenetic markers. Using DNA sequence and allozyme data, I studied the phylogeography and post-Pleistocene range expansion of two widely distributed European oak gallwasp species, <i>Andricus quercustozae </i>and <i>Biorhiza pallida. </i>Patterns of genetic diversity in these species have been shaped by their association with their obligate hosts, the oaks (both species), and by the bacterial endosymbiont <i>Wolbachia </i>(<i>B. pallida</i>). These studies revealed the existence of multiple distinct European and Anatolian refuges and suggested that the species’ post-glacial distribution range has been determined by the presence/absence of specific oak species in central and northern Europe. Using mitochondrial DNA sequence data, I generated a phylogeny of the various European gallwasp genera, verifying the existence of various conserved clades and suggesting that many species are non-monophyletic due to lineage sorting of ancestral polymorphisms and / or hybridisation. For a subset of this phylogeny - the genus <i>Andricus</i> - the evolution of shift(s) in the sexual generation oak hosts and host organs galled were analysed, using additional nuclear data. Finally, I surveyed member species of most gallwasp tribes for infection with the bacterial endosymbiont <i>Wolbachia</i> and showed that: (i) the prevalence of <i>Wolbachia</i> differs between lineages with different reproductive modes; (ii) <i>Wolbachia</i> is not associated with thelytoky in the cyclical parthenogenetic gallwasp lineage (in contrast, thelytoky in herb and rose gallwasps is, most likely, <i>Wolbachia-</i>induced); and (iii) horizontal transfer of <i>Wolbachia </i>is likely to have occurred between gall-inducers and their associated inquilines.

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This thesis has three major aims: (i) to utilise phylogenetic approaches to address a specific set of phylogeographic questions; (ii) to develop bioinformatics methods; and (iii) to improve understanding of the evolutionary history of the Western Palaearctic oak gallwasps and oak inquilines. A review of the literature on Western Palaearctic phylogeography reveals that relatively few studies address the aims of longitudinal phylogeography. Within these studies, an emerging pattern of eastern origin of widespread Western Palaearctic taxa is identified and further investigated using the oak gallwasps as a model system. Eastern origins are identified in three widespread species of oak gallwasp, with a common timescale of origin approximately corresponding to the onset of the Pleistocene. Model-based trait mapping techniques are adopted for phylogeographic reconstruction, and a model reduction technique is developed that allows directions of longitudinal range expansion to be inferred. Given the potential importance of longitudinal phylogeographic concordance, a direct comparative method is proposed to allow quantitative comparison of intraspecific phylogenies. A further method is developed to allow consistent sets of molecular taxa to be identified across multiple genes, allowing DNA bar-coding to be applied to identify taxa in situations where data are missing for some genes in some samples, which should facilitate longitudinal phylogeography where morphological taxonomy is unresolved. This thesis resolves some of the outstanding issues in the oak gallwasp and oak inquiline research. Cryptic lineages are identified in areas to the east of Europe, highlighting the importance of these areas as cradles of oak gallwasp diversity. The potential for human activity to alter longitudinal phylogeographic patterns is demonstrated for the oak gallwasp <i>Andricus kollari,</i> whose gals were historically important in trade. The scale of this trade is illustrated by the transfer of an entire phylogeographic clade into the UK from its region of origin to the east of the Mediterranean. Molecular taxonomy of the oak inquiline Synergini is shown to be inconsistent with the current morphological taxonomy, which will require extensive revision.

Extreme variation exists in hypotheses of the taxonomy, systematics and phylogeny of the phylum Nematoda. That nematodes are important and require a unified systematic approach is not in doubt; of the organisms that are not nematodes, few can avoid their influence one way or another. The vast majority of nematodes are free-living and although they have significant impact on the composition of the biota, have little measured direct impact on humans and thus remain largely unidentified. A notable exception is the model organism <i>Caenorhabditis elegans,</i> of which more is known than possibly any other eukaryote. Other nematodes, most notably parasites of plants and animals, have received widespread attention. In between, lie a myriad of life-history, developmental, ecological, structural, and functional relationships waiting to be resolved. This requires phylogeny. The data used to infer this phylogeny must itself be unified from all available reliable sources. In this work, current molecular tools combined with analytical observation are used to address some important junctures in nematode evolution. These are assessed in terms of temporal and spatial radiations inferred by SSUrDNA phylogeny. An objective approach to phylogeny is implemented where no <i>a priori</i> assumptions are made on the data. Phylogenies, and underlying evolutionary models are statistically evaluated. Morphological and ecological corroboration for observed phylogenetic patterns is sought. This combined approach is essential to help reconcile taxonomy with a systematic approach based on an effective consolidated phylogenetic perspective. Special reference is made to Strongyloidoidea and the genus <i>Strongyloides</i> in particular for which a strategy for extraction of quality DNA from formalin fixed <i>Strongyloides</i> samples is implemented.

Circadian rhythms in DNA synthesis have been shown to be present in the epithelium of whole chick lenses. These rhythms are a reflection of the mitosing epithelial cells and are strain specific. Three chick strains were studied: By-l, By-2 and N. The results suggest that the cell cycle in L.B. cells is under genetic control. Synchronous cultures of L.E. have been induced in vitro by two different methods: mitotic selection and a cell cycle arrest method. Protein synthesis studies of these synchronised cells showed that no qualitative differences were apparent at different times during the cell cycle. Several instances of quantitative changes were found including an increase in 6-crystallin synthesis during S-phase and an increase in actin synthesis during the transition into S-phase. An increase in newly synthesised actin associated with the membrane was also found at this time. Few other changes in the L.E. cell membrane polypeptides during the cell cycle could be resolved by SLR-polyacrylamide gel electrophoresis. In apparent contrast, differences were found in the lectin binding capacity of L.B. cells during the cell cycle. Binding of all lectins under study was found to be greatest during mitosis. Strain differences were apparent: strains By-1 and By-2 showed greater lectin binding than strain N both during mitosis and interphase. Insulin, foetal calf serum and a retinal extract were found to induce changes in growth rate, cell morphology and crystallin synthesis in L.B. cultures of the 3 strains of chick under study. In all cases strain differences were apparent. The role of external signals to the lens is discussed in the context of lens epithelial cell differentiation.

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