| Summary: | By means of introduction, I look here to vignette the general structure of my thesis and how it represents the body of work conducted over my PhD. Abstracts that more generally place individual pieces of work within the context of the rest of the scientific literature prepend each chapter. Figure 1 describes the projects that I have been involved in, the time periods that work was conducted over and where in this thesis those projects are documented. They detail: • 'The Impact Of Horizontal Gene Transfer (HGT) Upon The Tree Of Life', where I attempt to refute claims that rampant HGT renders ,even the concept of a bifurcating tree of evolutionary relation obsolete. This is presented in Part ii: Chapter 2 & Chapter 3. • 'Evolution Of The Transcribed Human Proteome' in Chapter 4 (Part iii), where I investigate the history of use of structural protein innovation in Homo sapiens using cell-type specific digital expression data from the FANTOM5 consortium. • 'Multicellular Phenotype In Yeast' in Chapter 5 (Part iv), which describes attempts to create a multicellular phenotype of Saccharomyces cerevisiae by directed evolution before extracting nucleic material so as to study. the genetic underpinnings of such behaviour. • 'The Gene Core Of E. Coli' in Chapter 1 (Part i), where I investigate anomalous values for a consensus gene set in the bacterial species Escherichia coli and show that confusion arises from a misunderstanding of the meaning of a significant E-value for popular biological sequence search tools.
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