Lateral gene transfer (LGT) is an important factor contributing to the evolution of prokaryotic genomes. The Aquificae are a hyperthermophilic bacterial group whose genes show affiliations to many other lineages, including the hyperthermophilic Thermotogae, the Proteobacteria, and the Archaea. Here I outline these scenarios and consider the fit of the available data, including two recently sequenced genomes from members of the Aquificae, to different sets of predictions. Evidence from phylogenetic profiles and trees suggests that the ?-Proteobacteria have the strongest affinities with the three Aquificae analyzed. However, this phylogenetic signal is by no means the dominant one, with the Archaea, many lineages of thermophilic bacteria, and members of genus Clostridium and class ?-Proteobacteria also showing strong connections to the Aquificae. The phylogenetic affiliations of different functional subsystems showed strong biases: as observed previously, most but not all genes implicated in the core translational apparatus tended to group Aquificae with Thermotogae, while a wide range of metabolic systems strongly supported the Aquificae - ?-Proteobacteria link. Given the breadth of support for this latter relationship, a scenario of ?-proteobacterial ancestry coupled with frequent exchange among thermophilic lineages is a plausible explanation for the emergence of the Aquificae.

<p>Currently centered on molecular data, bacterial and archaeal relationships are often based on their relative branching in 16S rRNA based phylogenetic trees. The availability of numerous bacterial genome sequences over the past two decades has provided new information for insights previously inaccessible to the field of taxonomy. Through utilization of comparative genomics, numerous molecular markers in the form of insertions and deletions within conserved regions of proteins, also known as Conserved Signature Indels or CSIs, have been discovered for various prokaryotic taxa. Using these techniques, we have analyzed relationships among the bacterial phyla of Thermotogae and Synergistetes and the conglomeration of bacterial organisms known as the PVC super-phylum. Through identification of large numbers of CSIs we have described the phyla Thermotogae and Synergistetes, and their sub-groups, in molecular terms for the first time. The identified molecular markers support a reconstruction of the current taxonomic divisions of these phyla. Similarly, previously only observed to group in phylogenetic trees, we have identified molecular markers for the PVC clade of bacterial phyla which are indicative of their shared ancestry. Further, in response to recent suggestions of extensive lateral gene transfer masking evolutionary relationships, an argument in favour of Darwinian mode of evolution for prokaryotic organisms is made using the identified molecular markers identified here along with markers previously identified in similar studies. Due to their taxonomic specificity, the markers that we have discovered provide useful tools for biochemical tests aiming for an understanding of the unique characteristics of the bacterial groups to which they are specific.</p> / Master of Science (MSc)