The central tree metaphor has been challenged over the last couple of decades
with the observation of incongruent trees derived largely from protein-coding genes in
prokaryotic genomes. There are an increasing number of evolutionary processes and
entities that confuse and confound the traditional understanding of evolution. As a
result, these processes and entities are very often omitted from phylogenetic studies
altogether.
In this thesis I attempt to uncover the importance of non-tree like evolution. I
discuss the types of genes that do not adhere to vertical patterns of inheritance such as
fusion genes and mobile genetic elements. Furthermore I explore the alternative of
using network structures in describing the evolutionary history of bacteria.
This thesis recounts two key uses of networks for revealing the less commonly
noted aspects of bacterial evolution. Firstly I present each stage in the development of
a new method for identifying fusions of unrelated genes from conception of the idea,
through the implementation to its application to data. Secondly I use networks of gene
sharing to elucidate patterns of divergence among a group of closely related bacteria
that would have once formed a single species cloud.
These studies reveal an abundance of the types of genes that contradict
traditional tree-thinking and support the notion that a strictly vertical view of
evolution is inadequate when describing bacterial relationships
