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.