Evolution of Mobile Promoters in Prokaryotic Genomes

Mobile genetic elements are important factors in evolution, and greatly influence the structure of genomes, facilitating the development of new adaptive characteristics. The dynamics of these mobile elements can be described using various mathematical and statistical models. In this thesis, we focus on a specific category of mobile genetic elements, i.e. mobile promoters, which are mobile regions of DNA that initiate the transcription of genes. We present a class of mathematical models for the evolution of mobile promoters in prokaryotic genomes, based on data obtained from available sequenced genomes. Our novel location-based model incorporates two biologically meaningful regions of the genome: promoter regions and other sites in the genome. We find the best model to describe the process using model selection techniques and reveal the most influential parameters in this dynamic process. We then compare the dynamics in these two regions of the genome with regards to the rates of four key processes: duplication, loss, diversification and horizontal gene transfer (HGT).