Modeling Genome Evolution : Creation, Change and Destruction

Historically, evolution has been studied either by looking at morphological traits in living organisms and the fossil record, or by using bioinformatics and comparative genomics. While highly useful for deducing evolutionary history, these approaches are not particularly well suited for studying the mechanisms of evolution. In order to address such issues, other methods are needed. Mathematical modelling is one of the most powerful options available, and it is the approach used in this thesis. By constructing models of biological systems, the work aims to resolve some of the many unresolved questions regarding evolutionary processes, such as how new genes evolve and how selection acts in fragmented populations. Some answers have been reached, and thus the thesis makes a small contribution to our overall understanding of evolution. The creation of novel genes was studied both directly and by extension of an analogous system, which revolved around reversion of a frameshift mutant. The results pointed to gene amplification as a likely mechanism for both reversion of the frameshift mutant and creation of new genes. Selection in fragmented populations is shown to be effective even when sub-populations, rather than individuals, are competing against each other. Modeling of a system of bacterial symbionts living in aphids indicates that, although the bacterial population within a single host is small and subject to rampant genetic drift, the bacterial population as a whole is regulated by selection on the host level. Thus, deleterious mutations do no accumulate and the population maintains its fitness over time