Mechanisms of genome evolution in flowering plants: Transposable elements and indel-associated mutation

In chapter one I use a phylogenetic approach to show that Helitron transposable elements (TEs) have recently proliferated in the Arabidopsis thaliana genome, that the spread of different Helitron subsets through A. thaliana populations has been checked by varying degrees of natural selection that seem to depend on shared features of these subsets. Helitron proliferation has also led to the close association of several insertions with protein-coding genes.;The second chapter examines the evolutionary consequences of silencing TE insertions by sRNA-directed DNA methylation in the A. thaliana genome. I show that unmethylated TEs are clustered around genes, and that methylated TEs are associated with reduced neighboring gene expression independent of genomic location. Using population genetic data, I show that methylated TEs near genes are subject to weak purifying selection and that their distribution shifts away from genes over evolutionary time, which is corroborated by an examination of the genomic distribution of ancient TE insertions.;The third chapter examines the interrelation between two types of genetic mutation, insertions/deletions and point mutations. Starting from the recent proposal that Heterozygosity at indels can elevate the point mutation rate at nearby nucleotides, I investigate the repercussions of this proposal for populations with differing levels of Heterozygosity arising from differences in the rate of inbreeding.