How genomes evolve through time and how they change in response to selective pressures remains a key area of research in genomics and evolutionary biology. Genome organization is now known to play a significant role in the regulation of expression patterns with significant clustering according to various parameters of gene expression having been reported in all major taxa. In this thesis I present a comprehensive analysis of sex-biased gene expression in the primate genome and show that there is a significant degree of similarity in sex-biased gene expression among neighbouring genes. Whether this clustering of genes with similar expression profiles is functional or instead the result of transcriptional interference with adjacent genes displaying non-functional but significant similarity in patterns of gene expression has only recently started to be addressed. A recent study suggested that although Drosophila melanogaster exhibits significant similarities in gene expression among neighbouring genes, these clusters are not conserved across evolutionary time in the Drosophila lineage. Chapter three of this thesis presents a comprehensive analysis of the conservation of testis overexpressed gene clusters. I show that, as has been found for other Drosophila expression clusters, testis overexpression clusters are also not conserved throughout evolution. Finally, in chapter 4 I present an analysis of allele frequency changes in the Arabidopsis thaliana genome in experimentally selected lines for early flowering under two different growth conditions resembling winter and spring growth seasons. My results reveal widespread changes in allele frequencies in response to selective pressures with a significant degree of parallel changes for independent lines under selection in similar growth conditions. Importantly, from the point of view of conservation crop efficiency efforts, no significant parallel changes were observed when examining the similarity in allele frequency changes across both growth conditions suggesting that adaptation for a particular trait might be only relevant in specific environmental conditions. Together these observations suggest that allele frequencies change on a global scale in response to selective pressures and that while the observed changes are mirrored across replicas in similar environments this is not the case for lines selected under different growth conditions.Overall, the results I present in this thesis provide valuable insights into how gene order relates to gene expression profiles and its functional relevance as well as presenting evidence for patterns of allele changes in response to selective pressures.
|Date of Award||10 May 2015|
|Supervisor||Araxi Urrutia (Supervisor) & Laurence Hurst (Supervisor)|