Patterns and processes in the evolution of genomic expression

Genomic regulation and expression are key to cellular differentiation, tissue morphogenesis, physiology, and development. Increasing evidence indicates that evolutionary diversity from cellular to organismic phenotypes may also be, in large part, the result of variation in the regulation of genomic expression. The most direct phenotypic outcome of diversity in genomic expression is variation in RNA abundances, including the differential specification of the rate and timing of gene expression between individuals. In particular, understanding how underlying variation in genetic parameters maps into variation that is expressed between phenotypes is of fundamental relevance. This is because such maps mediate the interaction of genomes with the environment and are of fundamental interest in that it may allow the link between natural selection and genome evolution to be made. Hence, gene expression levels may merit detailed analyses of phenotypic evolution and genomic architecture. Here studies were carried out aimed at bridging the gap towards achieving this goal. Chapter 1 reports regulatory effects of diverse Y-chromosomes placed on a common background of autosomes and X chromosome. It adds to the growing number of studies reporting abundant regulatory variation in natural populations. Chapter 2 addresses the relative merits of mutation, genetic drift, directional selection, and stabilizing selection in shaping levels of variation in gene expression. It indicates that stabilizing selection greatly prevents larger levels of gene expression variation between populations. Chapter 3 and 4 report the association between levels of evolutionary variation in gene expression and a number of biological attributes, including protein sequence evolution and protein-protein interactions. It is an initial step towards reconstructing the selective landscape underlying evolutionary variation in gene expression levels. Chapter 5 uses gene expression levels as a model phenotype to test specific hypotheses about patterns of phenotypic evolution. In particular, the underlying causes for the differential robustness of gene expression levels to dramatic changes in genomic background as observed between inbreed parental genotypes are investigated, including the effects of expression networks, and mutational and environmental sensitivities.