Evolutionary Genomics from Ontogeny to Phylogeny

Abstract

<p> Much speculation has been made about the relative importance of changes in developmental regulation of gene expression in determining major phylogenetic patterns observed both in extant and extinct species. However, most of these hypotheses have been formulated based on data obtained from the comparison of very distantly related organisms (e.g., between animal phyla). Another approach to answering questions about development (ontogeny) in the context of evolution (phylogeny) is to observe how developmental patterns diverge between closely related species, in order to obtain a better understanding of the population level processes underlying phyletic change. With the intent of addressing this possibility, the principle work outlined in this thesis investigated patterns of divergence between closely related species of Drosophila at the level of both the nucleotide coding sequence as well as gene expression levels in the context of ontogeny. The results show that the stage during which genes are expressed has a significant impact on their patterns of divergence, acting both to constrain (earlier stages) and accelerate (later stages) their rates of evolution - the latter being largely the result of sexual selection pressure. However, we also find that intermediate stages of fly development, such as metamorphosis, may experience a greater degree of conservation of the elements regulating gene expression than other stages. Nonetheless, we do find evidence that both gene expression and coding sequences may be subject to similar selection pressures, yet there also appears to be substantial uncoupling of the two, as evidenced by our observation of stage-specific, autonomous patterns of hybrid misexpression manifested in interspecific hybrids. The data presented herein shed new light on patterns of divergence between species, specifically with regards to how various selection pressures affect different stages of ontogeny.</p>