The evolution of genetic networks and gene families

A fundamental challenge in evolutionary biology is to explain the extensive diversity among different species. Because the adult phenotype is the result of an ontogenic process, phenotypic variation must reside in differences generated during development. Surprisingly, animal development relies on a conserved set of gene families and signaling pathways that diversified early in metazoan evolution. The occurrence of gene families, however, raises the questions of how individual members of gene families evolve specialized functions and how the origin of gene duplicates contributes to organismal function and innovation. Further, almost all organismal function is controlled by pathways composed of interacting genetic components, yet the relationship between pathway structure and the evolution of individual components is not completely understood. The main objectives of this dissertation were to (i) clarify the influence of the structure of genetic pathways and networks on the rate of protein evolution, (ii) investigate the hypothesis that transcription factor sequence evolution is highly constrained, (iii) investigate the evolutionary paths leading to functional diversification following gene duplication. The analysis of olfactory pathways in nematodes reveals that selective constraints need to be considered within larger networks. Investigation of transcription factor evolution in the context of the yeast gene regulatory network highlights the role of network structure on protein evolution but indicates that the effect of gene position is dependent on the function of the network under study. Next, the analysis of allelic variation in natural populations illustrates that transcription factors are not as highly constrained as commonly thought. Importantly, this work suggests that the role of divergence of regulatory genes during the evolution of gene regulatory networks requires further attention. Finally, examination of the functional diversification of the FgfD subfamily identifies processes that are likely to be applicable to the evolution of many vertebrate multigene families. The work presented here on the evolution of genetic networks and gene families contributes to our understanding of the origin of phenotypic diversity by expanding the analysis of molecular evolution from the level of single genes to interacting genetic systems.;This dissertation includes previously published and co-authored materials.