<p>Understanding the mechanisms that underlie the formation of, and innovation in biochemical pathways is an important goal in evolutionary biology. The following work addresses the problem of biochemical pathway evolution in two ways. In the first chapter, I combine genetic manipulations and population genetic analyses to investigate the whether flux control in the aliphatic glucosinolate pathway of <italic> Arabidopsis thaliana</italic> drives evolutionary rate heterogeneity. My results indicate that the first enzyme in the pathway, CYP79F1, has majority flux control and is the only one to show convincing evidence for positive selection. The second chapter builds on the first by asking whether flux control is stable under a variety of environmental conditions. I find that flux control remains with CYP79F1, in all my environmental treatments. In the final chapter, I address the evolution of one enzyme in this pathway from <italic>Boechera stricta</italic> that is responsible for a gain-in-function polymorphism that results in increased fitness in nature. With molecular phylogenetic analysis, site-directed mutagenesis, structural biology and enzymatic assays, I determine what residues are under selection and test their functional effects. I find that just two mutations in this enzyme are responsible for the change in function, and discuss their position within the enzyme. Strikingly, the enzyme with majority flux control in <italic>A. thaliana</italic> is homologous to the enzyme responsible for the novel function in <italic>Boechera</italic>. Together these results suggest that selection may predictably exploit the same small subset of genes to optimize biochemical pathway output and for evolutionary innovation.</p> / Dissertation