Efforts to understand genes and genomes are greatly enhanced by evolutionary analyses. Clark’s group combines evolutionary inference with direct experiments to determine the relationships between genes and to reveal the genetic changes underlying adaptation between species. Current projects include identification of coevolutionary signatures between genes that function in a common pathway or complex to infer new genetic interactions and reveal deeper relationships between entire genetic pathways. Clark’s lab has studied the evolving genomes of 18 yeast species and 22 mammalian species, looking particularly at genes that are involved in meiosis and DNA repair. They have found parallel changes, such as acceleration or deceleration, in evolutionary rates among not only genes encoding proteins that physically interact with each other, but also among those that had no direct contact but still participated in meiosis or DNA repair pathways. By tracking complementary rate changes, it could be possible to identify which genes participate in the same important pathways, providing clues to their function.