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Speciation is a process by which 1 population splits into 2 distinct populations that in time acquire reproductive isolation (RI). Interestingly, the speed at which RI is attained can be influenced by several factors. My thesis work focuses on how protein-protein interactions affect this process, either by impeding or expediting the acquisition of RI. Here, I present an analysis of cascading positive selection in a group of centromere associated proteins in the Drosophila melanogaster subgroup. Within this group, there are proteins known to interact with rapidly evolving DNA elements located at the centromere, as well as other proteins. While previous work has shown that proteins binding rapidly evolving DNA elements are prone to rapid evolution, I provide evidence that this cascade of positive selection can further extend to other interacting partners. This group of rapidly evolving proteins provides a prime example of protein-protein interactions driving speciation. I also present evidence of protein-protein interactions impeding the process of speciation. Specifically, this work focuses on the sister species D. yakuba and D. santomea. This species pair is of particular interest because previous work has demonstrated that he mitochondrial genome completely introgressed from D. yakuba to D. santomea replacing the native form. By assessing nuclear genes encoding proteins that interact with mitochondrial proteins in the Oxidative Phosphorylation (OXPHOS) pathway, I have identified specific cases of co-introgression in which nuclear encoded mitochondrial partners have introgressed with the mitochondrial genome to allow for the maintenance of physical function, thus maintaining similarities between species, ultimately impeding the process of speciation.