The Evolution of a Transcription Factor: Divergence in DNA Binding Behavior of the Sex-Determination Gene hermaphrodite in the Genus Drosophila

Changes in transcriptional regulatory networks are thought to underlie most morphological change observed across taxa, but the general principles of how such networks change and why remain unknown. While many studies have focused on evolutionary changes in cis-acting components of transcriptional networks (enhancers and transcription factor binding sites), changes in the transcription factor proteins which bind these sites have been mostly overlooked. In this thesis I identify the putative Drosophila transcrtiption factor hermaphrodite (her) as having a highly divergent DNA-binding domain, and examine its DNA-binding profile in two fruitfly species, Drosophila melanogaster and Drosophila pseudoobscura. I find evidence for a large-scale divergence in the distribution of HER binding, as well as a possible difference in DNA-binding preference between these two species. This establishes Drosophila her as an excellent system for the study of regulatory evolution through changes in transcription factors.