This hypothesis-driven laboratory exercise teaches how DNA evidence can be used to investigate an organism's evolutionary history while providing practical modeling of the fundamental processes of gene transcription and translation. We used an inquiry-based approach to construct a laboratory around a nontrivial, open-ended evolutionary question about the relationship of five species of "Drosophila". In the course of answering this question, students at the early college biology level learn how the information in DNA can be extracted and used by both the cell and scientists. This dual proximate-ultimate approach introduces students to the techniques of PCR, DNA sequencing, and phylogenetic sequence analysis while simultaneously providing a concrete pen-and-paper model of the cellular processes of transcription and translation. The laboratory has been successfully employed over 3 years with first-year college students and has proven its versatility by being easily adapted to a "dry lab" form with advanced high school students.