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This dissertation describes evolutionary patterns of female and male reproductive proteins and their potential contribution to speciation in deer mice (Peromyscus). Proteins involved in reproduction are among the most rapidly evolving genes in many taxa. This striking pattern is of particular interest because reproductive proteins mediate species-specific fertilization, and thus changes in these proteins have the potential to contribute to reproductive isolation. In internally fertilized taxa, knowledge of the evolutionary dynamics of reproductive proteins in closely related species is limited primarily to seminal proteins expressed in accessory glands of Drosophila. Investigation of additional taxa and functional classes of proteins is necessary to determine if there is a general pattern of adaptive evolution of reproductive proteins between recently diverged species. In mammals, positive selection has been documented in …