Novel morphological structures have always fascinated scientists. Developmental processes give rise to structures and morphologies that are often functionally necessary for an organism’s survival and reproduction. But how does evolution shape these developmental processes to give rise to new phenotypes? How do these new phenotypes ultimately give rise to new species? And, how do these new phenotypes interact and coevolve between the sexes, particularly in the context of reproduction? Most studies that have focused on the evolution of novel traits focus on the importance of transcription factors and their pathways, and many studies have shown that evolution in regulatory regions and/or coding regions of transcription factors often gives rise to differences between species. In this dissertation, I investigated how novel traits diverge among the four sister species of Drosophila melanogaster and how novel traits are shaped by female sensory variation, focusing on an unconventional candidate. In Chapter 1, I used a genetic introgression line called 4C2(A) to identify genes that are involved in the development of a novel male reproductive structure of the external genitalia of the four sister species. The introgression lines were created by crossing a D. mauritiana male carrying a P-element with a D. sechellia white (w) female and back-crossing it to D. sechellia w male for 15 generations to have a small D. mauritiana region in an otherwise D. sechellia w genetic background. These secondary sexual structures are called epandarial posterior lobes (ePLs) and help the male to grasp the female during mating and ensure a tight genital coupling. Using a series of mapping experiments and functional genetic tests, I identified Allnighter (Aln), a pseudokinase, as a gene that directs the development of ePLs. Using additional functional genetic experiments, I showed that Aln is necessary for specifying ePL size differences among the four sister species. Furthermore, our data showed that Aln had a more prominent role when flies developed under stressful thermal conditions. Specifically, when Aln null individuals developed in higher temperatures, they exhibited an even smaller ePL size and an incomplete genitalia rotation, resulting in upside-down male genitalia. This work suggests the co-option of the cellular stress response pathways can result in divergent morphologies and highlights the role of cellular stress response pathways in evolutionary developmental biology. Most, if not all, traits on the male genitalia are under sexual selection, and no study will be complete without investigating how females respond to and co-evolve with these novel male reproductive traits. Previous studies have shown that when D. melanogaster females mate with males that have smaller or misshapen ePLs, they reduce the number of eggs they lay. In Chapter 2, I studied whether the gene or genes that specify ePLs size and female egg-laying are in the same region or even the same gene. I investigated the effect of the entire collection of available D. sechellia-D. mauritiana introgression lines that had smaller or misshapen ePLs on female egg-laying, with a focus on 4C2(A). We showed that when 4C2(A) females mate with 4C2(A) males, they do not reduce their egg-laying amounts, which suggests that a gene or genes in this region affect the female egg-laying phenotype. I tested the egg-laying amount of Aln null females, and our results show that these females laid significantly fewer eggs compared to the control females. These results demonstrate that Aln specifies not only male genital morphology, but also female reproductive behavior, providing a basis for sexual selection to act on males and females in concordance. These findings have important implications for our understanding of the co-evolution of male and female reproductive traits. In Chapter 3, I delved deeper into the egg-laying phenotype and how females control this key reproductive event. I conducted a literature review and summarized the studies that show how specific neurons, whether from the peripheral nervous system or the central nervous system, modulate the action of egg deposition or the movement of the egg into the oviduct and other phenomena in the egg-laying behavior. Furthermore, by looking at other insect examples, I show that there are more components in the egg-laying behavior that require further study in Drosophila. Neuronal control of egg-laying in Drosophila provides many understudied avenues and has the potential to provide more robust evidence for phenomena like cryptic female choice. In Chapter 4, I further explored how females sense the ePLs during mating and how they regulate their reproductive output/responses as a consequence of variation in ePL morphology. First, I identified candidate sensory neurons on female genitalia at the site where the ePLs make contact with the female during copulation. The candidate neurons I identified are mechanosensory sensilla on the epigynial ventral lobe. Interestingly, these bristles vary in average number among the four sister species. I showed that the neurons attached to the sensilla express Piezo, a mechanoreceptor gene, and are cholinergic. My results showed that Piezo knockout females mate normally but lay significantly fewer eggs compared to control females. On the other hand, although Piezo knockout males sire slightly fewer offspring, the difference in the number of eggs laid by females mated to Piezo knockout males compared to females mated to control males is not significant. Laser ablation of only some of these epigynial sensilla does not affect the female egg-laying output. However, when all of these sensilla were ablated, females laid close to no eggs. Additionally, we showed that axons of these neurons arborize the abdominal neuromere through the main abdominal nerve. The abdominal neuromere houses both motor neurons that modulate the female egg-laying and interneurons that carry the sensory signal to the brain, suggesting that the information carried by the epigynial sensilla neurons has the potential to influence the output of central nervous system neurons. Taken together, these neurons are promising candidates for future studies about sensing ePLs. In summary, my studies showed that the co-evolutionary dynamics between male and female reproductive traits are complex. Variation in peripheral sensory neurons can drive the evolution and diversification of novel traits and change in a gene like Aln not only provides the developmental raw material to diversify the size of the ePLs in the males but also reinforces the egg-laying bias in females.