Evolutionary and functional genomics of genetic novelties and expression adaptation in Drosophila

Adaptive transcriptome evolution likely underlies a substantial component of all adaptations. Here I propose to study two main types of transcriptome evolution using Drosophila. First, we will identify transcriptome novelties in Drosophila melanogaster, focusing on reproductive tissues. We will then investigate the functions of these novelties using CRISPR and RNAi to learn about the possible agents of selection acting on them. Second, we will investigate convergent local adaptation at the transcriptome level in two distantly related species, D. simulans and D.hydei, and identify the underlying regulatory basis to determine whether convergent expression adaptation has a shared genetic basis or whether it generally proceeds by different trajectories in different species. Finally, we will carry out a more general investigation of the role of directional selection in driving expression divergence between Drosophila species.