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

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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 genetic novelties, focusing on reproductive tissues, including analysis at the single-cell level. We will then investigate the functions of these novelties in two species using a variety of genetic and biochemical tools, including CRISPR and RNAi to learn about the agents of selection acting on these novelties. Second, we will use population approaches to characterize adaptive transcriptome divergence contributing to local adaptation within species, and transcriptome adaptation over longer timescales between species. We will then use these results to infer the fraction of the transcriptome evolving adaptively for multiple tissues and species. We will use genetic and ATAC-seq experiments to investigate whether convergent expression adaptation generally has a shared genetic basis or whether adaptation generally proceeds by different trajectories in different species.