Advances in genomics offer new opportunities for identifying loci that behave unusually against a background of neutral variation. Detecting divergent sites among related individuals and taxa can shed light on the process of adaptive divergence, from non-random mating to the establishment of reproductive barriers. Conversely, identifying convergent sites among unrelated taxa can offer insights into deeper level ecological radiations. This project will study genes underpinning evolutionary divergence at several stages. Discovering genome-wide ‘gene outliers’ presents enormous challenges. I argue these can be overcome by combining and applying phylogenetic and evolutionary analyses with deep sequencing to exceptional study systems. Among mammals, bats are unique in having independently evolved laryngeal echolocation and nectarivory, both implicated in their unparalleled adaptive radiation. We will (i) use a novel phylogenomic approach to identify genes under convergent and divergent selection associated with acoustic and dietary diversification. (ii) We will then discover additional loci implicated in diverging incipient sympatric taxa that have undergone recent dramatic call frequency shifts. (iii) We will identify genome-wide loci that show anomalous divergence and non-random combinations between faithfully breeding pairs of bats in a population where outbreeding increases fitness. These complementary studies will produce a database of candidate loci implicated in ecological divergence. We will then verify and synthesize our results by screening the genes in a taxonomically wider range of species. We hope to provide a comprehensive assessment of the relative numbers and importance of different types of loci in multiple stages of evolutionary divergence in a mammalian system. As such these results will significantly extend the current frontier of our knowledge about how new taxa form.