"More than 150 years after the publication of Charles Darwin’s The Origin of Species, the identification of the processes that govern the emergence of novel species remains a fundamental problem to biology. Why is it that some groups have diversified in a seemingly explosive manner, while others have lingered unvaried over millions of years? What are the external factors and environmental conditions that promote organismal diversity? And what is the molecular basis of adaptation and diversification? A key to these and related questions is the comparative study of exceptionally diverse yet relatively recent species assemblages such as Darwin’s finches, the Caribbean anole lizards, or the hundreds of endemic species of cichlid fishes in the East African Great Lakes, which are at the center of this proposal. More specifically, I intend to conduct the so far most thorough examination of a large adaptive radiation, combining in-depth eco-morphological assessments and whole genome sequencing of all members of a cichlid species flock. To this end, I plan to (i) sequence the genomes and transcriptomes of several specimens of each cichlid species from Lake Tanganyika to examine genetic and transcriptional diversity; (ii) apply stable-isotope and stomach-content analyses in combination with underwater transplant experiments and transect surveys to quantitate feeding performances, habitat preferences and natural-history parameters; (iii) use X-ray computed tomography to study phenotypic variation in 3D; and (iv) examine fossils from existing and forthcoming drilling cores to implement a time line of diversification in a cichlid adaptive radiation. This project, thus, offers the unique opportunity to test recent theory- and data-based predictions on speciation and adaptive radiation within an entire biological system – in this case the adaptive radiation of cichlid fishes in Lake Tanganyika."