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However, the large sizes and complexity of most radiations such as those of the cichlids in the African Great Lakes make it impossible to infer the exact evolutionary history of any population divergence event. The genus<jats:italic>Alcolapia,<\/jats:italic>a small cichlid lineage endemic to Lakes Magadi and Natron in East Africa, exhibits phenotypes similar to some of those found in cichlids of the radiations of the African Great Lakes. The simplicity within<jats:italic>Alcolapia<\/jats:italic>makes it an excellent model system to investigate ecological diversification and speciation. We used an integrated approach including population genomics based on<jats:styled-content style=\"fixed-case\">RAD<\/jats:styled-content>\u2010seq data, geometric morphometrics and stable isotope analyses to investigate the eco\u2010morphological diversification of tilapia in Lake Magadi and its satellite lake Little Magadi. Additionally, we reconstructed the demographic history of the species using coalescent simulations based on the joint site frequency spectrum. The population in Little Magadi has a characteristically upturned mouth\u2014possibly an adaptation to feeding on prey from the water surface. Eco\u2010morphological differences between populations within Lake Magadi are more subtle, but are consistent with known ecological differences between its lagoons such as high concentrations of nitrogen attributable to extensive guano deposits in Rest of Magadi relative to Fish Springs Lagoon. All populations diverged simultaneously only about 1100 generations ago. 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