It has been a major challenge to resolve the evolutionary relationships (phylogeny) between cichlid species. The difficulty is partly the result of the young age of these species - they diverged fairly recently in evolutionary time, and haven’t acquired the kind and number of genetic differences normally used to build phylogenies. Recently, researchers used next generation genome sequence technology to get around this problem, by essentially gathering an enormous amount of genome sequence data to use for phylogeny-building. The result is perhaps the best resolved phylogenetic tree for such a young group of cichlid species.
Wagner, et.al. - Genome-wide RAD sequence data provide unprecedented resolution of species boundaries and relationships in the Lake Victoria cichlid adaptive radiation.