Genetic mapping of horizontal stripes in Lake Victoria cichlid fishes: benefits and pitfalls of using of dense linkage mapping in non-model organisms

The genetic dissection of naturally occurring phenotypes sheds light on many fundamental and longstanding questions in speciation and adaptation and is a central research topic in evolutionary biology. Until recently, forward-genetic approaches were virtually impossible to apply to non-model organisms, but the development of next-generation sequencing techniques eases this difficulty. Here, we use the ddRAD-seq method to map a color trait with a known adaptive function in cichlid fishes, well-known textbook examples for rapid rates of speciation and astonishing phenotypic diversification. A suite of phenotypic key-innovations are related to speciation and adaptation in cichlids, among which body coloration features prominently. The focal trait of the present study, horizontal stripes, evolved in parallel in several cichlid radiations and is associated with piscivorous foraging behavior. We conducted interspecific crosses between Haplochromis sauvagei and H. nyererei, and constructed a l...