The genomic substrate for adaptive radiation in African cichlid fish

Cichlid fishes are famous for large, diverse and replicated adaptive radiations in the Great Lakes of East Africa. To under- standthemolecularmechanismsunderlying cichlidphenotypic diversity,wesequencedthegenomesandtranscriptomes of fivelineages of Africancichlids: theNile tilapia (Oreochromis niloticus),anancestral lineagewithlowdiversity;andfour members of the East African lineage: Neolamprologus brichardi/pulcher (older radiation, Lake Tanganyika),Metriaclima zebra(recent radiation,LakeMalawi),Pundamilianyererei (veryrecentradiation,LakeVictoria),andAstatotilapiaburtoni (riverine species aroundLakeTanganyika).Wefound an excess of gene duplications in the East African lineagecompared to tilapia and other teleosts, an abundance of non-coding element divergence, accelerated coding sequence evolution, expression divergence associated with transposable element insertions,and regulationby novel microRNAs. In addition, we analysed sequence data from sixty individuals representing six closely related species from Lake Victoria, and show genome-widediversifying selectiononcodingandregulatoryvariants,someofwhichwererecruited fromancientpoly- morphisms.Weconclude that anumberof molecular mechanismsshaped East African cichlid genomes, and that amass- ing of standing variation during periods of relaxed purifying selectionmayhavebeenimportantin facilitating subsequent evolutionary diversification.