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 understand themolecularmechanisms underlying cichlid phenotypic diversity,wesequenced the genomesand transcriptomes of five lineages of Africancichlids: theNile tilapia (Oreochromis niloticus), an ancestral lineagewith low diversity; and four members of the East African lineage: Neolamprologus brichardi/pulcher (older radiation, Lake Tanganyika), Metriaclima zebra (recent radiation, LakeMalawi),Pundamilia nyererei (very recent radiation, LakeVictoria), andAstatotilapia burtoni (riverine species around Lake Tanganyika).Wefound an excess of gene duplications in the East African lineage compared to tilapia and other teleosts, an abundance of non-coding element divergence, accelerated coding sequence evolution, expression divergence associated with transposable element insertions, and regulation by novel microRNAs. In addition, we analysed sequence data from sixty individuals representing six closely related species from Lake Victoria, and show genome-wide diversifying selection on coding and regulatory variants, some of which were recruited fromancient polymorphisms. Weconclude that a numberof molecular mechanisms shaped East African cichlid genomes, and that amassing of standing variation during periods of relaxed purifying selectionmayhave been important in facilitating subsequent evolutionary diversification.