Subterranean Fishes of the World

5273

2014

Nature

375-381

513(7518)

Cichlid fishes are famous for large, diverse and replicated adaptive radiations in the Great Lakes of East Africa. To under-stand the molecular mechanisms underlying cichlid phenotypic diversity, we sequenced the genomes and transcriptomesof five lineages of African cichlids: the Nile tilapia (Oreochromis niloticus), an ancestral lineage with low diversity; and fourmembers of the East African lineage:Neolamprologus brichardi/pulcher(older radiation, Lake Tanganyika),Metriaclimazebra(recent radiation, Lake Malawi),Pundamilia nyererei(very recent radiation, Lake Victoria), andAstatotilapia burtoni(riverine species around Lake Tanganyika). We found an excess of gene duplications in the East African lineage comparedto 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 showgenome-wide diversifying selection on coding and regulatory variants, some of which were recruited from ancient poly-morphisms. We conclude that a number of molecular mechanisms shaped East African cichlid genomes, and that amass-ing of standing variation during periods of relaxed purifying selection may have been important in facilitating subsequentevolutionary diversification.

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