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Cichlid fishes are famous for large, diverse and replicated adaptive radiations in the Great Lakes of East Africa. To understand the molecular mechanisms underlying cichlid phenotypic diversity, we sequenced the genomes and transcriptomes of five lineages of African cichlids: the Nile tilapia (Oreochromis niloticus), an ancestral lineage with low diversity; and four members of the East African lineage: Neolamprologus brichardi/pulcher (older radiation, Lake Tanganyika), Metriaclima zebra (recent radiation, Lake Malawi), Pundamilia nyererei (very recent radiation, Lake Victoria), and Astatotilapia burtoni (riverine species around Lake Tanganyika). We found 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 from ancient polymorphisms. We conclude that a number of molecular mechanisms shaped East African cichlid genomes, and that a massing of standing variation during periods of relaxed purifying selection may have been important in facilitating subsequent evolutionary diversification.
Wide variation in the rates of diversification among lineages isa feature ofevolutionthathasfascinated biologistssince Darwin1,2.Withapprox- imately 2,000 known species, hundreds of which coexist in individual African lakes, cichlid fish are amongst the most striking examples of adaptiveradiation, the phenomenonwherebya singlelineage diversifies into many ecologically varied species in a short span of time3 (Fig. 1). The largest radiations, which in Lakes Victoria, Malawi and Tanganyika,have generated between 250 (Tanganyika) and 500 (Malawi and Victoria) speciesperlake, took no more than 15,000to 100,000 yearsfor Victoria and less than 5 million years for Malawi3-5, but 10-12 million years for Lake Tanganyika6. The radiations in Lake Victoria and Malawi thus dis- playthehighestsustainedratesofspeciationknowntodateinvertebrates7. The evolutionof these lineagesand their genomes has presumably been shaped by cycles of population expansion, fragmentation and contrac- tion as lineages colonized lakes, diversified, collapsed when lakes dried up, and re-colonized lakes, and by episodic adaptation to a multitude of ecologicalniches coupledwith strongsexualselection. Geneticdiversity withinlake radiations has beeninfluenced byadmixture following mul- tiple colonization events and periodic infusions throughhybridization8,9.
Cichlid phenotypic diversity encompasses variation in behaviour, body shape,coloration andecologicalspecialization.Thefrequentoccurrence of convergent evolution of similar...