Population genomics of cichlid fish adaptive radiation
Cichlid fishes are famous for large, diverse and replicated adaptive radiations in the Great Lakes of East Africa. To make a start towards understanding what molecular mechanisms may have played a role in the rapid origins of cichlid phenotypic diversity, a large group of cichlid researchers under the leadership of the Broad Institute 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, LakeMalawi), Pundamilia nyererei (very recent radiation, LakeVictoria), Astatotilapia burtoni (riverine species around Lake Tanganyika).
We observed several remarkable and interesting patterns. We saw what seems to be an excess of gene duplications in the ancestor of the East African lineage compared to tilapia and other teleost fishes, an abundance of non-coding element divergence, accelerated coding sequence evolution, expression divergence associated with transposable element insertions, and regulation by novel microRNAs. We analyzed Restriction Site Associated DNA (RAD) sequence data from sixty individuals representing six closely related species from Lake Victoria, and showed that differentiation among these extremely closely related and occasionally hybridizing species affects many regions on all chromosomes, includes coding and potentially regulatory variants, and quite a few of these were recruited from ancient polymorphisms that by far predates the origin of the radiation. We interpret these data as evidence for amassing of standing variation prior to the onset of radiations, possibly associated with periods of relaxed purifying selection. It will be interesting in the future to investigate whether this period of relaxed selection may have been important in facilitating subsequent evolutionary diversification.