The genomic substrate for adaptive radiation in African cichlid fish

In African lakes, cichlid fishes are famous for large, diverse and replicated adaptive radiations. Nearly 1,500 new species of cichlid fish evolved in a few million years when environmentally determined opportunity for sexual selection and ecological niche expansion was met by an evolutionary lineage with unusual potential to adapt, speciate and diversify. The phenotypic diversity encompasses variation in behaviour, body shape, coloration and ecological specialization. The frequent occurrence of convergent evolution of similar ecotypes suggests a primary role of natural selection in shaping cichlid phenotypic diversity.

To identify the ecological and molecular basis of divergent evolution in the cichlid system, David et al. [1] sequenced the genomes and transcriptomes of five lineages of African cichlids, Pundamilia nyererei (endemic of Lake Victoria); Neolamprologus brichardi (endemic of Lake Tanganyika); Metriaclima zebra (endemic of Lake Malawi); Oreochromis niloticus (from rivers across northern Africa); Astatotilapia burtoni (from rivers connected to Lake Tanganyika). These five lineages diverged primarily through geographical isolation, and three of them subsequently underwent adaptive radiations in the three largest lakes of Africa. Authors comprehensively investigate the features from these massive genomic data. Here is some interesting finding:

Accelerated gene evolution was assessed by non-synonymous/synonymous ratio. Compare with stickleback fish, O. niloticus has significant higher ranks. And three gene, a ligand (bmp4), a receptor (bmpr1b) and an antagonist (nog2) in the BMP pathway, all known to influence cichlid jaw morphology, show accelerated rates of protein evolution in haplo-chromine cichlids.

East African cichlids, including O. niloticus, possess an unexpectedly large number of gene duplicates. The author found 280 duplication events in the lineage leading to the common ancestor of the radiations. And that was 4.5- to 6-fold increase in gene duplications relative to other clades, normalizing by the branch length. But again, same as high dN/dS analysis, there is no significant enrichment for particular gene pathway.

For the transposable elements insertion in different lineage, the authors claimed that there were three waves of TE insertions. And the TE inserted near the 5’ UTR increased gene expression significantly. Surprisingly, none of the five cichlid genomes showed any deficit of sense-oriented LINE insertions, which correspond to a time of transposable element insertions in the common ancestor of the haplo-tilapiine cichlids. This suggests that ancestral East African cichlids went through an extended period of relaxed purifying selection.

For people who interested in small RNA, the authors also found surprising excess number of novel microRNA emerge in cichlid and with wet lab experiment confirmation, these novel miRNAs were believed to alter gene expression in multiple organs.

Last but not the least, they also did a lot of population genetic analysis in closely related species of the genera Pundamilia, Mbipia and Neochromis, all of which are endemic to Lake Victoria. Because Lake Victoria is where the most recent radiation happened. Several hundred endemic species emerged within the past 15,000–100,000 years. Their results from Fst comparing suggests that (1) variation in coding sequence is most likely to be involved in the divergence of physiological and/or terminally differentiated traits like color; (2) regulatory variation is more important in morphological changes involving genes that have pleiotropic effects in developmental networks.


Sometimes with massive interesting point, it is hard to get the simple answer for the ultimate question, why some species diversify so dramatically, some species did not. Here is the case for cichlid, which they try to address the question of what is the genomic substrate for adaptive radiation. The author’s conclusion is neutral and adaptive processes both make important contributions to the genetic basis of cichlid radiations.


  1. Brawand D, Wagner CE, Li YI, Malinsky M, Keller I, Fan S, Simakov O, Ng AY, Lim ZW, Bezault E, Turner-Maier, J. Johnson J, Alcazar R, Noh HJ, Russell P, Aken B, Alföldi J, Amemiya C, Azzouzi N, Baroiller J-F, Barloy-Hubler F, Berlin A, Bloomquist R, Carleton KL, Conte MA, D’Cotta H, Eshel O, Gaffney L, Galibert F, Gante HF, et al.: The genomic substrate for adaptive radiation in African cichlid fish. Nature 2014.