Genomics of adaptation and speciation in cichlid fishes: recent advances and analyses in African and Neotropical lineages

Abstract

Cichlid fishes are remarkably phenotypically diverse and species-rich. Therefore, they provide an exciting opportunity for the study of the genetics of adaptation and speciation by natural and sexual selection. Here, we review advances in the genomics and transcriptomics of cichlids, particularly regarding ecologically relevant differences in body shape, trophic apparatus, coloration and patterning, and sex determination. Research conducted so far has focused almost exclusively on African cichlids. To analyse genomic diversity and selection in a Neotropical radiation, we conducted a comparative transcriptomic analysis between sympatric, ecologically divergent crater-lake Midas cichlids (Lake Xiloá Amphilophus amarillo and Amphilophus sagittae). We pyrosequenced (Roche 454) expressed sequence tag (EST) libraries and generated more than 178 000 000 ESTs and identified nine ESTs under positive selection between these sister species (Ka/Ks > 1). None of these ESTs were found to be under selection in African cichlids. Of 11 candidate genes for ecomorphological differentiation in African cichlids, none showed signs of selection between A. amarillo and A. sagittae. Although more population-level studies are now needed to thoroughly document patterns of divergence during speciation of cichlids, available information so far suggests that adaptive phenotypic diversification in Neotropical and African cichlids may be evolving through non-parallel genetic bases.

Figure 1.

Cichlid fishes show a rich array of coloration and behavioural phenotypes that have recently been investigated using genomic and transcriptomic approaches. (a) A breeding pair of Midas cichlids (Amphilophus xiloaensis) from crater Lake Xiloá, Nicaragua. The female has the ‘gold’ (amelanic) coloration and the male shows the typical ‘dark’ coloration of white and black bars. See §1b for more details. Photo credit: Ad Konings. (b) The haplochromine cichlid Paralabidochromis ‘red fin piebald’ from Lake Victoria, Africa, showing (i) a typical orange blotch (OB) phenotype and (ii) a typical white blotch (WB) phenotype. See §1b,c for more details. Photo credit: P. Eriksson. (c) Neolamprologus pulcher is a cooperatively breeding cichlid from Lake Tanganyika. This image shows two helpers-at-the-nest (left) and a breeder female (right). See §1d for more details. Photo credit: J. Desjardins.

Figure 2.

(a) Lake Xiloá is an isolated crater lake in western Nicaragua. Lake Apoyo is a larger and older crater lake to the south. (b) Amphilophus amarillo is a benthic and Amphilophus sagittae a limnetic Midas cichlid species.

Figure 3.

The distribution of Ka/Ks for high-quality ESTs between Lake Xiloá A. amarillo and A. sagittae. Expressed sequence tags with Ka/Ks <1 fall above the grey line.