Genetic rewiring drives species variation in East African cichlids

What drove the explosion of diversity in an East African cichlid freshwater fish that radiated into more than 2,000 species in the last few million years?

A recent study explores how genetic rewiring – changes in gene regulatory networks (GRNs) at non-coding regions – contributed to the cichlid's rapid adaptation to different ecological niches in East African lakes and rivers.

The work appears in the Jan. 8 journal BMC Genome Biology. The study was led by Sushmita Roy from the University of Wisconsin, Madison, and Federica Di-Palma from the University of East Anglia, Norwich, in collaboration with Earlham Institute, a life science research center, in Norwich.

The researchers note that the surprisingly large number of cichlid species arose from only "one or a few ancestral lineages." Tilapia, a popular food fish, is a one of the more familiar cichlid species.

The study focused on the opsin genes of the cichlid visual system, for which they "report striking cases of network rewiring" to support different functions. They used a novel computation framework, called a computational pipeline, to investigate how cichlid gene regulatory networks became specialized for different environmental niches.

In their case study, the researchers compare gene expression patterns from six particular tissues between five representative East African cichlids to see what changed in the cichlid adaptation to different environments. For a case study, they applied their method to the visual system because it is well-studied.

The researchers hypothesized that species with similar food-foraging habits would "share conserved regulatory genotypes," while species with dissimilar foraging habits would segregate or have different gene regulatory sites. Using a computational pipeline, they analyzed 157,232 genetic sites.

Their results suggest gene co-expression differences, which underpin the variation of traits in cichlids, are due to transcriptional rewiring and alterations in transcription factor binding sites, not mutations in protein coding regions. The study concludes GRN adaption is driven by "discrete changes at regulatory binding sites, and network rewiring events."

In a Norwich Research Park news release on the study, Di-Palma comments: “We have released an impressive amount of expression data which will further aid studies into the adaptive radiation of cichlids for the future. We are now deciphering the complexity of these cis-regulatory regions by using genome-wide CRISPR screens. 

“The wider impact of our regulatory gene network approach will also help inform evolution of agriculturally important traits for tilapia such as growth rate and tolerance to different local water conditions, as well as for general aquaculture and fisheries.”