2.2 Experimental design
To determine how alternative feeding regimes affected gene expression and the cis -regulatory system, we used a benthic diet or pelagic diet to impose a power or speed demand, respectively, on the oral jaw. This experimental design was used in two cichlid species,Tropheops sp. “red cheek” (TRC) and Maylandia zebra (MZ) (Figure 1A-D) to compare species differences in plasticity. Diet treatments for RNA-seq ran for 17 days, and 28 days for ATAC-seq (Figure 1E). The combination of approaches allowed us to examine both differential expression and differential chromatin accessibility between species and environments. That the experiments were performed at two different time-points following the onset of foraging challenges, allowed us to identify loci with effects over extended periods of time.