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.