Extended Data Fig. 9: Fixed and reset methylome variation among wild populations of Lake Masoko A. calliptera cichlids.
From: Epigenetic divergence during early stages of speciation in an African crater lake cichlid fish
a. Plot showing the proportion of fixed versus reset DMRs between each pairwise comparison upon common garden experiment. b. Violin plots showing length in base pair (bp) of fixed and reset DMRs found for each pairwise comparison. y-axis, logarithmic scale. Median lengths for all fixed and reset DMRs are indicated above the graphs. Two-way ANOVA, P < 4.6e-05. c. GO analysis for reset DMRs associated with differentially expressed genes (DEG). d. Methylome profiles of the genes eklf and epoR for wild and common garden (‘Tank’) populations showing reset methylome patterns in benthic fish upon environmental perturbation. e. Example of fixed benthic-specific hypomethylation in an uncharacterised non-coding RNA gene associated with its downregulation in benthic fish only. f-g. Box plot showing gene expression profiles for the genes dpp4 and ces2, associated with fixed benthic-specific methylome patterns. B, benthic; L, littoral; R, river populations, respectively. Box plots indicate median (middle line), 25th, 75th percentile (box), and 5th and 95th percentile (whiskers) as well as outliers (single points).
