Fig. 3: Common-garden experiment results in both global resetting of methylome profiles in wild benthic and littoral fish to resemble riverine methylome profiles and inheritance of fixed methylome differences.
From: Epigenetic divergence during early stages of speciation in an African crater lake cichlid fish
a, Heatmap of the average DNA methylation levels (mCG/CG, %) at all DMRs found in wild populations in Fig. 1g for all wild and common-garden fish. Methylome profiles revealed global epigenetic resetting in wild benthic and littoral fish to resemble neighbouring river fish methylome profiles, which were mostly unaffected by environmental perturbation. b, The proportion of reset (on common-garden experiment and within one generation) and population-fixed DMRs between littoral and benthic fish. See Extended Data Fig. 9a for the other pairwise comparisons. c, GO analysis showing significant enrichment for fixed and reset DMRs in genes involved primarily in developmental and metabolic processes, respectively. d,e, Examples of DMRs fixed between populations (d) in wild and common-garden fish, with some fixed DMRs also associated with altered transcriptional activity in the liver (liver DEG; using Wald test FDR-adjusted two-sided P value using Benjamini–Hochberg <0.05; see Extended Data Fig. 9f–h for P values associated with each DEG) and of DMRs reset on the common-garden experiment, all associated with population-specific transcriptional differences (e). Each bar represents the average mCG/CG levels in 50 bp-long non-overlapping windows for each fish population (n ≥ 2 biological replicates). DMRs are highlighted in red and the length (bp) of each DMR is indicated in black.
