Extended Data Fig. 3: Properties of the WGBS-DMRs found between wild populations of Lake Masoko and riverine A. calliptera ecomorph populations.
From: Epigenetic divergence during early stages of speciation in an African crater lake cichlid fish
a. Total count of differentially methylated regions (DMR) found between each pairwise comparison using the WGBS dataset (B, benthic, L, littoral and R, river; v., versus; see Fig. 1g) and total number of unique DMRs (found in ≥1 pairwise comparison; in grey). b. Histograms of methylation difference (mCG/CG ∆) at DMRs found for each pairwise comparison. For each pairwise comparison, DMRs are split between Gain-/Loss-DMRs for gain/loss of methylation. Gain-DMRs in benthic, littoral or river fish, respectively, are indicated with histograms of different colors (blue, yellow, or red, respectively). Average DMR methylation difference (mean ± sd) is shown above/below each graph. c. Violin plots showing average DMR mCG/CG levels for each DMR group found in (c). Values on the left of each graph represent mean ± sd for mCG/CG levels. d. Left: Violin and box plots of the length (bp, log10 y-axis) of all unique DMRs found in ≥1 comparison. Right: violin plots showing the number of CG sites within all precited DMR sequences found between each pairwise comparison (log10 y-axis). Red dots and black horizontal bars represent mean and median values, respectively. Box plots indicate median (middle line), 25th, 75th percentile (box), and 5th and 95th percentile (whiskers) as well as outliers (single points). e. Circos plot showing DMR density found between each pairwise comparison (from Fig. 1g) across all chromosomes (data shown only for linkage groups LG [putative chromosomes] 1-23 in GCF_000238955.4 M_zebra_UMD2a). f. Example of methylome landscape (mean mCG/CG over 50 bp-long windows) at four highly diverged regions (HDRs between littoral and benthic populations, in green; from Malinsky et al., 2015) for wild-caught (w) fish from river (R), littoral (L) and benthic populations (B). n, number of biological replicates. DMR, differentially methylated regions in the three pairwise comparisons (v, versus; in purple). HDR annotations refer to Ref. 16.
