Extended Data Fig. 8: Mapping results, methylome variation and PC analysis for Common-Garden/tank-reared WGBS fish samples.
From: Epigenetic divergence during early stages of speciation in an African crater lake cichlid fish
a. Mapping rates for Common Garden fish WGBS reads aligned to M. zebra_UMD2a reference genome (see Methods). Black midlines and whiskers represent mean ± sd of mapping rates within each population. Average mapping rates shown at the bottom of each graph (mean ± sd). b. Violin plots of average mCG/CG levels in 1kbp-long non-overlapping windows genome-wide for common garden (cg) fish of each population. Black circles and lines indicate mean and median values, respectively. c. PCA of liver methylome variation in wild (shades of purple) and common garden (shades of green) A. calliptera populations reveals global methylation remodeling in wild benthic and littoral fish (Wild Masoko) to resemble river fish methylome profiles. Upper- and lower-case letters distinguish wild from common garden fish for each population (river R/r, benthic B/b, littoral L/l). Biological replicates: wild fish: Benthic (B), n = 3; Littoral (L) and Riverine (R), n = 2; common garden fish: benthic (b), littoral (l) and riverine (r), n = 2.
