Fig. 1: The methylome of Lake Malawi cichlids.

a Map of Africa (main river systems are highlighted in white) and magnification of Lake Malawi (scale bar: 40 km). b Photographs (not to scale) of the six Lake Malawi cichlid species part of this study spanning five of the seven described eco-morphological groups. The symbols represent the different habitats (pelagic/benthic [wave symbol], rock/sand-dwelling/littoral [rock symbol] and adjacent rivers part of Lake Malawi catchment), and the type of diet (fish, fish/zooplankton, algae, invertebrates) for each group. The species representing each group are indicated by their initials (see below). c Diagram summarising the sampling and sequencing strategies for liver and muscle methylome (whole-genome bisulfite sequencing, WGBS) and whole transcriptome (RNAseq) datasets. See “Methods”, Supplementary Fig. 1 and Supplementary Table 1. d Violin plots showing the distribution of liver DNA methylation levels in CG sequence context (averaged mCG/CG levels over 50 bp-long bins genome-wide) in different genomic regions: overall, gene bodies, exons, promoter regions (TSS ± 500 bp), CpG-islands in promoters and outside (orphan) and in repeat/transposon regions. mC levels for two different repeat classes are given: DNA transposon superfamily Tc2-Mariner (n = 5,378) and LINE I (n = 407). e Average liver mCG profiles across genes differ depending on their transcriptional activity in liver: from non-expressed (0) to genes showing low (1), intermediate (2), high (3) and highest (4) expression levels (“Methods”). Results shown in (d, e) are for Mbuna MZ (liver, n = 3) and are representative of the results for all other species, and are based on average mC/C in 50 bp non-overlapping windows. RL, Rhamphochromis longiceps; DL, Diplotaxodon limnothrissa; MZ, Maylandia zebra; PG, Petrotilapia genalutea; AS, Aulonocara stuartgranti; AC, Astatotilapia calliptera. Credits—Fish photographs: Hannes Svardal and M. Emília Santos. Geographical map modified from www.d-maps.com/.