The methylomes of Lake Malawi cichlids reveal epigenetic variation associated with phenotypic diversification

Epigenetic variation modulates gene expression and can be heritable. However, knowledge of the contribution of epigenetic variation to diversification and speciation in nature remains limited. Here, we present the first genome-wide methylome study in a large vertebrate evolutionary radiation, focussing on liver and muscle tissues in six genetically similar but eco-morphologically divergent cichlid fishes from Lake Malawi. In both tissues we find substantial methylome divergence in DNA sequences conserved between species and differentially methylated regions (DMR) are signifi-cantly enriched in recently active transposable elements. DMRs in the liver are associated with transcription changes of genes with hepatic functions, pointing to a link between dietary ecology and methylome divergence. Unexpectedly, DMRs shared across adult tissues are enriched in genes involved in embryonic and developmental processes, suggesting roles in early embryogen-esis. Our study provides initial evidence for DNA methylation contributing to phenotypic diversifi-cation of cichlids, and represents an important resource for further work.