Abstract
Chromatin modifications provide a substrate for epigenetic variation with evolutionary potential. To quantify the contribution of this layer of variation during speciation in crows, we leveraged genome and methylome sequencing data from an incipient avian species: all‐black carrion crows, grey‐coated hooded crows, and their hybrids. Combining controlled experimentation under common garden conditions and sampling of natural genetic variation across the hybrid zone, we show that 5mC methylation variation was largely explained by genome properties and the ontogenetic programme of the organism. Taxonomically related methylation divergence clustered in intergenic space, with the only genomic region of strongly elevated genetic differentiation encoding the diagnostic colour contrast between taxa. We conclude that methylation variation with relevance to speciation largely follows cis ‐genetic polymorphism in this system and does not constitute an autonomous axis of evolution.