Epigenetic signatures of migratory orientation in a songbird hybrid zone

Epigenetic marks are strong candidates for elements controlling environmentally mediated behaviours like migration. Understanding the potential role of epigenetics in migratory behaviour is increasingly important, as rapidly changing environmental conditions threaten many migratory populations. Here, we report a methylome-wide analysis to identify differentially methylated CpG sites (DMSs) associated with migratory orientation in the Swainson's thrush (Catharus ustulatus), a migratory songbird with two subspecies that show distinct migratory pathways. We compared birds with extreme autumn migration orientations, including pure forms and early-generation hybrids, and contrasted our epigenomic results with genomic variation. We found weak methylome-wide differentiation, largely explained by ancestry and heterozygosity, but identified a small number of DMSs based on migratory orientation. These DMSs were located within transposable elements, while others were evenly distributed between promoters and gene bodies. Genes with annotated roles in olfaction were enriched near these DMSs, supporting growing evidence for their role in migratory orientation. Many DMSs were also linked to genetic variants in trans-regulatory regions, suggesting that methylated sites may interact with distant genetic variants to influence migratory orientation in response to environmental cues. These findings advance our understanding of the molecular mechanisms that control differences in migratory orientation, providing empirical evidence of epigenetic divergence with potential implications for intraspecific divergence in migratory behaviour. This article is part of the theme issue 'Ecological epigenetics at the intersection of behaviour and life history variation in non-model animals'.