Epigenetic changes as regulatory mechanism for the expression of life history stages in <i>Zonotrichia capensis</i> inhabiting an aseasonal environment

Seasonal life‐history stages (LHS) in birds are typically regulated by environmental cues such as photoperiod and temperature. However, rufous‐collared sparrows Zonotrichia capensis inhabiting river valleys of the Atacama Desert exhibit an atypical, seasonal life cycle, including frequent overlap between reproduction and molt. This system provides an opportunity to investigate regulatory mechanisms underlying life‐history expression under reduced seasonal entrainment. Using GBS‐MeDIP, we characterized genetic and epigenetic variation in individuals sampled across different LHS. We identified 11 860 single nucleotide polymorphisms (SNPs) and 19 688 methylation windows that passed quality control. Individuals were genetically homogeneous and showed no clustering by LHS; however, we showed that subsets of SNPs and differentially methylated regions (DMRs) are associated with specific LHS. SNPs followed the classic pattern of standing genetic variation, accumulating predominantly in distal intergenic regions and being depleted in coding and promoter regions, consistent with long‐term mutation–selection processes. In contrast, DMRs were enriched in promoters and exons and depleted in distal intergenic space, indicating preferential association with regulatory genomic elements compared to the neutral genomic background. Overlap between genetic and epigenetic variation was limited, with only two CpG‐SNPs identified in functionally annotated regions. Together, these results suggest that DNA methylation is associated with regulatory variation linked to the expression of LHS in this weak seasonal system, and may contribute to phenotypic flexibility under relaxed seasonal constraints.