Conserved sex-biased DNA methylation patterns target key developmental genes and reproductive function in two Poeciliid species

Abstract

Sexual dimorphism provides a powerful framework for studying how regulatory mechanisms generate phenotypic divergence from a shared genome. Many sex-specific traits arise from differences in gene expression, which can be mediated by epigenetic mechanisms such as DNA methylation. These mechanisms contribute to the organisation of gene regulatory variation across tissues, genes, and chromosomes, with potential consequences for the emergence and maintenance of sexually dimorphic phenotypes. Using a comparative epigenomic approach we investigate sex-biased DNA methylation in gonad and muscle tissue across two closely related Poeciliid species, Poecilia reticulata and Poecilia wingei. We address three questions: (i) how conserved are sex-biased DNA methylation patterns across species and tissues; (ii) are conserved sex-biased methylation patterns associated with genes involved in developmental and transcriptional regulation; and (iii) are sex-biased epigenetic patterns enriched on the sex chromosome? We identify extensive conservation of sex-biased differentially methylated regions (DMRs) in gonadal tissue, with strong cross-species concordance, whereas muscle shows little conservation of sex specific differential methylation. Conserved male-hypomethylated regions are enriched near genes involved in developmental transcriptional regulation and gonadal differentiation. Methylation–expression coupling distinguishes sex-biased reproductive gene functions, with male-biased genes enriched for spermatogenesis and motility and female-biased genes enriched for sperm–egg interaction processes. Sex-biased DNA methylation is broadly distributed across the genome, with localized regulatory regions on the sex chromosome. Together, these results show that conserved sex-biased DNA methylation is highly tissue-specific and associated with reproductive regulatory function, supporting a model in which gonadal epigenetic architecture reflects conserved regulatory organisation underlying sexual dimorphism.