Epigenetic modifications, particularly DNA methylation, are increasingly recognized as mechanisms underlying phenotypic plasticity and potential mediators of transgenerational responses to environmental change. We investigated the persistence of early life temperature-induced DNA methylation changes and the role of parental life history in shaping methylation patterns in juvenile brown trout (Salmo trutta). Fertilized eggs from crosses of anadromous and resident trout were incubated under natural or elevated temperatures (by +3°C) until first feeding, after which all fish were reared under common conditions. Whole-genome bisulfite pooled sequencing was conducted on juveniles 10.5 months post-fertilization. We found weak and inconsistent evidence for persistent temperature-induced methylation changes, with little overlap among different parental cross types. In contrast, parental life history, particularly maternal origin, significantly influenced offspring methylation patterns. Maternally derived differences were more extensive than paternal effects and were enriched for genes related to metabolism, nervous system function, and digestion, suggesting potential adaptive relevance. These findings highlight a limited long-term impact of early-life thermal conditions on methylation and emphasize a stronger role of transgenerational epigenetic effects in brown trout. Given that climate change is expected to alter thermal regimes in future aquatic ecosystems, our results, along with other recent publications, suggest that parental environmental history may be a more significant driver of epigenetic variability than temperature experienced during eary life. Understanding such mechanisms is critical for predicting how populations may respond to ongoing and future climate change.

Epigenetic modifications, particularly DNA methylation, are increasingly recognized as mechanisms underlying phenotypic plasticity and potential mediators of transgenerational responses to environmental change. We investigated the persistence of early life temperature-induced DNA methylation changes and the role of parental life history in shaping methylation patterns in juvenile brown trout (Salmo trutta). Fertilized eggs from crosses of anadromous and resident trout were incubated under natural or elevated temperatures (by +3°C) until first feeding, after which all fish were reared under common conditions. Whole-genome bisulfite pooled sequencing was conducted on juveniles 10.5 months post-fertilization. We found weak and inconsistent evidence for persistent temperature-induced methylation changes, with little overlap among different parental cross types. In contrast, parental life history, particularly maternal origin, significantly influenced offspring methylation patterns. Maternally derived differences were more extensive than paternal effects and were enriched for genes related to metabolism, nervous system function, and digestion, suggesting potential adaptive relevance. These findings highlight a limited long-term impact of early-life thermal conditions on methylation and emphasize a stronger role of transgenerational epigenetic effects in brown trout. Given that climate change is expected to alter thermal regimes in future aquatic ecosystems, our results, along with other recent publications, suggest that parental environmental history may be a more significant driver of epigenetic variability than temperature experienced during eary life. Understanding such mechanisms is critical for predicting how populations may respond to ongoing and future climate change.

The role of methylation in adaptive, developmental and speciation processes has attracted considerable interest, but interpretation of results is complicated by diffuse boundaries between genetic and non-genetic variation. We studied whole genome genetic and methylation variation in the European eel, distributed from subarctic to subtropical environments, but with panmixia precluding genetically based local adaptation beyond single-generation responses. Overall methylation was 70.9%, with hypomethylation predominantly found in promoters and first exons. Redundancy analyses involving juvenile glass eels showed 0.06% and 0.03% of the variance at SNPs to be explained by localities and environmental variables, respectively, with GO terms of genes associated with outliers primarily involving neural system functioning. For CpGs 2.98% and 1.36% of variance was explained by localities and environmental variables. Differentially methylated regions particularly included genes involved in developmental processes, with hox clusters featuring prominently. Life stage (adult versus glass eels) was the most important source of inter-individual variation in methylation, likely reflecting both ageing and developmental processes. Demethylation of transposable elements was observed in European X American eel hybrids, possibly representing postzygotic barriers in this system characterized by prolonged speciation and ongoing gene flow. Whereas the genetic data are consistent with a role of single-generation selective responses, the methylation results underpin the importance of epigenetics in the life cycle of eels and suggests interactions between local environments, development and phenotypic variation mediated by methylation variation. Eels are remarkable by having retained eight hox clusters, and the results suggest important roles of methylation at hox genes for adaptive processes.