DOI: 10.5061/dryad.612jm64hn
title: Stronger parental than temperature effects on methylation in juvenile brown trout (Salmo trutta)

description: 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.
description: # Stronger parental than temperature effects on methylation in juvenile
 brown trout (Salmo trutta) File: methylation_merged.tsv.gz Description: *
 CpG sites and their methylation in 8 samples. * Combined coverage ranges
 between 120 and 800. * No missing values are allowed. Format: * The first
 5 columns are information columns for the CpG sites. * chr: chromosome. *
 start: 1-based starting position of C in the CpG site. * end: 1-based
 ending position of C in the CpG site. * strand: strand of the CpG site.
 "+" and "-" indicate forward and reverse strands,
 respectively. "*" indicates that the complementary CpGs were
 merged. * context: context of C. It can be one of CpG, CHG and CHH, where
 H represents A, T or G. For the current file, this column only contains
 CpG because this study only focuses on C's of CpG context. C's
 of CHG or CHH are hardly methylated in vertebrates. * The 6th column
 onwards specify the methylation in each sample. Each entry in the sample
 columns consists of two integers seperated by a colon. The two integers
 are the coverages of methylated and unmethylated CpGs. The sample names,
 i.e., the column names are explained in the manuscript (see Figure 1 and
 "Crosses and hatchery-rearing" of Materials and Methods). But
 here is a brief summary. * AA_cold: Pooled sample of offspring from
 crosses between anadromous females and anadromous males (AA). The
 offspring were raised in ambient (natural) temperature. * AA_warm: Pooled
 sample of offspring from crosses between anadromous females and anadromous
 males (AA). The offspring were raised in temperature 3^o^C higher than
 ambient temperature. * AR_cold: Pooled sample of offspring from crosses
 between anadromous females and resident males (AR). The offspring were
 raised in ambient (natural) temperature. * AR_warm: Pooled sample of
 offspring from crosses between anadromous females and resident males
 (AR). The offspring were raised in temperature 3^o^C higher than ambient
 temperature. * RA_cold: Pooled sample of offspring from crosses between
 resident females and anadromous males (RA). The offspring were raised in
 ambient (natural) temperature. * RA_warm: Pooled sample of offspring from
 crosses between resident females and anadromous males (RA). The offspring
 were raised in temperature 3^o^C higher than ambient temperature. *
 RR_cold: Pooled sample of offspring from crosses between resident females
 and resident males (RR). The offspring were raised in ambient (natural)
 temperature. * RR_warm: Pooled sample of offspring from crosses between
 resident females and resident males (RR). The offspring were raised in
 temperature 3^o^C higher than ambient temperature. md5sum value of the
 file. b810523d26970773fd232ef63ea7d91c methylation_merged.tsv.gz