Stronger parental than temperature effects on methylation in juvenile brown trout (Salmo trutta)
Data files
Aug 27, 2025 version files 760.45 MB
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methylation_merged.tsv.gz
760.44 MB
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README.md
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Abstract
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.
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 3oC 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 3oC 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 3oC 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 3oC higher than ambient temperature.
md5sum value of the file.
b810523d26970773fd232ef63ea7d91c methylation_merged.tsv.gz