Environmentally induced DNA methylation is inherited across generations in an aquatic keystone species
Nathalie Feiner,
Reinder Radersma,
Louella Vasquez,
Markus Ringnér,
Björn Nystedt,
Amanda Raine,
Elmar W. Tobi,
Bastiaan T. Heijmans,
Tobias Uller
Affiliations
Nathalie Feiner
Department of Biology, Lund University, Lund, Sweden; Corresponding author
Reinder Radersma
Department of Biology, Lund University, Lund, Sweden; Centrum Wiskunde & Informatica, Amsterdam, The Netherlands
Louella Vasquez
Department of Laboratory Medicine, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Lund University, Lund, Sweden
Markus Ringnér
Department of Biology, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Lund University, Lund, Sweden
Björn Nystedt
Department of Cell and Molecular Biology, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
Amanda Raine
Department of Medical Sciences, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
Elmar W. Tobi
Periconceptional Epidemiology, Department of Obstetrics and Gynaecology, Division of Obstetrics and Prenatal Medicine, Erasmus MC, University Medical Center, Rotterdam, The Netherlands; Division of Human Nutrition and Health, Department of Agrotechnology and Food Science, Wageningen University & Research, Wageningen, The Netherlands; Molecular Epidemiology, Department of Biomedical Data Sciences, Leiden University Medical Center, Leiden, The Netherlands
Bastiaan T. Heijmans
Molecular Epidemiology, Department of Biomedical Data Sciences, Leiden University Medical Center, Leiden, The Netherlands
Tobias Uller
Department of Biology, Lund University, Lund, Sweden; Corresponding author
Summary: Transgenerational inheritance of environmentally induced epigenetic marks can have significant impacts on eco-evolutionary dynamics, but the phenomenon remains controversial in ecological model systems. We used whole-genome bisulfite sequencing of individual water fleas (Daphnia magna) to assess whether environmentally induced DNA methylation is transgenerationally inherited. Genetically identical females were exposed to one of three natural stressors, or a de-methylating drug, and their offspring were propagated clonally for four generations under control conditions. We identified between 70 and 225 differentially methylated CpG positions (DMPs) in F1 individuals whose mothers were exposed to a natural stressor. Roughly half of these environmentally induced DMPs persisted until generation F4. In contrast, treatment with the drug demonstrated that pervasive hypomethylation upon exposure is reset almost completely after one generation. These results suggest that environmentally induced DNA methylation is non-random and stably inherited across generations in Daphnia, making epigenetic inheritance a putative factor in the eco-evolutionary dynamics of freshwater communities.
