The following depository contains raw phenotypic data and intermediate DNA methylation data presented in the article "DNA methylation in clonal Duckweed lineages (Lemna minor L.) reflects current and historical environmental exposures." : 1) Raw phenotypic data - Frond_area_Phase1_Phase2 -> Frond area measured at different time points (week 1, 6, 7 and 8) during the experiment. - Frond_number_Phase1_Phase2 -> Frond number measured at different time points (week 1, 6, 7 and 8) during the experiment. 2) Intermediate files obtained from running the epiGBS2 pipeline. The following files are available: - consensus_cluster.renamed.fa -> epiGBS de novo loci. This file consists of the de novo epiGBS reference sequence file obtained during the de novo reference creation. - methylation.filtMETH -> The filtered DNA methylation data. This data was obtained after filtering the raw DNA methylation data. Cytosines which had a 10X coverage or higher and which were present in 80% of all samples were kept for further analysis. Demultiplexed and raw data were deposited at NCBI: BioProject: PRJNA883550