Fig. 3

DNA methylation differences between male and female Daphnia pulex in Eloise Butler strain (genotypes EB31 and EB45), using a filtered dataset; CpGs not covered in all samples and with no methylated reads in more than half of the samples were excluded. a) Principal component analysis (PCA) of DNA methylation (CpG) levels. Samples are represented by points along PC1 (x-axis) and PC2 (y-axis), which account for the majority of variance in the data. Genotypes separate by PC1 which accounts for 47% of the variance in methylation and the sexes separate by PC2 which accounts for 41% of variance. b) Volcano plot of DNA methylation (CpG) differences between male and female. The differentially methylated CpGs (DMCs; FDR < 0.05) are indicated in red