Fig. 4

Analysis of somatic epimutations in poplar. a A single poplar (P. trichocarpa) tree was analyzed. Tree 13 and 14 are two main stems that have diverged early in development. Four branches from each tree were chosen and aged by coring. b Shown are the coring sites along with the coring-based branch ages. Age coring proved technically challenging at the bottom of the tree and led to unintelligible ring counts. An educated guess places the age of the tree between 250 and 350 years. c The tree can be presented as an intra-organismal phylogeny. Leaf methylomes were collected from each of the selected branches and served as input for AlphaBeta. d Overview of the data: N is the total number of sequenced samples; Seq depth is the average sequence depths of the samples; # TP is the number of unique time-points that are sampled; max. (Δt) is the maximum divergence time (in years) between leaf samples. eAlphaBeta was fitted to the global CG methylation divergence data of the complete tree data treating tree age as an unknown parameter. Model residual (LSQ) was minimized at an age of 330 years, which is our estimate of the age of the tree. f Model comparisons indicate that somatic epimutations accumulate neutrally in context CG (red) and CHG (orange) during aging, both at the global scale as well as within specific genomic features (exons, promoters, TEs). g, h Shown are the fits of model ABneutral to the global CG (red) and CHG (orange) methylation divergence data of the complete tree (intra-tree + inter-tree, g), as well as for tree 13 and tree 14 separately (intra-tree, h)