Fig. 1

Overview of the AlphaBeta computational pipeline. a Top panel: Construction of multi-generational (G0 to GN) mutation accumulation (MA) lines through sexual (selfing or sibling mating) or asexual (clonal) propagation. The different lineages (L1 to L3) can be represented as a pedigree. The pedigree branch point times and the branch lengths are typically known, a priori, from the experimental design. 5mC sampling can be performed at selected generations, either from plant material of direct progenitors or from siblings of those progenitors. The data can be used to estimate the rate and spectrum of “germline” epimutations. Bottom panel: Long-lived perennials, such as trees, can be viewed as a natural mutation accumulation system. The tree branching structure can be treated as an intra-organismal phylogeny of somatic lineages. 5mC samples can be performed on leaf tissues from selected branches. Along with coring data, the leaf methylomes can be used to estimate the rate and spectrum of somatic epimutations. b Data pre-processing: AlphaBeta requires methylation data and pedigree data as input. File conversion: Using the input files, AlphaBeta calculates the 5mC divergence (D) as well as divergence time (Δt) between all sample pairs. Model estimation: AlphaBeta fit competing epimutation models to the data. The model parameters are estimated using numerical non-linear least squares optimization. Model comparisons allow for tests of selection and neutrality