Fig. 3

We propose a heuristic model whereby genomic changes and spontaneous epimutations occur simultaneously, and contribute to interspecific or intraspecific methylome diversity over evolutionary time. For illustrative purposes, we assume that lineages descended from a common founder plant at time 0. The rapid accumulation of heritable epimutations dominates methylome diversity over short timescales but quickly converges to an equilibrium diversity value that is defined by the magnitude of forward and backward epimutation rates as well as by their ratios (i.e., the epimutation bias parameter). By contrast, genomic changes accumulate more gradually among lineages, and begin to dominate methylome diversity after longer evolutionary divergence times. An important empirical challenge is to delineate the relative contributions of these two processes based on methylome diversity data collected at any point along this evolutionary trajectory. Recent theoretical models for the analysis of the methylation site frequency spectrum (mSFS) provide an important step in this direction