An evolutionary epigenetic clock in plants
Nanyu Yao, Zhilin Zhang, Lei Yu, Rashmi R. Hazarika, Chao Yu, Hosung Jang, Lisa M. Smith, Jurriaan Ton, Liang Liu, John J. Stachowicz, Thorsten B. H. Reusch, Robert J. Schmitz, Frank Johannes
Abstract
Molecular clocks are the basis for dating the divergence between lineages over macroevolutionary timescales (~10 5 to 10 8 years). However, classical DNA-based clocks tick too slowly to inform us about the recent past. Here, we demonstrate that stochastic DNA methylation changes at a subset of cytosines in plant genomes display a clocklike behavior. This “epimutation clock” is orders of magnitude faster than DNA-based clocks and enables phylogenetic explorations on a scale of years to centuries. We show experimentally that epimutation clocks recapitulate known topologies and branching times of intraspecies phylogenetic trees in the self-fertilizing plant Arabidopsis thaliana and the clonal seagrass Zostera marina , which represent two major modes of plant reproduction. This discovery will open new possibilities for high-resolution temporal studies of plant biodiversity.