Yao N, Zhang Z, Yu L, Hazarika R, Yu C, Jang H, Smith L M, Ton J, Liu L, Stachowicz J, Reusch Tbh, Schmitz R J, Johannes F
Department of Genetics, University of Georgia, Athens, USA.
Plant Epigenomics, Technical University of Munich, Freising, Germany.
bioRxiv. 2023 Mar 16:2023.03.15.532766. doi: 10.1101/2023.03.15.532766.
Molecular clocks are the basis for dating the divergence between lineages over macro-evolutionary timescales (~10 -10 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 possess a clock-like 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 intra-species phylogenetic trees in the selfing plant and the clonal seagrass , which represent two major modes of plant reproduction. This discovery will open new possibilities for high-resolution temporal studies of plant biodiversity.
分子钟是在宏观进化时间尺度（约10⁻¹⁰年）上确定谱系间分化时间的基础。然而，传统的基于DNA的分子钟走得太慢，无法为我们提供有关近期历史的信息。在这里，我们证明植物基因组中一部分胞嘧啶的随机DNA甲基化变化具有类似时钟的行为。这种“表观突变钟”比基于DNA的分子钟快几个数量级，并能够在数年至数百年的时间尺度上进行系统发育探索。我们通过实验表明，表观突变钟能够重现自花授粉植物和克隆海草这两种植物主要繁殖模式的种内系统发育树的已知拓扑结构和分支时间。这一发现将为植物生物多样性的高分辨率时间研究开辟新的可能性。
