An evolutionary epigenetic clock in plants

• 成果类型: Article
• 署名作者: Yao, N.; Zhang, Z.; Yu, L.; Hazarika, R.; Yu, C.; Jang, H.; Smith, L. M.; Ton, J.; Liu, L.; Stachowicz, J. J.; Reusch, T. B. H.; Schmitz, R. J.; Johannes, F.
• 署名单位: University System of Georgia; University of Georgia; Technical University of Munich; Helmholtz Association; GEOMAR Helmholtz Center for Ocean Research Kiel; University of Sheffield; University System of Georgia; University of Georgia; University of California System; University of California Davis
• 刊物名称: SCIENCE
• ISSN/ISSBN: 0036-12709
• DOI: 10.1126/science.adh9443
• 发表日期: 2023-09-29
• 页码: 1440-1445
• 关键词: maximum-likelihood-estimation; arabidopsis-thaliana; substitution rates; molecular-clock; methylation; phylogenies; divergence; mutations; spectrum; genome

摘要

Molecular clocks are the basis for dating the divergence between lineages over macroevolutionary timescales (similar to 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.