Nuclear Phylogenomics Sheds Light on Traits- and Environment-Driven Diversification in Prunus s.l. (Rosaceae)

Understanding how a lineage originates, diversifies, and adapts through interactions between intrinsic traits and the environment is a central question in evolutionary biology and ecology. Prunus L., one of the morphologically diverse genera in the Rosaceae, holds considerable ornamental and economic importance. However, the drives of its remarkable diversity and how it responds to environmental change throughout its diversification history remain poorly understood. Here, we reconstruct a comprehensive nuclear phylogeny of Prunus by integrating universal Angiosperms353 genes and lineage-specific orthologous genes, providing a robust framework for investigating the spatiotemporal dynamics of diversification and trait-mediated environmental adaptation. Our comparative analyses date the crown age of Prunus to the early Paleocene (~63 Million year ago, Ma) and identify the onset of accelerated diversification accompanied by at least one major rate shift. Pronounced diversification pulses were associated with paleotemperature, as well as interactions between climatic effects and intrinsic traits, particularly ploidy level and inflorescence types, which facilitated ecological expansion and promoted lineage radiation. Ancestral state reconstructions indicate that the most recent common ancestor of Prunus was deciduous, racemose, polyploid, and possessed a glabrous ovary. Together, these results show that the evolutionary trajectory of Prunus has been jointly shaped by climatic change and key biological traits, providing a robust macroevolutionary framework for future evolutionary, and comparative studies in Rosaceae.