Nuclear phylogenomics reveals trait- and environment-associated patterns of 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 factors associated with its remarkable diversity and its responses 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 their correlations with trait variation and environmental conditions. Our comparative analyses date the crown age of Prunus to the early Paleocene (∼63 million years ago, Ma) and identify increased diversification rates, including at least one major rate shift. Pronounced diversification pulses were associated with variation in paleotemperature, as well as interactions between climatic variables and intrinsic traits, particularly ploidy level and inflorescence types. These associations are consistent with patterns of ecological expansion and 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 shaped by both climatic change and key biological traits, providing a robust macroevolutionary framework for future evolutionary, and comparative studies in Rosaceae.