The R codes used for building the Apocynaceae phylogeny.

Investigating the evolutionary history and species diversification patterns in hyperdiverse lineages isessential for understanding how species diversity accumulates and how floras assemble historically across diverseregions. A large angiosperm family, Apocynaceae, exhibited remarkable diversity in functional traits includinggrowth form, fruit types, and pollen aggregation, which may have a substantial impact on species diversificationrates. However, the lack of a robust and well dated phylogeny has hindered our understanding of Apocynaceaediversification. To address this gap, we reconstructed a robust phylogeny covering 22 of 25 tribes using plastomesequences, then employed this framework to estimate divergence times, analyze diversification patterns,and investigate associations between species diversification and functional traits. The plastome phylogeniesreceived strong nodal support across most branches. Among higher taxonomic groupings, three subfamilies(Asclepiadoideae, Secamonoideae, and Periplocoideae) were monophyletic. At the tribal levels, 19 tribes werestrongly supported as monophyletic except Melodineae, Willughbeieae, and Vinceae. Additionally, five genera(Vincetoxicum, Cynanchum, Hoya, Marsdenia, and Aganosma) were identified as nonmonophyletic. Our analysesrevealed that Apocynaceae originated in the paleotropics during the middle Late Cretaceous. Integrating binarystate speciation and extinction (BiSSE), hidden state speciation and extinction (HiSSE), and fast, intuitive state‐dependent speciation‐extinction (FiSSE) analyses, we found that species with pollinia had a higher speciation ratethan those without. Dry‐fruited species had a higher speciation rate than those with fleshy fruits. Furthermore,Bayesian analysis of macro‐evolutionary mixtures (BAMM) detected a diversification rate increase coinciding withthe evolution of pollinia with clip‐type attachment mechanisms in the subfamily Asclepiadoideae. Herbs had thehighest speciation rate, followed by climbers and self‐supporting species. Our findings contribute tounderstanding the historical assembly of floras in tropical and subtropical Asia.