Phylogenomic analysis reveals convergent evolution of shrubby Clematis species

<em>Clematis </em>of the buttercup family is one of the most popular garden flowers in the world, being crowned as the “Queen of Climbers.” It is well known for its climbing habit, but it also has shrubby members with poorly known evolutionary origins. The relationships among the major <em>Clematis </em>groups still remain controversial. In this study, we assembled the complete plastome and nrDNA sequences of 56 <em>Clematis </em>species representing most of the sections, and reconstructed the phylogenetic framework using both datasets. Our sampling covered all species of the shrubby <em>C</em>. sect. <em>Fruticella s. str.</em> and the taxonomically controversial species allied to the section to test the monophyly of section <em>Fruticella </em>and trace the evolution of habits in the genus. Using both likelihood and Bayesian methods, the two datasets of DNA sequences generated similar, but not identical, phylogenetic relationships. The complete plastome sequences delivered a better resolved phylogeny, supporting five well-resolved major clades for all sampled species, except for a first-diverged African species. Many of the morphological characters widely used for taxonomy were shown to represent parallel or convergent evolution. Molecular dating inferred that all major <em>Clematis </em>clades radiated during the early Pliocene, with a species radiation during the Quaternary. The erect, shrubby habits of <em>Clematis </em>were inferred to have evolved multiple times in eastern Asia. <em>Clematis</em> sect. <em>Meclatis</em> is likely sister to <em>C</em>. sect.<em> Fruticella</em>, and the latter diversified during the late Quaternary. The cold, dry Quaternary climate was hypothesized to have facilitated species diversification and dispersal of <em>C</em>. sect. <em>Fruticella.</em>