Worldwide phylogeny and integrative taxonomy of Clematis: Insights from phylogenomics

The genus <i>Clematis</i> (Ranunculaceae) comprises over 300 species with remarkable morphological and ecological diversity worldwide. Despite its horticultural, medicinal, and ecological importance, a well-resolved phylogeny and coherent infrageneric classification are still lacking. Here, we reconstruct a robust phylogeny for <i>Clematis</i> using a phylogenomic approach and revise its infrageneric taxonomy. We incorporated 198 samples representing 151 species, two subspecies, and 12 varieties, covering all subgenera and most sections worldwide, obtained from both fresh and herbarium material. Nuclear single nucleotide polymorphisms (SNPs) and complete plastid genomes were assembled for phylogenetic analyses. We also prepared a nuclear ribosomal ITS (nrITS) dataset comprising 171 species, two subspecies, and 12 varieties (217 samples) to include as many species as possible for phylogenetic inference. Phylogenies based on plastid genomes and nrITS exhibited limited resolution and modest support, highlighting challenges in resolving certain relationships. Nuclear SNP analyses yielded a robust phylogenetic tree with 22 well-supported clades corresponding to 22 sections, with most previously recognized subgenera and sections not recovered as monophyletic. Ancestral state reconstruction of 12 key morphological characters revealed multiple independent origins of character states. This study presents the first comprehensive sectional classification for <i>Clematis</i> based on robust phylogenomic evidence, redefines morphological characteristics for each section, and resolves long-standing taxonomic ambiguities. Our results establish a framework for future studies on the evolution, ecology, and horticultural potential of this globally significant genus.