Phylogenomics ofAristolochiasubg.Siphisia (Aristolochiaceae) reveals widespread incomplete lineage sorting and supports a novel pollinator-filtering hypothesis

AristolochiasubgenusSiphisiaconstitutes a monophyletic lineage of predominantly lianescent species, with occasional shrubs or herbs, and is characterized by remarkable diversity in perianth morphology. Members ofSiphisiaserve as larval hosts for endangered Lepidoptera and are widely used in traditional medicine. Despite its ecological and ethnobotanical significance,Siphisiasystematics remains unresolved due to limited genomic resources and insufficient phylogenetic signal across previously sampled loci. Here, we present a phylogenomically informed framework forSiphisia, integrating 46 newly collected accessions and seven public datasets across 44 taxa. Using genome skimming (∼30× coverage) and HybPiper, we recovered Angiosperms353 nuclear loci, including supercontigs, for phylogenetic reconstruction via concatenation and coalescent approaches. The resulting species trees resolve seven strongly supported monophyletic clades, each defined by distinct biogeographic patterns and morphological synapomorphies. Comparative plastome analyses fromde novoassemblies explored quadripartite structure, plastid phylogeny, GC content, and gene synteny. Cytonuclear discordance was concentrated in species-rich Asian clades, while hybridization signals were rare and limited to deep backbone nodes in North American lineages. These results indicate that incomplete lineage sorting, rather than introgression, accounts for most gene–species tree conflicts and likely reflects strong reproductive isolation following speciation. We also revise a previously taxonomically ambiguous complex—the now well-supportedA. versicolorspecies group—based on integrated phylogenomic and morphological evidence. Within this group, we describe five previously unrecognized cryptic species and identify a novel pollination syndrome involving floral adaptations for pollinator filtering. This syndrome may contribute to prezygotic isolation and recent diversification, and it challenges the prevailing assumption thatAristolochiapollination is universally governed by a trapping–release mechanism—suggesting this model may not apply to subg.Siphisia.