Genomic and morphological data help resolve phylogenetic conflicts and establish revised, stable classifications: A synthetic insight into Carex sect. Mitratae s.l. (Cyperaceae)

: Phylogenetic incongruences and taxonomic discrepancies often go hand in hand, confounding taxonomic classifications due to the conflicting signals between molecular and morphological data. The internal organization of Carex (Cyperaceae), a genus with over 2,200 species, presents substantial phylogenetic and taxonomic challenges due to pervasive homoplasy of key morphological characters. Although sequence data from Hyb-Seq approaches have recently provided a preliminary infrageneric framework, the underlying causes of deep gene tree discordance and unresolved relationships in rapidly radiating shallow lineages remain insufficiently understood, thereby introducing uncertainty into taxonomic classifications. In this study, we focused on the alliance known as Carex sect. Mitratae s.l., a typical case of shallow rapid phylogenetic radiation, to address these issues. Using deep genome skimming data, from which we recovered 4,975 single-copy orthologs (SCOs), we reconstructed a robust phylogenetic backbone of the group and its relatives. We demonstrated that incomplete lineage sorting (ILS), introgression, and hybridization collectively explain the pervasive gene tree discordance affecting sect. Mitratae . Integrating phylogenetic and morphological evidence, we propose a revised taxonomy of the group recognizing five monophyletic sections within the alliance: sects. Foraminatae (sect. nov.), Cryptostachyae , Digamae , Truncatiglumae , and Mitratae . Our study not only resolves the long-standing taxonomic controversies regarding the limits of sect. Mitratae s.l., but also provides an empirical case demonstrating how integration of genomic data, phylogenetic methods, and morphological evidence can help decipher the complex evolutionary history of a rapid radiation in a megadiverse genus, ultimately establishing a revised, stable classification.