Phylogenetic investigation and taxonomic revision of the subgenus Anguinum ( Allium , Amaryllidaceae) using multi-omics data

Abstract Resolving phylogenetic relationships in recently diverged plant lineages is challenging, yet essential for understanding plant evolution and taxonomy. The Allium subgenus Anguinum represents a taxonomically complex group with blurred species boundaries and pronounced phylogenetic conflicts. To clarify its evolutionary history and address long-standing taxonomic uncertainties, we applied integrative multi-omics approaches covering all 10 Anguinum species and two varieties. A phylogenetic framework of Allium was constructed using 113 chloroplast genomes and 188 nuclear ITS sequences. By further integrating 18 transcriptomes and 21 chloroplast genomes from subg. Anguinum, we confirmed the subgenus’s monophyly and its primary division into the East Asian (EAL) and Euro–North American (ENAL) lineages. Comparative chloroplast genome analyses revealed substantial divergence, mainly in intergenic regions and selected protein-coding genes, despite a conserved quadripartite structure. Codon usage, nucleotide diversity, and selection analyses highlighted heterogeneous evolutionary dynamics among chloroplast genes. A multi-omics genomic analysis based on 1531 nuclear single-copy genes and 77 chloroplast coding sequences reconstructed the evolutionary history of the subgenus. Phylogenetic reconstructions consistently resolved two major lineages (EAL and ENAL), with A. funckiifolium nested within the A. ovalifolium group (AO group) in the EAL. Molecular, morphological, and ecological evidence consistently supports the reclassification of A. funckiifolium as a variety of A. ovalifolium. Discordance between nuclear and chloroplast trees, coupled with quartet concordance, ABBA–BABA, and f4-ratio analyses, revealed extensive gene flow, particularly within the A. ovalifolium–A. funckiifolium complex. Coalescent simulations indicated that most conflicts result from incomplete lineage sorting with hybridization-mediated gene flow contributing. This study refines species delimitations and establishes a complete taxonomic framework for Anguinum, reveals the mechanisms of taxonomic discordance, and provides key insights and a representative case for understanding phylogenetic incongruence and evolutionary dynamics in Allium.