Exploring evolutionary relationships within the species-rich and taxonomically complex Allium section Codonoprasum using nuclear and plastid DNA regions

Abstract The genus Allium has been extensively studied in recent decades to elucidate the evolutionary processes shaping its phylogeny and taxonomic relationships. However, significant gaps remain, particularly concerning infrageneric classification and evolutionary relationships within several sections. One such example is section Codonoprasum, comprising approximately 160 diploid and polyploid taxa centred mainly in the Mediterranean and western Irano–Turanian regions. High species diversity in this section is accompanied by taxonomic inconsistencies and a poorly resolved phylogenetic structure. Here, we improve current understanding of the evolution of section Codonoprasum by analysing sequence variation in three genomic loci (nrITS, trnH–psbA, and trnL–ndhJ) and by mapping selected plant traits onto the resulting phylogenetic trees. Our dataset includes 48 taxa—around 30% of the total diversity of the section—each represented by multiple accessions. The results support the monophyly of section Codonoprasum and indicate a close relationship with section Cupanioscordum. Within section Codonoprasum, five major lineages (clades I–V) were identified, some of which were further subdivided into morphologically and/or karyologically distinct subclades. The placement of taxa within these lineages is evaluated in the light of existing knowledge on their morphology, karyology, and geographic distribution. Overall, the phylogenetic patterns recovered here are incongruent with traditional subsectional taxonomy. Genome size appears to follow a more punctuated than gradual mode of evolution along the phylogeny. We interpret these findings with a focus on lineage composition, interclade relationships, and their implications for understanding evolutionary patterns and taxonomy within this diverse section.