Phylogenomic evidence provides insights into the phylogeny and speciation patterns in the subgenus Caloscordum (Allium, Amaryllidaceae).
Phylogenomics with abundant informative sites offers a powerful means for elucidating complex diversification history. Here, we collected 22 samples from 18 populations representing all species of subgenus Caloscordum (Allium). Using transcriptome and whole-genome resequencing data, we generated 1755 low-copy nuclear genes and 81 plastid genes. By integrating morphological and phylogenomic evidence, we clarified the subgenus's complex evolutionary histories and speciation patterns. A total of 18 morphological characteristics were analysed, with a taxonomic framework established. Our analyses resolved robust species relationships despite detecting extensive phylogenetic discordances, which were attributed to incomplete lineage sorting (ILS) and hybridization. Specifically, our results suggest that A. inutile originated via rapid budding speciation from the widespread A. tubiflorum. This process likely coincided with mid-Pleistocene glacial-interglacial cycles and may have been reinforced by geographic isolation and ecological adaptation. In contrast, the sole tetraploid species, A. peikingense, was confirmed to be of hybrid origin, derived from A. neriniflorum and A. tubiflorum. This allopolyploidization event appears to have been facilitated by secondary contact between the parent species, which was likely associated with climatic oscillations within the 35° N-45° N arid belt. Overall, our findings elucidate the intricate speciation patterns within Caloscordum and highlight how the interplay of polyploidization, ecological isolation, and tectonic uplift-driven aridification has shaped plant diversity in East Asia.