Integrating morphological and phylogenomic data reveals the taxonomic puzzles, incongruence in phylogenies and cryptic species in <i>Allium</i> section <i>Bromatorrhiza</i> Ekberg

Phylogenomic data from enriched informative loci yield higher resolution insights for clarifying taxonomic relationships and reconstructing the evolutionary histories of complex taxa. Section Bromatorrhiza (Allium, Amaryllidaceae), a small taxon of 11 species, has long been plagued by taxonomic controversies and persistent, unresolved phylogenetic incongruence. Here, we collected transcriptome and plastome data from 34 samples representing multiple populations across all species in this section. From these, 1993 low-copy nuclear genes and 110 plastid genes were extracted for phylogenetic reconstruction. Integrating phylogenomic and morphological approaches, we investigated species relationships and the causes of phylogenetic discordance. Our results provide robust clarification of interspecific relationships and identify 10 diagnostic morphological traits in this section. The Allium hookeri Alliance (AHA) was resolved as a monophyletic clade comprising seven species. We elevated Allium hookeri var. muliense to species status, formally describing it as A. muliense, and newly describe a cryptic species as Allium xui Y. Wang, D.F. Xie & X.J. He, sp. nov. Furthermore, we demonstrate that extensive phylogenetic discordance within this section is primarily attributable to incomplete lineage sorting (ILS) and reticulate evolution. By synthesizing phylogenetic and morphological evidence, we propose refined taxonomic treatments. Our findings resolve long-standing taxonomic ambiguities and phylogenetic discordance in section Bromatorrhiza.