Species delimitation in the <i>Polygonatum odoratum</i> complex (Asparagaceae) based on phylogenomic and morphometric data

Abstract Defining species and delineating boundaries among closely related species is challenging particularly for species complexes with a recent history of diversification. The Polygonatum odoratum complex, consisting of seven taxa, presents a compelling example showing unresolved taxonomic boundaries. Here, we aim to delimit taxonomic boundaries in the complex using genomic and morphometric data. Target enrichment was employed to analyze 40 accessions representing the seven taxa in the complex. We inferred the species tree using coalescent and maximum likelihood approaches with nuclear and plastid data. Additionally, we examined 14 morphological characters from 851 herbarium specimens and conducted morphometric analysis using factor analysis of mixed data. The phylogenomic analysis, based on 297 genes, strongly supports the presence of three monophyletic clades with a recent diversification history (&lt;4 million years). Coupled with our morphological examinations, our findings demonstrate the existence of three distinct species, revising the previous classification of seven taxa. By applying an integrated species concept, our study resolves the species boundaries and updates the taxonomy of the P. odoratum complex.