A phylogenomic framework for species delimitation in Kirganelia (Phyllanthaceae): Tracing a history of reticulate evolution

Kirganelia (Phyllanthaceae) is a palaeotropical genus recently reinstated as separate from Phyllanthus, yet species boundaries remain unclear, especially within the widespread and morphologically variable K. reticulata complex. To resolve this, we generated Angiosperms353-based phylogenomic data from 233 samples and applied an integrative framework combining maximum likelihood and coalescent-based trees, ADMIXTURE analysis, phylogenetic networks (PhyloNet, SplitsTree), and diagnostic traits. These approaches consistently supported three main lineages and justified the recognition of 30 clades of individuals, here hypothesized to represent species. One lineage—including K. zippeliana, K. glaucina, four undescribed taxa, and Moeroris retinervis—is sufficiently distinct to be treated as a new section within Kirganelia, with nomenclatural changes to follow. Within the K. reticulata complex, we recognize five species: two from Africa (K. polysperma and a yet unpublished species), and three non-African species (K. baccata, K. microcarpa, K. reticulata). Network analyses revealed hybrid ancestry in multiple taxa, particularly within the “Malagasy” clade, highlighting reticulate evolution as a key driver of morphological overlap and phylogenetic discordance. These findings demonstrate the limitations of relying solely on monophyly for species delimitation in recently diverged lineages and support using multiple lines of evidence to define coherent evolutionary units. This work provides an evolutionary foundation for future studies of Kirganelia taxonomy, diversity, and biogeography.