Integrating Morphology and Chloroplast Genomics: A New East Asian Species of Aletris (Nartheciaceae) With Insights Into Regional Phylogeny and Evolution.

The genus Aletris L. (Nartheciaceae) encompasses approximately 21-24 species distributed in East Asia and North America, yet taxonomic ambiguity persists due to overlapping morphological traits among closely related species. During fieldwork in southeastern Xizang, China, a morphologically distinct candidate species, Aletris medogensis, was discovered. To validate its taxonomic status and explore evolutionary relationships within East Asian Aletris, we integrated detailed morphological observation with comparative chloroplast phylogenomics. The newly proposed species is characterized by creeping stolons, narrow leaves, and glandular-pubescent inflorescences. Comparative analysis of 14 East Asian Aletris complete chloroplast genomes revealed a conserved quadripartite structure with species-specific variations, including pseudogenization of ycf1, loss of rrn4.5, and shifts in IR boundaries. Phylogenomic analyses strongly supported A. medogensis as a distinct species closely related to A. alpestris. We identified 18 hypervariable regions as potential molecular markers and detected signals of positive selection in genes ccsA, cemA, and rps12, suggesting adaptive evolution. This study confirms the recognition of A. medogensis as a new species endemic to the eastern Himalayas and demonstrates the utility of chloroplast genomics in resolving taxonomic complexity and understanding evolutionary mechanisms in Aletris.