Integrative evidence reveals a new species and traces of hybridization in Fritillaria (Liliaceae) from the Qinghai‐Tibet Plateau

Abstract The genus Fritillaria presents significant taxonomic challenges due to its morphological plasticity and complex evolutionary history. We herein describe Fritillaria elegans , a new species from Sichuan and Qinghai Provinces, China, and investigate the phylogenetic relationships and speciation processes within the plateau endemic clade using an integrative approach. Morphological comparisons and geographic distribution clearly distinguish F. elegans from its close relatives, F. sichuanica and F. przewalskii . Phylogenetic analyses based on both chloroplast genomes and 4752 nuclear single‐copy orthologous genes (SCOGs) support the monophyly of F. elegans. We also detected significant cytonuclear discordance within F. sect. Fritillaria from the Qinghai‐Tibet Plateau and adjacent regions, and identified ancient hybridization as its primary cause. Major phases of plateau uplift and climatic oscillations since the Pliocene likely drove both allopatric speciation and secondary contact. Our study not only adds a new species to Fritillaria but also demonstrates that hybridization has been a crucial mechanism in shaping the diversity of high‐altitude Fritillaria species. Furthermore, it highlights the efficacy of integrated genomic approaches for resolving complex phylogenetic relationships in this genus.