Plastid genome data provide new insights into the phylogeny and evolution of the genus Epimedium.

[Display omitted] • The phylogeny and evolution of Epimedium based on 45 plastomes were first studied systematically. • Four types of plastomes were recognized according to the variation of inverted repeat boundary. • A strong support for the sister relationship of sect. Macroceras and sect. Diphyllon was revealed. • The diversification of Epimedium was estimated in the early Pleistocene (∼2.11 Ma). • Long spur (large-flowered group) constituted the plesiomorphic state of Epimedium. • Disharmony existed between molecular phylogeny and traditional classification of sect. Diphyllon. Epimedium L., the largest herbaceous genus of Berberidaceae, is one of the most taxonomically difficult representatives. The classification and phylogenetic relationships within Epimedium are controversial and unresolved. For the first time, we systematically studied the phylogeny and evolution of Epimedium based on plastid genome (plastome) data for better understanding this enigmatic genus. We explored the molecular phylogeny, assessed the infrageneric classification, estimated the divergence times, and inferred the ancestral states for flower traits of Epimedium based on 45 plastomes from 32 species. The Epimedium plastome length ranged from 156,635 bp to 159,956 bp. Four types of plastome organization with different inverted repeat boundary changes were identified. Phylogenetic analysis revealed a strong support for the sister relationship of sect. Macroceras and sect. Diphyllon but did not provide a distinct route for petal evolution in sect. Diphyllon. Disharmony between phylogenetic relationships and traditional classification of sect. Diphyllon was observed. Results from divergence time analysis showed that Epimedium diverged in the early Pleistocene (~2.11 Ma, 95% HPD = 1.88–2.35 Ma). Ancestral character state reconstructions indicated transitions from long spur (large-flowered group) to other petal types (small-flowered group) in Epimedium. These findings provide new insights into the relationships among Epimedium species and pave the way for better elucidation of the classification and evolution of this genus. [ABSTRACT FROM AUTHOR]