Incomplete lineage sorting, hybridization and polyploidization blurred phylogenetic relationships of gentians from...

Resolving evolutionary relationships among species undergoing radiation is challenging. Gentiana is a species-rich genus with a sub-cosmopolitan distribution, in which several sections have undergone recent radiation. In this study, we reassessed the phylogeny of Gentiana with particular focus on the controversial section Kudoa, and elucidated the complex phylogenetic relationship as well as their underlying causes in this section. Combining with a large number of single-copy orthologous genes and complete chloroplast genome sequences, we revised the delimitation of sections Kudoa and Isomeria, and proposed a new section Uniflorae. Our results suggested that G. yakushimensis, one of the most controversial species in Gentiana, should be transferred from section Kudoa to Pneumonanthe. The revised section Kudoa comprised two morphologically distinct series, and was composed of five genetic clades, with one clade corresponding to series Verticilatae. Although the backbone of Kudoa phylogeny was clear, current genetic data were insufficient to clarify species boundaries for several species. Evidence from single-copy orthologous genes and genome-wide SNPs revealed widespread hybridization against a background of extensive incomplete lineage sorting (ILS) in section Kudoa, accounting for the gene tree discordance. Genome size data indicated that tetraploids occurred in three out of the five clades, demonstrating that polyploidization further complicated the phylogeny of section Kudoa. In summary, Gentiana comprises 14 sections under our revised classification, and ILS, hybridization and polyploidization collectively contributed to the phylogenetic ambiguity of section Kudoa.