Target enrichment phylogenomics and biogeographic analyses unravel rapid radiation and reticulate evolution between Hainan-South China mainland -Vietnam in Section Nintooa (Lonicera, Caprifoliaceae)

Abstract

The South China mainland and nearby islands are biodiversity hotspots. Section Nintooa, widely distributed across mainland China, Vietnam, and Hainan Island, exhibits a typical disjunct distribution pattern. However, the origins of the flora of Hainan Island and the phylogenetic relationships within Section Nintooa remain contentious. In this study, we collected 81 samples encompassing all recognized species of Section Nintooa, along with samples from other sections of Lonicera. We reconstructed the phylogenetic relationships using 491 orthologous nuclear genes and complete plastomes generated by target enrichment and genome skimming sequencing. Our nuclear gene-based species and concatenated trees support the monophyly of Section Nintooa. The species tree indicates that the Vietnamese and Hainan populations form sister clades. However, the plastome results indicate that Section Nintooa is polyphyletic, with subsection Volubilis forming a monophyletic group and subsection Calcaratae forming a sister clade with other members of subgenus Chamaecerasus. Our hybridization network analysis reveals extensive gene flow within Section Nintooa, whereas subsection Calcaratae shows no gene flow with subsection Volubilis, leaving the origin of Calcaratae unclear. Lonicera species from Hainan Island exhibit unstable phylogenetic positions and underwent a rapid radiation during the Miocene. Biogeographical results indicate that populations from Vietnam and Hainan both originated from mainland China. Overall, our findings enhance the understanding of the evolutionary diversification history of Lonicera.