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

Abstract

The South China mainland and nearby islands are biodiversity hotspots. SectionNintooa, 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 SectionNintooaremain contentious. In this study, we collected 81 samples encompassing all recognized species of SectionNintooa, along with samples from other sections ofLonicera. 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 SectionNintooa. The species tree indicates that the Vietnamese and Hainan populations form sister clades. However, the plastome results indicate that SectionNintooais polyphyletic, with subsectionVolubilisforming a monophyletic group and subsectionCalcarataeforming a sister clade with other members of subgenusChamaecerasus. Our hybridization network analysis reveals extensive gene flow within SectionNintooa, whereas subsectionCalcarataeshows no gene flow with subsectionVolubilis, leaving the origin ofCalcarataeunclear.Loniceraspecies 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 ofLonicera.