Target sequence capture data shed light on the deeper evolutionary relationship on the subgenus Chamaecerasus of Lonicera (Caprifoliaceae)

Abstract The genus Lonicera L. is widely distributed and is well-known for its high species richness and morphological diversity. Previous studies have suggested that many sections of Lonicera are not monophyletic and phylogenetic relationships within the genus are still poorly known. In this study, we sampled 37 accessions of Lonicera , covering four sections of subgenus Chamaecerasus plus six outgroup taxa to recover the main clades of Lonicera based on sequences of nuclear loci generated by target enrichment and cpDNA from genome skimming. We found extensive cytonuclear discordance across the subgenus. Both nuclear and plastid phylogenetic analyses supported subgenus Chamaecerasus sister to subgenus Lonicera . Within subgenus Chamaecerasus , sections Isika and Niatoon were polyphyletic. Based on the nuclear and chloroplast phylogenies we propose to merge Lonicera korolkowii into section Coeloxylosteum and Lonicera caerulea into section Nintooa. In addition, Lonicera is estimated to have originated in the late Miocene (19.84 Ma). The stem age of section Nintooa was estimated to be 17.97 Ma (95% HPD: 13.31- 22.89). The stem age of subgenus Lonicera was estimated to be 16.35 Ma (95% HPD: 9.33- 45.15). Ancestral area reconstruction analyses indicate that Lonicera originated in the Qinghai Tibet Plateau (QTP) and Asia, with subsequent dispersal into other areas. The aridification of the Asian interior possibly promoted the rapid radiation of Lonicera within this region, and the uplift of the QTP appears to have triggered the dispersal and recent rapid diversification of the genus in the QTP and adjacent regions. Overall, this study provides new insights into the taxonomically complex lineages of Lonicera at the section level and the process of speciation.