A phylogenomic analysis of Lonicera and its bearing on the evolution of organ fusion

Abstract Premise The ~140 species of Lonicera are characterized by variously fused leaves, bracteoles, and ovaries, making it a model system for studying the evolution and development of organ fusion. However, previous phylogenetic analyses, based mainly on chloroplast DNA markers, have yielded uncertain and conflicting results. A well‐supported phylogeny of Lonicera will allow us to trace the evolutionary history of organ fusion. Methods We inferred the phylogeny of Lonicera using restriction site–associated DNA sequencing (RADSeq), sampling all major clades and 18 of the 23 subsections. This provided the basis for inferring the evolution of five fusion‐related traits. Results RADSeq data yielded a well‐resolved and well‐supported phylogeny. The two traditionally recognized subgenera ( Periclymenum and Chamaecerasus ), three of the four sections ( Isoxylosteum , Coeloxylosteum , and Nintooa ), and half of the subsections sampled were recovered as monophyletic. However, the large and heterogeneous section Isika was strongly supported as paraphyletic. Nintooa , a clade of ~22 mostly vine‐forming species, including L. japonica , was recovered in a novel position, raising the possibility of cytonuclear discordance. We document the parallel evolution of fused leaves, bracteoles, and ovaries, with rare reversals. Most strikingly, complete cupules, in which four fused bracteoles completely enclose two unfused ovaries, arose at least three times. Surprisingly, these appear to have evolved directly from ancestors with free bracteoles instead of partial cupules. Conclusions We provide the most comprehensive and well‐supported phylogeny of Lonicera to date. Our inference of multiple evolutionary shifts in organ fusion provides a solid foundation for in depth developmental and functional analyses.