Phylogenomic analyses of the East Asian endemic Abelia (Caprifoliaceae) shed insights into the temporal and spatial diversification history with widespread hybridization

• Background and Aims Abelia (Caprifoliaceae) is a small genus with five species, including one man-made hybrid and several natural hybrids. The genus has a discontinuous distribution in Mainland China, the Taiwan Island, and the Ryukyu Islands, providing a model system to explore mechanisms of species dispersal in the East Asian flora. However, the current phylogenetic relationships within Abelia remain uncertain.

• Methods In this study, we reconstructed the phylogenetic relationships within Abelia using nuclear loci generated by target enrichment and plastomes from genome skimming. Divergence time estimation, ancestral area reconstruction, and ecological niche modelling (ENM) were used to examine the diversification history of Abelia.

• Key Results We found extensive cytonuclear discordance across the genus. By integrating lines of evidence from molecular phylogenies, divergence times, and morphology, we propose to merge A. macrotera var. zabelioides into A. uniflora. Network analyses suggested that there have been widespread and multiple hybridization events among Abelia species. These hybridization events may have contributed to the speciation mechanism and resulted in a high observed morphological diversity. The diversification of Abelia began in the early Eocene, followed by A. chinensis var. ionandra colonizing the Taiwan Island in the Middle Miocene. The ENM results suggested an expansion of climatically suitable areas during the Last Glacial Maximum and range contraction during the Last Interglacial. Disjunction between the Himalayan-Hengduan Mountain region (HHM) and the Taiwan Island is most likely the consequence of topographic isolation and postglacial contraction.

• Conclusions We used genomic data to reconstruct the phylogeny of Abelia and found a clear pattern of reticulate evolution in the group. In addition, our results support shrinkage of postglacial range and the heterogeneity of the terrain have led to the disjunction of the Mainland China-Taiwan Island. This study provides important new insights into the speciation process and taxonomy of Abelia.