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.