A phylogenomic perspective on gene tree conflict and character evolution in Caprifoliaceae using target enrichment data, with Zabelioideae recognized as a new subfamily

The use of diverse data sets in phylogenetic studies aiming for understanding evolutionary histories species can yield conflicting inference. Phylogenetic conflicts observed animal and plant systems have often been explained by hybridization, incomplete lineage sorting (ILS), or horizontal gene transfer. Here, we used target enrichment data, tree, network approaches to infer the backbone phylogeny family Caprifoliaceae, while distinguishing among sources incongruence. We 713 nuclear loci 46 complete plastome sequence from 43 samples representing 38 all major clades reconstruct using concatenation coalescence approaches. found significant tree conflict as well cytonuclear discordance. Additionally, coalescent simulations analyses suggested putative ancient hybridization subfamilies which seems be main source Ancestral state reconstruction six morphological characters revealed some homoplasy each character examined. By dating branching events, inferred origin Caprifoliaceae at approximately 66.65 Ma late Cretaceous. integrating evidence molecular phylogeny, divergence times, morphology, here recognize Zabelioideae a new subfamily Caprifoliaceae. This work shows necessity combination multiple identify Our study also highlights importance both plastid genomes deep shallow phylogenies plants.