Hyb-Seq data of 43 species of the plant Caprifoliaceae and three species from closely related genera Targeted loci Genome sequencing and assembly

The use of diverse datasets in phylogenetic studies aiming for understanding evolutionary histories of species can yield conflicting inference. Phylogenetic conflicts observed in animal and plant systems have often been explained by hybridization, incomplete lineage sorting (ILS), or horizontal gene transfer. Here, we use target enrichment data and species tree and species network approaches to infer the backbone phylogeny of the family Caprifoliaceae, while distinguishing among sources of incongruence. We explore the phylogenetic conflict in Caprifoliaceae using 43 samples representing 38 species from seven major clades. We used a target enrichment approach to generate 713 nuclear loci and 46 protein-coding sequences of plastome data to reconstruct the phylogeny of the group using concatenation and coalescence approaches.