Phylogenomics unravels the early divergence and diversification in Bignoniaceae

Bignoniaceae, a pantropical family comprising 79 genera and 901 species, exhibits remarkable morphological and ecological diversity, including lianas, shrubs, trees, and high-elevation herbs. Reconstructing the early evolutionary history of Bignoniaceae has been particularly challenging due to ancient hybridization/introgression and incomplete lineage sorting (ILS). In this study, we re-evaluated the deep branching relationships within Bignoniaceae using phylogenomic data from 1275 single/low-copy nuclear genes and the Angiosperms353 dataset, complemented with chloroplast genomes and quantified the roles of hybridization, and ILS in shaping the family's evolutionary history. Our results robustly resolved Bignoniaceae into ten major clades, with the Argylia clade sister to a clade containing Oroxyleae, the Delostoma clade, Catalpeae, Bignonieae, the Tabebuia alliance, and the Paleotropical clade, while the Delostoma clade and Catalpeae formed a monophyletic lineage. Divergence time estimation revealed a rapid diversification during the early Eocene, coinciding with the Early Eocene Climatic Optimum. Several lines of evidence indicate that the predominant factor underlying phylogenetic conflicts across deep nodes is ILS. Introgression/hybridization also contributed significantly, with at least three ancient events detected: between Tourrettieae and the Delostoma clade, between the Delostoma clade and Bignonieae, and a major introgression from the Argylia clade to the Oroxyleae- Delostoma -Catalpeae-Bignonieae- Tabebuia -Paleotropical clade. This study provides a robust phylogenetic foundation and comprehensive evolutionary synthesis for Bignoniaceae, shedding new light on its early diversification. • Phylogenomic analyses of early-diverging Bignoniaceae were conducted based on chloroplast genome and nuclear genes. • Robust phylogeny resolved Bignoniaceae into ten major clades. • Early Bignoniaceae evolution was driven by ILS • Divergence time estimation revealed that rapid radiation of Bignoniaceae occurred during the early Eocene.