Abstract: Due to the high cost of whole-genome and the sampling difficulty of transcriptome sequencing in non-model plants, evolutionary studies often depend on next-generation sequencing (NGS) data. Nonetheless, current approaches typically focus on assembling chloroplast genomes or a few nuclear loci, leaving much of the genomic information from NGS underexploited. In this study, we employed multi-genomic datasets and advanced analytical pipelines to reconstruct a robust phylogenetic framework for 39 Bupleurum. Nuclear gene datasets and organellar genomes derived from next-generation sequencing were analyzed. We successfully reconstructed a robust phylogenetic framework for East Asian Bupleurum, in which two clades are strongly supported and all intersectional relationships are resolved. Phylogenetic discordance was mainly caused by incomplete lineage sorting and hybridization. Divergence dating estimated the origin of Bupleurum at approximately 50.76 Ma, with the two subgenera (Penninervia and Bupleurum) diverging at 42.26 Ma. The East Asian lineages emerged around 22.85 Ma, with Group I diverging at 11 Ma and Group II at 8.72 Ma. Notably, diversification rates remained stable within both East Asian groups. Combined with geological events and gene-environment correlations, precipitation seasonality (PSN) showed the strongest phylogenetic signals with SCO tree. The arid event in Central Asia may have driven the adaptation of East Asian Bupleurum (especially in East Asian Group II species) to arid, sun-exposed environments. By integrating phylogenetics, geology, and environmental data, this study provides a comprehensive understanding of the evolutionary history and adaptive strategies of Bupleurum in East Asia, offering valuable insights into the interplay between genetic and ecological factors in plant diversification.

Key words: Bupleurum, diversification, hybridization, phylogenomics