Phylogenomics of the <i>Bupleurum</i> in East Asia: Insights into distribution patterns and diversification

Abstract Due to the high cost of whole‐genome sequencing 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 multigenomic data sets and advanced analytical pipelines to reconstruct a robust phylogenetic framework for 39 Bupleurum . Nuclear gene data sets and organellar genomes derived from NGS were analyzed. We successfully reconstructed a robust phylogenetic framework for East Asia (EA) Bupleurum , in which two clades were strongly supported and all intersectional relationships were resolved. Phylogenetic discordance was mainly caused by incomplete lineage sorting and hybridization. Divergence dating estimated the origin of Bupleurum at ∼50.76 Ma, with the two subgenera ( Penninervia and Bupleurum ) diverging at 42.26 Ma. The EA 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 EA groups. Combined with geological events and gene–environment correlations, precipitation seasonality (PSN) showed the strongest phylogenetic signals with the Single Copy Orthologue (SCO) tree. The arid event in Central Asia may have driven the adaptation of EA Bupleurum (especially in EA 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 EA, offering valuable insight into the interplay between genetic and ecological factors in plant diversification.