Data from: Geography and admixture shape the genome-scale phylogeny of North American Delphinium

The genus Delphinium exemplifies the complexity of plant diversification in mountainous regions, where rapid speciation, hybridization, and morphological convergence frequently obscure species boundaries. The North American lineage Delphinium sect. Diedropetala has rapidly radiated across a range of ecological habitats, from alpine tundra to desert grasslands, forming an iconic component of western wildflower communities. Despite decades of taxonomic study, phylogenetic relationships within this group remain poorly resolved. Here, we present a genome-scale phylogeny of 34 taxa using ddRAD-seq data from 150 individuals sampled across their geographic ranges. Our results reveal strong phylogenetic structure corresponding to biogeographic regions, including several well-supported clades that cut across existing taxonomic subsections, emphasizing the need for taxonomic revision. Hybridization and introgression are widespread, occurring both within and between these regional clades. Most species are connected through a syngameon-like network of introgression, with few widespread species acting as central hubs. We describe six higher-level clade names and use an agent-based artificial intelligence analysis to identify morphological synapomorphies that align with our genomic findings. Our study demonstrates that geography and gene flow have played a dominant role in shaping the evolutionary history of Delphinium, offering a framework for revising its taxonomy and informing future conservation efforts.