Abstract
Past studies of Sophora sect. Edwardsia using traditional phylogenetic and population genetic markers have been unable to produce a resolved species phylogeny of this recent radiation of shrubs and trees. Here we examined the relationships within and between the New Zealand species of Sophora sect. Edwardsia using next‐generation sequencing. We generated genome‐wide SNP data with double‐digest restriction site‐associated DNA sequencing (ddRADseq). Sophora prostrata was resolved as sister to the remaining species in all analyses. Relationships between the remaining taxa exhibited a high level of conflict with many of the genetic clusters reflecting geography rather than species boundaries. This result contrasts with a previous study, which was able to differentiate most species using genotype data from nine microsatellite loci. Overall our ddRADseq results indicate a high level of interspecific hybridisation and introgression within the group, which blurs the taxonomic boundaries throughout the distributional ranges of most species. Hybridisation and introgression among regional metapopulations comprising closely related species may increase the adaptive potential to respond to changing local conditions, and at the same time selection acts to maintain their genetic identity in the face of ongoing gene flow.