Diversification and hybridization in Andinocleome (Cleomaceae)

Andinocleome sensu lato of the Andean clade of Cleomaceae contains eight species and presents an important study group for research in population dynamics, species boundaries, and hybridization as there are morphological variations within species (particularly A. anomala), questionable species boundaries, and hypothesized hybridization in the genus. In this research, we used target sequence capture and the Angiosperms353 probe set to generate data from 65 herbarium vouchers. These data were combined with previously published sequence data from an additional 112 specimens in the genus to resolve species boundaries and identify genetic diversity within species. The Hyb-Seq nuclear phylogenetic tree resolved species boundaries and provides an important framework for future studies in Andinocleome. Few studies in plants have applied the Angiosperms353 probe set to address population level dynamics using herbarium specimens, and our study expands on this research. We identified genetic variation between intraspecific populations by sampling from two "mass collections" representing morphological variation in the species A. anomala, in addition to sampling across the genus. We also used off-target chloroplast regions to construct a chloroplast phylogenetic tree; discordance between the nuclear and chloroplast trees indicated introgressive hybridization within Andinocleome. STRUCTURE, principal component analyses, SNaQ, and HyDe analyses further supported hybridization between multiple species within the clade. Our study resolves species boundaries despite significant hybridization and represents the most comprehensive genetic study to date in Andinocleome. We demonstrate that the Angiosperms353 probe set can be appropriate for identifying population structuring within species, even when utilizing herbarium specimens.