Phasing Hyb-Seq loci from two combined bait sets to investigate phylogenetic patterns of hybridization within Boechera s.s. (Brassicaceae)

Background and Aims The complex landscape of hybridization and apomixis that characterizes the genus Boechera (Brassicaceae) is only beginning to be understood. Boechera, with over 80 recognized sexual species predominantly in North America, has emerged as a key model system for studying apomixis, primarily because of its remarkable capacity to form apomictic hybrids. This study builds on recent Hyb-Seq analyses by incorporating seven phased apomictic taxa into an existing topology of 108 sexual samples, thereby enhancing the existing phylogenetic framework and refining our understanding of the taxonomy of Boechera. Methods A modified version of HybPhaser was used to phase 1114 Hyb-Seq loci from two bait sets, Angiosperms353 (with broad applicability across flowering plants) and a Brassicaceae-specific bait set (designed for use in the mustard family). These loci were phased for seven samples hypothesized to be apomictic diploids of hybrid origin based on pollen morphology and microsatellite data. Phylogenies were subsequently constructed with RAxML-NG and wASTRAL. Key Results We successfully phased all seven putative diploid hybrids of Boechera across 1114 loci, incorporating 14 phased hybrid tips into an existing phylogeny that previously included only sexual diploids. These results robustly support previously hypothesized hybrid relationships based on microsatellite data. Conclusions In this proof-of-concept study, we integrated phased hybrid tips into an existing phylogeny of sexual diploid Boechera species to reveal the intricate evolutionary history of the group and showcase the utility of phasing multiple Hyb-Seq bait sets. By exploring hybridization in Boechera we aim to uncover the underlying genetic and ecological factors that contribute to the remarkable diversity observed in this genus and related groups. The dynamic evolution of Boechera exemplifies the significant roles of hybridization and apomixis in shaping biodiversity and adaptive landscapes within flowering plants.