Genomic analysis reveals population structure and guides conservation actions of the endangered plant, Pedicularis furbishiae (Orobanchaceae)

Abstract Pedicularis furbishiae is a globally rare, hemiparasitic perennial restricted to dynamic riverbank habitats along the Wolastoq (Saint John) River in Maine, USA, and New Brunswick, Canada. The species now faces severe threats from habitat fragmentation, altered hydrology, and demographic collapse—particularly in New Brunswick, where several subpopulations have been recently extirpated and where recovery activities are being undertaken to protect the species from further decline. In this study, we assembled the first reference genome for P. furbishiae and conducted reduced-representation genotyping by sequencing (GBS) across 69 individuals sampled from all major subpopulations. Despite recovering a modest number of SNPs (152), we identified four genetically distinct populations: one in Maine with some subpopulation structure and three isolated subpopulations in New Brunswick. Genetic diversity was low overall, with elevated inbreeding coefficients in Grand Falls and Medford populations. All subpopulations contain private alleles, indicating the importance of conserving even the most demographically vulnerable sites. These findings support an integrated conservation strategy combining seed banking, ex situ propagation, and genetic rescue through controlled outcrossing among subpopulations, and provide a critical genomic baseline to inform the recovery of this imperiled species through population reinforcement and reintroduction across its range.