Patterns of Genetic Variation in the endangered Harper's Beauty Harperocallis flava

Objectives: Preserving genetic variation in endangered species is critical to protecting their long-term evolutionary potential. Here, we examine genetic variation in the US federally endangered plant Harperocallis flava McDaniel (Harper's Beauty), an extremely rare plant with a distribution limited to a few occurrences near a single national forest, using whole genome skim sequencing and microsatellites.Results: We identify 15064 single nucleotide polymorphisms segregating in H. flava, as well as over 300 potential short nucleotide repeats. We characterized variation in SNPs across 48 individuals and microsatellites in a larger panel of 59 individuals. Patterns of genetic variation indicate that the remaining occurrences of H. flava have low levels of genetic variation and that a moderate amount of clonal reproduction occurs, although individuals are not genetically identical. We find limited genetic differentiation between stands in different management units (average FST of 0.07 in SNPs), either on a roadside or in forest interior sites. The roadside sites do bear genetic variation not present in the forest interior, making it worthy of conservation. We advocate for continued protection of the roadside habitat, with monitoring of existing stands and ex situ preservation.