Population genetic structure and patterns of hybridization of the rare Lupinus tidestromii and its congener L. chamissonis (Fabaceae) inform seed sourcing strategies for population augmentation and reintroduction

Human activities can impact the genetic diversity of populations, making them more vulnerable to extinction. Rare species are at an increased risk of negative genetic consequences of human activities, but understanding genetic diversity in rare species requires comparison to more common congeners. Hybridization, a common phenomenon in plants, can provide genetic rescue of genetically depauperate populations or put rare species at risk of being “swamped” out of the population. Human-mediated dispersal can create novel sympatry between previously allopatric species, fostering hybridization. The endangered Tideström’s lupine (Lupinus tidestromii Greene), endemic to the coastal dune ecosystem of California, co-occurs and hybridizes with the more common dune bush lupine (L. chamissonis Eschsch.). We characterized 532 individuals from sympatric and non-sympatric sites across both species’ entire geographic ranges using genotyping-by-sequencing technology to identify 1,377 single-nucleotide polymorphisms. We analyzed population structure, genetic diversity within and among populations, and hybridization between L. tidestromii and L. chamissonis. Genetic diversity was lower in L. tidestromii than in the more common L. chamissonis. Both species showed strong population structure which coincided with a deep intraspecific split between populations north and south of San Francisco. Hybridization was confirmed at all sites of co-occurrence. Evidence of hybridization at multiple non-sympatric sites indicated former co-occurrence and recent local extirpations. From these results, we make specific management recommendations for L. tidestromii. Seeds from large populations in the north can be used to augment the smaller populations in this region and to reintroduce this endangered species back to extirpated sites. Our results highlight how studies considering spatial patterns of genetic diversity, hybridization and private alleles can be used to make clear recommendations for conservation actions.