Population Genomic Survey of Six Rare Plant Species in San Diego County: raw sequence data. San Diego Rare Plants

San Diego County is a hotspot of biodiversity, situated at the intersection of the Baja peninsula, the California floristic province, and the desert southwest. Much of what qualifies this region as a hotspot is the high number of rare and endemic species, which persist alongside a major urban epicenter. San Diego County has implemented a strategic management plan that identifies species, based on low numbers of occurrences or high risk of threat, for which management practices are recommended. In creating a management plan for rare species, it is important to strike a balance between preserving locally adapted traits and maintaining genetic diversity, as species’ ranges fluctuate due to a changing climate and habitat fragmentation. This project, in partnership with the San Diego Natural History Museum, aims to provide a reference point for the current status of genetic diversity of rare plant species that will inform future preservation and restoration efforts. We focused on six threatened or endangered plant species: Acanthomintha ilicifolia, Baccharis vanessae, Chloropyron maritimum ssp. maritimum, Deinandra conjugens, Dicranostegia orcuttiana, and Monardella viminea. For each species, botanists from the San Diego Natural History Museum visited all known occurrences in San Diego County and collected leaf tissue for genetic and cytological analysis. We then developed a panel of genetic markers to estimate genetic diversity and population structure. This population genetic survey provided insight into the amount of gene flow occurring within each species’ range, identified isolated occurrences subject to inbreeding or genetic bottlenecks, and identified areas that are rich sources of allelic diversity. Finally, we convened a panel of experts to review results and develop specific recommendations for each species. A summary of the workshop is included in this report. Overall, we found low genetic differentiation for all species across the San Diego region, with the exception of A. ilicifolia. Relative inbreeding was low and consistent across sites and genetic diversity across sites was variable but not concerning, with noted exceptions. These positive findings allow for a wide array of management options that are compatible with panmictic population structure.