San Diego Management & Monitoring Program


Population Genomic Surveys for Six Rare Plant Species in San Diego County, California

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Type: report

Article abstract: 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 in response 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 genetic differentiation across each species’ range, identified isolated occurrences potentially 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 compatible management options for each species. A summary of the management workshop is included in this report. Overall, we found low genetic differentiation among occurrences across the San Diego region for all species, with the exception of A. ilicifolia. Relative inbreeding was low and consistent across sites, and genetic diversity across sites was variable, with noted exceptions. These findings allow for a wide array of management options that are compatible with panmictic population structure in five of the six surveyed species.

Number of pages: 72

Authors: Milano, Elizabeth; Vandergast, Amy;

Day: 19

Month: November

Year: 2018

Publisher: U.S. Geological Survey

Prepared for: San Diego Association of Governments;

Prepared by: U.S. Geological Survey, Western Ecological Research Center;

Keywords: genetic; genetic sampling; genetic studies; population genetic structure; Rare plant;

Species: Encinitas baccharis; San Diego thorn-mint; Otay tarplant; Willowy monardella; Orcutt's birds-beak; Salt marsh bird's-beak

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