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

Open-File Report 2018-1175
Prepared in cooperation with the San Diego Association of Governments
By:  and 



San Diego County is a hotspot of biodiversity, situated at the intersection of the Baja peninsula, the California floristic province, and the desert southwest. This hotspot is characterized by a 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 level 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 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.

Suggested Citation

Milano, E.R., and Vandergast, A.G., 2018, Population genomic surveys for six rare plant species in San Diego County, California: U.S. Geological Survey Open-File Report 2018–1175, 60 p., https://doi.org/10.3133/ofr20181175.

ISSN: 2331-1258 (online)

Study Area

Table of Contents

  • Acknowledgments
  • Abstract
  • Introduction
  • Methods
  • Results and Discussion
  • References Cited
  • Glossary
  • Appendix 1
  • Appendix 2
Publication type Report
Publication Subtype USGS Numbered Series
Title Population genomic surveys for six rare plant species in San Diego County, California
Series title Open-File Report
Series number 2018-1175
DOI 10.3133/ofr20181175
Year Published 2018
Language English
Publisher U.S. Geological Survey
Publisher location Reston, VA
Contributing office(s) Western Ecological Research Center
Description vii, 61 p.
Country United States
State California
County San Diego County
Online Only (Y/N) Y
Google Analytic Metrics Metrics page
Additional publication details