Population Genetic Analysis of 6 Rare Plant Species in San Diego County

The first phase (years 1-2) of this research task focused on genetic and cytological screening to determine potential ploidy and population genetic differences among occurrences within species. Upon completion, an expert panel convened to review results of the genetic studies and develop specific recommendations for each species relative to the MSP management objectives planned for that species. These recommendations included designing appropriate common garden or reciprocal transplant studies to determine the fitness consequences of using seed from different populations to increase population size or establish new occurrences. The recommendations also addressed MSP objectives involving seed banking and seed bulking needs for each species. The expert panel also made recommendations on genetic management of populations, including whether genetic connectivity needs to be enhanced or restored to maintain or increase genetic diversity. Recommended and approved studies will be added in the second phase (beginning in year 3). The following questions were specifically addressed in phase 1: 1. What is the status of documented occurrences? 2. Is there evidence of mixed ploidy levels among or within occurrences? 3. What is current genetic structure among and within occurrences in the MSPA? How vulnerable are the occurrences to genetic drift and loss of genetic diversity and is there gene flow between occurrences? 4. Are there signatures of genetic bottlenecks or lower genetic diversity in populations that have undergone recent reductions due to fire, drought, or other causes, or evidence of local adaptation? 5. Based on the cytological and genetic analysis, what are the recommendations for common garden and reciprocal transplantations, for collecting, bulking and distributing seeds for enhancing existing occurrences, and for establishing new occurrences?

Genetic study
Rare Plants
in progress
Project Focus

Encinitas baccharis, Orcutt's bird's-beak, Otay tarplant, saltmarsh bird's-beak, San Diego thorn-mint, Willowy monardella

Amy Vandergast; Jon Rebman

San Diego Natural History Museum; U.S. Geological Survey, Western Ecological Research Center

Amy Vandergast

Project Protocol

Orcutt's birds-beak Dicranostegia orcuttiana

Goal: Maintain or enhance existing Orcutt's bird's-beak occurrences and establish new occurrences, as needed, to ensure multiple conserved occurrences with self sustaining populations to increase resilience to environmental and demographic stochasticity, maintain genetic diversity, and ensure persistence over the long term (>100 years) in coastal sage scrub vegetation communities.

Regional NFO 2017 SL

Management units: 1, 3

In 2017, complete the study begun in 2016 to characterize the population genetic structure, gene flow, and genetic diversity for Orcutt's bird's-beak occurrences (see occurrence table). The study will determine if there is evidence of mixed ploidy levels within or among occurrences; evaluate vulnerability of occurrences to genetic drift and loss of genetic diversity; assess the level of gene flow among occurrences; identify if there are signatures of genetic bottlenecks or low genetic diversity in occurrences that have undergone recent reductions; and look for evidence of local population adaptation. Based on the results of the genetic analyses, management recommendations will include whether common garden and reciprocal transplantations are necessary before proceeding with population enhancement or restoration and will provide specific recommendations for collecting, bulking and distributing seed to enhance existing occurrences or establish new occurrences.

Action Statement Action status Projects
RES-1 Use BMPs to collect plant material for genetic samples at Orcutt's bird's-beak occurrences in the MSPA. In progress Population Genetic Analysis of 6 Rare Plant Species in San Diego County
RES-2 Hold a workshop of scientists, rare plant experts, and land managers to develop management recommendations based upon the results of genetic analyses. In progress
RES-3 Evaluate the overall long-term genetic trajectory for Orcutt's bird's-beak. In progress
RES-4 Submit project metadata, genetic datasets and analyses, and report with management recommendations to the MSP Web Portal. In progress
Criteria Deadline year
Genetic Study with Management Recommendations Completed in 2017 2021
Threat Name Threat Code
Loss of connectivityLOSCON
Code Obj. code Statement
DICORC-6 MGT-PRP-SBPL In 2020, begin preparing an Orcutt's bird's-beak section in the MSP Seed Collection, Banking and Bulking Plan that incorporates best science and management practices (Wall 2009, KEW 2016) to preserve genetic diversity and rescue occurrences in case of catastrophic disturbance. The plan should include recommendations from 2017-2019 seed collection and bulking efforts conducted by San Diego Zoo's Institute for Conservation Research and from the 2016-2017 genetic study to collect and store seeds over the long term at a permanent, established conservation seed bank (e.g., Institute for Conservation Research Native Plant Seed Bank, Rancho Santa Ana Botanic Garden Seed Conservation Program) and for providing a source of seeds for management purposes. The plan should include recommendations for: collecting and storing seeds for conservation banking; management oriented research; rescuing occurrences after catastrophic disturbances; and seed bulking and out-planting to augment extant occurrences or to establish new occurrences with consideration of genetic implications for population sustainability.
DICORC-8 MGT-PRP-MGTPL In 2020, begin preparing an Orcutt's bird's-beak section in the MSP Rare Plant Management Plan that prioritizes management actions to maintain large occurrences and expand at least 3 small occurrences on Conserved Lands (see occurrence table) based upon an assessment of data on occurrence status, habitat and threats. Prepare management recommendations for re-establishment of historic occurrences or establishment of new occurrences if determined to be necessary for gene flow and for long term persistence. Minimum criteria for enhancement are to reduce invasive annual nonnative plants and thatch to less than 20% absolute cover within the occurrence
File name Lead Author Year Type
Population Genomic Surveys for Six Rare Plant Species in San Diego County, California Milano, Elizabeth; Vandergast, Amy 2018 report
Rare Plant Genomics Methods and Timeline Vandergast, Amy 2016 other
SDNHM 2018 Rare Plant Genetic Sampling Final San Diego Natural History Museum 2018 report