San Diego Management & Monitoring Program


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

in progress

Project description

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?


Project protocol

Name: Rare Plant Genomics: 2016-2017

Description: DNA will be extracted from leaves using standard CTAB protocol or plant extraction kits to generate a large quantity of high quality DNA. We will use an adapted RAD-Seq or genotyping by sequencing (GBS) protocol to identify SNPs for each species. These methods use restriction enzymes to sample the same set of loci across individuals. DNA samples for each individual are digested using restriction enzymes such as ApeKI, a common-cutting enzyme that works well in plants, and PstI, a rare-cutting enzyme. Following digestion, PCR adapters and unique individual barcodes are ligated to samples, and these gene regions are PCR amplified. Sequencing will be performed on an Illumina or equivalent platform, capable of producing 150-250 bp reads. In order to keep sequencing costs minimal, all samples will be processed and sequenced together in large batches. Resulting reads will be processed and assembled for further genetic analysis.


Project spatial boundary

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Project focus

Project type: Genetic study

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


Implementing entities

Investigator: Amy Vandergast; Jon Rebman

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

Point of contact: Amy Vandergast


Files and documents