Genetic Analysis of Six Rare Plant Species

By Cindy Burrascano, Chapter Book Sales

San Diego Management and Monitoring Program (SDMMP) funded and organized a study to look at the genetics of 6 rare plant species that occur in San Diego: Acanthomintha ilicifolia (San Diego Thornmint), Baccharis vanessae (Encinitas Baccharis), Chloropyron maritimum ssp. maritimum (Salt Marsh Bird’s-beak), Dicranostegia orcuttiana (Orcutt’s Bird’s-beak), Deinandra conjugens (Otay Tarplant) and Monardella linoides (Willowy Monardella). The project was headed by Amy Vandergast of the U.S. Geologic Survey (USGS) and Jon Rebman of the San Diego Natural History Museum (SDNHM). Margie Mulligan (SDNHM) collected specimens, visiting numerous populations for the species, documenting the population sizes in either 2016 or 2017 and the general conditions at the sites, and collecting material for genetic analysis by USGS staff. Salt marsh bird’s-beak was sampled throughout its range (Punta Azufre and Bahia Falsa near San Quintin in Baja California, Mexico; and in California at Newport Bay in Orange County; Naval Base Ventura/Point Mugu in Ventura County; Ormond Beach, Carpinteria, in Santa Barbara County; and Morro Bay in San Luis Obispo County) and work was partially funded by the U.S. Navy. They were also fortunate to have Marine Corps Base Camp Pendleton and Marine Corps Air Station Miramar participate in the studies by allowing visits to the bases and collection of materials, which was particularly critical for understanding Willowy Monardella. Margie’s report A Report of Genetic Sample Collections and Curation for Six Rare Plants within the San Diego MSPA San Diego County, California, can be viewed and downloaded from the SDMMP website ( The report from the genetic analysis portion of the study will be posted at the website, hopefully, in the near future. If you have never looked through the reports posted at the website you are in for a treat. A variety of studies have been conducted on various animal and plant species. I unfortunately have misplaced my notes on the meeting that was held and only really remember those aspects pertinent to populations I work with. I guess we will all have to go to the SDMMP webpage periodically to see if the report is posted yet to get the information.

Depending on the population size, Margie sampled up to 20 individuals for each occurrence. Five of the individuals were collected for ploidy analysis. One voucher specimen was collected for each occurrence and is housed at the SDNHM.

San Diego Thornmint is an annual that grows on clay soils in many parts of the county from Carlsbad to the Otay Lakes area to Alpine. Weeds are an issue for most occurrences of the species. Population size varies in any given year largely depending on rainfall levels. 47 occurrences were identified; 7 of these are believed extirpated and site visits for this study found no plants in 8 additional occurrences. Margie found population sizes from 0 to 750,000 plants. She found 2 large populations (35,000 and 750,000 plants), 5 with 1,000 to 5,000 plants and 18 that had less than 300 plants.

Ploidy difference has been documented in the past for San Diego Thornmint (DeWoody et al. in Conservation Genetics 2018) although the current study did not confirm that finding. In the prior study, 4 of 21 occurrences examined were tetraploid, 11 were a mix of diploid and tetraploid, 4 were a mix of tetraploid and hexaploid, 1 was mostly tetraploid but had a few diploid and hexaploidy, and 1 population was hexaploid. The paper can be downloaded from the SDMMP website as it contains far more information than discussed here, including common garden experiments.

Encinitas Baccharis also has a wide distribution, from Camp Pendleton to Otay Mountain to Escondido, and can be found on sandy soils in Encinitas to metavolcanic soils on Otay Mountain, although it was reported all populations were found on sandy soil. It is likely this species has more populations, as it does not stand out and is easily overlooked. It is a dioecious shrub, meaning there are male plants and female plants. Sixteen sites were reported for the species. Population sizes ranged from 9 to 700 plants with 12 of the populations having less than 50 plants.

There were 29 occurrences of Salt Marsh Bird’s-beak with only 7 being in the Master Occurrence Matrix database. Twenty-two occurrences were added to the database, with 3 at Tijuana Estuary, one at Camp Surf on Naval Base Coronado, 3 from Baja California, Mexico, 5 at Naval Base Ventura, 2 at Carpinteria Marsh, 4 at Morro Bay, 2 at Ormond Beach and 2 at Newport Bay. The reports of plants at Border Field State Park and the Naval Radar Receiving Facility, Naval Base Coronado, could not be confirmed as currently present and may have been extirpated from the sites. Populations ranged from 3 to 3,000 individuals with distributions restricted by slight elevational changes meaning global warming will impact the species distribution. Populations thought to be established by human hand tended to have lower diversity (Sweetwater Marsh, Dog Beach).

Otay Tarplant occurs in the southern part of the county, in Dennery Canyon and Chula Vista east to Rancho Jamul Ecological Reserve. This annual is also very responsive to rainfall. Weed competition is an issue for the species with 15 of 17 of the sites visited having prominent levels of weeds, mostly Brachypodium distachyon (Purple False Brome) or Centaurea melitensis (Tocalote). Five of the occurrences had vegetation defined by a non-native species (Bromus rubensAvena barbata, etc.). The species grows on clay soils with the exception being a population in Paradise Valley growing on sandy loam or loam soils.

Nine occurrences of Orcutt’s Bird’s-beak are known with the species growing in the south coastal part of the county. Permission was granted to visit 8 of the sites but only 7 supported the species and a landowner prohibited collection from one site. Population sizes ranged from 50 to 10,000 plants with no plants being found at Dennery Ranch. All sites that supported the species had sandy soils and non-natives were observed in 50% of the sites. Asphodelus fistulosus (Onionweed) was called out as dominating the Rice Canyon site in Chula Vista that supports the species, although other weedy species were also present at other sites. Staff recommended looking to Baja California for long term preservation of the species as only one site has a sizable population of 10,000 plants (California Terraces project). Border Field State Park had 1,634 plants, Otay River Valley 800 plants, Rice Canyon 50 plants, Tijuana River Valley/Spooner Mesa 150 plants and Valle Tranquilo, Fusiques Arroyo in Baja, 300 plants.

Willowy Monardella is a small shrub largely occurring on Marine Corp Air Station Miramar. It grows in ephemeral drainages where, when urbanization occurs around the canyons like in Mira Mesa and San Clemente Canyon, water gets dumped into the canyons and habitat converts to a wetter environment than the plant tolerates or erosion becomes a problem washing away plants. Freeway construction has also physically eliminated parts of populations (I-15 and SR-52). If this species persists, we will have the military to thank, first the Navy and now the Marines.

Genetics Analysis

DNA was extracted from leaves using standard CTAB protocol or plant extraction kits to generate a large quantity of high quality DNA. An adapted RAD-Seq or genotyping by sequencing (GBS) protocol was used 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 were 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 were ligated to samples, and these gene regions were PCR amplified. Sequencing was performed on an Illumina or equivalent platform, capable of producing 150-250 bp reads. To keep sequencing costs minimal, all samples were processed and sequenced together in large batches. Resulting reads were then processed and assembled for further genetic analysis.