San Diego Zoo Global

Sula Vanderplank, San Diego Zoo Global

The cross-border seedbanking initiative affectionately known as ‘Baja Rare’ targets around 65 taxa that are documented to be rare, threatened or endangered both sides of the MX/US border.  Many of these plants are far better-known in the US than in Mexico and as a result, our program has had to start with significant reconnaissance and surveys to find the populations historically documented.  In four cases (Streptanthus campestris, Navarrettia peinsularis, Erythranthe purpurea and Acmispon haydonii), expert botanical participation has revealed mis-identifications which make each of these three plants significantly rarer than previously assumed.  This project has also revealed at least one new highly restricted endemic taxon and multiple taxa worth of further study.  The role of the expert botanist is essential.

Date Recorded: 
Friday, October 9, 2020

Authors: Stacy Anderson, Tobin Weatherson, Joe Davitt - San Diego Zoo Native Plant Seed Bank

We are all taught in school that water expands when frozen. That's why ice floats, sealed bottles explode in the freezer, and frost kills living tissues. All living cells are comprised largely of water and can rupture and die when the water they contain expands under freezing conditions. The cells of seeds are no different.  Research has shown there is a "goldilocks zone" of relative humidity that our seeds must reach before freezing. This perfect range of relative humidy is greater than 25% and less than 35%. The final and most crucial step before freezing our seeds, is testing their relative humidy to ensure it lies within this range. At SDZGs native plant seed bank we use small air tight desiccation chambers and color changing silica gel to obtain the relative humidity needed in our seed accessions. It's also common to use salt solutions to desiccate. We have found that a very quick and convenient way to read the relative humidy is to place a BlueMaestro Tempo Disc inside our sealed chambers. Given amble time to stabalize, we can infer the seeds reach an equalibrium with their ambient environment. These discs can quickly tell us the relative humidy inside the desiccation chambers without opening them and exposing the contents to humid air. There is a simple app on our phones that gives us temperature and relative humidity levels, and makes it easy to track these data over time. It's important to note that the size of the desiccation chamber, the amount of silica or salt solution, the number of seeds, and the type of seeds can all affect the time it takes to reach equilibrium (within a sealed chamber). For a more precise relative humidity measurement, or if we are unsure about the equilibrium within a chamber, we use The Rotronic HygroPalm. This hygrometer is also useful for obtaining a baseline RH reading from fresh seeds. The HygroPalm uses a small cup to measure the relative humidity of a sample.We attach the probe to the connection port, and turn it on by pressing the red button. We fill this small cup to the line with seeds and the probe tightly covers the sample. It then slowly draws in air and in about 5 minutes gives a very accurate reading. Note some of the drawbacks of using this hygrometer. Sometimes we have very small amounts of seeds in many maternal lines that we can not combine. We don't always have a large enough sample for this cup. We also have to open our chambers and disrupt equilibrium to test. For this reason, we use both the ibuttons and the hygrometer. We have designated desiccation chambers that are very stable and hold small accessions that stabilize quickly, and others for large bulked accessions. We always open and close these chambers as quickly as possible.  When we know that it is safe to freeze the seed, we place the accession into foil lined bags and heat seal them. The bags are now ready to freeze for long term storage, where they can survive for hundreds or even thousands of years, be preserved for generations to come and act as a safe guard against extinction.

Date Recorded: 
Wednesday, October 14, 2020

Katherine D. Heineman, Christa Horn, Naomi Fraga, Cheryl Sevilla, Heather Schneider, Vanessa Handley, Holly Forbes, Brett Hall, Evan Meyer, Tony Gunroe, Shannon Still, David Magney, Stacy Anderson, Bart O’Brien, Joyce Maschinski

Center for Plant Conservation, San Diego Zoo Institute for Conservation Research, Rancho Santa Ana Botanic Garden, Santa Barbara Botanic Garden, University of California Botanic Garden, University of California-Santa Cruz Botanic Garden & Arboretum, University of California-Los Angeles, Mildred E. Mathias Botanic Garden, San Diego Botanic Garden, University of California-Davis, Botanic Garden & Arboretum, California Native Plant Society, Regional Parks Botanic Garden

California is home to one third of the globally rare plant species in the United States. To secure this incredible flora, ten botanical institutions in California have joined together to form the seed banking collaborative, California Plant Rescue. By sharing our accession data and integration of combined dataset with our natural heritage database, we created a suite of tools in support of seed collections. These tools include a web-based accessions database, a mapping application for collections targeting, and a web-app that prioritizes species for collection based on location, conservation status, and phylogenetic diversity. From our dataset, we also conducted a gap analysis of current collections in order to direct our seed strategy moving forward. Our analysis evaluated the spatial, phylogenetic, landownership, and ecological patterns of seed collections in California. Some patterns were intuitive: Our seed collections were heavily biased toward Southern California where the majority of our permanent seed banks, including our most prolific collector, is located. Ecological patterns were somewhat less intuitive: despite high interannual variation in population size, annuals are more likely to be represented in seed collection than perennials perhaps owing toward larger seed set and lower incidence of recalcitrance. Finally, our landownership analysis demonstrated that the greatest potential for seed collection in California is on US Forest Service land, which has the highest density of extant rare plant occurrences. We identified five specific National Forests which are home to 20 or more uncollected rare species, an insight that will be crucial for prioritizing permitting and relationship building with agency collaborators. In 2019, California Plant Rescue was awarded $3.6 million by the State of California to seed bank the remaining 650 rarest plant species in California. We will leverage these tools and insights to take full advantage of this exciting opportunity.

Date Recorded: 
Wednesday, March 4, 2020

Joe Davitt, Institute for Conservation Research, San Diego Zoo Global

Maintaining a plant species’ genetic diversity can contribute to adaptive potential, prevent inbreeding effects, and potentially preserve traits such as drought tolerance and disease resistance, all of which are critical in a changing climate. Seed collections are often the best method of conserving the genetic diversity of rare plant populations ex-situ, however most seed collections are made with no available genetic data from the target species. Ideally, this genetic data would give us a clear picture of which populations are the most critical to conserve and how genetically structured a species’ populations are in relationship to one another, but this can be a time consuming and costly process. Seed collection protocols, such as those published by the Center for Plant Conservation, can inform our general best practices, but as seed collectors we must also infer best practice on a species by species basis. The life history and reproductive biology of the target species, as well as our sampling methods can greatly impact the effectiveness of seed collections to capture the entire target populations’ genetic diversity. Taking all available information about a species into consideration, we can infer the best seed collection methods to ensure genetic conservation.

Contributing Author(s): 
Date Recorded: 
Tuesday, September 10, 2019

Christy Powell, San Diego Zoo Global

San Diego Zoo Global's Christy Powell opens the 2019 Plant Genetics Conservation workshop at San Diego Zoo Global with a welcome to participants, some background on San Diego Zoo Global, and an inspirational story about a fern that has benefitted from conservation efforts.

Contributing Author(s): 
Date Recorded: 
Tuesday, September 10, 2019

Christy Powell, Brian Dorsey, San Diego Zoo Global, Huntington Botanical Garden

As the most endangered group of plants on the planet, cycads (Cycadales) face a number of threats to their continued existence. Efforts to preserve these iconic plants (in situ reserves and ex situ collections) could benefit greatly from a better understanding of population genetic dynamics and recent demographic history. We have shown that within the genus Dioon most species likely diverged between 30-80 kya. This very recent divergence along with long generation times suggests the possibility of shared polymorphisms across species and potentially incomplete speciation between accepted taxa. Conversely, the distribution of populations and the pollination/dispersal system suggests that migration rates may be quite low. Determining the relative influence of these processes will better inform conservation efforts. Given the nearly 50 Gb genomes of this group, we are using a hybrid of two RADseq methods to produce high coverage/highly multiplexed reduced representation data sets to assess connectivity, historical demography, and genetic diversity. While data for Dioon is still coming in, we have a pilot study using the same technique to assess the genetic diversity among Encephalartos latifrons plants held in botanical gardens in the USA, which we plan to extend to include wild populations with similar goals.

Contributing Author(s): 
Date Recorded: 
Tuesday, September 10, 2019

Oliver A. Ryder, Director, Conservation Genetics, Kleberg Endowed Chair, San Diego Zoo Institute for Conservation Research

In January, 1975 genetics studies commenced at the San Diego with group of researchers who would become the core of CRES, the Center for Reproduction of Endangered Species – now the San Diego Zoo Institute for Conservation Research. Founded by Kurt Benirschke, MD, cell culture and chromosomal analyses were first established. In June of that year, the first postdoctoral fellow joined the team, Oliver Ryder. By the time that Dr. Benirschke left the employ of the Zoo (to join its Board of Trustees), the research disciplines had expanded to include reproductive sciences, endocrinology, behavior and virology. Ryder oversaw the continuing development of the Frozen Zoo® and projects in molecular evolution, systematics, hybridization, speciation, kinship analyses, and population genetics, each area evolving as new technologies became available. An historical overview, the continuing development of conservation genetics at ICR in the era of genomics, and the incorporation of advanced cellular technologies for genetic rescue into our Conservation Genetics toolkit will be presented.

Date Recorded: 
Tuesday, September 10, 2019

Dr. Stephanie Steele, San Diego Zoo Global 

The Torrey pine (Pinus torreyana) is a rare, iconic species that occurs naturally in only two locations in Southern California: in coastal San Diego County and on Santa Rosa Island. The species is of particular conservation concern due to prolonged drought which has increased susceptibility of trees to attack by the bark beetle Ips paraconfusus. The Ips beetle has posed a significant challenge for trees in the mainland population in recent years. While Torrey pines harbor a remarkably low level of genetic diversity, it is possible that genetic variation underlies resistance to beetles and thus determines, at least partially, which trees survive. To test this, we are using RNA-Seq to survey functional genetic diversity in Torrey pines that either succumb to mortality by bark beetles or remain asymptomatic. We aim to 1) characterize functional genetic diversity in the species, particularly in defense-related genes, 2) test for genetic differentiation between affected and asymptomatic trees, and 3) identify whether specific genetic variants are associated with survival. This work will offer insight into the adaptive potential of Torrey pines to respond to continued bark beetle outbreaks and will inform future restoration efforts for this iconic species.

Contributing Author(s): 
Date Recorded: 
Wednesday, September 11, 2019

Cynthia Steiner, Aryn Wilder, Debra Shier and Natalie Calatayud, San Diego Zoo Institute of Conservation Research

Among the main roles of conservation management is to mitigate the negative effect of anthropogenic activities in nature by ensuring the persistence of biodiversity and species in the wild. Conservation geneticists have recently developed a new toolbox of genomic methods to address the management of species in-situ and ex-situ. Among these approaches, the reduce representation or ddRADseq method allows to sample a fraction of the genome-wide genetic variation to estimate population summary statistics and individuals’ relationships for breeding management. The study of the southern mountain yellow-legged frog, an endemic and critically endangered amphibian species from southern California provides importance lessons about the use of ddRADseq in species with large genome size, in terms of quality/quantity of DNA samples required for generating genomic libraries, quality control of restriction enzymes chosen, optimization of parameters in the STACK pipeline for data analysis and selection of criteria for filtering genetic variants.

Date Recorded: 
Tuesday, September 10, 2019

Dr. Aryn Wilder, Institute for Conservation Research, San Diego Zoo Global

Human activity has left species worldwide on the brink of extinction, where they are susceptible to the loss of genetic diversity and the accumulation of deleterious mutations that reduce adaptive potential and increase extinction risk. The application of modern genomic tools allows us to more accurately assess the conservation status of populations and examine the genetic factors that contribute to extinction. I will present case studies from animal populations where we are applying genomics as a conservation tool. First, we compared genomic characteristics of two closely related white rhino subspecies, the northern white rhino (NWR) which has been driven effectively to extinction, and the southern white rhino which has mounted a remarkable recovery, to provide insight into the potential for restoration of NWR. Second, we are currently generating low-coverage, whole genome sequence data from hundreds of wild and captive Pacific pocket mice. Combined with imputation, low coverage sequencing provides a cost-effective way to infer genotypes across the genome for a large number of individuals, providing statistical power needed to measure the genetic basis of fitness-related traits. The advancement and increasing cost-effectiveness of genomic technologies will continue to provide valuable insights applicable to conservation across taxa.

Date Recorded: 
Tuesday, September 10, 2019