San Diego Zoo Global

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
Photo Categories: 
Photo Credit: 
Christa Horn
Tobin Weatherson from the San Diego Zoo Native Plant Seed Bank Collecting Field Data
Photo Categories: 
Photo Credit: 
Joe Davitt
The San Diego Zoo Native Plant seed bank made six seed collections of this federally endangered plant in 2019
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Photo Credit: 
Joe Davitt