For 50 years, scientists at the San Diego Zoo have been collecting and storing cells from rare and endangered species in its Frozen Zoo with an eye to the future.
The future is here. The San Diego Zoo Wildlife Alliance earlier this month announced it had entered into a partnership with gene-sequencing giant Illumina to use advanced DNA technology to sequence thousands of specimens that have been cryopreserved.
The hope is that generating whole-genome sequencing data from the samples will uncover insights that will help threatened species in the wild and in zoos.
“Sequencing samples represented in the Frozen Zoo is not new — we have been doing this for decades and learning much about the conservation status and evolutionary history of species,” said Megan Owen, vice president of wildlife conservation science with the alliance. “It is the volume of samples that we’ll be able to sequence with Illumina’s support that is truly unique here.”
Owen said partnering with the San Diego-based biotechnology company will help accelerate discoveries that can be made from material in the biobank. Genetic discoveries can help scientists assess the status of inbreeding in a species and identify how its genetic makeup might contribute to diseases or hinder reproduction, she said.
“If we are going to leverage these kinds of materials and these types of analyses to try to halt and reverse declines in wildlife, we really need to pick up the pace and increase the scale of these analyses,” she said.
Under the agreement, Illumina will provide whole-genome sequencing for up to 4,000 samples from 1,300 species. Data from the samples will be shared with the zoo and its collaborators to advance conservation science.
“Our partnership amplifies conservation science by turning a priceless biological archive into a powerful, data-driven tool that can be shared with collaborators across the globe and help scientists make better, more informed decisions to protect species now and in the future,” said Ashley Van Zeeland, Illumina’s vice president of corporate development.
The hope is that scientists use the genomic data to apply insights toward real-world conservation challenges. Such discoveries could bring changes to wildlife medicine, evolutionary biology and biodiversity preservation.
The Frozen Zoo was started in 1975 by Dr. Kurt Benirschke, a renowned pathologist and expert in reproductive medicine at UC San Diego who became the director of research at the zoo and later served as chair of its Board of Trustees. On his own, he began freezing living cells from endangered animals, even though he didn’t have a clear idea how they’d be used. His thinking? “You must collect things for reasons you don’t yet understand.”
Cells banked in the Frozen Zoo have been used to clone two critically endangered species, the black-footed ferret and Przewalski’s horse. Zoo officials say that work fuels hope that genetic material can help rebuild a species’ future by “reintegrating lost genetic diversity.”
Benirschke died in 2018 at the age of 94. His son, former Chargers kicker Rolf Benirschke, the current chair of the alliance’s Board of Trustees, said his father would be “smiling” knowing his vision led to the collaboration with Illumina. Benirschke said he expects the work to “dramatically expand and amplify the science of conservation.”
Owen said understanding the status of species through their genetic health will help conservation scientists make better decisions about what work to prioritize and whether to pursue conservation interventions. One example, she said, could be using information to try to bolster genetic diversity by moving or “translocating” animals to a different location to breed.
“So if we have populations that through these types of analyses look like they are genomically isolated, then we can develop a strategy for translocation that would basically mix the genes,” she said.
Over the past five years, the zoo and Illumnia have worked together on several conservation-focused projects, including analyzing the genomes of endangered lemurs in Madagascar, elephant genetic mapping in Africa and a project on koala genomics, which is providing insights into koala cancer risks.
The latest agreement to sequence the Frozen Zoo seemed a natural “next step,” Van Zeeland said.
“The agreement reflects a mutual desire to work more closely together and to scale the impact of genomics for wildlife conservation in ways that neither organization could achieve alone,” she said.
She said the sequencing plan will focus on generating genomic data from one representative sample per individual rather than sequencing every stored tissue or sample in the Frozen Zoo. The work will include mammals, birds, reptiles, amphibians, fish and some invertebrates.
Zoo officials say the partnership comes at a time when conservation scientists are racing against the clock to collect samples from threatened and endangered species. Illumina’s genetic sequencing can turn that material into knowledge that can guide their next steps.
“Biotechnology is just transforming before our eyes. It’s just an area of incredibly rapid innovation,” Owen said. “This kind of partnership with the private sector really helps us accelerate our discoveries. And we really need that because, as you know, the pace and scale of biodiversity loss is just accelerating.”