The world’s first successfully cloned Black-footed ferret has been born, marking the first time a U.S. endangered species has been cloned. “Elizabeth Ann” was born on December 10, 2020, and is the clone of “Willa,” a wild-caught Black-footed ferret whose cell line was cryopreserved in 1988. A genomic study led, funded, and developed by Revive & Restore in 2014 helped determine that Willa’s genome possessed nearly three times more genetic diversity than the current Black-footed ferret population. This means that her clone Elizabeth Ann is now the most genetically valuable Black-footed ferret alive. This birth is the result of a long-standing genetic rescue effort for the Black-footed ferret species, the goal of which is to increase the genetic diversity and fitness of one of America’s most endangered species to help ensure its full recovery in the wild.
PRESERVING GENETIC DIVERSITY
Willa was among the sole surviving wild population found living near Meeteetse, Wyoming. Hoping to save the species from the ravages of disease and habitat loss, conservationists managed to capture the last 18 of these animals, including Willa, before disease wiped them all out. A captive breeding program was established to safeguard the species and grow their numbers until reintroductions were possible.
Willa lived until January 23, 1988, but she never bred in captivity. Forward-thinking conservationists at the Wyoming Department of Game and Fish, knowing that Willa’s genetic diversity was likely unique and no longer represented in the Black-footed ferret population, sent her tissue samples to the Frozen Zoo® at San Diego Zoo Wildlife Alliance (SDZWA). There, a cell line was established and cryopreserved three days after she died. While the technology did not yet exist, this ensured the cell line’s viability for cloning now three decades later. Learn More About The Species.
POTENTIAL FOR AN EIGHTH FOUNDER
Several of those last 18 wild-caught Black-footed ferrets did not breed successfully. In fact, only seven became founders of today’s population. Now numbering between 250 to 350 ferrets maintained in captivity and 300 more spread across 29 reintroduction sites in the wild, all Black-footed ferrets are descendants of just those seven founders. Over 20 generations later, all Black-footed ferrets alive today are as closely related as siblings or cousins.
If Elizabeth Ann successfully breeds, however, she will become an eighth founder for her species. This was the reason for cloning from Willa’s cell line. It is a second chance to bring Willa’s genetic contribution into the breeding population. This clone is being cared for by her surrogate domestic ferret mother and the staff at the National Black-footed Ferret Conservation Center (NBFFCC) in Colorado. She may soon be joined by other kits cloned from Willa’s cell line as well as a historic male cell line known only as “Studbook 2” or “SB2,” a potential ninth founder. Research to follow will evaluate the clones’ health and safety before any of the clones are integrated into the breeding population. If the clones do successfully breed, the Willa cell line, those cloned from it, and their offspring offer the Black-footed ferret species a better chance at recovery in the wild. Greater genetic diversity supports fitness and adaptability. This will also validate cloning as a legitimate, safe, and useful reproductive technology for the conservation management of Black-footed ferrets and other U.S. endangered species.
This achievement is the result of years of careful planning, permitting, and research, which began in 2013 with a partnership between Revive & Restore and the Black-footed ferret Recovery Implementation Team. The partnership has grown to include the expertise and resources of many organizations and individuals, especially those at the SDZWA Frozen Zoo® and ViaGen Pets & Equine. Learn More.
CLONING FOR CONSERVATION
After years of initial research, design, and development Revive & Restore partnered with ViaGen Pets & Equine to clone Willa. In November 2020, that team successfully created embryos from her cell line and implanted them into a domestic ferret surrogate. The surrogate mother was transferred from ViaGen to the U.S. Fish and Wildlife Service (USFWS) National Black-footed Ferret Conservation Center where the cloned kit Elizabeth Ann was born. Read the Press Release.
If we do not intervene to increase genetic diversity now, the black-footed ferret population is likely to suffer from the ongoing effects of inbreeding and genetic drift, which may begin to drive the population toward extinction. Lower levels of genetic diversity also make it less likely that the species will be able to adapt to existing or future threats
CREATING RESILIENCE TO SYLVATIC PLAGUE
While significant progress has been made in re-establishing Black-footed ferret populations, removing this iconic North American carnivore from the federal endangered species list remains elusive. Currently, a carefully orchestrated breeding program led by the Black-Footed Ferret Recovery Implementation Team manages the species’ low genetic diversity to stave off inbreeding. On top of this effort, the USFWS must also vaccinate the Black-footed ferret population to protect them from sylvatic plague. Plague is 100% lethal to unvaccinated Black-footed ferrets.
This project began when the Recovery Implementation Team approached Revive & Restore to see if we could help the species overcome both challenges. To succeed will mean the Black-footed ferret will be closer to joining 47 other species successfully recovered under the Endangered Species Act.
The long-term high-level goal is to enable black-footed ferrets to thrive in the wild despite plague and without human intervention. Genetic rescue to overcome susceptibility to sylvatic plague may help ensure the successful recovery of the black-footed ferret. Revive & Restore has been awarded a Recovery Challenge Grant from USFWS to conduct foundational research that uses the domestic ferret as an experimental model for testing immunity to plague.
Until black-footed ferrets are able to coexist with sylvatic plague, their populations will remain vulnerable to lethal outbreaks. If nothing is changed, Black-footed ferrets will remain conservation-reliant as the population grows and will never be truly wild.
INCREASING GENETIC DIVERSITY
At first, the true extent of the species’ genetic diversity problem had not been empirically assessed. The potential for historic cell lines to help in the matter was unknown. Genome sequencing data was needed to fill in the details that a careful pedigree analysis could not provide
GENOMIC STUDY COMPARING ‘HISTORIC’ CELL LINES WITH THE LIVING POPULATION
Revive & Restore initiated a genomic study in 2014 with CoFactor Genomics, sequencing the genomes of two historic cell lines and two Black-footed ferrets from the current population. The Genomics Working Group has continued to sequence additional genomes to build upon the initial findings. The current state of Black-footed ferret genomics knowledge is detailed below.
SDZWA provided DNA samples from two cryopreserved cell lines from two individuals that have no living descendants (in grey). Together, their genomes provide a measure of genetic variability from the historic wild population:
- “Willa” (Studbook 10), the female captured on November 2, 1985, that did not breed in captivity but whose cell line has now been cloned for genetic rescue (“Elizabeth Ann” in teal).
- “SB 2,” a male among the first six wild BFF captured in 1985. Canine distemper killed SB2 before he could breed.
The Recovery Implementation Team provided DNA samples from four living BFF:
- “Cheerio” (SB 6573), “Cadbury” (SB 7462), and “Thorpe” (SB 8055) were all born in the captive breeding program (in red) and their genomes offer insight into the BFF population’s current genetic variability.
- “Balboa” (SB 6815), a male born in 2010, the result of an earlier genetic rescue effort (in teal). He was produced through artificial insemination using sperm cryopreserved in the early 1990s from “Rocky,” a wild BFF (in purple) captured at Meeteetse.
GENOMIC STUDY RESULTS
Comparing these six sequenced genomes confirmed wild-caught Black-footed ferrets from the 1980s possessed more genetic diversity than the current Black-footed ferret breeding population. The breeding program has been largely successful at maintaining individual heterozygosity (possessing two different variants of a particular gene, one unique variant inherited from each parent). Genomic analysis of corroborated pedigree analysis estimates that heterozygosity declined by just 15%. However, individual heterozygosity is only one aspect of genetic diversity. Individual genetic variation is the measure of unique genetic variants between individuals. Whole genome sequencing of the six genomes described above revealed that individual genetic variation in the Black-footed ferret population had declined significantly. In fact, genetic variation had declined by an average of 55% since the 1980s.
Genetic rescue efforts aim to restore genetic variation to inbred populations. Balboa’s genome revealed the real-world potential that genetic rescue offers the species. Balboa’s individual heterozygosity was fully recovered to historic levels and his individual genetic variation was rescued nearly 25%. This showed that advanced reproductive technologies applied to biobanked or cryopreserved resources can help increase genetic diversity for captive breeding populations.
This led to the conclusion that cloning cryopreserved cell lines and integrating the offspring into the breeding population is a viable route of genetic rescue. The results spurred on the cloning of the Willa cell line. Plus it led to a separate line of work: clearing canine distemper from the SB2 cell line so that it too may be viable for cloning and provide a potential ninth founder for the species.
Klaus-Peter Koepfli, of the Smithsonian-Mason School of Conservation, now leads an expansive genomics research program that builds upon this initial Black-footed ferret genomic study. Hundreds of genomes are now being sequenced to build genomic insight tools that can guide future management and genetic rescue decisions.
ENDANGERED SPECIES RECOVERY PERMIT
After those conclusions, it became clear that permits were needed. In 2018, Revive & Restore received a first-of-its-kind Endangered Species Recovery Permit from the United States Fish & Wildlife Service to initiate the foundational laboratory research for the genetic rescue of the Black-footed ferret. The permit authorized the lab work needed to explore:
- The viability of using cloning techniques to bring cryopreserved cell lines and the genetic diversity they possess back into the population.
- The viability of various potential methods to provide inheritable resistance for sylvatic plague.
Importantly, Revive & Restore’s current permit from the USFWS meets the public review standards of the National Environmental Policy Act that encourages public and agency review of the proposed activities. We look forward to future rounds of public engagement on the genetic rescue of the Black-footed ferret.
DEVELOPING INHERITABLE IMMUNITY TO SYLVATIC PLAGUE
Sylvatic plague, accidentally brought to America from Asia, is the greatest threat to the wild recovery of Black-footed ferrets. Unlike domestic ferrets, Black-footed ferrets are intolerant of sylvatic plague infection. They succumb to the disease so quickly that their immune system does not have time to develop a response. Vaccination, however, is effective. With help, the Black-footed ferret species is capable of developing a sufficient immune response.
In 2019, Revive & Restore developed a research pathway to test if upregulating antibody expression might help Black-footed ferrets establish inheritable immunity to plague. Earlier research in mice demonstrated that plague immunity can be antibody-mediated and inoculation or temporary expression of plague-binding antibodies increases an individual’s ability to survive infection. Therefore, an inherited lifelong expression of a plague-binding antibody could provide protection against plague infection in the Black-footed ferret.
As a first step, work is now underway to test this method in mice. Texas A&M Institute for Genomic Medicine has developed transgenic mice that will be used in plague challenges at the US Geological Survey (USGS) National Wildlife Health Center. This proof-of-concept study may also lead to a means for establishing innate, inheritable immunity (or tolerance) to other exotic bacterial diseases in other mammalian species.