Phase One

 

Black-footed Ferret Genomic Study 2014 – 2016 

Genomics can be used in many of ways to improve the conservation of the Black-footed Ferret.
Black-footed Ferret breeding has been intensely managed using theoretical measures of genetic diversity based on kinship. But because all living ferrets share the same ancestry at a kinship level between first cousins and siblings, it very difficult to choose mate pairs. Genome sequencing can create an empirical decision matrix that will allow breeders to selecting mate-pairs based on the unique genetic contribution their offspring will receive, rather than on kinship. Whole genome analyses can identify maladaptive genes responsible for traits associated with inbreeding depression, such as low sperm mobility, cryptorchidism, and kinked tails, and prevent the accumulation of these traits in the population.  Studying genomes of wild-born ferrets can help identify what alleles are selected in the wild in order to breed ferrets in captivity more suited to their particular release sites.

In order to maximize the benefits of genomic technologies in the recovery of ferrets requires building a databank of genomic knowledge, which Revive & Restore initiated in 2014.

In 2014, in partnership with San Diego Zoo Global’s (SDZG) Frozen Zoo and Cofactor Genomics, Revive & Restore sequenced the genomes of four, carefully selected Black-footed Ferret samples to assess some preliminary questions about the species’ history and its conservation:

  • How diverse was the last wild population of ferrets that founded the captive breeding program?
  • Has overall genomic diversity decreased over the past 30 years?
  • Does integrating historic individuals restore genomic diversity?
  • How much diversity might be gained with continued genetic rescue efforts?

The study individuals include two unique individuals captured at Meeteetse, Wyoming in the 1980s, a living ferret born in 2009 whose genetics is representative of the current captive population, a unique individual born in 2010 as the result of artificial insemination using semen cryopreserved in the 1980s. (This was an early genetic rescue attempt to restore lost diversity.) The DNA samples of two living ferrets born in captivity were provided by the Black-footed Ferret Recovery Team, while the Frozen Zoo provided the historic samples for the two individuals born in the wild. Both these ferrets were members of the population that founded the captive breeding program, so their genomes represent a sample of the genetic diversity of the founding generation of all living ferrets. However, these ferrets’ unique genetic lineages were lost completely during the captive breeding program. Therefore, their cryopreserved cells are a resource for cloning, for restoring lost genetic diversity, and for infusing new genetic variation.

2014 - 2016

The Study Individuals

Cheerio: Studbook number SB6573

Studbook number SB6573 was a male named Cheerio, born 2009. Cheerio’s genome shares ancestry from all seven founders, presumably in equal amounts. All living ferrets are presumed to share similar ancestry to all seven founders, thus Cheerio is the proverbial “every ferret” of the living population for this research. Cheerio died shortly after our genomic study, after a long and productive life siring 10 kits to continue Black-footed Ferret recovery.

Balboa: Studbook number SB6815

Studbook number SB6815 was a male named Balboa, born 2010. Balboa is unique; he was born by artificial insemination, using the cryopreserved sperm of Rocky, a ferret captured in the 1980s at Meeteetse and assumed to be the son of one of the founders, Scarface. This form of “cryogenic artificial insemination” is a viable genetic rescue method, partially restoring the genetic diversity lost over 20 years and 11 generations. Balboa died in spring 2016. He sired 4 kits through natural breeding, which are the 4 most genetically diverse living Black-footed Ferrets.

Studbook Number 2

Studbook Number 2 was an unnamed wild male captured at Meeteetse in 1985. This male was among the first six wild ferrets captured for captive breeding, but all six died of canine distemper before they could be bred in captivity. However, tissue samples of this male were shipped to the San Diego Frozen Zoo where cell cultures were grown and cultured.

Willa: Studbook number SB10

Studbook number SB10 was a wild female named Willa, captured at Meeteetse between 1986 and 1987. Willa successfully bred in captivity, but her kits died without leaving any descendants.

Study Results

For each of the four Black-footed Ferret study individuals, 90 percent, or 2.2 billion base pairs of DNA, were mapped successful to the publicly available domestic ferret reference genome.

The genomic analysis found that the level of diversity between the four individuals amounted to approximately 2 million variable mutations, which is roughly similar to overall diversity exhibited by other endangered carnivores. Some of these variations were shared between two or three of the study individuals, but some were completely unique to specific individuals. By comparing the shared and unique diversity of the four ferrets, we found that Black-footed Ferrets in the 1980s possessed more genetic diversity than living ferrets, suggesting that some diversity has been lost by the breeding pedigree, as predicted. A secondary analysis further confirmed that living ferrets have suffered a small degree of inbreeding.

However, the results also showed that genomic diversity can be improved through techniques of genetic rescue. The genome of Balboa, the study individual born via artificial insemination and advanced reproductive techniques, was as diverse as that of Willa, a ferret born in the wild and captured for the captive breeding program in the 1980s. This indicates that it is possible to slow, or possibly reverse, the genetic erosion of the captive breeding program. Cloning the two cell cultures housed in the Frozen Zoo and integrating them into to the breeding program would potentially introduce a substantial amount of unique diversity relative to the diversity of living ferrets.

Phase Two


With only four individuals analyzed, it is not yet possible to know how much variation has truly been lost from the seven captive breeding founders and how much of that variation can be restored through cloning or artificial insemination. In order to answer these questions and to begin researching genetic rescue techniques for Sylvatic plague resistance, Revive & Restore and SDZG has partnered with the lab of Federica DiPalma at the Earlham Institute to compare more individuals. The DiPalma group has sequenced the genomes of four Black-footed Ferrets born in the wild that descended from successful reintroductions at Shirley Basin, Wyoming and Badlands National Park, South Dakota.

Thus far, the DiPalma group has sequenced DNA from over 90 strains of domestic ferret as well as other wild species of ferret, including the Siberian Polecat, the closest relative to the Black-footed Ferret, which is also susceptible to Sylvatic Plague. With a focus on the genetics of the immune system (termed the immunome), the DiPalma group has improved our understanding of the genes that comprise ferret immune systems and of their evolution. By comparing the immunomes of a diverse sample of individuals of these three ferret species, we can begin to identify the genes that may be involved in Sylvatic Plague resistance and susceptibility. From our preliminary study, we’ve found that the Black-footed Ferret and domestic ferret genomes are approximately 99.6% identical, meaning the key differences that make domestic ferrets resistant to Sylvatic Plague is contained in a small number of mutations.