RESEARCH QUESTIONS

Running_black_footed_ferret

Goal: To understand how the black-footed ferret gene pool has changed from the founding population to the current generation.

Background

The extensive efforts and successes of the Black-footed Ferret Recovery Program saved the species from the brink of extinction in the 1980s, when fewer than 30 ferrets remained alive. Today, through captive breeding and wild release, the program has produced over 8,300 kits (baby ferrets) and re-introduced ferrets to over 19 sites in the wild of its former range. In doing so, the program has produced a known family tree of thousands of ferrets, jotted down observations of health, and among records and records of data, it has preserved various tissues from many individuals – all resources necessary for researching the genetic rescue of the black-footed ferret.

Because so few ferrets were alive to breed for repopulation, the past 25+ years of captive breeding has led to a loss of genetic diversity. Genetic diversity has been shown in conservation to be directly related to the health or long-term survival/adaptability of a species. Genetic rescue for the black-footed ferret means finding ways to bring back the diversity lost from inbreeding. The recovery program has already gone so far as to pioneer genetic rescue techniques with advanced reproductive technologies: producing ferrets from “cryogenic artificial insemination” using 20-year-old cryopreserved spermatoazoa to fertilize living females. These ferrets, born from parents spanning 20 years of generations, may bring back genetic diversity lost through inbreeding.

The black-footed ferret recovery program designed its breeding management to preserve as much genetic diversity as possible and to prevent problems related to inbreeding depression. These goals have been designed through quantitative models that have yet to be tested with whole genome sequencing, until now.

We want to determine how accurate the quantitative predictions of genetic diversity have been. Genetic diversity is assessed by heterozygosity within an individual’s genome, although a population also includes the total variations of genes (called alleles) present between all individuals. In the black-footed ferret population we expect both the individual heterozygosity to decrease as well as the total diversity of alleles in the population. This phenomenon is a result of genetic drift – a process that acts on small populations more powerfully than any other evolutionary process. At this point the recovery program does not know the actual genetic diversity of the Meeteetse population, nor how closely related were the founders of the captive breeding program. These missing pieces of information may greatly influence how ferret breeding is managed in the future, and will certainly have bearing on decisions to introduce genetic rescue efforts into the program.

Whole genome sequencing allows us to characterize the genetic diversity that existed in the Meeteetse population from which the founders were captured, and compare it to the current genetic diversity of ferrets after the past 25 years of managed breeding.

We’ve selected four study individuals to specifically address questions related to genetic diversity and to genetic rescue. Other conservation questions can be posed to this data: questions concerning  the evolution of ferret species, the historic demography of the Meeteetse population, genetic diversity in specific types of genes, and even analyzing the effects certain mutations may have (especially if they may cause a problem to the gene in which they occur).

Help us investigate four key questions. You can submit your answers to us. To learn more about how you can participate, go to the How to Participate in Research page.

Key Questions to Investigate

Black-Footed FerretThe four sequenced BFF genomes can be used within many disciplines from biomedical to evolutionary studies and conservation. The purpose of study shapes the questions asked of the data, and the questions asked of the data shape what data is needed and how it is analyzed. Our first four genomes comprise the genomic resources needed to begin exploring major research questions for the species.

Below are the primary questions driving the study of black-footed ferret genomes for conservation.

The process of answering these questions will lead to the development of new analytical questions directed and articulated specifically for the data. Each analytical question gives a piece of the answer that with the other “pieces of the puzzle” from multiple analytical questions form the conclusions for a major research question.

Question #1: What is the total loss of genetically variable sites (heterozygosity) from 1985 (the ferret cell cultures in the Frozen Zoo) to the current generation (Cheerio)?

  • How many positions in the genome that were heterozygous in the ferrets sampled from 1985 have become homozygous in Cheerio and Balboa?
  • Are losses in heterozygosity from 1985 that occur in protein coding regions more numerous than in non-coding regions?
  • Is genetic diversity of Balboa, the black-footed ferret, produced by artificial insemination from a 1985 male with a female from a recent generation greater than that present in Cheerio and by how many variable positions (SNPs)?

Question #2: What gene functions may have been lost from black-footed ferrets in comparison to domestic ferrets.

  • Are there variant forms of genes (alleles) involved in immunity or reproduction that are absent in the living ferrets (Cheerio and Balboa) that were present in the samples from the 1985 ferrets?

Question #3: Without sequencing the genomes of additional black-footed ferrets, how could you estimate the amount of genetic variation that the cells from the two ferrets from 1985 could contribute to the current gene pool?

Question #4: How would sequencing additional ferrets from the current population refine these answers?

  • How would specific types of ferret genomes refine these answers? (e.g. generation 2 ferrets, generation 10 ferrets, wild-born ferrets, 19th century ferrets, etc.)
  • What new questions can be explored with additional genomes?

Get involved!
To learn more about how you can participate and submit your answers to us, go to the How to Participate in Research page.