FIF Supports Research into the Impact of a Genetic Bottleneck on Island Foxes

When a population declines to a small number of survivors and then increases dramatically over the next few generations, there are always questions about genetic issues.

Meet Elisabeth Leung a student at the University of California at Riverside. Working with her advisor Professor Ellie Armstrong, Leung is “Exploring founder contributions from the captive island fox breeding programs for Santa Rosa and San Miguel Island using genomic sequencing.”

FIF is supporting Leung’s research because she is delving into an important question with long-lasting consequences for island foxes.

 

Around 26 years ago, the island fox populations on Santa Rosa and San Miguel Islands dropped to a critically low number: 15 surviving individuals on each island. When we look at Santa Rosa’s estimated population of 2,536 island foxes in 2023, all of them have descend from just 12 individuals in captive breeding: 4 males and 8 females.

Elisabeth Leung’s investigation will look directly at the genetics of the original founding individuals on Santa Rosa Island and San Miguel Island and compare their DNA to their descendants on the islands today.

 

Why is this important? Typically a population has some members with genetic-related health issues, maybe a tendency toward heart problems, a physical deformity, or an increased occurrence of specific cancers. Usually, these individuals are a small minority in the population because they are less successful passing on their genes before they die. When survivors are randomly chosen, rather than because they have traits that drive their success, traits that are not necessarily beneficial can increase across a population; this is called “genetic drift.”

With just 4 males contributing to the first generation of captive-born island foxes on Santa Rosa Island, if just one of those males carried a gene that increased health risks, a greater percentage of the population could be impacted. The recovered population might then have higher numbers of individuals with non-beneficial genetic traits. Overtime this would be expected to cause “inbreeding depression”–a magnification of negative traits and reduction in species vigor.

The Florida panther (Puma councilor coryi) is a well-known example of “inbreeding depression.” Genetic problems arose as the population became very small, leading to reduced male fertility and noticeably kinked tails. The inflammation response of Santa Catalina Island foxes to ear mite infestation may be linked to genetics or epigenetics and is currently being investigated by Alexandria DeCandia at the Smithsonian.

biologist examines island fox ear during health check

Though geneticists have raised concerns about island foxes, there is no evidence of current genetic problems.

Today genetic research can delve deeper into DNA and health-related issues than it could 26 years ago. See FIF Grant for Transcriptomic Research

Leung’s research will help us understand the evolutionary impact of recovering from a small founding population. Has there been genetic drift in the fox populations on these two islands? What has changed or not changed in island fox genes?

To examine these changes, the lab at UC Riverside is also creating the first island fox reference genome. The island fox pictured here is fox “25205” on Santa Rosa Island. Blood samples from this island fox will be used to assemble the first complete island fox genome.

Genetic research has entered a golden age and donors like you are helping uncover important genetic information to help island foxes survive into the future.

FIF 2024 Research Grant Investigating Link Between Island Fox Genetics and Health

Meet Kimberly Schoenberger, recipient of FIF’s 2024 Island Fox Research Grant and a PhD candidate at the University of Southern California (USC) Dornsife College of Marine and Environmental Biology.

Schoenberger is initiating the first investigation of island fox genetics using transcriptomics. This leading-edge research uses RNA (the copier of DNA) to look at a species’ genetic material and evaluate it for protein production and vital cell functions. Transcriptomics provides insight into how genes turn on or off in cells and how this may influence health or disease.

 

The project will analyze three important aspects of island fox genetic expression: 1) what are the genetic differences between the six island fox subspecies; 2) how do different environmental conditions and demographics impact gene expression; and 3) will identify genes that are being influenced by disease or parasite exposure.

(As Catalina Island foxes were recovering from a severe population low, they experienced high levels of cancer due to an extreme immune system response to ear mites. This condition does not occur on other islands. Dr. A. DeCandia’s microbiome investigation identified a connection with specific bacteria (elaborated on by Jasmine Lu paper). Husbandry efforts currently control the ear mites, but the epigenetic link between the inflammation and eventual cancer remains unknown.)

Disease and parasites pose some of the greatest current threats to island fox survival. This project could provide valuable insight into which island fox subspecies have the greatest genetic vulnerabilities and help inform conservation measures.

Another important element of Schoenberger’s project is that it integrates directly into the current protocols for health checks. Biologists are currently in the field across the Channel Islands counting island foxes, providing health checks, and administering vaccinations. As part of the 2024 health checks, some individual island foxes will provide a blood sample for transcriptomics. Schoenberger’s genetic study will compliment and build on the individual island fox data currently being collected on diet, microbiome, territory, and health.

Schoenberger was able to travel out to Santa Rosa Island and engage with the National Park biologists as they took samples. She also met individual island foxes that will be part of her investigation.

At USC, Schoenberger explains that she puts the blood samples through a centrifuge “to separate RNA from other particles.”

The samples then go through a chemical processing to isolate and purify the RNA for sequencing.

Schoenberger says: “Transcriptomics can allow insights into gene expression patterns that underlie population health and disease by providing molecular-level understanding of island fox physiology and how they function and respond to differing environmental conditions.” Friends of the Island Fox is thrilled to support Kimberly Schoenberger’s research which will provide a baseline on the differences between populations and “shed light on key genes that are affected by environmental differences and may be crucial for adaptation and survival of the island fox.”

Your donations make this research possible.

photo courtesy of P Bronstein

 

FIF Research Grant to Investigate Diversity of Island Fox Microbiome

Friends of the Island Fox is happy to announce Alexandra DeCandia, Ph.D. is the recipient of FIF's 2020 Research Grant.

You may remember DeCandia's article from April 2020 regarding her doctoral work at Princeton University: Mites, Microbes, and Cancer in Santa Catalina Island Foxes. Microbes can be found on the skin, in the digestive system, and in connection with the body's openings.

A healthy animal has a diversity of microbes. In this way, a single island fox is like an island. If something should happen to the biodiversity of microbes on an individual, the ecosystem on that individual might become out of balance. Some microbes might thrive, while others perish. An imbalance of microbes can impact an animal's overall health.

When island foxes on a specific island go through a near-extinction population bottleneck, there is a potential for a loss of microbe diversity that can be passed on to surviving island foxes. 

DeCandia investigated if there was a connection between the diversity of microbes on Catalina Island foxes and an unusual prevalence of cancer in this subspecies.

Looking into island fox ear canal

What she found was "evidence of disrupted microbial communities in mite-infected ear canals that may contribute to sustained inflammation." Inflammation can play a role in cancer and this microbial imbalance may be connected to why Santa Catalina Island foxes are the only island foxes known to develop cancerous tumors in their ear canals.

DeCandia's work was published in Molecular Ecology and when she presented her findings at the Annual Island Fox Conservation Working Group Meeting in May of this year, everyone was intrigued. A healthy microbial biome is vital to healthy digestion, immune response to disease, behavior, and even development. Because island foxes on five islands have been through population bottlenecks, where the number of surviving individuals was very low, there is a potential that island foxes on other islands may have disrupted microbial communities as well.

As island foxes are counted and given health checks across the islands this year, they are also getting swabbed for microbes in their ear canals and at their anuses. DeCandia describes the process as "similar to cleaning your ears with a cotton swab, except you don't throw away the swab afterwards." The swab samples will be sent to DeCandia at the Smithsonian Conservation Biology Institute in Washington D.C.

 

 

DeCandia in the lab

FIF Research Grant funding will be used to extract DNA samples and process DNA sequencing to identify the various microbes in island fox ear canals and digestive systems. 

This investigation provides a unique opportunity to do comparative analyses between subspecies of island foxes on different islands. DeCandia hopes to:

1. survey variation of microbes within island foxes on each island
2. characterize the differences between islands
3. identify the drivers of ear canal tumors on Santa Catalina Island
   

This work is at the cutting edge of science and may have important consequences for the long term survival of the island fox.

If you are an FIF donor, 

you are making this important work possible.

 

If you haven't donated yet, Please Donate 

This is Science, For Fox Sake!

 

Mites, Microbes, and Cancer in Santa Catalina Island Foxes by Alexandra DeCandia

(Thank you to our guest blogger Alexandra DeCandia a doctoral candidate at Princeton University)

Over the last few decades, we've realized that organisms are far more complicated than they initially appear. What may look like an individual fox is actually an ecosystem containing trillions of microorganisms on every square inch. [Figure 1]

Despite their tiny size, microbes influence important host functions, such as development, digestion, stress tolerance, behavior, and even immunity. Therefore learning more about these hidden actors can inform wildlife conservation of at-risk species in the modern molecular era.

Looking into the ear canal of an island fox.

Microbes may be particularly important to species that lack genetic diversity, such as Channel Island foxes, especially where disease threatens long-term persistence. On Santa Catalina Island, scientists discovered extremely high rates of ear canal tumors, where roughly half of adult foxes have growths in their ears. Although the exact cause is unknown, researchers linked ear mite infection to tumor growth and development. The most prominent hypothesis states that infection with ear mites leads to inflammation and rampant cell growth in the ear canal, which in turn leads to tumors. Thankfully, treating foxes with the acaricide Ivermectin has already decreased mite burdens and tumor rates in these foxes.

However, there's more to this story. We still don't fully understand how mite infection leads to tumor growth. In particular, my collaborators and I wondered whether microbes play a role in this system. For example, do mites disrupt healthy microbes and cause secondary bacterial infections? And do those infections then contribute to the chronic inflammation that precedes tumor growth?

Figure 2: Island fox is swabbed during health check

To address these questions, my collaborators at the Catalina Island Conservancy collected microbe samples by swabbing ear canals (and a few other body sites) of healthy and mite-infected foxes. [Figure 2] (This process is similar to cleaning your ears with a cotton swab, except you don't throw away the swab afterwards.) Once a bunch of foxes were swabbed, all samples were sent to New Jersey, where I extracted DNA, collected genetic sequences, and analyzed the data.

 The results came back loud and clear: microbes differed between mite-infected and uninfected ear canals. Rather than a rich community of diverse microbes (as seen in healthy ears), mite-infected ear canals had fewer microbial species present. We further found that the balance of microbes (know as "relative abundance") differed between infection groups.  [Figure 3]

Figure 3: Classes of bacteria found in swab samples

As it turned out, this pattern was almost entirely driven by an overabundance of one bacterial species: Staphylococcus pseudintermedius (Class: Bacilli, shown in brown in Figure 3).

Even though this microbe is commonly found on canid species (such as domestic dogs and foxes), it can become an opportunistic pathogen when healthy communities are disrupted. Once it proliferates, it can be incredibly difficult for the immune system or even antibiotics to eradicate, leading to chronic inflammation.

We now hypothesize that mite infection and secondary bacterial infection with Staphylococcus pseudintermedius contribute to chronic inflammation and tumor growth in Santa Catalina Island foxes. 

Photo courtesy of Glenn Jensen

Although further tests are needed to definitively establish causation, these insights into the microbial dynamics of mite infection can help us monitor the population for antibiotic resistant forms of Staphylococcus pseudintermedius that could cause a disease outbreak. They can further help us explore other open questions, such as why Santa Catalina Island foxes are the only subspecies with ear canal tumors, despite ear mites on other islands. As always in science, answers lead to more questions. But at least one thing is clear: there's more to this story (and indeed, to all organisms) than what initially meets the eye.  

Alexandra DeCandia, Department of Ecology & Evolutionary Biology, Princeton University, Princeton, New Jersey.

Read the full paper: Ear mite infection is associated with altered microbial communities in genetically depauperate Santa Catalina Island foxes (Urocyon littoralis catalinae)

More Research Regarding Island Foxes:

Origins of the Island Fox

New Findings on Island Fox Diet

Epidemic Disease Threats to the Island Fox

More