Collaboration is the lifeblood of island fox research

It’s no understatement to say that collaboration is the lifeblood of research and survival for the island fox—for genetics researchers like myself, this is especially true.

The decline and recovery of the Channel Island fox (Urocyon littoralis) in the 1990s and early 2000s is one of the most remarkable instances of intervention and conservation success of an endangered species. The charismatic fox, endemic only to the Channel Islands of California, approached extinction for four subspecies, with population drops of up to 90% due to factors related to human activity, including introduced disease, predation by invasive species, and habitat degradation.

In response, a wide-ranging team launched a recovery effort. It involved conservation groups, government agencies, zoos, volunteers, researchers, and many more—a collection of individuals we like to call the “fox family.” The key actions of the recovery plan involved captive breeding, removal of non-native predators and invasive species, disease management through vaccination efforts, and continual monitoring of the population for the years following reintroduction.

Today, we are able to witness the results of this intensive collaboration. Fox numbers have increased substantially and have had all-time population highs in the last year on almost all islands, according to data collected through ongoing seasonal monitoring.

Current risks and research goals

Although we have seen a general increase in fox numbers, there are still a range of factors that put the species’ health and longevity at risk. The population bottlenecks and subsequent flatlining of genetic diversity left the foxes highly vulnerable to changing climate and novel diseases. On the southern islands, ear mite infections are abundant, and have been linked to tumor development in Catalina foxes. This is especially noteworthy because the population decline on Catalina in the 1990s was also driven by disease, specifically an outbreak of canine distemper virus (CDV).

My work seeks to identify how these vulnerabilities manifest by exploring immune-related gene expression of all six island fox subspecies using RNA sequencing (RNA-seq) from whole-blood samples. This work, known as transcriptomics, enables insights into which genes are surfacing (being expressed) under certain conditions. This is a complement to genomics, which looks at all genes in an organism’s DNA (its genome). By contrasting the gene expression for foxes on the six different islands and their six unique environments, we aim to identify the cracks in the immune foundation, and hopefully, inform intervention methods to support and repair them.

In contrast to DNA, which essentially contains the list of all possible instruction manuals for anything that the body needs to do or build, RNA is the messenger—converting those instructions into usable proteins to carry out required tasks. This allows RNA to function as a “snapshot” of what is happening in the body at a specific point in time, breaking down after its job is complete. This is a problem for sampling because RNA degrades quickly, even more so once outside the body or in deceased organisms. As such, it requires collection from living tissues and immediate preservation to provide the most informative data. In short, in order to accomplish my research goals, I had to enlist help to collect fresh blood from wild foxes. 

Building on a foxy foundation

Fortunately, because of the existing infrastructure of collaboration and island fox research, this was not as big of a hurdle as I originally anticipated. Blood draws are a routine component of the ongoing fox monitoring, which allows conservation groups to track general aspects of fox health, much like getting bloodwork done during a routine physical. My sample collection would fit in seamlessly, without causing any additional duress to the island foxes or creating more work for the monitoring teams.

Though it varies slightly depending on the organization, the main goal of monitoring is to keep tabs on the populations on each island. This takes the form of grid trapping, where small subsets of the islands are set up with traps for 5-6 nights, during which traps are checked and reset daily. Captured foxes are tagged with passive integrated transponder (PIT) tags, which help serve as individual identification. Grids are staggered throughout the trapping season to ensure that every trap can be checked every morning it is open, so that foxes spend the least amount of time contained. This method is highly effective in capturing a whole picture of the fox population on each island, and it is equally effective in getting a whole picture of the gene expression for my research.

Connected by the incredible team at Friends of the Island Fox (FIF), I put out my request to the different groups responsible for managing the islands where the foxes live—the National Park Service (NPS), The Nature Conservancy (TNC), Catalina Island Conservancy (CIC), the Institute for Wildlife Studies (IWS), and the U.S. Navy—to take extra blood samples into special RNA-preservation tubes. I was blown away by the response. Not only was everyone on board, but they were excited!

I was able to put together a team consisting of representatives from each island, meeting with everyone to flush out the feasibility of a sampling plan, narrowing down what variables were possible and how many samples I would be able to collect. Following this, the RNA collection tubes were shipped out to the six islands for sampling. I got the privilege of volunteering alongside the core team members on Santa Rosa for a portion of the season—getting to provide hands-on support to the people making my research possible.

What does this sample collection and monitoring actually look like?

First, to get out to Santa Rosa Island, you have to take a three-and-a-half-hour boat ride across the Santa Barbara Channel. Then, once set up at park housing, the work can start.

The first day of a new grid, we set up traps at the long-term sites according to their designated GPS coordinates (this ensures consistent data across trapping years). The traps are lined with grass for bedding and baited with kibble and scented loganberry lure. Then, trap checking begins the following day. Out on Santa Rosa, our daily monitoring team consisted of a combination of biologists from NPS, TNC, the California Institute of Environmental Studies (CIES), and researchers like myself from USC and Caltech.

For each day of a grid, we got up around 5 a.m. to get everything ready for the day and hit the long and bumpy dirt roads before sunrise. Once loaded in, each ride can take 45-90 minutes to get to the start of the grids, dropping off each person like a reverse school bus. Then, we hike from trap to trap through thick grassland, steep cliffsides, sandy beaches, and all manner of terrain to check for foxes.

What happens if there’s a fox in the trap?

If there is a fox in the trap, a series of steps need to take place for a full workup and health check, all of which is recorded on data sheets. For most of these steps, a blinder is placed over the fox’s eyes, which helps to keep them calmer during the process.

1. Weigh in: First, the trap gets weighed with the fox still inside—the trap is then weighed again after the fox is released and subtracted from the first measurement to calculate the actual fox weight.
2. PIT tag check: Then, we use a PIT tag scanner to check if the fox has been previously tagged. If the scanner shows an ID, we are then able to look up the individual to see previous data such as age, sex, vaccination status, and other info on its history (this is kind of the equivalent of your pet’s vet history). If there isn’t a PIT tag, then this fox hasn’t been trapped before, and will receive a tag and be entered into the system. On the first day of a new grid, typically every fox will receive a full workup, described in the following steps. On following days, if the PIT tag is from a fox that already received a workup this year, this is referred to as a “recapture” and the fox is simply released from the trap.
3. Collars: Some of the foxes also have radio collars—these are what are referred to as “sentinel” foxes. The radio collars allow for spatial monitoring of behavior like home range, habitat usage, and also provide specific signals if a fox has died (this “mortality beep” is triggered by complete stillness for 6 hours). Radio collared foxes are important to monitoring because these foxes do not receive any vaccinations—serving as “sentinels” for disease monitoring and other potential population threats. If a fox has a collar, we may change the battery or provide fit adjustments.
4. Teeth check: Checking the wear of the teeth on a fox lets us sort foxes into different age classes: 0 = new pup, 1 = yearling/juvenile, 2 = young adult, 3 = adult, 4 = old adult. These are not ages in years, but groupings more like kid, teenager, adult, senior, etc. This is important for documenting the age range of the overall population, particularly for determining the success of reproduction and “pupping” for a given year.
5. Body condition: This is the part of the work-up that gives an overall idea of the fox’s health. Here, we check for amount of body fat, sex and reproductive status, presence of any injuries, and other general physical health traits. Small scrapes or obstructions are treated if possible.
6. Ectoparasites: A comb is used to check the fur for fleas, ticks, and other possible ecto- (external) parasites. If identified, ticks are removed, and sometimes collected for research. On the southern islands, ears are checked for the presence of mites using an otoscope (the same tool your doctor uses to check your ears!). If abundant, they are treated with a topical medication.
7. Sample collection: Once these initial steps are taken, samples for ongoing research projects and internal health checks can now be collected. Some of these include whisker collection for dietary studies, ear and anal swabs for microbiome studies, and blood draws to test for diseases and organ function and to support genetic studies like mine. Blood samples are collected in one overall draw, then can be distributed to different chemical tubes for different purposes—including my RNA blood tubes!
8. Vaccines: Unless flagged as a sentinel for disease monitoring, the majority of foxes trapped receive two vaccines—one for rabies and one for canine distemper virus (CDV). In addition to the overall population monitoring, this is one of the most vital components of fox trapping. Currently, neither disease has been found on any of the Channel Islands since the outbreak of CDV on Catalina in the 2000s. Vaccination efforts have been a crucial component to protecting the recovered population there ever since, and creating a defensive barrier on the other islands to prevent such events from transpiring.
9. Release: Once the workup is done, the blinders are removed, and the foxes are released to go about their lives.
10. Trap reset: After the fox workup, we empty the contents of the trap, add fresh grass, kibble, and loganberry lure, and reset it to be checked the following day. At the end of the 6 days of monitoring for a given grid, the traps are removed.

After the trap check is complete, we pack everything up and hike on to the next trap to check for more foxes and start the whole process over again.

Once all traps on the grid have been checked, worked up, and reset for the day, the “school bus” picks up everyone at their designated end points to head back to housing. There, the samples are processed and stored, data sheets logged, and field kits repacked to get ready to do it all again the next day. 

The best thing is that after all of this long day and hard work–once everyone gets cleaned up and washes the field off–the team still wants to spend time together. After a brief lull where folks take naps and reenergize, everyone crowds into one of the houses for a beloved “family” dinner.

By the numbers

Last year’s field season, over 1,000 unique foxes underwent health checks across all of the islands, and over 2,000 fox captures contributed to population estimates. Consider the work that goes into getting all the way out to a single grid of 12 traps, into a single fox health check—now consider that happening a thousand more times. The sheer scale of teamwork required is nothing short of incredible.

Of these 1,000 unique foxes, 88 individuals provided RNA samples for my research across the six islands. Those samples have since been extracted in the lab and sequenced through support by FIF, and I am in the process of analyzing the data in the hopes of finding answers to questions of immune susceptibility in the island fox populations.

What I’ve shared here is a small snapshot into what sampling for a wild, protected mammal looks like. For every blood sample that was collected for my RNA work, someone had to travel across the ocean, drive a long bumpy dirt road, hike out to a GPS-specified location, hope that there was a fox in the trap, check that the fox fit our sample plan, take a blood sample, transport the sample back to basecamp, freeze it, and somehow get the sample off the island and back to me for downstream lab work and data analysis. For every one of the 88 blood samples that I received back, and every one of their 88 data points used in my analysis, I am deeply thankful for both the fox that provided it and the fox family member that collected it.

Kimberly Schoenberger’s summer research is supported by the Gerald Bakus Graduate Fellowship in Marine and Environmental Biology. Her work is part of a larger, long-term study on Channel Island foxes, led by USC professor Suzanne Edmands. This long-term study is supported by the Offield Family Foundation through the Wrigley Institute for Environment and Sustainability and by Dornsife College of Letters, Arts and Sciences.

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