Metabarcoding Reveals the Genetic Fingerprints of Prey in Scat

 

Scat samples from island spotted skunks and island foxes were collected last December on Santa Cruz Island. The samples were part of a trial research project to determine if a conservation working dog, Moose, could accurately locate and identify island spotted skunk scat. Meet Moose; How accurate was Moose?

A total of 15 island spotted skunk scats were compared to island fox scats using metabarcoding. 

Metabarcoding is a process that takes a general biological sample and sifts out short sections of DNA and matches them to known strands of DNA representing different species. Using this process, a sample of pond water can provide a list of species that have been in that pond. In the Florida Everglades biologists are using metabarcoding to locate invasive pythons. The pythons shed DNA into the environment and metabarcoding can identify their presence.

 

In a scat sample, metabarcoding can help identify food items that an animal has eaten, especially when that prey may not leave exoskeletons, seeds, fur, or bones visible in the scat. (Scat & fox diet)

If island foxes and island spotted skunks are competing for the same food resources, the growing number of island foxes could have a population-limiting impact on the smaller species, the island spotted skunks. (Island foxes and island spotted skunks)

The preliminary results are very interesting.

There was an overlap in some prey species. Both island foxes and island spotted skunks were consistently consuming Jerusalem crickets in the fall of 2024. This large insect is an important food resource for both species. 

Jerusalem cricket

Deer mice appeared to be more important in the diets of island foxes than island spotted skunks. Both species also preyed on katydids, millipedes, and crane fly (most likely the larva which can be large and pump in the fall). For these three arthropods, island foxes were more likely to include them in their diet than island spotted skunks.

 

There were also a large number of prey items that were unique to either foxes or skunks.

Island foxes were frequently eating ground beetles and earwigs, which skunks were not eating. They were eating faster-moving diurnal species like: grasshoppers, song birds and quail. They were consuming fly and moth species that were different from those consumed by the skunks. Island foxes were also occasionally consuming snails. While snails might seem a slow-moving, nocturnal prey, their DNA did not show up in the skunk scat. 

Island spotted skunks were also consuming unique prey species. Several moth species were detected and more than a third of skunk scats revealed moth DNA. Island spotted skunks are strictly nocturnal and it's not a surprise that nocturnal species like moths and field crickets would be prey. Surprisingly, petrel DNA, a sea bird, was also found in about a third of the scats. These are small marine birds nesting in sea caves on the islands. Slender salamanders, a small terrestrial species most likely found in moist canyon soils were a common food source, while weevils and butterflies (possibly overwintering chrysalis) were occasionally eaten.  

While this was a preliminary study over a short amount of time with a small sample size, it suggests that, at least in the fall, there is not a lot of overlap in resource use between island foxes and island spotted skunks. We don’t know how many different island foxes or island spotted skunks are represented by the scat samples and more data is definitely needed.

The scat samples are currently being evaluated for plant DNA.

Island Foxes and Beach Foods

In 2018 Juliann Schamel was the recipient of Friends of the Island Fox's first Research Grant. Her investigation of island fox diet through stable isotopes in whiskers has evolved and deepened to look for connections between diet and surviving drought conditions. 

In 2019 FIF continued to fund Schamel's research as she followed the foxes and the potential of "beach foods" in their diet. It is no coincidence that the island fox above is in a beach area. 

If you look closely at the pile of kelp washed up on the beach, or "beach wrack," you'll see island fox foot prints all around it.

photo courtesy of Nick Schooler, UCSB

Combining her stable isotope research with collaborators at the University of California, Santa Barbara, Schamel has revealed that some island foxes are making use of food resources connected to sandy beaches. Tiny arthropods called "beach hoppers" live in the sand and emerge to eat the kelp that washes up on the beach. Look closely and you will see a group of them feeding on the edge of the kelp blade pictured. 

Some island foxes are eating these tiny, quick moving creatures. If you've turned over a clump of beach wrack and seen little hopping critters, commonly referred to as sand fleas, you've seen beach hoppers. They are not fleas at all; they are more closely related to shrimp.

Juliann Schamel recently presented a poster at the 2022 Wildlife Society Conference. POSTER

And her paper Diet of a threatened endemic fox reveals variation in sandy beach resource use on California Channel Islands with Henry M. Page, Marine Science Institute, UCSB, et. al. was published in PLOS ONE. Read the Paper

Your support for FIF helped fund this important research. The island fox and the beach hopper demonstrate an intertwining of terrestrial and marine ecosystems on the Channel Islands.

FIF Research Grant to Investigate Island Fox Diet Through Whiskers

photo courtesy of P. Bronstein

Island foxes have lots of long black whiskers. These specialized hairs hold important information on diet that could inform decisions on island fox conservation.

Friends of the Island Fox is happy to announce: 

Juliann Schamel is the recipient of the first FIF Research Grant

Schamel is a Biological Science Technician at Channel Islands National Park and the $5,000 grant will help fund research on "The Channel Island Food Web–A Decade of Dietary Resource Use in Channel Island Fox: Implications for Reproduction, Recruitment, and Resilience in a Changing Climate."

It's a big title reflecting the broad range of important data that may be revealed. 

Schamel's work will build on important past research.

island fox scat (or poop)

In 2009, researchers collected island fox scat samples to look at seasonal diet across all six islands. Their 2014 paper revealed diet varied from island to island and included a higher frequency of insects and fruit than expected. They cautioned that islands with poor native plant diversity offered fewer food options for island foxes in the event of drought. 

photo courtesy of P. Bronstein

Just as the science warned, during the consecutive years of the recent drought, island foxes were challenged to find enough food on San Miguel and San Nicolas Islands. Decline of San Nicolas Island fox. During this time a new parasite entered the San Miguel Island fox's diet causing fox deaths.

While scat successfully reveals visual items, (insect exoskeletons, cactus fruit skin and seeds), it may not visually capture everything in the fox's diet. Also, scat data is limited to recording diet in an individual over a short time period, a few days.

In 2010, building on work done on the San Joaquin kit fox, a small sample of island fox whiskers were investigated using stable isotope analysis. 

You are what you eat. Food items (prey and plant) have their own isotope fingerprint. Carbon and nitrogen isotopes consumed by the fox are laid down in the hair shaft documenting an individual's diet over months. 

Since 2010, biologists have been gathering whisker samples from individual island foxes during health checks on the northern islands. These samples have been cataloged by year and with individual fox identification. 

FIF is excited to support Schamel's research using whiskers because it has the potential to:

• Compare diet between successful mothers and unsuccessful mothers
• Discover dietary differences between coastal living island foxes and interior living foxes
• Document changes in diet over the past 9 years, through the drought and as the fox populations have grown
• Possibly reveal prey items that are a vector for the intestinal parasite on San Miguel Island which has caused fox deaths

Whiskers are amazing! Not only do they offer an opportunity to invest in greater knowledge about the secret lives of island foxes, whiskers grow back and their collection is non-invasive. 

FIF will be bringing you more on Juliann Schamel and her research as her work progresses.

Thank you to all of the 2018 grant applicants for sharing your research goals with FIF. There is so much more to learn about island fox health, behavior, and interactions with other species.

Application for the 2019 Research Grant

will be available April 15, 2019

Fox Foto Friday - Island Fox Eating Redberry

Island foxes love their native fruit! Across the Channel Islands native fruit sometimes makes up over 50% of the island fox's diet. 

Researcher Todd West observed this island fox eating island redberry. From toyon and lemonade berry, to Catalina Island cherry and prickly pear cactus, if the native fruit is red, island foxes eat it.

Thank you, Todd, for sharing your photo with Friends of the Island Fox. More of Todd's photos. More island foxes eating.

Do you have a great photo of an island fox? Share it with Fox Foto Friday - islandfoxnews@gmail.com 

How can you help island foxes?

Island Foxes With a Sweet Tooth

What is that island fox doing?

On a December trip to Santa Cruz Island several observers documented a number of island foxes busily searching the ground under the eucalyptus trees.

courtesy of Douglas E. Welch

Initially we thought they were finding food debris left by campers, but the more we watched the more it became apparent that the island foxes were licking something on the leaf litter. The December day was unusually warm and dry. (This was while the Thomas Fire in Ventura was blazing.) We watched foxes in close proximity to each other completely engaged in their search and paying no attention to us or each other. At one point there were seven foxes in this small area. -
Douglas Welch

bloom after island fox licked it

The red gum eucalyptus trees were in bloom. One young island fox stood on its hind legs and pulled down a low branch so it could access the flowers. One at a time, it stuck it's muzzle into the eucalyptus blooms, licking and nibbling them. I've been visiting Santa Cruz for over 10 years. I've never seen this behavior before. - Keri Dearborn 

Little beads of sticky sap were on the tables and benches. I touched my finger to the sap and tapped it on my tongue–it was sweet.  - Michael Lawshe

One island fox wandered within several feet of me. Each time it found a drop of sweet sap, it would lick it up and make a soft sound, almost like a purr. - Keri Dearborn
 
On this dry hot day in December, the island foxes were licking up the sweet eucalyptus sap. While this is not known to be a typical behavior, it is another example of the adaptive nature of these unique canines. Typical island fox diet. Island foxes eating toyon berries that same day.

Re-examining Island Fox Diet

What do island foxes eat?

Island fox scat with native fruit seeds

It is a common question and examining island fox scat (or poop) has provided some of the best answers. In 2009 a year-long study examined island fox scat over four seasons and across the six islands where they live. New Findings on Island Fox Diet.

The findings from this study, however, were done before multi-year drought impacted vegetation across California and on several islands. Have island foxes shifted their diet to other foods to make-up for the decreased availability of some plant foods or prey species?

Island fox scat with insect exoskeleton remnants

In 2009, island fox populations were recovering on four islands from near extinction and their population numbers were still relatively low. Most fox pairs could establish a territory in an area with abundant resources. Now that the populations have recovered, are island foxes eating a more diverse diet to meet their food needs? Are beetles and insects still the most frequently eaten prey? Have island foxes in marginal territories started to consume other food items? 

In addition to scat, whisker samples can provide evidence of what an island fox has eaten over several months. Whiskers are specialized hairs that grow over an extended amount of time. Trimming an inch or two off the end of a whisker, can provide researchers with information on what a specific individual fox has been eating. Isotopes laid down in the hair shaft document the kinds of proteins and plant matter consumed.

 While we don't think of island foxes eating marine animals, during a limited test study, one individual island fox was found to have isotope markers that signaled it was eating marine proteins, fish or crustaceans. Was this individual unusual?

Research on island fox diet is an on-going project. Biologists in the field counting island foxes on the northern islands were taking whisker samples this year.

Whether it is scat or whisker samples, it is time to add a new chapter to research on island fox diet.

Island Fox Origins and the Truth Behind Eagle Diets

Are you looking for information on the origin of island foxes; how they evolved and their biology? Perhaps you’ve heard people question whether golden eagles were actually preying on island foxes. Answer your questions with information from the primary sources.

Friends of the Island Fox is honored to make information available from top researchers and biologists working with the island fox and the Channel Island ecosystem.


Paul W. Collins, Curator of Vertebrate Zoology at the Santa Barbara Museum of Natural History recently gave two presentations from his accumulated research at an Island Fox Workshop sponsored by the Santa Barbara Museum, Ty Warner Sea Center, Santa Barbara Zoo and Friends of the Island Fox. Both of these presentations are now available through links from the Friends of the Island Fox Educational Research Library.

• Origin, Evolution and Biology of the Island Fox - looks at genetic, morphological, and archeological data regarding island fox origins and the basics of island fox biology, size, behavior, reproduction and diet

• Diet of Bald and Golden Eagles on the Channel Islands - looks at the role eagles played in the decline of island foxes on the Northern Channel Islands and compares the diet of bald and golden eagles on the islands by examining prey remains in nests.

These two slideshow presentations can be found in the Educational Research Library

Under: “Island Fox Fact Sheets & Current Research”

Under: “Links to Research Sources”

Friends of the Island Fox is endeavoring to create the Internet’s most current library of information regarding island foxes. If you are a researcher or biologist and would like us to link to or host your published work relating to the island fox or the Channel Island ecosystem, please contact the Friends of the Island Fox Webmaster at islandfoxnews@gmail.com