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.

Stable Isotopes Document Decade of Dietary Change in Island Foxes

Juliann Schamel has been researching island fox diet using stable isotopes in whisker samples since 2018. Friends of the Island Fox has supported the processing of whisker samples through several Research Grants. In November of 2023, Schamel presented the following poster of her latest work at the California Islands Symposium.

Using Stable Isotopes to Assess a Decade of Dietary Resource Use in Two Sympatric Island Endemics: The Island Fox and the Island Spotted Skunk (link to complete poster)

Island foxes and island spotted skunks live together on two islands, Santa Rosa and Santa Cruz. When island fox numbers crashed due to predation by golden eagles, island spotted skunk numbers appeared to increase dramatically. In 2011, on Santa Rosa Island, there were still fewer than 90 island foxes in the wild. During annual health checks, whisker samples were collected from both island foxes and island spotted skunks in a northern area of the island and stored for later analysis of what food resources each species was using.

In 2011, island spotted skunks out numbered island foxes in the wild. Stable isotope analysis shows that the skunks and foxes were using different resources. 

J. Schamel, 2023 poster

 

Carbon and nitrogen isotopes travel up the food chain leaving a specific isotope signature for plant and animal resources. Literally, you are what you eat and isotopes from a mammal's diet are laid down chronologically in hair or fur. A single island fox whisker can provide 5–6 months of weekly diet data. On the graph above, native terrestrial plant foods, like manzanita berries, are high in Carbon and low in Nitrogen. A deer mouse is the accumulation of its own, mostly plant diet; it has a mid-range Carbon and Nitrogen signature. In the graph above, the blue data points represent island fox diet and the orange data points represent island spotted skunk diet. 

In 2011, when island fox numbers in the wild were low, their diet tended to be higher on the food chain or trophic level: deer mice, birds and reptiles. The data suggested separate diet niches for island foxes and island spotted skunks. The skunks were eating primarily, lower level prey, like insects, and some plant foods.

J. Schamel, 2023 poster

In 2014, continuing drought influenced wildlife survival; island fox and island spotted skunks were nearly even in number on Santa Rosa Island. Island foxes expanded their diet, including marine resources, and island spotted skunks preyed more on deer mice and higher level prey. The two predators began competing for resources.

J. Schamel, 2023 poster

By 2018, the island fox population had recovered, but island spotted skunks appeared to decline in number. (Counting island spotted skunks) As island fox density increased across the island, they dramatically broadened their diet–from native fruit through a range of prey species. The spotted skunks maintained a more narrow diet, but they were now in constant competition with island foxes. What will this mean for the two species?

Schamel's work also revealed that individual island foxes are becoming specialized in their diet.

J. Schamel, 2023 poster

 

In the graphic above, each circle of data points represents an individual island fox and its diet. Some individuals appear to be specializing in fruit and insects, while others are eating predominately terrestrial prey. How is island fox diet continuing to change?

Save the date of April 30th at 6:30 pm PT 

Juliann Schamel will talk about her work on 

FIF's "Date with a Fox" webinar

sign-up for FIF's e-newsletter to receive an invitation

Measuring out a whisker sample

Whisker samples continue to be collected for both species. 

designed by island biologist, Stacy Baker

When you purchase an island spotted skunk pin, 

you send a sample of island spotted skunk whisker 

to the mass spectrometer to reveal stable isotopes.

Island Fox Whiskers Go to the Lab

Schamel with island fox pup

FIF Research Grant recipient Juliann Schamel has been collecting island fox whiskers to study the diet of island foxes through stable isotope analysis. Her research project is in conjunction with Dr. Seth Newsome and the Center for Stable Isotopes at the University of New Mexico.

Juliann says "Once I learned how stable isotope ecology works and what we could learn about island fox ecology from this method...I was hooked. The invisible chemical world can reveal fascinating connections within food webs and beyond." More on stable isotopes

"This year, with the support of Friends of the Island Fox and [another conservation fund], we are able to investigate a variety of conservation-geared questions about island fox diet on San Miguel and Santa Rosa Islands. We are looking into how diet differs among habitats on the islands, among demographic groups, and between island fox and island skunk. We are also assessing if and how fox diet has changed over time (2010–present) in response to things like density changes in the fox population and rainfall (drought conditions). This last question may have important implications for the ecology of the acanthocephalan worm, a novel parasite that appeared in the San Miguel Island fox in 2012 (at the beginning of the drought) and has spread through the fox population."

The spiny-headed worm, a species of Acanthocephala, has been implicated in the low population numbers on San Miguel in recent years. Parasite threatening San Miguel Island Fox.

"By using whisker samples that are linked to a known individual with a known history within the island fox monitoring program," Schamel says, "we are able to track the diet of individuals over time to see if and how their diet may have fluctuated during the drought or as they moved to a new habitat."

A number of whisker specimens were collected this winter, including in the beach/dune habitat on Miguel and Rosa where island foxes are not typically counted. This will provide data on dietary resources in the marine adjacent habitat that has not been collected before. Schamel says "I am very excited to run these samples!"

Collected whisker samples are sorted, inventoried, and cataloged. Once they are cleaned, rinsed, and dried, each individual whisker is placed in vial.

Newsome and his lab manager at UNM use a razor and tweezers to divide each whisker into sub-samples: 0.2mg (weighed precisely with a micro-scale).

Schamel explains these sub-samples are fed into "the mass spectrometer, which consumes the samples and spits out data on carbon and nitrogen isotope ratios." The ratios are compared to a library of food resources and their known isotope ratios. "The FIF funding is actually paying the mass spectrometer for its time."

Schamel in the field on Santa Rosa Island.

So far ~100 island fox samples from Santa Rosa have been analyzed from a variety of habitats. In addition ~200 island fox whisker samples from San Miguel have been analyzed from 2010–2012, before the drought. Schamel will be at UNM this spring working on samples from 2014–2016. "There are many samples from the same individuals across this time frame, which will be exciting to see!"

Juliann Schamel hopes to present preliminary data at the 2019 Island Fox Conservation Working Group Meeting in May. 

Research like Juliann Schamel's is vital to understanding island fox health and long-term survival.  This research is only possible with donations from people like you.

Applications for the 2019 Friends of the Island Fox Research Grant will be available on islandfox.org on April 15, 2019.