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.

A Nose for Identifying a Species

Last December, Friends of the Island Fox worked with The Nature Conservancy and Working Dogs 4 Conservation on a project to see if a specially trained dog could track down island spotted skunk dens and scat. (See Moose the conservation working dog)

courtesy of TNC and WD4C

 

In the initial project, Moose used his specially trained nose to locate 11 scat samples. Two scat samples were also found by humans. The samples were sent to the Genetics Lab at UC Davis and Friends of the Island Fox helped fund the genetic testing of the samples. How well did Moose do identifying island spotted skunk scat from island fox scat?

Moose: 9 out of the 11 scats came from island spotted skunks. 1 sample was too degraded for DNA analysis (it might have been skunk) and 1 sample was island fox scat. 90% accurate!

Humans: 1 of the 2 scats came from an island spotted skunk, the other was island fox. 50% accurate!

 

Obviously, Moose is better than humans at detecting island spotted skunk scat.

island fox scat

The next questions: 

• Is there enough quality DNA in a scat sample to determine the identity of an individual island spotted skunk?
• It would cost $7,000 to develop island spotted skunk genetic markers to determine individuals. Can enough scat be located to establish a population estimate and would it be fiscally feasible to count the population this way?

 

The other information obtained from the scat samples pertains to diet. Island spotted skunk scat was compared with island fox scat. Stay tuned for more on metabarcoding.

Why do we need to count island spotted skunks?