The Scoop on Scat Sampling

One of our goals during Sierra Nevada Red Fox surveys is to identify, collect, and record the locations of any scat we find out on the trail. While scat has been used in animal tracking for as long as humans have tracked anything, and obviously helps confirm a fox's presence in an area, recent scientific breakthroughs have revealed new uses for yesterday's meals.

​Scat has long been used to tell what animals are living in the area, as well as approximate their diet through cataloguing the scat’s contents. This data is particularly invaluable for understanding rare carnivores, when direct observation is unfeasible or would disrupt their natural behavior. For example, using scat, researchers were able to determine that whitebark pine trees are crucial for the winter survival for mountain dwelling red fox like the Sierra Nevada red fox (also known as SNRF). A Yellowstone winter study revealed that red fox scat was made up of an average of 61 percent Whitebark pine seeds (1). Whitebark pine is in decline due to an introduced pathogen, so this finding has important ecological and management implications. (As a side note, foxes are classified as carnivores primarily because they belong to the order Carnivora; they are not strictly carnivores.) Individual scats are not only useful for identification and diet, counting scats across the  landscape can also establish rough population estimates through mathematical modeling. Just looking at scat can tell us many important things!

Whitebark pine trees at Kings Canyon National Park provide an important food source for foxes (Credit: NPS)

Over the last decade and a half, scat surveys have become even more useful, due to breakthroughs in genetic analysis. Previously, studies relied on a scat’s visual characteristics to determine which species it belonged to. These visual characteristics are highly valuable for some species, but an inexact science for others. In some cases scats from two entirely different species can share nearly identical characteristics, generating accidental bias in studies.  Around the mid-2010s, researchers began using genetic information extracted from fresh scat samples to confirm the species identity. A 2015 study utilizing these new DNA identification techniques on snow leopards found that, out of 100 samples collected by researchers, more than half of the scat identified in the field as snow leopard (Panthera uncia) actually belonged to the red fox (Vulpes vulpes), since both species have nearly identical scat characteristics (5). Breakthroughs in genetic analysis have allowed researchers to move forward with more confidence in the data generated by scat.

Red fox scat (credit: Poo Museum)

Snow Leopard scat (Credit: Phuntsho Thinley)

​Over time the analysis of DNA from scat became a hallmark tool used by wildlife managers and researchers to gain even more information on rare species. Breakthroughs in genetic sequencing made fresh scat not only useful for identifying species, but also for identifying each individual animal as well. With this non-invasive ability to identify individuals, researchers and wildlife managers can now monitor a whole new dimension of rare carnivore life, including survival rates, breeding success, and overall population dynamics. ​

To do the genetic analysis, the DNA is put into solution and thousands of copies are made, making it easier to “see” the DNA’s characteristics. Genetic analysis is a fast evolving science. In the most recent breakthrough in 2025, Smithsonian researchers studying the reintroduction of swift foxes in Montana, applied a new amplification technique to the DNA, borrowed from archeologists, that improved the resolution of the DNA, allowing even degraded samples to provide useful data. This breakthrough raised the bar in what could be done, making scat ever and ever more relevant to conservation.

Agarose gel electrophoresis allows scientists to visualize bands of DNA based on a pattern left in the gel after the process is complete. (Credit: Ultrabem)

​The Sierra Nevada Red Fox Conservation Strategy outlines key steps needed to conserve the species, with the goal of “long-term persistence of viable populations of SNRF within their historical range.” The strategy also identifies current roadblocks, the main one being the lack of data on current populations. This key issue is outlined in the opening paragraphs - “Progress in SNRF conservation is hindered by our limited understanding of several basic characteristics of extant SNRF populations.” The strategy lists scat surveys as a critical method for understanding small populations like the one on Mt. Hood. The strategy refers to the need to gather data year after year in a noninvasive way, something that scat surveys excel at. This scat will determine not only if Sierra Nevada red foxes are present, but also their sex, age, familial relationships, minimum reproductive output, minimum survival rates, residency status (including population of origin for immigrants), and ancestral composition (3).

A SNRF rock den site observed in the Central Cascades. (Credit: ODFW)

​Thanks to these scientific breakthroughs and the data collected during scat surveys, we will all continue to learn even more about the rare and unique carnivores in our local ecosystems.

​Sources:
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1. https://www.fs.usda.gov/r6/issssp/downloads/xvertebrates/ssa-ma-vulpes-vulpes-necator-201802.pdf
2. https://www.dfw.state.or.us/resources/hunting/small_game/docs/forest_carnivore_project_report_hiller.pdf
3. https://www.dfw.state.or.us/wildlife/management_plans/docs/A%20Conservation%20Strategy%20for%20the%20Sierra%20Nevada%20Red%20Fox_2022.pdf
4. https://nationalzoo.si.edu/news/new-dna-analysis-allows-scientists-identify-specific-animals-their-feces
5. https://pmc.ncbi.nlm.nih.gov/articles/PMC4790252/