Ecologists Use DNA to Study Wild Herbivore Diets

Utah State University

LOGAN, UTAH, USA – It's not easy eating green. Most plants are heavily defended with chemicals to deter plant eaters. For these herbivores, getting enough to eat, while minimizing exposure to toxins, is a persistent challenge that shapes their foraging choices.

Understanding how these animals navigate these choices is fundamental to understanding what these creatures need to survive and how species respond to changing conditions, says Utah State University ecologist Sara Weinstein.

Woodrats (genus Neotoma) provide an unexpected model for studying animal diets, she says. Native to North America, these herbivorous rodents consume a wide variety of plants.

"Woodrats are remarkable in their ability to eat truly awful, toxic plants," says Weinstein, assistant professor in USU's Department of Biology and Ecology Center. "If there are no other options, woodrats can consume plants like creosote bush, mesquite and juniper, which are full of disagreeable compounds like alkaloids and terpenes."

Weinstein, along with University of Utah scientists Denise Dearing and Dylan Klure, USU adjunct faculty colleague Marc Mayes at Spatial Informatics Group-Natural Assets Laboratory in Pleasanton, California; and research partners at ARUP Laboratories in Salt Lake City, San Francisco State University and the North Carolina Museum of Natural Sciences, reports findings from a nearly eight-year, large-scale survey of woodrat populations throughout North America in the Sept. 15, 2025 issue of the Proceedings of the American Academy of Sciences.

The research was supported by the National Science Foundation.

"Woodrats are a phenomenal model organism for understanding how wild animals make choices about what to eat," says Weinstein, "They live in a landscape with varied food options, some better than others, and we can use this natural variation to understand how they decide what to consume."

Unlike rats typically found in urban and suburban areas, woodrats shy away from humans.

"Woodrats are very distant cousins of the better known, and omnivorous, New York pizza rat," she says. "You are unlikely to see woodrats, unless you're in relatively undeveloped habitat."

Yet the timid woodrats live throughout the United States and their large numbers make them excellent study subjects, Weinstein says.

"They're everywhere, with multiple species often present in the same area, which gives us lots of replication to look at what determines diet breadth at the individual, population and species level," she says.

Observing how woodrats choose foods at an individual level, as well as at the population level, Weinstein says, reveals how the animals are balancing the challenges of finding enough to eat without poisoning themselves.

The animals' small size also makes them easy-to-manage research subjects.

"Compared to large herbivores like deer, moose or elephants, woodrats are much easier to capture and handle," she says. "They also readily provide us with material for diet analyses, because they tend to defecate in traps."

These droppings provide a treasure trove of information.

"Each sample combines about a day of food choices," Weinstein says. "We can get a snapshot of everything the animal has eaten.'

Advancements with DNA metabarcoding, facilitated by next-generation sequencing over the past decade, have revolutionized our ability to analyze animal diets, she says. "It's a very powerful and accessible technique to characterize the unseen."

This information is critical for understanding species' resilience, yet Weinstein says dietary niche breadth remains poorly understood in mammalian herbivores. Results from species, population and individual level surveys suggest that costs of both specialization and generalization dictate diet breadth.

"A longstanding notion is that if you're highly specific in what you eat – you only eat one thing – then, if you lose access to that plant – say, it disappears because the ecosystem changes or an invasive species pushes it out – you're going to be in trouble," she says.

If you're a generalist and able to pivot quickly to an alternative food source, your chances of survival improve.

"Most woodrat populations are generalists, but at the individual level, these generalists' diets may not be as broad as we previously assumed," Weinstein says. "We tend to think of generalists as being a jack-of-all-trades, master of none. However, it looks like most generalists are more aptly described as jacks-of-all trades, master of some."

Individuals appear to select a consistent subset of plants, she says, which likely helps them to manage the costs and risks of consuming potentially poisonous food.

"Ultimately, these constraints on animal diets have important implications for our understanding of food webs, species interactions and which populations are more likely to persist in changing ecosystems," Weinstein says.

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