Stanford researchers develop a DNA approach to predicting ecosystem changes

When the wolves returned to Yellowstone in 1995, no one imagined that predators would literally change the course of rivers in the national park through cascading effects on other animals and plants. Now, an approach developed by Stanford University holds the promise of predicting such ecosystem changes as some species become more widespread or vanish altogether.

Outlined in Borders in ecology and evolution, the fast, low-cost technique is the first to analyze DNA left in animal feces to map complex networks of species interactions in a terrestrial system. It could help redefine conservation as we know it, identify otherwise difficult-to-find species, and lead a global effort to rebuild large areas through the reintroduction of locally eradicated species.

“It’s not just that we can quickly capture an area’s biodiversity,” said study lead author Jordana Meyer, a PhD student in biology at the Stanford School of Humanities and Sciences. “We can also quantify the extent of indirect links between species, such as how the behavior of a specific predator affects the vegetation in an area. This allows us to measure the impacts on species that are essential to the system or particularly. vulnerable “.

Just as the introduction of species, such as Yellowstone wolves, can have widespread effects, their demise can be devastating in ways that are hard for scientists to predict. Meyer, whose work primarily focuses on African wildlife, has seen the impact firsthand in the Democratic Republic of the Congo. There, the loss of large herbivores, such as rhinos and elephants, has led to the shrinking of the once huge grasslands that the creatures once grazed.

As human impacts on wilderness accelerate, effective conservation and ecosystem management will require faster, inexpensive and non-invasive technologies to capture changes in biodiversity and quantify interactions between species. One of the most promising tools is the study of so-called environmental DNA in animal materials left behind, such as hair and skin. After extracting the DNA, scientists sequence it and compare it with online databases to identify organisms present in a given area. It is a relatively quick and low maintenance process compared to traditional approaches, such as live-trapping, animal tracking, and cam trapping.

Working at Stanford’s 1,193-acre Jasper Ridge Biological Preserve, the researchers used their technique to analyze the feces of carnivores such as mountain lions, omnivores such as gray foxes and herbivores such as black-tailed deer. By identifying DNA in the diets of these animals, the researchers built an extraordinarily detailed and data-rich food web and accurately captured the biodiversity of the area compared to other animal surveys and a long-term camera trap study in the reserve.

Among other surprises, the new analysis revealed the indirect effects of a cascade of predators on vegetation and allowed the researchers to determine exactly how the predators competed with each other. These findings were validated against evidence from camera trap data collected at Jasper Ridge over the past seven years in which the return of mountain lions, the ecosystem’s main predator, caused a decline in the presence of deer and coyotes. Without its coyote competitor, the former rare gray fox has returned to Jasper Ridge. Gray foxes survive more on plants, namely fruits and seeds, than coyotes. Therefore, the increase in gray foxes can lead to alterations in the distribution and abundance of fruit plants in the reserve because the seeds often remain viable after being digested by mammals. Armed with this kind of knowledge, managers can predict the impacts of changing animal and plant communities, which in turn can provide a framework for conservation-relevant decisions.

The DNA the researchers collected in the animal feces also identified plant and animal species that were unknown within the reserve, providing an early warning of invasive species.

“We are excited about this approach because it will not only help us understand how and why species survive in protected areas based on what they eat, but also whether animals are able to take advantage of non-native plant and animal species,” he said. said the study senior author Elizabeth Hadly, Professor Paul S. and Billie Achilles of environmental biology at Stanford’s School of Humanities and Sciences. Hadly’s lab pioneered work with ancient and abandoned DNA in the United States, South America and India.

These methods could help rebuild protected areas by allowing researchers to model how ecosystems will respond to certain species before they are actually reintroduced. For example, before reintroducing the African lion to protected parts of Africa, scientists could first study the biodiversity and connectivity of the areas and predict how lions could impact prey populations and other knock-on effects they could trigger in the whole ecosystem.

The researchers plan to expand their model into protected areas in Africa to assist in strategic adaptive management and restoration strategies. “I hope that techniques like this can help us protect and monitor natural spaces on a global scale,” Meyer said.

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Hadly is also a faculty director of Stanford’s Jasper Ridge Biological Preserve, a member of Stanford Bio-X and a senior fellow at the Stanford Woods Institute for the Environment. Co-authors of the study include Kevin Leempoel and Gianalberto Losapio, postdoctoral fellows in biology at Stanford at the time of the research.