Soil DNA analysis could be an effective way to track animals

IMAGE: A night vision camera trap captured this image of mountain lions drinking from a stream in Stanford’s Jasper Ridge Biological Reserve.
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Credit: Jasper Ridge Biological Preserve

It’s difficult to protect something you can’t find. A new Stanford study reveals that soil sampling for the left DNA of animals can provide valuable information for conservation efforts – with significantly lower costs and times – than currently used methods, such as photo traps.

The trial, outlined on January 14 in Proceedings of the Royal Society B, have also proven effective in distinguishing genetic differences between animals that would otherwise appear identical, an arduous task with traditional localization approaches, and may also have revealed a previously unknown species diversity, according to the researchers. Although the technique still needs improvement, the authors are optimistic that one day it could revolutionize the study of species in nature.

“We need a quantum leap in the way we identify and follow animals,” said lead author of the study Kevin Leempoel, postdoctoral researcher in biology at Stanford. “It could be this.”

A confident solution

The extinction spectrum hangs over over a quarter of all animal species, according to the best estimate of the International Union for Conservation of Nature, which maintains a list of endangered and extinct species. Conservationists have documented extreme dips in animal populations in every region of the Earth.

One of the most promising tools for biodiversity monitoring – key to large-scale conservation efforts – is the study of environmental DNA, or eDNA, in discarded animal materials, such as hair, feces, skin and saliva. After extracting the DNA, the scientists sequence and compare the online DNA sequence databases to identify the species. It is a relatively fast, low-maintenance process compared to traditional approaches, such as live trapping, animal monitoring and camera trapping, to study species diversity, distribution and abundance. The researchers spent approximately $ 4,500 on all supplies of the study, except for laboratory equipment. A similar study with cameras could cost more than double.

Despite the obvious advantages, questions remained about the effectiveness of eDNA analyzes. This is partly due to the fact that most research has so far been conducted only in ocean and freshwater environments. Of the few studies conducted on earth, most took place in closed areas, such as zoos, or limited to a limited number of species.

See the invisible

Working at the 1,193-acre Jasper Ridge Stanford Biological Reserve, Leempoel and his colleagues studied soil eDNA. Not only did they identify nearly all the animals that nearby photo traps had spotted in the previous four years, they also found genetic evidence of a number of small mammals, including bats and voles, rarely if ever seen on cameras. These creatures had probably escaped the gaze of the cameras because they were too small to trigger them. Overall, there was an 80% chance of finding an animal’s eDNA in an area within 30 days of the animal’s presence there.

Another advantage of eDNA is the ability to distinguish similar species. For example, the researchers found the DNA of the Norwegian rat in soil samples, confirming for the first time the presence of this species in the area. Previous polls on the camera could not distinguish between Norway and black rats.

Compared to camera recordings and other observations, eDNA identifications appeared to be closely related to the frequency and recent presence of animals in the area. The analysis revealed no sign of badgers – not recorded on cameras in the previous four years – domestic cats or weasels – captured by the camera only a few times in the previous two years.

“By validating animal photographs with their genetic remains in the environment, this study reveals both the biodiversity hidden in a terrestrial ecosystem and how these eDNA techniques will work in other places,” said senior writer Elizabeth Hadly, Paul S. and Billie Achille Professor of environmental biology at Stanford’s School of Humanities and Sciences.

Towards a new paradigm

Despite these positive results, questions remain about the potential of eDNA analysis. Scientists don’t know how often an animal has to go through a certain area to be detectable in an eDNA sample or how recent this step must be. If the size of an animal influences the amount of DNA left behind, as researchers speculate, some animals would be sampled only rarely while others would be overrepresented. Nobody knows the precise volume and the number of samples that should be collected for maximum accuracy, which environmental source – soil or something else – is the most versatile or if all species are even detectable by eDNA analysis.

The results of the study seemed to represent excessively some species, such as mountain lions and lynx, probably due to the habit of felines to frequently mark their territory with urine and feces and because they frequently use paths such as those in which the researchers have taken soil samples. In general, it is impossible to know whether pieces of dry skin, fur or scat were carried by the wind or by other species that had consumed the animal as prey.

Perhaps most importantly, incomplete DNA databases and the study’s design limitations made it difficult to detect all species present in the area and caused at least two inconsistent results among the genetic sequencing approaches used by researchers. The analysis of eDNA remains relatively time-consuming since proven protocols have not yet been established. However, researchers are optimistic about the promise of the approach.

“Its overall accuracy, coupled with reduced costs of genetic sequencing and new portable sequencers, makes eDNA a likely candidate to become the standard for biodiversity investigations in the next decade,” said Leempoel.

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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 member at the Stanford Woods Institute for the Environment. Trevor Hebert, an academic technology specialist at Jasper Ridge Biological Preserve, also co-authored the study.

The research was funded by the Swiss National Science Foundation, the Stanford University’s Mellon Grant and the Howard Hughes Medical Institute.

Contact

Kevin Leempoel, Biology: (650) 229-9482, [email protected]

Elizabeth Hadly, Biology: (650) 245-1775, [email protected]

Rob Jordan, Stanford Woods Institute for the Environment: (650) 721-1881, [email protected]

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