Tracking animals without seeing them

This night-vision camera trap picture of mountain lions drinking from a stream at the Jasper Ridge Biological Preserve in the US looks great, and is valuable, but getting such images is a bit hit and miss.

Sampling the DNA that animals leave behind in the soil might be a better way of gaining information about what’s where for conservation purposes, argue researchers from Stanford University.

In a paper in the journal Proceedings of the Royal Society B, Kevin Leempoel and colleagues say environmental DNA (eDNA) also helps distinguish genetic differences between animals that otherwise look identical – an arduous task with traditional tracking approaches.

It’s not a new approach, and it’s a relatively straightforward process. After sequencing DNA extracted from discarded animal materials, such as hair, faeces, skin and saliva, scientists compare it to online DNA sequence databases to identify the species. 

Questions remain about its efficacy, however, in part because most eDNA research to date has been done in ocean and freshwater environments. Of the few studies on land, the majority have been in enclosed areas, such as zoos, or limited to a small number of species.

So Leempoel and colleagues decided to trial it across the 480 hectares of Jasper Ridge, which Stanford owns.

They report that they not only identified almost every animal that nearby camera 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 by the cameras. 

These creatures had likely escaped the cameras’ gaze, they say, because they are 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.

And they were able to distinguish between species. For example, they found the DNA of the Norway rat (Rattus norvegicus) in soil samples, confirming its presence in the area for the first time. Camera surveys could not tell the difference between Norway rats and black rats.

At the same time, they could confirm what hadn’t been around. They found no sign of badgers – which had been not been caught on camera for the four years – or domestic cats and weasels, which have been recorded only a few times in the past two.

Despite these positive results, questions remain, the researchers acknowledge. 

Scientists do not know how frequently an animal must pass by a given area to be detectable in an eDNA sample, for example, or how recent that passage must be. If an animal’s size affects the amount of DNA it leaves behind, as the researchers speculate, some animals would only rarely be sampled while others would be overrepresented. 

No one knows the precise volume and number of samples that should be collected for maximum accuracy, which environmental source – soil or something else – is the most versatile, or whether all species are even detectable via eDNA analysis.

The study results appeared to overrepresent some species, such as mountain lions and bobcats, possibly due to their habit of frequently marking their territory with urine and faeces, and because they regularly use trails such as those where the researchers took soil samples. 

In general, it’s also impossible to know whether pieces of skin, fur or dried scat were transported by wind or by other species that had consumed the animal as prey.

And while getting results is easier than hoping to catch an animal on camera, analysing eDNA is relatively time-consuming because proven protocols have yet to be established. 

Leempoel and his colleagues remain positive about the potential, nonetheless.

“Its overall accuracy, combined with decreasing costs of genetic sequencing and new portable sequencers, makes eDNA a likely candidate to become the standard for biodiversity surveys in the next decade,” he says.

“We need a quantum leap in the way we identify and track animals,” he adds. “This may be it.”