Tracking Plants And Animals With The DNA They Leave Behind

Sep 23, 2020

Dr. Kellie Carim samples for bull trout in a Western Montana creek outside of Missoula Montana.
Credit Photos courtesy of USFS National Genomics Center for Wildlife and Fish Conservation

It's a bit like CSI - if the cops suspect someone has been there, they check for DNA, take it back to the lab, and figure out who it belongs to. Only these researchers aren't looking for crooks - they're looking for endangered or invasive species, using environmental DNA (eDNA).

eDNA is the tiny bits of genetic material that an organism sheds into their surrounding environment. A researcher can collect samples that contain eDNA much quicker and cheaper than a researcher looking for an individual of a certain species, especially if it's rare or endangered. This is because they don't have to physically find or collect an organism.

Filtered water is collected as a sample in an area where the species may be. Then it's tested for this shed DNA. Oftentimes these samples can only let you know if an organism is there or not, though some sampling methods can give rough population estimates.

Dr. Kellie Carim and Dr. Taylor Wilcox discuss eDNA results from the quantitative PCR machine pictured to the right.
Credit Photos courtesy of USFS National Genomics Center for Wildlife and Fish Conservation

Organizations like the National Genomics Center for Wildlife and Fish Conservation, housed in the U.S. Forest Service's Rocky Mountain Research Station (RMRS), have been using eDNA to monitor the spread of invasive species.

"When something comes into the system, they're at really, really low density. It's really hard to find them going out there. And Wyoming's vast. The area you might think has been invaded is huge," said RMRS Wildlife Science Program Manager and Director of National Genomics Center Mike Schwartz. "So how do you find that smaller area? How do you go find that one, that needle in the haystack? So this is where environmental DNA is really helpful."

According to Schwartz, samples are taken down the length of a stream to test for the front lines of an invasion. Then, when the invasive species is detected, agencies can strike quickly in the right areas.

"Because when an invasive species is just getting established, that is really the best time to try to put in some mitigation efforts, some control efforts, to get rid of that species because we know once that invasive species is in the ecosystem they're very hard to remove," said Schwartz.

Ph.D. Candidate Jessie Golding samples snow on the Beaverhead Deer lodge National Forest.
Credit Photos courtesy of USFS National Genomics Center for Wildlife and Fish Conservation

eDNA can also help wildlife managers keep track of endangered species in the area, especially if they spend some time in the water or walk through some snow.

"If you went out in the winter, and you saw an animal walk through and leave a track, you're right there after it leaves the track, you'd have a pretty clear print of what that animal leaves," said Schwartz "But give it three, four or five days later, that track starts to melt down, it starts to change form. You can't always tell what animal was there."

But if you collected the snow and melted it down, it could be analyzed in the lab for the presence of eDNA and used to identify the track. This can even be used for tracks that have been buried if you know how far down in the snow to go for the sample.

According to Schwartz, the ways eDNA can be used continues to evolve.

"Every time we think we hit a limit on what this technology can do, we find there's a new thing we can do, there's a new way we can be more efficient," said Schwartz. "And it's just been really fun because you see the excitement that our management partners have in getting some of this information and how it's 10 times more efficient than a lot of the other ways in which we sampled in the past. So it just feels good to be able to provide data that that's of use to our management colleagues."

Those interested in finding out where aquatic eDNA samples have been collected can visit the open access eDNAtlas. The database contains information from samples collected by multiple agencies across the country.

Have a question about this story? Contact the reporter, Ivy Engel, at iengel@uwyo.edu.