DNA Detective Work Offers New Way to Survey Wildlife

Aug 27, 2019

Forensic scientists (at least on TV shows) collect DNA to figure out who was at the scene of a crime. What if you could use the same technique to discover when a mountain lion crossed a river or what kind of fish live in a lake? A team at Embry Riddle Aeronautical University in Prescott is working on that idea as a new, faster way to survey wildlife. KNAU’s Melissa Sevigny reports.

Credit Judi Rochford

The Verde River is murky and green through this stretch of desert near Clarkdale. Its water contains secrets that a team of scientists hope to uncover.  

Katie Benson takes a water sample from the Verde River
Credit Judi Rochford

"I’ve done a lot of falling in rivers the last year!" wildlife biologist Katie Benson laughs as wades into the water to dip a small sample jar. "I’m basically positioning myself in the middle of the flow... then I usually wait a few seconds, because I’ve kicked up sediment and things on the way out here, so wait a few seconds, then open up my filter housing and dip it in the water upstream from myself."

Matt Valente sets up the vacuum pump
Credit Judi Rochford

The water is full of DNA—not just from fish and frogs, but from a lot of other animals that drink from, swim through, or fly over the river. Benson’s vision is one day wildlife biologists will be able to make a list of every vertebrate species in a watershed – just with a scoop of water.

"This is still quite a bit of work, but it is definitely not as labor intensive as some of the traditional surveys," Benson says.

In traditional surveys biologists have to go into the field to count birds or net fish. It takes a long time and it can be stressful for wildlife. Hillary Eaton, Embry-Riddle forensic scientist, says "I was actually kind of shocked at the way they would monitor animals… electrofishing, traps."

Eaton wanted to know if forensic techniques could help. "It’s less invasive, less stressful, especially when you’re talking about threatened and endangered species and having to trap them or tranquillize them. If you don’t have to do that, let’s maybe not do that."

Water is filtered through a vacuum pump
Credit Connor McShane / Embry Riddle

So far they’ve sampled DNA from the Verde River, Fossil Creek, Oak Creek, and even a few stock ponds. The technique has to be tweaked for each ecosystem, and for things like temperature and time of year. Eaton says it’s not new to use DNA to study wildlife, but most methods target a specific species, "verses our method, you can find whatever’s there, whether it’s supposed to be there or not."   

DNA is extracted in the lab
Credit Connor McShane / Embry Riddle

On the riverbank, the scientists sterilize their gloves with bleach to prevent contamination. Biologist Matt Valente uses a pump to squeeze the water sample through a filter. "So this is from an autoparts store, a little vacuum pump that’s operated by hand, it’s used for draining brake lines usually," he says.

They’ll put the DNA-drenched filter on ice to take back to the laboratory. In the lab they’ll extract the DNA and make copies of a single gene that acts like a “barcode.” These sequences are uploaded to a worldwide database of more than four hundred thousand species called GenBank.  

Valente says, "Some of them we have found out match perfectly to other species in the database, and some of them don’t. That’s when the detective work starts to try to figure out, OK, what are we missing that should be here?"

They’ve identified tiny, rare fish like the Gila topminnow and black bears that went for a bath. And the results turned up one case of mistaken identity. Everybody thought the Verde River was full of an exotic fish called the smallmouth bass. DNA proved it was actually the red-eyed bass all along.

"One of the foundations of all biology is knowing what species are where," Valente says. "And we may not fully understand how to use it all yet, but there’s a lot of power there that really we haven’t had access to in the past."

This forensic technique can ’t replace traditional surveys completely. It gives only the presence or absence of a species, not population numbers. But Valente thinks it’ll be a critical first step in the future. It shows what’s really in the ecosystem, including surprises that nobody knew to expect.