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How do you track turtles that spend most of their time in muddy water and also look like rocks? It turns out, scientists have found a way to track such hidden animals using eDNA.

Hosted by: Michael Aranda

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[♪ INTRO].

Imagine that you’re a scientist trying to track a species that’s notoriously hard to find. Maybe you’ll look for footprints, or droppings.

Perhaps you’ll put out camera traps hoping to spot them as they move about. Or you could just scoop up a bottle of stream water or a cup of dirt and look for DNA fragments instead! That’s the amazing potential of environmental DNA, or eDNA— and scientists are already using it to study animals in all sorts of ways. eDNA is DNA that can be extracted from an environmental substrate, like soil or water.

You see, all living things leave their DNA behind like a trail of breadcrumbs thanks to biological castoffs like saliva, feces, urine, or skin cells. And scientists can use this eDNA to essentially press rewind and see what’s passed through an area recently. That’s because species have unique genetic codes.

Even regions of DNA that look broadly similar between species have unique differences that can be used to separate one from another. So a researcher can collect a cup of soil or water and sequence the DNA in it to see what species are around. Often, this is done by looking for fragments of mitochondrial DNA.

And, as the name implies, that’s the DNA found inside of mitochondria, the cell’s energy factories. Each cell can have dozens or even thousands of these mitochondria, so there are generally more copies of mitochondrial DNA than nuclear DNA per cell—and that makes these sequences easier to find in environmental samples, especially ones where the DNA may be degraded or dilute. The tricky part is translating a presence/absence signal into a reliable estimate of how many individuals of a species there are.

And scientists are still trying to figure that all out, as there are a lot of factors that affect how much DNA is shed from an animal and how long a given bit of DNA sticks around. For example, DNA may decay faster in a hot environment than in a cold one, or dilute and disperse more in streams and oceans than in soil. But even with these challenges, eDNA is already helping scientists manage and conserve species, because it can be used to monitor animals that are rare, like to hide, or are otherwise hard to see.

Take the bluegill sunfish, for example. Native to North America, this freshwater fish was introduced to Japan in the 1960s and has now become one of their most notorious invasive species. It eats basically anything it can, and has the potential to push species towards extinction, so some areas are trying to get rid of them to help conserve native freshwater ecosystems.

But in order to do that, scientists have to know where the bluegills are. And if you’ve ever tried to spot a fish from shore before, you know this can be difficult: what you see can be influenced by the fish’s size, behavior, and habitat. So, in a 2013 study, a group of researchers tried using eDNA to find bluegills in 70 ponds in Japan.

They collected water samples from each pond, but also walked along the shore to see if they could spot the fish themselves. They saw bluegills in 8 of the 70 ponds, and were able to successfully find bluegill DNA in the matching water samples. But they also found bluegill DNA in 11 additional ponds!

So eDNA gave them a more complete picture of the fish’s distribution. And sometimes, eDNA reveals animals that scientists aren’t expecting to find. For example, scientists in the Baltic Sea were testing an eDNA protocol for detecting harbor porpoises in sea water when they found something surprising.

Their results showed DNA from a long-finned pilot whale. These whales are rarely seen in the area, with only two unconfirmed sightings. eDNA analysis in the ocean is a bit harder than in freshwater: the larger body of water creates more opportunity for dilution and dispersal of DNA. That means the authors couldn’t rule out the possibility that the DNA had drifted over a long distance or originated from a dead animal.

But, the results still suggest that eDNA can be used to detect hard to observe animals in areas they rarely frequent. And eDNA can also help spot animals in their native habitats when they’re just really hard to find. In Virginia, wood turtles are declining in number because people are destroying their habitat and poaching them to keep as pets.

They’re considered both an endangered species and a management priority, so scientists really want to know exactly where these turtles are. But… they’re turtles. Not only do they spend a lot of time underwater in muddy streams, they also tend to look like rocks.

It can take years and lots of money to train people to spot them reliably. So, a team of scientists decided to try eDNA as a potentially easier and cheaper solution. They looked for turtles at 37 locations across Virginia by wading through streams with nets and aquatic view scopes—contraptions that look a bit like an overturned bucket with a lens at the end which allowed them to peek below the water’s surface.

And at each site, they also carefully filtered water samples to collect eDNA. They saw turtles at 17 of the sites, and found positive eDNA hits at 13 of those. Those false negative results—where the eDNA did not correspond to visual sightings— revealed factors that impact successful eDNA monitoring, like turtle density, days since last rainfall, and water temperature.

By understanding these, the team was able to optimize their protocol to improve detection and sensitivity in future studies. But despite these limitations, the group found eDNA at 3 sites where turtles were not seen by the surveyors. The researchers think those sites were likely places where they had missed the turtles visually because there were so few of them around. eDNA surveying also wound up being more cost efficient than human surveys, so the team recommended it for monitoring these threatened turtles in Virginia and beyond.

And these are just a few of the many ways eDNA is already helping scientists track and find species. It’s also tracking invasive golden mussels, dangerous mosquito larvae, and vulnerable manatee populations, for example. A 2019 study even suggested eDNA could tell us how much coral there is on a reef.

And it isn’t just for aquatic animals. eDNA has also been used to look at things like earthworm communities and adorable lemurs called aye-ayes. And at least one project is trying to ID birds by sequencing eDNA pulled from the air. There are some kinks to be worked out, but ultimately, eDNA could completely change how we find and monitor all sorts of living things.

And with thousands of species on the brink of extinction, the unique insights we’re getting from eDNA may be more important than ever. Thanks for watching this episode of SciShow, which is produced by Complexly. If you liked learning about this neat way scientists study living things, you might like another one of our channels: Nature League.

In every episode, host Brit Garner explores the diversity of life on Earth and questions what we think we know about the natural world. [♪ OUTRO].