Scraps of DNA Are Helping Scientists Track Down Nature's Most Elusive Creatures

The rare crayfish’s habitat
Photo: Eric R. Larson

In the forest-flanked waters of the Eleven Point River in southern Missouri’s Ozarks, scientists are on the hunt for one of the rarest crayfishes in the United States. To evaluate the status of their populations, researchers are using two very different methods—one of which is an emerging high-tech tool that may change how conservation biologists locate some of the planet’s most elusive species.

The cold-water crayfish (Faxonius eupunctus) is exceptionally rare, thought to live only within a 30-mile-long section of the river. But scientists don’t know just how rare the crayfish is, information that’s needed if the animal is to be listed under the Endangered Species Act. That’s why researchers at the University of Illinois and the Illinois Natural History Survey are scouring the cold-water crayfish’s habitat to get an idea of how many individuals exist, and where.

Faxonius eupunctus crayfish caught in a mesh
Photo: Eric R. Larson

The first trick is finding the buggers. Crayfish aren’t exactly the most eye-catching aquatic animals around. Many species remain hidden during the day, under submerged vegetation, logs, or rocks.

Traditionally, field biologists interested in surveying invertebrates in rocky streams like this have used “kick-seining”, which involves standing out in the water with a mesh seine suspended between two poles, while someone upstream kicks the riverbed, rolling the rocks and dislodging any crayfish. The crayfish float downstream and get caught in the mesh. It may sound inelegant, but it works, allowing the efficient capture of the animals and all the critical data they provide (size, number, sex, etc.).

Research team members searching the mesh seine for crayfish
Photo: Eric R. Larson

But the fieldwork is still labor intensive with sample area limitations—and rivers like the Eleven Point are big. Enter environmental DNA (eDNA)—DNA left behind by organisms in their environment, detectable in water, soil, or scat samples. Animals like crayfish are constantly shedding cells and secretions into their watery environment, so by taking a water sample, analyzing it through DNA sequencing and “metabarcoding” to identify what organisms the DNA in the sample came from, scientists can find out if the target species was present without a single rock kick. Since DNA degrades quickly in the environment, it’s likely the signal is from an animal that passed through recently.

To put eDNA analysis to the test for cold-water crayfish, the research team compared the old-school and newfangled methods side by side. They randomly selected 39 sites throughout the river system, and sampled those areas using kick-seining. Those sites also had their water collected, filtered, and analyzed for the presence of F. eupunctus eDNA.


Kick-seining uncovered crayfish at 21 of the 39 sites. The team also detected signs of the rare species’ DNA at 19 of those sites, all of which were among the 21 where they found live animals. These results, published in a recent paper in the journal Freshwater Biology, suggest that eDNA is a fairly reliable indicator of the presence of these crayfish.

The study also revealed some of eDNA’s limitations. eDNA failed to corroborate with two sites with known crayfish, and the eDNA detection probability increased as you go downstream, which is unrelated to any gradients in population density. It’s likely that in a river system, eDNA accumulates as it floats downstream, meaning it’s not a great way to figure out how many crayfish are in a specific location in the river. For that, kick-seining is still the way to go.


This comparison is invaluable for scientists conducting population surveys with eDNA, according Anna MacDonald, a biologist at the Australian National University with expertise in conservation genetics and eDNA who was not involved with this study.


“This sort of validation study will be really important to people who need to make sense of eDNA results,” MacDonald told Earther.

Indeed, eDNA’s ability to detect rare or imperiled creatures in a totally non-invasive manner has made it increasingly attractive to conservation biologists, especially as DNA sequencing technology becomes cheaper. It’s now being used to detect endangered sturgeon in Alabama, rare trout in the Rockies, and giant salamanders in Japan, among many other organisms.


eDNA can find land-lubbers, too. MacDonald’s past work involved testing DNA in the droppings of small, marsupial carnivores in Australia (like Tasmanian devils and quolls), both to identify what predatory species the poop came from, but also what that animal had eaten. This is useful for determining the range of threatened native carnivores, but also for seeing if introduced carnivores (like foxes and cats) are eating threatened wildlife, according to MacDonald.

“We’ve been able to detect DNA from the eastern barred bandicoot—a vulnerable species—from both feral cat and Tasmanian devil scats,” she said.

Eastern barred bandicoot (Perameles gundii), a threatened marsupial being consumed by non-native predators
Photo: JJ Harrison

MacDonald explained that while the future is likely bright for the application of eDNA to wildlife conservation, there are challenges and knowledge gaps that research groups around the world are working to solve. How do you avoid sample cross-contamination? How does DNA move through the environment? How accurately can we ID species?


“I’m really excited about the potential of eDNA for biodiversity monitoring, where DNA from many species can be detected at once,” MacDonald said. “You can’t conserve what you do not know about, and eDNA provides another window into this world that we cannot see.”

As for the cold-water crayfish, it only showed up through either method in the main river, crucial information for any future conservation plan. Such a tiny distribution leaves the species vulnerable to conservation threats like habitat degradation or invasive species.


Jake Buehler is a Seattle area science writer with an adoration for the Tree of Life’s weird, wild, and unsung—follow him on Twitter or at his blog.

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About the author

Jake Buehler

Jake Buehler is a science writer living on Washington’s Olympic Peninsula with an adoration for the Tree of Life’s weird, wild, and unsung.