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More than 140 years ago, a Rio Grande siren—a slippery, two-legged, one-foot-long salamander—was found near Eagle Pass on the U.S.-Mexico border. Protected by the State of Texas. But in 2019, biologist Krista Ruppert, now a Ph.D. student at Mississippi State University, realized she didn’t need sirens to prove they were still there.

All she needs is a can of muddy water to filter.

In Eagle’s mouth, Rupert found enough environmental DNA — traces of genetic material left behind when organisms crawl, swim or flutter in life — to determine that the elusive amphibian still lives in the area, where they have the westernmost edge of the known range.

In the past decade or so, environmental DNA, or eDNA, has revolutionized marine and aquatic research by allowing scientists to sample “whole ecosystems” with a liter of water. Now, after a series of experiments on land over the past few years, eDNA has become biologists’ master key. It’s a relatively inexpensive, non-invasive and simple technique that can be modified to study any form of life, and it generally requires less time and labor than previous methods.

Here’s a sample of the most surprising places scientists have found hidden DNA — from beaches to beetles to the wind — and what those discoveries teach us.

stop and wipe the roses

In 2017, researchers from Aarhus University in Denmark took the plunge – they picked a bunch of wildflowers from two fields in Denmark and put them in a chemical bath to extract any DNA on their surface.

“We’re actually really not sure if this will work,” said assistant biology professor Eva Egelyng Sigsgaard.

To their surprise, a single wild celery flower carried DNA from 25 species of insects, spiders and other arthropods. In 56 blooms, they detected eDNA from at least 135 species with enormous diversity, from a multitude of pollinators including moths and bees to predatory beetles.

“What’s impressive here is that we get species with very short time spans of interaction” — like the few seconds a butterfly sips nectar before flying away — “a species that completes its entire life cycle on a flower” , for example, says Philip Francis Thomsen, another associate professor of biology at Aarhus University who has been studying eDNA for more than a decade.

Environmental DNA samples taken from flowers can provide much-needed insight into the most active pollinators in an area or plant species. For example, scientists believe that the contributions of moths and flies are greatly underestimated, and they could be important targets for conservation efforts.

Pathogens in the sand

Florida’s white sand beaches are littered with eDNA—and not just from tourists. A team of scientists at the University of Florida has recovered genetic material from flipper prints left by individual loggerhead turtle hatchlings, which are up to two-quarters of their weight, and enter the sea from their nests.

Further analysis of the sand samples showed that eDNA could help researchers not only monitor species, but also the spread of disease.

The tiny orbitals also contained eDNA from ChHV5, the virus that causes the debilitating cancerous growths of fibromapillomatosis in hatchlings of many species. The finding challenges the dominant theory that the disease is spread horizontally, either through the water column or between direct contact between hatchlings.

“The detection of the virus in an entirely new larva raises the very big question of whether vertical transmission from mother to larva’ is also at work,” said Jessie, a recent Ph.D. graduate from the University of Florida and lead author of the study. Caffarrell said. Research.

This “will have a very big knock-on effect on how we try to mitigate this disease in the future,” she said.

clear blue sky

At the height of the lockdown in 2020, Christina Lynggaard, then a postdoc at the University of Copenhagen, used a variety of vacuum cleaners to suck up air at Copenhagen Zoo. She and her advisor, Kristine Bohmann, associate professor of molecular ecology, didn’t have high hopes—if she stood in the okapi’s stable, she thought, maybe she would Get DNA from your body.

But the results were beyond their wildest dreams. By filtering the air at multiple locations in the zoo, Lynggaard eventually detected 49 species of animals, some of which lived hundreds of yards away—birds, reptiles, mammals, and even fish that hunted predators.

“We had goosebumps and tears in our eyes,” Berman said. “Lynggaard has shown something that could change the entire field of terrestrial vertebrate monitoring,” referring to vertebrate land animals.

Unbeknownst to Lynggaard, a near-identical study was being conducted at a British zoo at the same time. Their results echo those of the Danish team, which found 25 species—happily, keepers often see a wild Eurasian hedgehog roaming the zoo.

The two discoveries became a watershed moment in eDNA history, but what they missed was almost as fascinating as what they caught. Some species have never been found, and the size and number of individuals in animals do not always seem to correlate with the strength of the readings.

“When I was walking around the zoo, I had an idea that if I could smell an animal, I might be able to detect it,” said Beth Claire, assistant professor of biology at York University in Canada and leader of the UK Foundation. Research.

“I thought, if I smell anything — hormones, pheromones, or the smell they give off — of course, those droplets must be carrying DNA.” But the zoo’s smelliest inhabitants, the maned wolf’s eDNA, steer clear their filters.

Now, both teams are working to improve their technology. Claire and colleagues have deployed four-wheeled prototypes in natural environments from Ontario to the tropics, and are experimenting with passive collection (that is, without the use of vacuum filters) of eDNA from dust, she said.

“Our most interesting finding is that these materials don’t just accumulate randomly,” she said. “When animals are active, they are found, [and] When they sleep, so do signals. ”

The new findings, which are currently under review for publication, are a major consolation for Claire, and an auspicious sign for the future of airborne eDNA.

“One of the early concerns [was] There won’t be a real signal — the risk of ‘everywhere’,” she explained. “It has been suggested that the wind just moves the DNA to make it a homogeneous soup. Our data suggest the opposite. ”

open ocean

The population dynamics of the whale shark, a mysterious giant that prefers deep water in the open ocean and doesn’t need to surface for air, remains a mystery to scientists.

To understand the relationship between different populations of endangered sharks, scientists routinely use hand spears to take biopsies from their bodies.

“It’s like you get a little cylinder — basically a cross-section of skin and fatty tissue,” about the size of “the tip of your little finger,” said University of Western Australia doctoral student Lawrence Dougal.

But new research, published in 2021, has found another way to access whale shark genes — by leaning over the whale shark and opening the cap of a Nalgene bottle.

By collecting eDNA samples just a few meters behind the whale shark, Dugal and her team obtained readouts clear enough to determine an individual shark’s haplotype, a genetic marker that provides information about where its ancestral lived and its relatedness to other populations. They are a perfect match for traditional biopsies taken from the same person.

“I found it very surprising that we were able to detect such a dominant signal from them in all of this water,” she explained.

informative invertebrates

But DNA isn’t always forgotten — some small animals naturally collect genetic material from the organisms they interact with throughout their lives.

A booming subfield of eDNA is iDNA, or DNA obtained from invertebrates, where “nature samplers” provide scientists with a convenient shortcut.

Earlier studies of sponges found that they accidentally create eDNA reservoirs when they filter their feed, while leeches contain genetic records of their past blood diets that can last up to four months. The researchers also recovered species-level DNA from the guts of dung beetles that feed on the dung of other animals, including material from bearded pigs and sambar deer.

Tea leaves about the past

Researchers from the University of Trier and the Max Planck Institute in Germany have brought their eDNA research close to home — perhaps so uncomfortable. In June, the team reported finding eDNA from 1,279 different species of insects, spiders and other arthropods in tea and spices bought in German grocery stores.

Green tea took first place (or last, depending on how you look at it), with an average of 449 in each sample, extending to every cup of tea. The samples of parsley and chamomile, mint and green tea contained, on average, eDNA from 200 species.

The authors say the discovery that eDNA is well-preserved on dry plant matter stored at room temperature opens up a potential treasure trove of new data. Historical botanical specimens collected around the world over the centuries may contain untapped information about the species that live around them.

No “silver bullet”

But the new discipline is not without its drawbacks: Even eDNA’s biggest proponents say it complements, not replaces, traditional field sampling techniques.

So far, eDNA cannot reveal the age, sex or physical condition of an organism, and despite some recent progress, it can be difficult to tell how many people are behind a species’ eDNA readout. We’ll need camera traps and old-fashioned in-person observation for many years to come. While sample collection is fairly low-tech, contamination is a threat to both the laboratory and the field.

Still, scientists’ sense of wonder at the power of this technology cannot be overstated.

“If you’ve been to the rainforest, you’ve seen all these natural performances, and you know there’s a lot of life there,” Berman said. “Then you get there and you can barely see anything. You have to sit still and if you’re lucky you hear something jumping away. But with eDNA you suddenly get a picture of what’s out there Snapshot – the whole world of diversity is open to you.”

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