Hidden DNA reveals secrets of animal life

It’s been more than 140 years since the Rio Grande siren – a slippery, two-footed salamander protected by the state of Texas – was found near Eagle Pass, a town on the US-Mexico border. But in 2019, Krista Robert, a graduate student at the University of Texas, realized she didn’t need a siren to prove they were still there.

She only needed a jug of muddy water to filter.

In Eagle Pass, Robert Found enough environmental DNATracing genetic material left as organisms crawl, swim or flutter their way through life — to prove that elusive amphibians still live in the region, at the westernmost edge of their known range.

In the past decade or so, environmental DNA, or eDNA, has revolutionized marine and aquatic research by allowing scientists to sample an “entire ecosystem” using a liter of water. Now, after a series of experiments on land in the past several years, eDNA has become the key to biologists’ skeletons. It is a cheap, non-invasive and relatively simple technique that can be modified to study any life form, often requiring less time and labor to employ than previous methods.

Here’s a sampling of some of the most surprising places scientists have found in hidden DNA – from beaches to beetle stomachs to the wind – and what these discoveries have taught us.

stop and wipe the roses

In 2017, researchers from Aarhus University in Denmark knocked out a limb – their Picking a bouquet of wildflowers from two Danish fields and put them in a chemical bath to extract any DNA on their surface.

“We weren’t really sure if this would work,” says the assistant professor of biology. Eva Ageing Sieggaard.

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

“What’s impressive here is that we get species that have a very short period of time from interactions” — like the seconds it takes a butterfly to pick up nectar before it flies away — “to species that complete their full life cycle on the flower,” says Manna. Philip Francis Thompsonanother associate professor of biology at Aarhus University who has been researching eDNA for more than a decade.

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

pathogens in sand

The dna covers Florida’s white sandy beaches — and it’s not just tourists. A team of scientists from the University of Florida Genetic material recovered from fin prints The young loggerhead turtles, which weigh about two quarters, leave them and make their way from the nest to the sea.

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

Small pathways also contain eDNA from ChHV5, a virus that causes the debilitating cancerous growth of fibropapilloma In young turtles of many species. This discovery challenges the main theory that the disease is transmitted horizontally, either through the water column or between direct contact between baby turtles.

says Jessica Farrell, a recent PhD graduate from the University of Florida and first author of the study book.

“This is going to have a really big impact in terms of how we try to mitigate this disease in the future,” she says.

clear blue sky

At the height of the 2020 lockdowns, Christina Lingard, who was then a postdoctoral researcher at the University of Copenhagen, used a variety of vacuums to suck air at the Copenhagen Zoo. she and her advisor, Kristen Bowmanassociate professor of molecular ecology, wasn’t expecting much — she might pick up DNA from okapi I thought that if she stood in the stable kind.

But the results far exceeded their wildest dreams. by air filter At several locations across the zoo, Lingard eventually discovered 49 species of animals, some harboring hundreds of meters away — birds, reptiles, mammals, and even fish that were feeding on predatory species.

“We had chills, tears in our eyes,” Bowman says. “Lynggaard showed something that could completely change the field of terrestrial vertebrate observation,” referring to the animals that live on land.

Unbeknownst to Lingard, almost identical study It was conducted at one time in a zoo in the UK. Their findings echoed those of the Danish team, where they found 25 species — including, delightfully, a wild Eurasian hedgehog whose keepers regularly watched the roving zoo property.

The twin discoveries marked a watershed moment in eDNA history, but what they missed was almost as remarkable as what they caught. Some species have never been discovered, and the animal’s body size and number of individuals do not always seem to have an effect on how strong the readings are.

“When I was walking around the zoo, I had the idea that if I could smell an animal, I could probably spot it,” Beth Claireassistant professor of biology at York University in Canada and study leader in the United Kingdom.

“I thought, if I’m smelling whatever — hormones, or pheromones, or the scent they put off — sure, there must be DNA carried with these drops.” But the eDNA of one of the zoo’s most stinky inhabitants, a burrowing wolf, has evaded its filters.

Now, both teams are working on improving their techniques. Claire and her colleagues have deployed four rounds of prototypes in natural environments from Ontario to the tropics, she says, and are experimenting with passive assembly (that is, the filters without spaces) of eDNA from dust.

“The most important thing we’ve found is that the material does not accumulate randomly,” she says. “When the animals are active, they are caught, [and] When they go into hibernation, the signal does so.”

These new findings, which are currently under review for publication, are a huge relief to Claire and an auspicious sign for the future of airborne eDNA.

One of the early concerns [was] She explains that there will be no real signal – the danger of “everything is everywhere”. “It has been suggested that the wind will move DNA everywhere making it a homogeneous soup. Our data suggest otherwise.”

open ocean

The population dynamics of the whale shark, a mysterious giant that prefers the deep waters of the open ocean and does not need the surface for air, remains a mystery to scientists.

To get a sense of how different groups of endangered sharks are related, scientists typically use hand spears to take biopsies from their bodies.

“It’s like a little roller that you get – basically a cross-section of the skin and in the fatty tissue” about the size of the “pinky tip”, Lawrence DougallPhD student at the University of Western Australia.

But New research published In 2021, another way was found to learn about the genes of a whale shark – go to the side of the monster and unscrew the cap of the Nalgene bottle.

By collecting eDNA samples a few meters away from whale sharks, Dugal and her team obtained enough clear readings to identify the sharks’ haplotypes, genetic markers that provide information about where their ancestors lived and their relationship to other populations. It was a perfect match for conventional biopsies from the same individuals.

“I found it quite surprising that we were able to detect such a dominant signal from them in all of these waters,” she explains.

Invertebrate informants

But DNA isn’t always left behind – some tiny creatures naturally collect genetic material from organisms they interact with throughout their lives.

The burgeoning subfield of eDNA is iDNA, or DNA acquired from invertebrates, where “natural specimens” provides a useful shortcut for scientists.

Early studies on sea sponges found that they create Episodic eDNA repositories During forage filtering, while leeches contain a genetic record of previous blood meals that It can last for up to four months. The researchers also recovered species-level DNA from the guts dung beetles that feed on the feces of other animals, Including articles from bearded pigs and sambar deer.

Tea leaves that tell us about the past

Researchers from the University of Trier and the Max Planck Institute in Germany have brought their eDNA-related research nearby — perhaps uncomfortably so. In June, the team reported finding eDNA from 1,279 distinct species of insects, spiders and other arthropods in tea and spices purchased from German grocery stores.

Green tea took home the first (or last, depending on how you look at it) prize with an average of 449 species in each sample and, by extension, each tea cup. A sample of parsley, chamomile, mint and green tea contains an average of 200 eDNA.

The authors say the finding that eDNA is well preserved in dry plant matter stored at room temperature opens up a potential treasure trove of new data. Historical plant specimens collected around the world for centuries can contain as yet unexamined information about the species that have surrounded them in life.

No “silver bullet”

But the new system is not without flaws: Even eDNA’s biggest proponents say it’s a complement, not a replacement, to traditional field sampling techniques.

To date, eDNA cannot reveal an organism’s age, sex, or body condition, and while recent progress has been made, it is difficult to know how many individuals are behind the eDNA reading of a species. We’ll need old-fashioned camera and personal surveillance traps for many years to come. And while sample collection can be fairly low-tech, contamination is a hazard both in the lab and in the field.

However, it’s hard to overstate the scientists’ sense of surprise at the technology’s power.

“If you’ve ever been to a rainforest, you’ve seen all these nature shows and you know there’s a lot of life out there,” Bowman says. “Then you get there and you hardly see anything. You have to sit really still, and if you’re lucky, you’ll hear something jump away. But with eDNA, all of a sudden you get this shot of what’s out there — that world of diversity opens up to you.”

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