DNA in desert pools could help park service track rare animals

In a quiet canyon on the east side of Saguaro National Park, researchers wearing surgical gloves scooped water samples from a shrinking, stagnant pool.

The hum of thirsty bees filled the air. Native frogs perched at the edge of the water, then threw themselves into the murky stew when people got too close.

It wasn’t a crime scene, but it felt a little bit like one.

On Tuesday, members of a National Park Service team collected and strained yellow-green “biological soup” from Madrona Pools, so they could send the filters off to be tested for DNA left behind by the animals drawn to the water — some of them native, some not.

If this were a television show, it would be called “CSI: Rincon Mountains” or maybe “Forensic Files for Frogs.”

Technology commonly associated with solving murders or fighting global pandemics is now being used by environmental scientists to track wildlife on a widening scale.

“It’s revolutionized what we’re doing,” said ecologist Andy Hubbard, program manager for the park service’s Sonoran Desert Network. “It’s wicked cool.”

From the roughly 4 cups of water collected on Tuesday, researchers hope to tease out DNA shed by some of the rare native amphibians and reptiles that might be living there.

They’re also looking for the genetic traces of dangerous invaders, such as non-native bullfrogs, chytrid fungus and ranaviruses, all of which can wipe out the locals.

“There’s a couple serial killers out there,” Hubbard said in his best crime drama voice.

Bullfrogs are especially menacing, because they eat native frogs and can cross 10 miles or more of open desert in search of new aquatic habitat to populate.

Worse still, these imported predators — introduced to the West on purpose a century ago as game animals, if you can believe it — appear more resistant to chytrid than other frog species are, making them carriers for the amphibian-killing fungus.

As Hubbard put it: “It’s two riders of the apocalypse.”

Native species like the threatened Chiricahua leopard frog, the lowland leopard frog and the Arizona toad were once common at aquatic sites in Saguaro National Park and elsewhere across the region, but their numbers have declined dramatically during the 21st century.

Last year, the park service began sampling for DNA in almost 50 springs, pools and streams on parkland in Arizona and New Mexico. No Chiricahua leopard frogs were detected in any of them.

Pond to lab

Hubbard and his team send the samples they collect to a lab at Washington State University, where ecologist and associate professor Caren Goldberg tests them for the DNA of several target organisms, including chytrid and ranaviruses.

“That’s one of the great things about this: We can pick up the pathogens as well as the vertebrates,” she said.

Goldberg is a pioneer in the field of environmental DNA, or eDNA for short. She is also a former Wildcat, who earned her master’s degree from the University of Arizona with a thesis on barking frogs in the Huachuca Mountains.

She has also slogged her way through a few leopard frog surveys in Southern Arizona, so she knows firsthand how hard it can be to find them in a muddy stretch of water, even when you know they are there. To be able to detect their presence with a water sample can be a powerful tool, she said, especially for a federal agency charged with protecting their habitat.

Ultimately, though, advances in DNA testing can’t replace the vitally important work biologists routinely perform in the field, Goldberg said.

“It can tell us if a population is there,” she said of eDNA. “It doesn’t tell us how that population is doing.”

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Hubbard said scientists have been using DNA to study specific species and even individual animals for the past 20 years or so. Until recently, though, such analysis was extremely expensive and limited only to a handful of high-profile endangered animals for which a genome — or genetic blueprint — had been mapped.

Researchers can now take what he called a “tree of life” approach to genetic sampling, thanks to new techniques, the declining cost of DNA processing and an ever-expanding, worldwide library of published genomes. Instead of looking for the genetic fingerprints of a single species of interest, they can sample whole habitats and identify a broad range of creatures that are found there.

From the waters at Saguaro and other southwestern parks, Hubbard and company have Goldberg testing for both Chiricahua and lowland leopard frogs, as well as for threatened northern Mexican gartersnakes.

Though eDNA is most effective for identifying frogs, fish and other species that live directly in the water sampled, in rare cases it can also pick up animals that merely stop by for a drink or a bathroom break on their way through. That’s why Hubbard tagged another creature of interest for Goldberg to scan for: jaguar.

So far, no big-cat DNA has turned up in any of the samples.

Hubbard said the lab at Washington State charges them about $140 per sample, “a screaming deal” compared to the thousands of dollars they would have had to pay another DNA lab five or 10 years ago to get results severely limited by the paltry number of genomes available back then.

Goldberg’s lab is also archiving what it processes for Hubbard so it can be reexamined in the future, as more species have their genetic codes sequenced.

“Magic” to reality

The eDNA work is part of a larger, five-year effort to assess and restore sensitive wetlands at eight park service sites: Saguaro and Carlsbad Caverns national parks; Chiricahua, Gila Cliff Dwellings, Montezuma Castle, and Tuzigoot national monuments; Coronado National Memorial and Fort Bowie National Historic Site.

The park service is slated to receive almost $1 million through the Inflation Reduction Act and the Bipartisan Infrastructure Law to eradicate bullfrogs, bring back rare native amphibians and snakes and improve their habitats.

The most recent installment of the money is being used to hire staff, conduct field work and buy equipment, including a portable sampling unit designed to collect eDNA from flowing water, Hubbard said. The $8,000 instrument is mounted to a backpack that weighs about 40 pounds and looks more like something an astronaut might carry.

Right now, park researchers are only collecting the water samples once a year and waiting as long as six months to get results back from the lab, so eDNA does not yet provide an early-warning system for sudden changes to a population or an ecosystem, Hubbard said.

But that could soon change.

He said at least one company is already marketing a DNA detector it says can be used to identify a targeted species in the field almost in real time, without having to send samples to a lab.

“That still seems a little magical to me, but that’s the future,” Hubbard said.

Lately, “the virus world” has been driving advances in DNA research, he said. A prime example is the increasingly common practice of tracking COVID-19 infections by sampling for the virus’ genetic markers in community wastewater streams.

Hubbard said the protocols he and his team now use to collect and preserve eDNA from places like Madrona Pools were developed with the help of a visiting virologist from Scotland.

He expects more technological leaps in coming years, as the cost of genetic analysis keeps dropping and the mapping of new animal genomes accelerates.

Inevitably, that could lead to a day when Hubbard won’t need help from Goldberg’s lab anymore. Researchers like him will be able to cheaply and easily do their own DNA sequencing, either right there in the field or very quickly afterwards.

“That is like Mr. Spock’s tricorder. That is like magic,” he said. “It opens up possibilities that we just didn’t think were real.”