Hiding in plain sight, ‘cryptic species’ may be all around us

The curious case of New York’s chuck-calling frog helps explain why we’re discovering more of them.

By Zach St. George
Published 15 Feb 2022, 11:51 GMT
naturepl_01159005
Scientists announce dozens of new species each year, many of them so-called cryptic species that appear nearly identical. Until 2014, Staten Island’s leopard frogs were classified as southern leopard frogs (above), but research showed they were a “new” and distinct species.
Photograph by Doug Wechsler, Nature Picture Library

On a warm evening in the spring of 2020, Jeremy Feinberg stood at the edge of a moonlit pond. He was on the Delmarva Peninsula, on the east side of Chesapeake Bay, an estuary in the eastern United States. “Chuck!” Feinberg called across the water. “Chuck! Chuck!” He cupped his hands behind his ears and swivelled back and forth, listening for a reply. Nothing. He called again. “Chuck! Chuck! Chuck!”

Feinberg is an ecologist. He was calling for frogs.

In the late 2000s, when Feinberg was studying southern leopard frogs for his Ph.D. at Rutgers University, in New Jersey, he discovered that the leopard frogs on nearby Staten Island didn’t sound right. They looked like southern leopard frogs, but instead of the southern leopard frogs’ usual rolling chuckle, they had a more staccato style. Their call sounded more like chuck. The frogs’ DNA confirmed Feinberg and his colleagues’ suspicions—the frogs weren’t southern leopard frogs at all. The scientists gave this new frog a Latin binomial, Rana kauffeldi, and a common name, the Atlantic Coast leopard frog.

Word of the discovery appeared in dozens of magazines and newspapers. Imagine, reporters marvelled, a new frog, right in New York City! In tone, these articles were typical of the new-species genre. Every year, scientists describe thousands of new species, and the media follow, announcing them to the world. In 2021, the most widely publicised new species included an octopus, two species of electric eel, and a beaked whale. (Learn more about electric eels.)

But these reports often miss a key detail. Many of these species aren’t exactly new. As with Feinberg’s Atlantic Coast leopard frog, people had seen the creature before. They just hadn’t realised that the creature was its own species.

Cryptic species

Biological taxonomy, the science of discovering, naming, and classifying living things, is in the middle of a sweeping reassessment. Over the past two decades, the increasing sophistication and availability of genetic sequencing have allowed scientists to reexamine species we thought we knew. Often, what they’ve found is not one species, but two or more. These morphologically cryptic species, as they’re called, look identical but are genetically or otherwise distinct. The look-alikes are everywhere, even among the most intensely studied life-forms. The number of primate species, for instance, has doubled since 1982. Scientists have discovered cryptic fish, butterflies, lizards, sea squirts, and pine trees.

“It’s like the invention of the microscope,” said Princeton ecologist Rob Pringle, speaking of the effect of molecular technologies on taxonomy and species recognition. “Something snaps into focus that wasn’t there before—like, Oh my god, this drop of water is full of living things!”

The growing realisation that we might be misunderstanding many of the species around us has a range of implications. Some are mundane: “The field guides will have to be updated,” Feinberg noted. Others are serious. Pharmaceutical companies, for instance, have long used leopard frogs to test the toxicity of their drugs—even though taxonomists now know that “leopard frogs” aren’t a single thing. “Now you’re testing a drug on four or five different species, some of which might have a different response to different stimuli, but you’re testing them as though they’re one,” Feinberg said.

But as the story of the Atlantic Coast leopard frog illustrates, for the creatures involved, the consequences of human misidentification can be more serious still—even existential. As Feinberg put it, “We can only protect what we know.”

A new way of seeing

People—Homo sapiens sapiens, that is—have a characteristic way of seeing the living world. We sort living things into nested categories based on their similarities and differences. The Swedish naturalist Carl Linnaeus echoed earlier so-called folk taxonomies when he created the framework for modern scientific taxonomy in the 1700s. Both the folk and Linnaean taxonomies began with broad categories, like “animal” and “plant,” followed by narrower categories like “tree,” “fish,” and “bird,” and finally, categories like “red oak,” “American robin,” and “silver salmon”—what we now refer to as “species.”

But while we intuitively categorise the creatures around us into species, the reality is often messy. In the process of evolution, populations of organisms are separated from others, either in space or in habit. Small variations accumulate in these populations, by chance or because they bestow some advantage, until eventually what was one species has become two. The cumulative nature of this process means that species exist on a continuum, with some creatures more distinct from one another, others less so.

A two-barred flasher feeds at a flower in Panama. In 2004, scientists announced that what had previously been considered one species of this butterfly was in fact 10, a discovery made possible by studying their mitochondrial DNA.
Photograph by Neil Bowman, Minden Pictures

In the scientific sense, therefore, a species is a hypothesis, one that can be supported along various lines of evidence—geographical distribution, ecology, courtship displays, nesting habits. But taxonomists have always relied most heavily on one line of evidence: appearance. Humans are visual creatures, understanding the world first by how it looks. Closeness of physical appearance, taxonomists long assumed, suggested closeness of relationship.

There have long been hints that this heavy reliance on a single line of evidence might be blinding us to some of the creatures around us. Charles Darwin, for instance, pointed to a group of European wrens that are almost physically identical but easily differentiated by their calls, nests, and feeding habits. The trouble was that while taxonomists could, with relative ease, sort creatures based on physical appearance using preserved specimens in their labs, gathering other lines of evidence required extensive observation in the field.

For most of the 19th and 20th centuries, there came a slow trickle of discoveries of morphologically cryptic species—firefly species marked by their varied flashing patterns, birds by their calls, tree frogs by their mating habits. It was clear that “cryptic species exist in a diversity of taxonomic groups,” wrote one researcher in a 1984 paper, announcing a morphologically cryptic bat. “What is not clear … is the frequency of the phenomenon.”

Then, in the early 2000s, the trickle of discoveries turned into a flood. New DNA technologies allowed scientists, with relative ease, to compare two or more creatures based on stretches of their DNA. While this data alone didn’t resolve the old question of where one species ended and another began, it provided a new and widely accessible form of evidence—and one that deftly overcame the old visual bias.

Many scientists highlight a pivotal moment in the study of morphologically cryptic species. In 2004, a group of researchers led by University of Guelph geneticist Paul Hebert published a paper that examined a specific region of the mitochondrial DNA of some 484 two-barred flashers, a type of butterfly scientifically known as Astraptes fulgerator. The size of a silver dollar, with dusky brown wingtips and electric-blue head and shoulders, this common butterfly ranged from the southern United States to northern Argentina. But in Costa Rica, researchers had noticed that the butterfly’s caterpillars had irregular patterning and colouration, and that they seemed to eat an unusually wide range of plants.

The butterflies’ mitochondrial DNA confirmed what the caterpillars suggested: A. fulgerator, the scientists wrote, contained distinct groupings whose differences were greater than typical of a single species’ members. The butterfly, that is, was more than one species. But it wasn’t just two or three, the researchers thought. The title of the paper announced their conclusion: “Ten Species in One.”

In the years that followed, scientists announced the discoveries of morphologically cryptic amphipods (a small crustacean), calico flowers, deep-sea limpets, mayflies, winter wrens, hairy snails, geckos, cicadas, fruit flies, caddisflies, sponges, kiwi birds, catfish, corals, earthworms, field voles, wobbegong sharks, spiders, and seaweed, among many other new species.

The morphologically cryptic species and their previously recognised counterparts might be physically indistinguishable to human eyes, but it’s almost certain the creatures themselves can tell which is which, whether by smell, sound, or other cues, said Sonal Singhal, an evolutionary biologist at California State University, Dominguez Hills, who studied a group of morphologically cryptic lizards in Australia. They’re only “cryptic to us, and our limited sensory perception,” she said.

As taxonomists increasingly adopted molecular technologies, DNA often provided the first hint of a hidden species. Other times it reaffirmed old suspicions. So it was with Jeremy Feinberg’s discovery of the Atlantic Coast leopard frog. At Rutgers, Feinberg was investigating the apparent disappearance of southern leopard frogs from Long Island and Staten Island in the early 2000s. He’d conducted extensive field surveys and was confident that the frogs were indeed gone. But then, one of his colleagues told him to take another look at the northwest corner of Staten Island, at a large, seasonally flooded meadow near the Goethals Bridge, just 20 minutes from Feinberg’s home in Brooklyn.

Evidence had been building for decades that Africa’s savanna elephants (above) and its forest elephants should be considered separate species. In 2021, the split was formally acknowledged by the International Union for the Conservation of Nature.
Photograph by Jessica Semler, Nat Geo Image Collection

He first visited the meadow on a dark, rainy night in February 2008. It was too early in the year to catch the frogs calling, but Feinberg found a single frog hopping across the road. He immediately noticed that “something was funky.” Compared to the southern leopard frogs he’d seen elsewhere, the Staten Island frog looked unusually dull. He returned to the meadow the next month and found more frogs on the road, both alive and dead. They were all just as dull as the first. “They were all just this drab brown,” he said. The next month, he returned to the meadow a third time. It was then, on a warm night, that he heard what he was certain meant the frogs were something new.

It was a vast sound, thunderous, rolling across the landscape: thousands of frogs in chorus, all singing chuck.

Chucks and quacks

On n autumn afternoon, many months after the trip to the Delmarva Peninsula, I met Jeremy Feinberg at his home in Richmond, Virginia. We sat in his backyard, at a table perfectly sized for his four-year-old daughter. Feinberg spread butcher paper and plastic wrap over the table. Then he showed me his collection of pickled frogs.

“To be honest, I don’t remember what’s in what,” he said as he dug through a stack of cardboard boxes. He pulled out a bottle that contained an alcohol-soaked brown snake and a Dasani bottle that held a pickerel frog. He looked through a tray of vials containing tiny leopard frogs, some of which had turned to frog soup.

At last he found what he was looking for: one southern leopard frog, Rana sphenocephala, and one Atlantic Coast leopard frog, Rana kauffeldi. He set them on clear plastic plates, where they lay with all the briny vitality of a pair of kosher dills. They were each a couple of inches long, olive with dark spots, and were, to my eyes, completely indistinguishable.

Feinberg, it turned out, wasn’t the first to notice the unusual leopard frogs of New York. Soon after he first heard the spring chorus on Staten Island, he began searching for written records of the mis-calling leopard frogs. There were abundant accounts, it turned out, including one from 1913 that described a call like quack, quack, quack. Other people, meanwhile, had noted that certain populations of what were thought to be southern leopard frogs had unusually drab colouring, as Feinberg had noticed on his first trip to the meadow on Staten Island. (Feinberg and his colleagues eventually discovered that the two species of leopard frogs can usually, but not always, also be distinguished by the shading on the inside of their thighs.)

But despite this long history of people noticing that something was amiss with the southern leopard frogs, nobody had connected all the pieces. The chuck-calling frog’s DNA, which Feinberg and his colleagues found to be markedly different from that of the southern leopard frog, provided the final link. In 2014, the frog from Staten Island became the Atlantic Coast leopard frog.

How many are there?

The amphibian now had a name, but it was still a scientific mystery. “All kinds of very basic natural history questions came up,” said zoologist and species co-discoverer Matthew Schlesinger, with the New York Natural Heritage Program, a partnership between the State University of New York and the state’s conservation department. “Where does it live? What are its habitat needs? How are its habits different from those of the known species? Are the things we thought we knew about the known species wrong, because it turns out it was this newly described thing instead that we were studying the whole time?”

The Tapanuli orangutan was identified as a species distinct from the Sumatran orangutan in 2017. Its range is limited to a single forest, called Batang Toru, in North Sumatra.
Photograph by Andrew Walmsley, Minden Pictures

Of particular concern was the frog’s conservation status. One of the biggest problems with mis-categorising species “is that conservation is primarily talked about in terms of species,” said Mort Isler, a taxonomist and research associate at the Smithsonian Institution who works on antbirds, a group of 230 similar-looking bird species. “And the species need a lot of work.”

Any time taxonomists split one species into two or more, the first becomes less common than previously thought. The new, morphologically cryptic species is frequently rare, which may be part of why it went unnoticed in the first place. In 2017, for example, researchers split the Sumatran orangutan species (Pongo abelii) in two. The new species, the Tapanuli orangutan (Pongo tapanuliensis), comprises fewer than 800 individuals, making it the rarest great ape in the world. (Left with a population of roughly 13,000, the Sumatran orangutan is also critically endangered.) In another example, from the early 2000s, researchers split the North Island brown kiwi into three species, one of which, Apteryx rowi, numbers only 600 birds.

It seemed possible that the Atlantic Coast leopard frog, known to exist only in one of the most densely peopled corners of the U.S., would be similarly imperiled. Soon after announcing their discovery, Feinberg, Schlesinger, and a team of scientists and land managers began working to understand the frog’s range. Dozens of volunteers visited more than a thousand sites scattered from Massachusetts to North Carolina, listening and looking for the frog. These searches were similar to my expedition with Feinberg along the Delmarva Peninsula, though “Jeremy’s the only one I know who mimics their call to get them to call back,” Schlesinger said.

In the end, the story of the Atlantic Coast leopard frog turned out to be a relatively happy one. While it is indeed rare in New York and other northern U.S. states, the species is far more common in Delaware, Virginia, and North Carolina. “It’s doing just fine in large parts of its range,” Schlesinger said. The International Union for the Conservation of Nature, the environmental organisation that compiles the widely used Red List of Endangered Species, recently judged the species to be of “least concern.” But the fortunes of even common species can turn, and the frog still faces threats in many parts of its range. The meadow where Feinberg first heard the frog, for example, was recently turned into warehouses for Amazon and Ikea.

Millions of species unknown

Morphologically cryptic species defy our age-old expectation that the world around us can be understood simply through close observation. It is a hard expectation to shake. Even professional ecologists overestimate their ability to recognize the members of the ecosystems they study, said Rob Pringle, the Princeton ecologist. “For the vast majority of biodiversity, it’s really hard to say for certain what it is,” he said. “We’re just peeling back the layers of the onion.”

On the taxonomic map of life on Earth, vast regions still lie dark. Since Linnaeus began applying his two-part names to animals and plants, scientists have formally described between 1.5 million and 1.8 million species. Of these, only a relative handful are known in any detail—how they communicate with other members of their species, for example, or what they eat, or what eats them. It is also unclear what portion of Earth’s species that number represents. Some estimates put the total number of species on Earth around three million. Most are much higher.

One of the highest estimates, of between 200 million and six billion species, came from a 2017 paper by a team led by evolutionary biologist John J. Wiens, at the University of Arizona, in Tucson. The large numbers are partly due to the researchers’ assumption that much of life’s diversity is composed of bacteria but also to their assumption that, among multi-cellular creatures, many—if not most—species are morphologically cryptic.

Six billion species is a figure beyond comprehension, certainly beyond the current ability of taxonomists to prove or disprove. It is perhaps best taken instead as a reminder of how much we still don’t know, and also of what we do know: that in a world of vast and hidden complexity, we are losing species we never knew existed.

One small remaining mystery concerns the Atlantic Coast leopard frogs of the Delmarva Peninsula. The surveys that Feinberg and Schlesinger led revealed a gap in the frog’s range along the Chesapeake Bay between Baltimore, Maryland, and Richmond, Virginia, one that Feinberg has long puzzled over. That spring night in 2020, we were chasing down a clue in the form of an audio clip reportedly made in northwestern Delmarva and posted to iNaturalist. Feinberg routinely scans the leopard frog sightings (and recordings) on the community-science app, looking for erroneous labels. He said the recording was unmistakably that of an Atlantic Coast leopard frog.

We drove up and down country roads, past large houses with No Trespassing signs, stopping at the edges of ponds and wetlands so Feinberg could listen for the frogs. After two fruitless hours, we arrived back at the pond where we had begun our search.

“Chuck!” Feinberg called. “Chuck! Chuck!” Nothing. The full moon shone on the water, spring peepers shrilled, and snow geese honked overhead.

Maybe the morphologically cryptic frogs weren’t there now. Maybe they had never been there.

“The maddening thing about this is they might still be there,” Feinberg mused. But if they were there, the frogs gave no sign.

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