In September, a frog died in an Atlanta botanical garden. With it went an entire species never to hop along the Earth again. Biologists at Zoo Atlanta who’d looked after the frog for the past 12 years called him “Toughie.” He was a charismatic, glossy-eyed specimen and the very last Rabbs’ fringe-limbed tree frog in the world.

Joseph Mendelson, the director of research at Zoo Atlanta, had been prepared for this. When the Rabbs’ frog was discovered in Panama in 2005, some 80 percent of the population had already been lost to disease. A few were removed in hope of a revival. Alas, the last female died in 2009. In 2012, when another male died, Toughie became the sole survivor of his kind.

Still, his death hurts, in part because of one of his beautiful biological quirks: The Rabbs’ were the only species in the world where the fathers let the babies eat the skin off their backs.

“The world has gotten so bad now that even the amphibians can’t tolerate it.”

“Allowing tadpoles to eat a [father’s] flesh, that’s never been documented in any animal in the world,” says Mendelson. “And we lost that.”

Frog like the Rabbs’ and other amphibians are dying off at an alarming rate. It’s estimated that 200 species of frogs have gone extinct since the 1970s, and many fear it’s a harbinger of greater biodiversity loss that will come for birds, fish, and mammals too.

Ecologists fear that the planet is in the midst of a mass extinction — the sixth in the long history of life on Earth. And it’s looking like amphibians are the most at-risk class of vertebrates.

This is particularly disturbing because amphibians — which include frogs, salamanders, and caecilians (they look like worms crossed with snakes) — have been around for hundreds of millions of years.

“During the great extinctions of the dinosaurs in the Pleistocene, amphibians made it through with no appreciable effect,” Mendelson says. “So they’re not the most delicate creatures in the world. But the world has gotten so bad now that even the amphibians can’t tolerate it.”

Broadly, that’s how it looks. But as with most stories of biology, this one is not so simple.

Some amphibians are revealing resilience even under significant threat. These amphibians are teaching humans critical lessons about what we need to do to protect and save more of them from extinction. To put it another way: As one frog dies, another one (the Sierra Nevada yellow-legged frog) is making a surprising comeback, offering a glimmer of hope for the amphibian Armageddon.

Amphibians have been dying off for decades

Herpetologists — the people who study amphibians — started to realize amphibians were dying off at an abnormally fast rate in the 1980s.

“At the first World Congress of Herpetology in 1989, a number of amphibian biologists were sharing anecdotes, and they were all strikingly similar,” Mendelson recalls. The scientists were telling one another that they were having trouble locating known populations of frogs. And it wasn’t just from one country: There were mysterious disappearances in Costa Rica, the United States, Australia. Something was happening.

So the scientists set out to document what was happening around the world. It was a massive effort that culminated in a worldwide comprehensive survey of 5,000-plus species of amphibian published in 2004 in Science. “The results demonstrate that amphibians are far more threatened than either birds or mammals,” the report stated. In all, it found 30 percent of amphibian species were at risk for extinction.

More surveys followed. In the United States, a 2013 national survey found the amphibian populations declined at a rate of 3.7 percent a year from 2002 to 2011. But what was surprising about those results was that the losses were not only taking “threatened” or “endangered” species. Even populations thought to be at low risk were declining at a rate of 2.7 percent a year. Even in protected conservation areas, there are declines.

In 2010, a survey of 25,780 species of vertebrates found that 41 percent of the amphibians were threatened with extinction. “On a per-species basis, amphibians are in an especially dire situation, suffering the double jeopardy of exceptionally high levels of threat coupled with low levels of conservation effort,” the study noted.

(Note: There’s some disagreement over whether the losses in amphibians are truly worse than the losses in birds and mammals. It’s just incredibly hard to do comprehensive assessments of all the thousands of species in the world for an exact comparison. At the very least, it’s safe to say that the amphibians’ situation is dire, if not somewhat worse than other animals.)

What’s killing the amphibians?

Historically, the Sierra Nevada yellow-legged frog was the most abundant amphibian in the mountain range that encompasses Yosemite National Park.

Now most visitors to Yosemite will never see one. “If all of the trees in the Sierra Nevadas suddenly disappeared, people would be very concerned,” Roland Knapp, a research biologist at UC Santa Barbara’s Marine Science Institute, says. That’s what happened with the frogs: Ninety-five percent of them have vanished.

“You’ve gone from hundreds of animals or thousands, to nothing. Truly nothing.”

And a great percent of the losses are due to one disease: Batrachochytrium dendrobatidis, sometimes called BD or the chytrid fungus, which is one of the biggest threats to amphibians worldwide.

“The chytrid is know to infect pretty much every species of amphibian,” says Reid Harris, a biologist and director of international disease mitigation at the Amphibian Survival Alliance. Not all species succumb to it, but the ones that do die off in horrifying fashion. It’s thought that BD is the main culprit behind the 200 frog species extinctions seen in the past several decades. That’s "the greatest disease-driven loss of biodiversity ever documented," the journal Nature reported in 2012.

BD is so devastating because it attacks frogs’ skin, which isn’t just an outer covering for these creatures. It's also their respiratory system and their excretory system. A chytrid infection is the equivalent of a disease in humans that takes out the lungs, kidneys, and skin in one shot.

The spores burrow a few cell layers down into an amphibian’s slick skin and then start reproducing inside the skin cells. The spores then burst out of the cells and can infect other cells, or other frogs. The spores disrupt the crucial exchange of salts across the frog’s skin. “It causes heart failure; that’s the bottom line,” Harris says.

After BD enters a waterway, “in a matter of weeks, typically, all the adults are killed; all the juveniles are killed as well,” Knapp says. “What’s left behind are tadpoles that are infected with the disease. They don’t die until they metamorphose — then they die as well. Within a year or two of the fungus arriving ... you’ve gone from hundreds of animals or thousands, to nothing. Truly nothing.”

Toughie somehow survived a rampant BD outbreak in his native Panama. When it was discovered in 2005, the Rabbs’ fringe-limbed tree frog in Panama was already suffering through huge declines because of BD, which killed as many as 85 percent of all the local amphibians. (No one really knows where BD originated — one guess is Africa. Regardless, it’s now on every continent where amphibians live.)

What’s concerning is that there’s a similar chytrid fungus that specifically attacks salamanders, another branch of the amphibian family tree. It’s called Bsal, and it has already wiped out entire populations of salamanders in Europe, where the animals have no natural immunity to it.

Bsal has yet to be found in the United States, but scientists fear it could arrive. Its potential to wreak havoc is not hyperbole: North America is home to 50 percent of all the salamander species in the world.

(If you’re thinking I’ve left out caecilians, be assured: The chytrid fungus can kill them too.)

It’s not just fungus

The experts I spoke to all agreed: Fungal infections can explain a lot of the decline in amphibian populations, but they can’t explain all of it. A 2015 study in Nature’s Scientific Reports tried to analyze amphibian declines in the United States, searching for a common stressor contributing to them all. The report concluded there was not one “smoking gun,” but instead amphibian declines were heavily influenced by local environmental changes.

Priya Nanjappa leads the amphibian and reptile conservation at the Association of Fish & Wildlife Agencies, and she explains there are six broad factors that can threaten amphibians:

Habitat loss: This is the biggest one. The ponds and forests where frogs and salamanders live are increasingly being turned into pavement. Diseases: Globalization has meant that deadly infections like BD and Bsal can run laps around the world. Climate change: Amphibians are dependent on water. Climate change–influenced droughts can limit frog population in areas. The US Forest Service also notes that a changing climate could influence the timing of amphibians’ life and reproductive cycles. Predatory invasive species, like fish that gobble up tadpoles. Commercial trade: Taking species from their habitats to sell in the pet trade or for bait. Pollutants in the air and water. (Recently The Guardian reported on the death of 10,000 endangered water frogs in lake Titicaca in Peru, with the likely culprit being pollution from sewage and industry.)

“A lot of these are so intertwined that it’s hard to tease out the one thing,” Nanjappa says.

But it does seem like amphibians are especially sensitive to a whole host of human-induced changes. And it could be a result of the fact that amphibians start their lives out in the water and then morph to live on land.

“They need a pretty wide diversity of habitats to accommodate not just the adult life forms but the aquatic life forms,” Knapp says. “They are entirely different ecosystems. If you lose either one of those, you’ve lost the amphibians.”

But there are some reasons to be hopeful

There is a new glimmer of hope for at least one species of frog: After decades of being devastated by chytrid disease and non-native predators, is returning in the mountain lakes and streams in Yosemite National Park.

According to a paper published recently in the Proceedings of the National Academy of Sciences, the species’ population is growing at a rate of 11 percent a year (after seeing a decline of 95 percent over the few preceding decades).

But why?

One reason is habitat. Until the 1970s, Yosemite stocked its waterways with non-native trout for fishing. Historically, the frogs developed without any predation from fish. As conservation efforts have removed the fish from the waterways, the frogs began to recover. But more exciting is this: There’s some evidence that the surviving frogs have become more resistant to BD.

Knapp is a co-author on this paper. He and his colleagues analyzed frog populations that had been exposed to BD and survived, and compared them with the skin of frogs that had never seen BD. Then in an experiment, both sets of frogs were exposed to BD.

At the end of a 15-week incubation period, there was five times more of the fungus in the naive frogs. Or, put another way: The frog populations that had encountered BD before appeared to have grown some immunity to it, perhaps by natural selection. And it might be helping their population numbers respond. More work needs to be done to describe the extent to which these frogs have become immune.

Knapp stresses these results don’t mean that simply nature will take care of itself. “That’s definitely the wrong conclusion,” he says. If anything, the results stress the need for increased conservation. In order for the frogs to develop an immunity, there need to be at least a few that survive an initial onslaught of BD.

And research groups are beginning to figure out how. Recently, KQED profiled a conservation project ongoing at the San Francisco Zoo. There, researchers are bringing in frogs from the Sierra, exposing them to the fungus to inoculate them, and then sending them back out into the wild.

A world without amphibians would suck

Science isn’t the only answer to save the amphibians. Policy can help too.

In January, the US Fish and Wildlife Service took the rare step of banning salamander imports, for fear of importing the deadly Bsal fungus. The US Department of Agriculture requires shipments of domesticated animals to be certified as disease-free, but the same safeguards don’t exist for wildlife. Nanjappa argues legislation should change that.

The stakes are high: A world without amphibians would be a worse place. Amphibians are a keystone of many ecosystems, and when they disappear, the environment changes dramatically. In many ecosystems, the population of amphibians outweighs all the other animals combined.

“In Central America, some of these amphibians would eat algae off rocks [in streams],” Nanjappa explains. “Now that the amphibians has disappeared, the algae is proliferating.” That subtly and profoundly changes the ecosystem. The spaces that would be created by removing the algae are homes for freshwater mussels and other invertebrates, she says.

Tiny, profound changes like that are happening the world over.

Aside from ecological collapse, scientists would also be missing out on potential medical discoveries. Salamanders are famous for being able to regenerate limbs and even regrow critical organs like the heart. Salamander skin also hosts an array of chemicals with potential medical importance. Same goes for frogs.

In Australia, a species called the gastric brooding frog used to do an incredible thing before it went extinct: It would suck tadpoles up into its stomach, where they would develop into adults. “The stomach would cease all digestive function,” Mendelson says. “What hormone ceases all digestive function? That would make ulcers and such incredibly more treatable. We lost that opportunity. [The hormone] is absolutely gone with it.”

Mendelson got into herpetology because he loved the thrill of discovering new species of frog. He was part of the team that discovered the Rabbs’ frog — which, remarkably, is not the first species he helped discover that he’s also seen go extinct.

Still, he thinks the tide could turn. “I have to find optimism, or I’d just lose it,” he says. Toughie may be gone, he says, but “we’re not going to lose all of them.”