For nearly 50 years, scientists have struggled to explain why frogs began disappearing from Brazil’s Atlantic Forest, one of the world’s richest regions for amphibian diversity. Beginning in the 1970s, researchers documented dramatic population declines, but the cause of these losses remained uncertain.
Now, scientists have uncovered compelling evidence pointing to a deadly fungal disease as the likely explanation. The findings, published in Molecular Ecology, come from researchers at the Center for Conservation Genomics at the Smithsonian’s National Zoo and Conservation Biology Institute (NZCBI) and Pennsylvania State University (PSU).
The suspected culprit is chytridiomycosis, often called chytrid, a disease caused by the microscopic fungus Batrachochytrium dendrobatidis. Scientists believe the pathogen originated in Asia before spreading around the world during the 1970s and 1980s. However, the fungus was not formally identified and described until 1999, long after devastating amphibian declines had begun.
By then, hundreds of amphibian species worldwide had been driven toward extinction, and some had already disappeared. Because so many populations collapsed before scientists knew the fungus existed, determining whether it was responsible has been particularly difficult.
“After almost 50 years, we still aren’t confident what caused many historical amphibian die-offs, making these declines some of the most enduring cold cases in wildlife epidemiology,” said Jack Boyette, an NZCBI graduate fellow and doctoral candidate at PSU who led the research.
A 50-Year-Old Mystery in Brazil’s Atlantic Forest
One of these longstanding mysteries centers on the Boracéia Biological Station in Brazil’s Atlantic Forest, where amphibian populations experienced severe declines between 1979 and 1982.
Some researchers previously suggested that climate change or unusually extreme weather might have triggered the disappearances. The new findings, however, provide evidence that an emerging fungal disease was spreading through the area at precisely the same time.
“While environmental factors could have played a role, our findings most directly implicate the chytrid fungus, revealing that regional invasion of the pathogen coincided with these unexplained amphibian disappearances,” Boyette said.
To investigate what happened, the researchers turned to an unexpected source of evidence: frogs preserved in museum collections decades earlier.
The Smithsonian’s National Museum of Natural History houses specimens collected by William Ronald Heyer, a former curator of amphibians and reptiles. Heyer conducted five collecting expeditions at Boracéia, including two during the 1970s before the major population declines and three during the 1980s after the die-offs had occurred.
These preserved animals offered scientists a rare opportunity to examine the period before and after the mysterious disappearances. By testing specimens collected at different times, researchers could investigate when the pathogen arrived and how rapidly it spread.
The team analyzed samples from more than 370 preserved amphibians representing 17 species, searching for evidence of chytrid infection and tracking how frequently the fungus appeared over time.
Museum Specimens Reveal a Deadly Fungal Outbreak
The results revealed a striking change. None of the specimens collected before 1979 showed evidence of chytrid infection. Among those collected during the 1980s, however, more than half tested positive for the fungus.
This sharp increase suggests that the pathogen arrived and spread through the local amphibian community around the same time that frog populations were collapsing.
But the researchers also uncovered a surprising pattern.
Species that suffered the most severe declines showed no detectable signs of infection in the preserved specimens. Meanwhile, species whose populations remained relatively stable frequently carried the fungus.
At first glance, these findings might seem to contradict the idea that chytrid caused the disappearances. The researchers believe the explanation may lie in differences in how individual species respond to the disease.
Some frogs may have been naturally capable of tolerating the infection, allowing them to survive even when the fungus was present. More vulnerable species, on the other hand, may have died so quickly after becoming infected that few or no infected individuals were ever collected.
“It’s important to keep in mind that not all species suffered catastrophic losses at Boracéia,” Boyette said. “The species that didn’t decline may have naturally tolerated the fungus, allowing them to become infected without suffering mass mortality. By contrast, the species that declined most dramatically may have been so susceptible that infected frogs died before Heyer could collect them.”
Together, the results suggest that chytrid spread rapidly among frogs with little previous exposure to the disease, with potentially devastating consequences for species unable to withstand infection.
Decades-Old Collections Help Solve a Wildlife Cold Case
For Michael Campana, a genomicist at NZCBI who contributed to the research, the findings demonstrate the extraordinary scientific value of natural history museums.
Specimens preserved many decades ago can contain biological evidence that researchers at the time had no way of recognizing. Modern testing methods now make it possible to revisit these collections and investigate outbreaks that occurred long before the responsible pathogens were discovered.
“Museum collectors could not have anticipated how important their collections would be to our modern conservation challenges, but without them, we would never be able to detect pathogens that went unnoticed for decades and reconstruct disease outbreaks that would otherwise remain a mystery,” Campana said.
Understanding these past outbreaks could also help scientists anticipate future threats.
One growing concern involves another fungal pathogen, B. salamandrivorans, which is threatening salamander populations in Europe and could pose a serious danger to salamanders in North America.
By reconstructing how earlier fungal diseases emerged, spread, and affected different species, researchers hope to improve their ability to recognize and respond to similar threats before they cause widespread damage.
Brazil’s Frogs Show Surprising Signs of Recovery
Despite the devastating losses recorded decades ago, the latest findings also offer encouraging evidence of recovery.
Working with researchers from the University of São Paulo, the team made six visits to Boracéia between 2022 and 2024 to investigate the amphibians living there today.
Of the 17 species represented in Heyer’s historical museum collection, researchers located 12 during their modern surveys. The remaining five were not found, leaving their current status uncertain and raising concerns that some may have disappeared from the site entirely.
Nevertheless, the surveys indicate that most amphibian species at Boracéia have recovered since the severe declines of the early 1980s.
The fungus has not disappeared. Chytrid infections are still present among local frogs, but the pattern of infection suggests that species once heavily affected by the disease may have developed greater tolerance over successive generations.
That increased tolerance could help explain why many populations have survived and rebounded despite continuing exposure to the pathogen.
The findings highlight an important distinction between infection and mortality. A species can carry a dangerous pathogen without necessarily suffering catastrophic losses, particularly if its members can tolerate the infection.
What the Discovery Means for Future Amphibian Survival
Although the evidence strongly implicates chytrid in the historic declines at Boracéia, the researchers caution that their findings apply to this particular location. The results cannot automatically explain amphibian disappearances elsewhere in the Atlantic Forest.
Still, the study provides a compelling explanation for a longstanding local mystery and demonstrates how scientists can use historical specimens to reconstruct outbreaks that would otherwise remain poorly understood.
The investigation is also continuing.
Researchers are now examining DNA recovered from museum specimens to identify the genetic mechanisms that influenced how amphibians responded to chytrid infections in the past. These analyses could help reveal why some species were devastated while others survived.
Separate projects are using ancient environmental DNA to help fill gaps in historical specimen records. This approach involves searching for genetic traces left behind by organisms in their surroundings, potentially providing evidence of species and pathogens that were never directly collected.
Together, these efforts could reveal a much clearer history of how chytrid emerged, spread, and affected amphibian biodiversity over the past century.
By uncovering the biological changes that helped some frogs survive and recover, scientists may also gain valuable insights into protecting vulnerable species from future fungal epidemics.
