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Colleen Handel has been wrestling with a mystery for almost 20 years, and it all started with an innocent phone call from a friend.

“It was really a serendipitous thing,” saysHandel, a biologist at the . In February 1998, her friend and colleague Sandy Talbot spotted a trio of Black-capped Chickadees at her home in Anchorage—a typical backyard scene, except there was something almost cartoonish about the birds. Their beaks were deformed, overgrown, and curved like pieces of elbow macaroni. Talbot called Handel and asked if she wanted to come take a look.

Based on their conversation, Handel didn’t think the deformities were unprecedented. Beaks get distorted every now and again: A birth defect or a collision with a window can cause them to grow in a weird way. But she did think it was interesting that three different birds all had similar deformities in the same area. She planned to go over and see the odd birds, but before she could, one came to her. When she opened up the Sunday edition of the Anchorage Daily News a few weeks later, there was a photo sent in by a reader of another chickadee with a warped beak.

The image had been taken in Big Lake, about 30 miles away from Talbot’s yard. “I knew that chickadees are resident species and they have very small territories to which they're very faithful,” Handel says, “so two sightings a fair distance apart but in the same general region should merit some attention.”

Handel and a few other researchers from the Alaska Science Center went back to Talbot’s yard to catch one of the little mutants. “We took a pretty close look at it and saw that this was really an unusual situation, and decided we better find out if there were more of these birds,” Handel says. They put the word out in the local ����APP newsletter and birding listservs, asking people to report any strange beak sightings. That opened up the floodgates. “I was blown away by people calling and reporting birds all over south-central Alaska with these abnormalities,” Handel says. This time it wasn’t just chickadees, but crows, magpies, nuthatches, and other species, too.

“Everyone, when they were seeing their birds in their backyards, thought ‘oh, well this is kind of weird, but these things happen.’ It wasn't until we started putting together the big picture that we realized that this was significant,” says Handel.

In the 18 years since, the number of affected birds has grown, the deformities have spread, and the mystery has deepened as Handel and her collaborators have struggled to find the culprit behind the Alaskan twisted-beak trend.

The Rise of an Epidemic

A year after the mutants were first noted, Handel and other researchers at the Alaska Science Center started the to monitor birds in south-central and southeast Alaska for what they started calling “avian keratin disorder.” Citizen scientists were recruited to set up nest boxes—built by Anchorage high school students in woodshop classes—in yards, parks, and rural areas so that chickadees could be captured and examined. The researchers also captured crows around Anchorage and several other coastal cities. They estimated that 6.5 percent of the state’s adult Black-capped Chickadee population was affected. The disorder was even more prevalent in Northwestern Crows, hitting around 17 percent of the adults.

These numbers far exceeded the background rate, or the level of anomalies seen under normal conditions, saysCaroline Van Hemert, a biologist who’s been working on the Beak Deformities Project since 2006. In total, the researchers have documented avian keratin disorder in more than 2,500 individuals belonging to 30 different species in Alaska, making this, they say, the ever recorded among wild bird populations.

Meanwhile, reports of similar mutations in dozens of other species trickled in from other parts of Alaska, the Pacific Northwest, and well beyond. “There have been clusters in several species of tits and rooks in the United Kingdom; there have been clusters of crows reported from India and Southeast Asia; and a number of species from South America,” Handel says. “Anytime you get a cluster, it raises a red flag. Whether or not these are all caused by the same thing, we don’t know, but it puts a different, global perspective on things.”

The severity of the defects varies between individuals. Some birds look like they have a slight overbite or underbite. In others, the upper or lower parts of the beak can grow to double their normal length and criss cross or curve to the side. The effects aren’t merely aesthetic: Disfigured birds have difficulty feeding and preening, making it harder for them to maintain weight and keep warm during the winter. “Birds with deformities also have more compromised health overall,” Van Hemert says. They’re more vulnerable to infections and illnesses like avian malaria, and have lower breeding success.

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Ruling Out Suspects

After realizing how severe and widespread the problem was, the team began hunting for an explanation. Since the sightings were first concentrated in a small area, they thought an environmental contaminant might be responsible. The adult chickadees, nestlings, eggs, and local supplies of bird seed for a wide range of contaminants. While they found that deformed adult birds had certain contaminants in their blood that resulted in chromosome damage, the concentrations of those contaminants were low. Plus, none of them had ever been linked to beak or keratin problems.

Other leads the group chased and ruled out include: nutritional deficiencies, fungal, bacterial, parasitic infections, and a heap of known viruses and diseases, like psittacine beak and feather disease, avian polyomavirus, and circovirus.

“It's been a really interesting ride down some blind alleys, and we found out some really fascinating things about these birds; but at this point we still don't know what’s causing the beak abnormalities,” Handel says. “When I first started out, I thought, ‘oh we'll figure this out right away.” She’s now approaching 20 years of work on the disorder—all on top of her regular research for USGS.

While the slog has been frustrating, the researchers aren’t ready to give up. “I’ll go through periods when I think it’s time to move on and I feel ready to write it off. But it doesn’t take more than going out in the field and seeing these birds with these grossly overgrown beaks to know it’s not going away,” Van Hemert says.

“Caroline and Colleen have worked their asses off,” says Bud Anderson, a biologist with the in Washington, who has been tracking similar deformities in raptors and sharing his reports with Alaskan team. “I think that those two are two of the most dedicated biologists I know."

A Break in the Case

There were no rewarding “a ha” moments in the investigation—until 2010, when San Francisco-based biologistJack Dumbacher provided a tip that may prove to be a gamechanger. He introduced Handel and her crew to a cutting-edge method for DNA analysis that’s allowing them to look for viruses they didn’t even know existed.

The latest expert on the case is Maxine Zylberberg, a post-doc at the University of California, San Francisco, who previously worked with Dumbacher on avian disease research. With traditional sequencing, scientists search for specific pieces of DNA or RNA in a biological sample, she says. “If you had a reason to suspect that a pox virus was causing a disease or if an individual was infected with a pox virus, you could target a sequence that you know is pox virus-specific and amplify it,” Zylberberg says. “But to do that you really need to know the exact sequence you're looking for.”

The newer method, known as deep sequencing, doesn’t require such meticulous search parameters. Instead, it takes all the genetic material in a sample (in this case, a ground-up bird beak), breaks it down into millions of pieces, and then sequences all of those pieces at once. Zylberberg compared the sequences she found in Handel’s shipments to databases of everything else that's ever been sequenced—animals, bacteria, viruses, etc. That's when she realized that her samples appeared to have a completely novel virus that's related to a group called the avian picornaviruses.

That virus, which has been dubbed poecivirus (after the genus that Black-capped Chickadees belong to, Poecile), is starting to look like the leading candidate behind avian keratin disorder. In published this week, Zylberberg, Handel, and other researchers screened both Black-capped Chickadees with or without deformities for poecivirus. All the bad-beaked chickadees tested positive, while less than 25 percent of the normal birds were infected. Two Northwestern Crows and two Red-breasted Nuthatches with the disorder were also confirmed to be viral.

As more proof pours in, the team will begin testing how poecivirus is causing the deformities—a vital step toward developing a treatment and preventative measures. And if it doesn’t turn out be the right culprit? “The simplest explanation is usually the best and right one, but we're quickly running out of those straightforward answers,” Handel says.

“It’s like a little Sherlock Holmes mystery,” she notes, “but we don’t know how long this book is and how close we are to the ending. I hope we figure it out pretty quickly.”