It’s a story about mystery, grime, and a phoenix rising from the ashes—so of course it started in Chicago.

The Field Museum, a Greco-Roman citadel of natural history on the shores of Lake Michigan, is famous for its Egyptology exhibit and for displaying Sue, the largest T. rex ever discovered. But among scientists and biologists, it carries a different distinction. In its basement and archives, the Field Museum holds more than 3 million specimens: drawers and drawers full of the stuffed corpses of long-dead creatures.

Among these dead are hundreds of Illinoisan birds, many of them captured and killed in the decades after the city’s founding. For years, curators and collection managers had noticed that something was off about some of them. Birds from the late 19th century were noticeably darker than other specimens of their own species from other time periods or other locations. They suspected the birds had been stained by the soot that once choked Chicago’s skies—but without looking at the birds more closely, they couldn’t be sure.

Two eastern towhees in the Field Museum’s collection: The bird at the top was collected in Chicago’s South Side in April 1906; the bottom in the heart of the city’s downtown 106 years later, in April 2012. (Carl Fuldner)

Their drabber colors remained a mystery until a few years ago, when two University of Chicago graduate students took an interest in the birds. In 2014, Carl Fuldner, a historian of photography, and Shane DuBay, an evolutionary biologist who studies alpine birds, secured a grant to photograph some specimens in the Field Museum’s collection.

Using a scanning electron microscope, they confirmed that the wings were covered in black carbon. Black carbon is a tiny waste product of coal combustion. It’s of great note to scientists: Black carbon contributes to global warming, but it’s also a potent form of toxic air pollution. A particle of black carbon is so small that it can penetrate deep into the lungs’ alveoli.

Now Fuldner and DuBay have brought their work further. They have photographed more than 1,300 birds from museum collections across the Midwest. Then they used the birds’ relative drabness to reconstruct a 130-year history of black-carbon pollution in the region surrounding the Great Lakes. Their results were published this week in the Proceedings of the National Academy of Sciences.

How Atmospheric Black Carbon Has Changed Over Time

The black line shows Fuldner and DuBay’s estimate of how atmospheric black carbon has changed in the Great Lakes from 1880 to present, with the gray area showing uncertainty. The purple line reflects a previous study which estimated atmospheric black carbon in the region by measuring what factories expended. The orange line shows total coal use in the United States over the same period. (PNAS)

“The birds are an incidental record—we’re using the birds as the tool, the resource, that captures the direct environmental sample from the past,” said DuBay.

Getting them to give up that data required some creativity. The pair photographed the birds in the Field Museum before realizing that their setup was imperfect, and that it allowed different amounts of light to leak onto the birds with every exposure. They had to go image all the birds again using a light box designed for commercial photography.

The pair also photographed birds at the Carnegie Museum of Natural History in Pittsburgh and the University of Michigan Museum of Zoology in Ann Arbor, Michigan.

They also used a piece of software called RawDigger to access the unedited brightness data from the photographs. This let them treat the digital camera’s output as an objective data set, rather than a subjective image. “We’re using the entire photographic apparatus as a kind of reflectance sensor,” said Fuldner.

Two red-headed woodpeckers from the Field Museum’s collection: at top, a sooty specimen collected in July 1901; at bottom, a much cleaner bird collected in June 1982 (Carl Fuldner)

But the technique worked. It largely matches earlier attempts to estimate the amount of coal burned in the region. “Seeing how coal consumption dropped right after the Great Depression began—and seeing that signal pop up really strongly in our dataset—really validated [this] in our minds,” said DuBay.

Their graph provides evidence that emissions rose during the late 19th century, previously the least understood period for North American emissions. The research also contained some geography-specific treats: Six of the 10 sootiest birds came from Joliet, Illinois, which held the country’s second-largest steel refinery for decades. Fuldner was even able to dig up old photographs of Joliet in the 1890s, its sky nearly black with smoke from the refinery.

“Who would’ve thought that people could mine the birds we collected over the last 150 years and get a climate record from it?” said Joe McConnell, a professor at the Desert Research Institute who was not connected to the study. His 2007 study of ice cores from Greenland also estimates the amount of black carbon released from North America over the last 200 years and lines up well with this new finding.

He said that the study, especially in its spatial precision, was important confirmation of what was already known about black-carbon concentrations during the late 19th century. He lamented that DuBay and Fuldner had not extended their record before 1880. “It would have been interesting to see if bird-feather records declined to preindustrial levels if you go back another 30 years,” he told me.

Fuldner and DuBay’s study is not the first to plumb the depths of the county’s natural-history collections. As my colleague Ed Yong has written, biologists have just started to use their contents to reveal entirely new species. And recently, a team of researchers at Princeton University used similar collections of dead plants to learn how flora had moved north and uphill in response to climate change.

The pair say they hope to continue their work in other parts of the world with deep collections and a long industrial history. (The United Kingdom comes to mind.)

“One of the things that has really excited me about this project is it’s more about the prospect of these collections being used by atmospheric scientists,” said DuBay. “This is really just the tip of the iceberg for other studies like this.”