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A few hours after sunset one night in July of 2016, a Ph.D. student walked into a New Jersey hotel carrying a bouquet of butterfly nets. The travelers who usually occupy the place looked up from their lonely business trips, curious to hear what Tim Fallon had caught. Tangled up in the mesh, he said, were about 100 fireflies, freshly nabbed from a local meadow as they blinked their way toward reproductive fulfillment.

He’d interrupted their mating dance for a worthy cause: figuring out how these insects first acquired the ability to glow — and hopefully, in the process, finding better laboratory tools for studying disease and developing treatments. Now, two years later, his team from the MIT-affiliated Whitehead Institute is publishing this firefly’s genome for the first time. It will appear next week in the journal eLife.

Among the key results: Bioluminescence evolved separately in fireflies and certain other species of beetles. But the findings won’t just be scoured by entomologists and evolutionary biologists.


“The data provided can (will) be used by others,” said Hugo Fraga, a biochemist at the Institut de Biologie Structurale, in Grenoble, France, who has done research on firefly chemistry, and who was not involved in this study. “The same way the human genome … provides a map for other researchers.”

Invertebrate evolution and biomedical research are more closely intertwined than you might think. In the mid-20th century, William McElroy, a biologist at Johns Hopkins University, began paying schoolchildren pennies for the fireflies they brought him. The bugs arrived by the thousands: In one photo, he sits behind a mound of them, like a lucky gambler behind a tower of chips. His project was partially an attempt to kindle students’ interest in science — but it also helped McElroy pick apart the chemistry inside fireflies’ lanterns.


What he described was a reaction between an enzyme called luciferase and a molecule called luciferin. Add a bit of fuel in the form of ATP — the compound that cells use to generate energy — plus some oxygen and a dash of magnesium, and you get a spark of greenish-yellow light.

Professor William D McElroy.
William McElroy, a professor at Johns Hopkins who enlisted schoolchildren to collect thousands of fireflies. Johns Hopkins University

It took millions of years for these soft-bodied beetles to perfect that chemical feat. But in the ’80s, just a few decades after McElroy’s discovery, biochemists had figured out how to clone the genetic bits responsible for luciferase and were soon lending fireflies’ fire to other creatures.

It was a nifty trick. Cancer biologists used it to make mouse tumors glow, watching through the rodents’ skin to see whether a drug could stop the spread of the disease. Pharmaceutical companies used it as a visual sign that a chemical would change the expression of specific proteins. NASA used it to check spacecraft for the presence of earthly microbes; because life forms all end up getting energy from ATP, the presence of the other firefly ingredients can make a living contaminant glimmer.

“It’s critical,” said Michael McManus, a professor at the University of California, San Francisco, who uses firefly luciferase for some of the experiments in his biomedical lab.

Fireflies aren’t the only spineless creatures from which we’ve borrowed glowing molecules for the lab. One kind of green fluorescent proteins — now ubiquitous in biomedicine — was discovered in a ghostly jellyfish of the Pacific Northwest. A sister molecule, this one red, was first isolated from a pet kept in the home aquarium of a coral enthusiast on the graffiti-covered outskirts of Moscow.

“Do you want to know how many times that paper has been cited?” asked Mikhail “Misha” Matz, an associate professor at the University of Texas, Austin, who was part of the gene-hunting expedition to the Russian suburbs. “Two thousand and ninety-five. It’s a lot, yup. This paper gets roughly a hundred citations a year, because everybody uses fluorescent proteins.” (When he says they’re fluorescent, he means they glow only when light is shone on them. Fireflies, on the other hand, produce their own light, called bioluminescence.)

Radim Schreiber/

Researchers use fluorescent molecules like GFP to tag proteins that would otherwise get lost in a cell or lab animal. Just as an ornithologist might put a radio transmitter on a migratory bird, to keep tabs on where it flies, so a biochemist might slip the gene for GFP or RFP into a specific bit of a creature’s genome. That way, when the genes they’re interested in are expressed, the resulting proteins will glow green or red under certain kinds of light.

As Matz explained, some of the atomic structures that make corals and jellyfish fluoresce are also present in other living things, which means that part of the signal you’re getting might be a bit gummed up by the surrounding visual noise. The advantage to luciferase-based tests is that they are very sensitive — so sensitive that a machine could potentially count the exact numbers of photons emitted.

But the downside is that, unlike for GFP and RFP, scientists don’t know how to insert all of the genes for the firefly’s glimmer into another creature. They figured it out for luciferase way back in the ’80s, but never did the same for luciferin. And luciferase without luciferin is like a match without a place to strike it.

That means that you can purchase luciferin commercially, but you have to keep adding it to your experiment, otherwise the glowing will stop. “It wanes away, so if you want to do long-term luminescence, you pretty much have to give a dose of luciferin every few hours,” said Jing-Ke Weng, a member of the Whitehead Institute, and the lead author of the new paper.

That’s where Fallon comes in. If he can figure out how fireflies evolved luciferin to light up their tails, he might just be able to isolate the genes responsible, which could then be inserted into creatures of the lab, much as researchers do with luciferase and GFP.

Once he’d driven the biggest of the New Jersey fireflies back up to Massachusetts, Fallon froze them with liquid nitrogen, crushed them up, and sent them off for genome sequencing. But on some of his other bugs, he was a bit more targeted, using needle-nosed tweezers to peel away layers until all that was left was the lantern itself. He wanted to figure out which genes were highly expressed in the firefly’s light-up rump, but were not as ubiquitous elsewhere.

“Before we started our study, there were only three or four genes that were known for the firefly,” Fallon said. “Now we know thousands.”

His team did similar work for a Caribbean click beetle with bioluminescent spots on its head, and a different species of firefly that a Japanese schoolteacher had been breeding for decades. By comparing those genomes, they could tell that the chemical reaction had evolved independently in the click beetle, as Charles Darwin himself had predicted. The two different lineages of fireflies, though, seem to have had some of that inner chemistry before they split off from each other.

“They diverged like a hundred million years ago, which is more than the time in the divergence between rats and humans,” Fallon said. “When dinosaurs were around, they probably saw flashing fireflies.”

He’s still working on co-opting the luciferin side of that chemistry to sell as a lab tool. From the sequencing data, he’s got a list of new, mysterious enzymes to work with. He’s also set up his own colony of Asian fireflies, in a closet-like space, established with eggs and larvae that the high school teacher sent from Japan. In their aquatic life stages, he gives them bladder snails as food, and watches them curl up, rolly-polly-like, under the pebbles in their tank.

He knows when it’s time to move them into his “mock riverbed”: When they’re ready to pupate, they start emitting an otherworldly glow.