How an Icon of Evolution Lost Its Flight

In 1835, the Galapagos Islands shaped the thoughts of a young British naturalist named Charles Darwin, and helped inspire his world-shaking theory of evolution. For that reason, the islands have become something of a Mecca for biologists, who travel there to see the same odd creatures that enthused Darwin.

“I like seeing wildlife in general, but some of these creatures have become iconic in evolutionary biology,” says Leonid Kruglyak from the University of California, Los Angeles, who visited the Galapagos in 2012. The famous finches, with their well-adapted and variously shaped beaks, are especially famous, but Kruglyak found them underwhelming. He was more drawn to the flightless cormorants.

There are around 40 species of these birds in the world, and all but one of them can fly. The sole exception lives on the Galapagos, and can be seen on the coasts of the Isabela and Fernandina islands, drying its shriveled and tatty wings in the sun. Compared to other cormorants, this one is about 60 percent bigger. Its wings are smaller and its feathers shorter. Its breast muscles, which would normally power a flapping stroke, are smaller, and the part of the breastbone that anchors those muscles is stubbier.

Kruglyak wanted to know why this bird couldn’t take to the skies. Specifically, as a geneticist, he wanted to know what genetic changes had grounded it. When he got back to his lab, he reached out to a research team that had collected blood samples from 223 flightless cormorants—almost a quarter of the total endangered population. He and his own team used these samples to sequence the cormorant’s genome, then compared its DNA to that of three other cormorant species, looking for mutations that are unique to the flightless one, and that are likely to alter its genes in important ways.

They found a long list of affected genes. Many of these, when mutated in humans, distort the growth of limbs, resulting in extra fingers, missing digits, and other similar conditions. Some of them are also responsible for a group of rare inherited disorders called ciliopathies, where cilia—small hair-like structures on the surface of cells—don’t develop correctly. Cells use cilia to exchange signals and coordinate their growth. If these hairs don’t form correctly, many body parts don’t develop in the usual way. In particular, some people with ciliopathies grow up with short limbs and small ribcages—a striking parallel with the stunted wings and small breastbone of the flightless cormorant.

All of this is circumstantial. It suggests, but doesn’t confirm, that the cormorant’s flightless wings might result of a kind of benign ciliopathy. To make a stronger case, Alejandro Burga, a member of Kruglyak’s team, focused his attention on a couple of genes. One of them—IFT122—controls the development of cilia across the animal kingdom. The Galapagos cormorant has a single mutation in a part of the gene that is always the same in other species.

The ideal experiment would be to alter the same gene in another species of cormorant, to see if they develop shorter wings. But cormorants aren’t exactly easy to work with in a lab, so Burga turned to a more amenable animal: the tiny roundworm, C. elegans. He used the gene-editing technique called CRISPR to change the worm’s version of IFT122 to match the cormorant’s. And sure enough, its cilia stopped working correctly.

Burga also focused on another gene called CUX1, which controls the activity of many other cilia-building genes. It’s especially active in the cartilage-making cells that lay the foundations for our skeletons. And here too, the cormorant has an unusual change—it’s missing a 12-letter stretch of DNA that’s present in almost all other back-boned animals. And when Burga deleted this same stretch from the mouse version of CUX1, the cartilage-making cells divide more slowly.  

All of these experiments paint a consistent picture. By building up mutations in several genes, the ancestors of the Galapagos cormorant changed the workings of its cilia and so altered the growth of the cells that form its skeleton. The result: shorter wings, smaller breastbones, and the loss of flight.

Still, there are plenty of missing details. As Kimberly Cooper, from the University of California, San Diego, notes in a piece that was published Kruglyak’s results, cilia play important roles all over the body, and humans with ciliopathies have problems with their kidneys, vision, and nervous system. How has the Galapagos cormorant escaped this fate? Do its mutations specifically affect the cilia in its limbs? Or has it evolved safeguards in other organs? Or “maybe they’re just weaker mutations, that tweak the function of the genes but don’t disrupt them to the same extent as in human ciliopathies,” says Kruglyak.

“I’d love to see similar studies in other lineages of flightless birds, because I imagine there are many different pathways to the loss of flight,” says Natalie Wright from the University of Montana, who studies the evolution of flightlessness. She notes that cormorants dive for their food, and shorter wings make them less buoyant and more streamlined underwater. Most species can only shrink their wings so far without disrupting their ability to fly. But when cormorants landed on the Galapagos, they found a paradise with year-round food and zero predators. They didn’t need to flee or migrate, so they could fully adapt to a diving life by shrinking their wings.

But other island birds that have become flightless, like rails, pigeons, parrots, owls, and songbirds, aren’t divers, and wouldn’t benefit from shorter wings. Wright suspects that they lost their flight for reasons of efficiency: It takes less energy to grow small flight muscles. “Perhaps different genes are involved,” she suggests.

A decade ago, it would have seemed implausible to ever test if Wright is right. But Kruglyak’s work show just how powerful genetics has become, and how quickly today’s scientists can uncover the evolutionary secrets of intriguing animals. “In five years, I went from seeing this unusual creature in the wild to doing its genome to getting a lot of good clues about what happened [to its wings],” he says.