The United States was a more colorful place when flocks of Carolina parakeets flew across the sky like daytime fireworks, flashing pops of orange, yellow, and green.

The country’s only native parrot species ranged from southern New England down to Florida and as far west as Colorado, but the last one died in captivity at the Cincinnati Zoo in 1918. Since then, the Carolina parakeet has symbolized the perils of extinction in the United States, much like the dodo has on the global stage.

A century after the last parakeet soared over America, a mystery endures: Was the demise of the 12-inch-long bird entirely driven by people? Farmers, who saw them as crop pests, easily eliminated whole flocks, since the animals had the unfortunate habit of gathering around their fallen comrades. Hunters killed the parakeets for their plumage, which was a popular hat accessory in the 20th century. And habitat loss—particularly land-clearing for agriculture—also removed trees the birds used or nesting. (Read how parrots may have become too popular for their own good.)

Reconstructed range of the extinct Carolina parakeet (Conuropsis carolinensis) Reconstructed range of the extinct Carolina parakeet (Conuropsis carolinensis) SOURCE: KEVIN R. BURGIO, CARY INSTITUTE OF ECOSYSTEM STUDIES

Even so, other experts have speculated other causes were at play: Natural disasters, such as fires and floods, could have fragmented the birds' habitat, and they may have been exposed to harmful diseases spread by poultry.

Now a group of international researchers has sequenced the Carolina parakeet genome and concluded that the bird’s rapid decline shows human interference drove their extinction, according to a study published today in the journal Current Biology.

Such research is crucial because it can help modern conservationists predict and help mitigate threats to species under siege today, says Kevin Burgio, an ecologist at the Cary Institute of Ecosystem Studies who not involved in the study.

For future conservation plans, “we need to get at which human activity was largely to blame and how we can prevent the same thing happening to others.”

Signs of a sudden end

Luckily, the scientists had samples of the femur and toe pads of a preserved specimen of Carolina parakeet in a private collection in Ginora, Spain, which was believed to have been collected in the early 20th century. But its DNA was too fragmented to use on its own.

So, to study the Carolina parakeet’s genome, the scientists first had to sequence the genome of its close, still-living relative, the South American sun parakeet.

“It is typical in [studying] ancient DNA that you need the genome of a close relative to be used as a reference to map the ancient one,” says study co-author Carles Lalueza Fox, a biologist at Pompeu Fabra University in Barcelona, Spain.

“For this reason, the Asian elephant genome is used as a reference for the mammoth genome,” he said via email.

Lalueza Fox and colleagues’ analysis of the DNA of both species, when compared with already established genomes of many other bird species, revealed that Carolina parakeets and sun parakeets diverged about three million years ago on the evolutionary tree. (Read how former pet parrots are thriving in 23 U.S states.)

View Images The last eggs from a captive Carolina parakeet, kept at the McGuire Center for Lepidoptera and Biodiversity in Gainesville, Florida. Photograph by Joel Sartore, National Geographic Photo Ark

The team first looked for signs of inbreeding, which can be easily observed in an animal’s genes and is a clue to a species having gone through a slow decline, rather than a more sudden end (when talking about evolutionary time, sudden would mean hundreds of years’ worth of hunting). The Carolina parakeet specimen showed no signs of inbreeding.

In fact, the Carolina parakeet genome is more genetically diverse than those of many birds alive today, which is “suggestive of an abrupt extinction process that left no marks in the parakeet genome,” Lalueza Fox says.

What’s more, diseases that would have been transmitted by domestic fowl, one of the suspected contributors to the bird’s demise weren’t found in the genetic analysis, Lalueza Fox says. But it’s still possible that the disease had some part in the parakeet’s die-off.

Staving off future extinction

Why Are Parrot Species in Decline? Highly intelligent and sociable, parrots are arguably the most popular pet birds. But they face dangers because of the pet trade and habitat destruction, making them among the most threatened species of birds.

“It is largely agreed upon by those who study the Carolina parakeet—myself included—that direct and indirect human activity led to the extinction of this species,” Burgio says.

Burgio has studied historical accounts and museum specimens to model the extinct species’ ecology, and suggests the bird’s range was actually smaller than previously believed, as well as that the eastern and western subspecies occupied different climates.

In a preprint paper, not yet peer-reviewed, Burgio claims the two subspecies of Carolina parakeet likely went extinct at least 30 to 40 years apart. It also notes the conditions under which that bird went extinct—such as rapid industrial expansion—are very much like the urbanizing world we live in today. (Meet the colorful people who devote their lives to parrots.)