Around the turn of the 20th century, naturalist Marià Masferrer returned to his tiny village in Spain with a striking addition to his natural history collection: a stuffed yellowish-green bird with a bright orange face. It was a Carolina Parakeet, the only parrot native to the United States. Little did he know, his specimen was one of the last of its kind. Within two decades the species would go extinct. 

The reason for the Carolina Parakeet’s demise remains a point of contention among scientists. They mostly agree some form of human pressure did the bird in. But was it from direct human involvement, like poaching birds considered agricultural pests or to harvest feathers for the plume trade? Or was it more inadvertent, like habitat destruction to clear farmland or disease spread? Finding the cause of their extinction wouldn’t just sate scientists’ curiosity, but it would also further our understanding how extinction happens so we might prevent it.

Some clues, it turns out, lay in that Carolina Parakeet specimen that Masferrer collected a century ago. When Carles Lalueza-Fox, a biologist specializing in historical DNA at the Institute of Evolutionary Biology in Spain, heard that the bird was still in great condition and surprisingly close to his lab, he saw an opportunity. Biologists like Lalueza-Fox have learned how to interpret patterns in DNA to track whether an extinction happened gradually due to natural causes or habitat loss, or abruptly due to human contact or disease.

In a new study, published today in Current Biology, a team led by Lalueza-Fox describes the first complete sequencing of the lost parrot’s genome from the one specimen. The reconstruction of its evolutionary history using DNA provides the best evidence to date that the Carolina Parakeet, a bird once common around places like Lake Erie and the Gulf of Mexico, went extinct abruptly and was almost definitely killed by direct human pressures.

The researchers looked at information from across the genome to reconstruct the colorful bird’s general population trends. One sign of gradual population decline from natural causes is inbreeding; when an endangered species has only a few members left, they often have no choice but to mate with relatives. But the parakeet’s genome showed no evidence of this. “The bird's genome does not show signals, such as sections of the genome with no variation, of progressive demographic declines that are sometimes associated with endangered species,” Lalueza-Fox says.

In fact, the study found no genetic trace of an extinction process at all. The Carolina Parakeet was there, and then it wasn’t. Its abrupt disappearance suggests that it was driven extinct by a relatively sudden event in history, like hunting, collecting, or disease, that killed many birds in a short period, rather than an extended decline through habitat loss or some other factor. 

“The value of the study is that it shows the species was not doing badly in terms of numbers,” says evolutionary biologist Leonardo Campagna with the Cornell Lab of Ornithology and who was not involved in the new DNA analysis. 

Some researchers studying the species have long suspected that disease, likely introduced through contact with domesticated poultry, was a major driver of the parrot’s rapid extinction. The new study did not find evidence of disease. Still, biologist Kevin Burgio with the University of Connecticut, who studies historical Carolina Parakeet sightings and collections and was not involved with the analysis, isn't fully convinced. Because the study’s single specimen was collected from an area isolated from poultry farms, he thinks more research into the genetics of other specimens is needed.

“I am not trying to say that other human-related problems such as habitat loss, being collected in the wild for the pet trade, or being shot as crop pests didn't play a role,” he says. “It's very likely that it was a combination of all of these factors that eventually led to their extinction.” 

Along with helping scientists better understand the bird's demise, mapping the Carolina Parakeet's entire genome informs the idea of “de-extinction,” or whether it’s possible to use DNA to bring species back. Alas, the study found that it would be nearly impossible to revive the Carolina Parakeet by combining its DNA with that of its closest living relative, South America’s Sun Parakeet. The two genomes have hundreds of genetic differences that “highlight the tremendous difficulties” involved in bringing the Carolina Parakeet back from extinction, Lalueza-Fox says. So for now, America's only parrot will remain in the past, a reminder of what we have lost and yet another cautionary tale from the Anthropocene.

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