Passenger pigeons just couldn’t adapt to having smaller populations.

JOEL SARTORE/National Geographic Creative

Four billion passenger pigeons vanished. Their large population may have been what did them in

Four billion passenger pigeons once darkened the skies of North America, but by the end of the 19th century, they were all gone. Now, a new study reveals that the birds’ large numbers are ironically what did them in. The pigeons evolved quickly, but in such a way to make them more vulnerable to hunting and other threats.

The pigeon’s fate may hold lessons for other animals under pressure from humans or other dangers, says A. Townsend Peterson, an evolutionary biologist at the University of Kansas in Lawrence who was not involved with the work.

Scientists have long blamed hunting and deforestation for the passenger pigeon’s disappearance—the birds destroyed the very trees in which they nested—but biologists still couldn’t make sense of why they declined so quickly and completely.

In 2014, Wen-San Huang, an evolutionary biologist at National Taiwan Normal University (NTNU) in Taipei, and colleagues turned to DNA in an attempt to solve the mystery. Genetic material from four 19th century museum specimens revealed that the species had relatively low genetic diversity—meaning that most individuals were remarkably similar to each other—and that its numbers had fluctuated 1000-fold for millions of years. Hunting and habitat loss came during a time when the species was already declining, the team concluded, which pushed the birds over the edge.

But the new study lays the lion’s share of the blame back on people. Beth Shapiro, a paleogenomicist at the University of California, Santa Cruz, and colleagues sequenced the complete genomes of two passenger pigeons, and analyzed the mitochondrial genomes—which reside in structures that power cells—of 41 individuals. The specimens came from throughout the bird’s range. In addition, they reanalyzed data from Hung’s group, and, for comparison, sequenced the bird’s closest living relative, the band-tailed pigeon.

DNA from passenger pigeon museum specimens provided key new insights into this species’s demise.

© Bailey Library and Archives, Denver Museum of Nature & Science

Like Huang’s study, Shapiro’s analysis found a remarkable lack of genetic diversity—given their population size—in passenger pigeons. Yet Shapiro’s team does not think this low genetic diversity resulted from populations fluctuations. Such fluctuations should affect all parts of the genome equally, but instead Shapiro and her colleagues saw concentrated pockets of low genetic diversity. What’s more, their analysis of the passenger pigeons’ mitochondrial genomes suggested that the bird’s population was stable for at least the last 20,000 years—countering the idea that the birds were already vulnerable when people began hunting them.

Instead, the passenger pigeon’s huge population is what made it vulnerable, Shapiro’s team reports today in Science. The birds were able to adapt faster to their environment—and spread these changes quickly within their population—but this also caused all of them to be fairly genetically similar. And when a new threat—like human hunters and habitat loss—came around, they suddenly found their physiology and behavior were poorly suited for their declining numbers. Their population “went from being superbig to supersmall so fast they didn’t have time to adapt,” in part because they lacked the diversity to cope with this new way of living, Shapiro says.

“This study suggests that the passenger pigeon’s most distinctive feature—its immense population size—left an enduring mark on its genome,” says Benjamin Van Doren, an evolutionary ecology graduate student at the University of Oxford in the United Kingdom not involved in the work.

“[Shapiro] did a great job to support the idea that natural selection works efficiently in large populations,” says evolutionary biologist Shou-Hsien Li, Huang’s co-author on the 2014 paper and colleague at NTNU. But Li and Huang say the work merely reinforces their team’s view that the bird’s low genetic diversity reflects an already tumbling population.

Some outside the camp agree with Shapiro’s interpretation, however. “The idea of wildly fluctuating passenger pigeon populations is deeply entrenched, Peterson says. But “I am persuaded by [Shapiro’s] argument, given this in-depth analysis of massive data resources.”

Regardless, says Van Doren, the passenger pigeon’s precipitous decline is a “a cautionary tale [that] teaches us that successfully conserving species with large populations may require keeping their numbers higher than we might otherwise expect.” If their numbers start to sink, they may lack the ability to persist, even though the absolute number might not be very low.