Martha, the last of her kind, resides in a glass case at the Smithsonian's National Museum of Natural History, perched on a thin branch.

She's a passenger pigeon, Ectopistes migratorius, and in the final years of her life, before her death in 1914 at the Cincinnati Zoo, she achieved fame as the last survivor of a species once so populous that its flocks could darken the noonday sky.

Martha is small and gray, with flecks of blue and green iridescence on the back of her neck. She is looking sharply to the right, as if looking over her shoulder - as if a bit wary. (You're not being paranoid when you're the only one left.)

"Some people find her a little plain looking," said Helen James, the Curator of Birds, who can put her hands on more specimens of passenger pigeons, older and unheralded, stored upstairs in the museum's ornithology collection.

How the passenger pigeon died out is hardly a whodunit. Humans exterminated them through ruthless and efficient hunting in the late 19th century.

We've driven plenty of species to extinction, but the case of the passenger pigeon is one of the most perplexing.

This had been the most abundant bird in North America and possibly the world. A single flock could contain more than a billion birds. Scientists still wonder: Why didn't some pigeons survive in remote areas?

A new study of the passenger pigeon's genome, published Thursday in the journal Science, dives into the debate over this famous extinction.

The paper argues that the passenger pigeon, contrary to what some scientists have said in recent years, did not suffer wild fluctuations in population before humans wiped them out.

Rather, the population was stable for thousands of years, even during periods of dramatic climate change, the paper states.

The study also bolsters research showing that the passenger pigeon didn't have very much genetic diversity across its vast population.

"We have this very large population size but not very large genetic diversity," said Gemma Murray, an evolutionary biologist at the University of California at Santa Cruz and the lead author of the Science paper.

The researchers studied the nuclear DNA of four passenger pigeon specimens, and also looked at the mitochondrial DNA of another 41 specimens.

They compared the genetic markers to the extinct bird's relative, the band-tailed pigeon.

The study concluded that much of the bird's genetic code shows signs of strong natural selection, and simultaneously a low level of genetic drift or "neutral" mutations - the kind of changes that may not have any obvious adaptive advantage in the short run but could serve as a hedge in the future if the ecosystem changed.

This finding fits a theoretical model that says that in species with large populations, adaptive advantages will quickly spread through the population while deleterious mutations will be weeded out.

The new study does not contend that the low level of genetic diversity led to the demise of the passenger pigeon. That's an extra leap.

It may be that even a bird with tremendous genetic diversity, nimble when ecosystems change suddenly, could not have withstood the onslaught of human predation.

"Our mass murder of them over the course of decades was just too fast for evolution to keep up," said Beth Shapiro, a professor of ecology and evolutionary biology at UC-Santa Cruz and another of the paper's co-authors.

"This species was abundant for tens of thousands of years in the face of major environmental changes to forest and climate, and despite all of that this species was resilient," said co-author Ben Novak, an ecologist with Revive and Restore, a nonprofit organisation that has explored ways of bringing back the passenger pigeon through genetic engineering.

He added, "It's impossible to adapt to gunfire."

Martha, in her case at the museum. (Photo by Joel Achenbach/The Washington Post)

Wen-San Huang, one of the co-authors of a 2014 paper arguing that the pigeon had a fluctuating population size, said in an email that the new study relies on "indirect evidence" for its claim that the population was stable.

Huang wrote, "[W]e cannot agree with the inference drawn by the authors, claiming that the passenger pigeon has had a stable population size through their demographic history based on the fact that it experienced a possibly stronger selection than its sister species."

The passenger pigeon clearly was adapted to large populations. What's unclear is what the minimum viable population size would be for the species.

Could it have survived in small flocks here and there? The researchers said it did, actually, for the last couple of decades that it existed. But the survival strategy of the birds had always been based on numbers - the birds far outnumbered their natural predators.

No predator could eat them all. "Predator satiation" as a survival strategy would presumably be less effective in small numbers.

Shapiro said there's a broader lesson in this research: No one should assume that numbers alone are a buffer against extinction. Other species may be numerous and yet more vulnerable than they appear at first glance.

"There's more that we should consider when we think about a population being endangered than just population size," Shapiro said.

The passenger pigeon lived in the Great Eastern Forest. John James Audubon, awed by the spectacle of passenger pigeons in Kentucky in the fall of 1813, wrote that "the light of noonday was obscured as by an eclipse; the dung fell in spots, not unlike melting flakes of snow; and the continued buzz of wings had a tendency to lull my senses to repose."

But in the decades that followed, hunters used new technologies to prey on the birds. By telegraph, they wired news of the migration of the great flocks and the locations where colonies were roosting.

By railroad, they sent dead birds stuffed in barrels to major cities for human consumption.

The last wild pigeons were seen soon after the start of the 20th century. On September 1, 1914, Martha was found dead in the bottom of her cage at the Cincinnati Zoo.

Zoo officials packed her in a 300-pound block of ice and shipped her by rail to the Smithsonian, according to James, the curator. Martha can be seen in the Objects of Wonders exhibition, displayed in a case next to the skulls of two mountain gorillas.

"This is a very American story," said Ed Green, a geneticist at UC-Santa Cruz who co-authored the new report. "And it's a terrible American story of extinction."

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