The first large study of North American wolf genomes has found that there is only one species on the continent: the gray wolf. Two other purported species, the Eastern wolf and the red wolf, are mixes of gray wolf and coyote DNA, the scientists behind the study concluded.
The finding, announced Wednesday, highlights the shortcomings of laws intended to protect endangered species, as such laws lag far behind scientific research into the evolution of species.
The gray wolf and red wolf were listed as endangered in the lower 48 states under the Endangered Species Act in the 1970s and remain protected today, to the periodic consternation of ranchers and agricultural interests.
In 2013, the United States Fish and Wildlife Service recognized the Eastern wolf as a separate species, which led officials to recommend delisting the gray wolf. Conservationists won a lawsuit that forced the agency to abandon the plan.
The new finding sharpens a scientific question at the heart of that debate: How should the Endangered Species Act address threatened animals that are hybrids?
“What’s very exciting about this paper is that it’s using extremely powerful tools to address longstanding, challenging questions in conservation,” said Ryan Kovach, a research wildlife biologist at the United States Geological Survey who was not involved in the new study.
When Europeans arrived in North America, wolves roamed much of the continent. Farmers and ranchers almost entirely eradicated them from what is now the United States.
Over the past four decades, conservation efforts have helped a few wolf populations recover in the Rocky Mountains and around the Great Lakes. In 2015, the Fish and Wildlife Service estimated there were 5,505 wolves in the continental United States.
Those efforts were possible because of the Endangered Species Act, established in 1973. The law led to a recovery program for a species known as the red wolf, or Canis rufus, believed to have originally lived in the Southeast. The last red wolves were removed from the wild in 1980, and captive-bred animals were released into the wild beginning in 1987.
The gray wolf, or Canis lupus, once ranged from the Rockies to New England. In 1978, the Fish and Wildlife Service declared it to be threatened in the lower 48 states.
In 2000, some scientists began to argue that the eastern population of gray wolves was in fact a separate species, which they called Canis lycaon. The Fish and Wildlife Service recognized that species in 2013, and officials argued that the gray wolf, now deemed to be limited to the western United States, was doing well enough to be taken off the list.
The new analysis, published in the journal Science Advances, paints a profoundly different portrait of the American wolf.
Bridgett M. vonHoldt of Princeton University and her colleagues sequenced the genomes of 12 gray wolves, six Eastern wolves, three red wolves and three coyotes, as well as the genomes of dogs and wolves from Asia.
Dr. vonHoldt and her colleagues found no evidence that red wolves or Eastern wolves belonged to distinct lineages of their own. Instead, they seem to be populations of gray wolves, sharing many of the same genes.
What really sets Eastern wolves and red wolves apart, the researchers found, is a large amount of coyote DNA in their genomes.
The new study revealed that coyotes and North American wolves shared a remarkably recent common ancestor. Scientists had previously estimated their ancestor lived a million years ago, but the new study put the figure at just 50,000 years ago.
“I could not have put money on it being so recent,” Dr. vonHoldt said.
That ancestor gave rise to two species — the predecessor of today’s gray wolves and that of today’s coyotes — somewhere in Eurasia. Dr. vonHoldt said that the two species then migrated into North America.
There, coyotes evolved into small predators that specialize in taking down smaller prey. Wolves took a different path, relying on their larger size and great speed to prey on moose and other big mammals.
As wolves were killed off in the East, coyotes spread from the Midwestern prairies over the past two centuries to take their place. Surviving wolves interbred with the coyotes, producing hybrid offspring.
Dr. vonHoldt and her colleagues found that the genomes of Eastern wolves that lived in Algonquin Provincial Park in Ontario were half gray wolf and half coyote. Red wolves are even more mixed: Their genomes are 75 percent coyote and only 25 percent wolf.
Some wolf experts were startled by the finding and said it would require further support.
Linda Y. Rutledge, an expert on Eastern wolves, questioned whether the new study was sufficient to reject them as a separate species. Two Algonquin wolves that were part of the new study, she said, lived during a period when hybridization between coyotes and wolves was unusually common.
“They’re potentially not representative at all,” she said.
Despite her concerns, Dr. Rutledge joined Dr. vonHoldt’s lab as a research associate last year to participate in a new study on wolves, called the Canine Ancestry Project. The researchers are pooling their samples of DNA to study up to 100 wolves, coyotes and dogs from every state in the continental United States, as well as in Canadian provinces.
Robert K. Wayne, an evolutionary biologist at the University of California, Los Angeles, who helped conduct the new study, said the mix of coyote and wolf DNA highlighted the need for a more sophisticated approach to conserving biological diversity.
Red and Eastern wolves still deserve protection despite their high level of coyote DNA, Dr. Wayne said, because they still carry the DNA of an endangered species: gray wolves.
With the proper management of the species’ habitat, he added, natural selection could help the wolf genes become more common again.
Yet the Endangered Species Act offers no guidance about what to do with hybrid animals.
“We put things in baskets, but it doesn’t work that way in nature,” Dr. Wayne said. “We need to have a hybrid policy.”
Even if they are not pure wolves, Dr. Rutledge said, hybrid animals still play a crucial role in eastern forests as top predators. “If it can kill deer in eastern landscapes, it’s worth saving,” she said.
Wolves are not the only animals challenging traditional taxonomy. Many related species are trading genes through hybridization, either naturally or because of human activity.
“It’s a fairly broad swath of diversity,” Dr. Kovach said. “And more concerning, it’s increasing.”