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.