How did a wild, fierce, nocturnal predator like the wolf evolve over the course of millennia into a friendly, domesticated companion who likes to sleep on our beds at night?

Evolutionary genetics says it’s in the genes, but which genes? A new study by researchers at the University of Michigan may point to an answer.

Amanda Pendleton, PhD, a postdoctoral research fellow in the Department of Human Genetics at Michigan Medicine in Ann Arbor, Michigan, was reviewing research on canine domestication and noticed something peculiar about the dog genome: At some places in the genome, the DNA of modern dogs didn’t appear to match the DNA of ancient dogs.

Somewhere along the line, something happened to the canine gene pool.

Most likely, it coincided with the rise of selective breeding around 300 years ago.

“We convinced ourselves that previous studies found many genes not associated with being a dog but with being a breed dog,” said Pendleton. Which means that breed dogs don’t fully reflect the genetic diversity found in dogs around the world.

Three-quarters of the world’s dogs, some 750 million, are village dogs, dogs who aren’t bred by humans or kept as pets, but roam unfettered and survive by scavenging for food near human populations. And unrestricted by the human hand of selective breeding, they mate freely.

They’re not the same as strays or mongrels, but they’re not feral, either.

What they are, are semi-wild, semi-socialized canines living in or near human settlements—and as close as researchers are going to get to the ancient dogs who first started to live alongside humans some 15,000 years ago.

That made them the perfect research subjects for Pendleton’s team, which looked at the DNA of 43 village dogs from places such as India, Portugal, and Vietnam. They compared that DNA to the DNA of ancient dogs found at 5,000-year-old burial sites, and the DNA of wolves.

What they found were more than 200 regions of the dog genome that could play a key part in the evolution of the domestic dog. These particular genes influence brain function, development, and behavior, and they appear to support something called the neural crest hypothesis of domestication.

Pendleton explains: “The neural crest hypothesis posits that the phenotypes we see in domesticated animals over and over again—floppy ears, changes to the jaw, coloration, tame behavior—can be explained by genetic changes that act in a certain type of cell during development called neural crest cells, which are incredibly important and contribute to all kinds of adult tissues.”

One gene in particular, RAI1, stood out.

Earlier studies suggest that RAI1 is involved in circadian rhythm and sleep in both dogs and humans. The researchers theorize that changes in this gene may help explain why domesticated dogs are now awake during the day rather than nocturnal like the wolves they’re descended from.

One thing’s for sure: It’s nice when everyone’s on the same schedule.

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