Ancient DNA tells of two origins for dogs

Dogs were domesticated at least twice, a new study suggests.

Genetic analyses of a 4,800-year-old Irish dog and 59 other ancient dogs suggest that canines and humans became pals in both Europe and East Asia long before the advent of farming, researchers report June 3 in Science. Later, dogs from East Asia accompanied their human companions to Europe, where their genetic legacy trumped that of dogs already living there, the team also concludes.

That muddled genetic legacy may help explain why previous studies have indicated that dogs were domesticated from wolves only once, although evidence hasn’t been clear about whether this took place in East Asia, Central Asia or Europe. The idea that dogs came from East Asia or Central Asia is mostly based on analysis of DNA from modern dogs, while claims for European origins have been staked on studies of prehistoric pups’ genetics. “This paper combines both types of data” to give a more complete picture of canine evolution, says Mietje Germonpré, a paleontologist at the Royal Belgian Institute of Natural Sciences in Brussels, who was not part of the study.

Understanding this domestication process may illuminate humans’ distant past — dogs were probably the first domesticated animal and may have paved the way for taming other animals and plants.

In the study, evolutionary geneticist Laurent Frantz of the University of Oxford and colleagues compiled the complete set of genes, or genome, of an ancient dog found in a tomb near Newgrange, Ireland. Researchers drilled into the hard-as-stone petrous portion of the dog’s temporal bone, which contains the inner ear, to get well-protected DNA, Frantz says.

IRISH HOUND A 4,800-year-old dog found in a tomb in Newgrange, Ireland, is the first ancient dog to have its entire genetic instruction book, or genome, deciphered.

The researchers don’t know much about what the midsize dog looked like; it doesn’t bear any genetic markers of particular modern dog breeds, Frantz says. “He wasn’t black. He wasn’t spotted. He wasn’t white.” Instead, the Newgrange dog was probably a mongrel with fur similar to a wolf’s.

But the ancient mutt has something special in his genes — a stretch of enigmatic DNA, says Germonpré. “This Irish dog has a component that can’t be found in recent dogs or recent wolves.” That distinct DNA could represent the genetic ancestry of indigenous European prehistoric dogs, she says. Or it could be a trace of an extinct ancient wolf that may have given rise to dogs (SN: 7/13/13, p. 14).

Unraveling the prehistoric mutt’s DNA may help researchers understand dogs’ history. Already, comparisons of the ancient Irish dog’s DNA with that of modern dogs reveal that East Asian dogs are genetically different from European and Middle Eastern dogs, the researchers have found. Other researchers may have missed the distinction between the two groups because they were working with subsets of the data that Frantz and colleagues amassed. Frantz’s team generated DNA data from the Newgrange dog and other ancient dogs, but also used data from previous studies of modern dogs, including the complete genomes of 80 dogs and less-complete sampling of DNA from 605 dogs, a collection of 48 breeds and village dogs of no particular breed.

The distinct genetic profiles of today’s Eastern and Western dogs suggests that two separate branches of the canine family tree once existed. The Newgrange dog’s DNA is more like that of the Western dogs. Since the Irish dog is 4,800 years old, the Eastern and Western dogs must have formed distinct groups before then, probably between about 6,400 to 14,000 years ago. The finding suggests that dogs may have been domesticated from local wolves in two separate locations during the Stone Age.

The ancient dog’s DNA may also help pinpoint when domestication happened. Using the Newgrange dog as a calibrator and the modern dogs to determine how much dogs have changed genetically in the past 4,800 years, Frantz and colleagues determined that dogs’ mutation rate is slower than researchers have previously calculated. Then, using the slower mutation rate to calculate when dogs became distinct from wolves, the researchers found that separate branches of the canine family tree formed between 20,000 and 60,000 years ago. Many previous calculations put the split between about 13,000 and about 30,000 years ago, but the new dates are consistent with figures from a study of an ancient wolf’s DNA (SN: 6/13/15, p. 10). Frantz and colleagues emphasize that their estimate doesn’t necessarily pinpoint the time of domestication. It could indicate that different populations of wolves were evolving into new species at that time. One of those could later have evolved into the ancestor of dogs.

Although the new study indicates there were two origin points for dogs, humans’ canine companions have since mixed and mingled. By comparing mitochondrial DNA, the genetic material inside energy-generating organelles, from 59 ancient European dogs and 167 modern dogs, the researchers determined that East Asian dogs at least partially genetically replaced European dogs in the distant past. Mitochondria are inherited from the mother. Ancient European dogs’ mitochondrial DNA varieties, or haplogroups, differed from those of modern dogs, the researchers found. Of the ancient dogs, 63 percent carried haplogroup C and 20 percent carried haplogroup D. But in present-day dogs, 64 percent carry haplogroup A and 22 percent carry haplogroup B. That shift and other evidence indicate that dogs from the East moved west with humans, and Eastern dogs passed more of their genetic heritage to descendants than Western dogs did.

Archaeological evidence backs up the dual origin story. Dogs as old as 12,500 years old have been found in East Asia. In Europe, dogs date back to 15,000 years ago. But there is a dearth of dog remains older than 8,000 years old in Central Eurasia. That lack possibly rules out this in-between region as a domestication site, despite some genetic evidence from village dogs that says otherwise (SN:11/28/15, p. 8). “The argument in this paper, pointing out a pattern in the archaeological data of an absence of early dog remains in the period [before] 10,000 years ago, should be taken very seriously,” says Pontus Skoglund, an evolutionary geneticist at Harvard University.

He’s not yet won over by the double-domestication hypothesis, though. The researchers admit they can’t yet rule out that dogs were domesticated once, then transported to different places where isolation, random chance and other factors caused them to drift apart genetically.

More ancient DNA may help clarify the still-hazy picture of dog domestication. Says Skoglund: “It’s going to be an exciting time going forward.”