2808. On the Origins of Dogs: The First Domesticated Animal

By Ed Yong, The Atlantic, June 2, 2016

Tens of thousands of years ago, before the internet, before the Industrial Revolution, before literature and mathematics, bronze and iron, before the advent of agriculture, early humans formed an unlikely partnership with another animal—the grey wolf. The fates of our two species became braided together. The wolves changed in body and temperament. Their skulls, teeth, and paws shrank. Their ears flopped. They gained a docile disposition, becoming both less frightening and less fearful. They learned to read the complex expressions that ripple across human faces. They turned into dogs.

Today, dogs are such familiar parts of our lives—our reputed best friends and subject of many a meme—that it’s easy to take them, and what they represent, for granted. Dogs were the first domesticated animals, and their barks heralded the Anthropocene. We raised puppies well before we raised kittens or chickens; before we herded cows, goats, pigs, and sheep; before we planted rice, wheat, barley, and corn; before we remade the world.

“Remove domestication from the human species, and there’s probably a couple of million of us on the planet, max,” says archaeologist and geneticist Greger Larson. “Instead, what do we have? Seven billion people, climate change, travel, innovation and everything. Domestication has influenced the entire earth. And dogs were the first.” For most of human history, “we’re not dissimilar to any other wild primate. We’re manipulating our environments, but not on a scale bigger than, say, a herd of African elephants. And then, we go into partnership with this group of wolves. They altered our relationship with the natural world.”

Larson wants to pin down their origins. He wants to know when, where, and how they were domesticated from wolves. But after decades of dogged effort, he and his fellow scientists are still arguing about the answers. They agree that all dogs, from low-slung corgis to towering mastiffs, are the tame descendants of wild ancestral wolves. But everything else is up for grabs.

Some say wolves were domesticated around 10,000 years ago, while others say 30,000. Some claim it happened in Europe, others in the Middle East, or East Asia. Some think early human hunter-gatherers actively tamed and bred wolves. Others say wolves domesticated themselves, by scavenging the carcasses left by human hunters, or loitering around campfires, growing tamer with each generation until they became permanent companions.

Dogs were domesticated so long ago, and have cross-bred so often with wolves and each other, that their genes are like “a completely homogenous bowl of soup,” Larson tells me, in his office at the University of Oxford. “Somebody goes: what ingredients were added, in what proportion and in what order, to make that soup?” He shrugs his shoulders. “The patterns we see could have been created by 17 different narrative scenarios, and we have no way of discriminating between them.”

The only way of doing so is to look into the past. Larson, who is fast-talking, eminently likable, and grounded in both archaeology and genetics, has been gathering fossils and collaborators in an attempt to yank the DNA out of as many dog and wolf fossils as he can. Those sequences will show exactly how the ancient canines relate to each other and to modern pooches. They’re the field’s best hope for getting firm answers to questions that have hounded them for decades.

And already, they have yielded a surprising discovery that could radically reframe the debate around dog domestication, so that the big question is no longer when it happened, or where, but how many times.

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On the eastern edge of Ireland lies Newgrange, a 4,800-year-old monument that predates Stonehenge and the pyramids of Giza. Beneath its large circular mound and within its underground chambers lie many fragments of animal bones. And among those fragments, Dan Bradley from Trinity College Dublin found the petrous bone of a dog.

Press your finger behind your ear. That’s the petrous. It’s a bulbous knob of very dense bone that’s exceptionally good at preserving DNA. If you try to pull DNA out of a fossil, most of it will come from contaminating microbes and just a few percent will come from the bone’s actual owner. But if you’ve got a petrous bone, that proportion can be as high as 80 percent. And indeed, Bradley found DNA galore within the bone, enough to sequence the full genome of the long-dead dog.

Larson and his colleague Laurent Frantz then compared the Newgrange sequences with those of almost 700 modern dogs, and built a family tree that revealed the relationships between these individuals. To their surprise, that tree had an obvious fork in its trunk—a deep divide between two doggie dynasties. One includes all the dogs from eastern Eurasia, such as Shar Peis and Tibetan mastiffs. The other includes all the western Eurasian breeds, and the Newgrange dog.

The genomes of the dogs from the western branch suggest that they went through a population bottleneck—a dramatic dwindling of numbers. Larson interprets this as evidence of a long migration. He thinks that the two dog lineages began as a single population in the east, before one branch broke off and headed west. This supports the idea that dogs were domesticated somewhere in China.

But there’s a critical twist.

The team calculated that the two dog dynasties split from each other between 6,400 and 14,000 years ago.  But the oldest dog fossils in both western and eastern Eurasia are older than that. Which means that when those eastern dogs migrated west into Europe, there were already dogs there.

To Larson, these details only make sense if dogs were domesticated twice.

Here’s the full story, as he sees it. Many thousands of years ago, somewhere in western Eurasia, humans domesticated grey wolves. The same thing happened independently, far away in the east. So, at this time, there were two distinct and geographically separated groups of dogs. Let’s call them Ancient Western and Ancient Eastern. Around the Bronze Age, some of the Ancient Eastern dogs migrated westward alongside their human partners, separating from their homebound peers and creating the deep split in Larson’s tree. Along their travels, these migrants encountered the indigenous Ancient Western dogs, mated with them (doggy style, presumably), and effectively replaced them.

Today’s eastern dogs are the descendants of the Ancient Eastern ones. But today’s western dogs (and the Newgrange one) trace most of their ancestry to the Ancient Eastern migrants. Less than 10 percent comes from the Ancient Western dogs, which have since gone extinct.

This is a bold story for Larson to endorse, not least because he himself has come down hard on other papers suggesting that cows, sheep, or other species were domesticated twice. “Any claims for more than one need to be substantially backed up by a lot of evidence,” he says. “Pigs were clearly domesticated in Anatolia and in East Asia. Everything else is once.” Well, except maybe dogs.

Other canine genetics experts think that Larson’s barking up the wrong tree. “I’m somewhat underwhelmed, since it’s based on a single specimen,” says Bob Wayne from the University of California, Los Angeles. He buys that there’s a deep genetic division between modern dogs. But, it’s still possible that dogs were domesticated just once, creating a large, widespread, interbreeding population that only later resolved into two distinct lineages.

In 2013, Wayne’s team compared the mitochondrial genomes (small rings of DNA that sit outside the main set) of 126 modern dogs and wolves, and 18 fossils. They concluded that dogs were domesticated somewhere in Europe or western Siberia, between 18,800 and 32,100 years ago. And genes aside, “the density of fossils from Europe tells us something,” says Wayne. “There are many things that look like dogs, and nothing quite like that in east Asia.”

Peter Savolainen from the KTH Royal Institute of Technology in Stockholm disagrees. By comparing the full genomes of 58 modern wolves and dogs, his team has shown that dogs in southern China are the most genetically diverse in the world. They must have originated there around 33,000 years ago, he says, before a subset of them migrated west 18,000 years later.

That’s essentially the same story that Larson is telling. The key difference is that Savolainen doesn’t buy the existence of an independently domesticated group of western dogs. “That’s stretching the data very much,” he says. Those Ancient Western dogs might have just been wolves, he says. Or perhaps they were an even earlier group of migrants from the east. “I think the picture must seem a bit chaotic,” he says understatedly. “But for me, it’s pretty clear. It must have happened in southern East Asia. You can’t interpret it any other way.”

Except, you totally can. Wayne does (“I’m certainly less dogmatic than Peter,” he says). Adam Boyko from Cornell University does, too: after studying the genes of village dogs—free-ranging mutts that live near human settlements—he argued for a single domestication in Central Asia, somewhere near India or Nepal. And clearly, Larson does as well.

Larson adds that his gene-focused peers are ignoring one crucial line of evidence—bones. If dogs originated just once, there should be a neat gradient of fossils with the oldest ones at the center of domestication and the youngest ones far away from it. That’s not what we have. Instead, archaeologists have found 15,000-year-old dog fossils in western Europe, 12,500-year-old ones in east Asia, and nothing older than 8,000 years in between.

“If we’re wrong, then how on earth do you explain the archaeological data?” says Larson. “Did dogs jump from East Asia to Western Europe in a week, and then go all the way back 4,000 years later?” No. A dual domestication makes more sense. Mietje Genompré, an archaeologist from the Royal Belgian Institute of Natural Sciences, agrees that the bones support Larson’s idea. “For me, it’s very convincing,” she says.

But even Larson is hedging his bets. When I ask him how strong his evidence is, he says, “Like, put a number on it? If was being bold, I’d say it’s a 7 out of 10. We lack the smoking gun.”

Why is this so hard? Of all the problems that scientists struggle with, why has the origin of dogs been such a bitch to solve?

For starters, the timing is hard to pin down because no one knows exactly how fast dog genomes change. That pace—the mutation rate—underpins a lot of genetic studies. It allows scientists to compare modern dogs and ask: How long ago must these lineages have diverged in order to build up this many differences in their genes? And since individual teams use mutation rate estimates that are wildly different, it’s no wonder they’ve arrived at conflicting answers.

Regardless of the exact date, it’s clear that over thousands of years, dogs have mated with each other, cross-bred with wolves, travelled over the world, and been deliberately bred by humans. The resulting ebb and flow of genes has turned their history into a muddy, turbid mess—the homogeneous soup that Larson envisages.

Wolves provide no clarity. Grey wolves used to live across the entire Northern Hemisphere, so they could have potentially been domesticated anywhere within that vast range (although North America is certainly out). What’s more, genetic studies tell us that no living group of wolves is more closely related to dogs than any other, which means that the wolves that originally gave rise to dogs are now extinct. Sequencing living wolves and dogs will never truly reveal their shrouded past; it’d be, as Larson says, like trying to solve a crime when the culprit isn’t even on the list of suspects.

“The only way to know for sure is to go back in time,” he adds.

The study informally known as the Big Dog Project was born of frustration. Back in 2011, Larson was working hard on the origin of domestic pigs, and became annoyed that scientists studying dogs were getting less rigorous papers in more prestigious journals, simply because their subjects were that much more charismatic and media-friendly. So he called up his longstanding collaborator Keith Dobney. “Through gritted teeth, I said: We’re fucking doing dogs. And he said: I’m in.”

Right from the start, the duo realized that studying living dogs would never settle the great domestication debate. The only way to do that was to sequence ancient DNA from fossil dogs and wolves, throughout their range and at different points in history. While other scientists were studying the soup of dog genetics by tasting the finished product, Larson would reach back in time to taste it at every step of its creation, allowing him to definitively reconstruct the entire recipe.

In recent decades, scientists have become increasingly successful at extracting and sequencing strands of DNA from fossils. This ancient DNA has done wonders for our understanding of our own evolution. It showed, for example, how Europe was colonized 40,000 years ago by hunter-gatherers moving up from Africa, then 8,000 years ago by Middle Eastern farmers, and 5,000 years ago by horse-riding herders from the Russian steppes. “Everyone in Europe today is a blend of those three populations,” says Larson, who hopes to parse the dog genome in the same way, by slicing it into its constituent ingredients.

Larson originally envisaged a small project—just him and Dobney analyzing a few fossils. But he got more funding, collaborators, and samples than he expected. “It just kind of metastasized out of all proportion,” he says. He and his colleagues would travel the world, drilling into fossils and carting chips of bone back to Oxford. They went to museums and private collections. (“There was a guy up in York who had a ton of stuff in his garage.”) They grabbed bones from archaeological sites.

The pieces of bone come back to a facility in Oxford called the Palaeo-BARN—the Palaeogenomics and Bioarchaeology Research Network. When I toured the facility with Larson, we wore white overalls, surgical masks, oversoles, and purple gloves, to keep our DNA (and that of our skin microbes) away from the precious fossil samples. Larson called them ‘spacesuits.’ I was thinking ‘thrift-store ninja.’

In one room, the team shoves pieces of bone into a machine that pounds it with a small ball bearing, turning solid shards into fine powder. They then send the powder through a gauntlet of chemicals and filters to pull out the DNA and get rid of everything else. The result is a tiny drop of liquid that contains the genetic essence of a long-dead dog or wolf. Larson’s freezer contains 1,500 such drops, and many more are on the way. “It’s truly fantastic the kind of data that he has gathered,” says Savolainen.

True to his roots in archaeology, Larson isn’t ignoring the bones. His team photographed the skulls of some 7,000 prehistoric dogs and wolves at 220 angles each, and rebuilt them in virtual space. They can use a technique called geometric morphometrics to see how different features on the skulls have evolved over time.

The two lines of evidence—DNA and bones—should either support or refute the double domestication idea. It will also help to clear some confusion over a few peculiar fossils, such as a 36,000 year old skull from Goyet cave in Belgium. Genompré thinks it’s a primitive dog. “It falls outside the variability of wolves: it’s smaller and the snout is different,” she says. Others say it’s too dissimilar to modern dogs. Wayne has suggested that it represents an aborted attempt at domestication—a line of dogs that didn’t contribute to modern populations and is now extinct.

Maybe the Goyet hound was part of Larson’s hypothetical Ancient Western group, domesticated shortly after modern humans arrived in Europe. Maybe it represented yet another separate flirtation with domestication. All of these options are on the table, and Larson thinks he has the data to tell them apart. “We can start putting numbers on the difference between dogs and wolves,” he says. “We can say this is what all the wolves at this time period look like; does the Goyet material fall within that realm, or does it look like dogs from later on?”

Larson hopes to have the first big answers within six to twelve months. “I think it’ll clearly show that some things can’t be right, and will narrow down the number of hypotheses,” says Boyko. “It may narrow it down to one but I’m not holding my breath on that.” Wayne is more optimistic. “Ancient DNA will provide much more definitive data than we had in the past,” he says. “[Larson] convinced everyone of that. He’s a great diplomat.”

Indeed, beyond accumulating DNA and virtual skulls, Larson’s greatest skill is in gathering collaborators. In 2013, he rounded up as many dog researchers as he could and flew them to Aberdeen, so he could get them talking. “I won’t say there was no tension,” he says. “You go into a room with someone who has written something that sort of implies you aren’t doing very good science... there will be tension. But it went away very quickly. And, frankly: alcohol.”

“Everyone was like: You know what? If I’m completely wrong and I have to eat crow on this, I don’t give a shit. I just want to know.”