Deeper Digging Needed to Decode a Best Friend’s Genetic Roots
By JAMES GORMAN
Published: May 21, 2012
As scientific puzzles go, the origin of dogs may not be as important as the origin of the universe. But it strikes closer to home, and it almost seems harder to answer.
Alen Popov
The Saluki has less mixed DNA than many other dogs.
Eric Isselée The Eurasier
The Basenji.
Cosmologists seem to have settled on the idea that 13.7 billion years ago the universe appeared with a bang (the big one) from nothing — albeit a kind of nothing that included the laws of physics.
With dogs, the consensus is that they came from wolves. Beyond that, there are varying claims. It seems dogs appeared sometime between 15,000 and 100,000 years ago, in Asia or Africa or multiple times in multiple places.
There is a reason for this confusion, according to Greger Larson at the University of Durham in England. In a new research paper, he argues that the DNA of modern dogs is so mixed up that it is useless in figuring out when and where dogs originated. “With the amount of DNA we’ve sequenced so far,” Dr. Larson said, “we’re lucky to get back a hundred years, max.” He says that only with the analysis of DNA from fossil dogs, now being done, will answers along this line emerge.
Dr. Larson, the first of 20 authors on a paper about the origin of dogs published Monday in The Proceedings of the National Academy of Sciences, argues that genetic study of modern breeds does not “get us any closer to understanding where and when and how dogs were domesticated.”
Adam Boyko of Cornell University, who has worked in the field of dog genetics but was not involved in the study, said that Dr. Larson’s group had a “fantastic data set,” and laid out clearly the current difficulties in nailing down the details of dog domestication. Dr. Larson and his colleagues analyzed 49,024 locations on dog DNA where the genetic code varies, so called SNPs (pronounced snips, for single nucleotide polymorphisms). They took the DNA from 1,375 dogs of 121 breeds, and 19 wolves.
What they found was that all the so-called modern breeds had been so mixed that their deep genetic history was obscured.
They also found six breeds that they called basal, meaning that their DNA was less mixed — the basenji, shar-pei, Saluki, Akita, Finnish spitz and Eurasier.
When they added these to eight breeds deemed ancient (older than 500 years) in other studies, what they found was that the dogs that were most genetically distinct were not from the places where the oldest archaeological and fossil evidence had been found. Dr. Larson said that the expectation was that if these breeds were closer genetically to the first domesticated dogs, they would be geographically closer as well, more likely to be found near the sites of early dog fossils, or archaeological records of ancient breeds.
Instead, the more genetically distinct dogs had been geographically isolated relatively recently in the history of domestication. For example, dingoes, basenjis and New Guinea singing dogs came from Southeast Asia and southern Africa, where dogs did not arrive until 3,500 and 1,400 years ago, respectively. Their distinctive genes were indications of relatively recent isolation.
But, he said, all is not lost. Humans have buried their dogs for a long time, and as a result there are fossils of truly ancient dogs, in the neighborhood of 15,000 years old, from which DNA can be extracted. Just as DNA from Neanderthals has helped illuminate the origins of modern humans, DNA from ancient dog fossils should help illuminate the story of early dog domestication in the next few years.
“Let’s step back,” he said. “Let’s take a breath. We’re not a million miles away” from figuring out when and where dogs appeared. “We’re close.”
A version of this article appeared in print on May 22, 2012, on page D3 of the New York edition with the headline: Deeper Digging Needed to Decode a Best Friend’s Genetic Roots.
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Update: According to the Verge citing other studies, “new findings published in Science this week suggest that they all can trace their relationship with humans back to Europe.
To determine where and when domestication occurred for canines, a team of scientists led by Olaf Thalmann at Finland’s University of Turku used mitochondrial DNA to establish links between a wide range of modern dog and wolf species with ancient canine fossils dated between 19,000 and 33,000 years old. The scientists saw that genetic sequences from modern dog breeds most closely matched those from both modern and ancient Europe. Thalmann was also able to extrapolate that because of the age of the oldest fossils employed in the study, wolves may have been domesticated during the hunter-gatherer period of human history.
Determining when dogs were domesticated has always been a complicated subject. An earlier study published in Nature in 2010 suggested that domestication events for dogs most likely occurred in the Middle East, while a 2011 Heredity study claimed that Y-chromosome DNA supported the theory that domestic dogs originated in Southeast Asia. This new research likely isn’t the final word on what’s become an ongoing debate.” Source: “DNA evidence suggests that dogs were domesticated in Europe“(Nov 14, 2013 The Verge)
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From the Dienekes’ Anthropology blog:
Science 15 November 2013: Vol. 342 no. 6160 pp. 871-874
Complete Mitochondrial Genomes of Ancient Canids Suggest a European Origin of Domestic Dogs
O. Thalmann et al.
The geographic and temporal origins of the domestic dog remain controversial, as genetic data suggest a domestication process in East Asia beginning 15,000 years ago, whereas the oldest doglike fossils are found in Europe and Siberia and date to >30,000 years ago. We analyzed the mitochondrial genomes of 18 prehistoric canids from Eurasia and the New World, along with a comprehensive panel of modern dogs and wolves. The mitochondrial genomes of all modern dogs are phylogenetically most closely related to either ancient or modern canids of Europe. Molecular dating suggests an onset of domestication there 18,800 to 32,100 years ago. These findings imply that domestic dogs are the culmination of a process that initiated with European hunter-gatherers and the canids with whom they interacted. Link
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An earlier post also from the Dienekes’ Anthropology blog, the evidence (Sarah Brown et al. study) reviewed suggested a Southeast-Asian origin of dogs:
PLoS ONE 6(12): e28496. doi:10.1371/journal.pone.0028496
Phylogenetic Distinctiveness of Middle Eastern and Southeast Asian Village Dog Y Chromosomes Illuminates Dog Origins
Sarah K. Brown et al.
Modern genetic samples are commonly used to trace dog origins, which entails untested assumptions that village dogs reflect indigenous ancestry or that breed origins can be reliably traced to particular regions. We used high-resolution Y chromosome markers (SNP and STR) and mitochondrial DNA to analyze 495 village dogs/dingoes from the Middle East and Southeast Asia, along with 138 dogs from >35 modern breeds to 1) assess genetic divergence between Middle Eastern and Southeast Asian village dogs and their phylogenetic affinities to Australian dingoes and gray wolves (Canis lupus) and 2) compare the genetic affinities of modern breeds to regional indigenous village dog populations. The Y chromosome markers indicated that village dogs in the two regions corresponded to reciprocally monophyletic clades, reflecting several to many thousand years divergence, predating the Neolithic ages, and indicating long-indigenous roots to those regions. As expected, breeds of the Middle East and East Asia clustered within the respective regional village dog clade. Australian dingoes also clustered in the Southeast Asian clade. However, the European and American breeds clustered almost entirely within the Southeast Asian clade, even sharing many haplotypes, suggesting a substantial and recent influence of East Asian dogs in the creation of European breeds. Comparison to 818 published breed dog Y STR haplotypes confirmed this conclusion and indicated that some African breeds reflect another distinct patrilineal origin. The lower-resolution mtDNA marker consistently supported Y-chromosome results. Both marker types confirmed previous findings of higher genetic diversity in dogs from Southeast Asia than the Middle East. Our findings demonstrate the importance of village dogs as windows into the past and provide a reference against which ancient DNA can be used to further elucidate origins and spread of the domestic dog.
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How the disparate findings of the various studies can be reconciled at the present moment, is not well understood and the job of untangling the history of wolf-dog breeding and the genetic trails is currently boggling scientists… more on this problem is elucidated at the NY Times article below:
Wolf to Dog: Scientists Agree on How, but Not Where by Carl Zimmer NY Times, Nov 14, 2013
“Where did dogs come from? That simple question is the subject of a scientific debate right now. In May, a team of scientists published a study pointing to East Asia as the place where dogs evolved from wolves. Now, another group of researchers has announced that dogs evolved several thousand miles to the west, in Europe
This controversy is intriguing even if you’re not a dog lover. It illuminates the challenges scientists face as they excavate the history of any species from its DNA.
Scientists have long agreed that the closest living relatives of dogs are wolves, their link confirmed by both anatomy and DNA. Somewhere, at some point, some wolves became domesticated. They evolved not only a different body shape, but also a different behavior. Instead of traveling in a pack to hunt down prey, dogs began lingering around humans. Eventually, those humans bred them into their many forms, from shar-peis to Newfoundlands.
A few fossils supply some tantalizing clues to that transformation. Dating back as far as 36,000 years, they look like wolfish dogs or doggish wolves. The oldest of these fossils have mostly turned up in Europe.
In the 1990s, scientists started using new techniques to explore theorigin of dogs. They sequenced bits of DNA from living dog breeds and wolves from various parts of the world to see how they were related. And the DNA told a different story than the bones. In fact, it told different stories.
In a 2002 study, for example, Peter Savolainen, now at the Royal Institute of Technology in Sweden, and his colleagues concluded thatdogs evolved in East Asia. Eight years later, however, Robert Wayne, a geneticist at the University of California, Los Angeles, and his colleagues analyzed some new dog breeds and concluded that the Middle East was where dogs got their start. (All such studies suggest that a few breeds may have been independently domesticated, although they differ on which ones and where.)
Dr. Savolainen and his colleagues continued to sequence DNA from more dogs, and they published more evidence for an East Asian origin of dogs ― narrowing it down to South China.
While early studies of canine origins were limited to fragments of DNA, scientists are now starting to sequence entire genomes of dogs and wolves. In May, for example, Dr. Salovainen and Chinese colleagues reported that Chinese native dogs had the most wolflike genomes. By tallying up the mutations in the different dog and wolf genomes, they estimated that the ancestors of Chinese village dogsand wolves split about 32,000 years ago.
If this were true, then the first dogs would have become domesticated not by farmers, but by Chinese hunter-gatherers more than 20,000 years before the dawn of agriculture.
Dr. Wayne and his colleagues think that is wrong.
A dog may have wolflike DNA because it is a dog-wolf hybrid. In a paper that is not yet published, they analyze wolf and dog genomes to look for signs of ancient interbreeding. They cite evidence that, indeed, some of the DNA in dogs in East Asia comes from wolf interbreeding.
“That’s going to pump up the resemblance,” Dr. Wayne said.
Now Dr. Wayne and his colleagues are introducing a new line of evidence to the dog debate: ancient DNA. Over the past two decades, scientists have developed increasingly powerful tools to rescue fragments of DNA from fossils, producing “an explosion in the samples,” said Beth Shapiro of the University of California, Santa Cruz, a collaborator with Dr. Wayne.
On Thursday in the journal Science, Dr. Wayne, Dr. Shapiro and their colleagues report on the first large-scale comparison of DNA from both living and fossil dogs and wolves. They managed to extract DNA from 18 fossils found in Europe, Russia and the New World. They compared their genes to those from 49 wolves, 77 dogs and 4 coyotes.
The scientists examined a special kind of DNA found in a structure in the cell called the mitochondrion. Mitochondrial DNA comes only from mothers. Because each cell may have thousands of mitochondria, it is easier to gather enough genetic fragments to reconstruct its DNA.
The scientists did not find that living dogs were closely related to wolves from the Middle East or China. Instead, their closest relatives were ancient dogs and wolves from Europe.
“It’s a simple story, and the story is they were domesticated in Europe,” Dr. Shapiro said.
Dr. Shapiro and Dr. Wayne and their colleagues estimate that dogs split off from European wolves sometime between 18,000 and 30,000 years ago. At the time, Northern Europe was covered in glaciers and the southern portion was a grassland steppe where humans hunted for mammoths, horses and other big game.
“Humans couldn’t take everything, and that was a great treasure trove,” Dr. Wayne said. Some wolves began to follow the European hunters to scavenge on the carcasses they left behind. As they migrated along with people, they became isolated from other wolves.
Dog evolution experts praised the scientists for gathering so much new data. “I think it’s terrific,” said Adam Boyko, a Cornell biologist. Dr. Savolainen agreed. “I think it’s a fantastic sample,” he said.
But Dr. Savolainen said the analysis was flawed. “It’s not a correct scientific study, because it’s geographically biased,” he said.
The study lacks ancient DNA from fossils from East Asia or the Middle East, and so it’s not possible to tell whether the roots of dog evolution are anchored in those regions. “You just need to have samples from everywhere,” Dr. Savolainen said.
He also rejects Dr. Wayne’s argument that interbreeding in East Asia creates an illusion that dogs originated there. Dr. Savolainen points out that the study suggesting interbreeding was based on a wolf from northern China. “What they need to have is samples from south China,” he said.
There’s just one catch. South China is now so densely settled by people that no wolves live there. A similar problem applies to the fossil record.
“It may be impossible to go this way,” Dr. Savolainen said.
Dr. Wayne is not quite so pessimistic. He and his colleagues are hoping to widen their scope and find more DNA from fossils of dogs outside of Europe, while also looking at the genes of living dogs that might hold important clues. Yet he thinks it unlikely that the new evidence will change the basic conclusion of his latest study.
“But there have been so many surprises in the history of this research on dog domestication that I’m holding my breath till we get more information,” Dr. Wayne said.”
Heritage of Japan 