Saturday, October 1, 2022

Largest study of ancient wolf DNA points to dogs’ mixed origins

Dogs are descended from at least two different populations of ancient wolves, one from eastern Eurasia and the other from around the Near East, a study suggests.

The research from an international team of geneticists and archaeologists is by far the largest study of ancient wolf genomes and also looks at the DNA of modern wolves and ancient and modern dogs. It indicates that dogs were domesticated in independent processes in two regions — or only in the more eastern region, with later gene flow between dogs moving west and local wolves.

Dogs descend from the grey wolf and were domesticated during the Ice Age, at least 15,000 years ago. Although they were the first animals to be domesticated, exactly when, where and how this occurred has long vexed experts.

A 32,000 wolf head from Yakutia. Photo: Love Dalén

For their study, published in Nature, the team analysed the genomes of 72 ancient wolves, 68 modern wolves, 33 ancient dogs and 369 modern dogs, spanning a total of 100,000 years. The ancient remains included the complete, well-preserved head of a Siberian wolf that lived 32,000 years ago.

Anders Bergström, joint first author and a post-doctoral researcher in the ancient genomics laboratory at the Francis Crick Institute, said: “Studying ancient wolves that lived close to the time of dog domestication, we found that dogs overall are more closely related to ancient wolves in Asia than to ancient wolves in Europe. This suggests that the domestication process occurred somewhere in the east — though outside of Siberia, where ancient wolves do not match dog ancestry.”

In their paper, the team said there were some indicators that this primary phase of domestication occurred around 28,000 years ago in or around East Asia although there was not yet enough evidence to be sure. The team also found that early dogs from Africa, the Near East and southern Europe had a genetic contribution from a second source population of wolves in western Eurasia, related to Near Eastern wolves.

Bergström said: “We can’t currently tell whether the second, western-related source of dog ancestry reflects an independent domestication process in the west. The other possibility is that there was only one domestication process in the east, followed by gene flow from local wolves as dogs arrived in the in Near East or surrounding regions. But in either case, we can’t say very much about the time at which this second source of ancestry would have emerged, only that it must have happened at some point prior to 7,200 years ago, when we have the earliest observation of this ancestry in an ancient dog in the Levant.

“It could have been much earlier than that, and future studies of earlier dogs in the region will be needed to learn more about the timing.”

He added that most dogs today descend from both these source populations of ancient wolves. “Many popular breed dogs are from Europe, and European dogs have approximately 15 per cent ancestry from the western-related source, and 85 per cent from the eastern-related source.”

We have greatly increased the number of sequenced ancient wolf genomes

Anders Bergström

A previous study, six years ago, also proposed that dogs may have been domesticated independently in western and eastern Eurasia. However, it suggested that ancestry from the former population was extinct or nearly extinct in modern dogs. Bergström and his colleagues said their new study demonstrated that ancestry from at least two wolf populations was “extant and ubiquitous” in modern dogs. It also indicated that ancient European wolves could not have been the western source population.

The processes by which fierce predators were domesticated to become man’s best friend remain contested. One theory is that domestication began when wolves scavenged around the camps of hunter-gatherers in East or Central Asia. They may have been trained by humans as hunting companions or guard dogs. If a separate process of domestication occurred closer to 7,200 years ago in the Near East, it could possibly have occurred after the development of agriculture, when dogs’ herding abilities would also have been useful.

As the 72 ancient wolf genomes spanned around 30,000 generations, the team were able to build a timeline of how wolf DNA has changed, showing natural selection in action.

For example, they observed that over a period of about 10,000 years, one gene variant went from being very rare to being present in every wolf, and is still present in all wolves and dogs. The variant affects a gene, IFT88, which is involved in the development of bones in the skull and jaw. It is possible that the spread of this variant could have been driven by a change in the types of prey available during the Ice Age, giving an advantage to wolves with a certain head shape.

Pontus Skoglund, senior author and group leader of the ancient genomics lab at the Crick, said: “This is the first time scientists have directly tracked natural selection in a large animal over a timescale of 100,000 years, seeing evolution play out in real time rather than trying to reconstruct it from DNA today.

“We found several cases where mutations spread to the whole wolf species, which was possible because the species was highly connected over large distances. This connectivity is perhaps a reason why wolves managed to survive the Ice Age while many other large carnivores vanished.

“Similar whole-genome time series from the Ice Age, in humans or other animals, could provide new information about how evolution happens.”

The team are continuing their search for the wolf ancestors of dogs. They are focusing on genomes from locations not included in this study, including more southerly regions.

Bergström said: “Through this project we have greatly increased the number of sequenced ancient wolf genomes, allowing us to create a detailed picture of wolf ancestry over time, including around the time of dog origins.”

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