July 28, 2017 6:00 AM

Old Dogs, New Tricks: DNA from Ancient Canines and Humans Can Teach Us a Lot

A study of DNA from prehistoric German dogs yielded new clues about how dogs became domesticated from wolves. The same techniques can teach us about our own ancient origins — and diseases that affect both species.

His laboratory sits in a medical school focused on human health. So why is a geneticist at the University of Michigan studying how wolves became domesticated into dogs?

Because, it turns out, old dogs can teach us new tricks.

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Jeffrey Kidd, Ph.D., and his colleagues study ancient DNA from both dogs and humans. They call the technique paleogenomics because they examine the full sample of DNA, or genome, found in ancient bones dug up from archaeological sites.

Using such samples, Kidd and his colleagues are tracing the history of our faithful companion animals and paving the way for research on the diseases that can affect both them and us.

Their latest paper reveals key information about the domestication of wolves into dogs. And related techniques have also revealed new clues about why certain genetic diseases afflict some human populations more than others.

Dogs from wolves: once, not twice

The latest discovery, published in Nature Communications by a team from Stony Brook University in New York and Kidd’s lab at the U-M Medical School, may help settle a debate about the transformation of wolves into humanity’s best friend.

In the study, the team used DNA from two ancient dog bones found in Germany — one 7,000 years old, when Europe’s humans were roaming hunters, and the other 4,700 years old, when farming had just begun in that region.

The team compared the DNA sequence with thousands of key areas of DNA from nearly 5,700 modern dogs and wolves.

Using advanced genetic sequencing and sophisticated computer models, they mapped the tiny variations among the DNA sequences. This allowed them to create a model of changes in canine DNA stretching back thousands of years.

They conclude that the ancestors of our modern dogs branched off from the gray wolf pack between 20,000 and 40,000 years ago in Europe. Long before humans had started taming wild plants or the ancestors of cows, chickens and horses, they found a way to connect with wolves and breed them for use in hunting.

The two ancient dogs’ DNA resembled that of modern dogs in many respects. The 4,700-year-old dog had DNA sequences resembling those of dogs now found mainly in India and central Asia. This might be attributable to the fact that Bronze Age Asian traders, with their dogs, came across the steppes for trade.

Other teams had suggested, based on their own DNA analysis of a 5,000-year-old Irish dog bone, that there had been two great wolf-domestication events.

But the new findings suggest that this happened only once.

While Kidd and his colleagues can’t say for sure exactly where it happened, or pinpoint the year during the Stone Age when it happened, they do note that the ancient German dogs hadn’t yet evolved the genetic machinery needed to digest starch — something that today’s dogs do have.

“Ancient DNA in humans reveals the rich history of population movements, and patterns of genetic flow that we were previously blind to, and the same appears to be true in dogs,” says Kidd, who has mainly focused his work on exploring how ancient changes affect modern human DNA. “Exactly where dog domestication happened remains controversial, and our samples aren’t old enough to be definitive about that. But our data are consistent with a single domestication.”

He notes that dogs suffer diseases that resemble human diseases more so than the mice normally used in lab experiments and that dogs traveled with our ancestors as they roamed across the globe. So having a better picture of ancient dog DNA may improve the ability to study such conditions — and to study the other animals and plants that humans domesticated.

“Coupled with dogs’ unique history of breed formation, this makes them a powerful mapping model,” he says.

Other research using paleogenomics

Dog origins are just one example of the kinds of things that paleogenomic techniques make possible. Kidd and his colleagues are now looking more closely at the exact genes that appear linked to dog domestication and which traits our ancestors tried to encourage through breeding.

SEE ALSO: Ancient Viruses Lurk in Our DNA

At the same time, he and his colleagues have many projects under way to apply these techniques to ancient and modern human DNA. It’s provided a wealth of information about global human diversity.

The genetic diversity of humans, like dogs, is shaped by a complex history of population movements.

In a 2016 paper in the Proceedings of the National Academy of Sciences, Kidd and his colleagues from Stony Brook, Stanford University, Switzerland and France looked at how patterns of disease-related mutations change based on ancient human migration patterns.

After Homo sapiens evolved on the African continent, our ancestors began migrating outward in waves, a process called expansion.

Using DNA information from seven human populations — from Namibia, Congo, Algeria, Pakistan, Cambodia, Siberia and Mexico — they look at how often various harmful mutations occur.

The project uses many of the same modeling and simulating techniques used in the dog study. In general, rates of harmful — called deleterious — mutations differed as predicted by models of human migration. These differences were particularly stark for recessive mutations, which lead to disease only if a person inherits the same mutation from both parents.

As time goes on, Kidd and his colleagues will continue to refine techniques to model human migrations, disease gene inheritance and the impact of humans on different crop, livestock and companion animal species.

Ancient DNA has many more things to teach, and paleogenomics is how we’ll learn.