Quirks & Quarks

Less than a teaspoon of dirt contains DNA that could hold the history of an entire landscape

Study finds many surprises, such as the fact that woolly mammoths survived 1,000 years longer than previously thought.

Study finds many surprises, like woolly mammoths survived 1000 years longer than previously thought

Tyler Murchie, a PhD candidate in professor Hendrick Poinar's lab at McMaster University, developed the technique that can tease out ancient DNA samples from soil. (Emil Karpinski/McMaster University)

It once required paleontological remains like fossilized bones to tell that an ancient animal species lived on a landscape. Now it can be done with a fraction of a gram of frozen soil. 

Scientists from McMaster University in Ontario collected permafrost soil samples from four sites in the Yukon. They then applied a new technique they'd developed that can isolate and identify DNA in soil that came from tiny traces of ancient plants and animals. These might have been microscopic fragments of decayed plant material, shed skin cells, hair or traces of feces. 

"You could identify that woolly mammoths were in that locality where you are standing currently, and horses and potentially animals that weren't or haven't been discovered from the paleontological remains," said team lead Hendrik Poinar. Poinar is a professor of evolutionary genetics at McMaster. 

Poinar and his colleagues discovered ancient genetic fingerprints of hundreds of animals and thousands of plants their groundbreaking new study. Their findings are already rewriting our understanding of which animals were present and the type of ecosystem they lived in during the last ice age and its aftermath. 

Their findings suggest, for example, that woolly mammoths were still roaming our northern landscape 9,700 years ago, a thousand years later than previously thought.

This shows the Klondike region in the Yukon, where the permafrost samples containing sediment DNA were collected. (Tyler Murchie/McMaster University)

Poinar says this new technique allows them to parse out a much clearer picture of the ancient past than ever before. For his field, he said, this was analogous to the way the microscope revolutionized biology — making the invisible visible. 

"This is a different kind of microscope that allows a resolution at the genetic level," Poinar said in conversation with Quirks & Quarks host, Bob McDonald. 

Identifying ancient DNA in soil teeming with life 

The team sampled soil going back thousands of years by coring permafrost. They then were able to select layers of different ages and selectively pull out soil from different snapshots in history. The soil contained massive amounts of DNA — much of it from microbes. So they had to isolate the DNA they were particularly interested in.

To do that, Tyler Murchie, the PhD candidate who led the study, designed special "genetic fishing hooks" to specifically target DNA from ancient plants and animals. 

It was overwhelming at first and nerve racking, but then also it was this really profound sense of like, 'Oh, I really did it. Like, this worked.'- Tyler Murchie, McMaster University

"We take elephant DNA, for example, and we make tiny little baits or tenterhooks of these fishing lines that will capture everything that is elephant-related," said Poinar. Since woolly mammoths are related to elephants, that's what stuck to their hooks. 

"That's the way [Murchie] managed to get rid of the 98 per cent of the bacteria and only pull up the less than two per cent, basically, that represented plants and animals." 

Poinar says this becomes a bit tricker with ancient species of pine or spruce that still exist in the nearby environment, but luckily, ancient DNA degrades in a predictable way, allowing them to tell ancient DNA from modern. 

"Imagine you have a sandwich with two loaves of bread, and the two loaves of bread represent your double-stranded DNA molecule. And what happens in the ancient DNA is the edges, so the crusts of that bread sort of peel away from each other over time," said Poinar.

The ancient DNA scientists from McMaster University extracted from soil samples are the first evidence of yaks living on the North American landscape thousands of years ago. (Kory Siegers/CBC)

Murchie said the first time he saw the readout of the ancient species present in the soil, he saw so many plant species, he thought he'd made a mistake. 

"It was overwhelming at first and nerve-racking, but then also it was this really profound sense of like, 'Oh, I really did it. Like, this worked.'"

One big surprise in the study was finding DNA from animals like the yak, whose remains have never been found in North America.

I think that at the human scale, it allows a resolution that will change our understanding of the people of North America and South America.- Hendrik Poinar, McMaster University

Rewriting our understanding of the ancient past

Another surprising discovery they made is the presence of pine trees in the far north approximately 9,600 years ago, which Poinar said means the boreal forest was expanding much more quickly than the pollen records suggest.

"One of the big, big purposes of this kind of work is really trying to understand how these environments respond to climate," said Poinar.

He said one of the reasons scientists thought woolly mammoths went extinct is because the boreal forests pushed out the open tundra landscapes, which these big herbivores relied upon.

Scientists can now identify long-extinct species, like the woolly mammoth, from ancient DNA in soil. This woolly mammoth skull, discovered at a Klondike mining property, is about 1.5 metres long and about one metre wide. (Grant Zazula/Government of Yukon)

"So I think this kind of movement of both pine — as well as birch, shrub, tundra and grasses, and willow — show a rapidly changing environmental biome that played a huge role in extinction." 

Poinar says this technique also has enormous potential for understanding human history as well — in particular our migration into the Americas. 

"I think that at the human scale, it allows a resolution that will change our understanding of the people of North America and South America."

Produced and written by Sonya Buyting

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