Oldest Known DNA Paints Picture of a Once-Lush Arctic

In the permafrost at the northern edge of Greenland, scientists have discovered the oldest known fragments of DNA, offering an extraordinary look at an extraordinary ancient ecosystem.

Thegenetic material dates back at least two million years — that’s nearly twice as old as the mammoth DNA in Siberia that held the previous record. And the samples, described on Wednesday in the journal Nature, came from more than 135 different species.

Together, they show that a region just 600 miles from the North Pole was once covered by a forest of poplar and birch trees inhabited by mastodons. The forests were also home to caribou and Arctic hares. And the warm coastal waters were filled with horseshoe crabs, a species that today cannot be found any farther north of Maine.

Independent experts hailed the study as a major advance.

“It feels almost magical to be able to infer such a complete picture of an ancient ecosystem from tiny fragments of preserved DNA,” said Beth Shapiro, a paleogeneticist at the University of California, Santa Cruz.

“I think it’s going to blow people’s minds,” said Andrew Christ, a geoscientist at the University of Vermont who studies the ancient Arctic. “It certainly did so for me.”

The discovery came after two decades of scientific gambles and frustrating setbacks.

One of the leaders of the project, Eske Willerslev, pioneered methods for pulling DNA out of sediment while he was a graduate student at the University of Copenhagen. In 2003, studying a chunk of Siberian permafrost, he and his colleagues found DNA from plants such as willow and daisies dating 400,000 years ago.

Kurt H. Kjær and Eske Willerslev dug for soil samples at the Kap København Formation.Credit…Svend Funder

That discovery set a record for the oldest DNA, and many scientists doubted it would be possible to find anything much older. But in 2006, Dr. Willerslev and Kurt Kjaer, a geoscientist at the University of Copenhagen, tried to defy the odds in northern Greenland. They made their way to a geological formation called Kap Kobenhavn, a series of bare hills as desolate as a moonscape. Previously, scientists had found plant fossils there that they estimated to be 2.4 million years old. Finding DNA in the sediments would have been astonishing.

“If you want to move things forward, you need to take some leaps,” Dr. Kjaer said.

The researchers dug up permafrost and brought it back to Copenhagen to search for DNA. They failed to find any.

In later years, Dr. Willerslev and his colleagues had more success when they examined younger sediments and bones from other parts of the world. They discovered a wealth of ancient human DNA that has helped reshape our understanding of our species’ history.

Along the way, the researchers tweaked their methods for extracting DNA from ancient samples and upgraded the machines they used to sequence it. As they became better at fishing for genes, they would take out more of the Kap Kobenhavn samples for another shot.

But for years they failed, again and again. From time to time they were tantalized by what looked like short bits of DNA, which are called reads. The researchers couldn’t rule out the possibility that bits of young DNA in Greenland, or even in their lab, had contaminated the reads.

Finally, after a major upgrade in their technology, they found DNA in the samples in 2017. The permafrost turned out to be loaded with genetic material. Before long they had collected millions of DNA fragments.

“It was a breakthrough,” Dr. Willerslev said. “It was going from nothing or very little that you don’t know is real, to suddenly: It’s there.”

The researchers lined up the fragments with DNA sequences of living species to figure out where they belonged on the evolutionary tree. They found 102 different kinds of plants — including 78 that had previously been identified from fossils and 24 new ones. The plant DNA painted a picture of forests dominated by poplar and birch trees.

Organic material in the coastal deposits, which showed traces of rich plant flora and insect fauna.Credit…Svend Funder

Other sequences come from land animals, including caribou, hares, mastodons, geese, lemmings and ants. The researchers also found marine species, such as horseshoe crabs, corals and algae.

“It superseded everything we imagined,” Dr. Kjaer said.

The researchers also searched the permafrost for new clues to the age of the fossils. They found layers in the sediment in which the minerals revealed that the Earth’s magnetic field had flipped. The age of those reversals helped the researchers determine that Kap Kobenhavn was at least two million years old, but they could not establish a clear upper limit. “My gut feeling as a geoscientist is that it’s older,” Dr. Kjaer said.

The researchers ruled out the possibility that the DNA came from younger species that contaminated the older permafrost. The DNA of the Kap Kobenhavn birch trees lacked many of the mutations that living species have, indicating that they were ancient. The DNA from Kap Kobenhavn also had a distinct pattern of damage that occurs only when the molecules have been sitting in sediment for geological stretches of time.

“It really helps show that this really is old DNA,” said Tyler Murchie, a postdoctoral researcher at McMaster University who was not involved in the new study.

The researchers were surprised by some of the species they found. Caribou live today in Greenland, as they do across much of the Arctic. But until now, their fossil record suggested they evolved a million years ago. Their DNA now doubles their evolutionary history.

Love Dalén, a paleogeneticist from Stockholm University who last year discovered mammoth DNA in Siberia that was 1.2 million years old, marveled that mastodons turned up in Greenland. “What the hell are they doing up there?” he asked.

Dr. Dalén noted that the nearest known mastodon fossils were 75,000-year-old remains in Nova Scotia — which are far younger than the Greenland DNA, and much farther south than Kap Kobenhavn. “You can’t go much further north on dry land,” he said.

A two-million-year-old trunk from a larch tree stuck in the permafrost within the coastal deposits. The tree was carried to the sea by the rivers that eroded the former forested landscape.Credit…Svend Funder

The Danish researchers determined that the mastodons in Greenland two million years ago belonged to a deep branch of the mastodon family tree, one that was previously unknown. “That could mean they are the ancestors of the late-Pleistocene mastodons that we know of, or that they could represent a new species,” Dr. Dalén said.

Ecologically, mastodons would fit in well in a poplar-birch forest in Greenland, as they did in North American woodlands. While caribou are most common on northern tundras, a subspecies lives in Canadian forests, offering clues to how the ancient caribou might have thrived. But the presence of horseshoe crabs in the shallow coastal waters suggests that the ocean and land alike were remarkably warm.

Dr. Willerslev and his colleagues are continuing to study the DNA for clues to how all these species were able to thrive a thousand miles north of the Arctic Circle. The trees, for example, had to survive half the year in darkness. The DNA preserved for two million years may hold their secrets of adaptation.

The scientists are also interested in how the DNA fragments managed to survive so long and defy expectations. Their research indicates that the DNA molecules can cling to minerals of feldspar and clay, which protect them from further damage.

Based on that discovery, the researchers are developing new methods that they hope will let them pull even more DNA out of ancient sediments. Dr. Kjaer and his colleagues are scouting four-million-year-old sites in Canada with the hope of breaking their own record.

Dr. Dalén said they might succeed. But the damage that both he and the Danish researchers are finding in the oldest DNA suggests to him that it will be impossible to find ancient genetic material older than about five million years. “This in no way suggests that there will be any DNA coming out of dinosaur-aged fossils,” he said.

Dr. Christ said that finding more DNA from places like Kap Kobenhavn may help them better understand how human-driven climate change will alter the Arctic. We should not assume, he said, that the region will resemble ecosystems in places farther south. After all, the ecosystem of Kap Kobenhavn two million years ago has no analog today.

“Life will adapt, but in ways we don’t expect,” Dr. Christ said.

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