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Lost world in northern Greenland conjured from DNA in ancient soil

In a bleak valley not far from Greenland’s massive ice sheet, scientists have reconstructed a rich ancient ecosystem, down to its roving mastodons and smooth-barked birch trees. The clues come from the oldest DNA ever recovered: 2-million-year-old snippets of genetic material from more than 100 kinds of animals and plants, extracted from buried sediments. The feat may provide a window into how life will evolve in our warming world and perhaps even allow scientists to resurrect long-lost genes to help modern species cope with climate change.

“It’s a tour de force. Simply astounding,” says Ross MacPhee, a paleontologist at the American Museum of Natural History who was not involved with the work, which appears today in Nature. “The idea that we can now recover these really short fragments of DNA and make sense of them is pretty exciting,” adds Beth Shapiro, an ancient DNA expert at the University of California, Santa Cruz, also not involved. “We can now extend further back in time than we thought was possible.”

The findings demonstrate the power of environmental DNA (eDNA)—genetic material extracted not from individual organisms, but from the environment—to reconstruct entire ecosystems: in this case, a coastal forest including poplars, thujas, and other conifers that no longer grow in Greenland, plus reindeer, lemmings, black geese, horseshoe crabs, and mastodons. “No one would have predicted an ecosystem like this. Some species you find further south in Greenland, but a number you don’t find in the Arctic at all,” says Eske Willerslev, a paleogeneticist at the University of Cambridge who led the 40-person team behind the findings. “It’s an ecosystem with no analog in the present day.”

Another surprise is that DNA—a fragile organic molecule—can stay intact for so long. Quartz and clay in the soil played a crucial role: The charged surfaces of the minerals captured the DNA and protected it from degrading enzymes and oxidizing agents, says study co-author Karina Sand, a geochemist at the Lundbeck Foundation GeoGenetics Centre at the University of Copenhagen. The onset of the ice ages—the Pleistocene Epoch—about 2.5 million years ago helped by keeping the DNA frozen to the present day.

That such a lush ecosystem could exist a half-million years into the Pleistocene suggests Greenland hadn’t yet fully glaciated, or the ecosystem arose during a warm interglacial period. Or, the recovered DNA may predate the Pleistocene—a possibility because the team opted for the most conservative interpretation of the site’s dating, Willerslev says.

Willerslev first thought of looking for ancient eDNA in 2000, as he was embarking on his Ph.D. in Copenhagen. He was idly looking out his apartment window, when “I saw a dog taking a crap on the street,” he says. He suggested to his Ph.D. supervisor that DNA from excrement and other organic material might persist in soil for thousands of years. “He just laughed. He said, ‘I never heard anything so stupid in my life.’”

Undeterred, Willerslev spent the next 2 years honing methods to extract DNA from permafrost. In December 2002, he hit literal paydirt, prying from Siberian soil the genetic remains ice age mammoths, musk ox, and all sorts of plants. The following year, his team extracted eDNA from ice cores near bedrock under the Greenland Ice Sheet, revealing a forest that existed there about 400,000 years ago.

It took ancient DNA pioneer Eske Willerslev and his team 15 years to succeed in prizing out of northern Greenland genetic secrets from the onset of the ice ages.NOVA, HHMI Tangled Bank Studios & Handful of Films

In the new work, Willerslev’s group turned to much older samples it had been collecting from northern Greenland since 2006. The researchers focused on the Kap København Formation, a sediment deposit nearly 100 meters thick that’s tucked in the mouth of a fjord. Discovered in 1978, the site’s sediments are thought to have accumulated during a 20,000-year period.

Today, the Kap København deposit is replete with petrified stumps and other remnants of an ancient boreal forest, but just one vertebrate fossil has ever been uncovered there: a hare’s tooth. Willerslev figured the soil must hold traces of other creatures, yet his team could not extract readable DNA from it. “We failed and failed and failed,” he says.

A breakthrough came after Sand realized DNA could stick to minerals in the sediments. “Karina was instrumental in breaking the Kap København curse,” Willerslev says. She and colleagues learned how to liberate nearly half the DNA bound to quartz—and much less of that bound to clay—in 41 sediment samples. They sequenced the extracted DNA in many short stretches and screened nearly 3 billion of these “reads” against libraries of living species.

Decipherable DNA belonged to 102 different plant genera. Some are familiar today, but a few dozen no longer exist in Greenland. Of the handful of animals identified, the mastodon “blew our mind,” says study co-author Mikkel Pedersen, a geoarchaeologist at the GeoGenetics Centre. No one expected the range of the extinct relative of elephants to extend that far north, he says.

Eske Willerslev and a colleague sample ancient sediments in Greenland for environmental DNA.NOVA, HHMI Tangled Bank Studios & Handful of Films

Paleoclimate studies suggest that when this ecosystem existed, Kap København’s temperatures were about 10°C higher, on average, then they are today. An eDNA window onto a balmier epoch may offer a preview of what climate change has in store for the high Arctic—and perhaps point to genetic adaptations that will allow species to thrive as their habitat warms.

Willerslev ventures that such genes could someday be plucked out of ancient genomes and, using CRISPR gene editing, stitched into present-day life forms. The borrowed genes might, for example, help crops germinate earlier during the high Arctic’s fleeting summers. “We could help evolution on its way,” Willerslev says.

For now, he’s satisfied with exploring the past. “We’ve shown that under the right circumstances, we can now go back further in time than anyone could have dared imagine,” Willerslev says. He expects to probe even deeper into the past—at this and other sites—as he and his colleagues continue to refine their methods.

That thrills Natalia Rybczynski, a paleontologist at the Canadian Museum of Nature. Still, she says, the further back in time paleogeneticists delve, the harder it will be to identify extinct life forms—especially those from dead-end lineages whose genomes likely bear scant resemblance to those of contemporary species. Indeed, Pedersen says, some of the Kap København eDNA “is a black box,” representing extinct creatures with only distant modern relatives.

As ancient DNA experts become more adept at summoning life forms from that black box, MacPhee says, “It’s possible to see a future in which what we now call paleontology all happens in a molecular biology lab.”

Source: Science Mag