DNA recovered from Arctic lakes holds clues for our future world

SAN FRANCISCO, CALIFORNIA—High in the Canadian Arctic on Baffin Island, beneath 10 meters of water and many more of mud, sits a refrigerated archive of Earth’s past life. The deep sediments in a small lake called CF8 hold ancient pollen and plant fossils. But it now appears that the mud harbors something else: ancient DNA from as far back as the Eemian, a period 125,000 years ago when the Arctic was warmer than today, left by vegetation that otherwise would have vanished without a trace.

“We feel confident that we are getting authentic results,” says Sarah Crump, a paleoclimatologist at the University of Colorado in Boulder who is presenting the work here this week at the annual meeting of the American Geophysical Union. She acknowledges the finding needs to be confirmed. But if it holds up, it could open a window on the ecosystems that flourished in the high Arctic at a time when temperatures were a few degrees warmer than today. It would also attest to the power of sedimentary DNA, as it’s called, to show how Arctic plants responded to past climate shifts—hinting at how they might respond in the future. “We are now at the point that this is a really useful signal for reconstructing biodiversity,” says Ulrike Herzschuh, a paleoecologist at the Alfred Wegener Institute in Potsdam, Germany, who uses the technique to study how the larch forests of Siberia in Russia reacted after the end of the last ice age some 12,000 years ago.

Although the search for bits of DNA preserved in sediments began 2 decades ago, it has taken off in the past few years as the cost of genetic sequencing has plummeted. Because cold temperatures help preserve DNA, the Arctic has been a prime hunting ground, drawing geneticists and geoscientists to sample permafrost, cave soils, and other settings, looking for molecular clues to the giant ice age animals that once roamed there.

Lately, Arctic lakes have emerged as the premier archive for sedimentary ancient DNA, because they collect clues to entire ecosystems. Leaves, flowers, dung—some part of every organism that lives around a lake ends up in the water. “You’ve got an incredibly complicated mixture of DNA there,” says Peter Heintzman, a molecular paleobiologist at the Arctic University of Norway (UiT) in Tromsø. DNA is sprung from its cells by decay, then attaches to mineral grains or organic compounds, which provide protection from ultraviolet radiation and oxidation. Temperatures at the lake bottom hover just above freezing, keeping the DNA stable. And year after year, the sediment keeps accumulating, its layers allowing clear dating of the DNA’s deposition.

Traditionally scientists have used pollen grains from lakebed cores to study past plant communities. But most plants in the Arctic are pollinated by insects, not by wind, so that little pollen ends up in the soil—and what’s there could have blown in from a distance. DNA in lake sediments more accurately reflects the plants and wildlife found nearby. For example, in a study published last month in Global Change Biology, Crump and others used ancient DNA to show that, after the planet warmed following the last ice age, dwarf birch arrived on Baffin Island some 2000 years later than researchers had concluded from pollen. “The pollen records are a bit biased,” Crump says, “leading us to believe migration was rapid, when it was in fact slower and inhibited by migration barriers.”

It’s not easy to extract the DNA. Scientists must be careful to collect a sample—typically 1 gram of mud—without contaminating it with modern DNA. Then, in a clean lab, the DNA must be extracted in a painstaking process of trial and error. “There’s not the most efficient way of pulling this stuff out,” says Beth Shapiro, an evolutionary biologist at the University of California, Santa Cruz. Organic-rich soils seem particularly problematic; they are ripe with molecules like humic acid, which behaves like DNA and can foul later sequencing.

To identify plant species in the resulting mélange of DNA—most of which comes from microbes—researchers often turn to metabarcoding, a technique that targets and amplifies a section of DNA that’s nearly universal in plants but is bracketed by sections that are distinctive to species. Other researchers simply sequence all the DNA in a sample and sift through the result for genetic gold or use genetic probes that can capture even short strands of plant DNA. But existing databases of plant sequences aren’t always reliable enough to identify the species in the sediment. “There were a lot of erroneous sequences uploaded,” says Inger Alsos, a paleobotanist at UiT.

To get around that problem, Alsos and her peers have almost finished creating a full genome reference library for Arctic plants, called PhyloNorway, that contains some 2000 species. (A similar effort for the Alps describes 4000 species.) Armed with these improved databases, Alsos and her collaborators are sampling more than three dozen lakes in northern Norway and the Alps, studying how shrubs spread across what had been tundra as the last ice age ended. Another European project, called Future Arctic Ecosystems, will examine a dozen lake cores from the continents ringing the Arctic, studying the dual roles played by climate and large herbivores, such as mammoths, in shaping past plant populations. Other researchers are sampling lakes in southeastern Tibet in China or the Tetons in Wyoming—anywhere cold where DNA could endure.

Early results challenge the simple notion that climate change triggers a wholesale turnover of plant species. “This is very often nonsense,” Herzschuh says. Take the Siberian larch forests she studies. Herzschuh found that certain larch species did not shift northward as the planet warmed after the last ice age, despite preferring a colder climate. Instead, she suggests, warming allowed the forest to grow denser, which favored a cold-loving larch. Alsos is studying a core from Lake Bolshoye Shchuchye, at the northern end of Russia’s Ural Mountains, that tells a related story. The DNA suggests taller plants invaded as the region warmed: first shrubs, then trees. But Arctic flowers persisted, perhaps by retreating uphill.

Future warming, however, may dislodge—or extirpate—these holdouts. For clues to the fate of ecosystems in an even warmer climate, researchers hope to find other ancient DNA records that stretch back to the Eemian. Herzschuh is hopeful: Her oldest Siberian record goes back 70,000 years so far, and DNA at its bottom is as well-preserved as at the top. “We do not see a clear decaying signal somewhere,” she says.

And as the lakes yield even older records, the field is inching toward studying not only the changes in plant diversity and abundance, but also how individual species adapted to climate change, Herzschuh adds. “We are not so far from tracing evolution through time.”