2-million-year-old DNA reveals surprising Arctic ecosystem | NOVA

Some 2 million years ago, the high Arctic was a much warmer, greener place—greener than many places on Earth are today. Paleontologists have found evidence of lush forests home to bears, beavers, and camel-like creatures in extreme northern latitudes.

But such fossil evidence is hard to come by, as the most recent Ice Age brought glaciers that repeatedly scoured the land clean, in some cases down to the bare rock. “For many years, people did not bother very much with places like northern Canada or northern Greenland, because you couldn’t expect to find very much,” says Ross MacPhee, senior curator at the American Museum of Natural History and expert in Ice Age mammals. “We only had our dreams and our imagination.”

Until now. In a study published today in the journal Nature, a team of scientists led by Eske Willerslev and Kurt H. Kjær of the University of Copenhagen reveals their remarkable feat: retrieving and analyzing 2 million-year-old DNA, pushing back the record by at least a million years. The DNA, retrieved from sediment cores at the northern edge of Greenland, reveals stunning information about the plants and animals that once inhabited the area: a blend of Arctic and temperate species unlike anything that exists today.  

The finding, experts say, could not only revolutionize paleontology, opening new windows onto ancient worlds, but also help us better understand how species adapted to a warming world in the past. “It’s as though we really do have a time machine in a way that we never expected,” MacPhee says.

Retrieving the oldest DNA

Though it may not be obvious, living organisms are always shedding DNA, sloughing it off in unneeded cells such as in skin flakes or dead leaves and excreting it in urine or feces. That DNA sticks around and, depending on the environment, can remain fairly intact for millenia. Over the past few decades, the study of this environmental DNA, or eDNA, has taken off. Scientists can now extract DNA from samples of soil, water, or air to understand what organisms live there currently or were present in the past. 

For their polar research, Willerslev and his colleagues analyzed DNA from 41 samples taken from a handful of sites in the Kap København formation in Greenland. They transported the cores to special “clean” labs that had been cleansed as much as possible of errant DNA from modern day microbes and the lab workers themselves.

Conventional wisdom, including predictions from Willerslev himself, held that DNA could only survive a few hundred thousand years, a million at most. But that prediction was based on how DNA behaves in liquid. This DNA had survived amazingly long, Willerslev explains, because it had become bonded to the clay, quartz, and other particles within the sediment. DNA carries a very slight electric charge, as do clay and quartz. That meant that, over time, the damaged bits of DNA got stuck to the minerals through electrostatic charge, which protected them from further damage and digestion by enzymes. But ironically, the very thing that made them so long lived also made them difficult to retrieve. Through more than a decade of trial and error, Willerslev and his team came up with increasingly targeted methods for getting the sediments to “release” the DNA stuck to them. 

Oldest DNA Ever Found Reveals Secrets of the Ancient Arctic:

Tom Gilbert, a geneticist at the University of Copenhagen who did not participate in the study, compares the process to getting burnt food off a pan. “You add detergent, and it basically breaks up the binding,” he says.

The next challenge was the sheer amount of DNA to sort through and the tiny size of the snippets they had gathered. eDNA researchers have historically used a process called “metabarcoding,” which searches for the chloroplasts or mitochondrial DNA from within a DNA soup, allowing them to focus on plants and animals but not the abundant bacteria. They then check the results against a huge library of known DNA sequences to identify specific species. Gilbert compares the process to hunting through a pile of ripped up pages trying to figure out what kind of books they come from. Metabarcoding would automatically identify and provide millions of copies of any title pages, so they’re much easier to find.

But that process would not have been practical for use in looking at the DNA of a whole ecosystem—and it also required longer DNA snippets than Willerslev’s team was finding. Instead, they used a newer technique known as “shotgun sequencing.” If metabarcoding is making copies of a few select pages in the pile, shotgun sequencing makes copies of every page of every book in a much larger pile in parallel, Gilbert says. Researchers can then compare them to that same library of every known DNA sequence. This process allows them to identify organisms using much shorter fragments. But it can be extremely expensive, in part because, as Willerslev points out, the vast majority of DNA in any soil is microorganisms. A lot of computing power in this process goes toward sorting through and discarding bacterial DNA. 

After years of work, and some 17 billion DNA fragments analyzed, the results were dramatic.

Willerslev and his colleagues were able to identify 102 plant genera in an area where paleontologists had previously identified only eight. And they pinpointed nine animal taxa where previous researchers had only found insects and a hare’s tooth. “We knew they had to be there, but this is science, right?” MacPhee says. “We had to get the empirical evidence.”

Filling in an “enormous blank”

Today, Kap København is a “wasteland,” Willerslev says. “It looks like you are in the Sahara, basically,” a polar desert slung with gray dunes and spotted with the occasional lichen or clump of moss. The findings begin to fill in what MacPhee refers to as “the enormous blank” in northern North America, painting a picture in unprecedented detail. Where now there is only desert, a lush forest once grew by the mouth of a river that emptied into a broad sea. Reindeer and hares grazed by the riverbank; geese flew overhead; mastodons crashed through the underbrush. 

Many of these animals’ modern counterparts have never been found so far north: caribou and mastodon were thought to be limited to more southern forests, while today horseshoe crabs thrive in much warmer water than now flows through the Arctic. Some 39% of the plant groups detected no longer grow in Greenland—and, perhaps even more unusually, they would have had to somehow survive half the year in polar darkness. (One hypothesis suggests that this is the origin of deciduousness: that trees evolved to lose their leaves to better protect themselves in these months of twenty-four hour darkness.)

In these forests, groups of plants we think of as more typically “Arctic” today also co-existed with trees better suited for warmer climes such as cedars, Willerslev says, in an ecosystem that exists nowhere on Earth today. This finding in particular shows that these communities’ capacity to adapt to a warming climate “is much greater than what we thought,” he adds, with these strange bedfellows representing a potentially positive harbinger in our warming world. 

But drawing conclusions from ancient genetic material isn’t simple. That’s partly because identifying mystery DNA requires matching that unknown sequence to a library of known sequences. What happens when the DNA is so old that the information it provides is limited or it’s from ancient creatures without a modern analogue? In the case of the mastodon Willerslev and his colleagues found evidence for at Kap København, the recovered DNA snippets may be too short to make such a positive identification, MacPhee says. For example, he wouldn’t rule out the possibility that that DNA could belong to another elephant-like creature such as a gomphothere, the mastadon’s often-forgotten cousin.

Paleobiologist Natalia Rybczynski of the Canadian Museum of Nature agrees, adding that it’s important to remember that any DNA sequencing effort is limited by its set of references. This research drew on a pre-existing DNA library of Pleistocene and modern animals—and that may not have included a gomphothere. At her own Arctic research site she and her colleagues identified a creature she terms a “very strange deer” from 20 million years ago. “Given what they have as their library to work with, they wouldn’t necessarily be able to pick up that deer,” she says. “It would be invisible.” 

Another challenge is the precision of dating. DNA itself can’t be dated the way carbon-based materials often are, making dating of the surrounding materials essential—and that is difficult to do precisely. A sediment layer is a “snapshot that might encompass a very large time period,” Gilbert says, depending on how it formed. An inch of soil can represent anywhere from a year to 10,000 years. In fact, Rybczynski wonders if some of the DNA might be significantly older than 2 million years. That’s really a “minimum age,” she says, based on the plant diversity and the site’s similarity to Pliocene-age areas she’s studied.

Willerslev points out that the samples did not turn up any carnivore DNA, indicating that the picture is still incomplete. Indeed, eDNA struggles to demonstrate what’s known in ecology as “relative abundance”—whether many mastodons or just one lived at Kap København; if there were more reindeer than mastodons, more hares than reindeer. If an elephant urinates tens of liters a day, its mastodon (or gomphothere) ancestor might have done similarly, Gilbert says. “Now, think about how much urine a mouse makes.” eDNA research can’t fix that imbalance.

The future of paleontology? 

MacPhee sees the Kap København findings not just as new data about the Arctic but also as representing a potential sea change for paleontology. Until now, he and his fellow paleontologists would go out on digs to look for “macrofossils,” such as bones and teeth, perhaps deriving clues about their ecological context based on lengthy, meticulous work. In contrast, the huge volumes of information that “nanofossils” like ancient DNA can provide in areas where there appear to be no fossil record is “mind blowing,” he says. “It’s really the most remarkable new thing since I’ve been working in this area.” He goes so far as to predict that his successors at the Museum of Natural History will all be versed in molecular biology, hopping between areas with promising sediment to explore our planet’s past.

This technique “opens up a whole new world for us,” Rybczynski says. But she sees a continuing role for traditional paleontology. Environmental DNA can tell us that caribou lived at a site, she says, but not what it ate or what it looked like—information that fossils like its bones, skull, and teeth would show. “These are really parallel lines of evidence,” she says, “and we want to work them together to develop a fuller picture of what it was like in the far north.”

In a catch-22, the clay that so wonderfully preserved the Kap København DNA also makes it difficult to access, meaning Willerslev and his team had to leave quite a bit unsequenced. “If we become better at releasing the DNA, it also means that we may most likely be able to go much further back in time,” he says.

For Gilbert, the most exciting next stop would be Antarctica, which is much colder than Greenland and which was last free of ice longer ago than Kap København. He too expects much older DNA to come. “Who knows what will be down there?” he says. “If you can go back far enough, you might find some very, very interesting things.”

Willerslev and Rybczynski also see an unusual opportunity to trace evolution directly. Even researchers studying good-quality macrofossil records can struggle to find the evolutionary connections between organisms, Rybczynski says. She points to elephants and elephant shrews, which look very different but share a common ancestor, as one example. Using the Kap København techniques, researchers could track changes in species’ genomes directly.

And MacPhee envisions a new generation of paleontologists, building a worldwide picture of ancient ecosystems brick by brick—even in places that aren’t as cold, dry, or undisturbed. Even now, researchers are collecting material from much warmer parts of Central America, South America, and Africa, he says. “It’s a brave new world, and a heck of an interesting one.”