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A 2-Million-Year-Old Ecosystem in the Throes of Climate Change Revealed in Environmental DNA
The reconstruction of a once-living landscape in northern Greenland from 2 million years ago, deduced from bits of DNA bound to minerals, reveals an Ice Age ecosystem in the throes of climate change that may suggest ways to mitigate rising global temperatures today. The collection, analysis, and interpretation of environmental DNA from this distant time and place provides a “genetic roadmap” for how organisms can adapt to a warming climate. The work is the cover story in Nature this week. Six of the 40-member multinational team discussed the findings at a news conference.
Environmental DNA – eDNA – is used to describe habitats both ancient and contemporary. Until now, the oldest eDNA was from a mammoth that lived in Siberia one million years ago.
The eDNA in the new study came from the Kap København Formation in the “polar desert” of Peary Land, North Greenland. Environmental DNA joins fossils and preserved pollen to paint portraits of long-ago habitats. The eDNA is not contained in cells. Especially hardy is DNA from mitochondria and chloroplasts, which is more abundant than nuclear DNA because these organelles are present in multiple copies in a cell. It is also more likely to persist because it is more highly fragmented compared to DNA in a nucleus.
Eske Willerslev, team leader and geogeneticist from the University of Cambridge, compared fossil to eDNA evidence. “For a fossil, you know that the DNA is from one individual. With sediments you can reconstruct a genome, but you don’t know if the genome is coming from one or multiple individuals. However, a huge benefit of environmental DNA is that you can get DNA of organisms that are not fossilized, and you can see the whole ecosystem.” Environmental context is important, too. Consider fossils from an elephant and a plant a few miles away. Finding DNA in the two places is not as meaningful as finding the plant DNA in the elephant’s intestine.
“DNA can degrade quickly, but we’ve shown that under the right circumstances, we can go back further in time than anyone could have dared imagine, opening a new chapter spanning one million extra years of history. For the first time we can look directly at the DNA of a past ecosystem that far back in time,” Willerslev said.
The Discovery Site
The researchers collected 41 usable samples from clay and quartz at five sites, each piece of genetic material a mere millionths of a millimeter long.
“The ancient DNA samples were buried deep in sediment that had built up over 20,000 years in a shallow bay. The sediment was eventually preserved in ice or permafrost and, crucially, not disturbed by humans for two million years,” explained geologist Kurt Kjaer, from the University of Copenhagen.
The sediment, nearly 400 feet thick, accumulated in the mouth of a fjord jutting into the Arctic Ocean in Greenland’s northernmost point. The climate in Greenland two to three million years ago, as the planet was emerging from the Pleistocene Ice Age, for a time oscillated between Arctic and temperate. Temperatures reached 50 to 62 degrees Fahrenheit warmer than today.
Reading the Stories in eDNA
A trio of technological leaps made the work possible, Willerslev said :
• discovering how DNA binds to mineral particles
• a new sequencing platform that can handle small pieces of frayed DNA
• collecting the ancient genetic material. (A cool tool is the Arctic PaleoChip, which sounds like a diet ice cream.)
Karina Sand from the University of Copenhagen shared details of interrogating the DNA-mineral interface, which played a crucial part in the preservation. “Marine conditions favored DNA absorption to minerals, and it binds quite tightly, which prevented enzymatic degradation. All the minerals in the formation could adsorb DNA, but at different strengths than we knew.”
Binding of DNA to minerals wouldn’t have happened in open seawater, Sand said. The researchers scrutinized modern DNA binding to surfaces using atomic force microscopy, manipulating parameters to recreate what might have happened to the preserved bits of DNA in the ancient sediments of Greenland.
The researchers then compared the short eDNA sequences to DNA databases of modern species. Some samples matched distant contemporary relatives, while others yielded no hits. Timeframes are applied to ancient DNA using known mutation rates of certain DNA sequences.
Once the species identifications began arriving with approximate timestamps, the investigators were at first confused, related Mikkel Pedersen from the University of Copenhagen. “When I got the data, it seemed crazy, I didn’t understand the time stamp. We got taxa (taxonomic groups) of different terrestrial plants and animals, and suddenly marine species showed up! That was really odd. So I ran to Kurt’s office and said, ‘what did you give me? Marine taxa, or terrestrial?’ It was a sign that soil had washed into a marine environment.”
Flora and Fauna of the Ancient Ecosystem
The portrait of the ancient ecosystem was like a huge jigsaw puzzle with only a few pieces – from fossils, preserved pollen, and DNA, particularly from the hardy chloroplasts and mitochondria. From these scant clues, the team identified 102 types of plants, from algae to trees, at the genus level – resolution wasn’t high enough to distinguish species, said Pedersen. “We found 9 taxa of animals, which were the most abundant in the landscape at the time (to have left DNA), and lots of bacteria and fungi. Most likely the vast majority of plants and animals are not detectable due to their persistent (small) biomass,” he added.
Fossils and DNA from the southern part of the area indicate poplars, red cedars, and firs. “Plants were growing together in ways we wouldn’t see today. It was an open boreal forest, with poplar, willow, birch and thuja trees and a mix of Arctic and boreal shrubs and herbs,” said Pedersen.
Mastodons lived in the area, which was surprising because they were only known, from their fossils, from North and Central America. The new info was possible due to the huge animal’s copious dung, which bears traces of the DNA of its diet of trees and shrubs.
DNA also revealed Atlantic horseshoe crabs farther south in the Atlantic than they are today, suggesting warmer surface waters during the Pleistocene. Tiny bits of DNA also came from geese, hares, reindeer, lemmings, a coral reef builder, and an ant and flea species.
Setting the Scene
Until the DNA discovery, the only trace of a mammal was a piece of a tooth. Willerslev recounted the team’s reaction to their find:
“When we got to the area in 2006, for a different project, we didn’t see much. It was similar to the Sahara, almost no life. Lichens, mosses, that was about it. So it was super exciting when we recovered the DNA and a very different ecosystem appeared. People had known from macrofossils that there had been a forest, but DNA identified many more taxa. Pollen and macrofossils had identified some species, but environmental DNA identified 102 plants!
When we found DNA from a mastodon, an animal associated with North America, we thought it must have been swimming in Greenland and crossing the ice!
We also found reindeers. Surprising! That was expected to be a much younger species. Reindeer hairs and horseshoe crabs in a marine setting suggest a much warmer climate.
Imagine standing in the bay with rubber boots on, looking up, and seeing a forest and mastodon and reindeer running around, and a river washing towards you bringing sediments and deposits from the land. That’s why the DNA is a mix of terrestrial and marine organisms. At some point the land rose, so now the huge mountains are inland and not at the shoreline anymore.”
A caveat to the power of eDNA research is the role of abundance: DNA from a species with a small population likely won’t show up. And that’s why carnivores weren’t part of the Greenland scene, according to the evidence.
It’s a numbers game, said Willerslev. “The more biomass, the more DNA is left. Plants are more common than herbivores, which are more common than carnivores. But if we continue taking samples and sequencing DNA, I predict that at some point we will see evidence of carnivores, perhaps an animal that ate mastodons.” He added that there’s no evidence of bears, wolves, and saber-toothed tigers, familiar inhabitants of Pleistocene scenes.
A Genetic Roadmap
Is the slice of time revealed in Greenland a harbinger of what’s to come as the current climate warms? Likely not, said Willerslev, but that isn’t necessarily bad news:
“This ecosystem and its mix of arctic and temperate species has no modern counterpart. That suggests that our ability to predict biological consequences of climate change is pretty poor. No one would have predicted this ecosystem from the range of present-day species. But it shows that the plasticity of organisms is greater and more complex than we imagined.”
What we do have, Willerslev stressed, is a “genetic roadmap of clues, in the form of genes, to how organisms adapt to very fast climate change. But many of those adaptations were likely lost because over a long time, they didn’t provide a benefit. Now climate change is happening extremely fast and evolution can’t follow. We should expect large extinctions.”
But what if we use the information from studies such as the Greenland one to get ahead of the DNA changes that propel adaptation to environmental change? Can biotechnology step in? Perhaps.
“Genetic engineering could mimic the strategy plants and trees developed two million years ago to survive in a climate of rising temperatures, and prevent the extinction of some species,” said Kjaer.
Willerslev foresees such efforts focusing, at first, on plants. “The roadmap can give information on where and how to edit the genome of a plant to make it more resilient to climate change. The tools are there. It sounds drastic, and I’m not saying this is how it should be, but it opens up a new possibility to try to mitigate the impact of climate change.”
But for now, helping species survive may be a race against time, even though climate has changed before. Pedersen presents a more sobering look:
“The data suggest that more species can evolve and adapt to wildly varying temperatures than previously thought. But, crucially, these results show they need time to do this. The speed of today’s global warming means organisms and species do not have that time, so the climate emergency remains a huge threat to biodiversity. Extinction is on the horizon for some species.”