As early as 2006, Eske Willerslev and members of her lab ventured into northern Greenland with a drill rig to extract sediment cores from the Kap København formation. They were looking for environmental DNA (eDNA), which makes it possible to estimate the biodiversity of an ecosystem in order to draw a portrait of the plants and animals present in the region two million years ago.
But for a long time they were left empty-handed. ” Every time we had improvements in terms of DNA extraction or sequencing technology, we re-examined these samples ,” says Eske Willerslev, an evolutionary geneticist at the University of Cambridge. Despite their efforts, the researchers did not achieve the desired result. So much so that they came to speak humorously of a ” curse of the formation of Kap København “.
But thanks to constant improvements in DNA extraction and sequencing technologies, the spell has been broken.
The team has just published the results of its 16 years of research on this prehistoric DNA in the journal Nature . They were able to sequence environmental DNA from 41 sediment samples that were 2 million years old and undisturbed by humans, collected in 2006, 2012 and 2016 from the Kap København formation. Their analyzes revealed that a lush forest teeming with reindeer, hares, mastodons and a wide variety of vegetation once stood in what is now a dull gray polar desert. For Eske Willerslev, a pioneering geneticist who had previously recovered environmental DNA from ice cores, considers this ” breakthrough is based on expertise, progress in genetic sequencing techniques and bioinformatics.
The floor is a storybook
DNA is not a particularly robust molecule. The bonds that hold it together are fragile and, over time, they degrade. This is why even though we have an abundance of dinosaur fossils, we don’t have DNA. Indeed, these animals died out 66 million years ago, and the DNA simply wouldn’t have survived that long.
As DNA degrades, its once-long strands of information break into smaller and smaller pieces. It becomes almost impossible to put these fragments back together in the correct configuration, especially if they are mixed with a lot of other DNA from the environment.
But under certain circumstances, DNA fragments can survive for a long time. The “ survival time of DNA in the environment is incredibly variable and highly dependent on the environment itself ,” notes Michael Knapp, ecologist and geneticist at the University of Otago in New Zealand.
Previously, the oldest DNA ever recovered came from mammoth fossils discovered in Siberian permafrost. In a 2021 paper in Nature , researchers showed that DNA from mammoth teeth was potentially around 1.6 million years old. The recovered DNA was broken into small fragments, but it was not degraded to the point that it could not be put back together. The extremely low temperature of the permafrost has certainly contributed to this conservation.
Eske Willerslev and co-workers speculate that the long survival time of DNA in their sediment cores was possible for two reasons. The first is the constant cold temperature of the polar desert. The second is the way DNA is bound to minerals in carrots, which prevents its degradation over longer time scales. The idea is that these mineral surfaces prevent enzymes from breaking down DNA.
Karina Sand, geochemist at the University of Copenhagen and co-author of the article, explains that one of the technological leaps that enabled this feat was the extraction of DNA from clay and quartz minerals. The latter provide abundant DNA, but it is more difficult to extract good DNA from the former. ” If we can get better at extracting DNA from clay minerals, we think we can go further back in time with DNA ,” she said.
The research team was able to extract DNA from the sediment cores and began reading the fragments. These were then compared to a database of genomes (complete DNA sequences) of modern plants and animals, looking for DNA matches. Little by little, they were able to reconstitute the rich ecosystem of ancient Greenland.
The ancient forest of Greenland
Two million years ago, Greenland was a totally different place.
“ The Kap København ecosystem, which has no current equivalent, existed at temperatures considerably higher than those we experience today ,” notes Mikkel Pederson, a geneticist at the Lundbeck Foundation Center for Geogenetics.
In northern Greenland, average temperatures at that time were probably more than 11 degrees Celsius higher than today. Previous studies at Kap København have shown it to be a boreal forest, but the environmental DNA extracted and analyzed in the new study paints a full picture of the region, adding megafauna and a wide variety of plants.
The most famous mammalian DNA found in carrots is undoubtedly the mastodon. It belonged to the family Elephantidae , which includes elephants, mammoths, and mastodons. One might assume that mastodons may have roamed Greenland 2 million years ago, but the researchers note that the evidence is not extremely strong and is based on relatively weak DNA matches.
The team also found DNA linked to reindeer, hares and rabbits, as well as a subfamily of animals that includes lemmings, voles and muskrats. In contrast, carnivore DNA is conspicuously absent. Researchers suggest this is due to their comparatively low biomass compared to herbivores.
One of the most intriguing DNA discoveries involves the Atlantic horseshoe crab. This species no longer occurs at such northern latitudes, which the authors say could mean that Kap København experienced higher sea surface temperatures 2 million years ago. Previous research has suggested that the sea surface is warmer at higher latitudes, and the discovery of horseshoe crab DNA lends further credence to this hypothesis.
Warmer temperatures are essential. Several authors of the article reiterated the importance of understanding an ecosystem like this, given the effects of global warming. Two million years ago the climate was changing and environmental DNA shows that arctic species lived with species that liked much warmer climates. This helps scientists understand how nature was adapting to these changes. In the DNA signatures may be hiding clues about how we could help modern flora and fauna survive extreme climate variations.
One of the important limitations of studying environmental DNA is that scientists must make assumptions about the types of species that lived at the time. Closely related ancient species may yield a DNA match, but this is still approximate. We may only be able to assign DNA to the level of a family or order, so we cannot know exactly what roamed the boreal forest of Greenland two million years ago. .
Even so, the recovery of such ancient DNA opens a new window into prehistoric Earth, a pathway for scientists and researchers to probe ecosystems that existed long before humans arrived. The team will travel to northern Canada next year to extract carrots and hope to go back even further in time.
This extraction method could even lend itself to DNA research in more humid climates around the world, such as Africa and Australia. ” If we can start exploring ancient DNA in the clay grains of Africa, we may be able to gather groundbreaking information about the origin of many different species – perhaps even new insights into early humans.” and their ancestors. The possibilities are endless ,” hopes Eske Willerslev.
