Two million years ago, northern Greenland had lush landscapes instead of a polar desert like today. Now researchers have found DNA from that time from many different creatures. The genome is a million years older than the oldest found in frozen mammoth bones in Siberia’s permafrost. The mini snippets come from animals, plants and microorganisms, including reindeer, rabbits, lemmings, geese, birches and poplars. The scientists hope that special genetic adaptations of the proven plants can be used to make today’s species more resistant to the current climate change.
Genetic traces of living beings can be found everywhere in the environment: they come from fallen hair and feathers, dander, faeces, pollen and many other things. In water and soil samples, the various animal species in the area can be identified solely from the DNA traces contained in them. One speaks of environmental DNA, also called eDNA – “e” from the English word “environmental”, “from the environment”. Under certain conditions, ancient environmental DNA can also be tracked down and examined, especially in permanently frozen sediment.
For the first time, DNA from a past ecosystem can now be viewed directly so far back in time, says study leader Eske Willerslev of the University of Cambridge. “DNA can decompose quickly, but we have shown that given the right circumstances, we can go further back in time than anyone could ever have imagined,” explains co-author Kurt Kjær from the University of Copenhagen. The environmental DNA was found buried deep in sediments that took 20,000 years to form. “The sediment eventually became conserved in ice or permafrost and, crucially, was not disturbed by humans for two million years.”
The success was made possible by a new generation of devices for DNA processing and decoding, as the team led by Willerslev and Kjær reported in the journal Nature. The microscopic DNA fragments, measuring just a few millionths of a millimetre, were found in Ice Age sediments in northern Greenland. They come from the Cape København Formation, a nearly 100 meter thick sedimentary deposit in the mouth of a fjord in the Arctic Ocean at Greenland’s northernmost point. The climate in Greenland then fluctuated between arctic and temperate and was 10 to 17 degrees warmer than today. The ecosystem was an open, so-called boreal forest with a mixed vegetation of poplar, birch and thuja trees as well as a variety of shrubs and herbs.
Some of the DNA fragments could easily be assigned to ancestors of modern species, others could only be assigned to a larger species group – and for some no match could be found in today’s DNA libraries. The scientists also found that the mastodon, a Ice Age mammal, once migrated as far as Greenland before becoming extinct. So far it has been assumed that the distribution area of the elephant-like animals did not extend from their areas of origin in North and Central America to Greenland.
The late Pliocene and early Pleistocene epochs, 3.6 to 0.8 million years ago, had a climate similar to that projected for future warming, the study says. The researchers hope their findings could help predict the long-term environmental consequences of ongoing global warming.
The data obtained in Greenland suggested that more species are able to evolve and adapt to sharply fluctuating temperatures than previously thought, says co-author Mikkel Pedersen from the University of Copenhagen. However, it is crucial that the results also show that they need time for this. “The rate of global warming today means organisms and species do not have that time, so the climate emergency remains a huge threat to biodiversity and the world – extinctions of some species, including plants and trees, are imminent.”
In the future, the researchers also want to use the genetic data to draw conclusions about the interaction with bacteria and other microorganisms in the former landscapes. They also hope that analyzes in much warmer regions will also be possible.
DNA generally survives best in cold, dry conditions, which prevailed for most of the time the material was deposited at Cape København, Willerslev explained. However, it is possible that ancient DNA was also preserved in clay in warm, humid environments, for example at sites in Africa. “If we can start studying ancient DNA in clay grains from Africa, we may be able to gather groundbreaking information about the origins of many different species, perhaps even new insights into early humans and their ancestors.” The possibilities are endless.”
Henrik Krehenwinkel from the University of Trier, who was not involved in the analysis himself, also believes that further “revolutionary new insights” are very possible. The successes achieved so far are primarily based on the major advances in sequencing technology, with which genetic material can be deciphered more and more quickly and cheaply. An end to the technical development is not foreseeable. Krehenwinkel does not see a time limit either. “Around ten years ago, experts still thought that it was not possible to go back much more than 100,000 years. Now we are at two million.”
“If the conditions are right, DNA can be very stable,” explains the Trier environmental scientist. Permafrost is ideal because the molecule then hardly degrades chemically and because no microbes are active that would decompose the DNA very quickly. If it were actually possible, as suggested by Willerslev, to find and decipher ancient DNA in the tropics as well, this would offer immense potential for evolutionary insights. “Biodiversity has always been huge in tropical areas and many species, including humans, have evolved in such regions,” says Krehenwinkel.
Environmental DNA has been used by scientists for a long time for analyses, but so far mainly for those on the current status. Years ago, for example, an eDNA study was used to observe the arrival of numerous marine migratory fish in New York waters – simply by analyzing regularly taken water samples. Such environmental DNA studies simplified and accelerated the monitoring of animal species considerably, the researchers wrote in the journal Plos One at the time.
Whale sharks in the world’s oceans can be detected in this way, as can invasive species or certain pathogens in lakes and rivers, without animals having to be caught or killed. Researchers led by Henrik Krehenwinkel have developed a method for extracting and evaluating genetic traces of insects from dried plants. Accordingly, DNA from up to 400 different insect species can be found in a single commercially available tea bag.
When a bee flies to a flower to pollinate, it leaves behind some saliva. A bug stings a leaf, a spider leaves silken threads. According to Krehenwinkel, this is enough to detect the DNA of the insects. The method presented in June in the specialist journal “Biological Letters” therefore opens up the possibility of analyzing old plant populations, for example from museums, and comparing their colonization with today’s.
“From this it is possible to deduce changes in species composition,” explains the Trier scientist. This is important, for example, for analyzes of insect decline, for which there is a lack of other data. A team led by Krehenwinkel used environmental DNA from leaf material archived for decades, for example, to investigate changes in the community of insect species and other arthropods living on it – several thousand species in total. The living communities have become more and more homogeneous in terms of time and space, according to the result.
The greatest challenge when analyzing environmental DNA is avoiding contamination, as Krehenwinkel says. Snippets of genetic material from the environment found their way into the analyzed sample extremely easily and falsified the result. A further problem, especially with traces deposited over long periods of time, is finding the comparatively rare species, such as those of a mastodon, among the snippets of frequently occurring species, such as those of microorganisms. “In order to identify such rare traces among the many others, you have to sequence vast amounts of DNA snippets.”
Ideally, with enough throughput, the entire genome of a species can even be assembled from the countless deciphered snippets. The analysis of the much more sensitive environmental RNA offers even more potential, adds Krehenwinkel. “Environmental RNA is still a very young topic.” It indicates which sections of the genome of the respective living organism are currently active. With a water sample, for example, it might be possible to check whether a fish population is currently under stress.
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