Taxonomic profiles of the set of plants found in metagenomes. Taxa in bold are genera found only as DNA and not as macrofossil or pollen. Asterisks indicate those found at other Pliocene Arctic sites. Extinct species identified by macrofossils or phylogenetic placements are marked with a dagger. Reads classified as Pyrus and Malus are marked with a pound symbol and are likely overclassified DNA sequences belonging to another species within Rosaceae that are not present as the reference genome. — University of Cambridge
Two million-year-old DNA has been identified for the first time, opening a new “game-changing” chapter in the history of evolution.
Microscopic fragments of environmental DNA were found in Ice Age sediment in northern Greenland. Using cutting-edge technology, the researchers discovered that the fragments are a million years older than the previous record of DNA extracted from a Siberian mammoth bone.
Ancient DNA has been used to map a two-million-year-old ecosystem that withstood extreme climate change. The researchers hope the results can help predict the long-term environmental cost of current global warming.
The discovery was made by a team of scientists led by Professor Eske Willerslev and Professor Kurt H. Kjær. Professor Willerslev is a Fellow of St John’s College, University of Cambridge and Director of the Lundbeck Foundation Center for Geogenetics at the University of Copenhagen, where Professor Kjær, an expert in geology, is also based.
The results of the 41 usable samples found hidden in clay and quartz are published today (Dec. 7, 2022) in Nature.
Professor Willerslev said: “A new chapter spanning an extra million years of history has finally opened, and for the first time we can look directly at the DNA of an ecosystem from far back in time.
“DNA can degrade rapidly, but we’ve shown that under the right circumstances, we can now go further back in time than anyone could have imagined.”
Professor Kjær said: “The ancient DNA samples were found buried deep in sediment that had accumulated over 20,000 years. The sediment was eventually preserved in ice or permafrost and, crucially, was undisturbed by humans for two million years.
The incomplete samples, a few millionths of a millimeter long, were taken from the København Formation, a nearly 100-meter-thick deposit of sediment hidden in the mouth of a fjord in the Arctic Ocean at the most north of Greenland. Greenland’s climate then varied between arctic and temperate and was 10–17 °C warmer than present-day Greenland. The sediment accumulated meter by meter in a shallow bay.
Scientists discovered evidence of animals, plants and microorganisms, including reindeer, hares, lemmings, birches and poplars. Researchers even found that Mastodon, an Ice Age mammal, made it all the way to Greenland before later becoming extinct. The range of the elephant-like animals was previously thought not to extend as far as Greenland from their known origins in North and Central America.
Detective work by 40 researchers from Denmark, the UK, France, Sweden, Norway, the US and Germany revealed the secrets of the DNA fragments. The process was painstaking: first they had to establish whether there was DNA hidden in the clay and quartz, and if there was, could they successfully separate the DNA from the sediment for examination? The answer, finally, was yes. The researchers compared each piece of DNA to extensive DNA libraries collected from living animals, plants and microorganisms. A picture of the DNA of trees, shrubs, birds, animals and microorganisms began to emerge.
Some of the DNA fragments were easy to classify as predecessors of current species, others could only be linked at the genus level, and some originated from species impossible to place in DNA libraries of animals, plants and microorganisms still living in the 21st century. .
The two-million-year-old samples are also helping academics build a picture of a previously unknown stage in the evolution of the DNA of a number of species that still exist today.
Professor Kjær said: “Expeditions are expensive and many of the samples were taken in 2006, when the team was in Greenland for another project, and have been in storage since then.
“It wasn’t until a new generation of DNA extraction and sequencing equipment was developed that we were able to locate and identify extremely small, damaged fragments of DNA in sediment samples. It meant we were finally able to map an ecosystem of two million years.”
Assistant Professor Mikkel W. Pedersen, co-first author of the paper and also based at the Center for Geogenetics at the Lundbeck Foundation, said: “The Kap København ecosystem, which has no modern equivalent, existed at considerably higher temperatures than the ones we have today, and because, at first glance, the climate appears to have been similar to the climate we expect on our planet in the future due to global warming.
“One of the key factors here is how well species will be able to adapt to changing conditions resulting from a significant increase in temperature. The data suggest that more species can evolve and adapt to widely varying temperatures than previously thought. thought. But above all, these results show that they need time to do so. The speed of current global warming means that organisms and species do not have that time, so the climate emergency remains a major threat to to biodiversity and the world: Extinction is on the horizon for some species, including plants and trees.”
While sifting through ancient DNA from the Kap København Formation, the researchers also found DNA from a wide range of microorganisms, including bacteria and fungi, which they continue to map. Future research will present a detailed description of how the interaction between animals, plants and single-celled organisms worked biologically within the ancient ecosystem at the northernmost point of Greenland.
It is now hoped that some of the two-million-year-old plant DNA ‘tricks’ discovered could be used to help make some endangered species more resilient to a warming climate.
Professor Kjær said: “It is possible that genetic engineering could mimic the strategy developed by plants and trees two million years ago to survive in a climate characterized by rising temperatures and avoid the extinction of some species, plants and trees. This is one of the reasons why this scientific breakthrough is so significant because it could reveal how to try to counteract the devastating impact of global warming.”
The findings of the Kap København Formation in Greenland have opened a whole new era in DNA detection.
Professor Willerslev explained: “DNA generally survives best in cold, dry conditions, such as those that prevailed for most of the period since the material was deposited at Kap København. Now that we have successfully extracted the Ancient DNA from clay and quartz, clay may have preserved ancient DNA in hot, humid environments in places in Africa.
“If we can begin to explore the ancient DNA in clay grains from Africa, we will be able to gather groundbreaking information about the origin of many different species, perhaps even new knowledge about early humans and their ancestors, the possibilities are infinite.”
A 2-million-year-old ecosystem in Greenland revealed by environmental DNA, data/statistical analysis
Astrobiology