Discovery of two-million-year-old DNA opens a game-changing new chapter

For the first time, scientists look directly at the DNA of a past ecosystem that far back in time.

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Late Pliocene and Early Pleistocene epochs 3.6 to 0.8 million years ago had climates resembling those forecasted under future warming. Palaeoclimatic records show strong polar amplification with mean annual temperatures of 11–19 °C above contemporary values. The biological communities inhabiting the Arctic during this time remain poorly known because fossils are rare.

In a new study, a team of scientists has discovered an ancient environmental DNA (eDNA) record describing the rich plant and animal assemblages of the Kap København Formation in North Greenland. This discovery breaks the record of the oldest DNA by one million years: this newly discovered eDNA dated to around two million years ago.

Scientists used this world’s oldest DNA to map a two-million-year-old ecosystem that weathered extreme climate change. According to scientists, the findings could help to predict the long-term environmental toll of today’s global warming.

Scientists found microscopic fragments in Ice Age sediment in northern Greenland. Using cutting-edge technology, they discovered that the fragments are one million years older than the previous record for DNA sampled from a Siberian mammoth bone.

Professor Eske Willerslev, fellow of St John’s College, University of Cambridge, said, “A new chapter spanning one million extra years of history has finally been opened, and for the first time, we can look directly at the DNA of a past ecosystem that far back in time.”

“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.”

“The ancient DNA samples were buried deep in sediment that had built up over 20,000 years. The sediment was eventually preserved in ice or permafrost and, crucially, not disturbed by humans for two million years.”

The fragmentary samples, which were only a few millionths of a millimeter long, were extracted from the Kbenhavn Formation, an Arctic Ocean sedimentary deposit almost 100 meters thick located in the northernmost tip of Greenland at the mouth of a fjord. Greenland’s climate at the period ranged from arctic to temperate and was 10–17°C warmer than it is now. In a little bay, the material accumulated one meter at a time.

Reindeer, hares, lemmings, birch, and poplar trees, as well as other animals, plants, and microbes, were found to have left fossils. Even the extinct Mastodon, an Ice Age mammal, was discovered to have wandered as far as Greenland. From their known origins in North and Central America, it was formerly believed that the elephant-like animals’ range did not reach as far as Greenland.

Forty researchers from Germany, Denmark, the UK, France, Sweden, Norway, the USA, and Denmark conducted a thorough investigation to uncover the mysteries of the DNA pieces. It was a laborious process since they first had to determine whether DNA was concealed in the clay and quartz and, if so, whether they could successfully separate the DNA from the silt to analyze it. Finally, the answer was yes. Every DNA fragment was compared with huge libraries of DNA that had been gathered from living animals, plants, and microbes. The DNA of trees, shrubs, birds, animals, and microorganisms started to take shape.

Some DNA fragments were easy to classify as predecessors to present-day species, others could only be linked at the genus level, and some originated from species impossible to place in the DNA libraries of animals, plants, and microorganisms still living in the 21st century. 

The two-million-year-old samples also help academics build a picture of a previously unknown stage in the DNA evolution of a range of species still in existence today. 

Professor Kjær said: “Expeditions are expensive, and many of the samples were taken back in 2006 when the team were in Greenland for another project, they have been stored ever since.”

“It wasn’t until a new generation of DNA extraction and sequencing equipment was developed that we’ve been able to locate and identify extremely small and damaged fragments of DNA in the sediment samples. It meant we were finally able to map a two-million-year-old ecosystem.”

Assistant Professor Mikkel W. Pedersen, co-first author on the paper and also based at the Lundbeck Foundation GeoGenetics Centre, said: “The Kap København ecosystem, which has no present-day equivalent, existed at considerably higher temperatures than we have today – and because, on the face of it, the climate seems to have been similar to the environment we expect on our planet in the future due to global warming.”

“One of the key factors here is to what degree species will be able to adapt to the change in conditions arising from a significant increase in temperature. The data suggests 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 and the world – extinction is on the horizon for some species, including plants and trees.”

The researchers discovered DNA from a variety of species, including bacteria and fungi when studying the ancient DNA from the Kap Kbenhavn Formation, which they are now mapping. In a subsequent research paper, a thorough explanation of the biological interactions that occurred inside the previous ecosystem at Greenland’s northernmost point involving animals, plants, and single-cell organisms will be presented.

It is now believed that some of the two million-year-old plant DNA’s “tricks” may be exploited to help make some endangered species more resistant 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 prevent the extinction of some species, plants, and trees. This is one of the reasons this scientific advance is so significant because it could reveal how to attempt to counteract the devastating impact of global warming.”

The findings from the Kap København Formation in Greenland have opened up a new period in DNA detection.

Professor Willerslev explained“DNA generally survives best in cold, dry conditions such as those that prevailed during most of the period since the material was deposited at Kap København. Now that we have successfully extracted ancient DNA from clay and quartz, it may be possible that clay may have preserved ancient DNA in warm, humid environments in sites found in Africa.”

“If we can begin to explore ancient DNA in clay grains from Africa, we may be able to gather ground-breaking information about the origin of many different species – perhaps even new knowledge about the first humans and their ancestors – the possibilities are endless.”

Journal Reference:

  1. Kjær, K.H., Winther Pedersen, M., De Sanctis, B. et al. A 2-million-year-old ecosystem in Greenland uncovered by environmental DNA. Nature 612, 283–291 (2022). DOI: 10.1038/s41586-022-05453-y