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Discovery of World’s Oldest DNA Reveals Ancient Ecosystem

Reconstruction of Kap København formation.
Reconstruction of Kap København formation two-million years ago in a time where the temperature was significantly warmer than northernmost Greenland today. Credit: Beth Zaikenjpg.
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A new study published in Nature describes the discovery and analysis of ancient DNA that is calculated to be two-million-years-old, breaking the record for the oldest DNA to be discovered and studied.

A breakthrough for the field of ancient DNA analysis

A new study marks a “game-changing” moment in the study of evolution, as the world’s oldest DNA is successfully sequenced.

The research was led by Professor Eske Willerslev, a fellow of St John’s College, University of Cambridge and director of the Lundbeck Foundation GeoGenetics Centre at the University of Copenhagen, and Professor Kurt H. Kjær, a geology expert also based at the University of Copenhagen.

“This is the longest study I have ever been involved in,” Willerslev said. It began in 2006, when a team of scientists journeyed to northern Greenland, reaching the København Formation, a geologic formation that lies within the mouth of a fjord in the Arctic Ocean. The team were visiting the area for a different project but, whilst there, decided to collect samples of clay and quartz from the site.  

A brief recap of ancient DNA analysis

The field of ancient DNA analysis has flourished over recent years due to advanced capabilities in next-generation sequencing (NGS) technologies, enabling the sequencing of small, degraded pieces of DNA. Earlier this year, the Nobel Prize in Physiology or Medicine was awarded to the Swedish geneticist Professor Svante Pääbo for his work studying the genomes of extinct hominins and human evolution.

The tools necessary for studying any DNA contained in the sediments did not exist at that time, and the samples were stored upon the researchers’ return. “Every time we saw improvements in methods for DNA extraction and sequencing technology, we tried to revisit the samples [for analysis], but we failed and failed,” Willerslev recalled. “Then, a couple of years ago, we had our breakthrough.”

Willerslev attributes the breakthrough to several developments. Firstly, Dr. Karina Sand, whose research focuses on understanding how DNA binds to minerals in the environment – and whether it can be extracted – joined the University of Copenhagen team. Secondly, the group obtained a novel sequencing platform that permits parallel DNA sequencing on a large scale, as well as the targeted sequencing of extremely small pieces of DNA.

A two-million-year-old ecosystem is uncovered

After Sand’s work established that DNA could be successfully detached from the clay and quartz samples, the microscopic DNA fragments were found to extremely damaged, suggesting they were most definitely “ancient”. What the team were perhaps not prepared for was exactly how ancient.

Willersleva and colleagues discovered that the ancient DNA was two-million-years-old, breaking the record for the oldest DNA discovered to date. This record belonged to one-million-year-old DNA extracted and sequenced from a Siberian mammoth bone.  

“The ancient DNA samples were found 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,” Kjær said.

The DNA fragments were compared to sequencing libraries of present-day organisms, including microorganisms, plants and animals, eventually building a picture of a two-million-year-old ecosystem that weathered extreme temperatures. “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 climate we expect on our planet in the future due to global warming,” said Professor Mikkel W. Pedersen, assistant professor at the Lundbeck Foundation GeoGenetics Centre and co-first author on the paper.

Evidence that reindeer, lemmings, birch and poplar trees – among other organisms – inhabited the region could be deciphered from the sequencing data. While some DNA samples were simple to classify as predecessors of present-day organisms, others could not be identified, as they likely do not have a predecessor still living in this century.

Technology Networks asked the research team to comment on the “most unexpected” finding from their analyses. “What blew our mind was the presence of Mastodon DNA,” they said. The Mastodon is an extinct mammal that originated in North and Central America. Previously, it was not known to exist as far north as Greenland. “Apparently they [mastodons] must have been swimming into Greenland at some point, or roaming on the ice,” the team added.

Using ancient DNA to support the future of our planet

Willerslev and colleagues are considering how their record-breaking finding could be used to support scientists and society in our fight against climate change. The extremely high temperatures of the Kap København region would have required adaptation from the organisms inhabiting it to withstand the rising temperatures. However, this process requires time, a luxury that we do not have. “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,” Pedersen said.

Could we use “clues” found within the ancient DNA to intervene? “It is possible that genetic engineering could [be used to] 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,” Kjær said. “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.” 

A new era in DNA detection

Among the DNA treasures already identified from the samples, there are a wide range of bacteria and fungi present. The scientists are exploring the interactions between ancient animals, plants and single-cell organisms, which they plan to map and publish at a later date.

The successful extraction of DNA from minerals also marks a new era in DNA detection, Willerslev emphasized: “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,” he concluded.

Reference: A 2-million-year-old ecosystem in Greenland uncovered by environmental DNA. Nature. 2022. doi: 10.1038/s41586-022-05453-y.