A new chapter in the history of evolution

Discovery of world’s oldest DNA breaks record by one million years

Two-million-year-old DNA has been identified for the first time opening a new chapter in the history of evolution.

Microscopic fragments of environmental DNA were found in Ice Age sediment in northern Greenland. The fragments are one million years older than the previous record for DNA sampled from a Siberian mammoth bone.

The ancient DNA has been used to map a two-million-year-old ecosystem which weathered extreme climate change. The results could help predict the long-term environmental toll of today’s global warming.

The discovery was made by a team of scientists led by Professor Eske Willerslev and Professor Kurt Kjær. Professor Willerslev is a Fellow of St John’s College, University of Cambridge and Director of the Lundbeck Foundation GeoGenetics Centre at the University of Copenhagen where Professor Kjær, a geology expert, is also based.

The results of the 41 usable samples found hidden in clay and quartz are published today in Nature.

“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,” says Willerslev.

“DNA can degrade quickly but we’ve shown that under the right circumstances, we can now go back further in time than anyone could have dared imagine.”

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

Close-up of organic material in the coastal deposits. The organic layers show traces of the rich plant flora and insect fauna that lived two million years ago in Kap København in North Greenland. Credits: Professor Kurt H. Kjær

The incomplete samples, a few millionths of a millimetre long, were taken from the København Formation, a sediment deposit almost 100 metres thick tucked in the mouth of a fjord in the Arctic Ocean in Greenland’s northernmost point. The climate in Greenland at the time varied between Arctic and temperate and was between 10-17C warmer than Greenland is today. The sediment built up metre by metre in a shallow bay.

Evidence of animals, plants and microorganisms including reindeer, hares, lemmings, birch and poplar trees were discovered. Researchers even found that Mastodon, an Ice Age mammal, roamed as far as Greenland before later becoming extinct. Previously it was thought the range of the elephant-like animals did not extend as far as Greenland from its known origins of North and Central America.

Detective work by 40 researchers from Denmark, the UK, France, Sweden, Norway, the USA and Germany, unlocked the secrets of the fragments of DNA. The process was painstaking – first they needed to establish whether there was DNA hidden in the clay and quartz, and if there was, could they successfully detach the DNA from the sediment to examine it? The answer, eventually, was yes. The researchers compared every single DNA fragment with extensive libraries of DNA collected from present-day animals, plants and microorganisms. A picture began to emerge of the DNA from trees, bushes, birds, animals and microorganisms.

A two million- year-old trunk from a larch tree still stuck in the permafrost within the coastal deposits. The tree was carried to the sea by the rivers that eroded the former forested landscape. Credits: Professor Svend Funder

Some of the DNA fragments were easy to classify as predecessors to present-day species, others could only be linked at 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 evolution of the DNA of a range of species still in existence today.

“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,” says Kjær.

“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.”

“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,” says co-first author Assistant Professor Mikkel Pedersen of the Lundbeck Foundation GeoGenetics Centre.

“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.”

While reviewing the ancient DNA from the Kap København Formation, the researchers also found DNA from a wide range of microorganisms, including bacteria and fungi, which they are continuing to map. A detailed description of how the interaction – between animals, plants and single-cell organisms – within the former ecosystem at Greenland’s northernmost point worked biologically will be presented in a future research paper.

It is now hoped that some of the ‘tricks’ of the two-million-year-old plant DNA discovered may be used to help make some endangered species more resistant to a warming climate.

“It is possible that genetic engineering could mimic the strategy developed by plants and trees two million years ago to survive in a climate characterised by rising temperatures and prevent the extinction of some species, plants and trees,” says Kjær. “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 whole new period in DNA detection.

“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,” says Willerslev. “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.”

Bibliographic information:

A 2-million-year-old ecosystem in Greenland uncovered by environmental DNA, Nature (7-Dec-2022), DOI: 10.1038/s41586-022-05453-y

Press release from the University of Cambridge on the discovery of world’s oldest DNA.

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Black Death shaped evolution of immunity genes, setting course for how we respond to disease today

An international team of scientists who analyzed centuries-old DNA from victims and survivors of the Black Death pandemic has identified key genetic differences that determined who lived and who died, and how those aspects of our immune systems have continued to evolve since that time.

Researchers from McMaster University, the University of Chicago, the Pasteur Institute and other organizations analyzed and identified genes that protected some against the devastating bubonic plague pandemic that swept through Europe, Asia and Africa nearly 700 years ago. Their study has been published in the journal Nature.

The same genes that once conferred protection against the Black Death are today associated with an increased susceptibility to autoimmune diseases such as Crohn’s and rheumatoid arthritis, the researchers report.

The team focused on a 100-year window before, during and after the Black Death, which reached London in the mid-1300s. It remains the single greatest human mortality event in recorded history, killing upwards of 50 per cent of the people in what were then some of the most densely populated parts of the world.

tooth Black Death shaped evolution of immunity genes, setting course for how we respond to disease today — Using DNA extracted from teeth of people who died before, during and after the Black Death pandemic, researchers were able to identify genetic differences that dictated who survived and who died from the virus. Credit: Matt Clarke/McMaster University

Researchers extracted DNA from the remains of people buried in the East Smithfield plague pits, which were used for mass burials in 1348 and 1349. Courtesy: Museum of London Archaeology (MOLA)

Black Death shaped evolution of immunity genes, setting course for how we respond to disease today — Researchers extracted DNA from the remains of people buried in the East Smithfield plague pits, which were used for mass burials in 1348 and 1349. Courtesy: Museum of London Archaeology (MOLA)

Evolutionary geneticist Hendrik Poinar has authored a new study, based on seven years of research, which found the genes that protected people against Black Death are associated with an increased susceptibility to autoimmune diseases. Credit: JD Howell/McMaster University

Members of the Barreiro lab conduct cell culture experiments. Courtesy: University of Chicago

More than 500 ancient DNA samples were extracted and screened from the remains of individuals who had died before the plague, died from it or survived the Black Death in London, including individuals buried in the East Smithfield plague pits used for mass burials in 1348-9. Additional samples were taken from remains buried in five other locations across Denmark.

Scientists searched for signs of genetic adaptation related to the plague, which is caused by the bacterium Yersinia pestis.

They identified four genes that were under selection, all of which are involved in the production of proteins that defend our systems from invading pathogens and found that versions of those genes, called alleles, either protected or rendered one susceptible to plague.

Individuals with two identical copies of a particular gene, known as ERAP2, survived the pandemic at a much higher rates than those with the opposing set of copies, because the ‘good’ copies allowed for more efficient neutralization of Y. pestis by immune cells.

“When a pandemic of this nature – killing 30 to 50 per cent of the population – occurs, there is bound to be selection for protective alleles in humans, which is to say people susceptible to the circulating pathogen will succumb. Even a slight advantage means the difference between surviving or passing. Of course, those survivors who are of breeding age will pass on their genes,” explains evolutionary geneticist Hendrik Poinar, an author of the Nature paper, director of McMaster’s Ancient DNA Centre, and a principal investigator with the Michael G. DeGroote Institute for Infectious Disease Research and McMaster’s Global Nexus for Pandemics & Biological Threats.

Europeans living at the time of the Black Death were initially very vulnerable because they had had no recent exposure to Yersinia pestis. As waves of the pandemic occurred again and again over the following centuries, mortality rates decreased.

Researchers estimate that people with the ERAP2 protective allele (the good copy of the gene, or trait), were 40 to 50 per cent more likely to survive than those who did not.

“The selective advantage associated with the selected loci are among the strongest ever reported in humans showing how a single pathogen can have such a strong impact to the evolution of the immune system,” says human geneticist Luis Barreiro, an author on the paper, and professor in Genetic Medicine at the University of Chicago.

The team reports that over time our immune systems have evolved to respond in different ways to pathogens, to the point that what had once been a protective gene against plague in the Middle Ages is today associated with increased susceptibility to autoimmune diseases. This is the balancing act upon which evolution plays with our genome.

“This highly original work has been possible only through a successful collaboration between very complementary teams working on ancient DNA, on human population genetics and the interaction between live virulent Yersinia pestis and immune cells,” says Javier Pizarro-Cerda, head of the Yersinia Research Unit and director of the World Health Organization Collaborating Centre for Plague at the Pasteur Institute.

“Understanding the dynamics that have shaped the human immune system is key to understanding how past pandemics, like the plague, contribute to our susceptibility to disease in modern times,” says Poinar.

The findings, the result of seven years of work from graduate student Jennifer Klunk, formally of McMaster’s Ancient DNA Centre and postdoctoral fellow Tauras Vigylas, from the University of Chicago, allowed for an unprecedented look at the immune genes of victims of the Black Death.

The research was funded in part by the Social Sciences and Humanities Research Council of Canada (SSHRC), The National Institutes of Health (NIH) and the Canadian Institute for Advanced Research, under the Humans and the Microbiome program.

Press release from McMaster University, by Michelle Donovan on how the Black Death shaped the evolution of immunity genes, setting course for how we respond to disease today.

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