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Ancient ecosystem reconstructed using 2-million-year-old DNA

Analysis of sediment samples from northern Greenland reveals traces of plant and animal inhabitants

by Laurel Oldach
December 7, 2022

A painting shows hares, geese, and mastodons in an open forest with shrubs and grass.
Credit: Beth Zaiken/Cambridge University
An artist's reconstruction shows northern Greenland as it would have appeared 2 million years ago based on animal and plant species identified from DNA found in sediments.

Researchers have sequenced the oldest DNA ever analyzed and used it to identify the plants and animals that populated northern Greenland 2 million years ago. The now cold and barren landscape was once a warm, grassy forest rich with mastodons, hares, and the ancestors of reindeer, the team reports (Nature 2022, DOI: 10.1038/s41586-022-05453-y). Understanding how those populations adapted as Greenland’s climate cooled may someday help guide conservation efforts to mitigate modern global climate change, the researchers say.

In 2006, a team from the University of Copenhagen and the University of Cambridge collected sediment samples from a geologic formation a few hundred miles from the North Pole. For years, lab members tried unsuccessfully to extract DNA from the samples. The work was so frustrating that the team joked about “the curse of the Kap København formation, because everybody who worked with these [samples] left science,” senior author Eske Willerslev said in a press conference.

A photograph shows two warmly dressed men digging on a sandy slope against a barren landscape.
Credit: Svend Funder/Cambridge University
Researchers Eske Willerslev and Kurt Kjær dig sediment samples at the Kap København formation in northern Greenland.

DNA binds tightly to clay and silicate particles, which slows decomposition and makes sediment an excellent storage medium. The sediment and chilly temperatures preserved fragments of DNA for more than twice as long as researchers had thought possible—but the tight binding also made the DNA very difficult to recover. After studying how modern DNA sticks to pure minerals, the researchers used a sediment extraction protocol they had optimized for other studies to finally shake loose some ancient DNA fragments. They sequenced the fragments and focused on mitochondrial DNA from mammalian and plant chloroplast genomes, which is more abundant than nuclear DNA. Combined with new bioinformatic approaches and reference databases, these techniques let the research team identify scores of ancient sequences almost to the species level.

“It feels somewhat magical to be able to infer such a complete picture of an ancient ecosystem from tiny fragments of damaged DNA,” Beth Shapiro, a paleogeneticist at the University of California, Santa Cruz, who was not involved with the study, says in an email.

The researchers found that temperate-dwelling species, such as horseshoe crabs and cedar trees, once lived side by side with organisms whose descendants are still in Greenland. Some species have adapted genetically to the colder environment, while others moved south or died out. The researchers hope that understanding how organisms adapted to a hotter ancient world might guide modern conservationists to genetically engineer plants and animals to survive rapid warming today.

According to Stockholm University sedimentary paleogeneticist Peter Heintzman, who was not involved in the study, such work would require much more complete genetic information and more precise sediment dating. Nonetheless, he says, “I’m really excited about the avenues for future research this [study] is going to enable.”



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