The dirt scattered on the floor of an ancient and remote cave in Mexico has produced a new viable source of old DNA.
For the first time, scientists have sequenced ancient DNA from soil samples – all thanks to Upper Paleolithic bears that prolifically used the cave as a toilet about 16,000 years ago.
Scientists describe their work as the “landing of the moon of genomics” because the discovery means that fossilized remains are no longer the only way to obtain ancient DNA. Moreover, it shows that ancient DNA can now be studied in the context of populations, rather than in scattered, fragmented individuals.
“When an animal or human urinates or defecates, the cells in the body are also excreted. And the DNA fragments in those cells are what we can detect in soil samples,” said geneticist Eske Willerslev of the University of Copenhagen in Denmark.
“Using extremely powerful sequencing techniques, we first reconstructed genomes – genetic profiles – based on these fragments. We showed that hair, urine and feces provide all the genetic material that, under the right conditions, can survive well over 10,000 years. years. “
Chiquihuite Cave, where the evidence was obtained, is well known as a site of historical significance. Many stone tools and fragments, dating back 25,000 to 30,000 years, show a period of human occupation – but humans were not the only ones to use the cave.
Bones and DNA traces also revealed the presence of a range of animals, including bears, bats, mosses, rodents and kangaroo rats. Using these samples, Willerslev and his team fully sequenced and recreated the genome of two Upper Paleolithic bears.
The first specimen was the ancestor of the modern American black bear (American bear), which still roam the forests of the North American continent. The second was the giant bear with the short face, now extinct (we Arctodus), one of the largest bears that ever lived, which died at the end of the last ice age about 11,000 years ago.
Sampling of different cultural layers in the cave. (Devlin A. Gandy)
The researchers then compared these genomes with those of other bears, including 83 current black bears in the US and Canada and three short-faced giant bears that lived in the Yukon in Canada about 22,000 years ago, based on an analysis of them. fossilized remains.
They found that Chiquihuite black bears are closely related to modern bears in North America, but also share ancestors with Alaska black bears. The researchers also found that Chiquihuite bears belong to the eastern offspring and that this offspring was the first to differ from other current populations of American black bears.
The DNA of the short-faced giant bears was split using the DNA of all eight modern bears in the Ursidae family, as well as three missing bears and the three short-faced giant bears in the Yukon Territory.
“Short-faced bears living in northern Mexico were different from the Mexican population [short-faced] bears living in northwestern Canada, “said geneticist Mikkel Winther Pedersen of the University of Copenhagen.
This is an excellent example of the new knowledge that suddenly becomes available when you reconstruct genomes based on DNA fragments extracted from the soil.
In addition to the findings of bears, which fill some gaps in our knowledge of America’s animal ancestors, the results show that we can now collect much more DNA from the environment than was previously possible, the researchers said.
DNA fragments found in sediments used to show only that a certain species was present and when. Now, using team techniques, scientists could learn more about these animals, such as where they fit into their family tree and how the animals migrated and diverged from their common ancestors.
“Everyone, everyone scientifically involved in the study of ancient DNA has recognized the need to reconstruct genomes from fragments found in soil or sediment. Being able to do this for the first time means we have opened a new frontier,” Willerslev said.
“Analysis of the DNA found in the soil could have the potential to expand the narrative about everything from species evolution to climate change – this is the monthly landing of genomics, because fossils will no longer be needed.”
The team ‘s research was published in Current biology.