The filth scattered across the floor of an ancient, remote cave in Mexico has yielded a new source of viable ancient DNA.
For the first time, scientists have sequenced ancient DNA from soil samples – and this is all thanks to the upper Paleolithic bears that used the cave on a large scale as their toilet about 16,000 years ago.
The scientists describe their work as “the lunar landing of genomics”, as the breakthrough means that fossilized remains are no longer the only way to obtain ancient DNA. Furthermore, it shows that ancient DNA can now be studied in the context of populations, rather than scattered, fragmentary individuals.
“When an animal or a human urinates or defecates, cells of the organism are also excreted. And the DNA fragments of these cells are what we can find in the soil samples,” explains geneticist Eske Willerslev of the University of Copenhagen in Denmark .
“Using extremely powerful sequencing techniques, we have reconstructed genomes for the first time – genetic profiles – based on these fragments. We have shown that hair, urine and feces all provide genetic material that can survive much longer than 10,000 in the right conditions. years. ‘
The Chiquihuite Cave, where the samples were obtained, is known as a place of historical interest. Many stone tools and fragments, dating from 25,000 to 30,000 years ago, show a period of human occupation – but humans were not the only ones to use the cave.
Bones and traces of DNA also revealed the presence of a variety of animals, including bears, bats, flies, rodents, and kangaroo rats. Using these monsters, Willerslev and his team now sequenced and recreated the genomes of two upper Paleolithic bears.
The first specimen was the ancestor of the modern American black bear (Ursus americanus), which is still roaming the forests of the North American continent. The second was the now extinct giant short-haired bear (Arctodus simus), one of the largest bears that ever lived, which died out at the end of the last ice age about 11,000 years ago.
Sampling of the different cultural layers in the cave. (Devlin A. Gandy)
The researchers compared this genome to that of other bears, including 83 modern-day black bears from the U.S. and Canada, and three giant short-sighted bears that lived in the Yukon in Canada about 22,000 years ago, based on an analysis of their fossilized remains.
They found that the Chiquihuite black bears are closely related to modern bears in North America, but also in Alaska of origin with black bears sharing. The researchers also discovered that the Chiquihuite bears belong to the eastern generation, and that this generation first differs from other contemporary American black bears.
The DNA of the giant short-sighted bears was pooled using the DNA of all eight modern bears in the Ursidae family, as well as three extinct bears, and the three giant short-sighted bears in the Yukon region.
‘The short-faced bears that lived in northern Mexico are clearly different from the population of [short-faced] bears 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 ground.”
In addition to the discovery of the bear, which fills some gaps in our knowledge of the origin of animals in the Americas, the results show that we can now extract much more from environmental DNA than was previously possible, the researchers said.
Fragments of DNA found in sediments previously only showed that a specific species was present, and when. Using the techniques of the team, scientists may be able to learn much more about these animals, such as where they fit into their pedigree, and how animals migrate and deviate from their common ancestors.
“Around the world, everyone who has been scientifically involved in the study of ancient DNA has recognized the need to reconstruct genomes from fragments found in soil or sediment. If we can do that for the first time, we have.” opened a new frontier, “said Willerslev. .
“Analysis of DNA found in the soil can expand the narrative on everything from species evolution to evolution in climate change – that’s the lunar landing of genomics because fossils will no longer be needed.”
The research of the team is in Current biology.