Dirt strewn across the floor of an ancient remote cave in Mexico has yielded a new viable source of ancient DNA.
For the first time, scientists have sequenced ancient DNA from soil samples, and it’s 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 lunar landing of genomics,” as the advance means that fossilized remains are no longer the only way to obtain ancient DNA. In addition, it shows that ancient DNA can now be studied in the context of populations, rather than scattered and fragmented individuals.
“When an animal or a man urinates or defecates, the body’s cells are also excreted. And the DNA fragments of those cells are what we can detect in soil samples,” he explained. geneticist Eske Willerslev of the University of Copenhagen in Denmark.
“Using extremely powerful sequencing techniques, we have for the first time reconstructed genomes (genetic profiles) based on these fragments. We have shown that hair, urine and feces provide genetic material that, under the right conditions, can survive for much longer. time than 10,000 years “.
Chiquihuite Cave, where the samples were obtained, is well known as a place of historical importance. Many tools and fragments of stone, dating back 25,000 to 30,000 years, show a period of human occupation, but humans were not the only ones to make use of the cave.
Bones and DNA traces also revealed the presence of a large number of animals, including bears, bats, mice, rodents and kangaroo rats. Through these samples, Willerslev and his team have now completely sequenced and recreated the Upper Paleolithic two-bear genome.
The first specimen was the ancestor of the modern American black bear (American bear), which still roams the forests of the American continent. The second was the short-faced giant bear already extinct (we Arctodus), one of the largest bears he ever lived, which died at the end of the last ice age about 11,000 years ago.
Sampling of the different cultural layers of the cave. (Devlin A. Gandy)
The researchers compared these genomes with those of other bears, including 83 current black bears from the United States 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 its fossilized remains.
They found that Chiquihuite black bears are closely related to modern bears in North America, but they also share ancestry with black bears in Alaska. The researchers also found that Chiquihuite bears belong to the eastern lineage and that this lineage was the first to diverge from other current populations of American black bears.
The DNA of the short-faced giant bears was joined using the DNA of the eight modern bears of the Ursidae family, as well as three extinct bears and the three short-faced giant bears in the Yukon Territory.
“The short – faced bears that lived in northern Mexico were clearly different from the population of [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 genomes are reconstructed from DNA fragments extracted from the soil.”
In addition to the bear’s discoveries, which fill some gaps in our knowledge of animal ancestry in the Americas, the results show that we can now extract much more from environmental DNA than was previously possible, the researchers.
DNA fragments found in sediments usually show that there was a specific species and when. Now, using the team’s techniques, scientists can learn much more about these animals, such as where they fit into their family tree and how animals migrated and diverged from their common ancestors.
“Everyone around the world who is scientifically involved in the study of ancient DNA recognized the need to reconstruct genomes from fragments found in soil or sediment. Being able to do this for the first time means we opened a new frontier, ”Willerslev said. .
“The analysis of DNA found in the soil could have the potential to broaden the narrative on everything from species evolution to climate change: this is the lunar landing of genomics. because fossils will no longer be needed. “
The team’s research has been published in Current biology.