The dirt scattered across the floor of an ancient remote cave in Mexico has provided a new source of viable ancient DNA.
For the first time, scientists have sequenced ancient DNA from soil samples – all thanks to the Upper Paleolithic bears who used the cave extensively as a toilet about 16,000 years ago.
The scientists describe their work as “the moon 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 human urinates or defecates, cells are also excreted from the organism. And we can detect the DNA fragments of these cells in the soil samples,” explains geneticist Eske Willerslev from the University of Copenhagen in Denmark.
“Using extremely powerful sequencing techniques, we reconstructed genomes – genetic profiles – from these fragments for the first time. We have shown that hair, urine, and feces all yield genetic material that, under the right conditions, can survive much longer than 10,000. years. “
The Chiquihuite Cave, where the samples were obtained, is known as a site of historical significance. Many stone tools and fragments, dating between 25,000 and 30,000 years ago, show a period of human habitation – but humans were not the only ones to make use of the cave.
Bones and traces of DNA also revealed the presence of a range of animals, including bears, bats, voles, rodents and kangaroo rats. Using those samples, Willerslev and his team have now fully sequenced and recreated the genomes of two Upper Paleolithic bears.
The first specimen was the ancestor of the modern American black bear (American bear), which still roams the forests of the North American continent. The second was the now-extinct giant short-headed bear (we Arctodus), one of the largest bears to ever live, which died 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 then compared these genomes with those of other bears, including 83 modern-day black bears from the US and Canada, and three giant short-headed bears that lived in Canada’s Yukon 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 share their ancestry with Alaskan black bears. The researchers also found that the Chiquihuite bears belong to the Eastern lineage, which is the first line to deviate from other current populations of American black bears.
The DNA of the giant short-headed bears was assembled using the DNA of all eight modern bears in the Ursidae family, as well as three extinct bears and the three giant short-headed bears in the Yukon area.
“The short-headed bears that lived in northern Mexico were markedly different from the population of [short-faced] bears that live in northwestern Canada, ”said geneticist Mikkel Winther Pedersen from the University of Copenhagen.
“This is an excellent example of the new knowledge that suddenly becomes available when you reconstruct genomes from DNA fragments extracted from the soil.”
In addition to the bear discoveries, which fill some gaps in our knowledge of the animals’ ancestors in America, the results show that we can now get much more out of environmental DNA than was previously possible, the researchers said.
Fragments of DNA found in sediments were used to show only when a particular species was present and when. Now, using the team’s techniques, scientists can learn a lot more about these animals, such as where they fit into their family tree and how animals migrated and diverged from their common ancestors.
“All over the world, everyone who was scientifically involved in the study of ancient DNA recognized the need to reconstruct genomes from fragments found in the soil or sediment. If we can do that for the first time, we will have a new one. border opened, “said Willerslev. .
“Analysis of DNA found in the soil could have the potential to expand the story on everything from the evolution of species to developments in climate change – this is the moon landing of genomics because fossils will no longer be needed.”
The team’s research is published in Current Biology