Scientists have sequenced ancient DNA from soil for the first time, and the advance will transform what is known about everything from evolution to climate change.
The study of ancient DNA has profoundly changed our image of ourselves: less fashioned by God as if from clay and more the spawn of prehistoric sex fiends. Now a new paper is changing our picture of the black bear of ancient Mexico – which, it turns out, did not relieve itself only in the woods.
Around 16,000 years ago, during the tail end of the Stone Age, black bears defecated in a cave. We know this thanks to researchers from the University of Copenhagen – led by Prof. Eske Willerslev – who recreated the genomes of plants, animals and bacteria from microscopic fragments of DNA detected in the soil of Chiquihuite Cave in northern Mexico. Their momentous discovery of ursine choices for defecation sites was published Monday in Current Biology.
DNA sampling from soil is a new wrinkle on the already-extraordinary technique of extracting and sequencing ancient genetic material from fossil bones. Last week a completely different study on DNA, extracted from cave sediments 50,000 to 200,000 years old in Spain and Russia, shed fresh light on the life and loss of Neanderthals, who apparently teetered on the brink of extinction more than once.
The paper by Willerslev and his team discusses the extraction of environmental DNA from soil and sediment of a cave – a huge advance in studying evolution, as it relieves researchers from having to find adequately preserved bones. And among the animals they identified was an ancestral American black bear, based on soil samples containing its bodily emissions.
Feces and urine, even in the fossil form known as coprolites, contain cells of the excreter, the team explains; the cells contain DNA.
It bears adding that the study of coprolites is a highly respected field. Just this week another coprolite study from a much more ancient time indicates that “herbivorous” dinosaurs in Utah also ate crustaceans. The animals in question were apparently duck-billed hadrosaurs. The University of Colorado Boulder paleontologists could reach no other conclusion; they had found crustacean shells in the feces of dinosaurs that had supped on maggot-rich rotting wood.
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Back in the cave in Mexico, the scientists were able to reconstruct a list of the site’s occupants using extremely powerful sequencing techniques on soil samples. “We have shown that hair, urine and feces all provide genetic material which, in the right conditions, can survive for much longer than 10,000 years,” Willerslev says.
To make a long story short, thanks to this breakthrough the researchers recreated the genetic code of two species of black bear: the Stone Age American black bear and the short-faced bear, Arctodus simus, which went extinct 12,000 years ago. By that time, humans had definitely reached the Americas, and a human presence has been correlated with many cases of megafaunal extinction. It is not known whether we killed off the short-faced mega-bear, which could be as tall as 2 meters when upright.
“The short-faced bears that lived in northern Mexico were distinctly different from the population of black bears living in northwestern Canada,” says Assistant Prof. Mikkel Winther Pedersen, the first author of the study. “This is an excellent example of the new knowledge that suddenly becomes available when you reconstruct genomes based on DNA fragments extracted from soil.”
We also know that humans also lived in Chiquihuite Cave, which is a high 2,750 meters above sea level, though no human DNA has been identified in the soil there. We know this because archaeologists found stone tools attesting to human occupation.
Which brings us to a heated argument. The researchers explain that DNA analysis of the plant and animal remains from the sediment in which the tools lie indicates that humans were there 25,000 to 30,000 years ago.
But humans are generally only thought to have reached the Americas around 15,000 years ago. Some would argue about the dating of the sediment, others about disruption of the archaeological layers, others that sometimes a supposed stone tool is just a rock. At least the evidence can be said to indicate that humans didn’t defecate in the cave.
Whether the black bears used the cave as home or as a toilet, other animals were there too; the scientists say they identified genes of mice, rodents, bats, voles and kangaroo rats. They probably did their business there too.