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A team member records where his team is collecting samples of cave sediments.

Devlin A. Gandy

Team recovers ancient genomes from dirt, revealing new history of North America’s bears

When scientists need ancient DNA, they typically have to drill into teeth or bones—a process that can destroy delicate, sometimes irreplaceable, samples. And that’s assuming they have those teeth or bones in the first place.

Now, researchers have shown they can recover not just high-quality ancient DNA from dirt, but also close approximations of whole genomes. The samples in question—from a cave floor in northern Mexico—not only reveal another way to get such genetic material, they help clarify the history of North America’s ice age bears.

The approach is a “huge breakthrough” for the ancient DNA field, says Anna Linderholm, an archaeologist at Texas A&M University, College Station, who was not involved with the work. “We are just scratching the surface of what is possible when retrieving ancient DNA from sediments.”

For the new study, molecular paleoecologist Mikkel Winther Pedersen from the University of Copenhagen’s GLOBE Institute revisited Chiquihuite cave in northern Mexico. Beginning in 2012, he and colleagues discovered stone tools there dating to about 30,000 years ago, and the team was curious about other inhabitants of the site, including ancient bears. The researchers took samples of sediments at different levels of the cave floor, recovering DNA from 48 of them.

Rather than simply focus on getting mitochrondrial DNA—the small amount of genetic material present in a cell’s powerhouses—as previous ancient soil DNA studies have done, the scientists sequenced all the DNA in each sample. To do this, they took advantage of techniques that make it possible to decipher billions of bases—or letters—of DNA in just a few days and developed computer software to handle and analyze all those data. As part of the analysis, they compared the sequenced fragments with bear DNA already in public databases.

From the mitochondrial DNA, the researchers were able to determine that black bears (Ursus americanus) had lived in the region of the cave for a long time—at least 3000 years.

Researchers explored the Chiquihuite cave in northern Mexico to learn more about bears.

Devlin A. Gandy

Analyzing the nuclear DNA was trickier, as the bear genome is billions of bases long, and the fragments were only thousands of bases at best. So, the team pieced those fragments together and assessed how much of the genome they had by matching the soil-derived DNA up with existing bear DNA.   

In the end, the researchers compiled rough genomes from three black bears and what proved to be a giant short-faced bear (Arctodus simus), an extinct species best known from fossils in CanadaPedersen calls his sequenced DNA “environmental genomes,” to differentiate them from the whole genomes now commonly obtained from living microbes and other organisms.

Researchers had not really known how bears fared during the last ice age and what happened when the planet warmed again. But by comparing the ancient black bear genomes with genomes of the same species from across North America, Pedersen’s team figured out that, as the ice disappeared across North America, some black bears headed as far north as Alaska. Others mated with black bears from farther west, with their descendants subsequently populating the U.S. Southwest, the team reports today in Current Biology.

The scientists don’t know exactly when these expansions into ice-free areas occurred, only that they happened as the world warmed 12,000 years ago. Some of those eastern bears interbred with other Alaskan black bears and migrated to a different part of Alaska. Knowing the relationships between bears living in different places can be important for conservation efforts, Pedersen says.

More than just providing insights into the history of North America’s bears, the paper is also “a proof of concept,” says Ron Pinhasi, a physical anthropologist at the University of Vienna, who has been studying ancient DNA for 10 years and is also sequencing genomes from ancient soils. “They showcase how it is possible to analyze ancient DNA from environmental samples in a similar manner as is currently done for DNA from fossil remains.”

In other words, stay tuned for more genomes from ancient dirt.