A team member records where his team collects samples of cave sediments.
Devlin A. Gandy
By Elizabeth Pennisi
When scientists need old DNA, they usually have to drill into teeth or bones – a process that can destroy delicate, sometimes irreplaceable samples. And this is the assumption that they have those teeth or bones in the first place.
Now researchers have shown that they can not only repair high-quality old DNA from dirt, but also close approaches of whole genomes. The specimens involved – from a cave floor in northern Mexico – not only reveal another way to obtain such genetic material, but also help to illuminate the history of the North American ice age.
The approach is a “major breakthrough” for the ancient DNA field, says Anna Linderholm, an archaeologist at Texas A&M University, College Station, who was not involved in the work. “We only scratch the surface of what is possible when we extract old DNA from sediments.”
For the new study, molecular paleoecologist Mikkel Winther Pedersen of the GLOBE Institute of the University of Copenhagen visited the Chiquihuite Cave in northern Mexico. Beginning in 2012, he and colleagues discovered stone tools there dating back 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 and recovered DNA from 48 of them.
Instead of simply concentrating on getting mitochondrial DNA – the small amount of genetic material that is in a cell’s power stations – as previous ancient DNA DNA studies have done, the scientists compiled all the DNA in each sample. . To do this, they used techniques that make it possible to decrypt billions of bases – or letters – of DNA in a matter of days, and developed computer software to handle and analyze all the data. As part of the analysis, they compared the successive fragments with bear DNA already in public databases.
From the mitochondrial DNA, the researchers were able to determine that black bears (Ursus americanus) lived for a long time in the region of the cave – at least 3000 years.
Researchers explored the Chiquihuite Cave in northern Mexico to learn more about bears.
Devlin A. Gandy
The analysis of the nuclear DNA was more difficult, as the bear genome is billions of bases long and the fragments were at best only thousands of bases. The team pooled the fragments and assessed how much of the genome they had by adapting the soil-derived DNA to existing bear DNA.
Eventually, the researchers compiled rough genomes from three black bears and what appeared to be a giant short-sighted bear (Arctodus simus), an extinct species best known from fossils in Canada. Pedersen calls his successive DNA ‘environmental genomes’ to distinguish it from the whole genome now commonly obtained from living microbes and other organisms.
Scientists did not really know how bears fared during the last ice age and what happened when the planet warmed up again. But by comparing the ancient black bear genome with genomes of the same species from across North America, Pedersen’s team realized that while the ice was disappearing over North America, some black bears were heading as far north as Alaska. Others were accompanied by black bears from further west, with their descendants populating the American southwest, the team reported today in Current biology.
Scientists do not know exactly when these extensions to ice-free areas occurred, only that they happened when the world warmed up 12,000 years ago. Some of the eastern bears bred with other Alaska black bears and migrated to another part of Alaska. Knowledge of the relationships between bears that live in different places can be important for conservation efforts, Pedersen says.
More than just the insight into the history of the bears of North America, the article is also ‘proof of concept’, says Ron Pinhasi, a physical anthropologist at the University of Vienna, who has been studying DNA for ten years and also sequence follows. taken from ancient lands. “They show how it is possible to analyze ancient DNA from environmental samples in a similar way as is currently done for DNA from fossil remains.”
In other words, keep an eye out for more genomes of antique dirt.