DNA from dirt can offer new view of ancient life

In this Spanish cave, white tags show layers of soil to be sampled for ancient DNA.

Zinovi Matskevich

For almost 2 decades, genomes isolated from fossils have galvanized the study of human evolution. Yet despite vast improvements in retrieving and analyzing that DNA, researchers have deciphered whole genomes from just 23 archaic humans, 18 of them Neanderthals. This week, however, marks the publication of the fourth study in less than 3 months describing isolation and sequencing of DNA from sediments. The studies reveal new details about which animals and humans lived in these areas over time—and when. Together, they also open the door to what will be a far more plentiful supply of ancient genetic material and a richer understanding of the life of the humans, bears, bison, and other organisms that supplied that DNA.

“These are very exciting papers that represent a big step forward in both ancient and environmental DNA,” says Neil Gemmell, a geneticist at the University of Otago. Mads Reinholdt Jensen, an environmental DNA researcher at Aarhus University, adds that by combining climate records with the new DNA from dirt, “we can begin to answer some exciting existential and evolutionary questions,” such as how the last ice age reshaped ecosystems, and, possibly, which species overlapped in time.

The pursuit of “environmental DNA,” the genetic material in soils, water, and even the air, dates to the 1990s. Microbiologists began by isolating the microbial DNA in a thimbleful of soil to see what genes and species were in the sample. But the soil also contained genetic material shed, sloughed off, or defecated by larger organisms. More and more researchers have begun to depend on this DNA to monitor the species in rivers, lakes, and other environments, even when individuals of the species are themselves elusive. “Modern environmental DNA research is taking off rapidly,” says Michael Knapp, a molecular ecologist at the University of Otago. 

In 2003, evolutionary geneticists reported this discarded DNA could persist for thousands of years. By 2015, researchers demonstrated that DNA could help reconstruct entire ancient ecosystems. Using environmental DNA was appealing, not just because fossils are rare, but also because DNA extraction from bones destroys part of invaluable specimens.

“There’s dirt everywhere!” says Benjamin Vernot, a geneticist from the Max Planck Institute for Evolutionary Anthropology (EVA). “If you can systematically get DNA from sediment samples, you can study people who lived at many hundreds or thousands of locations—even if they didn’t leave behind their remains.” That prospect is exciting, adds Viviane Slon, a paleogeneticist at Tel Aviv University: “This opens the possibility of gaining a much broader view on the genetic history of past populations.”

Until this year, researchers applied molecular probes—pieces of DNA that match the ancient DNA researchers wanted to study—to ancient soils. Those probes can pull out mitochondrial DNA (mtDNA), the genetic material in the mitochondria that is passed on from females, and reveal the species that were present. Now, researchers have shown that with a capful of dirt, they can sequence genetic material from across a whole genome—the nuclear DNA, which provides much more information about a species. “It is the more desirable target,” Knapp says.

Evolutionary biologist Pere Gelabert and archaeologist Ron Pinhasi from the University of Vienna and their colleagues used the technique at the Satsurblia Cave in western Georgia, where ancient tools, modern human, and other animal fossils had been found. The team collected six sediment samples from layers ranging from 32,000 to 17,000 years old. They found genetic material from a female modern human, as well as from what seemed to be a dog and cattle. They pieced this material into genomes to compare with modern genomes.

The woman represents a previously undiscovered group of modern humans who lived about 25,000 years ago. Her lineage contributed to modern Europeans and, to a much lesser extent, modern Asians, Gelabert and Pinhasi’s team reports report today in Current Biology. The work yielded just 0.5% of her genome, but that’s “still mightily impressive,” Gemmell says.

Pinhasi’s team compared the “dog” DNA to canine genomes and mtDNA and concluded it belonged to a now-extinct lineage of wolves that predated the ancestor of modern wolves and dogs. These data support a hypothesis that wolf populations reshaped as the last ice age ended, with this wolf population dying out as the climate changed, possibly because of a change in prey and competition from other species. None of its DNA existed in more recent sediments.  

The bovine genome belonged to a bison, and its mtDNA can be found in living bison. Taken together, this snapshot of ancient life from cave dirt shows “We have moved to the next phase” of ancient DNA, Pinhasi says, with enough high-quality sequences to do extensive evolutionary analyses.

But he cautions that “we have very little clue” about whether the species overlapped, as the animals could have occupied the cave hundreds or even thousands of years apart.

Anna Linderholm, an archaeologist at Texas A&M University, College Station, is thrilled with these genomes, even though they are incomplete. “With this one study, the team has demonstrated the untapped source of information [that] sediments are.”

The new study adds to a handful of others to show the power of DNA from ancient soils. While Pinhasi’s team was in western Georgia, molecular paleoecologist Mikkel Winther Pedersen from the University of Copenhagen was sifting through sediments in Chiquihuite Cave in northern Mexico. His team pulled out genomes from three black bears and what proved to be a giant short-faced bear—which was not known to range that far south.

Both Pedersen and Pinhasi relied on the ever-lower costs of DNA sequencing and took a brute force approach, looking at all the DNA in a sample using “shotgun sequencing,” the cheapest and most popular technique available. The teams then compared those sequenced fragments to DNA databases to sort those sequences by species and arrange them into genomes. “They don’t have to know what they’re looking for before they start,” Vernot says.

Vernot’s own work on sediments in a cave in Spain showed that a more targeted approach, in which researchers use molecular probes to pull out particular stretches of DNA, can also be used to get genomewide information. He used these data to piece together the history of Neanderthal occupation of the Estatuas Cave in northern Spain. In a similar manner, Matthias Meyer, a geneticist at EVA, and colleagues examined DNA from the soil of the famous Denisova Cave, where the first fossils of the eponymous extinct humans were found. They found that the cave hosted Neanderthals and modern humans as well as Denisovans, possibly at the same time.

“All [these] studies testify that the analysis of ancient environmental DNA is coming of age,” Meyer says.

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