Researchers at the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany, have successfully retrieved hominin DNA from cave sediments without relying on ancient bones or teeth.
The newly perfected technology instead focuses on traces of mitochondrial DNA preserved in mineral sediments in the soil, and has greatly expanded the horizons of ancient DNA research.
Shortage Of Ancient Human Fossils
The need for stepping up the game and devising new ways to get hold of ancient human DNA stems from the scarcity of skeletal remains.
Even though archaeologists have found a plethora of tools and other human-made artifacts in many prehistoric sites in Europe and Asia, not the same can be said about actual human remains.
Moreover, many of the recovered fossils don't have enough DNA to be used in genetic analysis.
Knowing that DNA binds to the mineral component of bones, the team, led by MPI geneticist Matthias Meyer, set out to establish if the same could happen in ancient sediments full of minerals.
As Meyer explains, bits of genes from ancient humans make up just a minute fraction of the DNA floating around in the natural world.
"In most excavation sites, if you find thousands of bones from animals, you're very lucky if you find one human tooth or a long-bone fragment," he said in a statement.
According to Meyer, their objective was "to investigate whether hominin DNA may survive in sediments at archaeological sites known to have been occupied by ancient hominins."
New Method Of Retrieving Early Human DNA
To test their theory, the researchers worked together with a large number of archaeologists from seven different sites in Belgium, France, Spain, Croatia, and Russia (including the Denisova Cave in Siberia) and collected 85 samples of sediment dated between 14,000 to more than 550,000 years ago.
Although DNA sticks to minerals and decayed plants in soil, scientists did not know whether it would ever be possible to fish out gene fragments that were tens of thousands of years old and buried deep among other genetic debris.
The team analyzed layers of sediment looking to discover if they preserved any genetic fingerprint, and was finally able to extract tiny DNA fragments that had once belonged to a variety of mammals, including our extinct human relatives.
Their efforts yielded DNA traces that once belonged to extinct species such as the woolly mammoths, woolly rhinoceroses, cave bears, and cave hyenas, as well as traces of Neanderthal DNA and Denisovan DNA.
"By automation-assisted screening of numerous sediment samples we detect Neanderthal DNA in eight archaeological layers from four caves in Eurasia. In Denisova Cave we retrieved Denisovan DNA in a Middle Pleistocene layer near the bottom of the stratigraphy," wrote the authors in the abstract of their paper, published April 27 in the journal Science.
The Mitochondrial DNA Technique
Mitochondrial DNA is the genetic material found in the mitochondria, the so-called "energy factories" of each cell. With only tiny amounts of material at their disposal, the scientists managed to recover and analyze mitochondrial DNA samples from twelve different mammal species.
At first, the team identified the animal DNA traces and then searched for ancient hominin DNA. Initially, the gathered samples seemed to contain too much of the other mammals' DNA and the team had trouble detecting the small traces of Neanderthal and Denisovan DNA.
At that point, the researchers "switched strategies and started targeting specifically DNA fragments of human origin," said study lead author Viviane Slon, a doctoral student at the German institute.
They found that nine of the samples, collected from four archaeological sites, contained enough ancient hominin DNA to advance their research. In the end, the team recovered Neanderthal mitochondrial DNA — belonging to either one or several individuals — from eight sediment samples, and Denisovan DNA from only one sample.
The majority of these samples came from sediment layers or sites where no hominin fossils were ever discovered. Instead, the DNA traces may have been left behind by animals that hunted the ancient humans and took shelter in the caves to eat their prey. Another possibility is that the samples are remnants of body parts or human waste.
Described as "a real evolution in technology," this method, developed over the course of several years, led to the retrieval of DNA even where it seemed impossibly scarce and degraded. DNA traces were recovered even from sediment samples that had been kept at room temperature for a long period of time.
"By retrieving hominin DNA from sediments, we can detect the presence of hominin groups at sites and in areas where this cannot be achieved with other methods", stated study co-author Svante Pääbo, director of the institute's Evolutionary Genetics department.
"This shows that DNA analyses of sediments are a very useful archaeological procedure, which may become routine in the future," he added.