Neanderthal DNA is preserved in archeological sediments

Researchers have discovered that DNA is sometimes preserved in the sediments surrounding archeological remains. This interesting finding raises the status of sediments from byproduct to useful tool. 

“The retrieval of ancient human and faunal DNA from sediments offers exciting new opportunities to investigate the geographical and temporal distribution of ancient humans and other organisms at sites where their skeletal remains are rare or absent,” said study senior author Matthias Meyer of Max Planck Institute for Evolutionary Anthropology in Leipzig.

In an attempt to discover the origins of the DNA, the researchers collaborated with a team of international geoarcheologists. Using pieces of sediment hardened by soaking in a polyester resin, the experts examined it under the microscope and attempted DNA extraction. 

DNA was successfully extracted from blocks of sediments that had been stored for up to 40 years. Mike Morely of Flinders University, who led some of the geo-archaeological analyses, said that the fact these blocks are an excellent source of ancient DNA – including that originating from hominins – provides access to a vast untapped repository of genetic information.

“The study opens up a new era of ancient DNA studies that will revisit samples stored in labs, allowing for analysis of sites that have long since been back-filled, which is especially important given travel restriction and site inaccessibility in a pandemic world,” said Morely.

The researchers looked at sediment from Denisova Cave in central Siberia, a place where DNA from Neanderthals, Denisovians and modern humans has been recovered. The scientists showed that organic particles yielded more DNA than randomly sampled sediment. 

“It clearly shows that the high success rate of ancient mammalian DNA retrieval from Denisova Cave sediments comes from the abundance of micro remains in the sediment matrix rather than from free extracellular DNA from feces, bodily fluids or decomposing cellular tissue potentially adsorbed onto mineral grains,” said study co-author Vera Aldeias from the University of Algarve.

According to study lead author Diyendo Massilani, he was able to recover substantial amounts of Neanderthal DNA from only a few milligrams of sediment. The genetic analysis of the DNA revealed the sex of the individuals and showed that they belonged to a Neanderthal population that has already been identified from the cave.

“The Neanderthal DNA in these small samples of plastic-embedded sediment was far more concentrated than what we typically find in loose material,” said Massilani.

“With this approach it will become possible in the future to analyze the DNA of many different ancient human individuals from just a small cube of solidified sediment. It is amusing to think that this is presumably so because they used the cave as a toilet tens of thousands of years ago.”

The study is published in the journal Proceedings of the National Academy of Sciences.

—By Zach Fitzner, Earth.com Staff Writer