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How does DNA survive thousands of years in ancient sediments?

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Ancient human and animal DNA can be found in sediments, preserved in microscopic bone and excrement fragments.

Most archaeologists have traditionally considered the sediments in which archaeological discoveries are embedded to be inconsequential by-products of excavations.

However, it has recently been discovered that sediments can contain ancient biomolecules such as DNA.

“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 Matthias Meyer, senior author of the study.

How does DNA survive thousands of years in ancient sediments?

Max Planck researchers teamed up with an international group of geoarchaeologists – archaeologists who use geological techniques to recreate the genesis of sediment and sites – to explore DNA preservation in sediment at a microscopic scale to understand the origin of DNA in the sediment.

They employed undisturbed sediment blocks saturated in synthetic plastic-like (polyester) resin that had previously been removed from archaeological sites.

The hardened blocks were transported to the laboratory, where they were split into sections for microscopic imaging and genetic research.

The researchers were able to extract DNA from sediment blocks that had been prepared as long as 40 years earlier in locations across Africa, Asia, Europe, and North America.

“The fact that these blocks are an excellent source of ancient DNA – including that originating from hominins – despite often decades of storage in plastic, 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”, added Mike Morley who led some of the geoarchaeological analysis.

Micro-remains in sediment matrix

The researchers used sediment blocks from Denisova Cave, a site in the Altai Mountains of South Central Siberia where ancient DNA from Neanderthals, Denisovans, and modern humans has been recovered, to show that microscopic organic particles yielded more DNA than silt collected at random.

“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 Vera Aldeias, co-author of the study.

“This study is a big step closer to understand precisely where and under what conditions ancient DNA is preserved in sediments,” said Morley.

The study’s method allows for highly targeted micro-scale sediment sample for DNA analysis, demonstrating that ancient DNA (aDNA) is not evenly distributed in the sediment and that certain sediment features are more favourable to ancient DNA preservation than others.

“Linking sediment aDNA to the archaeological micro-context means that we can also address the possibility of physical movement of aDNA between sedimentary deposits,” said Susan Mentzer.

The study’s lead author, Diyendo Massilani, was able to retrieve significant amounts of Neanderthal DNA from only a few milligrams of sediment. He was able to determine the gender of those who left DNA behind, indicating that they belonged to a group related to a Neanderthal whose genome had previously been reassembled from a cave bone fragment.

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

“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”.

Source: 10.1073/pnas.2113666118


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