How ancient human and animal DNA is preserved in archaeological sediments for thousands of years

Sampling of an intact block of impregnated sediment for old DNA analyzes. Credit: MPI f. Evolutionary anthropology

Ancient human and animal DNA may remain stably localized in sediment, preserved in microscopic fragments of bone and feces.

The sediments in which archaeological finds are embedded have long been viewed by most archaeologists as unimportant by-products of excavation. However, in recent years, it has been shown that sediments can contain ancient biomolecules, including DNA. “The recovery of ancient human and wildlife DNA from sediments offers exciting new opportunities to study the geographic and temporal distribution of ancient humans and other organisms at sites where their skeletal remains are scarce or absent. Says Matthias Meyer, lead author of the study and researcher at the Max Planck Institute for Evolutionary Anthropology in Leipzig.

To study the origin of DNA in sediments, Max Planck researchers have teamed up with an international group of geoarchaeologists – archaeologists who apply geological techniques to reconstruct the formation of sediments and sites – to study the preservation of DNA in sediment on a microscopic scale. They used blocks of undisturbed sediment that had been previously removed from archaeological sites and soaked in synthetic plastic-like resin (polyester). The hardened blocks were taken to the lab and sliced ​​into sections for microscopic imaging and genetic analysis.

Denisova cave sediment block

Surface of a section of intact boulder of impregnated sediment from Denisova cave. Credit: Mike Morley

The researchers succeeded in extracting DNA from a collection of sediment blocks prepared 40 years ago, from sites in Africa, Asia, Europe and North America. “The fact that these blocks are an excellent source of ancient DNA – including that from hominids – despite often decades of storage in plastic, provides access to a vast untapped repository of genetic information. The study opens a new era of ancient DNA studies that will revisit samples stored in laboratories, allowing the analysis of sites that have long been backfilled, which is especially important given travel restrictions and l ‘inaccessibility of sites in a pandemic world,’ said Mike Morley of Flinders University in Australia who led some of the geoarchaeological analyzes.

Abundance of microrests in the sedimentary matrix

Scientists used blocks of sediment from the Denisova Cave, a site in the Altai Mountains of southern central Siberia where ancient DNA from Neanderthals, Denisovans and modern humans was recovered, and showed that small organic particles produced more DNA than randomly sampled sediments. “This clearly shows that the high success rate of the recovery of ancient mammal DNA from the sediments of Denisova Cave stems from the abundance of microrestes in the sedimentary matrix rather than the extracellular DNA free from feces,” body fluids or decaying cell tissue potentially adsorbed onto mineral grains, ”says Vera Aldeias, study co-author and researcher at the University of Algarve in Portugal. “This study is a big step forward in understanding precisely where and under what conditions ancient DNA is preserved in sediment,” says Morley.

The approach described in the study allows very localized micro-scale sampling of sediments for DNA analysis and shows that old DNA (aDNA) is not uniformly distributed in the sediment; and that the specific characteristics of sediments are more conducive to the preservation of ancient DNA than others. “Linking the aDNA of sediments to the archaeological micro-context means that we can also address the possibility of physical movement of the aDNA between sedimentary deposits,” explains Susan Mentzer, researcher at the Senckenberg Center for Human Evolution and the paleoenvironment (Germany).

Diyendo Massilani, the study’s lead author, was able to recover substantial amounts of Neanderthal DNA from just a few milligrams of sediment. He was able to identify the sex of the individuals who left their DNA behind, and showed that they belonged to a population related to a Neanderthal whose genome had been reconstructed beforehand from a fragment of bone discovered in the cave. . “The Neanderthal DNA in these little plastic-encrusted sediment samples was much more concentrated than what we typically find in bulk material,” he says. “With this approach, it will become possible in the future to analyze the DNA of many different ancient human individuals from a small cube of solidified sediment. It’s funny to think that’s probably the case because they used the cave as a toilet tens of thousands of years ago.

Reference: “Microstratigraphic conservation of ancient DNA of fauna and hominids in the sediments of Pleistocene caves” December 27, 2021, Proceedings of the National Academy of Sciences.
DOI: 10.1073 / pnas.2113666118

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