DNA molecules in ancient dirt offer a treasure trove of clues to our past

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Archaeological deposits typically consist of a mixture of artefacts and remains of plants and animals – including the occasional human fossil – all preserved in a dirt matrix. But these days, we dig a lot besides fossils and artifacts.

Now we can find evidence of the past deep in the dirt we dig. Besides plant and animal remains, sediments in archaeological deposits may also contain ancient DNA particles that can be extracted and used to identify species that once lived there.

Such was the case at Denisova Cave in southern Siberia, where “sediment DNA” revealed the comings and goings of two now-extinct groups of humans who once lived there: Neanderthals and a mysterious group called Denisovans.

READ MORE: Dirty Secrets: Sediment DNA Reveals 300,000 Year Timeline of Ancient and Modern Humans Living in Siberia

Recent developments in this new area of ​​genetic research present exciting opportunities to study the geographic spread, timing, and behavior of previous human populations. The possibility of obtaining evidence from the DNA of the sediments is also important because human remains (bones and teeth) are rarely preserved at archaeological sites.

Our new research, published in the Proceedings of the National Academy of Sciences, reveals exactly the source of DNA in archaeological deposits — on a microscopic scale.

DNA in dirt

Together with colleagues from around the world, we extracted ancient DNA from intact blocks of resin-soaked sediments collected at 13 archaeological sites in Europe, Asia, Africa and North America. From these blocks, we identified a variety of mammals, including Neanderthals in a sample from Denisova Cave.

We recovered ancient DNA from 23 of the 47 blocks analyzed, including samples from Russia, Germany, France and Turkey, but not from samples collected at sites in Israel, Morocco, South Africa or the United States.

These results are consistent with previous reports about the limits of preservation of ancient DNA in bones and teeth. DNA survival depends on the complex interaction of environmental conditions, including temperature, humidity, and soil composition. It is usually better preserved in cool, dry environments than in deserts or tropical regions.

Sediment blocks from 13 sites were examined for the presence of ancient mammalian DNA, which was detected in blocks collected at the sites shown in red.

Although DNA can survive in sediments for tens of thousands of years under favorable conditions, lingering questions remain about where these DNA molecules originated, and whether they can be transported by water between archaeological layers.

In archaeological research, it is crucial to know the exact location of where a piece of evidence was found. The sediment layers were laid down over thousands of years, so if the DNA molecules found their way into older or younger layers, our estimates of their ages would likely be out by thousands of years.

Set the record straight

To check whether DNA molecules could indeed be transported by water from one archaeological layer to another, we looked at sediment samples from caves that humans and other animals have occupied in the past.

We cut resin-soaked blocks of cave sediments into thin slices for microscopic imaging and genetic analysis. From these, we have successfully extracted DNA from pieces excavated 40 years ago.

The blocks were originally collected and placed in reinforced resin to help understand how archaeological sites were formed. But our relatively new ability to retrieve ancient DNA from these samples opens up new possibilities for exploring the past.

Resin-soaked sediment block from Denisova Cave containing fossilized bones, stones, and droppings.

We used a dental drill to make small holes in the sediment strips and were encouraged to find the resulting powder containing ancient DNA. We therefore looked in detail at specific microscopic features preserved intact in the blocks from which we cut the slices, and targeted them for genetic analysis.

In our samples, ancient DNA was concentrated in millimeter-sized “hotspots”. These were usually associated with small fragments of bone – in fact, microfossils – or fossilized feces. With a better understanding of where DNA is preserved in sediments, we now know which microscopic features to target in future studies.

Drill sites in the sediment block from Denisova Cave (on the left, circles indicate sample size) and ancient mammal DNA recovered from them. Sites 5 and 16 yielded Neanderthal DNA.

The resin-hardened sediment masses are very stable over time and are not likely to be contaminated by other sources of DNA, such as modern DNA from present-day humans.

Lumps of resin-soaked sediments can be found in archaeological repositories around the world, providing a largely untapped store of clues about the ancient human groups and the animals and plants that lived alongside them.

Read more: Dirt removal: Sediment reveals famous human cave site was also home to hyenas and wolves

Excavation in the laboratory

In a pandemic world, where access to archaeological sites may be limited, these sediment clumps may also usher in a new era of “scientific exploration,” which is being done in the lab, not in the field.

Detailed analyzes of archived sediment blocks can reduce the need to travel to remote sites. It’s an already financially and environmentally costly practice, which has become even more difficult during the current pandemic.

Determining the origin of DNA in archaeological dirt will help us improve this understanding, especially at sites that lack ancient bones and teeth.

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