Neanderthal nuclear DNA unlocks ancient human history

Scientists have extracted Neanderthal nuclear DNA from cave sediments for the first time, greatly improving the scope of ancient DNA research to include whole populations.

Ancient DNA preserved in bones and teeth has previously revealed insights into ancient humans like Neanderthals and Denisovans. But since skeletal remains are exceedingly rare, archaeologists have turned to extracting DNA from cave sediments.

Key research points

  • Nuclear DNA from sediments have been extracted and analysed for the first time
  • This Neanderthal nuclear DNA allowed researchers to see whole population data of Neanderthals
  • A Russian cave site held a single population, while a Spanish cave held two distinct populations – one replacing the other

DNA exists in two places in the cell: the nucleus and the mitochondrion. The nuclear (or chromosomal) DNA exists as a set of chromosomes inherited from both parents and is about three million base pairs (units of DNA) long. This DNA codes for all of the proteins in the body.

The mitochondrial DNA, on the other hand, exists as small, circular pieces of DNA around 16,500 base pairs long, and holds information about what proteins to make specifically for the mitochondria to create energy. 

Unlike nuclear DNA, mitochondrial DNA is only inherited from the mother, which somewhat limits the amount of information that can be gleaned from it.

Previously, this was the only type of Neanderthal DNA that could be collected from sediment, because there is a greater volume of it, making it is easier to find and isolate.

Now, a team of researchers, led by Benjamin Vernot from the Max Planck Institute for Evolutionary Anthropology in Germany, has fine-tuned their extraction technique to unearth the history of Neanderthals from both nuclear and mitochondrial DNA, collected from 150 sediment samples across three caves.

Instead of relying on only a single bone, and therefore only one genome, their samples revealed multiple genomes of a whole population.

Researchers in galería de las estatuas cave site in northern spain
Galería de las Estatuas cave site in northern Spain. Credit: Javier Trueba – Madrid Scientific Films

“The dawn of nuclear DNA analysis of sediments massively extends the range of options to tease out the evolutionary history of ancient humans,” says Vernot.

For example, the chromosomal DNA from Chagyrskaya Cave in Russia belonged to a single population that occupied it for a short period of time, which was difficult to determine from a bone previously found in the cave.

“We took sediment samples from throughout the stratigraphy, and they all looked very similar to the DNA from the bone, even though the sediment DNA came from multiple individuals,” says Kseniya Kolobova from the Russian Academy of Sciences and lead archaeologist at Chagyrskaya Cave.

On the other hand, a site in northern Spain called Galería de las Estatuas housed two separate populations, where the original group was replaced by a second around 100,000 years ago.

“We wondered if these ‘radiations’, along with the population replacement in Estatuas, might have been tied to climate changes, or to changes in Neanderthal morphology that occurred around this time period – although we will need more data to say for sure,” says Juan Luís Arsuaga of Universidad Complutense de Madrid, who led the excavations in Spain.

In their paper, published in Science, the authors suggest that this technique can help us learn more about Neanderthal and Denisovan populations, how they interacted and interbred, and how the migrated.

“We can now study the DNA from many more human populations, and from many more places, than has previously been thought possible,” says Matthias Meyer, from the Max Planck Institute for Evolutionary Anthropology.

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