Researchers have come up with a new way to obtain Neanderthal DNA. 

DNA from our ancient Neanderthal cousins is extremely difficult to obtain. In fact, despite evidence of the species being uncovered at thousands o sites around the world, DNA has been salvaged from just 18 individuals. 

“Neanderthals lived for hundreds of thousands of years, spanning Europe and Asia, and we're representing them with 18 people,” says Benjamin Vernot, a postdoctoral scientist at the Max Planck Institute for Evolutionary Anthropology. 

“We sort of have hit a limit. Every once in a while, someone digs up a new Neanderthal bone, but a lot of the results that have come out so far are things that have been excavated in the '70s, '80s, or '90s.”

But in a new study, Dr Vernot and his colleagues reveal a resourceful technique to gather more ancient human DNA from dirt. 

One of the most prominent Neanderthal sites in the world is known as Galería de las Estatuas in Spain. The giant limestone cave area served as shelter, a workshop for making stone tools, and a kitchen for butchering animals. However, the only Neanderthal ever found fossil at the site is a single pinky toe bone - too small to obtain DNA from without completely destroying. 

But every handful of sediment from the floor of Galería de las Estatuas contains a wealth of DNA from the plants, animals and microbes that have lived there. 

In the new study, researchers employed an innovative technique to sift through the mass of jumbled-up genetic material to extract Neanderthal DNA. 

“You can imagine a Neanderthal woman sitting in the cave, butchering a deer, and she cuts herself. She bleeds on the floor a little bit, and that blood has DNA in it, which binds to the dirt in the floor,” said Dr Vernot. 

“Time passes, more dirt accumulates, and her DNA is trapped in the dirt. We can now go find it and learn about that person.”

Previous studies have been able to extract Neanderthal and Denisovan mitochondrial DNA from sediment, but this type of DNA is maternally inherited, so it cannot capture the complete genetic history of the archaic humans.  

The latest effort marks the first time that sediment-based nuclear DNA of archaic humans has been unearthed and analysed. 

“Obtaining DNA from cave sediments is a remarkable achievement and offers a tremendous way to unravel the later developments in human evolution,” says Richard Potts, director of the Human Origins Program at the Smithsonian's National Museum of Natural History, who was not involved in the research. 

“The study is a boon to figuring out what we now know, based on ancient DNA analyses, was a very complex history of how Neanderthals, Denisovans and Homo sapiens interacted and interbred.”

When Dr Vernot’s team first began looking at the sediment, they found over 99.9 per cent of the genetic material came from microbes, plants and other non-mammalian sources.

To search through the 0.1 per cent of mammalian DNA, they developed genetic probes to spot particular regions specific to the human genome. 

After using the probes to fish out human DNA from the samples, Vernot and his colleagues checked their findings against previously published ancient DNA extracted from other skeletal remains, and found they likely came from the same population of Neanderthals. 

Their findings suggest that a consistent Neanderthal population occupied the Galería de las Estatuas until about 100,000 years ago, when a distinct turnover seemed to occur. 

At that point, a different population took over, according to their data - an event possibly connected to the rapid cooling of the Earth at the beginning of a new ice age. 

“The fact that molecular genomes can be recovered from cave sediments, rather than by destroying parts of fossil bones and teeth, means that molecular studies can really ramp up,” said Dr Potts. 

“We can thus determine from sediments who exactly occupied particular caves in Europe and Asia and at what times.”

The study is accessible here.