New techniques for capturing DNA preserved in cave sediments now enable researchers to detect the presence of Neanderthals and other extinct humans. These ancestorsroamed the earth in front of and in some cases alongside Homo sapiens. The latest techniques allow scientists to learn about our early relatives without ever having to find their bones – just the dirt from the caves they were hanging out in.
Humans and animals are constantly losing genetic material when they pee, poop and bleed – and when they shed hair and dead skin cells. This genetic material ends up in the ground where, given the right conditions, it can remain for tens of thousands, if not hundreds of thousands of years – in dark, cold caves, for example.
“These are ancient caves where Neanderthals lived. They don’t know if people poop where they lived and worked. I would like not to think. But they make tools, you can imagine them cutting themselves. If they had kids, the kids might have pooped – they definitely didn’t have pampers, ”said lead author Benjamin Vernot, a population geneticist atGermany’s Max Planck Institute for Evolutionary Anthropology.
Vernot helped develop the new technique for capturing and analyzing DNA from cave sediments.
However, these findings concerned mitochondrial DNA, which is more common but less meaningful than nuclear DNA.
Vernot and his team are the first to extract human core DNA from cave debris.
“Mitochondrial DNA is only inherited from mother, it’s just a tiny thread of your ancestry and you lose a lot of complexity. If you look at the core genomes of humans, Neanderthals, or Denisovans, you can work out how they were related and how many there were at a certain time, “said Vernot.
Extracting and deciphering this DNA is not easy, but it is gradually changing our understanding of prehistory and allowing scientists to unravel some of the greatest mysteries of human evolution: how our ancestors spread around the world and how they interact with other ancient people – including the enigmatic Denisovans.
“I think the science paper is a remarkable technical achievement and opens up a lot of opportunities for future work in Eurasia on caves without Neanderthal (or Denisovan) fossils,” said Chris Stringer, research director of human origins and professor at the Natural History Museum in London. He was not involved in this latest study.
“Many temperate areas that currently have little or no archaic fossil human records can now potentially help build a population history of Neanderthals, Denisovans, and who knows – other human lineages,” Stringer said via email.
This breakthrough means that potentially much, much more DNA sequences can be obtained, even without skeletal remains, to create a more complete picture of the elderly.
Where does the DNA come from?
Vernot and his colleagues took around 75 samples from layers of sediment in three caves that have long been home to old people: the Denisova and Chagyrskaya caves in southern Siberia and the Galería de las Estatuas in the Atapuerca Mountains in northern Spain. About three-quarters of the samples the research team took had ancient human DNA.
“In the caves we sampled, archaeologists had already dug deep and exposed the various layers so we could access 40,000 years of history. We took tiny plastic tubes and wedged them into the cave sediments and twisted them a little.”
The detection of the Neanderthal DNA fragments in the cave sediment is not easy, said Vernot. The caves were inhabited by other animals that have similar stretches of DNA to humans. And these caves could also have been contaminated by DNA from archaeologists who worked in the cave.
The team compared the known genomes of Neanderthal fossils to those of 15 other mammals and developed chemical methods to target the unique Neanderthal portion of the genome that would be most telling.
“Humans weren’t the only things in this cave. We’re related to all living things on earth, and there are parts of our genome that are like bears or pigs. You really have to fish for human DNA. Human DNA fragments are one too.” a million. “
Ultimately, the scientists were able to determine when the Neanderthals lived in the cave, the genetic identity of the cave dwellers, and in some cases their gender. The oldest DNA the researchers could find was Denisovan, dating back 200,000 years.
The information the team received from the Spanish cave was particularly fascinating, Vernot said. While it had been a hangout for ancient people for more than 40,000 years and many stone tools were found in the sediment, the only Neanderthal fossil found there was a toe bone too small to be taken for DNA.
However, the DNA found and sequenced Vernot showed that two separate lines of Neanderthals had lived in the cave, with the later group developing much larger brains.
roll the dice
Vernot wants to apply these techniques to cave debris in places that may have been occupied by both Homo sapiens and Homo neanderthalensis around 40,000 years ago. It was at this point that early modern humans first came to Europe and met Neanderthals who had lived in the region for tens of thousands of years. It could shed some light on how the two groups interacted with each other.
“We know that early humans and Neanderthals mix. But we don’t really know about this interaction. Did they live together or did they meet and have a one-night stand?” Said Vernot.
“Early humans brought with them a new technology for making stone tools – more nuanced, with material from new places. We have locations with the old tools we associate with Neanderthals and new tools that we (early modern) people made, but we do don’t attract them. There are no bones attached to these tools. Chances are we met them and taught them how to do it. ”
“It’s not that DNA is better preserved in cave dirt, but you can roll the dice more often – there’s a lot more dirt than bones. There are a lot more needles in your haystack.”