For centuries, archaeologists have searched caves for teeth and bones entombed in sun-starved dirt in the hope of piecing together how our ancestors lived and what they looked like.
Now, new techniques to capture DNA preserved in cave sediment are allowing researchers to detect the presence of Neanderthals and other extinct humans. These ancestors roamed the Earth before 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 where they hung out.
Humans and animals constantly shed genetic material when they pee, poop and bleed — and from shedding hair and dead skin cells. This genetic material leaches into the soil, where it can remain for tens, if not hundreds, of thousands of years if the conditions are right — such as in dark, cold caves.
Researchers have, for the first time, retrieved detailed Neanderthal genetic material from DNA preserved in dirt in three different caves in Europe and Siberia, according to a study published in the journal Science in April.
“These are ancient caves where Neanderthals lived. You don’t know if people are pooping where they lived and worked. I’d like to think not. But they are making tools, you can imagine they cut themselves. If they had children, the children maybe pooped — they definitely didn’t have Pampers,” said lead author Benjamin Vernot, a population geneticist at Germany’s Max Planck Institute for Evolutionary Anthropology.
Vernot helped develop the new technique to capture and analyze the DNA from cave sediments.
The first human DNA gleaned from cave dirt came from Denisova Cave in Siberia in 2017. Last year, scientists were able to extract the DNA of Denisovans — a little-known human population for which we only have five definitive bone fragments — from dirt in a cave on the Tibetan plateau. That cave is where the first Denisovan fossil remains outside the eponymous Siberian cave had been found. The discovery provided more definitive evidence for their presence in Asia.
Those findings, however, were of mitochondrial DNA, which is more abundant but less informative than nuclear DNA.
Vernot and his team are the first to glean human nuclear DNA from cave dirt.
“Mitochondrial DNA is only inherited from the mother, it’s only one tiny thread of your ancestry and you lose a lot of complexity. If you look at the nuclear genomes of humans, Neanderthals or Denisovans, you can calculate how they were related and how many there were at a given time,” Vernot said.
Extracting and decoding this DNA isn’t easy, but it’s beginning to reshape our understanding of prehistory and may allow scientists to untangle some of human evolution’s biggest mysteries: how our ancestors spread around the world and how they interacted with other ancient humans — including the enigmatic Denisovans.
“I think the Science paper is a remarkable technical achievement and opens up many possibilities for future work in Eurasia on caves with no Neanderthal (or Denisovan) fossils,” said Chris Stringer, research leader in human origins and professor at the Natural History Museum in London. He wasn’t involved in this latest study.
“Many temperate areas that currently have little or no archaic fossil human record may now be able to contribute to building a population history of Neanderthals, Denisovans and – who knows? – yet other human lineages,” Stringer said via email.
Until recently, the only way to study the genes of ancient humans was to recover DNA from scarce fossil bones and teeth. To date, DNA has only been extracted from 18 Neanderthal bones, four Denisovans and the child of a Neanderthal and Denisovan.
This breakthrough means that many, many more DNA sequences can potentially be obtained, even without skeletal remains, to build up a more complete picture of ancient humans.
Where does the DNA come from?
Vernot and his colleagues took around 75 samples from sediment layers in three caves where ancient humans long have been known to have lived: 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 different layers so we were able to access 40,000 years of history. We took tiny plastic tubes and jammed them into the cave sediments and twisted them a bit.”
Detecting the Neanderthal DNA fragments in the cave sediment wasn’t easy, Vernot said. The caves were inhabited by other animals that have similar stretches of DNA to humans. And these caves also could have been contaminated by DNA from archaeologists who have worked in the cave.
The team compared the known genomes of Neanderthal fossils with those of 15 other mammals and designed chemical methods to target the uniquely Neanderthal part of the genome that would be most informative.
“Humans weren’t the only things in that cave. We are related to all living things In Earth, and there are parts of our genome that are similar to bears or pigs. You really have to fish for the human DNA. Human DNA fragments are one in a million.”
Ultimately, the scientists were able to tell when the Neanderthals lived in the cave, the genetic identity of the cave dwellers, and, in some cases, their sex. The oldest DNA the researchers managed to find was Denisovan and dated back 200,000 years.
The information the team gleaned from the Spanish cave was particularly intriguing, Vernot said. While it had been a hangout for ancient humans for more than 40,000 years, with many stone tools found in the sediment, the only Neanderthal fossil found there was a toe bone that was too small to sample for DNA.
However, the DNA Vernot found and sequenced showed that two separate lineages of Neanderthals had lived in the cave, with the later group evolving much bigger brains.
Using similar techniques, scientists announced last month that they had sequenced the genome of a prehistoric bear that lived more than 10,000 years ago using DNA fragments found in dirt in a cave in Mexico. The technique has wide applications to study the evolution of animals, plants and microorganisms, the researchers said.
Rolling the dice
In particular, Vernot wants to apply these techniques to cave dirt at sites that might have been occupied by both Homo sapiens and Homo neanderthalensis around 40,000 years ago. This is when early modern humans first arrived in Europe and encountered Neanderthals, who had lived in the region for tens of thousands of years. It could shed light on how the two groups interacted.
“We know that early humans and Neanderthals interbred. But we don’t really know about that interaction. Did they live together or run into each other and have a one night stand?” Vernot said.
“Early humans brought with them a new technology for making stone tools — more nuanced, with material from new places. We have sites with the old tools that we associate with Neanderthals and new tools we know (early modern) humans made but we don’t have bones associated with those tools. It’s entirely possible we met them and taught them how to do this.”
It could also help build up a more complete picture of ancient humans in southeast Asia — an exciting locale for paleoanthropology. It’s where some of the world’s oldest cave art has been found and the remains of puzzling archaic humans such as the Hobbits of Flores in Indonesia have been discovered. DNA degrades more easily in warmer climates, but these new techniques mean more DNA sequences potentially can be found.
“It’s not like DNA preserves better in cave dirt but it allows you to roll the dice more times — there’s a lot more dirt than bones. There’s a lot more needles in your haystack.”