How Neanderthal DNA from cave dirt is revealing details about how early humans lived

Early human DNA extracted from dirt can reveal details about ancient cave-dwelling Neanderthals.

(CNN)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 Galería de las Estatuas site in Burgos, northern Spain, is shown here.

      Unraveling mysteries

        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.