Several well-preserved Neanderthal remains have been found in the Vindija cave in Croatia (Credit: MPI f. Evolutionary Anthropology/ J. Krause)
When life gives you an ancient cave filled with dirt, look for DNA. That’s what paleontologists and those involved in the study of ancient humans will likely be doing in the future following the revelation of a breakthrough technique that enables hominin DNA to be recovered directly from sediments without the need for fossils.
Led by geneticist Viviane Slon as well as molecular biologist Matthias Meyer (both from Germany’s Max Planck Institute for Evolutionary Anthropology), the team is the first to extract Neanderthal and Denisovan DNA directly from dirt samples collected from archaeological caves in Europe where their existence has been documented. More interestingly, they were also able to recover DNA at sites where no bones were ever found.
All living things leave behind genetic traces of themselves as they go through life, and our ancient ancestors were no different. One of the advantages of using this “eDNA” (environmental DNA) to study ecosystems and the animals living in them is that all it requires is a water or soil sample.
Unsurprisingly, scientists have been applying this technique to prehistoric animals – evolutionary geneticist Eske Willersev made headlines back in 2003 when he became the first scientist to sequence the DNA from species such as woolly mammoths from Siberian permafrost. However this doesn’t make the new findings any less of a feat given how difficult it is to isolate ancient human DNA. For a start, there’s the fact that it exists in minuscule traces from decomposed bodies, blood or feces, which often get lost among the other biological material in the soil. Secondly, there’s the difficulty of distinguishing it from modern human DNA, which inevitably ends up contaminating samples when researchers handle them.
Sure enough, while it wasn’t a problem identifying the DNA of extinct animal species such as the woolly mammoth and woolly rhinoceros in the sediment samples that they collected, identifying ancient human DNA required a far greater degree of precision.
“From the preliminary results, we suspected that in most of our samples, DNA from other mammals was too abundant to detect small traces of human DNA,” says Slon. “We then switched strategies and started targeting specifically DNA fragments of human origin.”
As documented in their study, they developed a molecular probe based on modern human mitochondrial DNA – which was chosen due to its abundance – to extract similar sequences. The researchers then compared the samples they found to known variants associated with Neanderthals or Denisovans and checked for chemical damage consistent with ancient DNA to make sure that they were looking at the right genetic material.
To prevent modern human DNA from contaminating the sediments, archaeologists working at El Sidrón cave in Spain, one of the sites in the study, also developed a protocol called “clean excavation” that enables researchers to extract both nuclear and mitochondrial DNA from teeth and skeletal remains for comparison purposes.
The result: Not only were the researchers able to detect the presence of ancient hominin DNA in the sediment samples from four caves, they were also able to distinguish between species and even deduce when a specific group might have occupied a cave.
“This work represents an enormous scientific breakthrough,” explains paleontologist Antonio Rosas from the Natural Science Museum in Madrid, who was part of the study. “We can now tell which species of hominid occupied a cave and on which particular stratigraphic level, even when no bone or skeletal remains are present.”
A researcher carefully collects mud samples from El Sidrón cave in Spain (Credit: El Sidrón research team)Case in point: The researchers found that the Denisovans and Neanderthals had occupied the Denisova Cave at different points in time based on the soil layer in which their DNA was found. “The Denisovans appear in the bottommost stratum, that is, in the oldest of the deposits,” says Rosas. “Their DNA in this sediment, without being associated with any skeletal remains, is the oldest proof of their existence right now.”
(For the balance of this article please see: https://newatlas.com/prehistoric-human-dna-el-sidron/49274/)