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Ancient humans identified through DNA left in cave soil


Fleshing out the evolutionary record may no longer require finding bones, writes Tim Wallace.


No bones about it: Despite the absence of skeletal remains, DNA shows that ancient humans lived at Vindija Cave, Croatia.
Max Planck Institute for Evolutionary Anthropology / J. Krause

Just as a body is the prime evidence for crime-scene investigators to prove a homicide, old bones have been the key for Pleistocene investigators to know that a hominin – an ancient human – lived at a certain time and place.

But now a breakthrough in DNA extraction may revolutionise archaeology as much as it has criminology, with an international team of researchers successfully identifying the mitochrondrial DNA of ancient humans left in cave soil – deposited there when the occupants relieved themselves.

The breakthrough – described in a paper published in Science – looks likely to liberate archaeologists from the need to locate hard-to-find fossil remains of early humans in order to piece together a clearer picture of the evolution and dispersal of the human genus.

“Our work opens the possibility to detect the presence of hominin groups at sites and in areas where no skeletal remains are found,” write the researchers, led by evolutionary geneticist Viviane Slon, of the Max Planck Institute for Evolutionary Anthropology. Slon’s boss, institute head Svante Pääbo, envisages the new technique becoming a standard tool in archeology, as ubiquitous as carbon-dating.

Using a technique called “hybridisation capture”, the team successfully identified the mitochondrial DNA of Neanderthals, who went extinct about 40,000 years ago, and Denisovans, a less well-known group of archaic humans related to the Neanderthals believed to have diverged from the human lineage leading to modern humans about 400,000 years ago.

To piece together the DNA signature of the Neanderthal and Denisovan cave dwellers, the researchers took soil samples from seven archaeological sites – in Belgium, France, Spain, Croatia and Russia – determined to have been occupied by hominins between 14,000 and 550,000 years ago. They then finessed an intricate technique to filter out human DNA sequences from the abundance of other animal DNA in the samples, comparing them with known sequences extracted from Neanderthal and Denisovan bones.

Direct fossil evidence is not always necessary to deduce the presence of early humans at a site; it can be done, for instance, from the evidence of tools. In the case of one the surveyed sites – Trou Al’Wesse in Belgium – the presence of Neanderthals has been supposed from the existence of tool artefacts and animal bones with cut-marks, despite the absence of any hominin bones. Here the team verified the supposition by positively identifying Neanderthal mtDNA.

With automated laboratory procedure making it possible to undertake large-scale studies of DNA in sediments, the researchers express confidence their new technique will shed light on the genetic affiliations of the occupants of the many archaeological sites where no human remains are found.

One such site is near San Diego, California, where apparent evidence of butchery found on mastodon bones led this week to researchers suggest North America might have been settled by humans at least 115,000 years earlier than thought. The startling claim is still far from being accepted as fact, and would certainly gain weight from verifiable DNA evidence.

Tim Wallace is a contributor to Cosmos Magazine
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