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#AceHistoryDesk – Ancient human DNA extracted from 20,000-year-old deer tooth pendant found in Denisova Cave

Scraps of ancient DNA coaxed out of a deer tooth pendant show it likely hung around the neck of a woman or girl around 20,000 years ago.

We don’t know what she looked like, but she was related to a populationof humans further east of Denisova Cave in southern Siberia, in which the pendant was unearthed.

These insights into the pendant-wearer were made possible by a new technique — reported today in Nature — that can non-destructively extract ancient human DNA from objects made from porous materials like bone or teeth.

Denisova Cave has housed humans for nearly 300,000 years, by some estimates.

And it’s a “treasure box” for ancient human DNA, according to study lead researcher Elena Essel, a PhD student at the Max Planck Institute for Evolutionary Anthropology in Germany.

“It’s quite cool in there, almost like a fridge. The conditions for DNA preservation are perfect.”

Indeed, DNA analyses of skeletal remains and sediments show the cave has sheltered numerous populations of Homo sapiens, Neanderthals, and Denisovans over the years — and, sometimes, hybrids.

Cave excavations have also turned up a bunch of pendants and tools.

Generally, unless an artefact is found buried with a person, attributing an object to the specific person who made or used it is impossible.

But now, thanks to this new technique, researchers were able to establish a “direct link” between an artefact and the person who handled it thousands of years ago, said Bert Roberts, a geochronologist at the University of Wollongong who was not involved in the study.

Linking jewellery with the wearer

The pendant was made from a tooth belonging to a wapiti or elk (Cervus canadensis), and had a hole drilled through one end, presumably to thread a string or thin strap through.The wapiti is one of the deer family’s largest species.(Getty Images: Halamka)none

While reconstructing a long-dead person’s genome from a deer tooth pendant may seem like “the stuff of science fiction”, the idea’s been bandied around archaeological circles for a while now, said João Teixiera, a population geneticist at the Australian National University, who was also not involved with the study.

Bones, teeth, antlers and ivory — any part of a skeleton, really — contain a mineral called hydroxyapatite. It gives these structures strength, but also happens to hold onto and help preserve DNA.

And because such materials are porous, any bodily fluids that seep into their microscopic holes could leave DNA behind, clinging to hydroxyapatite.

The challenge for Ms Essel and her colleagues was getting the DNA out without damaging the pendant.

They first tested a range of different chemical cocktails on around a dozen other artefacts before settling on a mixture that successfully liberated trapped DNA.To avoid contaminating the tooth with her DNA while handling it, Elena Essel wore head-to-toe protective gear.(Supplied: Max Planck Institute for Evolutionary Anthropology)none

They then bathed the pendant in the solution to extract two types of DNA — nuclear DNA and mitochondrial DNA.

Nuclear DNA is inherited from both parents, and is generally considered our genetic blueprint. It’s stored as long, coiled strands, and each cell has a maximum of one copy.

From the bits of nuclear genome they managed to extract, the researchers deduced the pendant-wearer was female with north Eurasian ancestry.

Mitochondrial DNA, on the other hand, is passed down from mother to child. It’s a ring of DNA that resides in hundreds of tiny cell components called mitochondria.

The stability of the mitochondrial DNA ring, and the fact there are so many copies of it in our cells, means it’s more plentiful in — and more easily extracted from — ancient samples.

It can be used to trace maternal lineage, but it can also act as a “molecular clock” and calculate a sample’s age.

As mitochondrial DNA is passed down over the millennia, it accumulates mutations.

By comparing the number of mutations in an ancient mitochondrial genome with a present-day one, evolutionary biologists can estimate how long ago the individual lived.The pendant is only around 2.5 centimetres long.(Supplied: Max Planck Institute for Evolutionary Anthropology)none

Ms Essel and her crew calculated the age of the pendant from human and deer mitochondrial DNA to be roughly 19,000 and 25,000 years old respectively.

And the pendant remains intact.

New source of human DNA

Reconstructing part of a nuclear genome and almost an entire mitochondrial genome from fragments lodged in the ancient pendant “was really outstanding”, Dr Teixiera said.

“This opens up another source for human DNA.

“It’s now fair game for us to look at these types of objects and to seriously think about the possibility of matching the species that made or used these kinds of objects to their culture.”

But there is a catch. The technique can only be used on artefacts that are carefully excavated to avoid contamination from the people doing the digging.

That means wearing masks and gloves during a dig.

And what about other archaeological finds, such as stone tools — could the new technique get DNA from those too?

Ms Essel has tried, but so far has been unsuccessful.

“We currently have no idea if the DNA can actually bind to the stone tools and be preserved,” she said.

“So we want to check stone tools that are more porous, and that might have allowed some soaking of sweat or saliva or skin cells, and then we’ll give it another try.”

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