DNA from extinct humans discovered in caves without skeletal remains

Updated 2017-04-28 10:31:09 Xinhua
This image shows excavations at the site of El Sidron, Spain. (Credit: El Sidron research team)

This image shows excavations at the site of El Sidron, Spain. (Credit: El Sidron research team)

An international team of researchers has successfully retrieved DNA from ancient humans in cave sediments where no skeletal remains have been found, according to a study published Thursday.

The highly sensitive screening technique the team applied even identified ancient human DNA sequences from locations where the presence of an extinct human species called Neanderthals has been proposed but never demonstrated, said the study published by the U.S. journal Science.

"It's a great breakthrough," Chris Stringer, an anthropologist at the Natural History Museum in London, who was not involved in the study, told Science.

"Anyone who's digging cave sites from the Pleistocene now should put [screening sediments for human DNA] on their list of things that they must do," Stringer said.

While there are numerous prehistoric sites in Europe and Asia that contain tools and other human-made artefacts, skeletal remains of ancient humans are scarce and they are not always available or suitable for genetic analyses.

Researchers of the Max Planck Institute for Evolutionary Anthropology in Germany, have therefore looked into new ways to get hold of ancient human DNA.

"We know that several components of sediments can bind DNA," said Matthias Meyer of the Max Planck Institute for Evolutionary Anthropology in Germany and senior author of the study. "We therefore decided to investigate whether hominin DNA may survive in sediments at archaeological sites known to have been occupied by ancient hominins."

To this aim, Meyer and his team collaborated with a large network of researchers excavating at seven archaeological sites in Belgium, Croatia, France, Russia and Spain, where ancient humans are known to have lived.

Overall, they collected 85 sediment samples covering a time span from 14,000 to over 550,000 years ago.

Using tiny amounts of material, the researchers recovered and analyzed fragments of mitochondrial DNA, genetic material from the mitochondria, the "energy factories" of the cell, and identified them as belonging to 12 different mammalian families that include extinct species such as the woolly mammoth, the woolly rhinoceros, the cave bear and the cave hyena.

To capture ancient human DNA in the samples, they developed a delicate DNA hook crafted from modern human mitochondrial DNA to fish out the sequences that most resembled it.

It turned out that eight sediment samples from four caves contained Neanderthal mitochondrial DNA from either one or multiple individuals, while one sample from another cave contained DNA of Denisovans, another extinct human species.

Most of these samples originated from archaeological layers or sites where no Neanderthal bones or teeth were previously found.

"By retrieving hominin DNA from sediments, we can detect the presence of hominin groups at sites and in areas where this cannot be achieved with other methods," Svante Paabo, director of the Evolutionary Genetics department at the Max Planck Institute for Evolutionary Anthropology and co-author of the study, said in a statement.

"This shows that DNA analyses of sediments are a very useful archaeological procedure, which may become routine in the future."

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