Scientists Recover 15,000-Year-Old Human DNA Just From Dirt

Separation of DNA fragments by electrophoresis through an agarose gel. Guy Tear/Wellcome Collection (CC BY 4.0)

Archeologists have typically had to get their hands on skeletal remains to obtain the ancient DNA of a human, but a remarkable new study has managed to sequence the genome of a 15,000-year-old human – as well as a prehistoric wolf and bison – using just a handful of dirt.

Scientists have recovered genetic sequences from environmental sediments before, but this new study opens up the possibility of reconstructing the evolution of whole past ecosystems simply using dirt.

As reported in the journal Current Biology, the ancient sentiment was picked up from the cave of Satsurblia in the Caucasus, present-day western Georgia, known to be inhabited by humans in different periods of the Paleolithic. From a layer that dates back over a 25,000-year period, before the Ice Age, an international team of researchers led by the University of Vienna and Francis Crick Institute in London managed to obtain the DNA of a human. 

Using extensive sequencing and vast banks of data, the researchers were able to discover that this DNA belonged to a woman of Eurasian ancestry who lived around 15,000 years ago. In fact, she appears to represent a human extinct lineage that contributed to the present-day West-Eurasian populations.

To confirm this really was ancient DNA, the researchers then compared this environment DNA to genetic material obtained from bone remains of the nearby cave of Dzudzuana. This revealed distinct similarities in the genome, further affirming that this DNA was not simply modern contamination. 

Human DNA wasn’t the only genetic material recovered, however. From the sentiment, the researchers also managed to identify a wolf environmental genome that represents a previously unknown and likely extinct lineage, as well as a European bison genome that’s a relative of present-day populations.

Environment DNA, or eDNA, refers to scraps of stray genetic material that have been shed from an organism into the environment. It can come from an array of sources, such as shed skin, poop, blood, mucus, and so on. In a study published earlier this year, scientists demonstrated how eDNA can also be obtained from the surrounding air, not just the ground or surfaces.

Obtaining the genome of an ancient human from the environment, however, is a remarkable feat that could pave the way to some exciting new discoveries into the ancient ecosystems of the world. 

"Our results provide new insights into the Late Pleistocene genetic histories of these three species and demonstrate that direct shotgun sequencing of sediment DNA, without target enrichment methods, can yield genome-wide data informative of ancestry and phylogenetic relationships," the study authors conclude in their paper. 

"Genome-wide ancient sediment DNA might open new directions for the study of whole ecosystems, including interactions between different species and aspects of human practices linked to the use of animals or plants."

 


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