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Soil DNA sheds light on ancient human

habitation in ancient Siberian cave
DNA analysis of soil samples in Denisova Cave in Russia suggests that Denisovans,
Neanderthals and modern humans may have lived there at the same time.
FUNDAMENTAL
SOCIETY RESEARCH

SCIENTIFIC ADVANCES

In 2010, scientists transformed the landscape

© Shanvood, Shutterstock
of human evolution when they analysed the
DNA of a tiny finger bone found in the
Denisova Cave in Russia’s Altai Mountains.
Dating from about 30 000 to 48 000 years ago
and believed to belong to a small child, the
pinkie bone rocked the scientific world when it
was found not to come from any known group
of extinct humans. This new group of early
humans was aptly named the Denisovans.

Researchers believe that the Denisova Cave

was inhabited by archaic humans as far back as 280 000 years ago and then by
modern humans as recently as the Middle Ages. DNA evidence pointing to this
includes eight human fossils: four bones (including the finger bone) from Denisovans,
three bones belonging to Neanderthals, and one bone from a child with a
Neanderthal mother and Denisovan father. Clearly, eight bones aren’t nearly enough
to reconstruct the timing and sequence of early human occupation, so researchers
supported by the EU-funded 100 Archaic Genomes project looked for more
information in the cave’s soils.

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Led by the Max Planck Institute for Evolutionary Anthropology, Germany, the
scientists analysed the DNA of 728 sediment samples collected from layers dating all
the way back to the Pleistocene epoch. After isolating and sequencing the soil
samples, the research team found ancient animal and human DNA in 685 and 175 of
them, respectively. Their findings have been published in the journal ‘Nature’.

First came the Denisovans

The study shows that the first humans to inhabit the cave were Denisovans. This, the
authors report in the study, “is associated with early Middle Palaeolithic stone tools
that were deposited approximately 250,000 to 170,000 years ago.” The next
Denisovan appearance in the cave occurred some 20 000 years later, lasting until
130 000 years ago, and was followed by another 30 000-year period of inhabitation
starting about 80 000 years ago.

Neanderthals appeared around 190 000 years ago, with DNA evidence placing their
inhabitation of the cave until 40 000 years ago. Different Neanderthal groups used
the cave at various points in time, some of which overlapped with Denisovan use.

Ancient modern humans were the last to arrive on the scene, at least 45 000 years
ago, the study reports. Interestingly, the soil layer from that period containing modern
human DNA also contained Denisovan and Neanderthal DNA. “The time periods [of
each layer] are quite large, so we can’t concretely say if they overlapped or not,”
noted study first author Elena Zavala, a PhD student in evolutionary genetics at the
Max Planck Institute, in a news item posted on ‘Science’. However, archaeological
scientist Katerina Douka of the Max Planck Institute for the Science of Human
History added: “I cannot think of another site where three human species lived
through time.”

The combination of DNA data from the fossils and sediment samples is a promising
direction for future research of this type. According to Douka, the study partly funded
by 100 Archaic Genomes (Genome sequences from extinct hominins) could help
make ancient soil DNA “a mainstream archaeological tool.”

For more information, please see:

100 Archaic Genomes project

Keywords
100 Archaic Genomes, DNA, Denisova Cave, human, Neanderthal, Denisovan,
bone, fossil

Related projects
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 100 Archaic Genomes

Genome sequences from extinct

hominins

22 July 2021
PROJECT

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Last update: 7 September 2021

Record number: 430628

Permalink: https://cordis.europa.eu/article/id/430628-soil-dna-sheds-light-on-
ancient-human-habitation-in-ancient-siberian-cave

© European Union, 2021

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