Soil DNA sheds light on ancient human habitation in ancient Siberian cave

In 2010, scientists transformed the landscape 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.

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’.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.”

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100 Archaic Genomes project