25,000-year-old human genome recovered from cave soil

Further analysis revealed the genome derived from a female individual, or multiple females.

An international team of researchers have successfully obtained the genome of a human, a wolf, and a bison from a single sediment sample pre-dating the Ice Age from the Satsurblia Cave site in the Caucasus, western Georgia.

Previous bioarchaeological studies have proven that sedimentary layers from caves can preserve ancient DNA for thousands of years. Although this is useful in conducting studies where skeletal remains are absent, the low number of sequences retrieved means analysis is limited to identifying only the presence of different species, and may not provide ancestral or phylogenetic information.

Photograph taken during the 2017 excavations in Section B of the Satsurblia Cave, showing where the sediment sample was collected. (© Anna Belfer-Cohen).

As discussed in a paper recently published in Current Biology, a study led by Ron Pinhasi and Pere Gelabert of the University of Vienna, and in collaboration with researchers from the Francis Crick Institute in London, involved performing shotgun sequencing on six sedimentary samples collected from the Satsurblia Cave to screen for mammalian DNA.

From a single Pleistocene soil sample, radiocarbon dated to between 23,500 and 22,200 BC, the researchers successfully yielded a human environmental genome.

Further analysis revealed the genome derived from a female individual, or multiple females. It represents a now-extinct lineage that split from western hunter-gatherer populations around 45,000 years ago, and has contributed to modern-day western-Eurasian populations.

The sample also yielded a wolf environmental genome of a previously unknown, likely extinct, lineage, and a bison genome also distinct from present-day Eurasian bison. This reveals that population structures have changed substantially since the Last Glacial Maximum (c. 24,000-18,000 years ago).

The team will conduct further analyses of sediment samples from the Satsurblia Cave site to deepen our understanding of interactions between humans and extinct fauna, and of the impact of climate change on ecosystems.

Ultimately, this important study demonstrates the feasibility of recovering in-depth genomic information in the absence of skeletal remains.