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Study Finds Ancient Human DNA Leaked Into Cave Stone Surrounding Bone

NEW YORK – The calcite stone surrounding ancient human remains may contain genetic material that matches DNA found in corresponding bone samples, according to new research by a team from Italy, Germany, and Austria.

"[W]e aim to bring attention to such valuable mineralogical deposits that are found attached to archaeological findings in cave environments," senior and corresponding author Frank Maixner, coordinator at the Institute for Mummy Studies at Eurac Research in Bolzano, Italy, and his colleagues wrote. "We showed that they are not only representing mineralogical deposits, but rather an extension to the archaeological findings that retain and preserve historical information in the form of [ancient] DNA."

For a case study published in iScience on Tuesday, the investigators focused on a Late Bronze Age skeleton found surrounded by calcite deposits in an underwater limestone cave in a river in Germany, dated around 3,000 to more than 3,300 years old.

Using shotgun metagenomic sequencing and hybridization capture-based sequencing, they were able to assemble a mitochondrial genome and autosomal sequences from the X and Y chromosomes in the stone that matched the haplotype found in the sampled tibia bone it surrounded. Through comparisons with other ancient and modern DNA sequences, they found that the ancient individual clustered genetically with other Bronze Age representatives profiled for past studies.

The team noted that DNA appeared to be relatively well preserved in the stone samples, based on features such as the length of the ancient DNA fragments found. Both the bone and stone samples also contained sequences from ancient microbes, making it possible to put together de novo metagenome-assembled genomes for half a dozen bacteria or archaea, including bugs in the Clostridium and Streptosporangium genera.

"[W]e demonstrate the direct diffusion of human DNA from bones into the surrounding environment and show the potential to reconstruct ancient microbial genomes from such cave deposits, which represent an additional paleoarcheological archive resource," the authors reported.

Based on these and other results, they suggested that archaeologists and anthropologists may want to turn to unconventional sources, such as the archaeological site-adjacent mineralogical deposits in the German cave, when collecting and analyzing ancient DNA, particularly when it comes to testing procedures that are destructive to the samples being analyzed.

Such sites "are not only representing mineralogical deposits, but rather an extension to the archeological findings that retain and preserve its historical information in the form of [ancient DNA]," the researchers argued, noting that "these deposits could help to avoid future destructive sampling of similar archaeological remains, offering an additional paleogenetic archive that can be used to reconstruct ancient human genomes and ancient microbial communities."

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