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Research on ancient DNA is surging, but how can it be ensured that human remains of irreplaceable significance are preserved? This is the question investigated by an international research team led by the University of Bonn. Their findings have now been published in the journal “PLOS ONE.”
The petrous part of the temporal bone is the hardest bone in the human skeleton. It houses the inner ear, including the cochlea, thus protecting our sense of balance and our hearing organs. That’s pretty straightforward, for the layperson. This bone portion is of inestimable scientific value however, as it preserves information from bygone eras that is useful in several different fields of research. In the womb, the inner ear develops fully in eight weeks, and does not change thereafter. The cochlea, furthermore, is the densest, most mineralized part of the human skeleton. It thus remains exceptionally well preserved for centuries, making it an optimal source of ancient DNA and other biomolecules. This inconspicuous portion of bone has been used to analyze more than 10,000 genomes of pre-historic humans—in nearly half of all sequenced individuals, ancient DNA was extracted from the petrous bone.
Sustainable approach needed
There is however a downside to the popularity of this method, as Dr. Lumila Paula Menéndez of the University of Bonn Institute for Archaeology and Cultural Anthropology explains: “The structural stability of the petrous bone makes it possible to analyze fine morphological details and investigate random evolutionary changes. Beyond its usefulness for analyzing ancient DNA, the petrous bone is of great interest in other disciplines as well.” The problem is however that in current methods for extracting ancient DNA, the samples get destroyed, so nothing is left for use in other scientific projects.
“We need to think strategically about petrous bone sample analysis,” says Menéndez, “to arrive at a uniform scientific approach that will guarantee the preservation of human remains for further study in other projects and fields, keeping this scientific legacy available for future generations.”
The promise of micro-computed tomography
Micro-computed tomography holds promise as a method potentially allowing researchers to digitally preserve samples before they are ever used for DNA analysis. “There are concerns however,” Menéndez notes, “of possible DNA damage from the X-rays used in tomography.” This was the subject of the recently published study conducted by Dr. Menéndez and her colleagues, who analyzed 93 petrous bone samples from archaeological sites in Argentina dating from the middle to late Holocene (the span of time from 6,000 to 200 years ago). Of the 93 samples, 50 were micro-CT-scanned prior to molecular analysis; the other 43 samples were not. The researchers then compared the two groups of petrous bones in relation to six commonly applied parameters. “We looked at the endogenous DNA content, for example,” says Menéndez, “a parameter that reveals the relative proportion of endogenous DNA, i.e., how much DNA comes from the remains as opposed to microbial DNA from the environment.” Other parameters studied included the number of readable base pairs of the DNA and the extent to which mitochondrial and nuclear DNA was contaminated by foreign DNA.
The researchers found no statistically significant differences between the scanned and unscanned samples, leading to the proposal of a sustainable workflow that preserves petrous bones and all other human remains for future use in any number of research studies. “The multi-step approach proposed starts with a macroscopic condition assessment, i.e. what is visible to the naked eye, and proceeds on to digital preservation and sample collection,” explains Menéndez, who believes the method maximizes scientific information obtainable from skeletal collections while minimizing procedural steps that result in destruction of samples. The method simultaneously represents an answer to ethical concerns around the handling of human remains.
Institutions involved and funding secured: In addition to the University of Bonn, various universities and research institutions from Costa Rica, Argentina, Austria, France, the UK, the US, Mexico, Bolivia, Chile, Brazil and Spain were involved in the study. The project was funded by the Wenner-Gren Foundation ((grant no. 9708 and grant no. 10755), the German Research Foundation (project no. 415489479) and the European Research Council (grant no. 948800), the Institut Pasteur and CNRS (grant ANR-16-CONV-0005).
Dr. Lumila Paula Menéndez
Institute for Archaeology and Cultural Anthropology
University of Bonn
Email: menendez@uni-bonn.de
Lumila Paula Menéndez, et. al.: µCT Scanning Effects on a DNA and a Multi-Step Workflow for Archaeological Petrous Portions. PLOS ONE 2026. DOI: 10.1371/journal.pone.0334682
https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0334682
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