µCT Scanning Effects on DNA and a Multi-Step Workflow for Archaeological Petrous Bones

Abstract The petrous portion of the temporal bone is a key element in human evolutionary studies due to its exceptional preservation of biomolecules and morphological information. However, intensive and often redundant sampling has raised concerns about sustainability and long-term conservation. Here we present the first systematic evaluation of whether micro-Computed Tomography (µCT)—a widely used tool for digital preservation—affects ancient DNA (aDNA) integrity in human petrous bones. We analyzed 93 archaeological samples from Argentina, of which 50 had been scanned using µCT and 43 had not. We compared six molecular parameters, including endogenous content, read length, cytosine deamination patterns and contamination estimates. No statistically significant differences were observed between scanned and unscanned samples across any parameter (Mann-Whitney/Wilcoxon tests, p <0.05). Although mitochondrial contamination was marginally higher in scanned samples (p = 0.051), this was not driven by contamination estimates above the widely accepted 5% threshold for genomic analysis, Moreover, this pattern was not observed when considering nuclear contamination. These results indicate that, under appropriate scanning conditions, µCT imaging does not compromise DNA preservation. Building on this evidence, we propose a sustainable, multi-step workflow that integrates biological profiling, osteobiography, imaging, and compositional pre-screening prior to molecular sampling. This interdisciplinary approach maximizes the scientific information obtained from skeletal collections while minimizing destructive practices, thereby promoting ethical and sustainable research on irreplaceable anthropological remains, and fosters collaboration across research fields.