Genome-wide assessment of DNA preservation in non-skeletal human tissue using low-coverage shotgun sequencing

Forensic anthropological investigations frequently involve highly degraded and skeletonized human remains in which optimal skeletal elements may be absent, compromised, or only partially preserved. In such contexts, the integration of molecular analysis within forensic anthropology becomes essential to support biological profiling and identification. Non-osseous tissues—such as hair, nails, ossified cartilage, and atherosclerotic calcifications—are often recovered alongside skeletal elements, yet their genome-wide preservation patterns remain poorly characterized. In this exploratory study, we assessed DNA preservation and sequencing performance across multiple non-skeletal tissues using low-coverage shotgun sequencing, directly comparing them with skeletal reference samples from the same individuals. Endogenous DNA content, fragment length distribution, molecular damage patterns, mitochondrial genome reconstruction, and nuclear marker recovery were evaluated. Despite low endogenous DNA proportions and extensive fragmentation, mitochondrial haplotypes and sex-informative markers were successfully retrieved from several non-osseous substrates, with concordance observed relative to skeletal references. Genome-wide nuclear SNP concordance exceeded 99.6% across all comparisons, supporting the persistence of coherent nuclear DNA signals in non-skeletal substrates despite extensive degradation. Although non-skeletal tissues cannot replace optimal skeletal sampling, these findings highlight their potential as complementary substrates within a forensic molecular anthropology framework, particularly in scenarios involving advanced decomposition, partial remains, or restricted access to preferred skeletal elements.