DNA Yield and Degradation in Skeletal Remains from Two Slovenian Second World War Mass Graves: A Comparative Study of Different Bone Types

Background: The genetic identification of Second World War (WWII) victims in Slovenia is a significant forensic challenge due to the varying taphonomic conditions of mass graves and the high degradation of skeletal remains. While recent studies highlight the potential of small cancellous bones and petrous parts, the variability of DNA preservation across different mass grave contexts remains under-investigated. Objectives: This study aimed to compare DNA quantity and quality across different skeletal elements grouped by anatomical and structural characteristics, specifically evaluating how two distinct burial sites—Konfin II and Huda Jama—influenced DNA preservation. Materials and Methods: A complete dataset of 785 samples was analyzed, integrating 114 newly processed samples from Huda Jama with previously published data from both sites. DNA was extracted using a total demineralization protocol and purified via the Biorobot EZ1 system. Quantification and degradation assessment were performed using the PowerQuant qPCR kit. Skeletal elements were categorized into six groups: temporal—pars petrosa, big long bones, torso bones, small long bones, short/sesamoid bones, and teeth. Results: Statistical analysis revealed significant differences in DNA yield and degradation between the two sites. Huda Jama samples exhibited significantly higher DNA yields in small long bones and short/sesamoid bones compared to Konfin II. Conversely, Konfin II showed superior DNA yield in teeth and torso bones. Regarding DNA quality, teeth were significantly more degraded in Huda Jama, while big long bones showed significantly higher degradation in Konfin II. No significant differences in the degradation index were observed between the sites for other skeletal elements, including small long bones and short/sesamoid bones. The temporal—pars petrosa remained a high-performing element at both locations. Conclusions: DNA preservation is highly site-specific and influenced by the complex taphonomic conditions of the burial site. While small cancellous bones are excellent candidates for DNA recovery in some environments (Huda Jama), teeth and torso bones may provide higher yields in others (Konfin II). However, the rate of DNA fragmentation (degradation) varies independently of yield, as seen in the extreme degradation of teeth in Huda Jama. A multi-sample strategy, prioritizing the petrous bone while accounting for site-specific preservation patterns, is essential for maximizing identification success in highly degraded skeletal remains from WWII mass graves in Slovenia.