Abstract
Ancient DNA research is typically conducted in dedicated clean-room facilities; however, recent work in Slovenia has demonstrated that standard forensic technologies can also be successfully applied to archaeological remains. This article reviews studies conducted by our group on skeletal samples from different Slovenian sites. Comparative analyses of petrous bones from two archaeological contexts revealed how environmental conditions affect DNA preservation. Long-term storage effects were assessed by comparing freshly excavated remains with samples stored for 12 years under unregulated museum conditions. Intra-skeletal variability was examined through petrous bones, femurs, tali, calcanei, patellae, and teeth, and the potential of tooth cementum for minimally destructive extraction was evaluated. Differences in DNA quality between adult and non-adult skeletons were investigated. Genetic sexing was performed on 83 subadult skeletons to test the reliability of morphological methods, which often fail at this age. For optimized analyses, a DNA extraction protocol was developed that requires minimal bone powder. The PowerQuant real-time polymerase chain reaction (PCR) system proved a cost-effective predictor of successful short tandem repeat (STR) typing in degraded remains. Kinship studies, including that of four individuals from the 5th-6th century, demonstrated the utility of combining STR, single nucleotide polymorphism (SNP), and PCR-based massive parallel sequencing approaches, which improved statistical power and confirmed relatedness. Additionally, eye and hair color were predicted for skeletons dated to the 3rd-18th centuries. Overall, these results highlight that combining conventional forensic approaches with strict contamination control can generate reliable genetic data from archaeological samples and offer valuable insights into past populations.