Recent advances in ancient DNA research – including high-throughput sequencing technologies, refined DNA extraction procedures, and increasingly sophisticated analytical frameworks – have significantly advanced the field. While DNA in human skeletal remains can persist for thousands of years, its preservation is highly dependent on environmental factors that are still not fully characterized. Excavation can further accelerate degradation processes by introducing abrupt changes in environmental conditions, which can lead to the loss of valuable genetic information. For a comprehensive understanding of the impact of environmental factors and storage conditions on DNA preservation, systematic studies that compare DNA preservation in skeletal remains under different environmental conditions are therefore needed.
In this thesis, we investigated the impact of environmental factors on the preservation of DNA in human skeletal remains both before and after their excavation. Using statistical analysis, we compared the preservation of DNA in samples from two geographically distinct archaeological sites, Črnomelj and Ljubljana – Vrazov trg, as well as in samples from Ljubljana’s Vrazov trg and Njegoševa sites, which differed in post-excavation storage conditions. Petrous bones were selected for DNA isolation due to their dense structure, which offers optimal preservation of ancient DNA in human skeletal remains. DNA yield and DNA preservation of isolated DNA were assessed using quantitative PCR (qPCR). The results were analysed statistically using 95% confidence intervals for medians and median tests for independent samples.
The results showed statistically significant differences in DNA yield as well as degree of DNA preservation among samples originating from different geographical locations. According to the statistical analysis, DNA yield and preservation are significantly higher for petrous bones excavated from Ljubljana – Vrazov trg compared to those from Črnomelj. Additionally, a statistically significant decrease in DNA yield and an increase in the degree of DNA degradation was observed for samples stored in museum depots at unregulated conditions for several years. Our findings highlight the importance of environmental factors on DNA preservation in archaeological skeletal samples – both prior to excavation and during long-term storage – and reinforce the need to adhere to scientific recommendations regarding optimal temperature and humidity when handling skeletal material for genetic analyses
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