The Effectiveness of STR Genotyping Depends on the Organic Carbon Content in Ancient Samples

Abstract

Ancient DNA (aDNA) analysis is associated with significant difficulties due to its poor preservation and chemical modifications, which makes it important to develop reliable and cost-effective methods for preliminary sample selection. In this paper, we investigated the relationship between the success of STR genotyping of autosomal DNA, the yield of NGS data, and the content of total organic carbon (TOC) in ancient bone remains (7th–9th centuries, Rostov region). Correlation analysis showed that the efficiency of PCR decreases with increasing sizes of the amplified loci (as evidenced by the high frequency of allele dropout for fragments over 250 bp) and depends on the content of total organic carbon in the analyzed bone fragments. Based on the data obtained, a cost-effective strategy for screening paleobiological material is proposed. The protocol includes rejection of samples with TOC <8%, primary PCR genotyping for samples with TOC values of 8–9.9%, and prioritization of samples with TOC >9.9% for NGS analysis. This approach allows for optimized selection of the most promising samples, minimizing the costs of expensive studies and increasing the overall efficiency of paleogenetic projects.