Comparing the performance of three ancient DNA extraction methods for high-throughput sequencing. Improving DNA extraction from ancient bones

The DNA molecules that can be extracted from archeological and paleontological remains are often degraded and massively contaminated with environmental microbial material. This reduces the efficacy of shotgun approaches for sequencing ancient genomes, despite decreasing sequencing costs in the high-throughput sequencing (HTS) era. Improving the recovery of endogenous molecules from the DNA extraction and purification steps could, thus, help further advance the characterization of ancient genomes. Here, we apply the three most commonly used DNA extraction methods to five ancient bone samples spanning a ~30 thousand year temporal range and originating from a diversity of environments, from South America to Alaska. We show that methods based on the purification of DNA fragments using silica columns are more advantageous than in solution methods and increase not only the total amount of DNA molecules retrieved but also the relative importance of endogenous DNA fragments and their molecular diversity. Therefore, these methods provide a cost-effective solution for downstream applications, including DNA sequencing on HTS platforms.