Journal
MOLECULAR ECOLOGY RESOURCES
Volume 16, Issue 2, Pages 459-469Publisher
WILEY
DOI: 10.1111/1755-0998.12470
Keywords
ancient DNA; DNA extraction; palaeogenomics; ultrashort fragments
Funding
- Danish Council for Independent Research, Natural Sciences [FNU-4002-00152B]
- Danish National Research Foundation, 'Chaires d'Attractivite' IDEX, University of Toulouse [DNRF94]
- International Research Group Program Deanship of Scientific Research of King Saud University, Saudi Arabia [IRG14-08]
- FP7 Marie-Curie Intra-European Fellowship [328024]
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The DNA molecules that can be extracted from archaeological and palaeontological remains are often degraded and massively contaminated with environmental microbial material. This reduces the efficacy of shotgun approaches for sequencing ancient genomes, despite the decreasing sequencing costs of high-throughput sequencing (HTS). Improving the recovery of endogenous molecules from the DNA extraction and purification steps could, thus, help advance the characterization of ancient genomes. Here, we apply the three most commonly used DNA extraction methods to five ancient bone samples spanning a similar to 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.
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