Data from: Blocking human contaminant DNA during PCR allows amplification of rare mammal species from sedimentary ancient DNA

• Main Authors: Boessenkool, Sanne, Epp, Laura S., Haile, James, Bellemain, Eva, Edwards, Mary, Coissac, Eric, Willerslev, Eske, Brochmann, Christian
• Format: Article in Journal/Newspaper
• Language: unknown
• Published: 2011
• Subjects: Bioinfomatics/Phyloinfomatics; Mammals; DNA Barcoding; Genomics/Proteomics; permafrost; Siberia
• Online Access: http://hdl.handle.net/10255/dryad.34990; https://doi.org/10.5061/dryad.t33v4k14

Analyses of degraded DNA are typically hampered by contamination, especially when employing universal primers such as commonly used in environmental DNA studies. In addition to false-positive results, the amplification of contaminant DNA may cause false-negative results due to competition, or bias, during the PCR. In this study, we test the utility of human-specific blocking primers in mammal diversity analyses of ancient permafrost samples from Siberia. Using quantitative PCR (qPCR) on human and mammoth DNA we first optimised the design and concentration of blocking primer in the PCR. Subsequently, 454 pyrosequencing of ancient permafrost samples amplified with and without the addition of blocking primer revealed that DNA sequences from a diversity of mammalian representatives of the Beringian megafauna were retrieved only when the blocking primer was added to the PCR. Notably, we observe the first retrieval of woolly rhinoceros (C. antiquitatis) DNA from ancient permafrost cores. In contrast, reactions without blocking primer resulted in complete dominance by human DNA sequences. These results demonstrate that in ancient environmental analysis, the PCR can be biased towards amplification of contaminant sequences to such an extent that retrieval of the endogenous DNA is severely restricted. The application of blocking primers is a promising tool to avoid this bias and can greatly enhance the quantity and the diversity of the endogenous DNA sequences that are amplified.