A mobile laboratory for ancient DNA analysis

Mobile devices for on-field DNA analysis have been used for medical diagnostics at the point-of-care, forensic investigation and environmental survey, but still have to be validated for ancient DNA studies. We report here on a mobile laboratory that we setup using commercially available devices, including a compact real-time PCR machine, and describe procedures to perform DNA extraction and analysis from a variety of archeological samples within 4 hours. The process is carried out on 50 mg samples that are identified at the species level using custom TaqMan real-time PCR assays for mitochondrial DNA fragments. We evaluated the potential of this approach in museums lacking facilities for DNA studies by analyzing samples from the Enlène (MIS 2 layer) and the Western Portel cave (MIS 3 deposits), and also performed experiments during an excavation campaign at the Roc-en-Pail (MIS 5) open-air site. Enlène Bovinae bone samples only yielded Bison priscus DNA, whereas Western Portel cave coprolites contained cave hyena (Crocuta crocuta) DNA together, for some of them, with DNA for the extinct Bison schoetensacki/Bb1/X clade, thus highlighting the Crocuta crocuta diet. Roc-en-Pail Bovinae bone and tooth samples also contained DNA for the Bison schoetensacki/Bb1/X clade, and Cervidae bone samples only yielded Rangifer tarandus DNA. Subsequent DNA sequencing analysis confirmed that correct species identification had been achieved using our TaqMan assays, hence validating these assays for future studies. We conclude that our approach enables the rapid genetic characterization of tens of millennia-old archeological samples and is expected to be useful for the on-site screening of museums and freshly excavated samples for DNA content. Because our mobile laboratory is made up of commercially available instruments, this approach is easily accessible to other investigators.

Methods
NGS Amplicons reads of: Bison Priscus (Enlène cave) Bison schoetensacki (Le Portel cave), Bison schoetensacki (Roc-en-Pail), Rangifer tarandus (Roc-en-Pail)