A mobile laboratory for ancient DNA analysis

Abstract

Mobile devices for on-field DNA analysis have been used for medical diagnostics at the point-of-care, forensic investigations and environmental surveys, 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 Portel-Ouest 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 DNA for the extinct steppe bison (Bison priscus), whereas Portel-Ouest cave coprolites contained cave hyena (Crocuta crocuta spelaea) DNA together, for some of them, with DNA for the European bison sister species/subspecies (Bison schoetensacki/Bb1-X), thus highlighting the cave hyena 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 reindeer (Rangifer tarandus) DNA. Subsequent DNA sequencing analyses 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.

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“…Successful concentration DNA analysis was achieved for several coprolites' samples from human. Several lines of evidence support the notion that our method provides reliable data, notably that contamination and specificity issues were adequately addressed [23]. Our mobile platform consists of three devices for DNA extraction (water bath, mini centrifuge, and vortex).…”

Identification by High-Throughput Real-Time PCR of 30 Major Circulating Listeria monocytogenes Clonal Complexes in Europe

“…Recently developed portable fast thermocyclers are particularly useful for performing rapid real-time PCR analysis in the field ( 76 – 78 ). We developed the multiplex real-time PCR assay to be compatible with such mobile fast PCR thermocyclers.…”

Metagenomic analysis of coprolites from three Late Pleistocene megaherbivores from the Southwestern United States

“…Those evaluating gut microbiomes from coprolites using metagenomic techniques have primarily focused on humans (Wibowo et al 2021; Tito et al 2012; Rivera-Perez et al 2015; Cano et al 2014; Rampelli et al 2021a; Appelt et al 2014) and dogs (Hagan et al 2020; Borry et al 2020) from the Late Holocene. A study by Bon et al (2012) used shotgun metagenomics to evaluate hyena coprolites that likely originated from the Late Pleistocene, but the authors focused on vertebrate rather than microbial DNA (Bon et al 2012; Utge et al 2020).…”