A mobile laboratory for ancient DNA analysis.

José Utge,Anne-Marie Moigne,Jean-Marc Elalouf,Christine Verna,Sylvain Soriano,Robert Begouën,Anne-Sophie Lartigot-Campin,Frédéric Maksud,Régis Vézian,Noémie Sévêque,Agnès Testu

doi:10.1371/journal.pone.0230496

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.

Highlights

Over the last twelve years, the field of ancient DNA has experienced deep changes that come both from technological advances and the attention paid to a variety of DNA sources
We report here on the use of a mobile laboratory consisting of commercially available devices for DNA extraction and amplification, and of TaqMan probes [25] that we designed for real-time PCR analysis of the mitochondrial DNA of six animal species
Genetic studies revealed that the Eurasian cave hyena and the extant spotted African hyena are so closely related that the cave hyena should be considered as a chronospecies rather than a distinct species or even subspecies [11,53]

Summary

Introduction

Over the last twelve years, the field of ancient DNA has experienced deep changes that come both from technological advances and the attention paid to a variety of DNA sources. New experimental procedures for DNA extraction [13,14,15] or sampling [16,17] have been described. Despite these advances, days to weeks are required from the time a sample has been excavated to the delivery of DNA data. Days to weeks are required from the time a sample has been excavated to the delivery of DNA data This contrasts with the increasing use of physics methods to perform on-field analysis of archeological material, which enable for example to characterize the pigments of rock art paintings [18,19,20]

Methods

Results

Conclusion