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High‐Throughput DNA sequencing of ancient wood |
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| Authors: | Stefanie Wagner Frédéric Lagane Andaine Seguin‐Orlando Mikkel Schubert Thibault Leroy Erwan Guichoux Emilie Chancerel Inger Bech‐Hebelstrup Vincent Bernard Cyrille Billard Yves Billaud Matthias Bolliger Christophe Croutsch Katarina Čufar Frédérique Eynaud Karl Uwe Heussner Joachim Köninger Fabien Langenegger Frédéric Leroy Christine Lima Nicoletta Martinelli Garry Momber André Billamboz Oliver Nelle Antoni Palomo Raquel Piqué Marianne Ramstein Roswitha Schweichel Harald Stäuble Willy Tegel Xavier Terradas Florence Verdin Christophe Plomion Antoine Kremer Ludovic Orlando |
| Affiliation: | 1. BIOGECO, INRA, University of Bordeaux, Cestas, France;2. Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark;3. Laboratoire AMIS, CNRS, UMR 5288, Université Paul Sabatier (UPS), Toulouse, France;4. Museum Lolland Falster, Nyk?bing Falster, Denmark;5. Dendro‐Archaeology, CNRS, UMR 6566 CReAAH, University of Rennes, Rennes cedex, France;6. DRAC Basse Normandie, Alen?on, France;7. MCC/DRASSM, Marseille, France;8. Edytem, University of Savoie, Le Bourget‐du‐Lac, France;9. Siedlungs‐ und Unterwasserarch?ologie, Bern, Switzerland;10. Archéologie Alsace 11, Sélestat, France;11. UMR 7044, ARCHIMEDE, Strasbourg Cedex, France;12. Biotechnical Faculty, Department of Wood Science and Technology, University of Ljubljana, Ljubljana, Slovenia;13. Laboratoire EPOC, UMR 5805, University of Bordeaux, Pessac, France;14. Deutsches Arch?ologisches Institut, Zentrale, Referat Naturwissenschaften/Dendrochronologie, Berlin, Germany;15. Janus Verlag Freiburg im Breisgau, Freiburg im Breisgau, Germany;16. Museum of Archaeology, Laténium, Hauterive, Switzerland;17. Département des Recherches Archéologiques Subaquatiques et Sous‐Marines, Marseille, France;18. Dendrodata s.a.s., Verona, Italy;19. National Oceanography Centre, Maritime Archaeology Trust, Southampton, UK;20. Baden‐Wuerttemberg State Office for Cultural Heritage, Tree‐ring Lab, Hemmenhofen, Germany;21. Universitat Autònoma de Barcelona, Bellaterra, Spain;22. Amt fuer Archaeologie im Thurgau, Frauenfeld, Switzerland;23. Landesamt fuer Archaeologie, Dresden, Germany;24. Institute for Forest Growth, University of Freiburg, Freiburg, Germany;25. Spanish National Research Council, IMF – Archaeology of Social Dynamics, Barcelona, Spain;26. CNRS, UMR 5607 Ausonius, Maison de l'Archéologie, Pessac cedex, France;27. BIOGECO, INRA, University of Bordeaux, Cestas, FranceThese authors are joint last authors. |
| Abstract: | Reconstructing the colonization and demographic dynamics that gave rise to extant forests is essential to forecasts of forest responses to environmental changes. Classical approaches to map how population of trees changed through space and time largely rely on pollen distribution patterns, with only a limited number of studies exploiting DNA molecules preserved in wooden tree archaeological and subfossil remains. Here, we advance such analyses by applying high‐throughput (HTS) DNA sequencing to wood archaeological and subfossil material for the first time, using a comprehensive sample of 167 European white oak waterlogged remains spanning a large temporal (from 550 to 9,800 years) and geographical range across Europe. The successful characterization of the endogenous DNA and exogenous microbial DNA of 140 (~83%) samples helped the identification of environmental conditions favouring long‐term DNA preservation in wood remains, and started to unveil the first trends in the DNA decay process in wood material. Additionally, the maternally inherited chloroplast haplotypes of 21 samples from three periods of forest human‐induced use (Neolithic, Bronze Age and Middle Ages) were found to be consistent with those of modern populations growing in the same geographic areas. Our work paves the way for further studies aiming at using ancient DNA preserved in wood to reconstruct the micro‐evolutionary response of trees to climate change and human forest management. |
| Keywords: | ancient DNA chloroplast DNA degradation oak Quercus petraea/robur temperate trees |