1. New insights on lake sediment DNA from the catchment: importance of taphonomic and analytical issues on the record quality
- Author
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Gentile Francesco Ficetola, Jérôme Poulenard, Kevin Walsh, Fernand David, Erwan Messager, Elodie Brisset, Pierre Sabatier, Anne-Lise Develle, Laurent Fouinat, Ludovic Gielly, Fabien Arnaud, Rémi Sinet, Manon Bajard, Charline Giguet-Covex, Frédéric Guiter, Pierre Taberlet, Environnements, Dynamiques et Territoires de la Montagne (EDYTEM), Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Centre National de la Recherche Scientifique (CNRS), BioArch-Department of Archaeology, Environnements, Dynamiques et Territoires de Montagne (EDYTEM), Laboratoire d'Ecologie Alpine (LECA ), Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019]), Department of Environmental Science and Policy [Milano], Università degli Studi di Milano = University of Milan (UNIMI), Centre européen de recherche et d'enseignement des géosciences de l'environnement (CEREGE), Institut de Recherche pour le Développement (IRD)-Institut National de la Recherche Agronomique (INRA)-Aix Marseille Université (AMU)-Collège de France (CdF (institution))-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS), Institut méditerranéen de biodiversité et d'écologie marine et continentale (IMBE), Avignon Université (AU)-Aix Marseille Université (AMU)-Institut de recherche pour le développement [IRD] : UMR237-Centre National de la Recherche Scientifique (CNRS), Institut Català de Paleoecologia Humana i Evolució Social (IPHES), Àrea de Prehistòria, Universitat Rovira i Virgili, Universitat Rovira i Virgili, DiPEE Chambéry-Grenoble (University Grenoble Alpes and University Savoie Mont Blanc), the Zone Atelier Alpes (ZAA), the PEPS de site Grenoble and the Conseil Général of Isère (AAP on biodiversity), the Parc National des Ecrins, Centre National de la Recherche Scientifique (CNRS)-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry]), Università degli Studi di Milano [Milano] (UNIMI), Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Collège de France (CdF (institution))-Institut de Recherche pour le Développement (IRD)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA), Laboratoire d'Ecologie Alpine (LECA), Centre National de la Recherche Scientifique (CNRS)-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Université Joseph Fourier - Grenoble 1 (UJF)-Université Grenoble Alpes (UGA), Department of Environmental Science and Policy, Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Collège de France (CdF)-Institut national des sciences de l'Univers (INSU - CNRS)-Aix Marseille Université (AMU)-Institut National de la Recherche Agronomique (INRA), and Centre National de la Recherche Scientifique (CNRS)-Institut de recherche pour le développement [IRD] : UMR237-Aix Marseille Université (AMU)-Avignon Université (AU)
- Subjects
0301 basic medicine ,0106 biological sciences ,Geologic Sediments ,Taphonomy ,Earth science ,Drainage basin ,lcsh:Medicine ,EarthArXiv|Physical Sciences and Mathematics|Earth Sciences ,EarthArXiv|Life Sciences|Ecology and Evolutionary Biology ,01 natural sciences ,bepress|Life Sciences ,EarthArXiv|Life Sciences ,Limnology ,Human Activities ,Glacial period ,EarthArXiv|Physical Sciences and Mathematics|Earth Sciences|Sedimentology ,lcsh:Science ,ComputingMilieux_MISCELLANEOUS ,bepress|Life Sciences|Ecology and Evolutionary Biology|Terrestrial and Aquatic Ecology ,Multidisciplinary ,geography.geographical_feature_category ,EarthArXiv|Physical Sciences and Mathematics|Earth Sciences|Geology ,Palaeoecology ,Agriculture ,Plants ,[SDE]Environmental Sciences ,Erosion ,Soil horizon ,Molecular ecology ,Agricultural landscapes ,Environmental Monitoring ,bepress|Physical Sciences and Mathematics ,bepress|Physical Sciences and Mathematics|Earth Sciences|Sedimentology ,[SDE.MCG]Environmental Sciences/Global Changes ,010607 zoology ,bepress|Physical Sciences and Mathematics|Earth Sciences ,EarthArXiv|Physical Sciences and Mathematics|Earth Sciences|Soil Science ,bepress|Life Sciences|Ecology and Evolutionary Biology ,010603 evolutionary biology ,Article ,C2FN ,03 medical and health sciences ,Humans ,[SDU.ENVI]Sciences of the Universe [physics]/Continental interfaces, environment ,EarthArXiv|Life Sciences|Ecology and Evolutionary Biology|Terrestrial and Aquatic Ecology ,geography ,bepress|Physical Sciences and Mathematics|Earth Sciences|Geology ,lcsh:R ,Sediment ,EarthArXiv|Physical Sciences and Mathematics|Earth Sciences|Geochemistry ,DNA ,15. Life on land ,[SDE.ES]Environmental Sciences/Environmental and Society ,EarthArXiv|Physical Sciences and Mathematics ,bepress|Physical Sciences and Mathematics|Earth Sciences|Soil Science ,Lakes ,030104 developmental biology ,Soil water ,Environmental science ,bepress|Physical Sciences and Mathematics|Earth Sciences|Geochemistry ,lcsh:Q - Abstract
Over the last decade, an increasing number of studies have used lake sediment DNA to trace past landscape changes, agricultural activities or human presence. However, the processes responsible for lake sediment formation and sediment properties might affect DNA records via taphonomic and analytical processes. It is crucial to understand these processes to ensure reliable interpretations for “palaeo” studies. Here, we combined plant and mammal DNA metabarcoding analyses with sedimentological and geochemical analyses from three lake-catchment systems that are characterised by different erosion dynamics. The new insights derived from this approach elucidate and assess issues relating to DNA sources and transfer processes. The sources of eroded materials strongly affect the “catchment-DNA” concentration in the sediments. For instance, erosion of upper organic and organo-mineral soil horizons provides a higher amount of plant DNA in lake sediments than deep horizons, bare soils or glacial flours. Moreover, high erosion rates, along with a well-developed hydrographic network, are proposed as factors positively affecting the representation of the catchment flora. The development of open and agricultural landscapes, which favour the erosion, could thus bias the reconstructed landscape trajectory but help the record of these human activities. Regarding domestic animals, pastoral practices and animal behaviour might affect their DNA record because they control the type of source of DNA (“point” vs. “diffuse”).
- Published
- 2019
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