New insights on lake sediment DNA from the catchment: importance of taphonomic and analytical issues on the record quality

Charline Giguet-Covex (1, 2) , Gentile Franscesco Ficetola (3, 4) , Kevin Walsh (1) , Jérôme Poulenard (2) , Manon Bajard (2) , Laurent Fouinat (2) , Pierre Sabatier (2) , Ludovic Gielly (3) , Erwan Messager (2) , Anne Lise Develle (2) , Fernand David (5) , Pierre Taberlet (3) , Elodie Brisset (6, 7, 8) , Frédéric Guiter (6) , Rémi Sinet (6) , Fabien Arnaud (2)

1 BioArch-Department of Archaeology
2 EDYTEM - Environnements, Dynamiques et Territoires de la Montagne
3 LECA - Laboratoire d'Ecologie Alpine
4 Department of Environmental Science and Policy [Milano]
5 CEREGE - Centre européen de recherche et d'enseignement des géosciences de l'environnement
6 IMBE - Institut méditerranéen de biodiversité et d'écologie marine et continentale
7 IPHES - Institut Català de Paleoecologia Humana i Evolució Social
8 Àrea de Prehistòria, Universitat Rovira i Virgili

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").

Keywords: C2FN

Domains: Environmental Sciences; Sciences of the Universe [physics]; Continental interfaces, environment

Charline Giguet-Covex, Gentile Franscesco Ficetola, Kevin Walsh, Jérôme Poulenard, Manon Bajard, et al.. New insights on lake sediment DNA from the catchment: importance of taphonomic and analytical issues on the record quality. Scientific Reports, 2019, 9 (14676), pp.1-21. ⟨10.1038/s41598-019-50339-1⟩. ⟨hal-02320430⟩