Lake sediment DNA to trace past landscape and agricultural activities: the importance of taphonomy

International audienceke sediment DNA to trace past landscape changes (plant DNA), agricultural activities(plant, mammal and bacteria DNA) as well as the human presence (human-specific bacteriaDNA). However, as all sedimentologists know, the sedimentation in a lake can vary temporallyand spatially depending of the variations of processes at the origin of the sedimentformation. Moreover, depending on the geological, topographical, climatic and ecologicalcontexts, the sedimentation can be very different from a lake to another. These lake sedimentscharacteristics might affect the aDNA archiving in a various ways including potentialbiases related to both, the taphonomic processes (DNA source, transfer and deposit) andthe analytical process. Consequently, it is now crucial to study these processes to ensurereliable interpretations of the lake sediment DNA results and to improve its potential forpalaeoenvironmentalists, archaeologists and historians. In this aim, we combined sedimentological/geochemicalanalyses with DNA metabarcoding analyses (focused on plants andmammals) on three different mountain lake-catchment systems in the Alps (different relativeto their physico-chemical and biological characteristics). We showed the extracellular aDNAretrieved from the sediment mainly comes from upper soil horizons and is transported tothe lake being fixed into/onto soil particles. Lakes with high detrital inputs are thus moresuitable to archive terrestrial DNA than lakes dominated by autochthonous sedimentation.Furthermore, the hydrographical web has to be well developed to provide a good spatial∗Speakersciencesconf.org:pageschambery16:95824representativeness of possible plant patches in the catchment. Specific chemical/biologicalconditions affecting aDNA preservation and/or analysis success were also proposed as explanationfor the non-detection of aDNA in one of the lakes. Other less predictable factors,e.g. pastoral practices and animal behaviour, also affect the archiving of aDNA from domesticanimals. In particular, determining the type of source of DNA (”point” vs ”diffuse”),these factors will affect the detection probability of the animals. All the factors affecting theaDNA record in lake sediments can change over time and can thus significantly affect thereconstructions of plant cover and livestock farming/pasturing histories