Vegetation changes over the last centuries in the Lower Lake Constance region reconstructed from sediment‐core environmental DNA

Abstract Many European lake ecosystems, including their respective catchment areas, underwent anthropogenic environmental changes over the last centuries. This has resulted in changes in the aquatic and terrestrial vegetation, but historical records on the composition of the past vegetation on centennial scale are scarce. In this study, we examined changes in the terrestrial and aquatic plant communities in and around Lower Lake Constance using metabarcoding of sedimentary DNA (sedDNA) of three cores from different sub‐basins covering the past, up to 300 years. We successfully identified an average of c. 3000 sequence variants (molecular operational taxonomic units ‐ MOTUs) and obtained a taxonomically annotated dataset of 127 species, 104 genera, and 72 families. We could detect major changes in the terrestrial and aquatic vegetation of the Lower Lake Constance region by examining the cores. For example, alpha diversity decreased in the last c. 100 years, and this decrease was more pronounced in the terrestrial than in the aquatic plant community. Unlike the terrestrial plant community, the current aquatic plant‐community composition partially resembles the community from before the 20th‐century eutrophication phase of the lake. In addition to changes that can be attributed to anthropogenic impacts, we also captured the effect of DNA sedimentation on the terrestrial DNA diversity representation in sediments during periods of extensive flooding and potentially as a consequence of extremely cold winters. With sedDNA from Lower Lake Constance, we provide a new local dataset to investigate and extend the historical changes of different shoreline habitats and to identify characteristic and invasive plant species. Such highly resolved datasets spanning the past centuries can provide detailed information on human environmental history in densely populated regions that have undergone severe changes in the recent past.