Erosion regime controls sediment environmental DNA-based community reconstruction

Analysis of environmental DNA detected in lake sediments shows promise to become a great paleoecological technique that can provide detailed information about organism communities living in past environments. However, when interpreting sedimentary environmental DNA records, it is of crucial importance to separate ecosystem responses to large-scale environmental change from ‘noise’ caused by changes in sediment provenance or potential post-depositional DNA mobility. In this study, we show that plant and mammalian communities reconstructed from sediments are strongly affected by sediment provenance, but unaffected by vertical mobility of DNA after sediment deposition. We observe that DNA from aquatic plants was abundant in background sediment, while embedded detrital event layers (sediment deposited under erosion events) primarily contained terrestrial plants; hence, vertical mobility of aquatic plant DNA across sediment layers was negligible within our studied lakes. About 33% of the ide..., The uploaded material contains sediment DNA metabarcoding data targeting plants (trnL gene) and mammals (16S gene). It consists of two data sets:

Plant and mammalian DNA sequences from a Holocene sediment sequence that was retrieved from Lake Grosssee, Flumserberg, Eastern Switzerland.
Plant and mammalian DNA sequences from surface sediments that were recovered from seven lakes across the Central Alps.

The samples in each data set are paired to contain a sample of hemipelagic background sediment and a detrital event layer deposited during a heavy precipitation event, which is of similar age compared to the background sediment.
All DNA libraries include extraction blanks (named ‘K1_date’ and ‘K2_date’ for each of the extraction runs, respectively), which were run along the extractions with no sediment input, as well as PCR negatives (named ‘Neg1-8’), which contain PCR mix and primers, but no DNA. Sample tags are dual-unique (twin tagging) and hence, PCR blanks are not specifically outl..., Raw sequencing data in .fq.gz format. Files need to be decompressed and can be run through an Obitools3 pipeline, for example., # Erosion regime controls sediment environmental DNA-based community reconstruction

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Analysis of environmental DNA detected in lake sediments shows promise to become a great paleoecological technique that can provide detailed information about organism communities living in past environments. However, when interpreting sedimentary environmental DNA records, it is of crucial importance to separate ecosystem responses to large-scale environmental change from ‘noise’ caused by changes in sediment provenance or potential post-depositional DNA mobility. In this study, we show that plant and mammalian communities reconstructed from sediments are strongly affected by sediment provenance, but unaffected by vertical mobility of DNA after sediment deposition. We observe that DNA from aquatic plants was abundant in background sediment, while embedded detrital event layers (sediment deposited under erosion events) primarily contained terrestrial plants; hence, vertical mobility of aquatic plan...