Nature of agricultural and pastoral activities and main trees in Lake La Thuile catchment over the last 6400 years


Method used to produce the sedimentary DNA datasets: DNA sequences were produced by using g (5'-GGGCAATCCTGAGCCAA-3') and h (5'-CCATTGAGTCTCTGCACCTATC-3') primers for plants and MamP007F (5'-CGAGAAGACCCTATGGAGCT-3') and MamP007R (5'-CCGAGGTCRCCCCAACC-3') primers and the human-blocking primer (5'-GGAGCTTTAATTTATTAATGCAAACAGTACCC-3') for mammals. The sequences have been produced by the Illumina technology (HiSeq instrument). The bioinformatic treatment of the sequences was operated applying the Obitool program (Boyer, F. et al. OBITOOLS:aUNIX-inspired software package for DNA metabarcoding. Mol. Ecol. Resour. 16, 176–182 (2016)) and following the procedure described in Giguet-Covex et al. New insights on lake sediment DNA from the catchment: importance of taphonomic and analytical issues on the record quality. Scientific Reports. 9, 14676 (2019) (DOI Then, other filtering processing were performed as also described in Giguet-Covex et al. 2019. These second treatments allow for removing 1) taxa assigned to a reference taxon at <95 % of sequence identity, 2) potential contaminations (based on sampling, extraction and PCR controls, and recognition of exotic taxa) and 3) stochastic detections. Several analytical replicates by samples were performed (4 for the plants and 12 for the mammals). Data are presented in number of positive replicates by sample. A replicate is considered as positive if more than 5 sequences are detected.

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Metadata Access
Creator Giguet-Covex, Charline ORCID logo
Publisher PANGAEA
Publication Year 2023
Rights Creative Commons Attribution 4.0 International;
OpenAccess true
Resource Type Dataset
Format text/tab-separated-values
Size 722 data points
Discipline Earth System Research
Spatial Coverage (6.056 LON, 45.531 LAT); North-western Alps