Intensity index of pastoral activities reconstructed from Lake Savine sediments, over the last 6500 years


Method used to calculate the index: This index has been calculated on the basis of pastoral indicators obtained from the DNA metabarcoding approach targeting plants (ruderal/nitrophilous taxa associated with pastoralism) and mammals (for domesticated animals). The selected pastoral indicators, here, are Plantago sp. for plants, and Bos and Ovis for mammals. They are standardized by calculating a z-score. Then, the index is calculated as the average of all these standardized indicators.Method used to generate sediment DNA datasets: DNA sequences were generated 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 Further filtering treatments were then applied, as also described in Giguet-Covex et al. 2019. These second treatments allow the removal of 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. Multiple analytical replicates by samples were performed (12 for both, the plants and 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 252 data points
Discipline Earth System Research
Spatial Coverage (6.914 LON, 45.175 LAT); North-western Alps