Method used to calculate the index: This index has been calculated on the basis of agro-pastoral indicators obtained from the DNA metabarcoding approach targeting plants (ruderal/nitrophilous taxa associated with pastoralism and crops) and mammals (for domesticated animals). The selected agro-pastoral indicators, here, are Plantago sp., Rumex sp., Cannabis sativa, Vicia faba, Juglandaceae, Pyrus sp., Prunus sp., and Vitaceae 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 DNAmetabarcoding. 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 https://doi.org/10.1038/s41598-019-50339-1). 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 (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.
