Giguet-Covex, Charline (2023): Nature of agricultural and pastoral activities and main trees in Lake La Thuile catchment over the last 6400 years [dataset]. PANGAEA, https://doi.org/10.1594/PANGAEA.958842, In: Giguet-Covex, Charline; Chen, Wentao; Ficetola, Francesco Gentile; Gielly, Ludovic; Pansu, Johan (2023): Plant DNA analyses, nature and intensity of human activities, and erosion intensities in the North-western Alps over the last 4000-6000 years inferred from lake sediments [dataset bundled publication]. PANGAEA, https://doi.org/10.1594/PANGAEA.958732
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Keyword(s):
Related to:
Giguet-Covex, Charline; Bajard, Manon; Chen, Wentao; Walsh, Kevin; Rey, Pierre-Jérôme; Messager, Erwan; Etienne, David; Sabatier, Pierre; Ficetola, Francesco Gentile; Gielly, Ludovic; Blanchet, C; Guffond, Christophe; Chiquet, Patricia; Arnaud, Fabien; Poulenard, Jérôme (2023): Long-term trajectories of mountain agro-ecosystems in the North-Western Alps. Regional Environmental Change, 23(2), 58, https://doi.org/10.1007/s10113-023-02030-5
Coverage:
Latitude: 45.530587 * Longitude: 6.056265
Date/Time Start: 2010-04-26T00:00:00 * Date/Time End: 2010-04-26T00:00:00
Minimum Elevation: 874.0 m * Maximum Elevation: 874.0 m
Event(s):
Comment:
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 https://doi.org/10.1038/s41598-019-50339-1). 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.
Parameter(s):
| # | Name | Short Name | Unit | Principal Investigator | Method/Device | Comment |
|---|---|---|---|---|---|---|
| 1 | Lake | Lake | Giguet-Covex, Charline | |||
| 2 | AGE | Age | ka BP | Giguet-Covex, Charline | Age model, radiocarbon dates and short radionuclides | Geocode |
| 3 | Age | Age | a AD/CE | Giguet-Covex, Charline | Age model, radiocarbon dates and short radionuclides | |
| 4 | Period, cultural | Period cultural | Giguet-Covex, Charline | |||
| 5 | Bos | Bos | # | Giguet-Covex, Charline | DNA metabarcoding approach | Number of positive replicates over 12 |
| 6 | Ovis | Ovis | # | Giguet-Covex, Charline | DNA metabarcoding approach | Number of positive replicates over 12 |
| 7 | Abies | Abi | # | Giguet-Covex, Charline | DNA metabarcoding approach | Number of positive replicates over 4 |
| 8 | Fagus | Fag | # | Giguet-Covex, Charline | DNA metabarcoding approach | Number of positive replicates over 4 |
| 9 | Picea | Pic | # | Giguet-Covex, Charline | DNA metabarcoding approach | Number of positive replicates over 4 |
| 10 | Alnus | Aln | # | Giguet-Covex, Charline | DNA metabarcoding approach | Number of positive replicates over 4 |
| 11 | Plantago | Pla | # | Giguet-Covex, Charline | DNA metabarcoding approach | Number of positive replicates over 4 |
| 12 | Rumex | Rum | # | Giguet-Covex, Charline | DNA metabarcoding approach | Number of positive replicates over 4 |
| 13 | Cannabis sativa | Can.s | # | Giguet-Covex, Charline | DNA metabarcoding approach | Number of positive replicates over 4 |
| 14 | Vicia faba | Vic.f | # | Giguet-Covex, Charline | DNA metabarcoding approach | Number of positive replicates over 4 |
| 15 | Juglandaceae | Jugae | # | Giguet-Covex, Charline | DNA metabarcoding approach | Number of positive replicates over 4 |
| 16 | Prunus | Prn | # | Giguet-Covex, Charline | DNA metabarcoding approach | Number of positive replicates over 4 |
| 17 | Pyrus | Yus | # | Giguet-Covex, Charline | DNA metabarcoding approach | Number of positive replicates over 4 |
| 18 | Maleae | Maleae | # | Giguet-Covex, Charline | DNA metabarcoding approach | Number of positive replicates over 4 |
| 19 | Vitaceae | Viteae | # | Giguet-Covex, Charline | DNA metabarcoding approach | Number of positive replicates over 4 |
License:
Creative Commons Attribution 4.0 International (CC-BY-4.0)
Status:
Curation Level: Enhanced curation (CurationLevelC)
Size:
722 data points