Giguet-Covex, Charline; Chen, Wentao; Ficetola, Francesco Gentile; Gielly, Ludovic; Pansu, Johan (2023): Plant DNA taxa detected in Lake Verney sediments (North-western Alps) over the last 4600 years [dataset]. PANGAEA, https://doi.org/10.1594/PANGAEA.958683, In: Giguet-Covex, C et al. (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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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
Funding:
European Commission (EC), grant/award no. 655331: agroPastoral Activities and effects on Landscapes and ErOsion dynAmics in the alps: a new insight from Geological appRoaches and lake sedIment DNA (PALEO-AGRI)
Coverage:
Latitude: 45.687916 * Longitude: 6.057317
Date/Time Start: 2013-01-24T00:00:00 * Date/Time End: 2013-01-24T00:00:00
Minimum Elevation: 2090.0 m * Maximum Elevation: 2090.0 m
Event(s):
VER13_I * Latitude: 45.687916 * Longitude: 6.057317 * Date/Time: 2013-01-24T00:00:00 * Elevation: 2090.0 m * IGSN: IEFRA086X * Location: North-western Alps * Method/Device: Sediment corer (SEDCO)
Comment:
This dataset contains plant taxa detected by sedimentary DNA analyses. The dataset is presented in number of DNA sequences by replicate of analyses (12 PCR replicates). It has been generated applying the DNA metabarcoding approach on the upper 1.4-m of sediments. The 2.4-m long sediment core was retrieved by using an Uwitec piston coring device. The primers used are g (5'-GGGCAATCCTGAGCCAA-3') and h (5'-CCATTGAGTCTCTGCACCTATC-3') (Taberlet, P., et al. Power and limitations of the chloroplast trn L (UAA) intron for plant DNA barcoding. Nucleic acids research, 35(3), e14-e14. (2007)). The sequences were then 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.
Parameter(s):
| # | Name | Short Name | Unit | Principal Investigator | Method/Device | Comment |
|---|---|---|---|---|---|---|
| 1 | AGE | Age | ka BP | Giguet-Covex, Charline | Geocode | |
| 2 | Alchemilla | Alc | # | Giguet-Covex, Charline | DNA metabarcoding approach, gh primers | Number of DNA sequences by replicate of analyses |
| 3 | Anthyllis vulneraria | Any.v | # | Giguet-Covex, Charline | DNA metabarcoding approach, gh primers | Number of DNA sequences by replicate of analyses |
| 4 | Apiaceae | Apiae | # | Giguet-Covex, Charline | DNA metabarcoding approach, gh primers | Number of DNA sequences by replicate of analyses |
| 5 | Arctostaphylos uva-ursi | Arc.u-u | # | Giguet-Covex, Charline | DNA metabarcoding approach, gh primers | Number of DNA sequences by replicate of analyses |
| 6 | Asteraceae | Astae | # | Giguet-Covex, Charline | DNA metabarcoding approach, gh primers | Number of DNA sequences by replicate of analyses |
| 7 | Bartsia alpina | B. alpina | # | Giguet-Covex, Charline | DNA metabarcoding approach, gh primers | Number of DNA sequences by replicate of analyses |
| 8 | Betulaceae | Betaea | # | Giguet-Covex, Charline | DNA metabarcoding approach, gh primers | Number of DNA sequences by replicate of analyses |
| 9 | Caltha | Clh | # | Giguet-Covex, Charline | DNA metabarcoding approach, gh primers | Number of DNA sequences by replicate of analyses |
| 10 | Campanulaceae | Camae | # | Giguet-Covex, Charline | DNA metabarcoding approach, gh primers | Number of DNA sequences by replicate of analyses |
| 11 | Carex | Cax | # | Giguet-Covex, Charline | DNA metabarcoding approach, gh primers | Number of DNA sequences by replicate of analyses |
| 12 | Cerastium cerastoides | C. cerastoides | # | Giguet-Covex, Charline | DNA metabarcoding approach, gh primers | Number of DNA sequences by replicate of analyses |
| 13 | Colurieae | Colurieae | # | Giguet-Covex, Charline | DNA metabarcoding approach, gh primers | Number of DNA sequences by replicate of analyses |
| 14 | Cupressaceae | Cupae | # | Giguet-Covex, Charline | DNA metabarcoding approach, gh primers | Number of DNA sequences by replicate of analyses |
| 15 | Dryadoideae | Dryadoideae | # | Giguet-Covex, Charline | DNA metabarcoding approach, gh primers | Number of DNA sequences by replicate of analyses |
| 16 | Equisetum | Equ | # | Giguet-Covex, Charline | DNA metabarcoding approach, gh primers | Number of DNA sequences by replicate of analyses |
| 17 | Geranium | Ger | # | Giguet-Covex, Charline | DNA metabarcoding approach, gh primers | Number of DNA sequences by replicate of analyses |
| 18 | Helianthemum nummularium | Hel.n | # | Giguet-Covex, Charline | DNA metabarcoding approach, gh primers | Number of DNA sequences by replicate of analyses |
| 19 | Hypericum | Hyp | # | Giguet-Covex, Charline | DNA metabarcoding approach, gh primers | Number of DNA sequences by replicate of analyses |
| 20 | Mentheae | Mentheae | # | Giguet-Covex, Charline | DNA metabarcoding approach, gh primers | Number of DNA sequences by replicate of analyses |
| 21 | Myosotis | Mst | # | Giguet-Covex, Charline | DNA metabarcoding approach, gh primers | Number of DNA sequences by replicate of analyses |
| 22 | Onagraceae | Onaae | # | Giguet-Covex, Charline | DNA metabarcoding approach, gh primers | Number of DNA sequences by replicate of analyses |
| 23 | Picea | Pic | # | Giguet-Covex, Charline | DNA metabarcoding approach, gh primers | Number of DNA sequences by replicate of analyses |
| 24 | Pinaceae | Pinae | # | Giguet-Covex, Charline | DNA metabarcoding approach, gh primers | Number of DNA sequences by replicate of analyses |
| 25 | Pinus | Pin | # | Giguet-Covex, Charline | DNA metabarcoding approach, gh primers | Number of DNA sequences by replicate of analyses |
| 26 | Plantago | Pla | # | Giguet-Covex, Charline | DNA metabarcoding approach, gh primers | Number of DNA sequences by replicate of analyses |
| 27 | Poeae | Poeae | # | Giguet-Covex, Charline | DNA metabarcoding approach, gh primers | Number of DNA sequences by replicate of analyses |
| 28 | Potentilla | Pti | # | Giguet-Covex, Charline | DNA metabarcoding approach, gh primers | Number of DNA sequences by replicate of analyses |
| 29 | Ranunculus | Ran | # | Giguet-Covex, Charline | DNA metabarcoding approach, gh primers | Number of DNA sequences by replicate of analyses |
| 30 | Ranunculus | Ran | # | Giguet-Covex, Charline | DNA metabarcoding approach, gh primers | Number of DNA sequences by replicate of analyses |
| 31 | Rhodoreae | Rhodoreae | # | Giguet-Covex, Charline | DNA metabarcoding approach, gh primers | Number of DNA sequences by replicate of analyses |
| 32 | Rumex | Rum | # | Giguet-Covex, Charline | DNA metabarcoding approach, gh primers | Number of DNA sequences by replicate of analyses |
| 33 | Sagina | Sag | # | Giguet-Covex, Charline | DNA metabarcoding approach, gh primers | Number of DNA sequences by replicate of analyses |
| 34 | Saxifraga oppositofolia | S. oppositofolia | # | Giguet-Covex, Charline | DNA metabarcoding approach, gh primers | Number of DNA sequences by replicate of analyses |
| 35 | Sempervivum tectorum | S. tectorum | # | Giguet-Covex, Charline | DNA metabarcoding approach, gh primers | Number of DNA sequences by replicate of analyses |
| 36 | Solanaceae | Solae | # | Giguet-Covex, Charline | DNA metabarcoding approach, gh primers | Number of DNA sequences by replicate of analyses |
| 37 | Trifolium | Tri | # | Giguet-Covex, Charline | DNA metabarcoding approach, gh primers | Number of DNA sequences by replicate of analyses |
| 38 | Trifolium | Tri | # | Giguet-Covex, Charline | DNA metabarcoding approach, gh primers | Number of DNA sequences by replicate of analyses |
| 39 | Trifolium pallescens | Tri.pa | # | Giguet-Covex, Charline | DNA metabarcoding approach, gh primers | Number of DNA sequences by replicate of analyses |
| 40 | Vaccinium uliginosum | Vac.u | # | Giguet-Covex, Charline | DNA metabarcoding approach, gh primers | Number of DNA sequences by replicate of analyses |
| 41 | Vaccinium vitis-idaea | V. vitis-idaea | # | Giguet-Covex, Charline | DNA metabarcoding approach, gh primers | Number of DNA sequences by replicate of analyses |
| 42 | Veratrum | Vum | # | Giguet-Covex, Charline | DNA metabarcoding approach, gh primers | Number of DNA sequences by replicate of analyses |
| 43 | Veronica alpina | V. alpina | # | Giguet-Covex, Charline | DNA metabarcoding approach, gh primers | Number of DNA sequences by replicate of analyses |
| 44 | Caprifoliaceae | Capeae | # | Giguet-Covex, Charline | DNA metabarcoding approach, gh primers | Number of DNA sequences by replicate of analyses |
| 45 | Lathyrus pratensis | L. pratensis | # | Giguet-Covex, Charline | DNA metabarcoding approach, gh primers | Number of DNA sequences by replicate of analyses |
License:
Creative Commons Attribution 4.0 International (CC-BY-4.0)
Status:
Curation Level: Enhanced curation (CurationLevelC)
Size:
20328 data points
Download Data
View dataset as HTML (shows only first 2000 rows)