Giguet-Covex, Charline; Chen, Wentao; Ficetola, Francesco Gentile; Gielly, Ludovic; Pansu, Johan (2023): Plant DNA taxa detected in Lake Savine sediments (North-western Alps) over the last 8000 years [dataset]. PANGAEA, https://doi.org/10.1594/PANGAEA.958675, 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: 45.175070 * Longitude: 6.913838
Date/Time Start: 2014-03-05T00:00:00 * Date/Time End: 2014-03-05T00:00:00
Minimum Elevation: 2443.0 m * Maximum Elevation: 2443.0 m
Event(s):
SAV14 * Latitude: 45.175070 * Longitude: 6.913838 * Date/Time: 2014-03-05T00:00:00 * Elevation: 2443.0 m * IGSN: IEFRA0871 * 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 a 7.75-m long sediment cores retrieved by using an Uwitec piston coring device directly from the ice-covered surface of the lake. 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 analyse |
| 3 | Apiaceae | Apiae | # | Giguet-Covex, Charline | DNA metabarcoding approach, gh primers | Number of DNA sequences by replicate of analyse |
| 4 | Asteraceae | Astae | # | Giguet-Covex, Charline | DNA metabarcoding approach, gh primers | Number of DNA sequences by replicate of analyse |
| 5 | Asteraceae | Astae | # | Giguet-Covex, Charline | DNA metabarcoding approach, gh primers | Number of DNA sequences by replicate of analyse |
| 6 | Asteroideae | Asteroideae | # | Giguet-Covex, Charline | DNA metabarcoding approach, gh primers | Number of DNA sequences by replicate of analyse |
| 7 | Bartsia alpina | B. alpina | # | Giguet-Covex, Charline | DNA metabarcoding approach, gh primers | Number of DNA sequences by replicate of analyse |
| 8 | Betulaceae | Betaea | # | Giguet-Covex, Charline | DNA metabarcoding approach, gh primers | Number of DNA sequences by replicate of analyse |
| 9 | Boraginaceae | Borae | # | Giguet-Covex, Charline | DNA metabarcoding approach, gh primers | Number of DNA sequences by replicate of analyse |
| 10 | Brassicaceae | Braae | # | Giguet-Covex, Charline | DNA metabarcoding approach, gh primers | Number of DNA sequences by replicate of analyse |
| 11 | Campanulaceae | Camae | # | Giguet-Covex, Charline | DNA metabarcoding approach, gh primers | Number of DNA sequences by replicate of analyse |
| 12 | Cardamineae | Cardamineae | # | Giguet-Covex, Charline | DNA metabarcoding approach, gh primers | Number of DNA sequences by replicate of analyse |
| 13 | Carex | Cax | # | Giguet-Covex, Charline | DNA metabarcoding approach, gh primers | Number of DNA sequences by replicate of analyse |
| 14 | Carex | Cax | # | Giguet-Covex, Charline | DNA metabarcoding approach, gh primers | Number of DNA sequences by replicate of analyse |
| 15 | Caryophyllaceae | Cphae | # | Giguet-Covex, Charline | DNA metabarcoding approach, gh primers | Number of DNA sequences by replicate of analyse |
| 16 | Cerastium cerastoides | C. cerastoides | # | Giguet-Covex, Charline | DNA metabarcoding approach, gh primers | Number of DNA sequences by replicate of analyse |
| 17 | Colurieae | Colurieae | # | Giguet-Covex, Charline | DNA metabarcoding approach, gh primers | Number of DNA sequences by replicate of analyse |
| 18 | Cupressaceae | Cupae | # | Giguet-Covex, Charline | DNA metabarcoding approach, gh primers | Number of DNA sequences by replicate of analyse |
| 19 | Euphrasia | Eur | # | Giguet-Covex, Charline | DNA metabarcoding approach, gh primers | Number of DNA sequences by replicate of analyse |
| 20 | Mentheae | Mentheae | # | Giguet-Covex, Charline | DNA metabarcoding approach, gh primers | Number of DNA sequences by replicate of analyse |
| 21 | Myosotis | Mst | # | Giguet-Covex, Charline | DNA metabarcoding approach, gh primers | Number of DNA sequences by replicate of analyse |
| 22 | Onagraceae | Onaae | # | Giguet-Covex, Charline | DNA metabarcoding approach, gh primers | Number of DNA sequences by replicate of analyse |
| 23 | Oxyria digyna | Oxy.d | # | Giguet-Covex, Charline | DNA metabarcoding approach, gh primers | Number of DNA sequences by replicate of analyse |
| 24 | Plantago | Pla | # | Giguet-Covex, Charline | DNA metabarcoding approach, gh primers | Number of DNA sequences by replicate of analyse |
| 25 | Poeae | Poeae | # | Giguet-Covex, Charline | DNA metabarcoding approach, gh primers | Number of DNA sequences by replicate of analyse |
| 26 | Poeae | Poeae | # | Giguet-Covex, Charline | DNA metabarcoding approach, gh primers | Number of DNA sequences by replicate of analyse |
| 27 | Poeae | Poeae | # | Giguet-Covex, Charline | DNA metabarcoding approach, gh primers | Number of DNA sequences by replicate of analyse |
| 28 | Potentilla | Pti | # | Giguet-Covex, Charline | DNA metabarcoding approach, gh primers | Number of DNA sequences by replicate of analyse |
| 29 | Primulaceae | Priae | # | Giguet-Covex, Charline | DNA metabarcoding approach, gh primers | Number of DNA sequences by replicate of analyse |
| 30 | Ranunculaceae | Ranae | # | Giguet-Covex, Charline | DNA metabarcoding approach, gh primers | Number of DNA sequences by replicate of analyse |
| 31 | Ranunculus | Ran | # | Giguet-Covex, Charline | DNA metabarcoding approach, gh primers | Number of DNA sequences by replicate of analyse |
| 32 | Ranunculus glacialis | Ran.g | # | Giguet-Covex, Charline | DNA metabarcoding approach, gh primers | Number of DNA sequences by replicate of analyse |
| 33 | Rumex | Rum | # | Giguet-Covex, Charline | DNA metabarcoding approach, gh primers | Number of DNA sequences by replicate of analyse |
| 34 | Saxifraga | Sax | # | Giguet-Covex, Charline | DNA metabarcoding approach, gh primers | Number of DNA sequences by replicate of analyse |
| 35 | Saxifraga oppositofolia | S. oppositofolia | # | Giguet-Covex, Charline | DNA metabarcoding approach, gh primers | Number of DNA sequences by replicate of analyse |
| 36 | Sempervivum tectorum | S. tectorum | # | Giguet-Covex, Charline | DNA metabarcoding approach, gh primers | Number of DNA sequences by replicate of analyse |
| 37 | Silene acaulis | Sil.a | # | Giguet-Covex, Charline | DNA metabarcoding approach, gh primers | Number of DNA sequences by replicate of analyse |
| 38 | Solanaceae | Solae | # | Giguet-Covex, Charline | DNA metabarcoding approach, gh primers | Number of DNA sequences by replicate of analyse |
| 39 | Soldanella | Sld | # | Giguet-Covex, Charline | DNA metabarcoding approach, gh primers | Number of DNA sequences by replicate of analyse |
| 40 | Trifolium | Tri | # | Giguet-Covex, Charline | DNA metabarcoding approach, gh primers | Number of DNA sequences by replicate of analyse |
| 41 | Trifolium pallescens | Tri.pa | # | Giguet-Covex, Charline | DNA metabarcoding approach, gh primers | Number of DNA sequences by replicate of analyse |
| 42 | Vaccinium uliginosium | V. uliginosium | # | Giguet-Covex, Charline | DNA metabarcoding approach, gh primers | Number of DNA sequences by replicate of analyse |
| 43 | Veronica | Ver | # | Giguet-Covex, Charline | DNA metabarcoding approach, gh primers | Number of DNA sequences by replicate of analyse |
| 44 | Viola tricolor | Vio.t | # | Giguet-Covex, Charline | DNA metabarcoding approach, gh primers | Number of DNA sequences by replicate of analyse |
License:
Creative Commons Attribution 4.0 International (CC-BY-4.0)
Status:
Curation Level: Enhanced curation (CurationLevelC)
Size:
37152 data points
Download Data
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