Giguet-Covex, Charline; Ficetola, Francesco Gentile; Bajard, Manon: Plant DNA taxa detected in Lake Gers sediments (North-western Alps) over the last 4600 years [dataset]. PANGAEA, https://doi.pangaea.de/10.1594/PANGAEA.958665 (dataset in review), 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
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: 46.027233 * Longitude: 6.729512
Date/Time Start: 2016-01-18T00:00:00 * Date/Time End: 2016-01-18T00:00:00
Minimum Elevation: 1532.0 m * Maximum Elevation: 1532.0 m
Event(s):
Comment:
This dataset contains plant taxa detected by sedimentary DNA analyses. The dataset is presented in number of DNA sequences by replicate of analyses (8 PCR replicates). It has been produced by applying the DNA metabarcoding approach on a 5.8-m long sediment cores retrieved by using an uwitec piston corer. 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). Then, other filtering processing were performed as also described in Giguet-Covex et al. 2019. This second treatment 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 | Acer | Ace | # | Giguet-Covex, Charline | DNA metabarcoding approach, gh primers | Number of DNA sequences by replicate of analyses |
| 3 | Ajuga | Ajuga | # | Giguet-Covex, Charline | DNA metabarcoding approach, gh primers | Number of DNA sequences by replicate of analyses |
| 4 | Alchemilla | Alc | # | Giguet-Covex, Charline | DNA metabarcoding approach, gh primers | Number of DNA sequences by replicate of analyses |
| 5 | Alnus | Aln | # | Giguet-Covex, Charline | DNA metabarcoding approach, gh primers | Number of DNA sequences by replicate of analyses |
| 6 | Anemoneae | Anemoneae | # | Giguet-Covex, Charline | DNA metabarcoding approach, gh primers | Number of DNA sequences by replicate of analyses |
| 7 | Anthyllis vulneraria | Any.v | # | Giguet-Covex, Charline | DNA metabarcoding approach, gh primers | Number of DNA sequences by replicate of analyses |
| 8 | Apioideae | Apioideae | # | Giguet-Covex, Charline | DNA metabarcoding approach, gh primers | Number of DNA sequences by replicate of analyses |
| 9 | Aquifoliaceae | Aquifoliaceae | # | Giguet-Covex, Charline | DNA metabarcoding approach, gh primers | Number of DNA sequences by replicate of analyses |
| 10 | Asteraceae | Astae | # | Giguet-Covex, Charline | DNA metabarcoding approach, gh primers | Number of DNA sequences by replicate of analyses |
| 11 | Asterales | Asterales | # | Giguet-Covex, Charline | DNA metabarcoding approach, gh primers | Number of DNA sequences by replicate of analyses |
| 12 | Asteroideae | Asteroideae | # | Giguet-Covex, Charline | DNA metabarcoding approach, gh primers | Number of DNA sequences by replicate of analyses |
| 13 | Astrantia | Asr | # | Giguet-Covex, Charline | DNA metabarcoding approach, gh primers | Number of DNA sequences by replicate of analyses |
| 14 | Athyrium | Ath | # | Giguet-Covex, Charline | DNA metabarcoding approach, gh primers | Number of DNA sequences by replicate of analyses |
| 15 | Bartsia alpina | B. alpina | # | Giguet-Covex, Charline | DNA metabarcoding approach, gh primers | Number of DNA sequences by replicate of analyses |
| 16 | Veronica beccabunga | Ver.b | # | Giguet-Covex, Charline | DNA metabarcoding approach, gh primers | Number of DNA sequences by replicate of analyses |
| 17 | Betulaceae | Betaea | # | Giguet-Covex, Charline | DNA metabarcoding approach, gh primers | Number of DNA sequences by replicate of analyses |
| 18 | Boraginaceae | Borae | # | Giguet-Covex, Charline | DNA metabarcoding approach, gh primers | Number of DNA sequences by replicate of analyses |
| 19 | Campanulaceae | Camae | # | Giguet-Covex, Charline | DNA metabarcoding approach, gh primers | Number of DNA sequences by replicate of analyses |
| 20 | Epilobium angustifolium | Epi.a | # | Giguet-Covex, Charline | DNA metabarcoding approach, gh primers | Number of DNA sequences by replicate of analyses |
| 21 | Colurieae | Colurieae | # | Giguet-Covex, Charline | DNA metabarcoding approach, gh primers | Number of DNA sequences by replicate of analyses |
| 22 | Cupressaceae | Cupae | # | Giguet-Covex, Charline | DNA metabarcoding approach, gh primers | Number of DNA sequences by replicate of analyses |
| 23 | Dactylis glomerata | D. glomerata | # | Giguet-Covex, Charline | DNA metabarcoding approach, gh primers | Number of DNA sequences by replicate of analyses |
| 24 | Dryopteridaceae | Dryoceae | # | Giguet-Covex, Charline | DNA metabarcoding approach, gh primers | Number of DNA sequences by replicate of analyses |
| 25 | Epilobieae | Epilobieae | # | Giguet-Covex, Charline | DNA metabarcoding approach, gh primers | Number of DNA sequences by replicate of analyses |
| 26 | Euphorbia esula | E. esula | # | Giguet-Covex, Charline | DNA metabarcoding approach, gh primers | Number of DNA sequences by replicate of analyses |
| 27 | Euphrasia | Eur | # | Giguet-Covex, Charline | DNA metabarcoding approach, gh primers | Number of DNA sequences by replicate of analyses |
| 28 | Gentiana | Gen | # | Giguet-Covex, Charline | DNA metabarcoding approach, gh primers | Number of DNA sequences by replicate of analyses |
| 29 | Geranium | Ger | # | Giguet-Covex, Charline | DNA metabarcoding approach, gh primers | Number of DNA sequences by replicate of analyses |
| 30 | Hedysarum hedysaroides | Hdy.h | # | Giguet-Covex, Charline | DNA metabarcoding approach, gh primers | Number of DNA sequences by replicate of analyses |
| 31 | Helianthemum nummularium | Hel.n | # | Giguet-Covex, Charline | DNA metabarcoding approach, gh primers | Number of DNA sequences by replicate of analyses |
| 32 | Hypericum | Hyp | # | Giguet-Covex, Charline | DNA metabarcoding approach, gh primers | Number of DNA sequences by replicate of analyses |
| 33 | Knautia | Kna | # | Giguet-Covex, Charline | DNA metabarcoding approach, gh primers | Number of DNA sequences by replicate of analyses |
| 34 | Lamiales | Lamiales | # | Giguet-Covex, Charline | DNA metabarcoding approach, gh primers | Number of DNA sequences by replicate of analyses |
| 35 | Leontodon | Leontodon | # | Giguet-Covex, Charline | DNA metabarcoding approach, gh primers | Number of DNA sequences by replicate of analyses |
| 36 | Lotus | Lot | # | Giguet-Covex, Charline | DNA metabarcoding approach, gh primers | Number of DNA sequences by replicate of analyses |
| 37 | Luzula | Luz | # | Giguet-Covex, Charline | DNA metabarcoding approach, gh primers | Number of DNA sequences by replicate of analyses |
| 38 | Maleae | Maleae | # | Giguet-Covex, Charline | DNA metabarcoding approach, gh primers | Number of DNA sequences by replicate of analyses |
| 39 | Mentheae | Mentheae | # | Giguet-Covex, Charline | DNA metabarcoding approach, gh primers | Number of DNA sequences by replicate of analyses |
| 40 | Picea | Pic | # | Giguet-Covex, Charline | DNA metabarcoding approach, gh primers | Number of DNA sequences by replicate of analyses |
| 41 | Pinaceae | Pinae | # | Giguet-Covex, Charline | DNA metabarcoding approach, gh primers | Number of DNA sequences by replicate of analyses |
| 42 | Plantago | Pla | # | Giguet-Covex, Charline | DNA metabarcoding approach, gh primers | Number of DNA sequences by replicate of analyses |
| 43 | Poeae | Poeae | # | Giguet-Covex, Charline | DNA metabarcoding approach, gh primers | Number of DNA sequences by replicate of analyses |
| 44 | Polygonoideae | Polygonoideae | # | Giguet-Covex, Charline | DNA metabarcoding approach, gh primers | Number of DNA sequences by replicate of analyses |
| 45 | Polytrichaceae | Polytrichaceae | # | Giguet-Covex, Charline | DNA metabarcoding approach, gh primers | Number of DNA sequences by replicate of analyses |
| 46 | Populus | Pop | # | Giguet-Covex, Charline | DNA metabarcoding approach, gh primers | Number of DNA sequences by replicate of analyses |
| 47 | Potamogeton | Pot | # | Giguet-Covex, Charline | DNA metabarcoding approach, gh primers | Number of DNA sequences by replicate of analyses |
| 48 | Potentilla | Pti | # | Giguet-Covex, Charline | DNA metabarcoding approach, gh primers | Number of DNA sequences by replicate of analyses |
| 49 | Prunus | Prn | # | Giguet-Covex, Charline | DNA metabarcoding approach, gh primers | Number of DNA sequences by replicate of analyses |
| 50 | Ranunculus | Ran | # | Giguet-Covex, Charline | DNA metabarcoding approach, gh primers | Number of DNA sequences by replicate of analyses |
| 51 | Rhodoreae | Rhodoreae | # | Giguet-Covex, Charline | DNA metabarcoding approach, gh primers | Number of DNA sequences by replicate of analyses |
| 52 | Rosoideae | Rosoideae | # | Giguet-Covex, Charline | DNA metabarcoding approach, gh primers | Number of DNA sequences by replicate of analyses |
| 53 | Rubus idaeus | Rub.i | # | Giguet-Covex, Charline | DNA metabarcoding approach, gh primers | Number of DNA sequences by replicate of analyses |
| 54 | Rumex | Rum | # | Giguet-Covex, Charline | DNA metabarcoding approach, gh primers | Number of DNA sequences by replicate of analyses |
| 55 | Rumex scutatus | R. scutatus | # | Giguet-Covex, Charline | DNA metabarcoding approach, gh primers | Number of DNA sequences by replicate of analyses |
| 56 | Sanguisorbinae | Sanguisorbinae | # | Giguet-Covex, Charline | DNA metabarcoding approach, gh primers | Number of DNA sequences by replicate of analyses |
| 57 | Scorzoneroides | Scorzoneroides | # | Giguet-Covex, Charline | DNA metabarcoding approach, gh primers | Number of DNA sequences by replicate of analyses |
| 58 | Silene | Sil | # | Giguet-Covex, Charline | DNA metabarcoding approach, gh primers | Number of DNA sequences by replicate of analyses |
| 59 | Trifolium | Tri | # | Giguet-Covex, Charline | DNA metabarcoding approach, gh primers | Number of DNA sequences by replicate of analyses |
| 60 | Ulmaceae | Ulmeae | # | Giguet-Covex, Charline | DNA metabarcoding approach, gh primers | Number of DNA sequences by replicate of analyses |
| 61 | Urtica | Urt | # | Giguet-Covex, Charline | DNA metabarcoding approach, gh primers | Number of DNA sequences by replicate of analyses |
| 62 | Vaccinium | Vac | # | Giguet-Covex, Charline | DNA metabarcoding approach, gh primers | Number of DNA sequences by replicate of analyses |
| 63 | Vaccinium | Vac | # | Giguet-Covex, Charline | DNA metabarcoding approach, gh primers | Number of DNA sequences by replicate of analyses |
| 64 | Valeriana | Val | # | Giguet-Covex, Charline | DNA metabarcoding approach, gh primers | Number of DNA sequences by replicate of analyses |
| 65 | Veratrum | Vum | # | Giguet-Covex, Charline | DNA metabarcoding approach, gh primers | Number of DNA sequences by replicate of analyses |
| 66 | Veronica | Ver | # | Giguet-Covex, Charline | DNA metabarcoding approach, gh primers | Number of DNA sequences by replicate of analyses |
| 67 | Viola | Vio | # | Giguet-Covex, Charline | DNA metabarcoding approach, gh primers | Number of DNA sequences by replicate of analyses |
| 68 | Saxifraga rotundifolia | Sxf.r | # | 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) (License comes into effect after moratorium ends)
Status:
Curation Level: Enhanced curation (CurationLevelC)
Size:
17219 data points
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