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Data Publisher for Earth & Environmental Science

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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Keyword(s):
Alpes; Lake sediment core; Landscape; plant taxa; Sedimentary DNA
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)
Grenoble Alpes University (UGA), grant/award no. ANR-15-IDEX-02: CDP Trajectories
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):
#NameShort NameUnitPrincipal InvestigatorMethod/DeviceComment
AGEAgeka BPGiguet-Covex, CharlineGeocode
AlchemillaAlc#Giguet-Covex, CharlineDNA metabarcoding approach, gh primersNumber of DNA sequences by replicate of analyses
Anthyllis vulnerariaAny.v#Giguet-Covex, CharlineDNA metabarcoding approach, gh primersNumber of DNA sequences by replicate of analyses
ApiaceaeApiae#Giguet-Covex, CharlineDNA metabarcoding approach, gh primersNumber of DNA sequences by replicate of analyses
Arctostaphylos uva-ursiArc.u-u#Giguet-Covex, CharlineDNA metabarcoding approach, gh primersNumber of DNA sequences by replicate of analyses
AsteraceaeAstae#Giguet-Covex, CharlineDNA metabarcoding approach, gh primersNumber of DNA sequences by replicate of analyses
Bartsia alpinaB. alpina#Giguet-Covex, CharlineDNA metabarcoding approach, gh primersNumber of DNA sequences by replicate of analyses
BetulaceaeBetaea#Giguet-Covex, CharlineDNA metabarcoding approach, gh primersNumber of DNA sequences by replicate of analyses
CalthaClh#Giguet-Covex, CharlineDNA metabarcoding approach, gh primersNumber of DNA sequences by replicate of analyses
10 CampanulaceaeCamae#Giguet-Covex, CharlineDNA metabarcoding approach, gh primersNumber of DNA sequences by replicate of analyses
11 CarexCax#Giguet-Covex, CharlineDNA metabarcoding approach, gh primersNumber of DNA sequences by replicate of analyses
12 Cerastium cerastoidesC. cerastoides#Giguet-Covex, CharlineDNA metabarcoding approach, gh primersNumber of DNA sequences by replicate of analyses
13 ColurieaeColurieae#Giguet-Covex, CharlineDNA metabarcoding approach, gh primersNumber of DNA sequences by replicate of analyses
14 CupressaceaeCupae#Giguet-Covex, CharlineDNA metabarcoding approach, gh primersNumber of DNA sequences by replicate of analyses
15 DryadoideaeDryadoideae#Giguet-Covex, CharlineDNA metabarcoding approach, gh primersNumber of DNA sequences by replicate of analyses
16 EquisetumEqu#Giguet-Covex, CharlineDNA metabarcoding approach, gh primersNumber of DNA sequences by replicate of analyses
17 GeraniumGer#Giguet-Covex, CharlineDNA metabarcoding approach, gh primersNumber of DNA sequences by replicate of analyses
18 Helianthemum nummulariumHel.n#Giguet-Covex, CharlineDNA metabarcoding approach, gh primersNumber of DNA sequences by replicate of analyses
19 HypericumHyp#Giguet-Covex, CharlineDNA metabarcoding approach, gh primersNumber of DNA sequences by replicate of analyses
20 MentheaeMentheae#Giguet-Covex, CharlineDNA metabarcoding approach, gh primersNumber of DNA sequences by replicate of analyses
21 MyosotisMst#Giguet-Covex, CharlineDNA metabarcoding approach, gh primersNumber of DNA sequences by replicate of analyses
22 OnagraceaeOnaae#Giguet-Covex, CharlineDNA metabarcoding approach, gh primersNumber of DNA sequences by replicate of analyses
23 PiceaPic#Giguet-Covex, CharlineDNA metabarcoding approach, gh primersNumber of DNA sequences by replicate of analyses
24 PinaceaePinae#Giguet-Covex, CharlineDNA metabarcoding approach, gh primersNumber of DNA sequences by replicate of analyses
25 PinusPin#Giguet-Covex, CharlineDNA metabarcoding approach, gh primersNumber of DNA sequences by replicate of analyses
26 PlantagoPla#Giguet-Covex, CharlineDNA metabarcoding approach, gh primersNumber of DNA sequences by replicate of analyses
27 PoeaePoeae#Giguet-Covex, CharlineDNA metabarcoding approach, gh primersNumber of DNA sequences by replicate of analyses
28 PotentillaPti#Giguet-Covex, CharlineDNA metabarcoding approach, gh primersNumber of DNA sequences by replicate of analyses
29 RanunculusRan#Giguet-Covex, CharlineDNA metabarcoding approach, gh primersNumber of DNA sequences by replicate of analyses
30 RanunculusRan#Giguet-Covex, CharlineDNA metabarcoding approach, gh primersNumber of DNA sequences by replicate of analyses
31 RhodoreaeRhodoreae#Giguet-Covex, CharlineDNA metabarcoding approach, gh primersNumber of DNA sequences by replicate of analyses
32 RumexRum#Giguet-Covex, CharlineDNA metabarcoding approach, gh primersNumber of DNA sequences by replicate of analyses
33 SaginaSag#Giguet-Covex, CharlineDNA metabarcoding approach, gh primersNumber of DNA sequences by replicate of analyses
34 Saxifraga oppositofoliaS. oppositofolia#Giguet-Covex, CharlineDNA metabarcoding approach, gh primersNumber of DNA sequences by replicate of analyses
35 Sempervivum tectorumS. tectorum#Giguet-Covex, CharlineDNA metabarcoding approach, gh primersNumber of DNA sequences by replicate of analyses
36 SolanaceaeSolae#Giguet-Covex, CharlineDNA metabarcoding approach, gh primersNumber of DNA sequences by replicate of analyses
37 TrifoliumTri#Giguet-Covex, CharlineDNA metabarcoding approach, gh primersNumber of DNA sequences by replicate of analyses
38 TrifoliumTri#Giguet-Covex, CharlineDNA metabarcoding approach, gh primersNumber of DNA sequences by replicate of analyses
39 Trifolium pallescensTri.pa#Giguet-Covex, CharlineDNA metabarcoding approach, gh primersNumber of DNA sequences by replicate of analyses
40 Vaccinium uliginosumVac.u#Giguet-Covex, CharlineDNA metabarcoding approach, gh primersNumber of DNA sequences by replicate of analyses
41 Vaccinium vitis-idaeaV. vitis-idaea#Giguet-Covex, CharlineDNA metabarcoding approach, gh primersNumber of DNA sequences by replicate of analyses
42 VeratrumVum#Giguet-Covex, CharlineDNA metabarcoding approach, gh primersNumber of DNA sequences by replicate of analyses
43 Veronica alpinaV. alpina#Giguet-Covex, CharlineDNA metabarcoding approach, gh primersNumber of DNA sequences by replicate of analyses
44 CaprifoliaceaeCapeae#Giguet-Covex, CharlineDNA metabarcoding approach, gh primersNumber of DNA sequences by replicate of analyses
45 Lathyrus pratensisL. pratensis#Giguet-Covex, CharlineDNA metabarcoding approach, gh primersNumber of DNA sequences by replicate of analyses
Status:
Curation Level: Enhanced curation (CurationLevelC)
Size:
20328 data points

Data

Download dataset as tab-delimited text — use the following character encoding:


Age [ka BP]

Alc [#]
(Number of DNA sequences by re...)

Any.v [#]
(Number of DNA sequences by re...)

Apiae [#]
(Number of DNA sequences by re...)

Arc.u-u [#]
(Number of DNA sequences by re...)

Astae [#]
(Number of DNA sequences by re...)

B. alpina [#]
(Number of DNA sequences by re...)

Betaea [#]
(Number of DNA sequences by re...)

Clh [#]
(Number of DNA sequences by re...)
10 
Camae [#]
(Number of DNA sequences by re...)
11 
Cax [#]
(Number of DNA sequences by re...)
12 
C. cerastoides [#]
(Number of DNA sequences by re...)
13 
Colurieae [#]
(Number of DNA sequences by re...)
14 
Cupae [#]
(Number of DNA sequences by re...)
15 
Dryadoideae [#]
(Number of DNA sequences by re...)
16 
Equ [#]
(Number of DNA sequences by re...)
17 
Ger [#]
(Number of DNA sequences by re...)
18 
Hel.n [#]
(Number of DNA sequences by re...)
19 
Hyp [#]
(Number of DNA sequences by re...)
20 
Mentheae [#]
(Number of DNA sequences by re...)
21 
Mst [#]
(Number of DNA sequences by re...)
22 
Onaae [#]
(Number of DNA sequences by re...)
23 
Pic [#]
(Number of DNA sequences by re...)
24 
Pinae [#]
(Number of DNA sequences by re...)
25 
Pin [#]
(Number of DNA sequences by re...)
26 
Pla [#]
(Number of DNA sequences by re...)
27 
Poeae [#]
(Number of DNA sequences by re...)
28 
Pti [#]
(Number of DNA sequences by re...)
29 
Ran [#]
(Number of DNA sequences by re...)
30 
Ran [#]
(Number of DNA sequences by re...)
31 
Rhodoreae [#]
(Number of DNA sequences by re...)
32 
Rum [#]
(Number of DNA sequences by re...)
33 
Sag [#]
(Number of DNA sequences by re...)
34 
S. oppositofolia [#]
(Number of DNA sequences by re...)
35 
S. tectorum [#]
(Number of DNA sequences by re...)
36 
Solae [#]
(Number of DNA sequences by re...)
37 
Tri [#]
(Number of DNA sequences by re...)
38 
Tri [#]
(Number of DNA sequences by re...)
39 
Tri.pa [#]
(Number of DNA sequences by re...)
40 
Vac.u [#]
(Number of DNA sequences by re...)
41 
V. vitis-idaea [#]
(Number of DNA sequences by re...)
42 
Vum [#]
(Number of DNA sequences by re...)
43 
V. alpina [#]
(Number of DNA sequences by re...)
44 
Capeae [#]
(Number of DNA sequences by re...)
45 
L. pratensis [#]
(Number of DNA sequences by re...)
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