Citation:

PANGAEA.958732

Name: Plant DNA taxa detected in Lake Anterne sediments (North-western Alps) over the Holocene
Creator: Charline Giguet-Covex
License: https://creativecommons.org/licenses/by/4.0/
Keywords: Alpes; Lake sediment core; Landscape; plant taxa; Sedimentary DNA

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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: 45.991133 * Longitude: 6.797783

Date/Time Start: 2007-09-05T00:00:00 * Date/Time End: 2007-09-15T00:00:00

Minimum Elevation: 2063.0 m * Maximum Elevation: 2063.0 m

Event(s):

ANT07 * Latitude: 45.991133 * Longitude: 6.797783 * Date/Time Start: 2007-09-05T00:00:00 * Date/Time End: 2007-09-15T00:00:00 * Elevation: 2063.0 m * 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 (2 sample replicates, 2 extraction replicates by sample and 2 polymerase chain reaction (PCR) replicates by extractions, so 8 replicates in total). It has been generated applying the DNA metabarcoding approach on a 20-m long sediment cores retrieved by using a uwitec gravity corer and a NIEDERREITER 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 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). 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	Aconitum lycoctonum	A. lycoctonum	#	Giguet-Covex, Charline	DNA metabarcoding approach, gh primers	Number of DNA sequences by replicate of analyses
3	Aegopodium	Aeg	#	Giguet-Covex, Charline	DNA metabarcoding approach, gh primers	Number of DNA sequences by replicate of analyses
4	Ajuga pyramidalis	A. pyramidalis	#	Giguet-Covex, Charline	DNA metabarcoding approach, gh primers	Number of DNA sequences by replicate of analyses
5	Alchemilla	Alc	#	Giguet-Covex, Charline	DNA metabarcoding approach, gh primers	Number of DNA sequences by replicate of analyses
6	Alchemilla alpina	A. alpina	#	Giguet-Covex, Charline	DNA metabarcoding approach, gh primers	Number of DNA sequences by replicate of analyses
7	Alnus viridis	Aln.v	#	Giguet-Covex, Charline	DNA metabarcoding approach, gh primers	Number of DNA sequences by replicate of analyses
8	Alopecurinae	Alopecurinae	#	Giguet-Covex, Charline	DNA metabarcoding approach, gh primers	Number of DNA sequences by replicate of analyses
9	Anemone	Ane	#	Giguet-Covex, Charline	DNA metabarcoding approach, gh primers	Number of DNA sequences by replicate of analyses
10	Anthemideae	Antae	#	Giguet-Covex, Charline	DNA metabarcoding approach, gh primers	Number of DNA sequences by replicate of analyses
11	Anthriscus sylvestris	Ant.s	#	Giguet-Covex, Charline	DNA metabarcoding approach, gh primers	Number of DNA sequences by replicate of analyses
12	Anthyllis vulneraria	Any.v	#	Giguet-Covex, Charline	DNA metabarcoding approach, gh primers	Number of DNA sequences by replicate of analyses
13	Apiaceae	Apiae	#	Giguet-Covex, Charline	DNA metabarcoding approach, gh primers	Number of DNA sequences by replicate of analyses
14	Arabis	Arabis	#	Giguet-Covex, Charline	DNA metabarcoding approach, gh primers	Number of DNA sequences by replicate of analyses
15	Artemisia	Art	#	Giguet-Covex, Charline	DNA metabarcoding approach, gh primers	Number of DNA sequences by replicate of analyses
16	Asteroideae	Asteroideae	#	Giguet-Covex, Charline	DNA metabarcoding approach, gh primers	Number of DNA sequences by replicate of analyses
17	Asteraceae	Astae	#	Giguet-Covex, Charline	DNA metabarcoding approach, gh primers	Number of DNA sequences by replicate of analyses
18	Astragalus	Asg	#	Giguet-Covex, Charline	DNA metabarcoding approach, gh primers	Number of DNA sequences by replicate of analyses
19	Bartsia alpina	B. alpina	#	Giguet-Covex, Charline	DNA metabarcoding approach, gh primers	Number of DNA sequences by replicate of analyses
20	Betula	Bet	#	Giguet-Covex, Charline	DNA metabarcoding approach, gh primers	Number of DNA sequences by replicate of analyses
21	Polygonum bistorta	Pol.b	#	Giguet-Covex, Charline	DNA metabarcoding approach, gh primers	Number of DNA sequences by replicate of analyses
22	Bistorta vivipara	Bis.v	#	Giguet-Covex, Charline	DNA metabarcoding approach, gh primers	Number of DNA sequences by replicate of analyses
23	Brassicaceae	Braae	#	Giguet-Covex, Charline	DNA metabarcoding approach, gh primers	Number of DNA sequences by replicate of analyses
24	Caltha	Clh	#	Giguet-Covex, Charline	DNA metabarcoding approach, gh primers	Number of DNA sequences by replicate of analyses
25	Campanula	Cam	#	Giguet-Covex, Charline	DNA metabarcoding approach, gh primers	Number of DNA sequences by replicate of analyses
26	Campanulids	Campanulids	#	Giguet-Covex, Charline	DNA metabarcoding approach, gh primers	Number of DNA sequences by replicate of analyses
27	Cardamine	Ine	#	Giguet-Covex, Charline	DNA metabarcoding approach, gh primers	Number of DNA sequences by replicate of analyses
28	Carduinae	Carduinae	#	Giguet-Covex, Charline	DNA metabarcoding approach, gh primers	Number of DNA sequences by replicate of analyses
29	Carex	Cax	#	Giguet-Covex, Charline	DNA metabarcoding approach, gh primers	Number of DNA sequences by replicate of analyses
30	Orobanchaceae	Orobanchaceae	#	Giguet-Covex, Charline	DNA metabarcoding approach, gh primers	Number of DNA sequences by replicate of analyses
31	Cerastium cerastoides	C. cerastoides	#	Giguet-Covex, Charline	DNA metabarcoding approach, gh primers	Number of DNA sequences by replicate of analyses
32	Epilobium angustifolium	Epi.a	#	Giguet-Covex, Charline	DNA metabarcoding approach, gh primers	Number of DNA sequences by replicate of analyses
33	Dryas	Dry	#	Giguet-Covex, Charline	DNA metabarcoding approach, gh primers	Number of DNA sequences by replicate of analyses
34	Empetrum	Emp	#	Giguet-Covex, Charline	DNA metabarcoding approach, gh primers	Number of DNA sequences by replicate of analyses
35	Epilobium	Epl	#	Giguet-Covex, Charline	DNA metabarcoding approach, gh primers	Number of DNA sequences by replicate of analyses
36	Epilobium alsinifolium	E. alsinifolium	#	Giguet-Covex, Charline	DNA metabarcoding approach, gh primers	Number of DNA sequences by replicate of analyses
37	Equisetum	Equ	#	Giguet-Covex, Charline	DNA metabarcoding approach, gh primers	Number of DNA sequences by replicate of analyses
38	Erigeron	Erg	#	Giguet-Covex, Charline	DNA metabarcoding approach, gh primers	Number of DNA sequences by replicate of analyses
39	Eriophorum	Erp	#	Giguet-Covex, Charline	DNA metabarcoding approach, gh primers	Number of DNA sequences by replicate of analyses
40	Euphrasia	Eur	#	Giguet-Covex, Charline	DNA metabarcoding approach, gh primers	Number of DNA sequences by replicate of analyses
41	Festuca	Festuca	#	Giguet-Covex, Charline	DNA metabarcoding approach, gh primers	Number of DNA sequences by replicate of analyses
42	Filipendula ulmaria	Flp.u	#	Giguet-Covex, Charline	DNA metabarcoding approach, gh primers	Number of DNA sequences by replicate of analyses
43	Gentiana	Gen	#	Giguet-Covex, Charline	DNA metabarcoding approach, gh primers	Number of DNA sequences by replicate of analyses
44	Geranium sylvaticum	Ger.s	#	Giguet-Covex, Charline	DNA metabarcoding approach, gh primers	Number of DNA sequences by replicate of analyses
45	Geum	Geu	#	Giguet-Covex, Charline	DNA metabarcoding approach, gh primers	Number of DNA sequences by replicate of analyses
46	Gnaphalieae	Gnaphalieae	#	Giguet-Covex, Charline	DNA metabarcoding approach, gh primers	Number of DNA sequences by replicate of analyses
47	Hedysarum hedysaroides	Hdy.h	#	Giguet-Covex, Charline	DNA metabarcoding approach, gh primers	Number of DNA sequences by replicate of analyses
48	Leucanthemum	Leucanthemum	#	Giguet-Covex, Charline	DNA metabarcoding approach, gh primers	Number of DNA sequences by replicate of analyses
49	Hypericum	Hyp	#	Giguet-Covex, Charline	DNA metabarcoding approach, gh primers	Number of DNA sequences by replicate of analyses
50	Inula	Inu	#	Giguet-Covex, Charline	DNA metabarcoding approach, gh primers	Number of DNA sequences by replicate of analyses
51	Juniperus	Jun	#	Giguet-Covex, Charline	DNA metabarcoding approach, gh primers	Number of DNA sequences by replicate of analyses
52	Lamiales	Lamiales	#	Giguet-Covex, Charline	DNA metabarcoding approach, gh primers	Number of DNA sequences by replicate of analyses
53	Leontodon hispidus	Leo.hi	#	Giguet-Covex, Charline	DNA metabarcoding approach, gh primers	Number of DNA sequences by replicate of analyses
54	Lotus corniculatus	Lot.c	#	Giguet-Covex, Charline	DNA metabarcoding approach, gh primers	Number of DNA sequences by replicate of analyses
55	Luzula	Luz	#	Giguet-Covex, Charline	DNA metabarcoding approach, gh primers	Number of DNA sequences by replicate of analyses
56	Menyanthes trifoliata	Mey.t	#	Giguet-Covex, Charline	DNA metabarcoding approach, gh primers	Number of DNA sequences by replicate of analyses
57	Saxifraga stellaris	Sax.s	#	Giguet-Covex, Charline	DNA metabarcoding approach, gh primers	Number of DNA sequences by replicate of analyses
58	Myosotis alpestris	M. alpestris	#	Giguet-Covex, Charline	DNA metabarcoding approach, gh primers	Number of DNA sequences by replicate of analyses
59	Oxyria digyna	Oxy.d	#	Giguet-Covex, Charline	DNA metabarcoding approach, gh primers	Number of DNA sequences by replicate of analyses
60	Parnassia	Par	#	Giguet-Covex, Charline	DNA metabarcoding approach, gh primers	Number of DNA sequences by replicate of analyses
61	Pedicularis	Ped	#	Giguet-Covex, Charline	DNA metabarcoding approach, gh primers	Number of DNA sequences by replicate of analyses
62	Pedicularis verticillata	P. verticillata	#	Giguet-Covex, Charline	DNA metabarcoding approach, gh primers	Number of DNA sequences by replicate of analyses
63	Picea	Pic	#	Giguet-Covex, Charline	DNA metabarcoding approach, gh primers	Number of DNA sequences by replicate of analyses
64	Pimpinella saxifraga	Pim.s	#	Giguet-Covex, Charline	DNA metabarcoding approach, gh primers	Number of DNA sequences by replicate of analyses
65	Pinus	Pin	#	Giguet-Covex, Charline	DNA metabarcoding approach, gh primers	Number of DNA sequences by replicate of analyses
66	Plantago lanceolata	Pla.l	#	Giguet-Covex, Charline	DNA metabarcoding approach, gh primers	Number of DNA sequences by replicate of analyses
67	Plantago	Pla	#	Giguet-Covex, Charline	DNA metabarcoding approach, gh primers	Number of DNA sequences by replicate of analyses
68	Poeae	Poeae	#	Giguet-Covex, Charline	DNA metabarcoding approach, gh primers	Number of DNA sequences by replicate of analyses
69	Polygonaceae	Polae	#	Giguet-Covex, Charline	DNA metabarcoding approach, gh primers	Number of DNA sequences by replicate of analyses
70	Potentilla	Pti	#	Giguet-Covex, Charline	DNA metabarcoding approach, gh primers	Number of DNA sequences by replicate of analyses
71	Potentilla erecta	Pot.e	#	Giguet-Covex, Charline	DNA metabarcoding approach, gh primers	Number of DNA sequences by replicate of analyses
72	Pteridium aquilinum	Ptd.a	#	Giguet-Covex, Charline	DNA metabarcoding approach, gh primers	Number of DNA sequences by replicate of analyses
73	Pyrola	Pyo	#	Giguet-Covex, Charline	DNA metabarcoding approach, gh primers	Number of DNA sequences by replicate of analyses
74	Ranunculaceae	Ranae	#	Giguet-Covex, Charline	DNA metabarcoding approach, gh primers	Number of DNA sequences by replicate of analyses
75	Ranunculus	Ran	#	Giguet-Covex, Charline	DNA metabarcoding approach, gh primers	Number of DNA sequences by replicate of analyses
76	Ranunculus glacialis	Ran.g	#	Giguet-Covex, Charline	DNA metabarcoding approach, gh primers	Number of DNA sequences by replicate of analyses
77	Ranunculus platanifolius	R. platanifolius	#	Giguet-Covex, Charline	DNA metabarcoding approach, gh primers	Number of DNA sequences by replicate of analyses
78	Rhinantheae	Rhinantheae	#	Giguet-Covex, Charline	DNA metabarcoding approach, gh primers	Number of DNA sequences by replicate of analyses
79	Rhinanthus angustifolius	R. angustifolius	#	Giguet-Covex, Charline	DNA metabarcoding approach, gh primers	Number of DNA sequences by replicate of analyses
80	Rhodiola rosea	Rho.r	#	Giguet-Covex, Charline	DNA metabarcoding approach, gh primers	Number of DNA sequences by replicate of analyses
81	Rhododendron	Rho	#	Giguet-Covex, Charline	DNA metabarcoding approach, gh primers	Number of DNA sequences by replicate of analyses
82	Rosodae	Rosodae	#	Giguet-Covex, Charline	DNA metabarcoding approach, gh primers	Number of DNA sequences by replicate of analyses
83	Rumex	Rum	#	Giguet-Covex, Charline	DNA metabarcoding approach, gh primers	Number of DNA sequences by replicate of analyses
84	Saliceae	Saliceae	#	Giguet-Covex, Charline	DNA metabarcoding approach, gh primers	Number of DNA sequences by replicate of analyses
85	Sanicula europaea	San.e	#	Giguet-Covex, Charline	DNA metabarcoding approach, gh primers	Number of DNA sequences by replicate of analyses
86	Saxifraga	Sax	#	Giguet-Covex, Charline	DNA metabarcoding approach, gh primers	Number of DNA sequences by replicate of analyses
87	Saxifraga paniculata	S. paniculata	#	Giguet-Covex, Charline	DNA metabarcoding approach, gh primers	Number of DNA sequences by replicate of analyses
88	Saxifragaceae	Saxae	#	Giguet-Covex, Charline	DNA metabarcoding approach, gh primers	Number of DNA sequences by replicate of analyses
89	Selineae	Selineae	#	Giguet-Covex, Charline	DNA metabarcoding approach, gh primers	Number of DNA sequences by replicate of analyses
90	Senecioneae	Senecioneae	#	Giguet-Covex, Charline	DNA metabarcoding approach, gh primers	Number of DNA sequences by replicate of analyses
91	Sibbaldia procumbens	Sib.p	#	Giguet-Covex, Charline	DNA metabarcoding approach, gh primers	Number of DNA sequences by replicate of analyses
92	Succisa pratensis	Suc.p	#	Giguet-Covex, Charline	DNA metabarcoding approach, gh primers	Number of DNA sequences by replicate of analyses
93	Thymus	Thu	#	Giguet-Covex, Charline	DNA metabarcoding approach, gh primers	Number of DNA sequences by replicate of analyses
94	Trifolium repens	Tri.r	#	Giguet-Covex, Charline	DNA metabarcoding approach, gh primers	Number of DNA sequences by replicate of analyses
95	Trifolium spadiceum	Tri.s	#	Giguet-Covex, Charline	DNA metabarcoding approach, gh primers	Number of DNA sequences by replicate of analyses
96	Trifolium	Tri	#	Giguet-Covex, Charline	DNA metabarcoding approach, gh primers	Number of DNA sequences by replicate of analyses
97	Trollius	Tro	#	Giguet-Covex, Charline	DNA metabarcoding approach, gh primers	Number of DNA sequences by replicate of analyses
98	Vaccinium	Vac	#	Giguet-Covex, Charline	DNA metabarcoding approach, gh primers	Number of DNA sequences by replicate of analyses
99	Vaccinium vitis-idaea	V. vitis-idaea	#	Giguet-Covex, Charline	DNA metabarcoding approach, gh primers	Number of DNA sequences by replicate of analyses
100	Veratrum	Vum	#	Giguet-Covex, Charline	DNA metabarcoding approach, gh primers	Number of DNA sequences by replicate of analyses
101	Veronica	Ver	#	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:

37200 data points

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