Data from: Reconstructing long-term human impacts on plant communities: an ecological approach based on lake sediment DNA

Pansu J, Giguet-Covex C, Ficetola GF, Gielly L, Boyer F, Zinger L, Arnaud F, Poulenard J, Taberlet P, Choler P

Date Published: March 3, 2015

DOI: http://dx.doi.org/10.5061/dryad.6171j

 

Files in this package

Content in the Dryad Digital Repository is offered "as is." By downloading files, you agree to the Dryad Terms of Service. To the extent possible under law, the authors have waived all copyright and related or neighboring rights to this data. CC0 (opens a new window) Open Data (opens a new window)

Title Sample_Age
Downloaded 30 times
Description This file contains the age of each sample based on 14C measurements.
Download Sample_Age.xlsx (52.73 Kb)
Details View File Details
Title Unfiltered sequencing data (fasta format)
Downloaded 17 times
Description This fasta file contains unfiltered sequencing data (i.e. merged reads assigned to their original sample). Amplicons were amplified using the universal primers “g” (5’-GGGCAATCCTGAGCCAA-3’) and “h” (5’-CCATTGAGTCTCTGCACCTATC-3’) (Taberlet et al. 2007). Sequences were obtained by a 2 x 100 bp paired-end sequencing on Illumina HiSeq 2500 platform. First processing steps were performed using the OBITOOLS software (http://metabarcoding.org/obitools) as follows: (i) Direct and reverse reads corresponding to the same sequence were aligned and merged thanks to the IlluminaPairEnd program. Only merged sequences with a high alignment quality score were retained (>=40) (ii) Each merged sequence was assigned to its original sample using the tags information previously added to primers thanks to the ngsfilter program. For this step, only sequences containing both primers (with a maximum of 3 mismatches per primer) and exact tag sequences were selected. (iii) To reduce the file size, strictly identical sequences were merged together while keeping information about the origin of sequences.
Download anterne_gh_raw_data_uniq.fasta (192.9 Mb)
Download README (2.3 Kb)
Details View File Details
Title Unfiltered sequencing data (table format)
Downloaded 23 times
Description This table contains pre-filtered sequencing data (i.e. usable merged reads assigned to their original sample). Amplicons were amplified using the universal primers “g” (5’-GGGCAATCCTGAGCCAA-3’) and “h” (5’-CCATTGAGTCTCTGCACCTATC-3’) (Taberlet et al. 2007). Sequences were obtained by a 2 x 100 bp paired-end sequencing on Illumina HiSeq 2500 platform. First processing steps were performed using the OBITOOLS software (http://metabarcoding.org/obitools) as follows: (i) Direct and reverse reads corresponding to the same sequence were aligned and merged thanks to the IlluminaPairEnd program. Only merged sequences with a high alignment quality score were retained (>=40). (ii) Each merged sequence was assigned to its original sample using the tags information previously added to primers thanks to the ngsfilter program. For this step, only sequences containing both primers (with a maximum of 3 mismatches per primer) and exact tag sequences were selected. (iii) To reduce the file size, strictly identical sequences were merged together while keeping information about the origin of sequences. (iv) Sequences containing ambiguous nucleotides or shorter than 7 bp were discarded. (v) Pure singleton (sequences with 1 read among the whole dataset) were removed.
Download ME_Pansu_AS2-1.txt (68.38 Mb)
Download README (3.183 Kb)
Details View File Details
Title Filtered sequencing data
Downloaded 40 times
Description This table contains filtered sequences. Amplicons were amplified using the universal primers “g” (5’-GGGCAATCCTGAGCCAA-3’) and “h” (5’-CCATTGAGTCTCTGCACCTATC-3’) (Taberlet et al. 2007). Sequences were obtained by a 2 x 100 bp paired-end sequencing on Illumina HiSeq 2500 platform. Data were filtered according to the filterering procedure described in Pansu et al. (2014) :'Reconstructing long-term human impacts on plant communities : an ecological approach based on lake sediment DNA'.
Download ME_Pansu_AS1-1.xlsx (189.3 Kb)
Download README (3.753 Kb)
Details View File Details
Title Alpine reference database EMBL (gh)
Downloaded 15 times
Description This file contains dereplicated sequences of alpine taxa extracted from the EMBL nucleic database release 117 using the ecopcr program (http://metabarcoding.org/obitools). Sequences have been extracted using the primers “g” (5’-GGGCAATCCTGAGCCAA-3’) and “h” (5’-CCATTGAGTCTCTGCACCTATC-3’) (Taberlet et al. 2007). Then, only alpine taxa were selected.
Download alpine_referenceDB_gh_embl.fasta (398.8 Kb)
Download README.README (776 bytes)
Details View File Details
Title Global reference database EMBL (gh)
Downloaded 37 times
Description This file contains all dereplicated sequences of alpine taxa extracted from the EMBL nucleic database release 117 using the ecopcr program (http://metabarcoding.org/obitools). Sequences have been extracted using the primers “g” (5’-GGGCAATCCTGAGCCAA-3’) and “h” (5’-CCATTGAGTCTCTGCACCTATC-3’) (Taberlet et al. 2007).
Download global_referenceDB_gh_embl.fasta.zip (507.7 Kb)
Download README.README (710 bytes)
Details View File Details

When using this data, please cite the original publication:

Pansu J, Giguet-Covex C, Ficetola GF, Gielly L, Boyer F, Zinger L, Arnaud F, Poulenard J, Taberlet P, Choler P (2015) Reconstructing long-term human impacts on plant communities: an ecological approach based on lake sediment DNA. Molecular Ecology 24(7): 1485-1498. http://dx.doi.org/10.1111/mec.13136

Additionally, please cite the Dryad data package:

Pansu J, Giguet-Covex C, Ficetola GF, Gielly L, Boyer F, Zinger L, Arnaud F, Poulenard J, Taberlet P, Choler P (2015) Data from: Reconstructing long-term human impacts on plant communities: an ecological approach based on lake sediment DNA. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.6171j
Cite | Share
Download the data package citation in the following formats:
   RIS (compatible with EndNote, Reference Manager, ProCite, RefWorks)
   BibTex (compatible with BibDesk, LaTeX)

Search for data

Be part of Dryad

We encourage organizations to: