DOI: 10.5061/dryad.t8534
title: Data from: Long-lasting modification of soil fungal diversity associated with the introduction of rabbits to a remote sub-Antarctic archipelago

description: During the late nineteenth century, Europeans introduced rabbits to many
 of the sub-Antarctic islands, environments that prior to this had been
 devoid of mammalian herbivores. The impacts of rabbits on indigenous
 ecosystems are well studied; notably, they cause dramatic changes in plant
 communities and promote soil erosion. However, the responses of fungal
 communities to such biotic disturbances remain unexplored. We used
 metabarcoding of soil extracellular DNA to assess the diversity of plant
 and fungal communities at sites on the sub-Antarctic Kerguelen Islands
 with contrasting histories of disturbance by rabbits. Our results suggest
 that on these islands, the simplification of plant communities and
 increased erosion resulting from the introduction of rabbits have driven
 compositional changes, including diversity reductions, in indigenous soil
 fungal communities. Moreover, there is no indication of recovery at sites
 from which rabbits were removed 20 years ago. These results imply that
 introduced herbivores have long-lasting and multifaceted effects on fungal
 biodiversity as well as highlight the low resiliency of sub-Antarctic
 ecosystems.
description: Vegetation surveys
 dataThis file contains data
 from vegetation surveys performed in study sites in Kerguelen Islands.The
 first row represent the percentage of vascular plant cover in each plot.
 Other rows contain the number of contacts of each plant species per plot
 (maximum 200 contacts per plot).vegetation_survey_kerguelen.xlsxUnfiltered sequencing data for fungal metabarcode (table format)This table contains pre-filtered sequencing data (i.e. usable merged reads assigned to their original sample) for fungal metabarcode. Amplicons were amplified using the primers ITS5 : 5'-GGAAGTAAAAGTCGTAACAAGG-3' (White et al. 1990) and 5.8S_fungi : 5'- CAAGAGATCCGTTGTTGAAAGTT-3' primers (Epp et al. 2012). Sequences were produced by a 2 x 250 bp paired-end sequencing on Illumina MiSeq 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 (&gt;=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 100 bp were discarded. (v) Pure singleton (sequences with 1 read among the whole dataset) were removed.Pansu&al_BioLett_ITSfungi_unfiltered_dataset.txt.zipUnfiltered sequencing data for fungal metabarcode (fasta format)This fasta file contains unfiltered sequencing data (i.e. merged reads assigned to their original sample) for fungal metabarcode. Amplicons were amplified using the primers ITS5 : 5'-GGAAGTAAAAGTCGTAACAAGG-3' (White et al. 1990) and 5.8S_fungi : 5'- CAAGAGATCCGTTGTTGAAAGTT-3' primers (Epp et al. 2012). Sequences were produced by a 2 x 250 bp paired-end sequencing on Illumina MiSeq 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 (&gt;=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.Pansu&al_BioLett_ITSfungi_unfiltered_dataset.fasta.zipFiltered sequencing data (MOTUs) for fungal metabarcodeThis table contains filtered MOTUs for the fungal metabarcode. Amplicons were amplified using ITS5 : 5'-GGAAGTAAAAGTCGTAACAAGG-3' (White et al. 1990) and 5.8S_fungi : 5'- CAAGAGATCCGTTGTTGAAAGTT-3' primers (Epp et al. 2012). Sequences were obtained by a 2 x 250 bp paired-end sequencing on Illumina MiSeq platform. Data filtering and MOTUs clustering were performed according to the procedure described in the supplementary materials of Pansu et al. (2015): 'Long-lasting modification of soil fungal diversity associated with the introduction of rabbits to a remote sub-Antarctic archipelago'.Pansu&al_BioLett_ITSfungi_filtered_dataset.txtFiltered sequencing data for plant metabarcodeThis table contains the filtered sequences for the plant metabarcode. Amplicons were amplified using g (5'-GGGCAATCCTGAGCCAA-3') and h (5'-CCATTGAGTCTCTGCACCTATC-3') primers (Taberlet et al. 2007). The sequences have been produced by the Illumina technology (HiSeq 2500 platform, 2x100bp pair-end) and were filtered according to the filtering procedure describes in the supplementary materials of Pansu et al. (2015) ¬'Long-lasting modification of soil fungal diversity associated with the introduction of rabbit to a remote sub-Antarctic archipelago'.Pansu&al_BioLett_gh_filtered_dataset.txtUnfiltered sequencing data for plant metabarcode (fasta format)This fasta file contains unfiltered sequencing data (i.e. merged reads assigned to their original sample) for plant metabarcode. Amplicons were amplified using the universal primers g (5'-GGGCAATCCTGAGCCAA-3') and h (5'-CCATTGAGTCTCTGCACCTATC-3') primers (Taberlet et al. 2007). Sequences were produced 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 (&gt;=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.Pansu&al_BioLett_gh_unfiltered_dataset.fasta.zipPansu&al_BioLett_gh_unfiltered_dataset.txtThis table contains pre-filtered sequencing data (i.e. usable merged reads assigned to their original sample) for fungal metabarcode. Amplicons were amplified using the univerdal primers 'g' (5'-GGGCAATCCTGAGCCAA-3') and 'h' (5'-CCATTGAGTCTCTGCACCTATC-3') primers (Taberlet et al. 2007). Sequences were produced 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 (&gt;=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.