Data from: Nitrogen deposition alters plant–fungal relationships: linking belowground dynamics to aboveground vegetation change

 

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Title alpha diversity code
Downloaded 32 times
Description R code that tests for relationships between alpha diversity measures and treatment. Inputs are collated alpha diversity files produced in QIIME.
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Title NiwotDGF map
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Description Environmental mapping file, providing treatment, plot, DNA dilution, and sequencing run information for each sample.
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Title NMDS code
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Description R code to build NMDS plot of bray-curtis distance matrix describing distances between communities from each sample. Also a permutation test for correlations between treatments and community distances. Input is taxa x SampleID table produced in Qiime.
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Title ANOVA code, N effects per host
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Description R code to test individual taxa for correlation with N in each host
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Title ANOVA code, Nxhost
Downloaded 24 times
Description R code to test individual taxa for correlation with N or host, or interactions between the two.
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Title ANOVA code, remxN
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Description R code to test individual taxa for correlation with treatment or treatment interactions in single host
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Title rarefaction plot code
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Description R code to build alpha rarefaction plots (collated alpha rarefaction table produced in Qiime from taxa x SampleID tables)
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Title RDA code
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Description R code for RDA ordination and permutation tests
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Title SE of OTU and seq counts
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Description R code to calculate standard error of sequence and OTU counts for each host
Download SE otus seqs.R (428 bytes)
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Title OTU and sequence counts
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Description file containing sequence and OTU counts for each sample. These statistics are calculated for data that has been filtered for poor quality sequences, and seemingly contaminated samples have been removed.
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Title rarefied OTU table L2
Downloaded 19 times
Description Rarefied phyla x sampleID tables (there are 6 tables for 6 taxonomic levels, species through phylum. L7=species, L2=phylum). OTU table was rarefied to 557 sequences (size of smallest sample), then taxa were collapsed into phylum.
Download reduced_nosingles_rarefied_557_99_L2.csv (2.343 Kb)
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Title rarefied OTU table L3
Downloaded 16 times
Description Rarefied class x sampleID tables (there are 6 tables for 6 taxonomic levels, species through phylum. L7=species, L2=phylum). OTU table was rarefied to 557 sequences (size of smallest sample), then taxa were collapsed into class.
Download reduced_nosingles_rarefied_557_99_L3.csv (6.162 Kb)
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Title rarefied OTU table L4
Downloaded 14 times
Description Rarefied order x sampleID tables (there are 6 tables for 6 taxonomic levels, species through phylum. L7=species, L2=phylum). OTU table was rarefied to 557 sequences (size of smallest sample), then taxa were collapsed into orders.
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Title rarefied OTU table L5
Downloaded 13 times
Description Rarefied family x sampleID tables (there are 6 tables for 6 taxonomic levels, species through phylum. L7=species, L2=phylum). OTU table was rarefied to 557 sequences (size of smallest sample), then taxa were collapsed into family.
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Title rarefied OTU table L6
Downloaded 17 times
Description Rarefied genus x sampleID tables (there are 6 tables for 6 taxonomic levels, species through phylum. L7=species, L2=phylum). OTU table was rarefied to 557 sequences (size of smallest sample), then taxa were collapsed into genera.
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Title rarefied OTU table L7
Downloaded 13 times
Description Rarefied OTU x sampleID tables (there are 6 tables for 6 taxonomic levels, species through phylum. L7=species, L2=phylum). OTU table was rarefied to 557 sequences (size of smallest sample).
Download reduced_nosingles_rarefied_557_99_L7.csv (308.4 Kb)
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Title Unrarefied OTU table L7
Downloaded 14 times
Description Unrarefied OTU x sampleID tables (the paper includes analyses on 6 tables for 6 taxonomic levels, species through phylum. L7=species, L2=phylum. The other tables can be constructed from this one in QIIME).
Download reduced_nosingletons_sorted_host_L7.csv (440.0 Kb)
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Title Unrarefied OTU table L6
Downloaded 17 times
Description Unrarefied genus x sampleID tables (there are 6 tables for 6 taxonomic levels, species through phylum).
Download reduced_nosingletons_sorted_host_L6.csv (55.35 Kb)
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Title Unrarefied OTU table L5
Downloaded 18 times
Description Unrarefied family x sampleID tables (there are 6 tables for 6 taxonomic levels, species through phylum).
Download reduced_nosingletons_sorted_host_L5.csv (29.67 Kb)
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Title Unrarefied OTU table L4
Downloaded 14 times
Description Unrarefied order x sampleID tables (there are 6 tables for 6 taxonomic levels, species through phylum).
Download reduced_nosingletons_sorted_host_L4.csv (16.34 Kb)
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Title Unrarefied OTU table L3
Downloaded 12 times
Description Unrarefied class x sampleID tables (there are 6 tables for 6 taxonomic levels, species through phylum).
Download reduced_nosingletons_sorted_host_L3.csv (6.982 Kb)
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Title Unrarefied OTU table L2
Downloaded 21 times
Description Unrarefied phylum x sampleID tables (there are 6 tables for 6 taxonomic levels, species through phylum).
Download reduced_nosingletons_sorted_host_L2.csv (2.465 Kb)
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Title raw sequences
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Description raw sequence file, fasta format
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Title quality file
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Description quality score file
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Title observed_species_L2
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Description Phylum richness calculated for 100 rarefaction plots
Download observed_species_L2.csv (11.48 Kb)
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Title observed_species_L3
Downloaded 16 times
Description Class richness calculated for 100 rarefaction plots (there are 6 tables for 6 taxonomic levels, species through phylum. L7=species, L2=phylum)
Download observed_species_L3.csv (13.25 Kb)
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Title observed_species_L4
Downloaded 17 times
Description Order richness calculated for 100 rarefaction plots (there are 6 tables for 6 taxonomic levels, species through phylum. L7=species, L2=phylum)
Download observed_species_L4.csv (14.88 Kb)
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Title observed_species_L5
Downloaded 19 times
Description Family richness calculated for 100 rarefaction plots (there are 6 tables for 6 taxonomic levels, species through phylum. L7=species, L2=phylum)
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Title observed_species_L6
Downloaded 12 times
Description Genus richness calculated for 100 rarefaction plots (there are 6 tables for 6 taxonomic levels, species through phylum. L7=species, L2=phylum)
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Title observed_species_L7
Downloaded 16 times
Description OTU richness calculated for 100 rarefaction plots (there are 6 tables for 6 taxonomic levels, species through phylum. L7=species, L2=phylum)
Download observed_species_L7.csv (17.25 Kb)
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Title simpson_evenness_L2
Downloaded 22 times
Description Phylum evenness calculated for 100 rarefaction plots (there are 6 tables for 6 taxonomic levels, species through phylum. L7=species, L2=phylum)
Download simpson_e_L2.csv (48.03 Kb)
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Title simpson_evenness_L3
Downloaded 16 times
Description Class evenness calculated for 100 rarefaction plots (there are 6 tables for 6 taxonomic levels, species through phylum. L7=species, L2=phylum)
Download simpson_e_L3.csv (48.06 Kb)
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Title simpson_evenness_L4
Downloaded 15 times
Description Order evenness calculated for 100 rarefaction plots (there are 6 tables for 6 taxonomic levels, species through phylum. L7=species, L2=phylum)
Download simpson_e_L4.csv (48.07 Kb)
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Title simpson_evenness_L5
Downloaded 16 times
Description Family evenness calculated for 100 rarefaction plots (there are 6 tables for 6 taxonomic levels, species through phylum. L7=species, L2=phylum)
Download simpson_e_L5.csv (48.09 Kb)
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Title simpson_evenness_L6
Downloaded 16 times
Description Genus evenness calculated for 100 rarefaction plots (there are 6 tables for 6 taxonomic levels, species through phylum. L7=species, L2=phylum)
Download simpson_e_L6.csv (48.04 Kb)
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Title simpson_evenness_L7
Downloaded 18 times
Description Species evenness calculated for 100 rarefaction plots (there are 6 tables for 6 taxonomic levels, species through phylum. L7=species, L2=phylum)
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Title simpson_diversity_L2
Downloaded 17 times
Description Phylum level Simpson's diversity calculated for 100 rarefaction plots (there are 6 tables for 6 taxonomic levels, species through phylum. L7=species, L2=phylum)
Download simpson_L2.csv (48.00 Kb)
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Title simpson_diversity_L3
Downloaded 16 times
Description Class level Simpson's diversity calculated for 100 rarefaction plots (there are 6 tables for 6 taxonomic levels, species through phylum. L7=species, L2=phylum)
Download simpson_L3.csv (47.97 Kb)
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Title simpson_diversity_L4
Downloaded 15 times
Description Order level Simpson's diversity calculated for 100 rarefaction plots (there are 6 tables for 6 taxonomic levels, species through phylum. L7=species, L2=phylum)
Download simpson_L4.csv (48.12 Kb)
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Title simpson_diversity_L5
Downloaded 17 times
Description Family level Simpson's diversity calculated for 100 rarefaction plots (there are 6 tables for 6 taxonomic levels, species through phylum. L7=species, L2=phylum)
Download simpson_L5.csv (47.91 Kb)
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Title simpson_diversity_L6
Downloaded 13 times
Description Genus level Simpson's diversity calculated for 100 rarefaction plots (there are 6 tables for 6 taxonomic levels, species through phylum. L7=species, L2=phylum)
Download simpson_L6.csv (48.07 Kb)
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Title simpson_diversity_L7
Downloaded 13 times
Description OTU level Simpson's diversity calculated for 100 rarefaction plots (there are 6 tables for 6 taxonomic levels, species through phylum. L7=species, L2=phylum)
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Title READ ME
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Description file explaining sample ID codes, and contents of each data and code file uploaded to Dryad
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When using this data, please cite the original publication:

Dean SL, Farrer EC, Taylor DL, Porras-Alfaro A, Suding KN, Sinsabaugh RL (2013) Nitrogen deposition alters plant–fungal relationships: linking belowground dynamics to aboveground vegetation change. Molecular Ecology 23(6): 1364–1378. http://dx.doi.org/10.1111/mec.12541

Additionally, please cite the Dryad data package:

Dean SL, Farrer EC, Taylor DL, Porras-Alfaro A, Suding KN, Sinsabaugh RL (2013) Data from: Nitrogen deposition alters plant–fungal relationships: linking belowground dynamics to aboveground vegetation change. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.sv33f
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