Data from: Effects of sampling effort on biodiversity patterns estimated from environmental DNA metabarcoding surveys

Grey EK, Bernatchez L, Cassey P, Deiner K, Deveney M, Howland KL, Lacoursière-Roussel A, Leong SCY, Li Y, Olds B, Pfrender ME, Prowse TAA, Renshaw MA, Lodge DM

Date Published: June 13, 2018

DOI: https://doi.org/10.5061/dryad.40782nd

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Title MOTU Cleaning and Analyses Script
Downloaded 2 times
Description This script removes cleans the raw MOTU data and runs all of the analyses in the paper including within-sample metazoan MOTU accumulation curves, sample richness estimates, site metazoan MOTU accumulation curves by sample number or read count, dissimilarity NMDS ordination, dissimilarity by distance analysis for Adelaide sites, and metazoan MOTU richness estimates standardize to 20 samples across all sites. This script was written for R version 3.4.1, requires input files "Unfiltered_18S.csv", "Unfiltered_COI.csv", "SampleIDs_18S.csv", "SampleIDs_COI.csv", and "geo dists adelaide.csv", and requires packages "vegan", "reshape2", and 'iNEXT".
Download MOTU Cleaning and Analyses.R (54.25 Kb)
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Title Unfiltered 18S MOTU Dataset
Downloaded 1 time
Description This dataset contains all of the 18S MOTUs obtained after the bioinformatics pipeline described in the manuscript. For each MOTU, there is taxonomic assignment information from two algorithms – SAP and Geneious BLAST – and the number of reads per MOTU per sample. Field descriptions are: "OTU_ID" = unique MOTU identifier "SAP" = taxonomic assignment from the SAP algorithm "MetazoanPhylum_SAP" = Metazoan phylum assigned by SAP "Level1_SAP"= higher level SAP assignment (e.g., Metazoan, Fungi, etc.) "Geneious Accession" = the NCBI accession of the best BLAST hit "Geneious1"= higher level BLAST assignment (e.g., Metazoan, Fungi, etc.) “MetazoanPhylum_Geneious”= metazoan phylum of best BLAST hit “Geneious2”…”Geneious6”= progressively lower-level taxonomic assignment of best BLAST hit “Geneious_coverage” = Percent coverage of best BLAST hit “Geneious_identity” = Percent identity of best BLAST hit “Geneious_eval” = E-value of best BLAST hit “Level1” = final higher-level categorization of the MOTU “MetazoanPhylum” = final Metazoan phylum of the MOTU Other fields: See the SampleIDs_18S for more information
Download Unfiltered_18S.csv (4.991 Mb)
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Title Unfiltered_COI
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Description This dataset contains all of the COI MOTUs obtained after the bioinformatics pipeline described in the manuscript. For each MOTU, there is taxonomic assignment information from two algorithms – SAP and Geneious BLAST – and the number of reads per MOTU per sample. Field descriptions are: "OTU_ID" = unique MOTU identifier "SAP" = taxonomic assignment from the SAP algorithm "MetazoanPhylum_SAP" = Metazoan phylum assigned by SAP "Level1_SAP"= higher level SAP assignment (e.g., Metazoan, Fungi, etc.) "Geneious Accession" = the NCBI accession of the best BLAST hit "Geneious1"= higher level BLAST assignment (e.g., Metazoan, Fungi, etc.) “MetazoanPhylum_Geneious”= metazoan phylum of best BLAST hit “Geneious2”…”Geneious6”= progressively lower-level taxonomic assignment of best BLAST hit “Geneious_coverage” = Percent coverage of best BLAST hit “Geneious_identity” = Percent identity of best BLAST hit “Geneious_eval” = E-value of best BLAST hit “Level1” = final higher-level categorization of the MOTU “MetazoanPhylum” = final Metazoan phylum of the MOTU Other fields: See the SampleIDs_18S for more information
Download Unfiltered_COI.csv (6.695 Mb)
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Title SampleIDs_18S
Downloaded 1 time
Description Dictionary linking samples to sites and ports. Also provides the 18S sequencing ID and bioinformatics pipeline ID for each sample.
Download SampleIDs_18S.csv (5.397 Kb)
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Title SampleIDs_COI
Downloaded 1 time
Description Dictionary linking samples to sites and ports. Also provides the COI sequencing ID and bioinformatics pipeline ID for each sample.
Download SampleIDs_COI.csv (5.358 Kb)
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Title Adelaide Site Over-Water Distances
Downloaded 1 time
Description Over-water distances in kilometers between the seven Adelaide sites.
Download geo dists adelaide.csv (277 bytes)
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When using this data, please cite the original publication:

Grey EK, Bernatchez L, Cassey P, Deiner K, Deveney M, Howland KL, Lacoursière-Roussel A, Leong SCY, Li Y, Olds B, Pfrender ME, Prowse TAA, Renshaw MA, Lodge DM (2018) Effects of sampling effort on biodiversity patterns estimated from environmental DNA metabarcoding surveys. Scientific Reports 8: 8843. https://doi.org/10.1038/s41598-018-27048-2

Additionally, please cite the Dryad data package:

Grey EK, Bernatchez L, Cassey P, Deiner K, Deveney M, Howland KL, Lacoursière-Roussel A, Leong SCY, Li Y, Olds B, Pfrender ME, Prowse TAA, Renshaw MA, Lodge DM (2018) Data from: Effects of sampling effort on biodiversity patterns estimated from environmental DNA metabarcoding surveys. Dryad Digital Repository. https://doi.org/10.5061/dryad.40782nd
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