DOI: 10.5061/dryad.40782nd
title: Data from: Effects of sampling effort on biodiversity patterns estimated from environmental DNA metabarcoding surveys

description: Environmental DNA (eDNA) metabarcoding can greatly enhance our
 understanding of global biodiversity and our ability to detect rare or
 cryptic species. However, sampling effort must be considered when
 interpreting results from these surveys. We explored how sampling effort
 influenced biodiversity patterns and nonindigenous species (NIS) detection
 in an eDNA metabarcoding survey of four commercial ports. Overall, we
 captured sequences from 18 metazoan phyla with minimal differences in
 taxonomic coverage between 18 S and COI primer sets. While community
 dissimilarity patterns were consistent across primers and sampling effort,
 richness patterns were not, suggesting that richness estimates are
 extremely sensitive to primer choice and sampling effort. The survey
 detected 64 potential NIS, with COI identifying more known NIS from port
 checklists but 18 S identifying more operational taxonomic units shared
 between three or more ports that represent un-recorded potential NIS.
 Overall, we conclude that eDNA metabarcoding surveys can reveal global
 similarity patterns among ports across a broad array of taxa and can also
 detect potential NIS in these key habitats. However, richness estimates
 and species assignments require caution. Based on results of this study,
 we make several recommendations for port eDNA sampling design and suggest
 several areas for future research.
description: MOTU Cleaning and
 Analyses ScriptThis 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".MOTU Cleaning and
 Analyses.RUnfiltered 18S MOTU
 DatasetThis 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
 informationUnfiltered_18S.csvUnfiltered_COIThis 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 informationSampleIDs_18SDictionary linking samples to sites and ports. Also provides the 18S sequencing ID and bioinformatics pipeline ID for each sample.SampleIDs_COIDictionary linking samples to sites and ports. Also provides the COI sequencing ID and bioinformatics pipeline ID for each sample.Adelaide Site Over-Water DistancesOver-water distances in kilometers between the seven Adelaide sites.geo dists adelaide.csv