DOI: 10.5061/dryad.d47fm
title: Data from: The importance of standardization for biodiversity comparisons: a case study using Autonomous Reef Monitoring Structures (ARMS) and metabarcoding to measure cryptic diversity on Mo'orea coral reefs, French Polynesia

description: The advancement of metabarcoding techniques, declining costs of
 high-throughput sequencing and development of systematic sampling devices,
 such as autonomous reef monitoring structures (ARMS), have provided the
 means to gather a vast amount of diversity data from cryptic marine
 communities. However, such increased capability could also lead to
 analytical challenges if the methods used to examine these communities
 across local and global scales are not standardized. Here we compare and
 assess the underlying biases of four ARMS field processing methods,
 preservation media, and current bioinformatic pipelines in evaluating
 diversity from cytochrome c oxidase I metabarcoding data. Illustrating the
 ability of ARMS-based metabarcoding to capture a wide spectrum of
 biodiversity, 3,372 OTUs and twenty-eight phyla, including 17 of 33 marine
 metazoan phyla, were detected from 3 ARMS (2.607 m2 area) collected on
 coral reefs in Mo'orea, French Polynesia. Significant differences
 were found between processing and preservation methods, demonstrating the
 need to standardize methods for biodiversity comparisons. We recommend the
 use of a standardized protocol (NOAA method) combined with DMSO
 preservation of tissues for sessile macroorganisms because it gave a more
 accurate representation of the underlying communities, is cost effective
 and removes chemical restrictions associated with sample transportation.
 We found that sequences identified at ? 97% similarity increased more than
 7-fold (5.1% to 38.6%) using a geographically local barcode inventory,
 highlighting the importance of local species inventories. Phylogenetic
 approaches that assign higher taxonomic ranks accrued phylum
 identification errors (9.7%) due to sparse taxonomic coverage of the
 understudied cryptic coral reef community in public databases. However, a
 ? 85% sequence identity cut-off provided more accurate results (0.7%
 errors) and enabled phylum level identifications of 86.3% of the sequence
 reads. With over 1600 ARMS deployed, standardizing methods and improving
 databases are imperative to provide unprecedented global baseline
 assessments of understudied cryptic marine species in a rapidly changing
 world.
description: PGM_DATA_MotileExperimentThis file contains raw PGM (Ion Torrent, Life technology) data for adaptors 1, 2 and 3. See file "PGM_SequencingRuns" for corresponding samples.PGM_DATA_SessileExperiment_Run2This file contains raw PGM (Ion Torrent, Life technologies) data for adaptors 6, 13, 14 and 16. See file "PGM_SequencingRuns" for corresponding samples.PGM_DATA_SessileExperiment_Run3This file contains raw PGM (Ion Torrent, Life technology) data for adaptors 10, 11, 12 and 15. See file "PGM_SequencingRuns" for corresponding samples.PGM_DATA_SessileExperiment_Run4This file contains raw PGM (Ion Torrent, Life technology) data for adaptors 8 and 9. See file "PGM_SequencingRuns" for corresponding samples.PGM_SequencingRunsThe table presents the strategy used for multiplexing samples.Metabarcode_OTUrepresentativesThis file contains one representative sequence per OTUMetabarcode_OTUtablesThis file contains an OTU table from each experiment and identifications for each OTU from Biocode, NCBI, BOLD and SAP.