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

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.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.Funding provided by: National Science FoundationCrossref Funder Registry ID: http://dx.doi.org/10.13039/100000001Award Number: OISE-124354