10.5061/DRYAD.D47FM
Ransome, Emma
National Museum
Geller, Jonathan B.
Moss Landing Marine Labs, Moss Landing, California, United States of America
Timmers, Molly
University of Hawaii at Manoa
Pacific Islands Fisheries Science Center
Leray, Matthieu
Smithsonian Tropical Research Institute
Mahardini, Angka
Indonesian Biodiversity Research Center, Denpasar, Bali, Indonesia
Sembiring, Andrianus
Udayana University
Collins, Allen G.
National Museum
National Marine Fisheries Service
Meyer, Christopher P.
National Museum
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
Dryad
dataset
2018
Autonomous Reef Monitoring Structures
Operational Taxonomic Units
National Science Foundation
https://ror.org/021nxhr62
OISE-1243541
2018-03-23T00:00:00Z
2018-03-23T00:00:00Z
en
https://doi.org/10.1371/journal.pone.0175066
2863723488 bytes
1
CC0 1.0 Universal (CC0 1.0) Public Domain Dedication
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.
Moorea French Polynesia