DOI: 10.5061/dryad.5p1j3
title: Data from: A metagenetic approach for revealing community structure of marine planktonic copepods

description: Marine planktonic copepods are an ecologically important group with high
 species richness and abundance. Here, we propose a new metagenetic
 approach for revealing the community structure of marine planktonic
 copepods using 454 pyrosequencing of nuclear large subunit ribosomal DNA.
 We determined an appropriate similarity threshold for clustering
 pyrosequencing data into molecular operational taxonomic units (MOTUs)
 using an artificial community containing 33 morphologically identified
 species. The 99% similarity threshold had high species-level resolution
 for MOTU clustering but overestimated species richness. The artificial
 community was appropriately clustered into MOTUs at 97% similarity, with
 little inflation in MOTU numbers and with relatively high species-level
 resolution. The number of sequence reads of each MOTU was correlated with
 dry weight of that taxon, suggesting that sequence reads could be used as
 a proxy for biomass. Next, we applied the method to field-collected
 samples, and the results corresponded reasonably well with morphological
 analysis of these communities. Numbers of MOTUs were well correlated with
 species richness at 97% similarity, and large numbers of sequence reads
 were generally observed in MOTUs derived from species with large biomass.
 Further, MOTUs were successfully classified into taxonomic groups at the
 family level at 97% similarity; similar patterns of species richness and
 biomass were revealed within families with metagenetic and morphological
 analyses. At the 99% similarity threshold, MOTUs with high proportions of
 sequence reads were identified as biomass-dominant species in each
 field-collected sample. The metagenetic approach reported here can be an
 effective tool for rapid and comprehensive assessment of copepod community
 structure.
description: Sequence file for
 classificationSequence file for the
 naϊve Bayesian classifier implemented in mothurTaxonomy file for
 classificationTaxonomy file for the
 naϊve Bayesian classifier implemented in mothurAligned LSU sequences of
 copepodsAligned sequences of LSU
 D2 region registered in this study (GenBank accessions AB796399–AB796431
 and AB820728–AB820803)JH_copepod_LSU_aligned.fasMOTU table for artificial community sampleMOTU list for artificial community sample (33 morphologically identified species) at the 97% threshold, with information of number of sequence reads, Blast result and representative sequence.33sp_MOTU_list.xlsxMOTU table for field-collected samplesMOTU list for field-collected samples at the 97% similarity threshold, with information of number of sequence reads in each station, Blast result, and representative sequences. The taxonomic order determined by the naϊve Bayesian classifier implemented in mothur is also listed.Field_MOTU_list.xlsxRaw data of morphological analysisMorphological analysis of field-collected samples. Numbers of individuals (Inds.) and total dry weight (DW) for all species identified from each sampling location. Numbers of individuals and DW are calibrated into unsplit (1/1) samples.Morphological_data.xlsxMOTU table for field-collected samples (99% similarity)MOTU list for field-collected samples at the 99% similarity threshold, with information of number of sequence reads in each station, and representative sequences.99% sequence reads.xlsxMID tag informationMID tag used in this study. Each sample was differentiated by unique multiplex identifier (MID) adaptors in GS Titanium Rapid Library MID Adaptors Kit (Roche).MID_tag_information.xlsx