Fig 1.
Community composition of copepods based on the presence/absence of operational taxonomic units (OTUs).
(a) Sampling location. (b) Vertical profiles of environmental variables across latitudes (top: seawater temperature, middle: salinity, and bottom: chlorophyll a) obtained during north–south transect cruises along 170°W (points encircled in black lines in [a]); the North Pacific Intermediate Water (NPIW) and Antarctic Intermediate Water (AAIW) are shown in the salinity profile. (c) Cluster analysis of all copepod communities. Color code for warm-, Transition/California-, and cold-water communities in the epipelagic layer is illustrated in (a). (d) Multidimensional scaling analysis of all samples. Cold-water communities are encircled by black line. Details of the PERMANOVA are presented in S3 Table. Map was created by the authors in Generic Mapping Tools version 5 [30].
Fig 2.
Rarefaction curves for operational taxonomic units (OTUs) at different sequence reads.
(a) Results for all sequence reads and total sequence reads at each sampling layer (0–200 m, 200–500 m, and 500–1,000 m). (b) Results for each sample. Geological areas are represented by color.
Fig 3.
Community compositions at each layer based on presence/absence of operational taxonomic units (OTUs).
(a) Epipelagic layer (0–200 m). (b) Upper mesopelagic layer (200–500 m). (c) Lower mesopelagic layer (500–1,000 m). Cluster analyses were performed on warm-water groups. PERMANOVA at each sampling layer was performed on groups color-coded by the region, excluding the unclassified groups (gray) in the lower mesopelagic layer (details in S3 Table). Maps were created by the authors in Generic Mapping Tools version 5 [30].
Table 1.
Summary of distance-based linear model (DistLM) analyses based on presence/absence of operational taxonomic units (OTUs).
The best model of variables was selected based on the Akaike information criterion (AICc) for all locations in each sampling layer (0–200 m, 200–500 m, and 500–1,000 m) and throughout the sampling layers (0–1,000 m). The pseudo–F, P–value, and explained variation attributable to the model are indicated for each variable.
Fig 4.
Community compositions based on presence/absence of operational taxonomic units (OTUs) throughout the sampling layers (0–1,000 m).
(a) Cluster analysis. PERMANOVA was performed on the cluster groups represented by color (details in S3 Table). Taxonomic compositions of OTUs are shown for each sampling station at each layer. The arctic community is added to the epipelagic layer. (b) Multidimensional scaling analysis for warm-water groups. Cluster groups are connected by lines. (c) Geographic distribution of clustered groups. (d) Comparison of clustered groups and temperature-salinity (T-S) diagram to investigate the effect of water mass structures on copepod community composition. Map was created by the authors in Generic Mapping Tools version 5 [30].
Fig 5.
Cluster analysis based on quantitative data and proportions of reads of each major operational taxonomic unit (OTU) within a sample.
The cluster analysis was performed on all samples based on square root transformed proportions of sequence reads in OTUs, and the PERMANOVA was performed on clustered groups. The California Current region is included in the Transition region. The OTUs and the best-hit species identified by BLAST search are represented for major OTUs, which were selected by the SIMPER analysis. The numbers in parentheses indicate the similarity percentage of the best-hit species.
Fig 6.
The distribution of copepod diversity at different layers: (a) 0–200 m, (b) 200–500 m, (c) 500–1,000 m, and (d) all sampling layers (0–1,000 m). Colors indicate the number of operational taxonomic units (OTUs). Maps were created by the authors in Generic Mapping Tools version 5 [30].
Fig 7.
Horizontal and vertical patterns of copepod diversity.
(a) Number of operational taxonomic units (OTUs). (b) Simpson diversity index. (c) Phylogenetic diversity. The California Current region is included in Transition region. The diversity parameters were averaged for each region and scale bars indicate standard deviation. NS = not significant; * = P < 0.05; ** = P < 0.005; *** = P < 0.001 based on Kruskal-Wallis tests among geographic regions; + = P < 0.05; ++ = P < 0.005; +++ = P < 0.001 based on Kruskal–Wallis tests among sampling depths. Details of the statistical analyses are listed in S5 Table. Maps were created by the authors in Generic Mapping Tools version 5 [30].
Table 2.
Variables explaining operational taxonomic unit (OTU) numbers.
The best model of the variables was selected using a stepwise method in generalized linear model (GLM) analysis, and the pseudo R2 and Akaike information criterion (AIC) values are reported for the best models.
Fig 8.
Distribution patterns of copepod operational taxonomic units (OTUs) based on cold- and warm-water groups and water depth (0–200 m, 200–500 m, and 500–1,000 m).
Only the OTUs with ≥ 15 sequence reads in a single sample were analyzed, and proportions of numbers of OTUs with different distribution patterns are shown in each taxonomic group. The log scale total OTU numbers and average genetic distance among OTUs are represented as colors for each taxonomic group. The orders Calanoida and Cyclopoida were further classified into families. The superfamily names are indicated for the order Calanoida.
Fig 9.
Phylogenetic analysis of taxonomic groups of operational taxonomic units (OTUs) with warm-water and cold-water distributions.
OTUs with cold-water distribution are indicated by arrows. Bootstrap values at the nodes are inferred from maximum likelihood analysis (white, grey, black). Genetic lineages containing multiple OTUs with warm-water distribution are presented as triangles for simplicity, and the number of OTUs within each triangle is represented by the white–black spectrum. The length of each triangle corresponds to the length of the deepest node of each lineage. Scale bars indicate 0.02 genetic distances. The average nearest genetic distance is indicated for OTUs with warm-water and cold-water distributions in each taxon. The nucleotide substitution models used are indicated for each taxon (GTR: General Time Reversible; TN93: Tamura-Nei).