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Table S1 Sample metadata and distribution of sequence reads across 12 marine sites.

Table S2 Taxonomic Breakdown of all OCTUs recovered at 95% and 99% sequence identity cutoffs in the OCTUPUS pipeline, based on top-scoring BLAST matches obtained from two 18S gene regions.

Fig. S1 Eukaryotic community assemblages at Atlantic sites 22#1 and 25#2 following noise removal.

Fig. S2 Map displaying sample sites utilized in this study, representing Pacific (blue) and Atlantic (red) locations.

Fig. S3 Jackknife Cluster Analysis using an expanded SSU pyrosequencing dataset.

Fig. S4 Proportions of eukaryotic taxa recovered under relaxed (95%) and stringent (99%) clustering with UCLUST.

Fig. S5 Proportional changes observed for non-chimeric nematode OCTUs (BLAST-derived taxonomy) representing forward sequencing reads from both 18S loci.

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