Ecological analyses
In order to evaluate how exhaustively the zooplankton communities of each station were sampled, rarefaction curves of the detected ASVs were generated using the QIIME2 diversity alpha-rarefaction plugin, implementing the median frequency of the reads as the sequencing depth. Additionally, the number of obtained ASVs from each station was compared against the non-parametric species richness estimator Chao1 (Chao, 1984; Supplementary Information Fig. S2). The rarefied number of reads was used as an abundance proxy to estimate the Shannon diversity index and structural changes in the zooplankton community among spatial and temporal scales.
Differences in taxonomic structure among cruises were evaluated at the order level with bar-plots based on only the most abundant ASVs (cutoff at > 1% frequency) and at the ASV level by principal coordinate analysis (PCoA) based on Bray Curtis, Jaccard, and weighted and unweighted phylogenetic Unifrac distance metrics. The results of the PCoA were visualized with EMPeror (Vázquez-Baeza, Pirrung, Gonzalez, & Knight, 2013). Statistical differences were evaluated by a permutational multivariate analysis of variance (PERMANOVA) and were based on 4999 permutations usingbeta-group-significance plugin of QIIME2 v.2019.7 (Anderson, 2001). Also, shared and/or exclusive non-rarefied ASVs among the same stations from each cruise (n = 19 and 21 for 18S and COI, respectively) were visualized using Venn diagrams created with the open web-software InteractiVenn (http://www.interactivenn.net/ Heberle, Meirelles, da Silva, Telles, & Minghim, 2015). Significant differences in the zooplankton diversity index were evaluated with a one-way analysis of variance (ANOVA) conducted in Statistica (StatSoft Inc., Tulsa, USA) with statistical significance evaluated at α = 0.05 (p < 0.05). Finally, to determine which ASVs were primarily contributing to the observed spatial-temporal dissimilarities, a SIMPER analysis based on rarefied ASV abundance was implemented in PRIMER+P v.6 (K. R. Clarke & Warwick, 2001).