Sequencing results and overall taxonomic composition of the zooplankton community
A total of 242 (122 and 120 for 18S rRNA and COI, respectively) zooplankton community libraries were successfully amplified. Overall, sequencing produced more than 28.5 million paired-end reads, and 24.4 million sequences (~86% of the total number of reads) met quality control tests. After library curation, an inflection point in ASV abundance was observed at 1.2 and 1.3 log value for 18S rRNA and COI, respectively (Supplementary Information Fig. S1A and S1B). Moreover, ASVs below these threshold values were generally detected for only one station and were considered as in vitro local artifacts that likely rose during amplification and/or sequencing. Therefore, further analyses were carried out with ASVs with a minimum number of reads, namely 12 (log value ~1.1) and 21 (log value ~1.3) for 18S rRNA and COI, respectively. The final datasets included 13,088,619 reads representing 1,247 ASVs for 18S and 8,573,204 reads representing 14,795 ASVs for COI (Supplementary Information Table S2 and Table S3). The number of reads and ASVs removed during the quality control tests for both loci are reported in Supplementary Information Table S4.
According to the asymptotic shape of the rarefaction curves (Supplementary Information Fig. S3 and Fig. S4) and the closeness between the detected ASVs to Chao1 (Supplementary Information Fig. S2), zooplankton communities were exhaustively sampled for both genetic markers. The minimum number of reads was 20,076 and 57,585 for the COI and 18S datasets, respectively. Thus, the samples were rarefied to these read numbers.
Taxonomic classification varied somewhat depending on the molecular marker. For example, some taxa were exclusively detected with either 18S rRNA (e.g., Brachyopoda, Bryozoa, Ctenophora, Hemichordata, and Nemertea) or COI (e.g., Chordata and Rotifera). Moreover, we observed a discrepancy in the relative abundance of taxa depending on the locus (e.g., Calanoida and Euphausiacea; Fig. 2A and 2B). Specifically, the most common orders and their relative abundance based on COI and 18S rRNA, respectively, were (abundance percentages in parenthesis): Calanoida (42.5%, 51.1%), Euphausiacea (17.5%, 19.5%), Aphragmophora (9.3%, 2.3%), Halocyprida (8.7%, 1%), Siphonophorae (5.9%, 5.1%), Decapoda (2.6%, 2.1%), and Phyllodocida (0.06%, 1.2%) Oegopsida (2%, 0.1%). Additionally, the predominant orders detected only with COI were Myctophiformes (2%), Stomiiformes (1.6%), and Clupeiformes (1.6%), while those detected only with 18S rRNA included Salpida (1.3%) and Doliolida (1.3%).