Comparison of beta diversity patterns between bulk DNA and eDNA datasets of the five primer sets
The MDS plots illustrate that primer sets A and E have very similar community patterns, while primer sets B, C and D are similar to each other but clearly distinct from the other two primer sets (ESM Fig 5A). All five primer sets were able to differentiate the most diverse location (120) from the three other locations (ESM Fig 5B), but differences in the ability to differentiate the three other locations were observed between primer sets (Fig 4). MDS plots for the five primer sets separately showed that the offshore sandy locations with intermediate diversity (330 and 840) were more similar to each other than to the fine sandy (120) and fine muddy (ZVL) coastal locations (Fig 4). For primer sets A and E, all four locations were recovered as separate clusters when using Bray Curtis dissimilarity index (Fig 4). This separation was less clear when using the Jaccard index (ESM Fig 6). Permanova results were largely consistent across primer sets and between Bray Curtis and Jaccard distance metrics and showed highly significant differences between locations, between bulk DNA or eDNA and for primer sets B, C and D also the interaction effect was highly significant (Table 2). Observed differences between primer sets were the non-significant interaction term “Location x DNA source” for primer sets A and E when the Bray Curtis index was used and a non-significant “DNA source” effect and interaction term “Location x DNA source” for primer set A when the Jaccard index was used (Table 2). Nearly all permdisp results were significant for all primer sets and for both distance metrics (Table 2), indicating that the significant Permanova results were caused by both location effects and dispersion effects. Despite the differences in dispersion of the replicates within sampling locations, the MDS plots show a clear distinction between sampling locations which was supported by a significant main effect of location in Permanova (Table 2) as well as significant posthoc test results for all pairwise combinations of locations for primer sets A and E (ESM Table 6). Permanova revealed significant differences in community structure between bulk DNA and eDNA samples for all primer sets (Table 2).