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).