I deployed fouling panels at 4 different sites (2 seagrass sites and 2 marinas). The panels were in cages to prevent predation and allowed for communities to develop. At different times I added more at each site so that I had communities that were 30 days old, 60 days old, and 90 days old at each site and all in cages. After 90 days I removed all cages and exposed all panels to predation for 5 days. The question is how predation affected communities of different ages and at different sites. I also had control communities that had no cage for 90 days. This can be analyzed as community data (permanova) and further by individual taxonomic groups or species. I have attempted to do a permanova with Before/After Cage Removal, Habitat, Community Age, and Site (nested within Habitat). The results look right but I am curious as to what other might suggest.
I think it is good to do PERMANOVA what I do not know if you performed PERMANOVA unifactorial or multifactorial in this case fixing the elimination before / after the cage with the factors (habitat, age of the community, site).
Another analysis that you can do is multiple correlations to see which variable influences more in the predation suggest Mantel Test.
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