I'm a grad student in microbial ecology and I'm comparing some bacterial communities in experimental man made ponds. I've run the PCoA, NMDS, and CCA to see how various variables effect or influence the communities. Next I'd like to actually assess the similarity. I'm running betadisper to check the homoscedasticity and I'm finding that within the entire 2 year experiment, the ponds' dispersions are different between years, but similar within years, for untreated and treated ponds. Am I still allowed to run ADONIS and ANOSIM on this data even though I'm getting significant values in anova and TukeyHSD? Can anyone recommend any other tests I could use to assess community similarity or any other useful tests?
Thanks! I just joined the community and have been reading it a lot! thank to all the contributors!