I am currently analyzing next generation sequencing bacterial data and trying to figure out whether bacterial communities differ between regions (seems to exhibit this in nMDS).
When running adonis (vegan package) I got an r2 = 0.45, and p = 0.001. When I ran the betadisper and ran a subsequent permutation test I got an F = 1 and p = 0.3.
From my understanding my results are saying that there is an effect of region on bacterial communities and that the communities from each region display similar homogeneity. I'm not sure if that is correct or even if it would be "expected" or appropriate to have a significant adonis but insignificant betadisper. For both permutation tests I used the obligatory 999 permutations. Let me know if you need more information and thanks in advance for your help!