It is normal for significance to change when taking other effects into account. The R2 value is not an indicator of significance, though — when you say not significant, I assume you mean the P value no longer indicates significance.
You should check out these other topics for more insight:
Hi!
I'm a bit of a newbie with stats and I'm still trying to fully grasp things. I'm a bit confused on what exactly the test statistics are telling me for PERMANOVA (pseudo-F), ADONIS (R2) and ANOSIM (R), and what exactly I should be using for my question, that is: are there significant differences between locations?
From what I understand of permanova, pseudo-F tells me the ratio of between-group variation and within-group variation. A larger pseudo-F value means that the between-group variat…
An earlier post by @CarlyRae first introduced me to the fact that when examining beta diversity I need to consider not only the results of a multi or univariate anova, but also examining if the within-group distances to a centroid were equivalent among my groups. I'm wondering how to best interpret the situation where everything turns out to be significant. That is, if the results of both PERMANOVA and PERMDISP suggest significant differences, where do most people go next? I've run these tests b…