I’m asking another question which I’m quite confused with. What I understand is that alpha diversity is much about the richness and evenness within sample, and beta diversity is much about structure or composition across samples. The mothur SOP did a repeated measures ANOVA and found no difference regarding the early vs late for alpha diveristy, but what does that mean? That is we are comparing alpha diversity across samples and it is not significant? Not quite sure how to interpret the data.
I can understand for all the following beta diversity analysis (AMOVA) and it says there is a significant difference between early vs late groups. It will make sense because we can exactly find out what has been changed among groups (and figure out which OTU is responsible for the shift).
My point is how to understand no difference from alpha diversity but significant different for beta? Any comments would be appreciated!!! thanks a lot to all of you.