alpha diversity comparison vs beta diversity analysis

Hey everyone,

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.

As you say, the alpha diversity is a measure of evenness/richness but it doesn’t back into account what OTUs are making up the community. For example, if you had a community that comprised 3 species of Escherichia in a equal abundance, and another community with 3 Prevotella (equal abundance) then any alpha diversity statistic would be the same for these communities. It doesn’t mean that the communities are similar, only that the amount of diversity in each one is the same.

In contrast, the beta diversity measures the overlap in OTUs between the samples, so the fact that the communities are made from difference species would be reflected there.