Interpreting the n in a Unifrac Box Plot

Hi! I'm new to the microbiome world, but am trying to get a grasp on my data.

I'm comparing milk samples from "healthy" and "mastitic" quarters (cow udder teats). I'm considering the samples independent since that is one of the requirements of PERMANOVA, and quarters are technically closed off from each other. I have 36 milk samples of each type. I know the n number on the bottom of the plot is to show the number of pairwise comparisons. I understand where the n=630 is coming from [(36(36-1))/2] = 630. I am, however, confused as to where the second n is coming from. Since I had the same amount of samples in both groups, shouldn't they be the same?

Also, the plots look very similar to each other, even though the p-value is at a significant level (0.001). How would you interpret this?


This is right when you are counting the number of distances within the group (distances to group 1 within group 1).

The second boxplot in the first figure will show the distances of samples from group 2 to group 1, so it will be simple 36*36.

Second figure will show distances to group 2 within group 2 and distances to group 2 from samples of group 1.


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