Alpha diversity interpretation

Hi, I ran alpha diversity analysis with various alpha div metrics on two different sample categories. I found a statistical difference in diversity between the samples in chao1, shannon and observed OTUs but not with Faith’s PD and am not sure how to interpret this. I understand that Faith’s PD takes into account phylogenetic distance within samples, so do my results mean that I have more variation in the different OTUs observed in one of the categories, however these OTUs have a strong overlap with those observed in my other category?


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Hi @marianacosta,
Faith’s PD takes into account phylogenetic distance between OTUs by measuring the total branch lengths for the OTUs in each sample.
So if you do see a difference using other metrics, but not using PD, it likely means that your samples have different number (and richness) of OTUs, but those OTUs are from a similar distribution of clades in the tree.


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