Different Shannon diversity results between QIIME2 and phyloseq

[Felipe_Rocha]

Hello everyone,

as I was wondering today through my alpha diversity measures from QIIME2 and phyloseq I found differences in all my samples’ Shannon diversity measures, but curiously not in my Simpson diversity measures. I wonder why would that happen if the same table is being used in both programs. I checked samples, features abundances and they are the same, I guess the Shannon diversity formula implemented is the same either. Do you have any idea of what is going on?

I was going to check if there is a linearity between the Inverse Simpson index (1/D) calculated by phyloseq’s estimate richness, and the exponential of the Shannon index (e^H’) based on my H’ provided by QIIME2, as suggested by phyloseq’s supporting information. Right before doing it I found those differences.

I appreciate any help or insights,
Thank you,
Felipe.

[Nicholas_Bokulich]

Hi @Felipe_Rocha,
Please see here:

shannon index value

Hello Ana, A bunch of things can affect the Shannon index. Switching from OTUs to ASVs can change it. The Shannon index uses a log scale, but it can use log2 or log10 or natural log, and all of these are perfectly valid nobody EVER reports which one they are using! This sounds crazy. And it is. And yet if you look in the original Shannon entropy paper that has 69,200 citations, all three of these log bases are mentioned on page one: The choice of a logarithmi…

[Felipe_Rocha]

Thanks, @Nicholas_Bokulich, I haven’t thought about the log scale used. I think it might be it.

Do you know the log scale used by QIIME2?

[Nicholas_Bokulich]

looks like it’s base 2: http://scikit-bio.org/docs/0.5.4/generated/generated/skbio.diversity.alpha.shannon.html