How are diversity measures calculated in QIIME?

[Nicholas_Bokulich]

Hi @LVC,

I cannot really comment on QIIME 1 — I was not involved in QIIME 1 development, and you may want to post to the QIIME 1 forum to get QIIME 1-specific answers.

That said, I expect QIIME 1 probably used the same metric calculations that QIIME 2 does.

@LVC

Alpha diversity however, can also be influenced by the definition of a species - what is QIIME defining a species as for inclusion criteria?

The "species" definition entirely depends on the input. We call this metric "observed OTUs" in QIIME 2 to be somewhat more clear about this — unless if alpha diversity is being explicitly calculated on species (e.g., a feature table that has been annotated and collapsed with species-level taxonomy), then the "species" definition is going to be unique sequences observed (i.e., OTUs or ASVs, however unique seqs are defined).

@LVC

Secondly, are more closely related species being weighted together in QIIME? eg. considering 2 populations:

This is not considered explicitly in richness (i.e., "observed OTUs") calculations. However, the "Faith's PD" metric examines phylogenetic diversity richness (as branch length covered by a given sample).

@LVC

I would also like to be able to calculate hill numbers at all values of the order q. Is it possible to do this in QIIME2?

We do not have a method for calculating hill numbers in QIIME 2 (this would be a great addition if you would like to contribute!). However, reading this paper:

Parameter a determines special cases of Hill number, for example, N 0 as number of taxa, N 1 as exponential Shannon index, and N 2 as reciprocal Simpson index

So Shannon and Simpson's index can be calculated separately in QIIME 2.

@LVC

Finally, in QIIME1 the observed_otus and observed_species data are identical however, when I look at the biom table (converted into a .tsv for visualisation) there appears to be several OTUs for each observed species.

That sounds correct, those would be identical. OTUs are just unique sequences, and do not necessarily correspond to distinct species — they can be different strains or a species or even 16S variants from within the same cell (multi-copy heterogeneity) or sequence error. Alpha diversity gets pretty messy when looking at multi-copy microbial marker genes.

@LVC

When I convert Shannon entropy values calculated in QIIME into Shannon diversity values they are higher than the observed_species values for that sample.

@LVC

Having read up on the documentation I therefore think Shannon entropy is being calculated differently here and that the conversion should instead be:
Shannon diversity = 2^(Shannon entropy)
= 2^(7.241567)
= 151.33 < Observed Species of 678.5 which is a reasonable answer.

Am I correct in my thinking here?

Yes, you are correct. Shannon is often calculated as log base 10 or log base 2 (or base e). See this thread for a little more discussion.

I hope that helps!