I have atmospheric microbiome data and want to know how I should be analyzing alpha diversity. I used unweighted unifrac for beta diversity and thought that I should use Fath's PD but don't really understand the difference between Faith and Chao1.
I don't think Shannon is going to be good because my data has the presence of many low abundant taxa and is zero inflated.
Any help is greatly appreciated!
Hi,
The Faith's PD is an alpha-diversity metric which is based on the phylogeny. In fact, this index take in account the structure of the phylogenetic tree constructed with your sequences. It help you to consider if the diversity observed make a sense with a phylogenetic differences between your taxas.
The Chao1 is a richness index, which is used to predict the theorical number of taxa among your samples by extrapolating. It help you to estimate the richness in your samples when a large number of rare taxas could be underestimated.
Hope it helps.
Hello Justin,
May be this could help
Article Partitioning Diversity Into Independent Alpha and Beta Components
Hi Justin,
It really depends on your questions you are asking.
Since Alfa diversity is used to evaluate within sample's indices, the important parameters are Richness (number of OTUs, Chao1 as Benoit mentioned), Evenness, total diversity (such as Shannon but not only ) which basically takes into consideration both richness and evenness,
and the total number of cells in the sample.
Other indices such as dominance and more are also acceptable, again depends on your questions.
Nir
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