What do the values on the Faith PD plot mean?

[m7474]

Hi everyone,

I'm doing an analysis to determine whether drug treatment has an effect on the microbiome. I ran the Faith's PD test and understand that it is testing phylogenetic diversity within samples, but am unsure what the numbers on the y-axis mean. Do higher values signify higher phylogenetic diversity? I have done some searching but am mostly finding info about the test, not the specific values. I've attached an image of what my plot looks like, if that helps!

Thank you!

[timanix (Timur Yergaliyev)]

@m7474

Do higher values signify higher phylogenetic diversity?

Hi!
y-axis is the index itself for your samples, so yes

[jwdebelius (Justine Debelius)]

Hi @m7474,

To add on to @timanix’s good answer, Faith’s phylogenetic diversity measures the amount of the phylogenetic tree covered by the community. It’s a sum of the minimum branch lengths (however you measure branch lengths). So, a higher number means more branches, means more richness (more diversity).

There are a couple of caveats (yes, I’m here to rain on the parade (). First, as a richness metric, Faith’s PD is pretty sensitive to sequencing depth. The actual value of your numbers depends on your sequencing depth, denoising method, rarefaction depth, and phylogenetic tree. The absloute magnitude is less useful as you look across datasets.

The relationship between the samples should be fairly consistent for a complex community, mostly independent of technical factors.

Best,
Justine

[m7474]

Thank you so much! This really helped me understand how to interpret my results.

[m7474]

Thank you so much for responding!