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donovan-h-parks / PhyloRank

Assign taxonomic ranks based on evolutionary divergence.
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Biological inference from RED values? #11

Open Jigyasa3 opened 4 years ago

Jigyasa3 commented 4 years ago

Hey all!

Thank you for such an interesting analysis! I wanted to ask if we can draw some biological inferences from the RED output? For example, I ran the example data given with the Phylorank package, and the "rank_distribution.html" file (also shown below) suggests that some archaeal orders (eg- o_Methanomicrobiales) might be undergoing faster relative evolutionary divergence as compared to other taxa.

Can we use this information to extrapolate that o_Methanomicrobiales is under a faster rate of evolutionary divergence i.e. might be evolving faster than other archaeal orders?

I am working on gut microbes, and I am interested in using RED values to say something about how some taxa are evolving faster than others in the same gut environment. Would that be correct to infer?

image

Looking forward to your reply!

donovan-h-parks commented 4 years ago

Hi. I don't think you can conclude that Methanomicrobiales is under a faster rate of evolutionary divergence. Different archaeal Orders will, in general, have different RED values simply because of the exact node used to define these Orders. For example, perhaps we will soon discover a new lineage sister to what is currently labelled Methanomicrobiales. Since the RED of Methanomicrobiales is high relative to other archaeal Orders, this lineage would be made the most basal family within the Methanomicrobiales. This would move the RED for Methanomicrobiales to the left in the plot and perhaps make it look far more typical.

Jigyasa3 commented 4 years ago

Understood, thank you for replying!