Multiple OTUs for a given Taxonomy

Theory behind mothur
1

Hi,

I have 3-4 samples for a given condition. After following the Miseq SOP tutorial, I end up having more than one OTU to the same Taxonomy in the taxonomy file (at the genus level). Does it make (biologically and procedurally) sense ?
If two different OTUs belong to different species within the same genus, should I expect to see both of them in the taxonomy file? Shouldn’t they be clustered into a single OTU when running pre.cluster?

Thanks

2

Multiple OTUs in a given genus is what we expect when we look at 3% OTUs because we think those correspond roughly to species.

3

I see. Then I could use merge.otus command to merge such “species” into genus (or any other taxa), right? So that I can choose in downstream analysis which taxon to consider?

Would it be equivalent (looking at 3% OTUs and merging OTUs to genus afterwards) to look at 5% OTUs?

Thanks!

4

I am not a taxonomy person. I’m very firmly in camp OTU because the amount of diversity captured in a named genera/order/whatever says much more about who has studies an organism/group than anything about their evolution.

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