Is it technically correct to eliminate branches with low bootstrap ?

Question

[ddh8602]

Hello everyone. So I did a phylogenetic analysis of some closely related isolates, the problem is that I got very low bootstrap values for some of the branches. I am wondering if it is technically correct to eliminate bootstrap values < 70 for example using iTOL ? Just a note, eliminating this isolates will not affect my results in general, but I am concerned that it will affect the topology of the tree. I appreciate your suggestions.

Answer 1

[lieven.sterck]

Personally I would say no. The branch has low bootstrap, ok, but that does not mean it should not be there. What you could do is collapse them (== create for instance tri-furctation) but simply removing them will be a bit harsh.

You could also go back to square one and don't take the sequences into account that are on the low bootstrap branch(es) and start the phylogeny analysis over, but then here you are forcing things to be like you want them to be.

Answer 2

[Mensur Dlakic]

There is nothing wrong with having a branch support < 70, though I would not make a major argument that relies on tree topology in poorly-supported branches.

I interpret your question to mean "is it ethically correct to remove branches?" I would say it depends on whether one is doing it for substantive or decorative reasons. If it is in the peripheral area of the tree and you want to remove a potential distraction from the main point, I think that is acceptable, though probably unnecessary as I said above. Removing branches that directly contradict our preferred interpretation of results would be unethical.

Whatever the exact reason is for removing branches, it may very well change the overall topology, so that is a valid concern.