Is it appropriate to publish a phylogenetic tree with low basal bootstarp value
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4 months ago

I have a tree, some of the nodes have low bootstrap values which vary from 20~70 and I want to use it in my paper. And I previously read a paper "Shewanella nanhaiensis sp. nov., a marine bacterium isolated from sediment of South China Sea, and emended descriptions of Shewanella woodyi, Shewanella hanedai and Shewanella canadensis" in which, they only show the node with bootstrap value that is above 70%. I would like to ask if it is appropriate. Thanks!

DNA tree phylogenetic • 517 views
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Are these % values? Or bootstrap numbers? i.e. are we talking 20-70% or 20-70 replicates out of, say, 1000 runs?

I think Michael's answer is right in either case, but just for completeness..

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Yes, those are % values, thanks for your answer!

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I think, then it's ok. Just go ahead with your manuscript. If you are lucky you may get some more feedback on your methods during the review process.

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4 months ago
Michael 54k

I normally label the nodes with less than 100% or 99% bootstrap support. You can also use a color code or just add the numbers. If you provide the data accurately and most of your nodes have good support and you don't try to base firm conclusions on those clades then there should be nothing to complain about. There is not much you can do about these nodes anyway, except try to re-do the alignment in different ways and do a comprehensive model test or leave out the whole clade.

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Thank you for your answer!

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