Personally, I don’t think I’d have a problem with this approach (especially 
given the paper Liam cited) given that you are using a phylogeny (a model) to 
test a hypothesis, which is, after all, all we can ever do. You can always do 
more, so any threshold of phylogenetic tree “quality” is going to be somewhat 
arbitrary anyway. I don’t mean to sound defeatist — obviously you should do the 
best job that you can, and it sounds like you have done that given that the 
goal of your research is not to reconstruct a new phylogeny of the clade you’re 
studying. Perhaps you can try to explain this in your rebuttal. 

Or alternatively, use Liam’s awesome code (below) to generate all possible 
phylogenetic trees give your polytomies, and run your PGLS on all of them to 
see if its sensitive to topology. You could probably loop this up somehow 
without much effort. 


> On Sep 17, 2016, at 6:46 PM, Oscar Valverde <> wrote:
> Dear colleages
> I am working on an phylogenetic signal and PGLS analysis using a database
> with values for ~600 plant species. To construct my phylogeny I used the
> backbone Phylomatic supertree ( and
> added branch lengths with the based on a fossil calibration for angiosperms
> using the bladj function in phylocom, and resolved polytomies with the
> multi2di function in phylotools.
> Now that I am trying to publish the paper, some reviewers indicated that
> such tree is not suitable for statistical analysis because the level of
> resolution of the tree is too low (to the family level maybe?) and the
> uncertainty is too high to get any reliable result with respect to PGLS or
> phylogenetic signal of the traits. Instead, they suggest I should build my
> own tree based on sequences. Of course this is a major project to undertake
> and in my opinion far from the scope of my study. In fact, this position
> defies the whole reason to have websites like phylomatic where researchers
> can use a reliable resolved phylogenetic tree instead of creating a new one
> every time.
> I would just like to know if the position of my reviewers is a valid one,
> and it the answer is yes, what resource should I use to get a reliable
> phylogenetic tree without making my own version. Thanks in advance for any
> help.
> Oscar Valverde
> Post Doctorate Associate
> International Center on Tropical Botany
> Florida International University
> ‘Anything else you’re interested in is not going to happen if you can’t
> breathe the air and drink the water. Don’t sit this one out. Do something.
> You are by accident of fate alive at an absolutely critical moment in the
> history of our planet.’ ~Carl Sagan
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