There also are several empirical plant chronograms available for reuse:
check TreeBase, OpenTree, and Dryad. Or you could use something like phlawd
or supersmart (just out in SystBio) to make a phylogeny for your taxa.
Phylomatic is convenient and will have all your taxa placed in some way,
but it'd make your conclusions more robust to just download a tree, make
sure the taxa match yours (look at the taxize package), prune out the taxa
that don't match (treedata() in Geiger), and rerun. If the conclusions are
qualitatively the same, you satisfy the reviewer; if not, you may have
saved yourself from an error. Either way the paper is improved. I haven't
reviewed your paper, but if the central point is using a phylogeny to look
at signal (rather than have this be just one small part of a paper focused
on something else), then doing even more to get a better tree might be
worth it -- the tree is THE thing used in every analysis, may as well get
it right (or at least, less wrong). If the paper is mostly on something
else, though, this might be a good enough solution.

Two notes for disclosure: I've been on papers that make empirical trees, so
I suppose there's a minor COI there (I might get one more citation). I'm
also part of a project, phylotastic, that is working to make getting trees
easier. We're doing a soft release soon, but there's nothing I'd suggest
you try using yet (we know people are going to form a first impression and
then decide to come back based on that first impression -- we're not quite
ready for our debut yet, though it is all open). My part is to make it
easier to get dates on trees: there's an R package for this (datelife, on
github) and a website, but I'm still debugging -- don't use yet for
something that matters, but it should make all this easier in the future.
But it does give me an incentive to say, "get a better tree", so take that
into consideration.


Brian O'Meara,, especially Calendar
<>, CV
<>, and Feedback

Associate Professor, Dept. of Ecology & Evolutionary Biology, UT Knoxville
Associate Head, Dept. of Ecology & Evolutionary Biology, UT Knoxville
Associate Director for Postdoctoral Activities, National Institute for
Mathematical & Biological Synthesis <> (NIMBioS)
Communication Director, Society of Systematic Biologists

On Sat, Sep 17, 2016 at 11:38 PM, Jacob Berv <
> wrote:

> 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.
> multifurcations.html?m=1 <
> 2016/08/resolving-one-or-more-multifurcations.html?m=1>
> Jake
> > 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
> >
> >       [[alternative HTML version deleted]]
> >
> > _______________________________________________
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> >
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