Thanks for the advice. My tree includes all seed plants (Gymnosperms +
Angiosperms) which goes back long enough to have a solid resolved topology.
We identified 50 genera (~160 species out of 600) with more than two
congeneric species where the resolution of the clade could be a problem. I
like Jac
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'
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 t
I also should have mentioned that phylogenetic signal is expected to be
more sensitive to error in the phylogeny; however this error is in one
direction in that errors will tend to cause phylogenetic signal to be
underestimated.
Liam J. Revell, Associate Professor of Biology
University of Mass
Hi Oscar.
I can't tell you how reviewers will respond, but there is at least one
very nice paper about why the phylogenetic regression appears to be
robust to errors in the estimated phylogeny:
Stone, E. A. 2011. Why the phylogenetic regression appears robust to
tree misspecification. Syst.
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 (http://phylodiversity.net/phylomatic/) and
added branch lengths with the based on a fossil calibration fo
