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. Biol. 60 (3): 245-260. http://dx.doi.org/10.1093/sysbio/syq098

Many other forms of comparative analysis appear to be much more sensitive to error in the phylogeny, or have not yet been studied.

All the best, Liam

Liam J. Revell, Associate Professor of Biology
University of Massachusetts Boston
web: http://faculty.umb.edu/liam.revell/
email: liam.rev...@umb.edu
blog: http://blog.phytools.org

On 9/17/2016 5:46 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 (http://phylodiversity.net/phylomatic/) 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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