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 Massachusetts Boston
web: http://faculty.umb.edu/liam.revell/
email: liam.rev...@umb.edu
blog: http://blog.phytools.org
On 9/17/2016 6:15 PM, Liam J. Revell wrote:
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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