Joe is of course correct. However, if the tree is ultrametric than would
it not be the case that one zero length terminal edge implies that there
is zero branch length separating at least two terminal species? (I
believe this is right.)
All the best, Liam
Liam J. Revell, Assistant 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 7/31/2013 1:54 PM, Joe Felsenstein wrote:
Liam Revell wrote:
Yes, for zero length terminal branches it is inadvisable to add a
"tiny amount" to the terminal edge so that the analysis "works". An
easy way to think about this is in terms of Felsenstein's contrasts
method (which is a special case of PGLS). Contrasts are standardized
to have the same expected variance by dividing by the square-root of
the subtending edges. If you set some (terminal) branches to be very
small - then the corresponding contrast will be very large. (Going to
Inf as the edge lengths go to zero!) This will give this contrast very
high weight in your regression.
Part of the problem here stems from the different effective meaning of
a zero length terminal edge in molecular phylogenetics vs. comparative
biology. In the former - a zero length terminal edge probably means
that we don't have enough sequence data, and thus failed to sample any
substitutions along that edge. Depending on the amount of data that
you have, the edge could be 1000s to millions of years long. A zero
length terminal edge in comparative inference means that the tree ends
at a speciation event - no time elapsed between the speciation event
that created a lineage and the present time. Under those
circumstances, we should expect to find no phenotypic difference
between species separated by zero time! (And it makes sense that
comparative methods wouldn't like data that suggested otherwise.)
Surely the problem is when two sister species both have branch lengths
0.0, so the branch length separating them is zero?
If only one has a branch length of zero, that should not cause an error
message, unless the program writer forgot that case. It is easily dealt
with. Also ancestor estimation is trivial, since one of the species
*is* the ancestor, so the states of the ancestor are whatever we observe
in that species.
J.F.
----
Joe Felsenstein j...@gs.washington.edu <mailto:j...@gs.washington.edu>
Department of Genome Sciences and Department of Biology,
University of Washington, Box 355065, Seattle, WA 98195-5065 USA
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