Hi Liam, Thank you for your rapid and helpful comments (I really appreciate your including the IC example to help me understand the nature of the problem).
Just to clarify your point about using the method by Ives et al. (2007), my understanding is that this would essentially involve combining my taxa that are separated by 0 branch length distance (since they cannot be separated in the phylogeny as distinct species anyways) and using a combination of trait values. My question then is whether it is even worth attempting this if my trait values are substantially different and the most likely explanation for the 0 length branches is the need for more molecular data. In addition, should I be throw out both members of a zero length terminal branch pair, or am I justified in retaining one of the pair randomly? Best, Tom On Wed, Jul 31, 2013 at 12:31 PM, Liam J. Revell <liam.rev...@umb.edu>wrote: > Hi Tom. > > 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.) > > The best solution is to get more data to infer your tree. Failing that, > you could assume that there is the equivalent of one substitution > leading to the tips with zero length terminal edges. Alternatively, you > could assume that differences between species separated by no patristic > distance is 'sampling error' and use the method of Ives et al. (2007). > I'm not sure what approach is best or if you have other options other > than collapsing or throwing out data. > > 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 7/30/2013 3:35 PM, Tom Kraft wrote: > > Dear all, > > > > I am running a standard pgls analysis using a phylogeny that contains > > several terminal edges of length zero. The tree is ultrametric and was > > generated using molecular data. This results in a predictable error with > > solve when using pgls(). Looking into this issue, it seems I am faced > with > > the following possibilities: > > > > 1) Drop all taxa with terminal branch lengths of 0. > > > > 2) Add a very small number (i.e. 0.00001) to each terminal branch length > of > > 0. > > > > On Liam Revell's blog, he writes, "for zero length terminal edges it is > > probably reasonable to just add a very small length to that edge. For > many > > comparative analyses, this is inadvisable, but for ancestral state > > estimation it is probably OK...". This makes it seem like option 2 is > not > > very good, although losing taxa from the analysis is obviously not > > desirable either. > > > > Am I right that these are currently my options for dealing with this > > problem? And if so, what is recommended? If anyone has any suggestions > > about how to proceed with this analysis or links to relevant literature > > that I am missing, I would appreciate it very much. > > > > Thank you in advance, > > Tom > > > > Thomas Kraft > > PhD Student > > Department of Biology > > Dartmouth College > > > > [[alternative HTML version deleted]] > > > > _______________________________________________ > > R-sig-phylo mailing list - R-sig-phylo@r-project.org > > https://stat.ethz.ch/mailman/listinfo/r-sig-phylo > > Searchable archive at > http://www.mail-archive.com/r-sig-phylo@r-project.org/ > > > > > > [[alternative HTML version deleted]] _______________________________________________ R-sig-phylo mailing list - R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/
