Hi Graham, I, too, have done this under Brownian motion and "squared-change parsimony" reconstructions. In my experience (which was a while ago, and memory fades ...), the confidence intervals for nodes near to the one you constrain ("near" in terms of the length of the branches connecting the nodes) should be reduced, and sometimes substantially, if the constrained node is close by. Right?
Cheers, Ted Theodore Garland, Jr. Professor Department of Biology University of California, Riverside Riverside, CA 92521 Office Phone: (951) 827-3524 Wet Lab Phone: (951) 827-5724 Dry Lab Phone: (951) 827-4026 Home Phone: (951) 328-0820 Facsimile: (951) 827-4286 = Dept. office (not confidential) Email: tgarl...@ucr.edu http://www.biology.ucr.edu/people/faculty/Garland.html Experimental Evolution: Concepts, Methods, and Applications of Selection Experiments Edited by Theodore Garland, Jr. and Michael R. Rose http://www.ucpress.edu/book.php?isbn=9780520261808 (PDFs of chapters are available from me or from the individual authors) ________________________________________ From: r-sig-phylo-boun...@r-project.org [r-sig-phylo-boun...@r-project.org] on behalf of Graham Slater [gsla...@ucla.edu] Sent: Thursday, June 30, 2011 10:09 AM To: r-sig-phylo@r-project.org Subject: Re: [R-sig-phylo] ancestral state reconstruction with fixed internal node(s) Hi AnneMarie, The way Paolo suggests would be the best/right way to do this. We're working on some methods for incorporating fossil info in comparative methods and I have some code that will do this that i can send you off-list if you would like. I should add that, at least based on what we've found so far, doing this probably won't make much difference to your reconstructed ancestral states, simply because under BM, your CIs are so wide without constraining nodes that doing so has little effect. best, Graham On 06/30/2011 09:40 AM, ppi...@uniroma3.it wrote: > Hi AnneMarie, > I dont really know if this makes sense; in fact > ancestral state reconstruction is an ** a posteriori > estimation ** of nodal values starting from tips > observations. > > A trick could be to add a false taxon lnked to that > node and giving to it a 0 branch length (i.e. > plitomized - you can then resolve this during > computation using multi2di() ) and assigning your > desired trait value. > > I'm not sure if this helps.... > > Best > Paolo > > > > > > > Dear phylo-sig list people, > > I want to do ancestral state reconstruction > (preferably with ace) with > one (or more) of the internal nodes 'fixed' for a > range / a distribution > of values. For instance, I want a node leading to one > particular clade > that is present a subset of my trees to have a value > from 0.2-0.5, and > then do the ancestral state reconstruction with this > restriction on that > node. > > I have been searching the archives and the net for > discussion of this > (but maybe with the wrong search terms), and I cannot > find anything > about it - not how to do it in R or in any other > package. > > Thanks for your input! > Annemarie > > -- > Annemarie Verkerk, MA > Evolutionary Processes in Language and Culture (PhD > student) > Max Planck Institute for Psycholinguistics > P.O. Box 310, 6500AH Nijmegen, The Netherlands > +31 (0)24 3521 185 > http://www.mpi.nl/research/research-projects/evolutionary-processes > > _______________________________________________ > R-sig-phylo mailing list > R-sig-phylo@r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-phylo > > _______________________________________________ > R-sig-phylo mailing list > R-sig-phylo@r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-phylo _______________________________________________ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo _______________________________________________ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo