The independent contrasts algebra for what Joe is talking about can be found in these papers:
Garland, T., Jr., P. E. Midford, and A. R. Ives. 1999. An introduction to phylogenetically based statistical methods, with a new method for confidence intervals on ancestral values. American Zoologist 39:374-388. Garland, T., Jr., and A. R. Ives. 2000. Using the past to predict the present: Confidence intervals for regression equations in phylogenetic comparative methods. American Naturalist 155:346-364. Cheers, Ted Theodore Garland, Jr. Professor Department of Biology University of California, Riverside Riverside, CA 92521 Office Phone: (951) 827-3524 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 Joe Felsenstein [j...@gs.washington.edu] Sent: Thursday, July 14, 2011 6:35 AM To: ppi...@uniroma3.it Cc: r-sig-phylo Subject: Re: [R-sig-phylo] pic() vs gls() Paolo Piras wrote -- > Citing > http://www.r-phylo.org/wiki/HowTo/Ancestral_State_Reconstruction: > Using Felsenstein's (1985) phylogenetic independent > contrasts (pic); This is also a Brownian-motion based > estimator, but it only takes descendants of each node > into account in reconstructing the state at that node. > More basal nodes are ignored. > > I THINK that, on the opposite, more basal nodes are > NOT ignored in gls and for this reason results can > differ slightly > I'm wrong? The contrast algorithm if continued to the root, makes the correct ancestral reconstruction for the root. You are correct that values for higher nodes in the tree are not the correct ML reconstruction for those nodes. If the tree is rerooted at any interior node and the algorithm used for that, then that node's reconstruction will be correct. There are ways of re-using information so that the total effort of doing this for all interior nodes will be no worse than about twice that of a single pass through the tree. However people may prefer to use PGLS, which if properly done should give the proper estimates for all nodes. There is some discussion of this in Rohlf's 2001 paper in Evolution. Joe ---- Joe Felsenstein, j...@gs.washington.edu Dept. of Genome Sciences, Univ. of Washington Box 355065, Seattle, WA 98195-5065 USA _______________________________________________ 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
