Hi Sergio, I am not quite understanding the situation nor why you see a "problem." if I understand correctly, you are considering these five (5) alternative models for some sort of simple or multiple regression:
OLS = star phylogeny PGLS with real-time branch lengths (ultrametric) Pagel's lambda with real-time branch lengths (ultrametric) PGLS with all branch legnths equal to 1.0 Pagel's lambda with all branch lengths equal to 1.0 To help decide which model best fits your data, you can look at AIC or for some comparisons do a likelihood ratio test. My experience is that any of the transform models (Pagel's lambda, Grafen's rho, OU in various implementations, ACDC) can sometimes yield really bizarre results when you start with a non-ultrametric tree. You need to be careful and check the REML likelihood surface for multiple peaks, etc. 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 (not confidential) Email: tgarl...@ucr.edu http://www.biology.ucr.edu/people/faculty/Garland.html http://scholar.google.com/citations?hl=en&user=iSSbrhwAAAAJ Director, UCR Institute for the Development of Educational Applications Editor in Chief, Physiological and Biochemical Zoology Fail Lab: Episode One http://testtube.com/faillab/zoochosis-episode-one-evolution http://www.youtube.com/watch?v=c0msBWyTzU0 ________________________________________ From: R-sig-phylo [r-sig-phylo-boun...@r-project.org] on behalf of Sergio Ferreira Cardoso [sff.card...@campus.fct.unl.pt] Sent: Thursday, May 14, 2015 8:32 AM To: r-sig-phylo@r-project.org Subject: [R-sig-phylo] Non-ultrametric tree PGLS Hello all, I have an ultrametric phylogenetic tree with divergence times as branch lengths. To see if there was a big difference between using these branch lengths and equal (=1) branch lengths I set all lengths to 1 and ran a PGLS. I ran with Lambda transformations and the estimation is that Lambda is superior than 1 (both with ML and REML estimation). I suppose this is a consequence of the tree being non ultrametric. Is there a solution for this problem or should I, in this case, just ran a GLS (Brownian Motion) to avoid the over estimation of the phylogenetic signal? Best regards, Sérgio. -- Com os melhores cumprimentos, Sérgio Ferreira Cardoso. -------------------- Best regards, Sérgio Ferreira Cardoso MSc. Paleontology candidate Departamento de Ciências da Terra - FCT /Universidade Nova de Lisboa Geociências - Universidade de Évora Lisboa, Portugal ᐧ [[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/ _______________________________________________ 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/
