[R-sig-phylo] PGLS with non-ultrametric tree

Dear all, What are the pros and cons of the two methods to do pgls with a non-ultrametric tree? Many thanks! 1) Convert the additive tree to ultrametric using penalized likelihood (Sanderson 2002) with ape:: chronopl after cross-validation to find the best lambda. 2) Use weighted least-squares

Re: [R-sig-phylo] PGLS with non-ultrametric tree

Dear Solomon, I don;t know where you are trying to go with this, but any proper implementation of PGLS (I am not talking about methods that transform the branch lengths with things like Grafen's rho, Pagel's lambda or OU models) should be able to use any tree of any shape. This is the same as

[R-sig-phylo] testing for variation in rates of evolution among traits

Hi there, I've come across several methods to test for differences in the rate of evolution among branches in a tree, but I can't find methods to test for differences in rates of evolution of different traits on the same species (ex. if wing size evolution is faster than than overall body size

Re: [R-sig-phylo] PGLS with non-ultrametric tree

Hi Dr. Garland, I got the impression that an ultrametric tree is needed for comparative analysis from this book http://www.springer.com/us/book/9783662435496ch. 2 pg. 38: most comparative analyses assume that the tree is ultrametric, as the majority of analyses deal with evolution of phenotypic

[R-sig-phylo] Different Lambda estimations

Hello all, I'm trying to estimate a lambda for my phylogeny but something strange happened. I used 3 different packages to confirm the estimated lambda value. My tree is ultrametric (with branchlengths in million years), it has 59 tips and 58 internal nodes. Here is what I did:

Re: [R-sig-phylo] PGLS with non-ultrametric tree

I really think this post could be useful for the discussion https://stat.ethz.ch/pipermail/r-sig-phylo/2010-September/000773.html best paolo Da: R-sig-phylo r-sig-phylo-boun...@r-project.org per conto di Solomon Chak tc...@vims.edu Inviato: giovedì 16

Re: [R-sig-phylo] PGLS with non-ultrametric tree

Hi Solomon, Comparatives methods are routinely applied to non-ultrametric trees, contrary to the text you quoted. See the last chapter of that book. The phylogeny-based analyses that do generally require ultrametric trees are those that fit some form of a lineage diversification model, because

Re: [R-sig-phylo] PGLS with non-ultrametric tree

Yep, we've all been down this road before, but I'm too old to remember! Thanks and cheers, Ted From: Paolo Piras [paolo.pi...@uniroma3.it] Sent: Thursday, July 16, 2015 2:38 PM To: Solomon Chak; Theodore Garland Jr Cc: r-sig-phylo@r-project.org Subject: Re: [R-sig-phylo] PGLS with

Re: [R-sig-phylo] testing for variation in rates of evolution among traits

One approach is found in: Adams, D.C. 2013. Comparing evolutionary rates for different phenotypic traits on a phylogeny using likelihood. Systematic Biology. 62:181-192. Dean Dr. Dean C. Adams Professor Department of Ecology, Evolution, and Organismal Biology    Department of Statistics

Re: [R-sig-phylo] testing for variation in rates of evolution among traits

If everything is log-transformed then the variance of phylogenetically independent contrasts or, equivalently, the MSE (if I remember correctly) from a PGLS analysis is directly related to the rate of trait evolution. I'm not sure of the best way to test for statistical differences among