Dear Pas, I am wondering what the general aim of your study is?
I agree with Ted, that you should be careful about your assumptions and the tools you are using. Ted's point that K is a descriptive statistic is an important one. K describes the expected divergence among tip traits assuming a model of Brownian motion, in particular whether it is more or less than expected via BM. So if you find that BM doesn't fit, and then try to use K on it, what exactly are you hoping to understand? This is a bit like the tail wagging the dog. In general, I really don't like the term "phylogenetic signal" because BM is the reference model, it puts all evolutionary comparative analysis in a BM-centric perspective. That is, the null expectation is that trait diversity is produced by a BM process, and so we have to look at "everything else" for any ecological adaptation or other evolutionary influences. In practice, we can find many examples where alternative models explain the data much better, so BM doesn't fit, but that does not mean that there is no "phylogenetic signal" (whatever that means). Evolutionary history may have had a huge influence, but it may be via an adaptive or other model where adaptation and the history of selection has also been influential. It forces artificial distinctions and frames of reference. Anyway, what are you using to assess "performance"? Please be sure to use appropriate statistics to assess model fit, and use descriptive statistics for description. But please do make sure that the interpretation makes sense. Best of luck, Marguerite On Jan 24, 2013, at 11:03 AM, Paolo Piras <paolo.pi...@uniroma3.it> wrote: > Hi pas, > > Besides the other arguments, I think that one should test for phylogenetic > signal AFTER trasforming the tree according to the best mode of evolution IF > it is not brownian. Maybe someone else can add some more on this. > best > paolo > > > ________________________________________ > Da: r-sig-phylo-boun...@r-project.org [r-sig-phylo-boun...@r-project.org] per > conto di Theodore Garland Jr [theodore.garl...@ucr.edu] > Inviato: giovedì 24 gennaio 2013 21.30 > A: pasquale.r...@libero.it; r-sig-phylo@r-project.org Mailing-list > Oggetto: Re: [R-sig-phylo] R: Re: From ClustalW2 Tree to Heat Map in R > > Hi Pas, > > K is just a descriptive statistic for tip data on a tree with some specified > branch lengths. > Obviously, if you change the branch lengths (or the topology or the tip > data), then K will be different. > How much different depends on the details. > > It is likely that certain branch-length transformations (whether purely > statistical or designed to mimic something like an OU process) will tend to > make K either larger or smaller, at least when checked cross a large number > of examples. Somebody would need to do a lot of simulations to sort this > out. Some related relevant things are here: > > Revell, L. J., L. J. Harmon, and D. C. Collar. 2008. Phylogenetic signal, > evolutionary process, and rate. Syst. Biol. 57:591-601. > > In the original Blomberg et al. (2003) paper we avoided this issue entirely > by only reporting K using whatever tree the original paper used. We wanted > to be able to compare K values among traits and studies in some sort of > simple and "fair" way. > > If lambda and OU transforms are leading to very different K values (how > different?) that does not mean one K value is better than the other. But it > does mean you would want to be careful if you tried to compare your K value > with other studies that did not use lambda and/or OU transforms. > > 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 > http://scholar.google.com/citations?hl=en&user=iSSbrhwAAAAJ > > Experimental Evolution: Concepts, Methods, and Applications of Selection > Experiments. 2009. > 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 pasquale.r...@libero.it [pasquale.r...@libero.it] > Sent: Thursday, January 24, 2013 12:14 PM > To: r-sig-phylo@r-project.org Mailing-list > Subject: [R-sig-phylo] R: Re: From ClustalW2 Tree to Heat Map in R > > Hi Gents and Lads, > > I have a very rapid question with a perhaps not-so-obvious reply. I'm in the > process of testing a number of evolutionary models and estimating phylogenetic > signal on a certain univariate data set. So something very basic and very > simple. The point is, I found BM performs poorly as compared to OU (single > peak) and lambda. Thus, I transformed the tree by using the fitted lamdba > and/or alpha before calculating Blomberg et al's K statistic. Does this make > sense? > If yes, the competing models have similar Akaike weigths (OU = 0.5, lambda = > 0.3) but give very different estimates of K when their fitted parameters are > used to transform the tree branch lenghts. How does discriminate which K > estimate is best? > Translating in R-esque: > > > require(geiger) > require(phytools) > > fitContinuous(tree, x, model="OU") ## gives relatively low alpha (.07) > phylosig(ouTree(tree,alpha=alpha),x,method ="K", test =T, nsim =1000) ## gives > very low K > > > fitContinuous(tree, x, model="lambda") ## gives very high lambda (.95) > phylosig(lambdaTree(tree,lambda=lambda),x,method ="K", test =T, nsim =1000) ## > gives very high K > > > thanks for help, > > Pas > > _______________________________________________ > 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/ > _______________________________________________ > 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/ ____________________________________________ Marguerite A. Butler Associate Professor Department of Biology University of Hawaii 2450 Campus Rd., Dean Hall Rm. 2 Honolulu, HI 96822 Office: 808-956-4713 Dept: 808-956-8617 Lab: 808-956-5867 FAX: 808-956-9812 http://www.hawaii.edu/zoology/faculty/butler.html http://www2.hawaii.edu/~mbutler http://www.hawaii.edu/zoology/ [[alternative HTML version deleted]]
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