Hello Florian.

`I would agree that the value of K you have observed is very low. Since K`

`is a standardized variance ratio, this suggest that (controlling for the`

`phylogeny) most of the variance is partitioned within, rather than`

`between, clades.`

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`That being said, on large trees even small values of K can be`

`significant. For instance, if you try the following:`

phylosig(tree<-pbtree(n=1000), x<-fastBM(phytools:::lambdaTree(tree,0.2)), test=TRUE)

`only a very small number of simulations are required to produce one that`

`is significant and that has a very small value of K.`

`Enrico's recommendation to check against picante::phylosignal is wise.`

`In my tests, the two functions produce values of K that are identical`

`and value of P that are highly similar. (The latter are from`

`permutation, so they are not expected to be precisely the same.)`

- Liam Liam J. Revell, Associate Professor of Biology University of Massachusetts Boston web: http://faculty.umb.edu/liam.revell/ email: liam.rev...@umb.edu blog: http://blog.phytools.org On 12/1/2016 12:32 PM, enrico.reze...@roehampton.ac.uk wrote:

Dear Florian, following Ted's comment: 1) Is the data you are analyzing normally distributed? It is possible that you detect significant signal with a very low K in datasets that deviate substantially from normality. Note that under Brownian motion you'd expect something like a normal distibution of the phenotypic data, hence you may want to transform you data prior to the analysis of phylogenetic signal 2) You can run the same test with the package picante to ensure that results are consistent across packages (i.e., not a bug). Cheers Enrico On 12/1/16 14:19, Theodore Garland wrote: Dear Florian, A K values of 0.041 is very small. It is hard for me to imagine that the randomizaton test for the presence of phylogenetic signal (Blomberg et al. 2003), which is based on the MSE not K, is significant. I cannot vouch for what those R packages are doing. I would suggest that you get the authors of those packages to run your data for you and see what's up. sincerely, Ted On Thu, Dec 1, 2016 at 1:41 AM, Menzel, Dr. Florian <menz...@uni-mainz.de><mailto:menz...@uni-mainz.de> wrote:Dear Ted, yes. I have a trait with K = 0.041. According to randomization tests, K differs from the random expectation (p= 0.001; test from Blomberg et al. 2003, computed with 'phylosig' from the phylosig package) AND from the expectation under a Brownian Motion model (also p=0.001; simulated using 'brownie.lite'/'paintSubTree'). I had similar results for some more traits. Does this mean that there is less phylogenetic signal than expected under Brownian Motion, but more than expected at random? Or does it mean that the trait evolves even faster than expected at random, i.e. that closely related taxa differ more than expected from random? Thanks a lot! Florian Dr. Florian Menzel Department of Evolutionary Biology, Institute of Zoology University of Mainz Johannes-von-Müller-Weg 6 55128 Mainz, Germany phone: 0049-6131-3927848 http://www.bio.uni-mainz.de/zoo/evobio/73_ENG_HTML.php Gemeinsam einen Unterschied machen! www.synagieren.de<http://www.synagieren.de> 'For every complex problem there is an answer that is clear, simple, and wrong.' (Henry Louis Mencken) ------------------------------ *Von:* Theodore Garland <theodore.garl...@ucr.edu><mailto:theodore.garl...@ucr.edu> *Gesendet:* Mittwoch, 30. November 2016 18:38 *An:* Menzel, Dr. Florian *Cc:* r-sig-phylo@r-project.org<mailto:r-sig-phylo@r-project.org> *Betreff:* Re: [R-sig-phylo] phylogenetic signal different from BM and random Dear Florian, What do you mean, exactly? Do you mean the K statistics is, say, about 0.5, and that the randomizaton test for phylogenetic signal (Blomberg et al. 2003), which is based on the MSE not K, is significant, indicating that you do have some degree of signal (more than zero)? Cheers, Ted Theodore Garland, Jr., Distinguished 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<mailto: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 <http://idea.ucr.edu/>Educational Applications <http://idea.ucr.edu/> Editor in Chief, *Physiological and Biochemical Zoology <http://www.press.uchicago.edu/ucp/journals/journal/pbz.html>* Fail Lab: Episode One http://testtube.com/faillab/zoochosis-episode-one-evolution http://www.youtube.com/watch?v=c0msBWyTzU0 On Wed, Nov 30, 2016 at 8:50 AM, Menzel, Dr. Florian <menz...@uni-mainz.de<mailto:menz...@uni-mainz.de>wrote:Dear all, I am analysing phylogenetic signal using Blomberg's K. For several of my traits (univariate, continuous), the signal strongly deviates both from random and from the Brownian Motion. I am unsure how to interpret this. Can you give me some advice what this could mean? Thanks a lot! Florian Dr. Florian Menzel Department of Evolutionary Biology, Institute of Zoology University of Mainz Johannes-von-Müller-Weg 6 55128 Mainz, Germany phone: 0049-6131-3927848 http://www.bio.uni-mainz.de/zoo/evobio/73_ENG_HTML.php Gemeinsam einen Unterschied machen! www.synagieren.de<http://www.synagieren.de><http://www.synagieren.de> 'For every complex problem there is an answer that is clear, simple, and wrong.' (Henry Louis Mencken) [[alternative HTML version deleted]] _______________________________________________ R-sig-phylo mailing list - R-sig-phylo@r-project.org<mailto: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-ph...@r-project.org/<mailto:sig-ph...@r-project.org/>[[alternative HTML version deleted]] _______________________________________________ R-sig-phylo mailing list - R-sig-phylo@r-project.org<mailto: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/ -- Enrico L. Rezende Senior Lecturer Department of Life Sciences University of Roehampton | London | SW15 4JD enrico.reze...@roehampton.ac.uk<mailto:enrico.reze...@roehampton.ac.uk> | www.roehampton.ac.uk<http://www.roehampton.ac.uk/> Tel: +44 (0) 20 8392 4495 Follow us on Twitter<http://www.twitter.com/RoehamptonUni> | Find us on Facebook<http://www.facebook.com/roehampton.uni> Join our circle on Google+<https://plus.google.com/b/110466050670991984102/110466050670991984102/about> | Connect via LinkedIn<http://www.linkedin.com/company/university-of-roehampton?trk=cp_followed_name_university-of-roehampton> Consider the environment. Please don't print this e-mail unless you really need to. ________________________________ This email and any attachments are confidential and in...{{dropped:16}}

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