Re: [R-sig-phylo] variation in rates over time
I agree with the suggestions so far. I just wanted to point out a few more alternatives: You could use the geiger package to estimate the best scaling for the tworatetree transformation to do this (should be equivalent to the earlier solutions, though it would require running optimization). You could also use the OUwie package with a tree that has been given simmap mappings using phytools. The advantage of this is that you could evaluate Brownian models but you could also look at various Ornstein-Uhlenbeck models (though note that while there is information about different Brownian rates before and after a time slice, info about different alphas (strength of pull parameter) and thetas (the attractor, aka "optimal value") is rapidly (but not immediately) lost under an OU process). For completeness, especially for citations, note that O'Meara et al. (2006) and Thomas et al. (2006) independently arrived at essentially the same method, so it is worth reading both papers. Best, Brian ___ Brian O'Meara Assistant Professor Dept. of Ecology & Evolutionary Biology U. of Tennessee, Knoxville http://www.brianomeara.info Students wanted: Applications due Dec. 15, annually Postdoc collaborators wanted: Check NIMBioS' website Calendar: http://www.brianomeara.info/calendars/omeara On Mon, Sep 17, 2012 at 9:11 PM, Jason S wrote: > > > Thanks, guys. That's exactly what I needed. > > > > From: Liam J. Revell > To: Matt Pennell > > -project.org> > Sent: Monday, September 17, 2012 9:22 PM > Subject: Re: [R-sig-phylo] variation in rates over time > > Hi Jason. Matt is absolutely correct. You can do this with phytools. > Say, for instance, you have an ultrametric phylogeny with branches in > millions of years (tree) and data vector containing the trait values for > species (x) and you want to test the hypothesis that the last 3.4 my has > a different rate of evolution than the rest of the tree, you could do > this as follows: > > library(phytools) # load phytools > tree<-make.era.map(tree,c(0,max(nodeHeights(tree))-3.4)) > plotSimmap(tree,pts=F,lwd=3) # visualize > fit<-brownie.lite(tree,x) # fit model > > That's it. Good luck. Liam > > Liam J. Revell, Assistant Professor of Biology > University of Massachusetts Boston > web: http://faculty.umb.edu/liam.revell/ > email: liam.rev...@umb.edu > blog: http://phytools.blogspot.com > > On 9/17/2012 7:46 PM, Matt Pennell wrote: > > > Jason, > > > > I think the best way to do this is with the approach of O'Meara et al. > 2006 > > Evolution "Brownie". > > > > Liam Revell has implemented this in R in his package phytools. You can > > modify the steps taken in this tutorial here > > > http://phytools.blogspot.com/2011/07/running-brownielite-for-arbitrarily.html > > perhaps > > in conjunction with the function make.era.map() > > > http://phytools.blogspot.com/2011/10/new-function-to-plot-eras-on-tree.html > > though > > I admittedly have not tried this myself. > > > > Perhaps Liam or someone else has a better explanation but I hope this is > at > > least somewhat helpful. > > > > cheers, > > matt > > > > > > >> > >> > >> > Hello, > >> > >> I see that there are several interesting alternatives to test for > >> different rates among clades. However, I was wondering if there is a > method > >> to test for varying rates over time. I'm aware of Pagel's delta and the > EB > >> model, but I was thinking more in terms of testing if there is a > different > >> rate for the entire tree after a specified point in time. For instance, > if > >> a snail predator colonizes an island 3.4 Mya, is there evidence for an > >> increased rate of evolution in the prey after that point in time? > Something > >> like two lambdas, one for before and one for after that point in time. > >> > >> Thanks! > >> > >> Jason > >> [[alternative HTML version deleted]] > >> > >> ___ > >> R-sig-phylo mailing list > >> R-sig-phylo@r-project.org > >> https://stat.ethz.ch/mailman/listinfo/r-sig-phylo > >> > > > > [[alternative HTML version deleted]] > > > > ___ > > R-sig-phylo mailing list > > R-sig-phylo@r-project.org > > https://stat.ethz.ch/mailman/listinfo/r-sig-phylo > > > [[alternative HTML version deleted]] > > > ___ > R-sig-phylo mailing list > R-sig-phylo@r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-phylo > > [[alternative HTML version deleted]] ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
Re: [R-sig-phylo] variation in rates over time
Thanks, guys. That's exactly what I needed. From: Liam J. Revell To: Matt Pennell -project.org> Sent: Monday, September 17, 2012 9:22 PM Subject: Re: [R-sig-phylo] variation in rates over time Hi Jason. Matt is absolutely correct. You can do this with phytools. Say, for instance, you have an ultrametric phylogeny with branches in millions of years (tree) and data vector containing the trait values for species (x) and you want to test the hypothesis that the last 3.4 my has a different rate of evolution than the rest of the tree, you could do this as follows: library(phytools) # load phytools tree<-make.era.map(tree,c(0,max(nodeHeights(tree))-3.4)) plotSimmap(tree,pts=F,lwd=3) # visualize fit<-brownie.lite(tree,x) # fit model That's it. Good luck. Liam Liam J. Revell, Assistant Professor of Biology University of Massachusetts Boston web: http://faculty.umb.edu/liam.revell/ email: liam.rev...@umb.edu blog: http://phytools.blogspot.com On 9/17/2012 7:46 PM, Matt Pennell wrote: > Jason, > > I think the best way to do this is with the approach of O'Meara et al. 2006 > Evolution "Brownie". > > Liam Revell has implemented this in R in his package phytools. You can > modify the steps taken in this tutorial here > http://phytools.blogspot.com/2011/07/running-brownielite-for-arbitrarily.html > perhaps > in conjunction with the function make.era.map() > http://phytools.blogspot.com/2011/10/new-function-to-plot-eras-on-tree.html > though > I admittedly have not tried this myself. > > Perhaps Liam or someone else has a better explanation but I hope this is at > least somewhat helpful. > > cheers, > matt > > >> >> >> Hello, >> >> I see that there are several interesting alternatives to test for >> different rates among clades. However, I was wondering if there is a method >> to test for varying rates over time. I'm aware of Pagel's delta and the EB >> model, but I was thinking more in terms of testing if there is a different >> rate for the entire tree after a specified point in time. For instance, if >> a snail predator colonizes an island 3.4 Mya, is there evidence for an >> increased rate of evolution in the prey after that point in time? Something >> like two lambdas, one for before and one for after that point in time. >> >> Thanks! >> >> Jason >> [[alternative HTML version deleted]] >> >> ___ >> R-sig-phylo mailing list >> R-sig-phylo@r-project.org >> https://stat.ethz.ch/mailman/listinfo/r-sig-phylo >> > > [[alternative HTML version deleted]] > > ___ > R-sig-phylo mailing list > R-sig-phylo@r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-phylo > [[alternative HTML version deleted]] ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
Re: [R-sig-phylo] variation in rates over time
Hi Jason. Matt is absolutely correct. You can do this with phytools. Say, for instance, you have an ultrametric phylogeny with branches in millions of years (tree) and data vector containing the trait values for species (x) and you want to test the hypothesis that the last 3.4 my has a different rate of evolution than the rest of the tree, you could do this as follows: library(phytools) # load phytools tree<-make.era.map(tree,c(0,max(nodeHeights(tree))-3.4)) plotSimmap(tree,pts=F,lwd=3) # visualize fit<-brownie.lite(tree,x) # fit model That's it. Good luck. Liam Liam J. Revell, Assistant Professor of Biology University of Massachusetts Boston web: http://faculty.umb.edu/liam.revell/ email: liam.rev...@umb.edu blog: http://phytools.blogspot.com On 9/17/2012 7:46 PM, Matt Pennell wrote: Jason, I think the best way to do this is with the approach of O'Meara et al. 2006 Evolution "Brownie". Liam Revell has implemented this in R in his package phytools. You can modify the steps taken in this tutorial here http://phytools.blogspot.com/2011/07/running-brownielite-for-arbitrarily.html perhaps in conjunction with the function make.era.map() http://phytools.blogspot.com/2011/10/new-function-to-plot-eras-on-tree.html though I admittedly have not tried this myself. Perhaps Liam or someone else has a better explanation but I hope this is at least somewhat helpful. cheers, matt On Mon, Sep 17, 2012 at 7:33 PM, Jason S wrote: Hello, I see that there are several interesting alternatives to test for different rates among clades. However, I was wondering if there is a method to test for varying rates over time. I'm aware of Pagel's delta and the EB model, but I was thinking more in terms of testing if there is a different rate for the entire tree after a specified point in time. For instance, if a snail predator colonizes an island 3.4 Mya, is there evidence for an increased rate of evolution in the prey after that point in time? Something like two lambdas, one for before and one for after that point in time. Thanks! Jason [[alternative HTML version deleted]] ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo [[alternative HTML version deleted]] ___ 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
Re: [R-sig-phylo] variation in rates over time
Jason, I think the best way to do this is with the approach of O'Meara et al. 2006 Evolution "Brownie". Liam Revell has implemented this in R in his package phytools. You can modify the steps taken in this tutorial here http://phytools.blogspot.com/2011/07/running-brownielite-for-arbitrarily.html perhaps in conjunction with the function make.era.map() http://phytools.blogspot.com/2011/10/new-function-to-plot-eras-on-tree.html though I admittedly have not tried this myself. Perhaps Liam or someone else has a better explanation but I hope this is at least somewhat helpful. cheers, matt On Mon, Sep 17, 2012 at 7:33 PM, Jason S wrote: > > > Hello, > > I see that there are several interesting alternatives to test for > different rates among clades. However, I was wondering if there is a method > to test for varying rates over time. I'm aware of Pagel's delta and the EB > model, but I was thinking more in terms of testing if there is a different > rate for the entire tree after a specified point in time. For instance, if > a snail predator colonizes an island 3.4 Mya, is there evidence for an > increased rate of evolution in the prey after that point in time? Something > like two lambdas, one for before and one for after that point in time. > > Thanks! > > Jason > [[alternative HTML version deleted]] > > ___ > R-sig-phylo mailing list > R-sig-phylo@r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-phylo > [[alternative HTML version deleted]] ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
[R-sig-phylo] variation in rates over time
Hello, I see that there are several interesting alternatives to test for different rates among clades. However, I was wondering if there is a method to test for varying rates over time. I'm aware of Pagel's delta and the EB model, but I was thinking more in terms of testing if there is a different rate for the entire tree after a specified point in time. For instance, if a snail predator colonizes an island 3.4 Mya, is there evidence for an increased rate of evolution in the prey after that point in time? Something like two lambdas, one for before and one for after that point in time. Thanks! Jason [[alternative HTML version deleted]] ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
Re: [R-sig-phylo] alternative to Bartlett test of homogeneity of variances
Thanks, Ted. I got another question, but I guess it would be best to start a new thread. From: Theodore Garland Jr -project.org> Sent: Monday, September 17, 2012 5:16 PM Subject: RE: [R-sig-phylo] alternative to Bartlett test of homogeneity of variances Several. See these papers for starters: Garland, T., Jr. 1992. Rate tests for phenotypic evolution using phylogenetically independent contrasts. Am. Nat. 140:509-519. Garland, T., Jr., A. W. Dickerman, C. M. Janis, and J. A. Jones. 1993. Phylogenetic analysis of covariance by computer simulation. Systematic Biology 42:265-292. Hutcheon, J. M., and T. Garland, Jr. 2004. Are megabats big? Journal of Mammalian Evolution 11:257-276. Collar, D. C., P. C. Wainwright, T. J. Near. 2005. Comparative analysis of morphological diversity: does morphological disparity evolve at the same rate in two lineages of centrarchid fishes. Evolution 58:1783-1794. [first use of method by O'Meara et al., 2006] O'Meara, B. C., C. Ane, M. J. Sanderson, and P. C. Wainwright. 2006. Testing for different rates of continuous trait evolution using likelihood. Evolution 60:922-933. [full explanation of method used by Collar et al., 2005] Rezende, E. L., and J. A. F. Diniz-Filho. 2012. Phylogenetic analyses: comparing species to infer adaptations and physiological mechanisms. Comprehensive Physiology 2:639-674. 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 http://scholar.google.com/citations?hl=en&user=iSSbrhwJ 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] Sent: Monday, September 17, 2012 1:08 PM To: R-sig-phylo@r-project.org Subject: [R-sig-phylo] alternative to Bartlett test of homogeneity of variances Hi there, Is there a PCM that is analogous to the Bartlett test of homogeneity of variances? Thanks, Jason Mustakas [[alternative HTML version deleted]] ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo [[alternative HTML version deleted]] ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
Re: [R-sig-phylo] alternative to Bartlett test of homogeneity of variances
Several. See these papers for starters: Garland, T., Jr. 1992. Rate tests for phenotypic evolution using phylogenetically independent contrasts. Am. Nat. 140:509-519. Garland, T., Jr., A. W. Dickerman, C. M. Janis, and J. A. Jones. 1993. Phylogenetic analysis of covariance by computer simulation. Systematic Biology 42:265-292. Hutcheon, J. M., and T. Garland, Jr. 2004. Are megabats big? Journal of Mammalian Evolution 11:257-276. Collar, D. C., P. C. Wainwright, T. J. Near. 2005. Comparative analysis of morphological diversity: does morphological disparity evolve at the same rate in two lineages of centrarchid fishes. Evolution 58:1783-1794. [first use of method by O'Meara et al., 2006] O'Meara, B. C., C. Ane, M. J. Sanderson, and P. C. Wainwright. 2006. Testing for different rates of continuous trait evolution using likelihood. Evolution 60:922-933. [full explanation of method used by Collar et al., 2005] Rezende, E. L., and J. A. F. Diniz-Filho. 2012. Phylogenetic analyses: comparing species to infer adaptations and physiological mechanisms. Comprehensive Physiology 2:639-674. 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 http://scholar.google.com/citations?hl=en&user=iSSbrhwJ 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 Jason S [jas2...@yahoo.com] Sent: Monday, September 17, 2012 1:08 PM To: R-sig-phylo@r-project.org Subject: [R-sig-phylo] alternative to Bartlett test of homogeneity of variances Hi there, Is there a PCM that is analogous to the Bartlett test of homogeneity of variances? Thanks, Jason Mustakas [[alternative HTML version deleted]] ___ 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
[R-sig-phylo] alternative to Bartlett test of homogeneity of variances
Hi there, Is there a PCM that is analogous to the Bartlett test of homogeneity of variances? Thanks, Jason Mustakas [[alternative HTML version deleted]] ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
[R-sig-phylo] Phylogenetic quantile regression
Dear list, Anybody knows if it would be possible to do a phylogenetic quantile regression procedure in R or other software? Im trying to model a relationship in which other factors beyond the ones which entered in the analysis are potentially misleading the analysis results. Quantile regression seems to deal well in such situations. However, ive been looking through the internet but did not find a way to implment PGLS over quantile regression. Is it even possible? Thanks in advance. Agus -- Agustín Camacho Guerrero. Doutorando em Zoologia. Laboratório de Herpetologia, Departamento de Zoologia, Instituto de Biociências, USP. Rua do Matão, trav. 14, nº 321, Cidade Universitária, São Paulo - SP, CEP: 05508-090, Brasil. <>___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
