Re: [R-sig-phylo] testing for variation in rates of evolution among traits
Thank you all for the valuable input! cheers! Karla On Fri, Jul 17, 2015 at 12:17 AM, Giulio V. Dalla Riva gv...@uclive.ac.nz wrote: P.S. Rumbling on that: a proper answer, however, in a phylogenetic scenario would also require to try and estimate the evolution of the intralineage trait variance (an ancestral state reconstruction of the trait mean and variance) as the hypothesis that it has been constant during long times seems rather weak. In that case one should probably try to give a proper definition of phylogenetic haldanes, i.e., averaging between the variance at start and endpoint of each branch... Or am I completely wrong? Giulio Valentino Dalla Riva PhD candidate @ Biomathematics Research Centre University of Canterbury Christchurch, NZ Phone: +64 3642987 ext 4869 On 17/07/2015, at 3:41 am, Theodore Garland Jr theodore.garl...@ucr.edu wrote: 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 traits, but I am sure you could do this with simulations. 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=enuser=iSSbrhwJ 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 Karla Shikev [karlashi...@gmail.com] Sent: Thursday, July 16, 2015 2:13 PM To: r-sig-phylo@r-project.org Subject: [R-sig-phylo] testing for variation in rates of evolution amongtraits 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 evolution). Any suggestions? Thanks! Karla [[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/ [[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/
Re: [R-sig-phylo] testing for variation in rates of evolution among traits
Hi Karla, Looks like I missed out on an interesting conversation. If you are interested in seeing an application of some of the methods/issues discussed, we recently had a paper comparing rates of evolution among different color traits in birds (http://onlinelibrary.wiley.com/doi/10./evo.12575/abstract). Briefly, we fit various multivariate models in ouch and assessed whether diagonal elements of sigma2/alpha matrices differed from each other using parametric bootstrapping. I’d be happy to share the R code with you if it helps. Chad — Chad Eliason Postdoctoral Fellow, Clarke lab Department of Geological Science University of Texas at Austin On Jul 17, 2015, at 9:17 AM, Karla Shikev karlashi...@gmail.com wrote: Thank you all for the valuable input! cheers! Karla On Fri, Jul 17, 2015 at 12:17 AM, Giulio V. Dalla Riva gv...@uclive.ac.nz wrote: P.S. Rumbling on that: a proper answer, however, in a phylogenetic scenario would also require to try and estimate the evolution of the intralineage trait variance (an ancestral state reconstruction of the trait mean and variance) as the hypothesis that it has been constant during long times seems rather weak. In that case one should probably try to give a proper definition of phylogenetic haldanes, i.e., averaging between the variance at start and endpoint of each branch... Or am I completely wrong? Giulio Valentino Dalla Riva PhD candidate @ Biomathematics Research Centre University of Canterbury Christchurch, NZ Phone: +64 3642987 ext 4869 On 17/07/2015, at 3:41 am, Theodore Garland Jr theodore.garl...@ucr.edu wrote: 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 traits, but I am sure you could do this with simulations. 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=enuser=iSSbrhwJ 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 Karla Shikev [karlashi...@gmail.com] Sent: Thursday, July 16, 2015 2:13 PM To: r-sig-phylo@r-project.org Subject: [R-sig-phylo] testing for variation in rates of evolution amongtraits 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 evolution). Any suggestions? Thanks! Karla [[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/ [[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/
Re: [R-sig-phylo] testing for variation in rates of evolution among traits
Hi, don’t know if this is what you search, but have a look at following publication: Mayrose Otto 2011, A likelihood method for detecting trait-dependent shifts in the rate of molecular evolution. and function “traitrate” in package “ips” Best, Franz BSc. Franz Krah Mobile: 0170 5221189 Ecology, Phylogenetic Comparative Methods Personal Webpage: http://franzkrah.github.io http://franzkrah.github.io/ University: http://www.biodiv.wzw.tum.de/index.php?id=18 http://www.biodiv.wzw.tum.de/index.php?id=18 On 17 Jul 2015, at 16:57, Chad Eliason cm...@zips.uakron.edu wrote: Hi Karla, Looks like I missed out on an interesting conversation. If you are interested in seeing an application of some of the methods/issues discussed, we recently had a paper comparing rates of evolution among different color traits in birds (http://onlinelibrary.wiley.com/doi/10./evo.12575/abstract). Briefly, we fit various multivariate models in ouch and assessed whether diagonal elements of sigma2/alpha matrices differed from each other using parametric bootstrapping. I’d be happy to share the R code with you if it helps. Chad — Chad Eliason Postdoctoral Fellow, Clarke lab Department of Geological Science University of Texas at Austin On Jul 17, 2015, at 9:17 AM, Karla Shikev karlashi...@gmail.com wrote: Thank you all for the valuable input! cheers! Karla On Fri, Jul 17, 2015 at 12:17 AM, Giulio V. Dalla Riva gv...@uclive.ac.nz wrote: P.S. Rumbling on that: a proper answer, however, in a phylogenetic scenario would also require to try and estimate the evolution of the intralineage trait variance (an ancestral state reconstruction of the trait mean and variance) as the hypothesis that it has been constant during long times seems rather weak. In that case one should probably try to give a proper definition of phylogenetic haldanes, i.e., averaging between the variance at start and endpoint of each branch... Or am I completely wrong? Giulio Valentino Dalla Riva PhD candidate @ Biomathematics Research Centre University of Canterbury Christchurch, NZ Phone: +64 3642987 ext 4869 On 17/07/2015, at 3:41 am, Theodore Garland Jr theodore.garl...@ucr.edu wrote: 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 traits, but I am sure you could do this with simulations. 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=enuser=iSSbrhwJ 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 Karla Shikev [karlashi...@gmail.com] Sent: Thursday, July 16, 2015 2:13 PM To: r-sig-phylo@r-project.org Subject: [R-sig-phylo] testing for variation in rates of evolution amongtraits 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 evolution). Any suggestions? Thanks! Karla [[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/ [[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/ [[alternative HTML version deleted]]
Re: [R-sig-phylo] testing for variation in rates of evolution among traits
Warning: You'd have to ensure that the traits for which you are comparing rates are evolving independently, so that they do not covary in their evolutionary changes. I assume Dean Adams's paper involves some way of coping with this. The issue of log-transforms that Ted raised is very important, otherwise big measurements will tend have higher rates of evolution. Joe j...@gs.washington.edu [[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/
Re: [R-sig-phylo] testing for variation in rates of evolution among traits
Hi Karla,
Here a short simulated example of covarying traits just to illustrate the
general workflow:
library(mvMORPH)set.seed(14)
# Simulate a 50 tips treetree-pbtree(n=50)# Simulate correlated body size and
wing size traits (on empirical data you must log-transform the
data)data-mvSIM(tree, param=list(sigma=sigma, ntraits=2, mu=theta,
names_traits=c(wing.size,body.size)), model=BM1, nsim=1)
# Fit one model with different ratesfit1-mvBM(tree, data, model=BM1)
# Then fit one model with similar rates on both traitsfit2-mvBM(tree, data,
model=BM1, param=list(constraint=TRUE))
# Now compare the AICAIC(fit1)AIC(fit2)
# Or compute the LRT test to assess the significance of the
differencesLRT(fit1,fit2)
If the data are best fitted by another model, say for instance an
Ornstein-Uhlenbeck, the BM rates estimates are probably not appropriate but you
can compare the variance as Chad suggested (See for instance Hunt
(2012)-Paleobiology for detail on this issue and Price et al. 2013- Evolution
for en example and an other way (also based on simulations) to cope with this
problem...)
To compare the variance of an OU process:alpha-matrix(c(2,0.5,0.5,1),2)
sigma-matrix(c(0.1,0.05,0.05,0.1),2)
theta-c(0,0)# Simulated traits under OU
data-mvSIM(tree, param=list(sigma=sigma, alpha=alpha, ntraits=2, mu=theta,
names_traits=c(wing.size,body.size)), model=OU1, nsim=1)
fit3-mvBM(tree, data, model=BM1)
fit4-mvOU(tree, data, model=OU1)
# Compare the modelsAIC(fit3)AIC(fit4)
# Compare the variances on both traitsdiag(stationary(fit4))
To assess whether they significantly differ you can then use a parametric
bootstrap approach by simulating the traits under the maximum likelihood
estimates:
# 100 simulated datasetssimul-simulate(fit4,tree=tree,nsim=100)
# Then, fit and extract the diagonal elements of the stationary OU covariance
matrix... and so on... (wait few minutes)results-sapply(1:100, function(x){
diag(stationary(mvOU(tree, simul[[x]], model=OU1, method=sparse,
echo=FALSE, diagnostic=FALSE))) })
# compare the estimated OU variance...boxplot(t(results), main=traits
variance)
HTH,
Julien
From: dcad...@iastate.edu
To: j...@gs.washington.edu; gv...@uclive.ac.nz
Date: Fri, 17 Jul 2015 19:19:12 +
CC: r-sig-phylo@r-project.org; theodore.garl...@ucr.edu
Subject: Re: [R-sig-phylo] testing for variation in rates of evolution
among traits
These are very important points to consider.
And yes, my approach does allow one to account for the covariation among
traits when comparing their evolutionary rates. This is accomplished when
using the full evolutionary rate matrix for the test, which contains both the
evolutionary rates for each trait and the pairwise evolutionary correlations
between them.
Dean
Dr. Dean C. Adams
Professor
Department of Ecology, Evolution, and Organismal Biology
Department of Statistics
Iowa State University
www.public.iastate.edu/~dcadams/
phone: 515-294-3834
-Original Message-
From: R-sig-phylo [mailto:r-sig-phylo-boun...@r-project.org] On Behalf Of Joe
Felsenstein
Sent: Friday, July 17, 2015 2:08 PM
To: Giulio V. Dalla Riva gv...@uclive.ac.nz
Cc: r-sig-phylo mailman r-sig-phylo@r-project.org; Theodore Garland Jr
theodore.garl...@ucr.edu
Subject: Re: [R-sig-phylo] testing for variation in rates of evolution among
traits
Warning: You'd have to ensure that the traits for which you are comparing
rates are evolving independently, so that they do not covary in their
evolutionary changes.
I assume Dean Adams's paper involves some way of coping with this. The issue
of log-transforms that Ted raised is very important, otherwise big
measurements will tend have higher rates of evolution.
Joe
j...@gs.washington.edu
[[alternative HTML version deleted]]
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[R-sig-phylo] Bug in ape: dropping tips from a ladderized tree (still) randomly shuffles the node labels
Hello all, Recently I noticed a complex function of mine that does some tree transformations was randomly scrambling node.label elements. In the course of doing so, I found this old email (below) from Rebecca Best in 2012, which outlined an issue that occurred when a ladderized tree had tips dropped. It appears that bug has reappeared in more recent version of ape. Here's a slightly modified version of her example code, which appears to still replicate a node label shuffling in ape v3.3. # require(ape) #read tree mytree-read.tree() ((D,(E,G)1)1,((H,J)0.8,(K,(((L,M)0.5,(N,O)0.6)1,(P,(Q,R)1)1)0.7)1)1); #ladderize tree mytree.lad-ladderize(mytree) #node labels display on both trees correctly layout(1:2) plot(mytree,show.node.label=TRUE) plot(mytree.lad,show.node.label=TRUE) #drop tips from both trees drop.mytree-drop.tip(mytree,c(L,D,G)) drop.mytree.lad-drop.tip(mytree.lad,c(L,D,G)) #plot both trees, node labels are incorrect for ladderized tree dev.new() layout(1:2) plot(drop.mytree,show.node.label=TRUE) plot(drop.mytree.lad,show.node.label=TRUE) # Although I'm still in the process of dismantling my own issue, so I am not 100% certain, I strongly believe this is the culprit in my case, as my script partly drops.tips from an input tree (that happens to always be ladderized). Cheers, -Dave -- Forwarded message -- From: Rebecca Best rjb...@ucdavis.edu Date: Tue, Oct 2, 2012 at 12:26 AM Subject: [R-sig-phylo] ladderize + drop.tip = shuffled node labels To: r-sig-phylo@r-project.org Hi all I have been plotting some pruned trees recently, and have run into a problem using drop.tip() after ladderize(). If you ladderize() and then drop tips from the ladderized tree, then at least in my case the node labels are no longer correct. This may be an unlikely sequence of commands, but I thought I'd post this in case it is an easy fix, or it helps anyone else avoid issues. Thanks! Rebecca ## require(ape) #read tree mytree-read.tree() ((D,(E,G)1)1,((H,J)0.8,(K,(((L,M)0.5,(N,O)0.6)1,(P,(Q,R)1)1)0.7)1)1); #ladderize tree mytree.lad-ladderize(mytree) #node labels display on both trees correctly plot(mytree,show.node.label=TRUE) plot(mytree.lad,show.node.label=TRUE) #drop tips from both trees drop.mytree-drop.tip(mytree,c(L,D,G)) drop.mytree.lad-drop.tip(mytree.lad,c(L,D,G)) #plot both trees, node labels are incorrect for ladderized tree plot(drop.mytree,show.node.label=TRUE) plot(drop.mytree.lad,show.node.label=TRUE) ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo -- David W. Bapst, PhD Adjunct Asst. Professor, Geology and Geol. Eng. South Dakota School of Mines and Technology 501 E. St. Joseph Rapid City, SD 57701 http://webpages.sdsmt.edu/~dbapst/ http://cran.r-project.org/web/packages/paleotree/index.html ___ 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/
Re: [R-sig-phylo] testing for variation in rates of evolution among traits
Hi Karla,
Here a short simulated example of covarying traits just to illustrate the
general workflow:
library(mvMORPH)
set.seed(14)
# Simulate a 50 tips tree
tree-pbtree(n=50)
# Simulate correlated body size and wing size traits (on empirical data you
must log-transform the data)
data-mvSIM(tree, param=list(sigma=sigma, ntraits=2, mu=theta,
names_traits=c(wing.size,body.size)),
model=BM1, nsim=1)
# Fit one model with different rates
fit1-mvBM(tree, data, model=BM1)
# Then fit one model with similar rates on both traits
fit2-mvBM(tree, data, model=BM1, param=list(constraint=TRUE))
# Now compare the AIC
AIC(fit1)
AIC(fit2)
# Or compute the LRT test to assess the significance of the differences
LRT(fit1,fit2)
If the data are best fitted by another model, say for instance an
Ornstein-Uhlenbeck, the BM rates estimates are probably not appropriate but you
can compare the variance as Chad suggested (See for instance Hunt
(2012)-Paleobiology for detail on this issue and Price et al. 2013- Evolution
for en example and an other way (also based on simulations) to cope with this
problem...)
To compare the variance of an OU process:
alpha-matrix(c(2,0.5,0.5,1),2)
sigma-matrix(c(0.1,0.05,0.05,0.1),2)
theta-c(0,0)
# Simulated traits under OU
data-mvSIM(tree, param=list(sigma=sigma, alpha=alpha, ntraits=2, mu=theta,
names_traits=c(wing.size,body.size)), model=OU1, nsim=1)
fit3-mvBM(tree, data, model=BM1)
fit4-mvOU(tree, data, model=OU1)
# Compare the models
AIC(fit3)
AIC(fit4)
# Compare the variances on both traits
diag(stationary(fit4))
To assess whether they significantly differ you can then use a parametric
bootstrap approach by simulating the traits under the maximum likelihood
estimates:
# 100 simulated datasets
simul-simulate(fit4,tree=tree,nsim=100)
# Then, fit and extract the diagonal elements of the stationary OU covariance
matrix... and so on... (wait few minutes)
results-sapply(1:100, function(x){ diag(stationary(mvOU(tree, simul[[x]],
model=OU1, method=sparse, echo=FALSE, diagnostic=FALSE))) })
# compare the estimated OU variance...
boxplot(t(results), main=traits variance)
HTH,
Julien
From: dcad...@iastate.edu
To: j...@gs.washington.edu; gv...@uclive.ac.nz
Date: Fri, 17 Jul 2015 19:19:12 +
CC: r-sig-phylo@r-project.org; theodore.garl...@ucr.edu
Subject: Re: [R-sig-phylo] testing for variation in rates of evolution
among traits
These are very important points to consider.
And yes, my approach does allow one to account for the covariation among
traits when comparing their evolutionary rates. This is accomplished when
using the full evolutionary rate matrix for the test, which contains both the
evolutionary rates for each trait and the pairwise evolutionary correlations
between them.
Dean
Dr. Dean C. Adams
Professor
Department of Ecology, Evolution, and Organismal Biology
Department of Statistics
Iowa State University
www.public.iastate.edu/~dcadams/
phone: 515-294-3834
-Original Message-
From: R-sig-phylo [mailto:r-sig-phylo-boun...@r-project.org] On Behalf Of Joe
Felsenstein
Sent: Friday, July 17, 2015 2:08 PM
To: Giulio V. Dalla Riva gv...@uclive.ac.nz
Cc: r-sig-phylo mailman r-sig-phylo@r-project.org; Theodore Garland Jr
theodore.garl...@ucr.edu
Subject: Re: [R-sig-phylo] testing for variation in rates of evolution among
traits
Warning: You'd have to ensure that the traits for which you are comparing
rates are evolving independently, so that they do not covary in their
evolutionary changes.
I assume Dean Adams's paper involves some way of coping with this. The issue
of log-transforms that Ted raised is very important, otherwise big
measurements will tend have higher rates of evolution.
Joe
j...@gs.washington.edu
[[alternative HTML version deleted]]
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