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

[Julien Clavel]

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 
> Cc: r-sig-phylo mailman ; Theodore Garland Jr 
> 
> 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]]
> 
> ___
> 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/

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

[Julien Clavel]

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 
> Cc: r-sig-phylo mailman ; Theodore Garland Jr 
> 
> 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]]
> 
> ___
> 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

[Adams, Dean [EEOBS]]

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 
Cc: r-sig-phylo mailman ; Theodore Garland Jr 

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]]

___
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

[Joe Felsenstein]

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

[f.k...@mailbox.org]

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 
University: http://www.biodiv.wzw.tum.de/index.php?id=18 





> On 17 Jul 2015, at 16:57, Chad Eliason  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  wrote:
>> 
>> Thank you all for the valuable input!
>> 
>> cheers!
>> 
>> Karla
>> 
>> On Fri, Jul 17, 2015 at 12:17 AM, Giulio V. Dalla Riva 
>> 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 
>>> 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=en&user=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

[Chad Eliason]

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  wrote:
> 
> Thank you all for the valuable input!
> 
> cheers!
> 
> Karla
> 
> On Fri, Jul 17, 2015 at 12:17 AM, Giulio V. Dalla Riva 
> 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 
>> 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=en&user=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

[Karla Shikev]

Thank you all for the valuable input!

cheers!

Karla

On Fri, Jul 17, 2015 at 12:17 AM, Giulio V. Dalla Riva 
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 
> 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=en&user=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

[Julien Clavel]

Hi Karla,
You can test for differences in rates of evolution between different traits 
using the mvBM function in the mvMORPH package.You just need to use the 
argument "constraint" in the "param" list of the function.See for instance 
?mvBM example for comparing the likelihood of model assuming independent rates 
vs similar rates using the approach described by Adams (2013) Systematic 
Biology.
HTH
Best,
Julien
> Date: Thu, 16 Jul 2015 18:13:57 -0300
> From: karlashi...@gmail.com
> To: r-sig-phylo@r-project.org
> Subject: [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
> 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/
  
[[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

[Giulio V. Dalla Riva]

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  
> 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=en&user=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 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
> 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/

___
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

[Giulio V. Dalla Riva]

Well, I have the gut that depends also on the adopted units of measure for the 
different traits. That is: having only averaged species data, is 1cm of 
wingspan increase a greater change than 1kg of bodymass increase?

A solution would be to compare on each tip the inferred traits directional 
change (approximated by the difference between the values at the phylogeny 
nodes) with their variance. This would allow to use the same scale for the 
evolution of every trait, i.e. variance units.

I think that's the idea behind haldanes: see Gingerich 1993 
http://earth.geology.yale.edu/~ajs/1993/11.1993.17Gingerich.pdf

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 
mailto: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=en&user=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 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
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

[Theodore Garland Jr]

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=en&user=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 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
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/

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

[Adams, Dean [EEOBS]]

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
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 Karla 
Shikev
Sent: Thursday, July 16, 2015 4:14 PM
To: r-sig-phylo@r-project.org
Subject: [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 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/