Re: [R-sig-phylo] comparing rates of evolution of a phenotypic trait among clades

[Theodore Garland]

Hi Karla,

The original simple way to compare two clades, using phylogenetically
independent contrasts, is here.  Newer methods may have higher power, but
this method is straightforward.

Garland, Jr., T. 1992. Rate tests for phenotypic evolution using
phylogenetically independent contrasts. The American Naturalist 140:509–519.

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

http://www.biology.ucr.edu/people/faculty/Garland.html

http://scholar.google.com/citations?hl=en=iSSbrhwJ


Director, UCR Institute for the Development of
Educational
Applications 


Editor in Chief, *Physiological and Biochemical Zoology
*


Fail Lab: Episode One


*https://www.youtube.com/watch?v=c0msBWyTzU0
*

On Sat, Jul 22, 2017 at 7:07 PM, Liam J. Revell  wrote:

> Hi Karla.
>
> This is not yet possible, but it would be straightforward to add. For
> instance, we could let the user specify different models such as A==B!=C
> vs. A!=B==C and so on, and then compare this models in a standard way. I
> will try to do this soon and then get back to you & the list.
>
> All the best,
>
> 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 7/22/2017 8:51 PM, Karla Shikev wrote:
>
>> Thanks, Liam!
>>
>> Just a quick follow-up question: in the example I saw on your webpage
>> (with
>> three clades, one of which with a higher rate), how would you go about a
>> sort of "post-hoc" test to determine which clades differ significantly
>> from
>> one another in their rates?
>>
>> Karla
>>
>> On Sat, Jul 22, 2017 at 4:13 PM, Liam J. Revell 
>> wrote:
>>
>> Hi Karla.
>>>
>>> phytools has a function called ratebytree for this. This essentially
>>> corresponds to the 'censored' model of O'Meara et al. 2006, but we also
>>> have a submitted manuscript describing it. I can send you that in a
>>> second
>>> email.
>>>
>>> For more information about using the function you can search for
>>> 'ratebytree' on my blog, blog.phytools.org.
>>>
>>> All the best, 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 7/22/2017 3:10 PM, Karla Shikev wrote:
>>>
>>> Dear all,

 I'd like to test whether the rate of evolution of a phenotypic trait
 (e.g.
 body size) is significantly different among distantly-related clades
 (e.g.
 mammals vs birds). I got tip data and completely resolved and
 callibrated
 trees. One possibility would be to estimate rates and their confidence
 intervals for each clade and to compare them directly, but I'm sure
 there's
 a more elegant way to do this.

 Karla

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Re: [R-sig-phylo] comparing rates of evolution of a phenotypic trait among clades

[Julien Clavel]

Hi Karla,


Here is a way to compare nested models in order to assess the significance of 
rate differences for a given tree and mapped regimes (in a similar fashion to 
what is proposing Liam).


# Here a function to collapse the regimes

mappedTrees <- function(tree, names){

combined <- rowSums(tree$mapped.edge[,names])

allnames <- colnames(tree$mapped.edge)

to_remove <- allnames[!allnames%in%names]

newmat <- cbind(tree$mapped.edge[,to_remove], combined)

newnames <- c(to_remove,paste(names, collapse="_"))

colnames(newmat) <- newnames

tree$mapped.edge <- newmat

return(tree)

}


## A worked example

library(mvMORPH)

set.seed(1)

tree<-pbtree(n=80)

# Setting the regime states of tip species

sta<-as.vector(c(rep("Forest",20),rep("Savannah",30),rep("Mountains",30))); 
names(sta)<-tree$tip.label

# Making the simmap tree with mapped states

tree<-make.simmap(tree,sta , model="ER", nsim=1)

# Simulate the traits

sigma<-list(1,3,6)

theta<-c(0)

data<-mvSIM(tree, param=list(sigma=sigma, theta=theta), model="BMM", nsim=1)

# fit the models with common rate (fit_1), and different rates for each regimes 
(fit_2)

fit_1 <- mvBM(tree, data, model="BM1")

fit_2 <- mvBM(tree, data, model="BMM")


# Here a scenario where we assume that both Forest and Mountains regimes are 
similar

combined <- c("Forest", "Mountains")

treeForestMount <- mappedTrees(tree, combined)

fit_3 <- mvBM(treeForestMount, data, model="BMM")


# Then compare the three models

aicw(list(fit_1, fit_2, fit_3))


# Use LRT on the two multiple rates models

LRT(fit_2, fit_3)


All the best,


Julien




De : R-sig-phylo <r-sig-phylo-boun...@r-project.org> de la part de Liam J. 
Revell <liam.rev...@umb.edu>
Envoy� : dimanche 23 juillet 2017 04:07
� : Karla Shikev
Cc : R-sig-phylo@r-project.org
Objet : Re: [R-sig-phylo] comparing rates of evolution of a phenotypic trait 
among clades

Hi Karla.

This is not yet possible, but it would be straightforward to add. For
instance, we could let the user specify different models such as A==B!=C
vs. A!=B==C and so on, and then compare this models in a standard way. I
will try to do this soon and then get back to you & the list.

All the best,

Liam J. Revell, Associate Professor of Biology
University of Massachusetts Boston
web: http://faculty.umb.edu/liam.revell/
Revell lab at UMass Boston - umb.edu<http://faculty.umb.edu/liam.revell/>
faculty.umb.edu
Welcome to the Revell lab webpages. This website contains information about 
research in the laboratory of Dr. Liam Revell. Research in the Revell lab takes 
place in ...



email: liam.rev...@umb.edu
blog: http://blog.phytools.org
[http://2.bp.blogspot.com/-R--OyW00QOU/WB-UaQC7MLI/DRQ/afyJAHnQfCAKtRW4l1KE6EhtQKbq0ZE6gCK4B/s80/14915472_10154224922482872_7349753094314809681_n.jpg%253Foh%253D6b28620478ddf91f645e47f84b91f818%2526oe%253D5898CE31%2526__gda__%253D1485369678_e7db5dad2c7aa5d03d967bc8ccac9fab]<http://blog.phytools.org/>

Phylogenetic Tools for Comparative Biology<http://blog.phytools.org/>
blog.phytools.org
The following is a demo of the phytools functions & methods I used to create 
the graphics for my Evolution 2017 meeting talk entitled �Some additional new 
methods ...




On 7/22/2017 8:51 PM, Karla Shikev wrote:
> Thanks, Liam!
>
> Just a quick follow-up question: in the example I saw on your webpage (with
> three clades, one of which with a higher rate), how would you go about a
> sort of "post-hoc" test to determine which clades differ significantly from
> one another in their rates?
>
> Karla
>
> On Sat, Jul 22, 2017 at 4:13 PM, Liam J. Revell <liam.rev...@umb.edu> wrote:
>
>> Hi Karla.
>>
>> phytools has a function called ratebytree for this. This essentially
>> corresponds to the 'censored' model of O'Meara et al. 2006, but we also
>> have a submitted manuscript describing it. I can send you that in a second
>> email.
>>
>> For more information about using the function you can search for
>> 'ratebytree' on my blog, blog.phytools.org.
>>
>> All the best, Liam
>>
>> Liam J. Revell, Associate Professor of Biology
>> University of Massachusetts Boston
>> web: http://faculty.umb.edu/liam.revell/
Revell lab at UMass Boston - umb.edu<http://faculty.umb.edu/liam.revell/>
faculty.umb.edu
Welcome to the Revell lab webpages. This website contains information about 
research in the laboratory of Dr. Liam Revell. Research in the Revell lab takes 
place in ...



>> email: liam.rev...@umb.edu
>> blog: http://blog.phytools.org
[http://2.bp.blogspot.com/-R--OyW00QOU/WB-UaQC7MLI/DRQ/afyJAHnQfCAKtRW4l1KE6EhtQKbq0ZE6gCK4B/s80/14915472_1015422492

Re: [R-sig-phylo] comparing rates of evolution of a phenotypic trait among clades

[Liam J. Revell]

Hi Karla.

This is not yet possible, but it would be straightforward to add. For 
instance, we could let the user specify different models such as A==B!=C 
vs. A!=B==C and so on, and then compare this models in a standard way. I 
will try to do this soon and then get back to you & the list.


All the best,

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 7/22/2017 8:51 PM, Karla Shikev wrote:

Thanks, Liam!

Just a quick follow-up question: in the example I saw on your webpage (with
three clades, one of which with a higher rate), how would you go about a
sort of "post-hoc" test to determine which clades differ significantly from
one another in their rates?

Karla

On Sat, Jul 22, 2017 at 4:13 PM, Liam J. Revell  wrote:


Hi Karla.

phytools has a function called ratebytree for this. This essentially
corresponds to the 'censored' model of O'Meara et al. 2006, but we also
have a submitted manuscript describing it. I can send you that in a second
email.

For more information about using the function you can search for
'ratebytree' on my blog, blog.phytools.org.

All the best, 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 7/22/2017 3:10 PM, Karla Shikev wrote:


Dear all,

I'd like to test whether the rate of evolution of a phenotypic trait (e.g.
body size) is significantly different among distantly-related clades (e.g.
mammals vs birds). I got tip data and completely resolved and callibrated
trees. One possibility would be to estimate rates and their confidence
intervals for each clade and to compare them directly, but I'm sure
there's
a more elegant way to do this.

Karla

[[alternative HTML version deleted]]

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Re: [R-sig-phylo] comparing rates of evolution of a phenotypic trait among clades

[Karla Shikev]

Thanks, Liam!

Just a quick follow-up question: in the example I saw on your webpage (with
three clades, one of which with a higher rate), how would you go about a
sort of "post-hoc" test to determine which clades differ significantly from
one another in their rates?

Karla

On Sat, Jul 22, 2017 at 4:13 PM, Liam J. Revell  wrote:

> Hi Karla.
>
> phytools has a function called ratebytree for this. This essentially
> corresponds to the 'censored' model of O'Meara et al. 2006, but we also
> have a submitted manuscript describing it. I can send you that in a second
> email.
>
> For more information about using the function you can search for
> 'ratebytree' on my blog, blog.phytools.org.
>
> All the best, 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 7/22/2017 3:10 PM, Karla Shikev wrote:
>
>> Dear all,
>>
>> I'd like to test whether the rate of evolution of a phenotypic trait (e.g.
>> body size) is significantly different among distantly-related clades (e.g.
>> mammals vs birds). I got tip data and completely resolved and callibrated
>> trees. One possibility would be to estimate rates and their confidence
>> intervals for each clade and to compare them directly, but I'm sure
>> there's
>> a more elegant way to do this.
>>
>> 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-ph...@r-project.org/
>>
>>

[[alternative HTML version deleted]]

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Re: [R-sig-phylo] comparing rates of evolution of a phenotypic trait among clades

[Liam J. Revell]

Hi Karla.

phytools has a function called ratebytree for this. This essentially 
corresponds to the 'censored' model of O'Meara et al. 2006, but we also 
have a submitted manuscript describing it. I can send you that in a 
second email.


For more information about using the function you can search for 
'ratebytree' on my blog, blog.phytools.org.


All the best, 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 7/22/2017 3:10 PM, Karla Shikev wrote:

Dear all,

I'd like to test whether the rate of evolution of a phenotypic trait (e.g.
body size) is significantly different among distantly-related clades (e.g.
mammals vs birds). I got tip data and completely resolved and callibrated
trees. One possibility would be to estimate rates and their confidence
intervals for each clade and to compare them directly, but I'm sure there's
a more elegant way to do this.

Karla

[[alternative HTML version deleted]]

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