date:20200923

Re: [R-sig-phylo] evolutionary rate for species with low phylogenetic signal

2020-09-23 Thread Karla Shikev

Thanks, Liam! That was really helpful. But what would be an alternative to
estimate evolutionary rates in those cases? Simply the sigsq estimate under
a white noise model? (which I assume is simply the variance in the original
data?)

Karla

On Wed, Sep 23, 2020 at 10:23 PM Liam J. Revell  wrote:

> Hi Karla.
>
>  > I just wanted to make sure that the estimate of sigma^2 in a BM model
>  > in fitContinuous is a meaningful measure of the rate of evolution of
>  > the trait even if its phylogenetic signal is low.
>
> I would say that the answer to this question (if it were posed as one)
> is 'no.' Another way to put this is that sigma^2 is probably not a
> meaningful measure of the rate of evolution for your character if
> Brownian motion is a (very) poor fit to your data.
>
> It's kind of equivalent to saying 'is the slope of a fitted linear
> regression a good measure of the rate of change in y as a function of x
> if a linear model is a very poor fit to my data?' (That is, you can
> still find a value of the slope that maximizes the probability of your
> data under a linear model, and this slope accurately give the mean
> effect of x on y over the range of your observations for x - but it may
> not mean a whole lot about how x & y genuinely co-vary.)
>
> All the best, Liam
>
> Liam J. Revell
> University of Massachusetts Boston
> Universidad Católica de la Ssma Concepción
> web: http://faculty.umb.edu/liam.revell/, http://www.phytools.org
>
> Academic Director UMass Boston Chile Abroad:
> https://www.umb.edu/academics/caps/international/biology_chile
>
> On 9/23/2020 9:36 PM, Karla Shikev wrote:
> > **[EXTERNAL SENDER]
> >
> > Dear All,
> >
> > Thanks for your fantastic feedback. Just a bit more background: I'm
> > interested both in the phylogenetic signal and the evolutionary rate. I
> > just wanted to make sure that the estimate of sigma^2 in a BM model in
> > fitContinuous is a meaningful measure of the rate of evolution of the
> > trait even if its phylogenetic signal is low.
> >
> > thanks again!
> >
> > Karla
> >
> > On Wed, Sep 23, 2020 at 8:45 PM Theodore Garland
> > mailto:theodore.garl...@ucr.edu>> wrote:
> >
> > Carla, I can also suggest looking at some of the papers on this,
> > such as:
> >
> > Blomberg, S. P., T. Garland, Jr., and A. R. Ives. 2003. Testing for
> > phylogenetic signal in comparative data: behavioral traits are more
> > labile. Evolution 57:717–745.
> >
> >
> > Ives, A. R., P. E. Midford, and T. Garland, Jr. 2007. Within-species
> > variation and measurement error in phylogenetic comparative methods.
> > Systematic Biology 56:252–270.
> >
> >
> > Revell, L., L. Harmon, and D. Collar. 2008. Phylogenetic signal,
> > evolutionary process, and rate. Systematic Biology 57:591–601.
> >
> >
> > Hardy, O. J., and S. Pavoine. 2012. Assessing phylogenetic signal
> > with measurement error: a comparison of Mantel tests, Blomberg et
> > al.’s K, and phylogenetic distograms. Evolution 66:2614–2621.
> >
> >
> > Cheers,
> >
> > Ted Garland
> >
> >
> >
> >
> > On Wed, Sep 23, 2020 at 4:33 PM Liam J. Revell  > > wrote:
> >
> > Dear Karla.
> >
> > What do you want to use fitContinuous to do?
> >
> > fitContinuous fits multiple models, some of which will result in
> > low
> > values of lambda in a test of phylogenetic signal. In fact, this
> is
> > really the main point of fitContinuous: to compare alternative
> > models
> > for trait evolution. If you just want to estimate the
> > most-likely rate
> > of evolution assuming a Brownian evolutionary process, you could
> > just
> > compute the mean squared PIC value (this is the REML estimate of
> > sigma^2).
> >
> > fitContinuous can also take into account sampling error in the
> > estimation of species means, which can be a cause for low
> measured
> > values of phylogenetic signal.
> >
> > Hope this is of some help Karla.
> >
> > All the best, Liam
> >
> > Liam J. Revell
> > University of Massachusetts Boston
> > Universidad Católica de la Ssma Concepción
> > web: http://faculty.umb.edu/liam.revell/,
> > http://www.phytools.org
> > <
> https://nam10.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.phytools.org%2F=02%7C01%7Cliam.revell%40umb.edu%7C4b3649722f5c4a9bb0f508d86021d687%7Cb97188711ee94425953c1ace1373eb38%7C0%7C1%7C637365045732071994=L7HXU2Ljrj89dZ5ql%2FRWMB7ddrReMWnZxdufzJQ2Nvs%3D=0
> >
> >
> > Academic Director UMass Boston Chile Abroad:
> > https://www.umb.edu/academics/caps/international/biology_chile
> >
> > On 9/23/2020 8:21 PM, Karla Shikev wrote:
> >  > [EXTERNAL SENDER]
> >  >
> >  > Dear friends,
> >  >
> >  > I guess this is as much a philosophical question as it is
> >

Re: [R-sig-phylo] evolutionary rate for species with low phylogenetic signal

2020-09-23 Thread Liam J. Revell

Hi Karla.

> I just wanted to make sure that the estimate of sigma^2 in a BM model
> in fitContinuous is a meaningful measure of the rate of evolution of
> the trait even if its phylogenetic signal is low.

I would say that the answer to this question (if it were posed as one) 
is 'no.' Another way to put this is that sigma^2 is probably not a 
meaningful measure of the rate of evolution for your character if 
Brownian motion is a (very) poor fit to your data.

It's kind of equivalent to saying 'is the slope of a fitted linear 
regression a good measure of the rate of change in y as a function of x 
if a linear model is a very poor fit to my data?' (That is, you can 
still find a value of the slope that maximizes the probability of your 
data under a linear model, and this slope accurately give the mean 
effect of x on y over the range of your observations for x - but it may 
not mean a whole lot about how x & y genuinely co-vary.)

All the best, Liam

Liam J. Revell
University of Massachusetts Boston
Universidad Católica de la Ssma Concepción
web: http://faculty.umb.edu/liam.revell/, http://www.phytools.org

Academic Director UMass Boston Chile Abroad:
https://www.umb.edu/academics/caps/international/biology_chile

On 9/23/2020 9:36 PM, Karla Shikev wrote:

**[EXTERNAL SENDER]

Dear All,

Thanks for your fantastic feedback. Just a bit more background: I'm 
interested both in the phylogenetic signal and the evolutionary rate. I 
just wanted to make sure that the estimate of sigma^2 in a BM model in 
fitContinuous is a meaningful measure of the rate of evolution of the 
trait even if its phylogenetic signal is low.

thanks again!

Karla

On Wed, Sep 23, 2020 at 8:45 PM Theodore Garland 
mailto:theodore.garl...@ucr.edu>> wrote:

Carla, I can also suggest looking at some of the papers on this,
such as:

Blomberg, S. P., T. Garland, Jr., and A. R. Ives. 2003. Testing for
phylogenetic signal in comparative data: behavioral traits are more
labile. Evolution 57:717–745.

Ives, A. R., P. E. Midford, and T. Garland, Jr. 2007. Within-species
variation and measurement error in phylogenetic comparative methods.
Systematic Biology 56:252–270.

Revell, L., L. Harmon, and D. Collar. 2008. Phylogenetic signal,
evolutionary process, and rate. Systematic Biology 57:591–601.

Hardy, O. J., and S. Pavoine. 2012. Assessing phylogenetic signal
with measurement error: a comparison of Mantel tests, Blomberg et
al.’s K, and phylogenetic distograms. Evolution 66:2614–2621.

Cheers,

Ted Garland

On Wed, Sep 23, 2020 at 4:33 PM Liam J. Revell mailto:liam.rev...@umb.edu>> wrote:

Dear Karla.

What do you want to use fitContinuous to do?

fitContinuous fits multiple models, some of which will result in
low
values of lambda in a test of phylogenetic signal. In fact, this is
really the main point of fitContinuous: to compare alternative
models
for trait evolution. If you just want to estimate the
most-likely rate
of evolution assuming a Brownian evolutionary process, you could
just
compute the mean squared PIC value (this is the REML estimate of
sigma^2).

fitContinuous can also take into account sampling error in the
estimation of species means, which can be a cause for low measured
values of phylogenetic signal.

Hope this is of some help Karla.

All the best, Liam

Liam J. Revell
University of Massachusetts Boston
Universidad Católica de la Ssma Concepción
web: http://faculty.umb.edu/liam.revell/,
http://www.phytools.org

Academic Director UMass Boston Chile Abroad:
https://www.umb.edu/academics/caps/international/biology_chile

On 9/23/2020 8:21 PM, Karla Shikev wrote:
 > [EXTERNAL SENDER]
 >
 > Dear friends,
 >
 > I guess this is as much a philosophical question as it is
methodological. I
 > want to estimate the rate of evolution of a trait (e.g. using the
 > fitContinuous function), but the trait has low phylogenetic
signal (e.g.
 > lambda close to 0). Does it make sense to use fitContinuous
on a trait
 > evolving like that?
 >
 > Thanks for your input.
 >
 > Karla
 >
 >          [[alternative HTML version deleted]]
 >
 > ___
 > R-sig-phylo mailing list - R-sig-phylo@r-project.org

 >

Re: [R-sig-phylo] evolutionary rate for species with low phylogenetic signal

2020-09-23 Thread Karla Shikev

Dear All,

Thanks for your fantastic feedback. Just a bit more background: I'm
interested both in the phylogenetic signal and the evolutionary rate. I
just wanted to make sure that the estimate of sigma^2 in a BM model in
fitContinuous is a meaningful measure of the rate of evolution of the trait
even if its phylogenetic signal is low.

thanks again!

Karla

On Wed, Sep 23, 2020 at 8:45 PM Theodore Garland 
wrote:

> Carla, I can also suggest looking at some of the papers on this, such as:
>
> Blomberg, S. P., T. Garland, Jr., and A. R. Ives. 2003. Testing for
> phylogenetic signal in comparative data: behavioral traits are more labile.
> Evolution 57:717–745.
>
>
> Ives, A. R., P. E. Midford, and T. Garland, Jr. 2007. Within-species
> variation and measurement error in phylogenetic comparative methods.
> Systematic Biology 56:252–270.
>
>
> Revell, L., L. Harmon, and D. Collar. 2008. Phylogenetic signal,
> evolutionary process, and rate. Systematic Biology 57:591–601.
>
>
> Hardy, O. J., and S. Pavoine. 2012. Assessing phylogenetic signal with
> measurement error: a comparison of Mantel tests, Blomberg et al.’s K, and
> phylogenetic distograms. Evolution 66:2614–2621.
>
>
> Cheers,
>
> Ted Garland
>
>
>
>
> On Wed, Sep 23, 2020 at 4:33 PM Liam J. Revell 
> wrote:
>
>> Dear Karla.
>>
>> What do you want to use fitContinuous to do?
>>
>> fitContinuous fits multiple models, some of which will result in low
>> values of lambda in a test of phylogenetic signal. In fact, this is
>> really the main point of fitContinuous: to compare alternative models
>> for trait evolution. If you just want to estimate the most-likely rate
>> of evolution assuming a Brownian evolutionary process, you could just
>> compute the mean squared PIC value (this is the REML estimate of sigma^2).
>>
>> fitContinuous can also take into account sampling error in the
>> estimation of species means, which can be a cause for low measured
>> values of phylogenetic signal.
>>
>> Hope this is of some help Karla.
>>
>> All the best, Liam
>>
>> Liam J. Revell
>> University of Massachusetts Boston
>> Universidad Católica de la Ssma Concepción
>> web: http://faculty.umb.edu/liam.revell/, http://www.phytools.org
>>
>> Academic Director UMass Boston Chile Abroad:
>> https://www.umb.edu/academics/caps/international/biology_chile
>>
>> On 9/23/2020 8:21 PM, Karla Shikev wrote:
>> > [EXTERNAL SENDER]
>> >
>> > Dear friends,
>> >
>> > I guess this is as much a philosophical question as it is
>> methodological. I
>> > want to estimate the rate of evolution of a trait (e.g. using the
>> > fitContinuous function), but the trait has low phylogenetic signal (e.g.
>> > lambda close to 0). Does it make sense to use fitContinuous on a trait
>> > evolving like that?
>> >
>> > Thanks for your input.
>> >
>> > Karla
>> >
>> >  [[alternative HTML version deleted]]
>> >
>> > ___
>> > R-sig-phylo mailing list - R-sig-phylo@r-project.org
>> >
>> https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fr-sig-phylodata=02%7C01%7Cliam.revell%40umb.edu%7C238f2a4ce92f4b62411f08d86017813f%7Cb97188711ee94425953c1ace1373eb38%7C0%7C1%7C637365001363567653sdata=4u7Q9SP0M9b0l07P13q6zruhfqyMW0AEVIqa%2FT9p1Ko%3Dreserved=0
>> > Searchable archive at
>> https://nam10.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.mail-archive.com%2Fr-sig-phylo%40r-project.org%2Fdata=02%7C01%7Cliam.revell%40umb.edu%7C238f2a4ce92f4b62411f08d86017813f%7Cb97188711ee94425953c1ace1373eb38%7C0%7C1%7C637365001363567653sdata=sKb4MeniYVOo5pQSEUtWRIpz%2BAGHt6wccZ%2B5mPQl7qU%3Dreserved=0
>> >
>>
>> ___
>> 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]]

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Re: [R-sig-phylo] evolutionary rate for species with low phylogenetic signal

2020-09-23 Thread Theodore Garland

Carla, I can also suggest looking at some of the papers on this, such as:

Blomberg, S. P., T. Garland, Jr., and A. R. Ives. 2003. Testing for
phylogenetic signal in comparative data: behavioral traits are more labile.
Evolution 57:717–745.


Ives, A. R., P. E. Midford, and T. Garland, Jr. 2007. Within-species
variation and measurement error in phylogenetic comparative methods.
Systematic Biology 56:252–270.


Revell, L., L. Harmon, and D. Collar. 2008. Phylogenetic signal,
evolutionary process, and rate. Systematic Biology 57:591–601.


Hardy, O. J., and S. Pavoine. 2012. Assessing phylogenetic signal with
measurement error: a comparison of Mantel tests, Blomberg et al.’s K, and
phylogenetic distograms. Evolution 66:2614–2621.


Cheers,

Ted Garland




On Wed, Sep 23, 2020 at 4:33 PM Liam J. Revell  wrote:

> Dear Karla.
>
> What do you want to use fitContinuous to do?
>
> fitContinuous fits multiple models, some of which will result in low
> values of lambda in a test of phylogenetic signal. In fact, this is
> really the main point of fitContinuous: to compare alternative models
> for trait evolution. If you just want to estimate the most-likely rate
> of evolution assuming a Brownian evolutionary process, you could just
> compute the mean squared PIC value (this is the REML estimate of sigma^2).
>
> fitContinuous can also take into account sampling error in the
> estimation of species means, which can be a cause for low measured
> values of phylogenetic signal.
>
> Hope this is of some help Karla.
>
> All the best, Liam
>
> Liam J. Revell
> University of Massachusetts Boston
> Universidad Católica de la Ssma Concepción
> web: http://faculty.umb.edu/liam.revell/, http://www.phytools.org
>
> Academic Director UMass Boston Chile Abroad:
> https://www.umb.edu/academics/caps/international/biology_chile
>
> On 9/23/2020 8:21 PM, Karla Shikev wrote:
> > [EXTERNAL SENDER]
> >
> > Dear friends,
> >
> > I guess this is as much a philosophical question as it is
> methodological. I
> > want to estimate the rate of evolution of a trait (e.g. using the
> > fitContinuous function), but the trait has low phylogenetic signal (e.g.
> > lambda close to 0). Does it make sense to use fitContinuous on a trait
> > evolving like that?
> >
> > Thanks for your input.
> >
> > Karla
> >
> >  [[alternative HTML version deleted]]
> >
> > ___
> > R-sig-phylo mailing list - R-sig-phylo@r-project.org
> >
> https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fr-sig-phylodata=02%7C01%7Cliam.revell%40umb.edu%7C238f2a4ce92f4b62411f08d86017813f%7Cb97188711ee94425953c1ace1373eb38%7C0%7C1%7C637365001363567653sdata=4u7Q9SP0M9b0l07P13q6zruhfqyMW0AEVIqa%2FT9p1Ko%3Dreserved=0
> > Searchable archive at
> https://nam10.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.mail-archive.com%2Fr-sig-phylo%40r-project.org%2Fdata=02%7C01%7Cliam.revell%40umb.edu%7C238f2a4ce92f4b62411f08d86017813f%7Cb97188711ee94425953c1ace1373eb38%7C0%7C1%7C637365001363567653sdata=sKb4MeniYVOo5pQSEUtWRIpz%2BAGHt6wccZ%2B5mPQl7qU%3Dreserved=0
> >
>
> ___
> 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]]

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Re: [R-sig-phylo] evolutionary rate for species with low phylogenetic signal

2020-09-23 Thread Liam J. Revell

Dear Karla.

What do you want to use fitContinuous to do?

fitContinuous fits multiple models, some of which will result in low
values of lambda in a test of phylogenetic signal. In fact, this is
really the main point of fitContinuous: to compare alternative models
for trait evolution. If you just want to estimate the most-likely rate
of evolution assuming a Brownian evolutionary process, you could just
compute the mean squared PIC value (this is the REML estimate of sigma^2).

fitContinuous can also take into account sampling error in the
estimation of species means, which can be a cause for low measured
values of phylogenetic signal.

Hope this is of some help Karla.

All the best, Liam

Liam J. Revell
University of Massachusetts Boston
Universidad Católica de la Ssma Concepción
web: http://faculty.umb.edu/liam.revell/, http://www.phytools.org

Academic Director UMass Boston Chile Abroad:
https://www.umb.edu/academics/caps/international/biology_chile

On 9/23/2020 8:21 PM, Karla Shikev wrote:

[EXTERNAL SENDER]

Dear friends,

I guess this is as much a philosophical question as it is methodological. I
want to estimate the rate of evolution of a trait (e.g. using the
fitContinuous function), but the trait has low phylogenetic signal (e.g.
lambda close to 0). Does it make sense to use fitContinuous on a trait
evolving like that?

Thanks for your input.

Karla

[[alternative HTML version deleted]]

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Searchable archive at
https://nam10.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.mail-archive.com%2Fr-sig-phylo%40r-project.org%2Fdata=02%7C01%7Cliam.revell%40umb.edu%7C238f2a4ce92f4b62411f08d86017813f%7Cb97188711ee94425953c1ace1373eb38%7C0%7C1%7C637365001363567653sdata=sKb4MeniYVOo5pQSEUtWRIpz%2BAGHt6wccZ%2B5mPQl7qU%3Dreserved=0

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[R-sig-phylo] evolutionary rate for species with low phylogenetic signal

2020-09-23 Thread Karla Shikev

Dear friends,

I guess this is as much a philosophical question as it is methodological. I
want to estimate the rate of evolution of a trait (e.g. using the
fitContinuous function), but the trait has low phylogenetic signal (e.g.
lambda close to 0). Does it make sense to use fitContinuous on a trait
evolving like that?

Thanks for your input.

Karla

[[alternative HTML version deleted]]

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Re: [R-sig-phylo] evolutionary rate for species with low phylogenetic signal

Re: [R-sig-phylo] evolutionary rate for species with low phylogenetic signal

Re: [R-sig-phylo] evolutionary rate for species with low phylogenetic signal

Re: [R-sig-phylo] evolutionary rate for species with low phylogenetic signal

Re: [R-sig-phylo] evolutionary rate for species with low phylogenetic signal

[R-sig-phylo] evolutionary rate for species with low phylogenetic signal

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