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/,
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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
<theodore.garl...@ucr.edu <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 <liam.rev...@umb.edu
<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/,
https://nam10.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.phytools.org%2F&data=02%7C01%7Cliam.revell%40umb.edu%7Cc32f6ae954334ee27bbf08d860a9554a%7Cb97188711ee94425953c1ace1373eb38%7C0%7C0%7C637365627682724545&sdata=mPJpNrUUHdUZ7nGRvCSc0yJSGpec32VK8%2F5ijH3ATTw%3D&reserved=0
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Academic Director UMass Boston Chile Abroad:
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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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