[R-sig-phylo] phylogenetic signal-Blomberg's K

2016-09-26 Thread Menzel, Dr. Florian 
Dear r-sig-phylo community,

I am analysing phylogenetic signal in univariate quantitative traits in 
insects. I use Blomberg's K (command phylosignal, library picante). Here I have 
two questions:

- how can I test whether K differs from the Brownian Motion Model?

- is it safe to assume phylogenetic overdispersion if the phylogenetic signal 
differs both from random and from the BM model?


Thanks a lot for your help!


Florian


Dr. Florian Menzel
Department of Evolutionary Biology, Institute of Zoology
University of Mainz
Johannes-von-M�ller-Weg 6
55128 Mainz, Germany
phone: 0049-6131-3927848
http://www.bio.uni-mainz.de/zoo/evobio/73_ENG_HTML.php

Gemeinsam einen Unterschied machen!
www.synagieren.de

'For every complex problem there is an answer that is clear, simple, and 
wrong.' (Henry Louis Mencken)

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Re: [R-sig-phylo] phylogenetic signal different from BM and random

2016-12-01 Thread Menzel, Dr. Florian 
Dear Ted,

yes - I have a trait with K = 0.041. It differs significantly from random 
expectation (p = 0.001, command phylosig, package phylosig and command 
phylosignal, package picante). But it also differs from the Brownian motion 
model (p = 0.001, simulated with brownie.lite and fastBM). I obtained similar 
results for other traits, too.


Does this mean that the trait has less phylogenetic signal than expected under 
Brownian motion, but more than expected from random, or does that mean that 
closely related species are even more different than expected from random (i.e. 
'negative' phylogenetic signal)? I am not sure how to interpret these results...


Thanks a lot for your help!


Florian


Dr. Florian Menzel
Department of Evolutionary Biology, Institute of Zoology
University of Mainz
Johannes-von-M�ller-Weg 6
55128 Mainz, Germany
phone: 0049-6131-3927848
http://www.bio.uni-mainz.de/zoo/evobio/73_ENG_HTML.php

Gemeinsam einen Unterschied machen!
www.synagieren.de<http://www.synagieren.de>

'For every complex problem there is an answer that is clear, simple, and 
wrong.' (Henry Louis Mencken)



Von: Theodore Garland <theodore.garl...@ucr.edu>
Gesendet: Mittwoch, 30. November 2016 18:38
An: Menzel, Dr. Florian
Cc: r-sig-phylo@r-project.org
Betreff: Re: [R-sig-phylo] phylogenetic signal different from BM and random

Dear Florian,

What do you mean, exactly?  Do you mean the K statistics is, say, about 0.5, 
and that the randomizaton test for phylogenetic signal (Blomberg et al. 2003), 
which is based on the MSE not K, is significant, indicating that you do have 
some degree of signal (more than zero)?

Cheers,
Ted


Theodore Garland, Jr., Distinguished Professor

Department of Biology

University of California, Riverside

Riverside, CA 92521

Office Phone:  (951) 827-3524<tel:%28951%29%20827-3524>

Facsimile:  (951) 827-4286<tel:%28951%29%20827-4286> (not confidential)

Email:  tgarl...@ucr.edu<mailto: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 <http://idea.ucr.edu/> 
Educational Applications<http://idea.ucr.edu/>


Editor in Chief, Physiological and Biochemical 
Zoology<http://www.press.uchicago.edu/ucp/journals/journal/pbz.html>


Fail Lab: Episode One

http://testtube.com/faillab/zoochosis-episode-one-evolution

http://www.youtube.com/watch?v=c0msBWyTzU0


On Wed, Nov 30, 2016 at 8:50 AM, Menzel, Dr. Florian 
<menz...@uni-mainz.de<mailto:menz...@uni-mainz.de>> wrote:
Dear all,

I am analysing phylogenetic signal using Blomberg's K. For several of my traits 
(univariate, continuous), the signal strongly deviates both from random and 
from the Brownian Motion.


I am unsure how to interpret this. Can you give me some advice what this could 
mean?


Thanks a lot!


Florian


Dr. Florian Menzel
Department of Evolutionary Biology, Institute of Zoology
University of Mainz
Johannes-von-M�ller-Weg 6
55128 Mainz, Germany
phone: 0049-6131-3927848
http://www.bio.uni-mainz.de/zoo/evobio/73_ENG_HTML.php

Gemeinsam einen Unterschied machen!
www.synagieren.de<http://www.synagieren.de><http://www.synagieren.de>

'For every complex problem there is an answer that is clear, simple, and 
wrong.' (Henry Louis Mencken)

[[alternative HTML version deleted]]


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Re: [R-sig-phylo] phylogenetic signal different from BM and random

2016-12-01 Thread Menzel, Dr. Florian 
Dear Ted,

yes. I have a trait with K = 0.041. According to randomization tests, K differs 
from the random expectation (p= 0.001; test from Blomberg et al. 2003, computed 
with 'phylosig' from the phylosig package) AND from the expectation under a 
Brownian Motion model (also p=0.001; simulated using 
'brownie.lite'/'paintSubTree'). I had similar results for some more traits.


Does this mean that there is less phylogenetic signal than expected under 
Brownian Motion, but more than expected at random? Or does it mean that the 
trait evolves even faster than expected at random, i.e. that closely related 
taxa differ more than expected from random?


Thanks a lot!


Florian


Dr. Florian Menzel
Department of Evolutionary Biology, Institute of Zoology
University of Mainz
Johannes-von-M�ller-Weg 6
55128 Mainz, Germany
phone: 0049-6131-3927848
http://www.bio.uni-mainz.de/zoo/evobio/73_ENG_HTML.php

Gemeinsam einen Unterschied machen!
www.synagieren.de<http://www.synagieren.de>

'For every complex problem there is an answer that is clear, simple, and 
wrong.' (Henry Louis Mencken)



Von: Theodore Garland <theodore.garl...@ucr.edu>
Gesendet: Mittwoch, 30. November 2016 18:38
An: Menzel, Dr. Florian
Cc: r-sig-phylo@r-project.org
Betreff: Re: [R-sig-phylo] phylogenetic signal different from BM and random

Dear Florian,

What do you mean, exactly?  Do you mean the K statistics is, say, about 0.5, 
and that the randomizaton test for phylogenetic signal (Blomberg et al. 2003), 
which is based on the MSE not K, is significant, indicating that you do have 
some degree of signal (more than zero)?

Cheers,
Ted


Theodore Garland, Jr., Distinguished Professor

Department of Biology

University of California, Riverside

Riverside, CA 92521

Office Phone:  (951) 827-3524<tel:%28951%29%20827-3524>

Facsimile:  (951) 827-4286<tel:%28951%29%20827-4286> (not confidential)

Email:  tgarl...@ucr.edu<mailto: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 <http://idea.ucr.edu/> 
Educational Applications<http://idea.ucr.edu/>


Editor in Chief, Physiological and Biochemical 
Zoology<http://www.press.uchicago.edu/ucp/journals/journal/pbz.html>


Fail Lab: Episode One

http://testtube.com/faillab/zoochosis-episode-one-evolution

http://www.youtube.com/watch?v=c0msBWyTzU0


On Wed, Nov 30, 2016 at 8:50 AM, Menzel, Dr. Florian 
<menz...@uni-mainz.de<mailto:menz...@uni-mainz.de>> wrote:
Dear all,

I am analysing phylogenetic signal using Blomberg's K. For several of my traits 
(univariate, continuous), the signal strongly deviates both from random and 
from the Brownian Motion.


I am unsure how to interpret this. Can you give me some advice what this could 
mean?


Thanks a lot!


Florian


Dr. Florian Menzel
Department of Evolutionary Biology, Institute of Zoology
University of Mainz
Johannes-von-M�ller-Weg 6
55128 Mainz, Germany
phone: 0049-6131-3927848
http://www.bio.uni-mainz.de/zoo/evobio/73_ENG_HTML.php

Gemeinsam einen Unterschied machen!
www.synagieren.de<http://www.synagieren.de><http://www.synagieren.de>

'For every complex problem there is an answer that is clear, simple, and 
wrong.' (Henry Louis Mencken)

[[alternative HTML version deleted]]


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