[R-sig-phylo] Blomberg K Statistic

Theodore Garland Jr theodore.garland at ucr.edu
Fri Jan 20 18:49:49 CET 2012


Hi Daniel,

I see no reason NOT to calculate K and also to test for significance of the MSE.
Your study design is an excellent one for testing the habitat effect (as we have pointed out in some papers).  If habitat does have a strong effect, then you would expect the K value to be quite low.

Note that K does not need to be near 1.00 in order for the randomization test for phylogenetic signal using the MSE to be statistically significant.  Depending on sample size and so forth, many K statistics even below 0.5 can be associated with significant results in the randomization test for MSE (see Blomberg et al., 2003).

All this said, I'd like to see your tree and some tip data -- can you send it as a Nexus file I can read into Mesquite?

Cheers,
Ted

Theodore Garland, Jr.
Professor
Department of Biology
University of California, Riverside
Riverside, CA 92521
Office Phone:  (951) 827-3524
Wet Lab Phone:  (951) 827-5724
Facsimile:  (951) 827-4286 = Dept. office (not confidential)
Email:  tgarland at ucr.edu
http://www.biology.ucr.edu/people/faculty/Garland.html

Experimental Evolution: Concepts, Methods, and Applications of Selection Experiments
Edited by Theodore Garland, Jr. and Michael R. Rose
http://www.ucpress.edu/book.php?isbn=9780520261808
(PDFs of chapters are available from me or from the individual authors)

________________________________________
From: r-sig-phylo-bounces at r-project.org [r-sig-phylo-bounces at r-project.org] on behalf of dwelsh at life.illinois.edu [dwelsh at life.illinois.edu]
Sent: Friday, January 20, 2012 9:38 AM
To: liam.revell at umb.edu
Cc: r-sig-phylo at r-project.org
Subject: Re: [R-sig-phylo] Blomberg K Statistic

Hi Liam,
  Thanks for getting back to me.
  You are correct with #2- I have many bifurcations close to the present.
The reason for this is that I am comparing between two different
habitats of 21 different species.  So, essentially, for each species,
there are 2 tips (with branch lengths of 0)- 1 for each habitat (lentic
and lotic).
  So, from what you are saying, I can't use the K statistic.  Do you (or
anyone else on this list) have an idea on a better way to test for
phylogenetic significance on a tree where comparisons are made within
species (between different habitats) as well as between species?
  Thank you for your thoughts.





-Daniel


> Hi Daniel.
>
> I can think of two possibilities:
>
> 1) This is an error.
>
> 2) Your tree has an extremely unusual shape (for instance, it has many
> bifurcations very close to the present day).
>
> On constant rate Yule trees, substituting 1s for the true branch lengths
> does not (on average) bias K in any particular direction.
>
> If you share your tree and data I would be happy to look at the issue
> more closely.
>
> All the best, Liam
>
> --
> Liam J. Revell
> University of Massachusetts Boston
> web: http://faculty.umb.edu/liam.revell/
> email: liam.revell at umb.edu
> blog: http://phytools.blogspot.com
>
> On 1/19/2012 9:53 PM, dwelsh at life.illinois.edu wrote:
>> Hi,
>>    I'm using the Picante package in R to calculate the Blomberg K.  I'm
>> trying to test for a phylogenetic signal in my data.  I'm using a
>> dataset with the PC score for 21 different species on a tree with
>> varying branch lengths.  I did this using the code here:
>> http://bodegaphylo.wikispot.org/IV._Testing_Phylogenetic_Signal_in_R
>>
>>    I got a K statistic of 0.0006457603 and yet the resultant
>> PIC.variance.P
>> is 0.001.  If I'm correct, the PIC.variance.P is the p-value and
>> significant at 0.05.  Is that correct?
>>    I then decided to play with my data and set all branch lengths equal
>> to
>> 1 to see how that would affect things.  I got a K statistic of 2.921763
>> and a PIC.variance.P value of 0.001.  My understanding is that K
>> statistics close to 0 are not significant and become significant close
>> to and above 1.
>>    I'm confused why I got a significant p-value for both K statistics,
>> even
>> though one is very close to 0 (0.00065) and the other is above 2.  I
>> would appreciate any help in explaining Picante and the K statistic.
>> Thank you.
>>
>>
>>
>>
>> -Daniel
>>
>> ----><((((º>  -----><((((º>  ----><((((º>  ----><((((º>  ----><((((º>
>> ----
>>
>> Daniel P Welsh
>> PhD Candidate
>> Teaching Assistant
>> Department of Animal Biology
>> University of Illinois at Urbana-Champaign
>> 202 Shelford Vivarium
>> 606 E. Healey Street
>> Champaign, IL 61821
>> lab phone: (217) 333-5323
>>
>> _______________________________________________
>> R-sig-phylo mailing list
>> R-sig-phylo at r-project.org
>> https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
>


---- ><((((º> ----- ><((((º> ---- ><((((º> ---- ><((((º> ---- ><((((º> ----

Daniel P Welsh
PhD Candidate
Teaching Assistant
Department of Animal Biology
University of Illinois at Urbana-Champaign
202 Shelford Vivarium
606 E. Healey Street
Champaign, IL 61821
lab phone: (217) 333-5323

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