Thanks for the reply!
In fact, I would like to measure/quantify to which extent different traits
reflect habitat choice (i.e. correlate with environment) between parallel
habitat specialized species,
with conventional statistics we analyzed this by means of manova's but the
comments were that we need to take into account the effect of phylogenetic
relatedness.
A first datasets concerns ecological relevant traits such as colour and the
second dataset consist of genital traits for seven related species.
Hence I obtained species mean PCA values obtained from pca's for the
different datasets
I understand how to analyze correlations between the different traits with
pdap analysis in mesquite
but can I also correlate this with a discrete value nl. habitat?
or do I need to treat habitat as a continuous variable with habitat a =1 and
habitat b=0?
I also needed to transform the branch lengths exponentially to satisfy the
assumption of no significant regression between the absolute value of
standardized contrast and the square root of sum of corrected branch lengths
Greetings
Charlotte
-Original Message-
From: Theodore Garland Jr [mailto:theodore.garl...@ucr.edu]
Sent: Thursday, June 30, 2011 6:58 PM
To: charlotte De Busschere; r-sig-phylo@r-project.org
Subject: RE: [R-sig-phylo] small sample size and detecting phylogenetic
signal with Blombergs K statistic
Dear Charlotte,
No, you do not want to do this.
As shown in Blomberg et al. (2003), the tests for statistical significance
do not work well when you have fewer than about 20 species.
The estimate of the K statistic (indicating the amoung of phylogentic
signal) is fine for small sample sizes, but the test of its statistical
significance is not. You can compare your value of K against the many other
values reported in our paper to see if it is typical for that type of
trait.
Note that K can range from close to zero to somewhat grater than one for
real data. See the values in Blomberg et al. (2003). Typical values are in
the range of about 0.4 to 0.8, and those values are tyupically significantly
greater than zero when you have decent sample size (greater than 20 or so).
A value a bit below one does NOT mean no phylogenetic signal.
In general, it is better to use statistical models that simultaneously
estiumate the strength of phylogenetic signal and the other parameters
(e.g., partial regression slopes). However, unfortunately, this also does
not work well with small samples sizes.
So, I suggest you do both conventional statistical analyses and
phylogenetically independent contrasts (which is equivalent to PGLS models
without any sort of branch length transform). Hopefully, results will be
similar. If not, then you probably cannot conclude much from your data.
Sincerely,
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
Dry Lab Phone: (951) 827-4026
Home Phone: (951) 328-0820
Facsimile: (951) 827-4286 = Dept. office (not confidential)
Email: tgarl...@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-boun...@r-project.org [r-sig-phylo-boun...@r-project.org]
on behalf of charlotte De Busschere [charlotte.debussch...@ugent.be]
Sent: Thursday, June 30, 2011 8:45 AM
To: r-sig-phylo@r-project.org
Subject: [R-sig-phylo] small sample size and detecting phylogenetic signal
with Blombergs K statistic
Dear all,
I'm currently describing phenotypic divergence patterns of several traits
within a radiated genus (5 species). Several comparative studies suggest to
take into account the phylogenetic relationships among the species by means
of
PIC or PLGS etc. for which I agree
But before applying these methods I guess I should first detect whether
there
is Phylogenetic signal (PS)in the data and if not then I suppose I can use
classic statistical methods
(correct me if my reasoning is wrong)
Hence I calculated Blombergs K statistics with Picante and almost all traits
have K values1 i.e. no PS (but no p values 0.05)
hence my question concerns about the accuracy of this statistic in a small
data set (N=5)
Blomberg et. al. 2003 (Evolution) mentioned that it is practically
impossible
to get a statistical significant result if N7
Hence, can I put confidence in this statistic?
Sincerely greetings,
Charlotte
Drs. Charlotte De Busschere
Ghent University
Biology Department
Terrestrial Ecology Unit
Ledeganckstraat 35
B-9000 Gent
Belgium
tel:++32 (0)92645039
http://www.ecology.ugent.be/terec/personal.php?pers=cd
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