[adegenet-forum] DAPC and s.class

[Hanan Sela]

Hello
I am trying to study the genetic diversity of a collection of a wheat wild
relative. I have a matrix of 105 individuals and ~10000 SNP. Each
individual is assigned to a collection site (population). I have done
several analyses to investigate the genetic diversity and how it is
distributed geographically.
1.  dudi.pca followed by s.class of dudi.pca$li using the population origin
as the classing factor.
2. dapc using the population origin as the grouping factor.
3. dapc using the grouping results of find.clusters.

I have two problems:

A.  The centers of the populations of  s.calss from analysis 1 do not agree
with the centers of  dapc analysis 2 Meaning that some population centers
that are one near the other in analysis 1 are  very distant one from the
other in analysis 2 while the grouping of find.clusters is similar to the
plotting of dudi.pca and s.class.

B. In bouth dpac analyses all of individulas of each group have the excat
same coordiates.

Please help with interpetation of  the results. Which analysis represents
better the true genetic distances between populations?

Thank you

Hanan Sela Ph.D.
Curator of the Lieberman Cereal Seed Bank
The Institute for Cereal Crops Improvement
Tel-Aviv University
P.O. Box 39040
Tel Aviv 6139001
Israel

E: hans at tauex.tau.ac.il <hans at tauex.tau.ac.il>
P: 972-3-6405773
M: 972-50-5727458
F: 972-3-6407857
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