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<p class="MsoNormal"><span style="" lang="EN-GB">Dear Dr.
Jombart and Adegenet users,</span></p>
<p class="MsoNormal"><span style="" lang="EN-GB"> </span></p>
<p class="MsoNormal"><span style="" lang="EN-GB">I have some
questions about DAPC analysis. </span></p>
<p class="MsoNormal"><span style="" lang="EN-GB">I worked on
tetraploid plant, with 11 SSR markers, 15 populations sampled
with 30
individuals each. </span></p>
<p class="MsoNormal"><span style="" lang="EN-GB"> </span></p>
<p class="MsoNormal"><span style="" lang="EN-GB">1) When I ran
‘find.clusters’ function, elbow in the curve of BIC values was
not very clear
so I ran it many time. But I obtained different optimal number
of cluster even
if I increase “max.n.cluster” option.</span></p>
<p class="MsoNormal"><span style="" lang="EN-GB"><span style=""> </span>I
agree that it is made with Bayesian
computation, but in this case how can I choose the “best”
optimal number of
cluster?</span></p>
<p class="MsoNormal"><span style="" lang="EN-GB">Maybe,
these non-homogenous results between different runs are due to
the sampling
pattern of my populations which were along a corridor (thus
suggesting a
stepping-stone model of dispersal?)</span></p>
<p class="MsoNormal"><span style="" lang="EN-GB"> </span></p>
<p class="MsoNormal"><span style="" lang="EN-GB"><span style=""> </span>2)
Besides, if I took into account the most
frequent “k” after ten runs of “find.clusters” function (k=8), I
observed that actual
groups did not correspond to inferred group. I mean that in the
best case, only
17,5 % of my actual group are inferred to clusters revealed by
the analysis. Even
if individual posterior membership was upper than 75% in most of
case, I did
not know if the genetic structure revealed by the analysis is
supported or not?
</span></p>
<p class="MsoNormal"><span style="" lang="EN-GB"> </span></p>
<p class="MsoNormal"><span style="" lang="EN-GB">3)
Moreover, some of the clusters revealed by the analysis, are
made with
individuals having posterior membership probability <60%, how
interpreting
these clusters? I would tend to run again the analysis and
reduce “k”…?</span></p>
<p class="MsoNormal"><span style="" lang="EN-GB"> </span></p>
<p class="MsoNormal"><span style="" lang="EN-GB"> </span></p>
<p class="MsoNormal"><span style="" lang="EN-GB"> </span></p>
<p class="MsoNormal"><span style="" lang="EN-GB">Sorry for this
long mail, I hope it is sufficiently clear.</span></p>
<p class="MsoNormal"><span style="" lang="EN-GB">Thanks in
advance for your help.</span></p>
<p class="MsoNormal"><span style="" lang="EN-GB">Elodie </span></p>
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