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Dear adegenet team,<br>
<br>
has something changed in the find.clusters and/or dapc functions
from V1.4-2 and V2.01 of adegenet?<br>
<br>
I am re-doing an analysis that was first done in 2014 (with V1.4-2)
on a genind object of 158 diploid individuals and 70 snp and the
results are quite different (synthesis of 20 analyses using CLUMPP,
highly consistent in each case). Exactly the same dataset and the
same script. The only difference I can see between the 2 analyses is
the version of adegenet: has something changed in these 2 functions?<br>
<br>
Actually the individuals belong to an admixed population, we look
for the number of components and assignment of the individuals. The
difference is as follows:<br>
2014 analysis => 3 clear groups (136 individuals out of 158 have
a mean assignment probability >0.95 to one of the groups), one
group is more "compact" and consists of very related individuals <br>
2017 analysis => 2 clear groups (111 individuals with assignment
>0.95), all individuals previously assigned to the compact group
are still assigned to the same new group but now associated with
others, the other 2 previous groups do not relate well with the new
ones.<br>
<br>
Any suggestion to interprete this discrepancy is welcome,<br>
Thank you,<br>
<br>
François<br>
<a class="moz-txt-link-abbreviated" href="mailto:francois.lefevre.2@inra.fr">francois.lefevre.2@inra.fr</a><br>
<br>
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