[adegenet-forum] any change in find.clusters and/or dapc functions from V1.4-2 to V2.0.1 ?

[flefevre]

Dear adegenet team,

has something changed in the find.clusters and/or dapc functions from 
V1.4-2 and V2.01 of adegenet?

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?

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:
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
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.

Any suggestion to interprete this discrepancy is welcome,
Thank you,

François
francois.lefevre.2 at inra.fr

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