[adegenet-forum] When cross-validating DAPC (using web server), is it best to use 'group' or 'overall'?

[Stephanie Coster]

Thanks in advance!

I have a dataset of genotypes from microsatellite loci and I'm looking to
analyze population structure. Program STRUCTURE shows essentially no
clusters, and I'd like to use DAPC to get another perspective.

I've run the 'find.clusters' code and the BIC suggests K=2, but the
assignments are unreliable (equal assignments across all sites to both
clusters). I am interpreting this to mean that K=1 and all samples likely
form a single cluster.

Now, I'd like to use my apriori site groupings to draw a scatterplot and am
using the DAPC web server to cross-validate and suggest the number of PCs
to retain. I get notably different scatterplots depending on whether I
choose 'group' or 'overall' to assess. The sites have more spatial
differentiation when using 'group', and essentially all overlap when using
'overall'. I understand that success is calculated by my groups or overall
depending on the choice, but what does this mean in application? Can
someone help explain why these plots differ and which is better to use?

Many thanks!

Stephanie
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