[adegenet-forum] DAPC group choice

[J. Richardson]

Hi Dr. Jombart and Adegenet users,

I have a question related to DAPC that I have not found in the manual,
tutorials or forum archive.

I am wondering what the DAPC operation is doing (i.e. how it is configuring
clusters relative to each other) when you
do not use the groups created in "find.clusters" (i.e. grp$grp output), but
rather use the population of origin as the
group designation (i.e. dataset$pop)?

I ran "find.clusters" and performed the DAPC with these created groups. I
also performed a DAPC with the groups set
as the sampling sites (populations of origin) using the number of clusters
derived from k-means. Interestingly, the DAPC using the k-means
groupings don't make a lot of intuitive sense. However, the DAPC results
using the sampling sites/populations of origin for the group
designation make sense and correspond closely to the output from STRUCTURE
using their location prior.

So I am wondering if using the sampling site/population designation as the
group designation is (A) analogous to the
STRUCTURE operation using the location prior or "population flags", and (B)
if this is valid if you have good a priori information on
your population delineations (e.g. a species breeding in discrete,
contained habitats)?

Thank you so much in advance for any insight you can provide.

Jon
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