[adegenet-forum] DAPC/sPCA Over-parameterization issues?

[jaa695 at mail.usask.ca]

Dear all,

I've been trying to figure out the real meaning of my latest aedegenet analyses,
and hope some of you can help.
Study case: continuous sampling (i.e. no a priori defined populations) of a
large mammal (n= 500 individuals, 34 STR loci) at a regional scale.
Puzzling results: When using DAPC on my dataset I do find some evidence for the
existence of three differentiated clusters (lowest BIC= 3 clusters, and delta
BIC between clusters=1 and clusters =3 is 16, when plotting there is no overlap
among clusters. Assign.per.pop ranges from 0.97 to 0.99). However when looking
at my sPCA results I do not find any evidence for either local or global
structure. Although there are potential biological explanantions for the above
results (e.g. assortative mating) this are extremely unlikely, and my feeling
is that the DAPC cluster might be the result of over-parameterization (494 x
292 matrix of genotypes. Reatined PCs 75 (80-85% cumulative variance, 2
retained discriminant functions). Any thoughts?

THANKS!

/Jose