[adegenet-forum] interpretation sPCA

[Thomas, Evert (Bioversity-Colombia)]

Dear Thibaut,

I have a question regarding the interpretation of the sPCA scores as visualized in a color plot or interpolated lagged scores. I am working with intraspecific species data at continental level and found a strong gradient in my data  with a clear separation of a northern and southern group. Based on a number of grounds I believe that the center of origin of the species I am working with is located  at the "genotone" (or what to call this, I mean the grey area between both groups where the genetic differentiation is the steepest) . Does this make sense with the theory behind sPCA? I think the species moved north and south from the putative center of origin and developed into different genotypes which becomes apparent in the visualization of the sPCA... 

And should the outcome of an sPCA be somewhat reflected in the outcomes of discriminant analysis of principal components or are these really two different methods? (I apologize for my ignorance) 

Many thanks in advance

Evert