I am studying the genetic Variation of a plant with not much research. I m using AFlp primer to identify and check the genetic variation of the plant. It is suppose to be same species. I collected the samples from different locations. I m using different combination of flourcent labelled ECoR1 and unlabelled mse1 primers.Aflp primers shows 100% of polymorphism.. I m using past and genleax and xlstat for PCA and pCoA that is showing low variance percentage below 50%. Amova shows 99% of variance among population.

I wonder if my analysis are correct.?

And what does that mean to have 100% polymorphism with low pCoA and PCA variance and high amova variation.?

If itz not correct. What else analysis I need to do to check these things and what soft wares I should use.?

Please help me.

Thank you