exploring genetic differences among highly close populations

Question

[yzko]

Hello,

I'D like to explore the genetic differences among highly close populations.

These population are close, but exist different clade in phylogenetic tree based on core genome. These populations were also confirmed using population clustering methods.

I tried to population specific genes(using pan-GWAS methods) or SNPs(by Fst values of SNPs), but I couldn't obtain the good results.

Are there any suggestions?

Thanks