Lositan using 2 populations only? Loci falling in straight line where Fst=He

Question

[lauren.c.white89]

Hello,

I'm using Lositan with 2 populations and around 200 SNP loci.

Most of my loci fall in a straight line on the plot where He=Fst.

Is this an artefact of using just 2 populations?

How is Fst calculated?

Thank you for your help.