Hello all,
I am trying to infer local adaptation from Qst-Fst comparisons. I have 4 populations, say popA, popB, popC, popD. Each of the populations have 6 different genotypes and each genotype has 3 biological replicates. In total I have 72 samples. After sequence assembly, I obtained around 30000 genes for my dataset. What I would like to do now is calculate the Qst values. I already have the pairwise Fst values (i.e.,
- PopA-PopB
- PopA-PopC
- PopA-PopD
- PopB-PopC
- PopB-PopD
- PopC-PopD
I have a couple of questions:
1) How is the Qst calculation usually done? Is it done pairwise (since I have pairwise Fst values) or should I do it for all populations at once?
2) Based on the formula implemented in most of the papers, I got the following impression (please correct me if I am wrong):
For the pairwise PopA-PopB, Qst can be calculated as:
Gb = Variance calculated with PopA and PopB (pooled)
Gw = (Variance of PopA + Variance of PopB)/2
Qst = Gb / (Gb + 2 * Gw)
Please help!