I am encountering difficulty selecting a statistic to compare two distributions of Weir & Cockerham's Fst. While I know the distribution is non-normal for the two Fst distributions I am looking at, I cannot say they are independent. One is a comparison between populations A and B, and the other is between populations A and C - as you can see both involve data from population A.
I was wondering whether a Wilcoxon signed-rank test or Kolmogorov-Smirnov test would be appropriate for testing whether the two distributions significantly differ?
If not, could anyone suggest a better statistic? The samples are too large (millions of markers) for me to do this via bootstrapping.
Thank you for any help you may be able to offer.