Are negative values for the Population Branch Statistic (from Yi et al. 2010) meaningful? I obtained per SNP pairwise WC Fst from 3 populations of different sizes from Vcftools and calculated PBS. For some SNPs, the PBS is negative for a population and I am not entirely sure how to interpret that.
These are the pairwise Fst values. Negative Fst is meaningless but the issue still persists if I convert negative Fst to 0.
Pop 1 v Pop 2
Pop 1 v Pop 3
Pop 2 v Pop 3
Looking online, in some papers with Manhatten plots, PBS always cuts off at 0 but in others it is negative for some SNPs. I think it has something to do with differences in Fst when size of populations being compared are slightly different.