negative PBS values
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.
| Population | PBS |
|---|---|
| Population 1 | -0.0897514 |
| Population 2 | 0.08334723 |
| Population 3 | 0.6226846 |
These are the pairwise Fst values. Negative Fst is meaningless but the issue still persists if I convert negative Fst to 0.
| Comparison | Fst |
|---|---|
| Pop 1 v Pop 2 | -0.006404169 |
| Pop 1 v Pop 3 | 0.5329332 |
| Pop 2 v Pop 3 | 0.7060318 |
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.
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