HIgh Fst outliers in lositan

Question

[caicedo]

Hi,

I'm running lositan on GBS data in two populations. Overall Fst is high between the populations, close to 0.6. I have several loci that are fixed between the two populations - so they have an Fst of 1 and heterozygosity of 1. However, they do not come out as outliers in the analysis. Is there a reason why Fst = 1 loci are not considered outliers? Some other High Fst loci do come out as outliers.

Thanks,
Ana

[Zev.Kronenberg]

I have not used lositan, but is it possible those sites have many missing genotypes?

Answer 1

[tiagoantao]

If Hz is 1 then Fst can only be 1 with 2 populations. What this means is that different alleles have fixated in both populations, thus the only possible Fst value is 1. It is actually the one trivial case ;)

I would strongly suspect that at least one (if not both) of your populations are highly inbred given the mean Fst and fixated alleles.