Question: HIgh Fst outliers in lositan
gravatar for caicedo
5.8 years ago by
United States
caicedo10 wrote:


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.




lositan • 2.1k views
ADD COMMENTlink modified 5.8 years ago by tiagoantao670 • written 5.8 years ago by caicedo10

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

ADD REPLYlink written 5.8 years ago by Zev.Kronenberg11k
gravatar for tiagoantao
5.8 years ago by
United States of America
tiagoantao670 wrote:

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.

ADD COMMENTlink written 5.8 years ago by tiagoantao670
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