Question: What Makes Fst A Better Measure For Genetic Differentiation Than Allele Frequency Differences?
gravatar for Abdel
7.1 years ago by
Abdel340 wrote:

What makes Fst (fixation index) a better measure for genetic differentiation for a single locus than the allele frequency difference?

fst • 3.3k views
ADD COMMENTlink modified 7.1 years ago by tiagoantao660 • written 7.1 years ago by Abdel340
gravatar for tiagoantao
7.1 years ago by
United States of America
tiagoantao660 wrote:

I would be careful with the relationship between Fst and Hz. Fst explains the genetic diversity due to population sub-division and that can be framed in terms of Hz, but it is not, strictly speaking, taking Hz into account. See Allendorf and Seeb, 2000 for a good example. There are also a few examples of selection detection methods that add Hz to the mix (avoiding a self-cite here ;) )

More than saying anything, I strongly recommend reading Genetics in geographically structured populations: defining, estimating and interpreting FST Holsinger & Wier Nat Rev Gen

It is a complex subject, with lots of literature. The above paper is probably the anyone best hope to make sense of a complex topic...

But you are on to something: A recent paper used allelic differences to find a gene (EPAS1) under selection in high-altitude (Tibetan) populations: 2 caveats to think about: it did a pair-wise comparison of populations (i.e. only two populations) and used SNP data (i.e. bi-allelic). Have a think about how to expand simple allelic differences to many populations and many alleles/locus...

ADD COMMENTlink written 7.1 years ago by tiagoantao660
gravatar for Zev.Kronenberg
7.1 years ago by
United States
Zev.Kronenberg11k wrote:

1) Allele frequency differences does not take heterozygosity into account.

2) It is a common measure where zero = panmixis; 1=fixation.

3) Fst weights the subpopulations.

If you think that using differences in allele frequency distribution is a better measure have a look at this paper:


They use and compare several methods for detecting selection. They explain the equations if you want to implement them yourself. I have been very happy with directional Fst and log10(theta_fu/theta_fu).

ADD COMMENTlink written 7.1 years ago by Zev.Kronenberg11k
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