Question: What Makes Fst A Better Measure For Genetic Differentiation Than Allele Frequency Differences?
gravatar for Abdel
7.9 years ago by
Abdel360 wrote:

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

fst • 3.6k views
ADD COMMENTlink modified 7.9 years ago by tiagoantao660 • written 7.9 years ago by Abdel360
gravatar for tiagoantao
7.9 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 7.9 years ago by tiagoantao660
gravatar for Zev.Kronenberg
7.9 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 7.9 years ago by Zev.Kronenberg11k
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1845 users visited in the last hour