Need help with FST calculation (not homework)

In summary, the conversation discusses the use of FST estimator to measure genetic differences between populations. The original FST formula introduced by Wright has been replaced by the FST estimate by Cockerham and Weir in 1984 due to its flaws. Recent studies have produced tables of FST distances between populations, particularly in European and East Asian populations. The conversation also mentions the availability of FST modules in BioPerl and the use of algorithms derived from Weir and Cockerham's study.
  • #1
argiedude
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Hi, to all. The FST estimator can tell how different 2 populations are, genetically. The normal FST formula was introduced by Wright and can be found very easily, for example, in wikipedia. But it had some flaws, so it's use has now been completely replaced by the FST estimate introduced by Cockerham and Weir (1984). I've tried very hard to find this formula, but I can't.

This is the original study (it's not public access):

B. S. Weir and C. C. Cockerham.
Estimating f-statistics for the analysis of population structure
Evolution, 38:1358-1370, 1984

Recent studies, using 100,000's of mutations in the human dna (SNPs), have produced tables of FST distances between several populations. So far this has been done for several European populations (Heath, 2008), and just a few weeks ago a new study came out which included an FST comparison between 20 East Asian populations.

It's all extremely interesting. Here's a graph I made of the genetic distances from the Heath study:

FST-autosomalEuropeHeath2008.gif


Can you help?
 
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  • #2
https://en.wikipedia.org/wiki/Fixation_index FST modules are freely available in BioPerl for example.
Someone else may know precisely which algorithms (and in what software packages) are derived from Weir and Cockerham.
 
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What is FST and why is it important?

FST stands for Fixation Index and it is a measure of genetic variation within and between populations. It is important because it helps to quantify the genetic differences among populations and can provide insights into the evolutionary processes that have shaped these differences.

How is FST calculated?

FST is calculated by comparing the genetic variation within a population (called the expected heterozygosity) to the genetic variation among populations (called the observed heterozygosity). This can be done using various statistical methods, such as analysis of molecular variance (AMOVA) or using the Weir and Cockerham method.

What factors can affect FST values?

FST values can be affected by a variety of factors, including the level of gene flow between populations, the genetic structure of the populations, and the size of the populations. Additionally, the type of markers used for FST calculation and the statistical method used can also impact the resulting FST values.

How can FST be interpreted?

Interpretation of FST values can vary depending on the context and purpose of the study. Generally, higher FST values indicate greater genetic differentiation between populations, while lower values indicate more genetic similarity. However, the interpretation of FST values should always be accompanied by an understanding of the underlying genetic and demographic factors.

Are there any limitations to using FST?

Yes, there are some limitations to using FST as a measure of genetic variation. FST does not take into account the overall genetic diversity within a population, and can be influenced by factors such as sample size, selection, and genetic drift. Additionally, FST may not accurately reflect the genetic structure of populations if there is significant gene flow or if populations are not in a state of genetic equilibrium.

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