Nucleotide Diversity (Pi ) Test

Question

[zhuwei.cug]

Hi all, how do I identify significant artificial selection for regions on genomes based on nucleotide diversity?

I know Tajima's D could do this and I have tried, but I still want to know how is possible to do this by nucleotide diversity test.

Thanks

Answer 1

[Zev.Kronenberg]

The paper below discusses some measures using nucleotide diversity (PI).

Tests of Selection

Fst and Achaz's Y are two tests that are designed to find regions under selection (natural, or artificial). You could also look into XP-EHH or IHS.

Measuring a loss in heterozygosity is often easy and effective.

Answer 2

[AGS]

Consider also an HKA test.

In Maize

Another in Maize

And here

Consider also Fay and Wu's H if you have high(er) levels of polymorphism and want to look at the AFS.