Question: Nucleotide Diversity (Pi ) Test
1
gravatar for zhuwei.cug
5.0 years ago by
zhuwei.cug20
zhuwei.cug20 wrote:

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

test • 3.8k views
ADD COMMENTlink modified 5.0 years ago by AGS230 • written 5.0 years ago by zhuwei.cug20
2
gravatar for Zev.Kronenberg
5.0 years ago by
United States
Zev.Kronenberg11k wrote:

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.

ADD COMMENTlink modified 5.0 years ago • written 5.0 years ago by Zev.Kronenberg11k
0
gravatar for AGS
5.0 years ago by
AGS230
Brooklyn, ny
AGS230 wrote:

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.

ADD COMMENTlink written 5.0 years ago by AGS230
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