Nucleotide Diversity (Pi ) Test
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9.1 years ago
zhuwei.cug ▴ 30

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

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9.1 years ago

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.

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9.1 years ago
AGS ▴ 230

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.

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