Question: Neutrality Test With Arlequin
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gravatar for ficchio89
7.6 years ago by
ficchio890
ficchio890 wrote:

Hy. I have tested neutrality on 8 haplotypes with Arlequin software. I have used three different neutrality test at same time Tajima D, Fu's Fs and Ewens-Watterson tests. Tajima D and Fu's they give me p-values = 0.98000 and EW a p-value = 0.0000. How does it possible. Futhermore I have found an article that define significats these values and possible sings of overdominace selection at HLA-A locus :

N: sample size (individuals)
k: number of sequences detected
Fobs: observed homozygosity
Fexp: expected homozygosity
p EW: Ewens-Watterson’s p-value
theta S: θ estimator based on polymorphic sites (S)
theta Π: θ estimator based on the number of pairwise differences
Tajima's D: Tajima’s statistic
p Tajima: Tajima’s p-value

HLA-A

Population    N        k    F obs    F exp    p EW    theta S    theta Π    Tajima's D     p Tajima
Zulu          186    29    0.064    0.121    0.0034    10.778    20.843    2.709        0.99475

May someone can help me Thank you.

p-value test • 4.8k views
ADD COMMENTlink modified 4.7 years ago by Biostar ♦♦ 20 • written 7.6 years ago by ficchio890

What values did you get for _D_ and _F_s and what null hypothesis are those p-values testing? Both D an Fs and be significantly greater or less than 0. Depending on how Arlequin sets up the tests p > 0.975 could be "significantly positive" results (the example you seems to show this D is greater than 2 which is the rule of thumb for significance and the p-value is >> 0.975)

ADD REPLYlink written 7.6 years ago by David W4.8k

Tajima's D test

Sample size 320 32.000.000 0.00000

S 11 1.100.000 0.00000

Pi 400.729 400.729 0.00000

Tajima's D 296.944 296.944 0.00000

Tajima's D p-value 0.99200 0.99200 0.00000

Fu's FS test

No. of alleles(unchecked) 7 700.000 0.00000

Theta_pi 400.729 400.729 0.00000

Exp. no. of alleles 1.811.710 1.811.710 0.00000

FS 868.540 868.540 0.00000

FS p-value 0.99900 0.99900 0.00000

Here my results tab, the null hypotesis was based on neutral selection at the HLA haplotypes that I have tested. I would expect D ed F values positives as sing of overdominance selection. Thank you.

ADD REPLYlink written 7.5 years ago by ficchio890

I'm not sure what to make of this -- Pi can't equal 400?

ADD REPLYlink written 7.5 years ago by David W4.8k

You have something strange going on. Tajima's D of 296 would be the highest ever observed (I think) and still it's not significant. I know that Arlequin is tricky with formatting issues. Try starting from the example data they provide and modify the file step by step. Also, you could post the input data if someone is willing to try.

ADD REPLYlink written 7.4 years ago by Fabio Marroni2.6k
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