Neutrality tests using silent polymorphisms based on groups of loci with low and high levels of variation
No. loci | Sign testb | ||||||||
---|---|---|---|---|---|---|---|---|---|
Average | Pa | Variance | Pa | +2.5% | −2.5% | + | − | P | |
n = 128 loci without outgroup (low θ) | |||||||||
Tajima's D | −0.5634 | <0.0001* | 0.7813 | 0.0864 | 1 | 9 | 25 | 86 | <0.001* |
Fu and Li's D* | −0.5405 | <0.0001* | 1.0330 | 0.4658 | 1 | 8 | 36 | 75 | <0.001* |
D/Dminc | −0.3658 | <0.0001* | 0.3512 | 0.0616 | 0 | 0 | 25 | 86 | <0.001* |
n = 67 loci without outgroup (high θ) | |||||||||
Tajima's D | −0.3157 | 0.0316* | 1.4093 | <0.0001* | 2 | 8 | 25 | 41 | 0.064 |
Fu and Li's D* | −0.3632 | 0.0096* | 1.5954 | <0.0001* | 6 | 7 | 28 | 36 | 0.382 |
D/Dminc | −0.1739 | 0.0262* | 0.3563 | 0.0016 | 2 | 5 | 24 | 42 | 0.036* |
n = 31 loci with A. lyrata outgroup (low θ) | |||||||||
Fu and Li's D | −0.4576 | 0.0376* | 1.3092 | 0.1378 | 0 | 2 | 6 | 13 | 0.167 |
Fay and Wu's H | 0.0219 | 0.7748 | 0.5658 | 0.7378 | 2 | 1 | 17 | 9 | 0.169 |
n = 12 loci with A. lyrata outgroup (high θ) | |||||||||
Fu and Li's D | −0.3615 | 0.0636 | 2.1195 | 0.0014* | 2 | 4 | 4 | 8 | 0.388 |
Fay and Wu's H | −1.3131 | 0.725 | 6.8636 | 0.5724 | 1 | 1 | 5 | 7 | 0.774 |