TABLE 6

Neutrality tests using silent polymorphisms based on groups of loci with low and high levels of variation

No. lociSign testb
AveragePaVariancePa+2.5%−2.5%+P
n = 128 loci without outgroup (low θ)
 Tajima's D−0.5634<0.0001*0.78130.0864192586<0.001*
 Fu and Li's D*−0.5405<0.0001*1.03300.4658183675<0.001*
 D/Dminc−0.3658<0.0001*0.35120.0616002586<0.001*
n = 67 loci without outgroup (high θ)
 Tajima's D−0.31570.0316*1.4093<0.0001*2825410.064
 Fu and Li's D*−0.36320.0096*1.5954<0.0001*6728360.382
 D/Dminc−0.17390.0262*0.35630.00162524420.036*
n = 31 loci with A. lyrata outgroup (low θ)
 Fu and Li's D−0.45760.0376*1.30920.137802 6130.167
 Fay and Wu's H0.02190.77480.56580.73782117 90.169
n = 12 loci with A. lyrata outgroup (high θ)
 Fu and Li's D−0.36150.06362.11950.0014*24 4 80.388
 Fay and Wu's H−1.31310.7256.86360.572411 5 70.774
  • * Significant P-values (P ≤ 0.05).

  • a Two-tailed probability.

  • b Numbers of loci with a value above (+) and below (−) the median as calculated by coalescent simulations.

  • c Tajima's D divided by its minimum (Schaeffer 2002).