TABLE 6

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

					No. loci		Sign test^b
	Average	P^a	Variance	P^a	+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/D_min^c	−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/D_min^c	−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

↵* 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).