Table 1.

Estimates of the Neutrality Index (NI) and the Proportion of Amino Acid Substitutions Fixed by Positive Selection (α) Derived from the Ratios of Replacement and Silent Polymorphisms and Fixed Differences.

Subspecies	Polymorphism Cutoffa	Replacement Polymorphism	Replacement Fixed	Silent Polymorphism	Silent Fixed	Replacement Polymorphism/Silent Polymorphism	Replacement Fixed/Silent Fixed	NI	αˆ	CIb	Pearson’s χ2
M. m. castaneus	>0	339	89	1,332	222	0.25	0.40	0.64	0.36	0.17–0.51	10.75*
M. m. castaneus	>0.10	207	89	903	222	0.23	0.40	0.57	0.43	0.24–0.57	14.64**
M. m. castaneus	>0.20	151	89	636	222	0.24	0.40	0.59	0.41	0.21–0.56	11.61**
M. m. domesticus	>0	442	152	1,509	467	0.29	0.33	0.90	0.10	−0.10 to 0.27	0.96
M. m. domesticus	>0.10	352	152	1,243	467	0.28	0.33	0.87	0.13	−0.09 to 0.30	1.57
M. m. domesticus	>0.20	216	152	786	467	0.27	0.33	0.84	0.16	−0.07 to 0.34	1.96
M. m. musculus	>0	314	185	969	501	0.32	0.37	0.88	0.12	−0.09 to 0.30	1.47
M. m. musculus	>0.10	216	185	652	501	0.33	0.37	0.90	0.10	−0.15 to 0.28	0.87
M. m. musculus	>0.20	142	185	444	501	0.32	0.37	0.87	0.13	−0.11 to 0.33	1.24

^aThe polymorphism cutoff is given in terms of the MAF.

^bCIs for αˆ were derived via 1,000 bootstrap replicates. α cannot be less than 0. However, negative estimates of α do occur when the ratio of replacement polymorphism to divergence exceeds the ratio of silent polymorphism to divergence.

*P < 0.05, **P < 0.001.