TABLE 3.

Numbers of synonymous substitutions per synonymous site (d_S) and of nonsynonymous substitutions per nonsynonymous site (d_N) in comparisons of the remainders of coding regions (excluding epitopes) with the inoculum sequence

Coding region	Mean ± SE for host typea
	Homozygous (n = 9)		Heterozygous (n = 5)		All (n = 14)
	dS	dN	dS	dN	dS	dN
Gag	0.0104 ± 0.0027	0.0055 ± 0.0005	0.0053 ± 0.0011	0.0047 ± 0.0001	0.0086 ± 0.0018	0.0052 ± 0.0004
Pol	0.0080 ± 0.0012	0.0018 ± 0.0002***	0.0090 ± 0.0010	0.0018 ± 0.0001**	0.0084 ± 0.0009	0.0018 ± 0.0001***
Tat	0.0215 ± 0.0021	0.0038 ± 0.0006***	0.0188 ± 0.0013	0.0048 ± 0.0008**	0.0206 ± 0.0014	0.0042 ± 0.0005***
ARF1	0.0144 ± 0.0040	0.0168 ± 0.0020	0.0255 ± 0.0006	0.0117 ± 0.0048	0.0184 ± 0.0029	0.0150 ± 0.0021
Env	0.0178 ± 0.0019	0.0107 ± 0.0010***	0.0184 ± 0.0022	0.0093 ± 0.0006*	0.0180 ± 0.0014	0.0102 ± 0.0007***
Rev	0.0057 ± 0.0014	0.0159 ± 0.0014**	0.0049 ± 0.0011	0.0168 ± 0.0012**	0.0055 ± 0.0009	0.0162 ± 0.0010***
Nef	0.0048 ± 0.0012	0.0074 ± 0.0011*	0.0066 ± 0.0015	0.0071 ± 0.0014	0.0054 ± 0.0010	0.0073 ± 0.0008*

^aPaired t tests (two tailed) of the hypothesis that d_S is equal to d_N were done: *, P < 0.05; **, P < 0.01; ***, P < 0.001.