TABLE 2.

Saturation indices^a

Gene	First plus second codon positions		Third codon position
	Half of expected saturation index	Observed saturation index (range)	Half of expected saturation index	Observed saturation index (range)
gag	0.96	0.64 (0.59-0.68)	0.94	1.29 (1.24-1.34)
pol	0.96	0.62 (0.59-0.65)	0.90	1.22 (1.18-1.26)
vif	0.97	1.08 (1.02-1.15)	0.90	1.48 (1.38-1.59)
env	0.96	0.88 (0.84-0.92)	0.95	1.42 (1.39-1.46)
nef	0.91	0.93 (0.85-1.01)	0.94	0.94 (0.81-1.07)
vpu (all positions)	0.83	0.84-1.16

^aSaturation indices were calculated with the program DAMBE at different codon positions on the concatenated nucleotide alignment for the nonoverlapping gene sequences, including representatives of the six major SIV lineages plus the SIV gsn-99CM71 and SIVgsn-99CM166 strains. Saturation positions for the different genes with a saturation index exceeding half of the expected saturation index are underlined.