TABLE 3.

Differences in ratios of nonsynonymous to synonymous substitutions between major and minor groups in individual genes^c

Group	Gene	Characterizationa	NSyn	Syn	No. of codons	Ratio	Significanceb
Combined characterization of exposure status at codons
Major	VP2	B	62	1,172	162	0.053
Minor	VP2	B	22	340	162	0.065	NS
Major	VP3	B	82	973	130	0.084
Minor	VP3	B	19	268	130	0.071	NS
Major	VP1	B	138	1,117	157	0.123
Minor	VP1	B	25	318	157	0.071	NSB χ2 = 3.65; P value = 0.056
Major	VP2	E	254	777	97	0.363
Minor	VP2	E	123	248	97	0.496	SB χ2 = 9.64; P value = 0.0019
Major	VP3	E	257	847	107	0.294
Minor	VP3	E	100	246	107	0.406	SB χ2 = 5.19; P value = 0.023
Major	VP1	E	353	934	125	0.378
Minor	VP1	E	180	291	125	0.619	SB χ2 = 18.5; P value = 0.000017
Joint characterization of exposure status at codons
Major	VP2	R	42	414	53	0.101
Minor	VP2	R	29	124	53	0.234	SB χ2 = 9.64; P value = 0.0019
Major	VP3	R	82	563	69	0.146
Minor	VP3	R	33	153	69	0.216	NS
Major	VP1	R	166	674	91	0.246
Minor	VP1	R	85	220	91	0.386	SB χ2 = 8.12; P value = 0.0044
Major	VP2	R+S	192	325	40	0.591
Minor	VP2	R+S	89	111	40	0.802	NS
Major	VP3	R+S	174	303	37	0.574
Minor	VP3	R+S	67	92	37	0.728	NS
Major	VP1	R+S	187	260	34	0.719
Minor	VP1	R+S	95	71	34	1.338	SB χ2 = 10.9; P value = 0.00094

^aR, exposed by the rolling-only model; R+S, exposed by the rolling+structural model.

^bNS, not significant; SB, significant after Bonferroni correction; NSB, not significant after Bonferroni correction.

^cWe show the number of nonsynonymous changes (NSyn), the number of synonymous changes (Syn), and the number of codons for each class of codons (exposed [E] or buried [B]) in major- and minor-group lineages for each gene, along with the ratio of nonsynonymous to synonymous changes. The significance is based on a chi-square test of the 2-by-2 contingency table of nonsynonymous and synonymous changes for these two rows. Note that we did not include the five sites identified only by the structural model because they could not have produced a significant interaction.