TABLE 2.

Effect of substitutions on protein sequence and phage growth

				AGR
	Order	Substitution	AA change	Ancestor	Derived		RGR (mean ± SE)
Anc				81.96	74.17	P = 0.2533 (n = 10)	1.010 ± 0.146
Line 1	1	U862C	Mat: S → L	77.10	120.00	P = 0.0049 (n = 10)	1.545 ± 0.134
	2	U1741C	Lys: F → L	94.87	182.33	P < 0.0001 (n = 10)	1.975 ± 0.156
	3	A1199G	Mat: H → R	88.76	172.57	P = 0.0041 (n = 10)	2.183 ± 0.304
	4	A1860C	Lys: E → D Rep: S → R	68.96	149.58	P = 0.0087 (n = 11)	1.209 ± 0.285
Lines 2 and 3	1	G253C	Mat: G → R	92.82	152.22	P = 0.0003 (n = 20)	2.016 ± 0.304
	2	A1697G	Lys: Q → R Coat: silent	73.17	154.93	P < 0.0111 (n = 10)	2.346 ± 0.267
Line 2	3	A1599G + A1697G	Coat: I → V	104.50	241.72	P = 0.0006 (n = 10)	2.899 ± 0.631
	—	A1599G + U1691C		74.13	215.52	P < 0.0001 (n = 10)	3.458 ± 0.444
Line 3	3 + 4	U1756A + C3056T	Lys: Y → H Rep: silent	98.51	145.16	P = 0.0309 (n = 13)	1.797 ± 0.397
	—	C1692U	Lys: silent Coat: P → S	78.16	270.29	P = 0.0002 (n = 10)	3.833 ± 0.475

The effect of substitutions and high-frequency mutations on protein sequence and growth rate is shown. Mutations are identified by ancestral nucleotide state, the location, and the derived state. Some mutations did not occur in the absence of other mutations and so are shown together. Also indicated is the gene affected and the change in amino acid sequence, if any; as MS2 has overlapping genes, some mutations affect more than one gene. Absolute growth rates (AGR) of ancestral (control) phage and phage with the specified genotype shown were compared using paired t-tests. Relative growth rates (RGR) correspond to fitness as described in the text. Note that the value for relative growth rate given is the mean across replicates of AGR-derived/AGR-ancestral and thus is not equal to the ratio of the mean absolute growth rates.