TABLE 1.

Major haplotypes appearing in population samples through time

	Line 1					Line 2					Line 3
Site				Site				Site
1	1	1	1	1	1	1	1	1	1	1	1	1	3
8	1	7	8	2	5	6	6	2	6	6	7	7	7	7	8	0
6	9	4	6	5	9	9	9	5	9	9	3	4	5	6	7	5
Passage	2	9	1	0	Frequency	3	9	1	7	Frequency	3	2	7	7	1	6	4	5	6	Frequency
MS2anc	U	A	U	A		G	A	U	A		G	C	A	G	U	U	U	A	C
10	.	.	.	.	1.00	.	.	.	.	0.50	.	.	.	.	.	.	.	.	.	0.11
					(n = 11)	C	.	.	.	0.50	C	.	.	.	.	.	.	.	.	0.89
										(n = 18)										(n = 9)
20	.	.	.	.	0.64	.	.	.	.	0.06	C	.	.	.	.	.	.	.	.	0.40
	C	.	.	.	0.36	C	.	.	.	0.75	C	.	.	.	C	.	.	.	.	0.10
					(n = 11)	C	.	C	.	0.13	C	.	.	.	.	.	C	.	.	0.50
						.	.	.	G	0.06										(n = 10)
										(n = 16)
30	.	.	.	.	0.21	C	.	.	G	0.22	C	.	G	.	.	.	.	.	.	0.13
	C	.	.	.	0.43	C	.	C	.	0.44	C	.	.	.	.	.	.	.	.	0.13
	C	.	C	.	0.36	C	G	.	G	0.22	C	.	.	.	C	.	.	.	.	0.50
					(n = 14)	C	G	C	.	0.11	C	.	.	.	.	.	C	.	.	0.25
										(n = 9)										(n = 8)
35	.	.	.	.	0.13					—										—
	C	.	.	.	0.13
	C	G	C	.	0.63
	C	G	C	C	0.13
					(n = 8)
40	C	.	.	.	0.09	C	.	C	.	0.25	C	.	G	.	.	.	.	.	.	0.33
	C	G	C	.	0.45	C	G	.	G	0.50	C	.	.	.	.	.	.	.	.	0.33
	C	G	C	C	0.45	C	G	C	.	0.25	C	U	G	.	.	.	.	.	.	0.22
					(n = 11)					(n = 8)	C	.	G	.	.	A	.	.	U	0.11
																				(n = 9)
45											C	.	G	.	.	.	.	.	.	0.375
											C	U	G	.	.	.	.	.	.	0.5
											C	.	G	.	.	.	.	G	.	0.13
																				(n = 8)
50	C	G	C	.	0.18	C	.	C	.	0.22	.	.	.	.	.	.	.	.	.	0.06
	C	G	C	C	0.82	C	G	.	G	0.56	C	U	G	.	.	.	.	.	.	0.53
					(n = 11)	C	G	C	.	0.22	C	.	.	.	.	.	.	.	.	0.12
										(n = 9)	C	.	G	.	.	.	.	.	.	0.12
											C	.	G	.	.	A	.	.	U	0.18
																				(n = 17)
60					—	C	.	C	.	0.17	C	.	.	.	.	.	C	.	.	0.20
						C	G	.	G	0.83	C	.	.	.	.	.	C	.	U	0.10
										(n = 12)	C	.	G	.	.	.	.	.	U	0.10
											C	.	G	.	.	A	.	.	U	0.60
																				(n = 10)
70					—					—	C	.	G	.	.	A	.	.	U	0.38
											C	.	G	U	.	.	.	G	.	0.63
																				(n = 8)

Genotypes of phage at sites with high-frequency variants are shown. Numbers across the top of the table indicate the location of each site relative to GenBank reference sequence NC%20001417. The passage number indicates the number of serial passages since the experiment was initiated. Plaques isolated from the passage indicated were sequenced, representing an individual phage in the evolving population. Haplotypes shown here include only sites where mutations were fixed or occurred at high frequencies; variation in the entire sequenced region, including sites with low-frequency variants, is shown in the supplemental materials.