Table 3. Nucleotide sequences in the ancestral and evolved phage genomes.
| Phage Population | S/N | Gene | Genome position | Nucleotide (Anc) | Nucleotide (Evolved) | Gene position | Codon change | Amino acid change | ||||||||
| NCBI (AY099114) | Anc | M54 | M109 | M163 | M165_2 | S94_3 | S169_3 | S168_4 | ||||||||
| ± | – | UTR | 47 | G | A | – | – | – | ||||||||
| ± | + | ± | ± | – | 52 | A | G | – | – | – | ||||||
| ± | S | A2 | 66 | U | A | 6(2) | CCU→CCA | – | ||||||||
| + | ± | ± | N | 221 | U | G | 161(54) | CUA→CGA | Leu→Arg | |||||||
| ± | ± | ± | S | 519 | A | G | 459(153) | GAA→GAG | – | |||||||
| + | ± | + | + | + | + | + | + | + | N | 569 | G/A | A | 509(170) | GGG→GAG | Gly→Glu | |
| ± | S | 789 | C | U | 729(243) | GGC→GGU | – | |||||||||
| ± | + | ± | N | 830 | U | C | 770(257) | GUU→GCU | Val→Ala | |||||||
| + | ± | S | 1,257 | C | U | 1,197(399) | ACC→ACU | – | ||||||||
| ± | ± | N | 1,288 | A | G | 1,228(410) | AGU→GGU | Ser→Gly | ||||||||
| ± | S | A1 coat | 1,344 | A | G | 1(1) | AUG→GUG | Met→Met * | ||||||||
| + | N | 1,371 | G | C | 28(10) | GGU→CGU | Gly→Arg | |||||||||
| ± | N | A1 | 1,795 | U | C | 452(151) | AUU→ACU | Ile→Thr | ||||||||
| + | + | + | + | + | + | + | + | S | 2,249 | C | U | 906(302) | AGC→AGU | – | ||
Blank, “±,” and “+” in the phage population column indicate that the whole population showed the same sequence as Anc, heterogeneous with Anc and evolved sequence, and evolved sequence, respectively. S and N in the S/N column represent synonymous and non-synonymous mutations, respectively. UTR, untranslated region. Genome positions were counted from the G of the 5′ terminus of the Qβ genome as position 1. Gene position was counted from the A of the start codon (AUG) of each gene as position 1. The numbers in parentheses represent the amino acid positions of each protein. Position 569 of Anc was heterogeneous with G and A, although the Anc Qβ population was derived from cloned cDNA.
*This mutation was AUG to GUG in the start codon. If this protein was functional, the GUG start codon would be used to encode Met.
To determine mutation fixation and cumulative mutation numbers in Figure 7, polymorphic sites (shown as ±) were counted as 0.5, and monomorphic sites (shown as +) were counted as 1. For position 221 in line 1, a count of 1 was given from Anc(P) to M54(P), 0.5 from M54(P) to M109(P), and 0.5 from M109(P) to M163(P). For position 221 in line 2, a count of 1 was also given from Anc(P) to M54(P) and 0.5 from M54(P) to M165_2(P).