Table 2.
Site-by-site signals of positive and negative selection acting on movement protein (mp), coat protein (cp) and replication associated protein (rep) gene codons during the SSRV evolution experiment
| Gene | Codon | Methoda | Selectionb | Motif/domain (site underlined where relevant) |
| mp | 21 | R | + | |
| 63 | R | + | C-terminal boundary of hydrophobic domain | |
| cp | 3 | R | - | DNA Binding domain |
| 67 | R | - | DNA Binding domain | |
| 69 | R | - | DNA Binding domain | |
| 85 | FR | - | DNA Binding domain | |
| 105 | FR | - | DNA Binding domain | |
| 122 | FR | - | ||
| 136 | R | - | ||
| 157 | FRS | - | ||
| 180 | R | - | ||
| 201 | R | - | ||
| 217 | R | - | ||
| 219 | R | - | ||
| rep b | 7 | FR | - | |
| 28 | FR | - | RCR motif I (FLTYPHC) | |
| 30 | FR | + | ||
| 133 | FR | - | ||
| 147 | FR | - | ||
| 155 | FR | - | ||
| 158 | FR | - | ||
| 185 | FRS | - | Rep-Rep oligomerisation domain (ASKLFPDTVEEY) | |
| 321 | FR | - | ||
| 326 | FR | - | ||
| 356 | FRS | - | ||
a F = Fixed effects likelihood method; R = Relative effects likelihood method; S = Single likelihood ancestor counting method.
b + = evidence of positive selection (p-value < 0.1); - = evidence of negative selection (p-value < 0.1).
c Excludes codons 217–282 that are expressed in different frames in rep and repA.