Table 2. Mutations for which significant estimates of fitness effects have been obtained.
For each mutation, we indicate whether it already existed in the DCV starting stocks (and at which frequency) or arose during the evolution experiment. We also provide the estimated selection coefficient, its SEM and statistical significance. Cases significant after FDR correction are marked with an asterisk.
| Fly genotype | Biol. Rep. | Mutation | Standing variation (frequency) | Selection coefficient per passage (± SEM) | P |
|---|---|---|---|---|---|
| w1118 | 1 | VP2/G6311C R16P | Yes (0.0104) | 1.2039 ±0.2543 | 0.0418 |
| w1118 | 2 | VP3/U7824C | Yes (0.1457) | 0.4780 ±0.0617 | < 0.0001* |
| Dcr-2L811fsX/L811fsX | 1 | - | |||
| Dcr-2L811fsX/L811fsX | 2 | RpRd/U5302C | No | 0.3877 ±0.0973 | 0.0073 |
| VP1/C8227U H655Y | Yes (0.0147) | 0.3735 ±0.1368 | 0.0258 | ||
| VP1/C8424U | Yes (0.0139) | 0.3880 ±0.1407 | 0.0248 | ||
| Dcr-2R416X/R416X | 1 | VP2/C6932U A223V | Yes (0.0084) | 0.2135 ±0.0169 | < 0.0001* |
| Dcr-2R416X/R416X | 2 | VP2/G6379A A39T | Yes (0.0098) | 0.2074 ±0.0555 | 0.0057 |
| VP3/A7465G I401V | Yes (0.0088) | 0.1185 ±0.0338 | 0.0100 | ||
| VP3/U7824C | Yes (0.1457) | −0.2887 ±0.0884 | 0.0309 | ||
| Ago-2414/414 | 1 | - | |||
| Ago-2414/414 | 2 | 5’UTR/A280U | Yes (0.1176) | −0.1307 ±0.0376 | 0.0084 |
| VP3/U7824C | Yes (0.1457) | 0.5251 ±0.1050 | 0.0024 | ||
| VP1/C8227U H655Y | Yes (0.0147) | 0.6238 ±0.1077 | 0.0007 | ||
| VP1/C8424U | Yes (0.0139) | 0.6206 ±0.1252 | 0.0026 | ||
| Spz2/2 | 1 | 5’UTR/A280U | Yes (0.1176) | −0.2092 ±0.0735 | 0.0215 |
| VP2/G6931A A223T | No | 0.5420 ±0.1477 | 0.0105 | ||
| Spz2/2 | 2 | 2A/A1128C D110A | Yes (0.0041) | −0.0229 ±0.0065 | 0.0246 |
| 3C-Prot/A3787G | No | 0.5238 ±0.0757 | 0.0002* | ||
| 3C-Prot/G4394A V1199I | No | 0.5982 ±0.0764 | 0.0002* | ||
| VP1/G8536A V758I | No | 0.7038 ±0.0915 | 0.0006* | ||
| IGR/A6108G | Yes (0.0044) | 0.4873 ±0.0692 | 0.0002* | ||
| VP3/G8090A R609H | Yes (0.0200) | 0.4947 ±0.0722 | 0.0001* | ||
| Dif 1/1 | 1 | VP3/A7465G I401V | Yes (0.0088) | 0.3213 ±0.1173 | 0.0338 |
| VP3/G7956A | No | 0.2000 ±0.0335 | 0.0094 | ||
| Dif1/1 | 2 | 5’UTR/A280U | Yes (0.1176) | 0.5157 ±0.1289 | 0.0052 |
| VP1/U8629C S5058P | Yes (0.0898) | 0.4864 ±0.1175 | 0.0043 | ||
| RelE20/E20 | 1 | 5’UTR/A280U | Yes (0.1176) | 0.3430 ±0.1017 | 0.0097 |
| RdRp/A5404G | Yes (0.0929) | 0.3993 ±0.1217 | 0.0135 | ||
| VP2/U6303A N13K | Yes (0.0037) | 0.5724 ±0.1409 | 0.0036 | ||
| VP3/U7824C | Yes (0.1457) | −0.2804 ±0.0206 | 0.0467 | ||
| RelE20/E20 | 2 | 5’UTR/A280U | Yes (0.1176) | −0.0917 ±0.0277 | 0.0130 |
| 2B/C1412U | Yes (0.1301) | 0.4554 ±0.0119 | 0.0166 | ||
| VP3/C7760A T499N | No | 0.1340 ±0.0195 | 0.0005 | ||
| VagoΔM10/ΔM10 | 1 | 2B/C1412U | Yes (0.1301) | 0.2386 ±0.0549 | 0.0025 |
| 3C-Prot/A3703G | No | 0.2859 ±0.0537 | 0.0031 | ||
| RdRp/U5188A | Yes (0.1325) | 0.2869 ±0.0705 | 0.0268 | ||
| VP2/C6932U A223V | Yes (0.0084) | 0.1368 ±0.0553 | 0.0426 | ||
| VP1/C8227U H655Y | Yes (0.0147) | 0.1936 ±0.0291 | 0.0002* | ||
| VP1/C8424U | Yes (0.0139) | 0.1915 ±0.0283 | 0.0001* | ||
| VP1/U8697C | No | 0.2053 ±0.0325 | 0.0002* | ||
| 3’UTR/U9163A | No | 0.1473 ±0.0622 | 0.0497 | ||
| VagoΔM10/ΔM10 | 2 | 2C-Hel/G1756A | Yes (0.0059) | 0.3467 ±0.1293 | 0.0364 |
| VP2/A6300U E12D | No | 0.3681 ±0.1297 | 0.0470 | ||
| VP3/U7824C | Yes (0.1372) | 0.1517 ±0.0391 | 0.0060 | ||
| Egfrt1/t1 | 1 | 5’UTR/A280U | Yes (0.1176) | 0.1394 ±0.0364 | 0.0050 |
| 3C-Prot/U3643A | No | -0.2064 ±0.0592 | 0.0399 | ||
| VP1/A8201G Q646R | Yes (0.0045) | 0.3198 ±0.0736 | 0.0225 | ||
| VP2/A6660U | No | −0.1906 ±0.0641 | 0.0409 | ||
| VP2/G6868A V8162I | No | 0.3302 ±0.0389 | 0.0001 | ||
| VP3/A7465G I401V | Yes (0.0088) | −0.1053 ±0.0359 | 0.0261 | ||
| VP3/U7824C | Yes (0.1457) | 0.0997 ±0.0410 | 0.0411 | ||
| Egfrt1/t1 | 2 | 5’UTR/A198G | No | 0.1035 ±0.0363 | 0.0246 |
| RdRp/U4810C | Yes (0.1152) | −0.2635 ±0.0301 | 0.0128 | ||
| RdRp/C5713U | Yes (0.1148) | −0.3036 ±0.0276 | 0.0082 | ||
| VP2/G6379A A39T | Yes (0.0082) | 0.0630 ±0.0254 | 0.0381 | ||
| VP3/U7824C | Yes (0.1457) | −0.1090 ±0.0402 | 0.0421 | ||
| VP3/G8090A R609H | Yes (0.0200) | 0.0764 ±0.0289 | 0.0333 | ||
| VP1/U8250G H662Q | Yes (0.0201) | 0.1734 ±0.0326 | 0.0060 |