Table 1. Concordantly evolving sites of the SARS-CoV-2 S-protein with FDR less than 10% for both reconstructed phylogenies (see Text).
The following characteristics are shown: coordinates on the S-protein sequence, nominal p-values, the value of the epistatic statistics, the total number of consecutive mutation pairs for the two corresponding ordered site pairs, numbers of mutations in consecutive pairs at sites 1 and 2, total numbers of mutations at sites 1 and 2, and the distance in the protein structure (PDB ID: 7JJJ). Pairs of sites where non-consecutive mutations are further from each other than expected (suggesting both epistatic and episodic selection; p-value <0.05 after adjustment) are indicated in bold; pairs of sites where they are closer to each other than expected (suggesting episodic rather than epistatic selection) are indicated in italic (see Appendix 1—tables 10 and 12). Physical distance could not be calculated for site pairs (13,152) and (681,716) because sites 13 and 681 were absent in 7JJJ.
| site 1 | site 2 | cluster | p-value | epistatic statistics | #consec.pairs of mutations | #mutations in consec. pairs at site 1 | #mutations in consec. pairs at site 2 | #mutations at site 1 | #mutations at site2 | physical distance, Å |
|---|---|---|---|---|---|---|---|---|---|---|
| 13 | 152 | <2e-5 | 2.864 | 5 | 5 | 4 | 5 | 16 | - | |
| 20 | 417 | 4 | 2.2e-4 | 1.348 | 4 | 3 | 2 | 8 | 7 | 47.83 |
| 26 | 190 | 4 | 1.8e-4 | 1.029 | 4 | 4 | 3 | 12 | 3 | 18.4 |
| 63 | 213 | 3 | 4e-5 | 0.681 | 1 | 1 | 1 | 2 | 3 | 13.51 |
| 69 | 70 | 3 | <2e-5 | 1.125 | 2 | 2 | 2 | 5 | 4 | 1.3 |
| 70 | 144 | 3 | <2e-5 | 1.301 | 3 | 3 | 3 | 4 | 5 | 14.03 |
| 76 | 490 | 2.6e-4 | 0.22 | 1 | 1 | 1 | 3 | 3 | 45.18 | |
| 189 | 360 | 2 | 1.6e-4 | 0.544 | 2 | 1 | 2 | 3 | 3 | 29.89 |
| 190 | 417 | 4 | 0.0001 | 1.272 | 3 | 2 | 2 | 3 | 7 | 39.93 |
| 259 | 261 | 3 | <2e-5 | 1.35 | 1.5 | 2 | 1 | 4 | 2 | 3.81 |
| 356 | 360 | 2 | <2e-5 | 1.283 | 2.5 | 2 | 3 | 2 | 3 | 10.12 |
| 359 | 360 | 2 | <2e-5 | 0.976 | 1.5 | 1 | 2 | 2 | 3 | 1.34 |
| 439 | 441 | 1 | <2e-5 | 2.097 | 4 | 3 | 4 | 9 | 8 | 3.5 |
| 440 | 441 | 1 | 1.4e-4 | 1.505 | 3 | 3 | 3 | 12 | 8 | 1.33 |
| 440 | 442 | 1 | <2e-5 | 2.476 | 3 | 2 | 3 | 12 | 6 | 3.92 |
| 440 | 444 | 1 | <2e-5 | 2.515 | 3.5 | 2 | 5 | 12 | 7 | 5.6 |
| 441 | 442 | 1 | <2e-5 | 2.244 | 4 | 4 | 4 | 8 | 6 | 1.33 |
| 441 | 443 | 1 | 2e-5 | 1.281 | 5 | 4 | 2 | 8 | 2 | 3.23 |
| 441 | 444 | 1 | <2e-5 | 3.492 | 5.5 | 4 | 4 | 8 | 7 | 2.6 |
| 442 | 443 | 1 | 6e-5 | 1.301 | 4 | 4 | 2 | 6 | 2 | 1.32 |
| 442 | 444 | 1 | <2e-5 | 3.013 | 6 | 4 | 4 | 6 | 7 | 4.05 |
| 443 | 444 | 1 | 8e-5 | 1.043 | 2 | 2 | 2 | 2 | 7 | 1.32 |
| 501 | 1118 | 5 | 1.4e-4 | 2.737 | 16 | 13 | 12 | 40 | 22 | 131.71 |
| 681 | 716 | 5 | <2e-5 | 3.905 | 16.5 | 12 | 16 | 59 | 21 | - |
| 716 | 982 | 5 | 2e-5 | 2.001 | 15 | 9 | 11 | 21 | 15 | 81.66 |
| 716 | 1118 | 5 | 4e-5 | 2.382 | 13 | 8 | 12 | 21 | 22 | 22.29 |
| 859 | 950 | <2e-5 | 2.219 | 5.5 | 4 | 5 | 11 | 9 | 15.17 | |
| 982 | 1118 | 5 | 1.4e-4 | 1.637 | 15 | 11 | 8 | 15 | 22 | 94.63 |