Appendix 1—table 10. Coordinated episodic selection in concordantly evolving pairs predicted for the phylogeny reconstructed by IQ-TREE.
Z-scores < 0 and upper p-values after Benjamini-Hochberg adjustment < 0.05 indicate clustering of nonconsecutive mutations; z-scores > 0 and lower p-values after Benjamini-Hochberg adjustment < 0.05 indicate that nonconsecutive mutations tend to avoid each other. For site pairs with z-scores > 0, concordant evolution cannot be explained without positive epistatic interaction between the sites.
| site 1 | site 2 | #nonseq. pairs | zscore | lower pvalue | upper pvalue | lower pvalue adj. | upper pvalue adj. |
|---|---|---|---|---|---|---|---|
| 13 | 152 | 2569 | –0,724 | 0,7675 | 0,2325 | 1 | 0,5813 |
| 18 | 20 | 8610,5 | 1,148 | 0,1225 | 0,8775 | 0,3675 | 1 |
| 20 | 26 | 5719 | 2,444 | 0,0175 | 0,9825 | 0,1125 | 1 |
| 20 | 417 | 2533 | 1,738 | 0,04 | 0,96 | 0,2 | 1 |
| 26 | 190 | 3682 | 2,258 | 0,015 | 0,985 | 0,1125 | 1 |
| 63 | 64 | 124 | 1,736 | 0,06 | 0,94 | 0,2455 | 1 |
| 63 | 67 | 264 | 1,68 | 0,075 | 0,925 | 0,2596 | 1 |
| 63 | 69 | 239 | 2,224 | 0,025 | 0,975 | 0,1406 | 1 |
| 63 | 213 | 94 | 1,407 | 0,0825 | 0,9175 | 0,2652 | 1 |
| 64 | 67 | 1324 | 2,353 | 0,0125 | 0,9875 | 0,1125 | 1 |
| 64 | 69 | 1199 | 2,766 | 0,0025 | 0,9975 | 0,0281 | 1 |
| 67 | 69 | 2542 | 4,104 | 0 | 1 | 0,0281 | 1 |
| 69 | 70 | 2014 | 4,041 | 0 | 1 | 0,0281 | 1 |
| 70 | 144 | 627 | 2,952 | 0,0025 | 0,9975 | 0,0281 | 1 |
| 76 | 490 | 1748 | 0,632 | 0,25 | 0,75 | 0,5357 | 1 |
| 154 | 1071 | 502 | –1,357 | 0,925 | 0,075 | 1 | 0,225 |
| 155 | 157 | 482 | 0,671 | 0,2375 | 0,7625 | 0,5344 | 1 |
| 189 | 356 | 108 | –0,187 | 0,555 | 0,445 | 0,999 | 0,9536 |
| 189 | 360 | 58 | 0,927 | 0,17 | 0,83 | 0,4765 | 1 |
| 190 | 417 | 1631 | 0,099 | 0,445 | 0,555 | 0,8344 | 1 |
| 213 | 261 | 778 | –1,251 | 0,905 | 0,095 | 1 | 0,2672 |
| 259 | 261 | 736,5 | –2,384 | 0,9975 | 0,0025 | 1 | 0,0094 |
| 262 | 272 | 744 | 0,085 | 0,44 | 0,56 | 0,8344 | 1 |
| 356 | 357 | 65 | –0,797 | 0,7525 | 0,2475 | 1 | 0,5862 |
| 356 | 360 | 63,5 | –2,704 | 1 | 0,0025 | 1 | 0,0094 |
| 359 | 360 | 64,5 | –0,39 | 0,6275 | 0,3725 | 1 | 0,8381 |
| 439 | 441 | 1196 | –3,989 | 1 | 0,0025 | 1 | 0,0094 |
| 440 | 441 | 1647 | –3,55 | 1 | 0,0025 | 1 | 0,0094 |
| 440 | 442 | 822 | –3,23 | 1 | 0,0025 | 1 | 0,0094 |
| 440 | 443 | 931 | –2,124 | 0,995 | 0,005 | 1 | 0,0173 |
| 440 | 444 | 1591,5 | –3,511 | 1 | 0,0025 | 1 | 0,0094 |
| 441 | 442 | 446 | –5,063 | 1 | 0,0025 | 1 | 0,0094 |
| 441 | 443 | 505 | –4,26 | 1 | 0,0025 | 1 | 0,0094 |
| 441 | 444 | 864,5 | –5,337 | 1 | 0,0025 | 1 | 0,0094 |
| 442 | 443 | 251 | –3,988 | 1 | 0,0025 | 1 | 0,0094 |
| 442 | 444 | 429 | –4,727 | 1 | 0,0025 | 1 | 0,0094 |
| 443 | 444 | 491 | –3,972 | 1 | 0,0025 | 1 | 0,0094 |
| 484 | 655 | 18792 | 1,038 | 0,18 | 0,82 | 0,4765 | 1 |
| 501 | 1118 | 16121 | 1,443 | 0,07 | 0,93 | 0,2596 | 1 |
| 681 | 716 | 19375,5 | –0,962 | 0,8325 | 0,1675 | 1 | 0,4434 |
| 716 | 982 | 8267 | 0,58 | 0,3075 | 0,6925 | 0,629 | 1 |
| 716 | 1118 | 9986 | 1,65 | 0,05 | 0,95 | 0,225 | 1 |
| 859 | 950 | 3684,5 | 0,747 | 0,2075 | 0,7925 | 0,5188 | 1 |
| 982 | 1118 | 8103 | 0,757 | 0,2325 | 0,7675 | 0,5344 | 1 |
| 1258 | 1259 | 1053 | –1,435 | 0,9375 | 0,0625 | 1 | 0,2009 |