Extended Data Table 4. Episodic selection estimated across sites along internal branches of the phylogeny.
A branch-site evolutionary model provided a statistical framework to search for evidence of episodic selection on internal branches in the tree. The ω distribution is given for both internal and external branches.
| Subject ID | Gene | Branch-site ω distribution (internal branches) | Branch-site ω distribution (terminal branches) | P-value for episodic diversifying selection on internal branches |
|---|---|---|---|---|
| JS1774 | gag |
ω1 = 0.09 (81%) ω2 = 0.35 (5%) ω3 = 1.00 (14%) |
ω1 = 0.09 (69%) ω2 = 0.15 (14%) ω3 = 0.32 (17%) |
1.0 |
| JS1774 | pol (PR) |
ω1 = 0.03 (95%) ω2 = 0.07 (3%) ω3 = 1.00 (2%) |
ω1 = 0.09 (99.9%) ω2 = ∞ (0.1%) |
1.0 |
| JS1774 | pol (RT) |
ω1 = 0.11 (89%) ω2 = 0.35 (11%) |
ω1 = 0.16 (71%) ω2 = 0.22 (29%) |
1.0 |
| SM1727 | gag |
ω1 = 0.16 (91%) ω2 = 0.36 (9%) |
ω1 = 0.00 (87%) ω2 = 5.00 (13%) |
1.0 |
| SM1727 | pol (PR) |
ω1 = 0.05 (94%) ω2 = 0.24 (2%) ω3 = 1.00 (4%) |
ω1 = 0.09 (60%) ω2 = 0.21 (13%) ω3 = 0.25 (27%) |
1.0 |
| SM1727 | pol (RT) |
ω1 = 0.09 (87%) ω2 = 0.51 (2%) ω3 = 1.00 (11%) |
ω1 = 0.13 (99.6%) ω2 = ∞ (0.4%) |
1.0 |
| TM1679 | gag |
ω1 = 0.15 (63%) ω2 = 1.19 (37%) |
ω1 = 0.68 (100%) | 1.0 |
| TM1679 | pol (PR) |
ω1 = 0.14 (82%) ω2 = 0.54 (0.5%) ω3 = 1.00 (17%) |
ω1 = 0.19 (97%) ω2 = 0.15 (2.8%) ω3 = ∞ (0.4%) |
1.0 |
| TM1679 | pol (RT) |
ω1 = 0.19 (94.8%) ω2 = 0.93 (4.9%) ω3 = ∞ (0.3%) |
ω1 = 0.31 (100%) | 10−6 |