Table 3.
LRT Statistics for Models of Variable Selective Pressure along Branches and Branch-Site Tests
| Gene | Model | −2Δln L | Degrees of Freedom | P Value (Bonferroni Corrected P Value) |
|---|---|---|---|---|
| ALB, region 1 | M0 versus M1 | 418.74 | 105 | 4.71 × 10−39 (9.42 × 10−39) |
| ALB, region 2 | M0 versus M1 | 194.21 | 105 | 2.77 × 10−7 (5.54 × 10−7) |
| Single branch analysis | |||||
|---|---|---|---|---|---|
| Gene | Foreground Branch (MA versus MA1) | −2Δln L | Degrees of Freedom | P value (FDR Corrected P Value) | MEME-BEB Sites |
| ALB, region 1 | |||||
| Laurasiatheria | 5.27 | 1 | 2.16 × 10−2 (2.45 × 10−2) | — | |
| Cetartiodactyla | 5.06 | 1 | 2.45 × 10−2 (2.45 × 10−2) | — | |
| Pteropodidae | 5.88 | 1 | 1.53 × 10−2 (2.29 × 10−2) | — | |
| Lemuriformes | 14.66 | 1 | 1.29 × 10−4 (7.74 × 10−4) | E316, S513 | |
| Squirrel | 5.96 | 1 | 1.46 × 10−2 (1.75 × 10−2) | P142 | |
| Rhinoceros | 9.74 | 1 | 1.80 × 10−3 (2.94 × 10−3) | — | |
| ALB, region 2 | |||||
| Manatee | 12.19 | 1 | 4.81 × 10−4 (1.44 × 10−3) | K588 | |
| Black flying fox | 9.59 | 1 | 1.96 × 10−3 (2.94 × 10−3) | — | |
Note.—M0 and M1 are free-ratio models that assume all branches to have the same ω (M0) or allow each branch to have its own ω (M1). MA and MA1 are branch-site models that assume four classes of sites: The MA model allows a proportion of codons to have ω ≥ 1 on the foreground branches, whereas the MA1 model does not. 2Δln L is twice the difference of the natural logs of the maximum likelihood of the models being compared.