Table 1 Evolutionary rate analyses of S6PDH, SDH and SOT gene families using branch-specific model of PAML
Gene | Model | ω setting | -ln L | Estimated parameters | Likelihood ratio test |
|---|---|---|---|---|---|
S6PDH | One-ratio | Entire tree: ω0 | 6724.98 | ω0 = 0.164 |  |
Two-ratio | branch A & B: ω1 | 6718.04 | ω1 = 0.515 | two-ratio vs. one-ratio: P < 0.01 | |
|  | other branches: ω0 |  | ω0 = 0.148 |  | |
Three-ratio | Branch A: ω1 | 6714.01 | ω1 = 0.043 | Three-ratio vs. one-ratio: P < 0.01 | |
|  | Branch B: ω2 |  | ω2 = 0.629 |  | |
|  | Other branches: ω0 |  | ω0 = 0.152 |  | |
SDH | One-ratio | Entire tree: ω0 | 9280.82 | ω0 = 0.104 |  |
Two-ratio | branch A: ω1 | 9278.32 | ω1 = 0.211 | two-ratio vs. one-ratio: P = 0.03 | |
|  | other branches: ω0 |  | ω0 = 0.101 |  | |
SOT | One-ratio | Entire tree: ω0 | 28,847.56 | ω0 = 0.192 |  |
two-ratio | branch A&B&C: ω1 | 28,841.07 | ω1 = 0.412 | two-ratio vs. one-ratio: P < 0.01 | |
|  | other branches: ω0 |  | ω0 = 0.186 |  | |
Four-ratio | Branch A: ω1 | 28,840.62 | ω1 = 0.346 | Four-ratio vs. one-ratio: P < 0.01 | |
|  | Branch B: ω2 |  | ω2 = 0.374 |  | |
|  | Branch C: ω3 |  | ω3 = 0.581 |  | |
|  | Other branches: ω0 |  | ω0 = 0.186 |  |