Table 1.
PAML Branch-Specific Models.
| Model | NP | ML | NJ | Reconstructed |
|---|---|---|---|---|
| One-ratio (R1) | 1 | ωCenH3-1 = 0.283 | ωCenH3-1 = 0.290 | ωCenH3-1 = 0.285 |
| ωCenH3-2 = ωCenH3-1 | ωCenH3-2 = ωCenH3-1 | ωCenH3-2 = ωCenH3-1 | ||
| ωCenH3-out = ωCenH3-1 | ωCenH3-out = ωCenH3-1 | ωCenH3-out = ωCenH3-1 | ||
| ln L =−3011.832 | ln L = −3025.45 | ln L = −3089.698 | ||
| Two-ratios (R2) | 2 | ωCenH3-1 = 0.328 | ωCenH3-1 = 0.337 | ωCenH3-1 = 0.335 |
| ωCenH3-2 = 0.227 | ωCenH3-2 = 0.231 | ωCenH3-2 = 0.224 | ||
| ωCenH3-out = ωCenH3-1 | ωCenH3-out = ωCenH3-1 | ωCenH3-out = ωCenH3-1 | ||
| ln L =−3010.042 | ln L = −3023.51 | ln L = −3087.444 | ||
| 2ΔlR2:R1 = 3.579 | 2ΔlR2:R1 = 3.872 | 2ΔlR2:R1 = 4.509 | ||
| P = 0.059 | P = 0.0491 | P = 0.034 | ||
| Three-ratios (R3) | 3 | ωCenH3-1 = 0.321 | ωCenH3-1 = 0.339 | ωCenH3-1 = 0.330 |
| ωCenH3-2 = 0.227 | ωCenH3-2 = 0.231 | ωCenH3-2 = 0.224 | ||
| ωCenH3-out = 0.331 | ωCenH3-out = 0.337 | ωCenH3-out = 0.339 | ||
| ln L =−3010.034 | ln L = −3023.51 | ln L = −3087.438 | ||
| 2ΔlR3:R2 = 0.015 | 2Δl R3:R2 = 0.001 | 2Δl R3:R2 = 0.01 | ||
| P = 0.902 | P = 0.982 | P = 0.915 |
Note.—The ω values were estimated separately for all branches preceding the CenH3 duplication event (CenH3-out) and for both CenH3-1 and CenH3-2 branches following the duplication event. The analysis was performed using three phylogenetic trees that differed partially in topology (see fig. 6B–D). Below the ω estimates are logarithm likelihood values (ln L) and results of LRT (2Δl) with P-values (P) for comparing model R2 with R1 and R3 with R2. Note that the R2 model provided a significantly better fit (P < 0.05) of the data than the R1 model for two trees (marked in underline), indicating stronger purifying selection at the CenH3-2 branch. The R3 model did not provide better fit of the data than R2, suggesting that there is no significant difference between the CenH3-1 and CenH3-out branches. NP is the number of freely estimated ω ratios.