Table 1.
Analysis of dN/dS ratios (ω) for branches of the tree in Figure 2A, with bolded values indicating positive selection (ω > 1).
| PAML Analysis | |||||||
|---|---|---|---|---|---|---|---|
| Branch Model | Branch-Site Model | ||||||
| Branch | ω Branch | ω2 (positive sites) | ω1 (purifying sites) | Fraction Sites under Positive Selection (ω>1) | Fraction Sites under Purifying Selection (ω<1) | LRT statistic (2 lnL)a | Significant Positively Selected Amino Acids (posterior probability) |
| A | 0.548 | 1.73 | 0.029 | 0.363 | 0.628 | 0.904 | 1 M (0.997) 14 N (0.997) 36 R (0.966) 107 R (0.999) 167 E (0.998) 266 W (0.998) |
| B | 0.827 | 70.60 | 0.043 | 0.021 | 0.971 | 0.854 | – |
| C | 0.173 | 3.27 | 0.041 | 0.057 | 0.933 | 1.154 | 130 E (0.988) |
| D | 0.048**** | 13.28 | 0.043 | 0.010 | 0.979 | 3.780 | 41 A (0.984) |
| E | 0.103 | 999.00 (dS =0) | 0.042 | 0.020 | 0.968 | 13.807** | – |
| F | 0.097**** | 1.21 | 0.039 | 0.098 | 0.890 | 0.035 | – |
| G | 0.128* | 4.53 | 0.042 | 0.060 | 0.928 | 0.707 | 1 M (0.974) 43 C (0.983) 171 R (0.980) 182 V (0953) |
| H | 0.066 | 1.00 | 0.044 | 0.000 | 0.988 | 0.000 | – |
| I | 0.053**** | 4.91 | 0.041 | 0.045 | 0.942 | 5.298 | 97 R (0.978) |
| aBSREL Analysis (Branch-Site Model) | |||||||
| Branch | – | ω2 (positive sites) | ω1 (purifying sites) | Fraction of Sites under Positive Selection | – | p-value | Significant after multiple hypothesis testing? |
| A | – | 3.03 | 0.249 | 0.250 | 0.1356 | no | |
| E | – | 15.2 | 0.00 | .024 | 0.0293 | no | |
| G | – | 2000 | 0.147 | 0.058 | – | 0.0045 | yes |
*
= p <0.05,
**
= p < 0.01,
****
= p <10−4, corrected for multiple hypothesis testing.
a
LRT, Likelihood Ratio Test statistic, used in χ2. Critical values are 3.84 (5%) and 6.63 (1%).