Table 1. Positively selected sites detected by SLAC, FEL, REL and/or IFEL in HIV-1 and HIV-2 env C2, V3 and C3 regions1.
| HIV-1 | HIV-2 | ||||||||||||||||||
| Region | Codon | SLAC | FEL | REL | IFEL | Region | Codon | SLAC | FEL | REL | IFEL | ||||||||
| C2 | 283 | 0.249 | (0.083) | 0.017 | (0.027) | 0.282 | (0.950) | −0.007 | (0.237) | C2 | 267 | 1.805 | (<0.001) | 0.151 | (<0.001) | 1.007 | (1.000) | 0.147 | (0.004) |
| 291 | 0.252 | (0.096) | 0.011 | (0.334) | 0.005 | (0.277) | 0.008 | (0.648) | 270 | 1.561 | (0.003) | 0.171 | (<0.001) | 0.892 | (1.000) | 0.179 | (0.010) | ||
| 292 | 0.269 | (0.063) | 0.017 | (0.167) | 0.547 | (<0.001) | 0.014 | (0.419) | 295 | 1.049 | (0.051) | 0.134 | (0.095) | 0.070 | (0.910) | 0.109 | (0.316) | ||
| 293 | 0.401 | (0.066) | 0.024 | (0.230) | 0.924 | (0.972) | 0.063 | (0.050) | 300 | 0.787 | (0.210) | 0.130 | (0.077) | 0.714 | (<0.001) | 0.131 | (0.109) | ||
| V3 | 300 | 0.335 | (0.079) | 0.022 | (0.022) | 0.219 | (0.846) | 0.016 | (0.093) | V3 | 331 | −0.312 | (0.859) | 0.020 | (0.591) | 0.193 | (0.987) | 0.069 | (0.390) |
| 306 | 0.312 | (0.106) | 0.014 | (0.541) | 0.947 | (0.984) | −0.004 | (0.867) | |||||||||||
| 308 | 0.619 | (0.008) | 0.046 | (0.065) | 0.869 | (0.973) | 0.094 | (0.012) | |||||||||||
| 314 | 0.314 | (0.052) | 0.014 | (0.291) | 0.163 | (0.178) | −0.001 | (0.971) | |||||||||||
| 317 | 0.301 | (0.057) | 0.011 | (0.401) | 0.192 | (0.140) | 0.005 | (0.749) | |||||||||||
| C3 | 332 | 0.124 | (0.267) | 0.009 | (0.341) | −0.432 | (<0.001) | 0.031 | (0.093) | C3 | 346 | 0.478 | (0.236) | 0.051 | (0.173) | 1.008 | (1.000) | 0.050 | (0.397) |
| 334 | 0.543 | (0.004) | 0.041 | (0.027) | 1.142 | (0.997) | 0.065 | (0.024) | 351 | 0.207 | (0.298) | 0.018 | (0.087) | 0.114 | (<0.001) | 0.000 | (1.000) | ||
| 335 | 0.458 | (0.010) | 0.025 | (0.109) | 0.893 | (0.936) | 0.035 | (0.147) | 354 | 0.689 | (0.047) | 0.067 | (0.016) | 0.988 | (1.000) | 0.000 | (1.000) | ||
| 336 | 0.452 | (0.058) | 0.019 | (0.583) | 0.817 | (0.907) | 0.011 | (0.743) | 361 | 0.887 | (0.035) | 0.093 | (0.011) | 0.988 | (1.000) | 0.016 | (0.693) | ||
| 343 | 0.405 | (0.060) | 0.022 | (0.109) | 0.885 | (0.989) | 0.017 | (0.370) | 364 | −0.085 | (0.704) | 0.014 | (0.690) | 0.130 | (0.983) | −0.069 | (0.072) | ||
| 345 | 0.392 | (0.024) | 0.016 | (0.330) | 0.492 | (0.657) | 0.070 | (0.018) | 365 | 1.074 | (0.089) | 0.175 | (0.070) | 0.463 | (0.561) | −0.056 | (0.626) | ||
| 346 | 1.080 | (<0.001) | 0.128 | (<0.001) | 0.945 | (0.982) | 0.281 | (<0.001) | 378 | 0.415 | (0.088) | 0.030 | (0.043) | 0.116 | (<0.001) | 0.029 | (0.119) | ||
| 348 | 0.270 | (0.096) | 0.011 | (0.664) | 1.183 | (<0.001) | −0.005 | (0.899) | |||||||||||
| 353 | 0.319 | (0.143) | 0.018 | (0.476) | −0.118 | (0.347) | 0.120 | (0.035) | |||||||||||
| 359 | 0.558 | (0.022) | 0.117 | (<0.001) | 0.882 | (1.000) | 0.214 | (0.001) | |||||||||||
| 363 | 0.169 | (0.295) | 0.017 | (0.279) | 0.860 | (0.995) | 0.003 | (0.900) | |||||||||||
| 378 | 0.244 | (0.021) | 0.014 | (0.020) | 0.217 | (<0.001) | 0.000 | (1.000) | |||||||||||
PT dataset.
Codon – codons selected under 10% level of significance (SLAC, FEL and IFEL) or above a Bayes Factor of 50 (REL) and numbered according to codon env position of HIV-1 HXB2 for HIV-1 dataset or of HIV-2 ALI for HIV-2 dataset. Codons selected simultaneously by SLAC, FEL and REL methods are bold and underlined.
SLAC, FEL and IFEL – the first numbers are the dN-dS difference for each site scaled by the total codon tree length, the numbers in parenthesis show P-values for corresponding test of non-synonymous rate being superior to synonymous rate; REL - the first numbers are the expected posterior dN-dS difference for each site scaled to the total codon tree length, the number in parenthesis show the posterior probability of non-synonymous rate being superior to synonymous rate; Bold dN-dS differences correspond to significant P-values or posterior probabilities.