Table 4. Rates of evolution tested using CODEML implemented in PAML.
| Gene | Assumptions | K (ts/tv rate ratio) | w (omega Dn/Ds) 0 | w (omega Dn/Ds)1 | Likelihood Ratio Test Statistic (if greater than 3.84 reject H0) H0 = equal rates |
|---|---|---|---|---|---|
| WGS | UCBSV and CBSV equal rates | 5.90944 | 0.06358 | ||
| UCBSV and CBSV different rates | 5.9598 | 0.05518 | 0.07622 | 26.29* | |
| P1 | UCBSV and CBSV equal rates | 5.07336 | 0.10394 | ||
| UCBSV and CBSV different rates | 5.05456 | 0.09047 | 0.12203 | 4.61* | |
| P3 | UCBSV and CBSV equal rates | 5.17197 | 0.08635 | ||
| UCBSV and CBSV different rates | 5.20559 | 0.0764 | 0.10198 | 2.22 | |
| 6K1 | UCBSV and CBSV equal rates | 19.54143 | 0.00969 | ||
| UCBSV and CBSV different rates | 19.69676 | 0.01527 | 0.00316 | 3.01 | |
| CI | UCBSV and CBSV equal rates | 9.9388 | 0.01722 | ||
| UCBSV and CBSV different rates | 8.06276 | 0.0155 | 0.01977 | 0.73 | |
| 6K2 | UCBSV and CBSV equal rates | 8.40649 | 0.04684 | ||
| UCBSV and CBSV different rates | 8.82738 | 0.02354 | 0.11057 | 6.74* | |
| VPg | UCBSV and CBSV equal rates | 5.852 | 0.05759 | ||
| UCBSV and CBSV different rates | 5.87009 | 0.054 | 0.06323 | 0.29 | |
| NIa | UCBSV and CBSV equal rates | 8.01105 | 0.02932 | ||
| UCBSV and CBSV different rates | 8.68283 | 0.01408 | 0.06719 | 29.95* | |
| NIb | UCBSV and CBSV equal rates | 6.07872 | 0.05329 | ||
| UCBSV and CBSV different rates | 6.14047 | 0.0452 | 0.06508 | 5.18* | |
| HAM1 | UCBSV and CBSV equal rates | 7.25177 | 0.16144 | ||
| UCBSV and CBSV different rates | 7.2343 | 0.17929 | 0.14007 | 2.23 | |
| CP | UCBSV and CBSV equal rates | 13.09297 | 0.06075 | ||
| UCBSV and CBSV different rates | 13.26752 | 0.05606 | 0.07155 | 1.29 | |
| faster rate UCBSV | faster rate CBSV | *Rates are different |
HO was CBSV and UCBSV have equal rates of evolution (one omega; model = 0), while H1 was that CBSV and UCBSV have different rates of evolution (two omegas; model = 2).