Table 3.
PAML Analysis of pre-gagV1 and gagV1 from Simian Primates.
| Gene | Codon Frequency | ω0 | M1–M2 |
M7–M8 |
Tree Lengtha | dN/dS (%) | Residuesb with dN/dS of >1 and pr of >0.95 | ||
|---|---|---|---|---|---|---|---|---|---|
| 2δ | P Value | 2δ | P Value | ||||||
| pre-gagV1 | f3 × 4 | 0.3 | 1.01 | 0.604 | 2.91 | 0.233 | 1.4524 | N.S. | N.S. |
| f3 × 4 | 1.7 | 1.01 | 0.604 | 2.91 | 0.233 | 1.4524 | N.S. | N.S. | |
|
gagV1
(Segment A) |
f3 × 4 | 0.3 | 13.1 | 0.0014 | 16.25 | 0.0003 | 1.6499 | 2.78 (11.5) | 9Q, 45K |
| f3 × 4 | 1.7 | 13.1 | 0.0014 | 16.25 | 0.0003 | 1.6499 | 2.78 (11.5) | 9Q, 45K | |
|
gagV1
(Segment B) |
f3 × 4 | 0.3 | 5.33 | 0.0694 | 8.412 | 0.0149 | 1.2764 | N.S. | N.S. |
| f3 × 4 | 1.7 | 5.25 | 0.0724 | 8.486 | 0.0143 | 1.2764 | N.S. | N.S. | |
Note.—ωo, the initial seed value of ω used; 2δ, two times the difference of the natural log values of the maximum likelihood from pairwise comparisons of the different models; pr, posterior probability.
a
Tree length is defined as the sum of the nucleotide substitutions per codon at each branch.
b
Residue numbers are based on the human pre-gagV1 and gagV1 sequences.