TABLE 4.
ML and MCMC estimates of evolutionary rates for two FIVpco genes within naturally infected cougarsa
| Animal | Interval (yr) (no. of samples)b,c | Maximum time since infection (yr)d | Gene | No. of sequences | ML
|
MCMC
|
||
|---|---|---|---|---|---|---|---|---|
| Rate of change (%/site/10 yr) | Tree age (yr)c | Rate of change (%/site/10 yr) | Tree age (yr)c | |||||
| SR600 | 4.1 (3) | 7 | env | 23 | 0.95 (0.00-1.37) | 6.9 (6.1-NEe) | 1.19 (0.34-2.20) | 9.4 (4.9-15.5) |
| pol | 21 | 0.39 (0.00-1.11) | 11.6 (5.4-NE) | 1.38 (0.32-2.58) | 7.3 (4.2-12.5) | |||
| SR617 | 2.9 (2) | 7 | env | 17 | 0.65 (0.00-1.43) | 6.0 (4.1-NE) | 1.27 (0.29-2.51) | 7.7 (3.7-14.0) |
| pol | 25 | 0.50 (0.00-1.09) | 10.6(5.7-NE) | 1.07 (0.30-2.00) | 9.3 (3.9-17.4) | |||
| SR618 | 1.6 (2) | 8 | env | 19 | 2.30 (0.04-3.78) | 1.9 (1.9-52.6) | 1.67 (0.30-3.56) | 6.0 (2.0-13.8) |
| pol | 24 | 0.72 (0.00-1.30) | 4.6 (3.3-NE) | 1.03 (0.18-2.20) | 7.9 (2.3-12.5) | |||
| SR620 | 2.3 (3) | 3 | env | 22 | 3.88 (1.70-6.30) | 2.5 (2.4-3.0) | 3.89 (1.72-6.27) | 3.1 (2.5-4.2) |
| pol | 28 | 2.35 (0.08-3.85) | 8.3 (6.0-192.2) | 5.87 (2.47-9.48) | 5.74 (3.5-8.3) | |||
| SR623 | 1.3 (3) | 2 | env | 28 | 2.57 (0.52-4.07) | 2.2 (1.9-6.3) | 2.48 (0.64-5.63) | 5.4 (1.6-10.0) |
| pol | 23 | 0.52 (0.00-1.25) | 5.9 (2.9-NE) | 6.21 (1.66-11.84) | 1.9 (1.3-2.4) | |||
| SR626 | 0.8 (2) | 4 | env | 23 | 1.54 (0.00-2.47) | 2.1 (1.7-NE) | 3.47 (0.56-3.14) | 2.7 (1.1-5.4) |
| pol | 29 | 1.46 (0.00-2.26) | 1.8 (1.7-NE) | 2.83 (0.36-6.36) | 2.9 (1.0-6.1) | |||
| SR627 | 1.0 (2) | 5 | env | 17 | 0.06 (0.00-1.70) | 88.4 (4.1-NE) | 3.00 (0.73-6.07) | 4.2 (1.6-7.9) |
| pol | 23 | 1.84 (0.00-3.75) | 2.5 (1.6-NE) | 1.85 (0.28-4.06) | 5.4 (1.5-11.9) | |||
| SR630 | 0.7 (2) | 1 | env | 16 | 0.66 (0.00-2.61) | 4.3 (1.3-NE) | 3.03 (0.50-6.82) | 1.7 (0.8-3.1) |
| pol | 18 | 2.28 (0.00-6.02) | 1.5 (1.0-NE) | 4.75 (0.61-10.27) | 1.6 (0.8-2.8) | |||
| SR631 | 2.5 (2) | 6 | env | 11 | 0.13 (0.00-1.14) | 33.0 (4.6-NE) | 1.08 (0.17-2.24) | 7.3 (3.2-14.6) |
| pol | 14 | 1.35 (0.51-2.31) | 2.8 (2.6-5.1) | 1.22 (0.17-3.07) | 9.4 (2.7-21.0) | |||
a
Based on sequential samples (2 or 3 serial samples per individual) collected 9 to 49 months apart. Shown are means with 95% CIs in parentheses.
b
Time from earliest to latest sample.
c
Decimals represent fractions of a year.
d
Based on estimated age of animal or known time of seroconversion.
e
NE, upper boundary not estimable.