Table 2.
Positive selection in coding regions.
| LRT and parameters | prfA | plcA | hly | mpl | actA | plcB |
|---|---|---|---|---|---|---|
| M0 vs M3 LRTa | 6.5852 | 52.3129* | 5.0478 | 18.3828* | 153.0975* | 0.0 |
| ωb | 1.20 | 2.12 | 0.61 | 1.05 | 2.39 | 0.105 |
| pc | 0.0169 | 0.0696 | 0.0347 | 0.0917 | 0.0978 | 0.3034 |
| M1a vs M2a LRTa | 0.02886 | 5.2502 | 0.0 | 0.0019 | 12.3971* | 0.0005 |
| ωb | 1.20 | 2.12 | 1.00 | 1.04 | 2.55 | 1.00 |
| pc | 0.0169 | 0.0696 | 0.0109 | 0.0917 | 0.0771 | 0.00 |
| aa sites under pos. selectiond | - | - | - | - | 461 (97%) | - |
| M7 vs M8 LRTa | 2.1510 | 5.2529 | 0.7376 | 0.0097 | 13.7596* | 0.0 |
| ωb | 1.20 | 2.12 | 1.00 | 1.07 | 2.40 | 1.00 |
| pc | 0.0169 | 0.0696 | 0.0175 | 0.0882 | 0.0955 | 0.00 |
| aa sites under pos. selectiond | - | aa 119 | - | - | aa 112 (97%) | - |
| (95%) | aa 123 (96%) | |||||
| aa 291 (97%) | ||||||
| aa 449 (97%) | ||||||
| aa 461 (99%) | ||||||
| aa 522 (95%) | ||||||
| Lineage I LRTa | NAe | 0.0 | 0.0 | 6.2440* | 1.4834 | 0.0 |
| ωb | NAe | 1.00 | 1.00 | 7.28 | 6.77 | 1.00 |
| pc | NAe | 0.00 | 0.0056 | 0.0151 | 0.174 | 0.00 |
| aa sites under pos. selectiond | NAe | - | - | aa 103 | - | - |
| (98%) | ||||||
| Lineage II LRTa | 0.0 | 4.6409* | 1.1946 | 0.0001 | 5.0142* | 0.0 |
| ωb | 1.00 | 2.82 | 3.95 | 1.00 | 3.59 | 1.00 |
| pc | 0.00 | 0.0381 | 0.0044 | 0.0802 | 0.0245 | 0.2064 |
| aa sites under pos. selectiond | - | - | - | - | - | - |
This row reports the results for the likelihood ratio test (LRT) for different models (e.g., M0 versus M3; lineage specific tests are indicated as “Lineage I LRT” and “Lineage II LRT”); the value shown represents the likelihood ratio between the two models;
a indicates that the null model can be rejected in favor to the alternative model (P < 0.05; significance is calculated using a χ2-distribution with degrees of freedom equals the difference in the number of parameters estimated for the alternative model in comparison to the null model
ω = dN/dS for the site category that allows ω to be larger than 1 (i.e., ω2 in M2, M3, and the branch specific models; ω in M8)
p = the proportion of sites under positive selection
aa site identified by Bayes Empirical Bayes (BEB) as having probability > 95% of being under positive selection are shown; posterior probabilities are given in parenthesis; “−“ indicates that no sites showed probability ≥ 95% of having evolved by positive selection
NA, not assessed because no amino acid changes were observed within lineage I in prfA