Table 1.
Summary of CodeML-Positive Selection Analysis on TRIF-Related Immune Response Genes
| Gene Name | Type of Positive Selection Predicteda | Sitesb | P Value of Positively Selected Sitesc |
|---|---|---|---|
| TRIF | Lineage specific, mouse | 18, 218, 270, 318, 338, 360, 375, 387, 388, 512, 603 | 11 > 0.50, 3 > 0.90, 0 > 0.99 |
| Site specific | 180, 332, 362, 369, 406, 424, 425, 465, 479, 496 | 10 > 0.50, 4 > 0.90, 0 > 0.99 | |
| TLR3 | Lineage specific, mouse | 266, 297, 603 | 3 > 0.50, 0 > 0.90, 0 > 0.99 |
| IRF3 | Lineage specific, mouse | 96, 140, 152, 229 | 4 > 0.50, 2 > 0.90, 0 > 0.99 |
| p38-β/MAPK11 | Site specific | 16 | 1 > 0.50, 1 > 0.90, 1 > 0.99 |
| TNFα | Site specific | 16, 71, 74, 75, 163, 164, 173, 184, 186, 194, 249 | 11 > 0.50, 5 > 0.90, 2 > 0.99 |
| IL-1B | Site specific | 109, 143, 245, 246, 247, 252, 281, 284, 285, 289, 291, 308, 332, 360, 400, 445, 456 | 17 > 0.50, 2 > 0.90, 0 > 0.99 |
| IL-6 | Site specific | 102, 128, 149, 156, 164, 166, 173, 176, 187, 231, 250, 254, 255, 258, 259, 262, 273, 286, 287, 288, 289, 292, 298, 299, 320, 324, 328, 333, 335 | 29 > 0.50, 4 > 0.90, 0 > 0.99 |
| IL-12A | Site specific | 21, 110, 152, 178, 190, 277, 281, 327 | 8 > 0.50, 2 > 0.90, 0 > 0.99 |
| INF β1 | Site specific | 25, 26, 28, 36, 37, 43, 48, 50, 52, 78, 82, 90, 111, 114, 119, 122,135, 137, 138, 140, 145, 153, 156, 157, 173, 188, 191 | 27 > 0.50, 8 > 0.90, 1 > 0.99 |
a
For site-specific selection, results are based on model M8 alone (reporting BEB sites).
b
For genes under site-specific selection, site numbers refer to position in the multiple sequence alignment used for CodeML analysis. For lineage-specific selection, site number (in red) refers to the amino acid position in lineage/species where selection has been detected.
c
The associated posterior probability is indicated through formating: underlined >0.90, in bold >0.99, and no formatting implies 0.50 < PP < 0.90.