Table 1.
Genes with Data from At Least Three Bird Species that Were Identified as Targets of Positive Selection
| Gene Symbol | Number of Bird Species | χ2 | P value | Number (and identity) of Positively Selected Sites, from PAML | Number (and identity) of Positively Selected Sites, from HyPhy |
| BLB2 (MHCIIB) | 9 | 118.605 | <0.0001 | 10 (34–37, 81, 91, 94, 95, 97, 101) | 7 (36, 38, 39, 64, 83, 97, 104) |
| BF2 (MHCI) | 7 | 37.888 | <0.0001 | 6 (66, 79, 86, 124, 126, 165) | 4 (81, 103, 184, 366) |
| B-NK | 4 | 16.576 | 0.0003 | 3 (5, 6, 60) | 6 (83, 84, 85, 86, 98, 156) |
| IL1B | 8 | 16.666 | 0.0002 | 2 (47, 192) | 7 (50, 53, 60, 76, 77, 224, 255) |
| MX1 | 6 | 12.291 | 0.0021 | 3 (212, 388, 436) | 16 (20, 130, 230, 241, 265, 318, 345, 357, 406, 454, 486, 506, 537, 538, 539, 585) |
| IFNG | 6 | 6.974 | 0.0306 | 1 (111) | 2 (111, 159) |
| CD9 | 8 | 5.534 | 0.0629 | 0 | 8 (39, 92, 152, 169, 174, 179, 186) |
| B2M | 3 | 3.950 | 0.139 | 0 | 3 (37, 73, 113) |
| CD44 | 3 | 1.187 | 0.552 | 0 | 11 (127, 184, 242, 245, 268, 277, 282, 285, 292, 299, 393) |
| PIK3AP1 | 3 | 0.804 | 0.669 | 0 | 8 (55, 62, 81, 166, 508, 664, 752, 760) |
Codons with a posterior probability greater than 95% for being under positive selection (calculated in PAML and HyPhy) are indicated. For plots of codon-wise ω and posterior probability of positive selection across the length of these genes, see Additional figs. 1–10.