Table 2 Molecular evolutionary analysis of APMAP, CD166, and thyroglobulin
From: The acquisition of novel N-glycosylation sites in conserved proteins during human evolution
Protein |  | Model | ln L | ω | 2Δl | P value | Positively selected sites a |
|---|---|---|---|---|---|---|---|
APMAP | Branch models | M0 (one ratio) | −2042.0968 | ω0 = 0.07385 |  |  |  |
|  |  | Free ratio | −2035.7572 | See Additional file 4 | (M0 vs Free ratio) 12.6792 | 0.1234 |  |
|  |  | Two ratio | −2038.4530 | ω0 = 0.05733, ω1 = 999.000 | (M0 vs Two ratio) 7.2876 | 0.006943** |  |
|  | Branch-site models | Model A | −2038.4530 | ω0 = 0.05732, ω1 = 1, ω2 = 999.000 |  |  | Val-100, Asn-196 |
|  |  | Null model A | −2039.0253 | ω0 = 0.05746, ω1 = 1, ω2 = 1 | (Model A vs Null model A) 1.1446 | 0.2847 |  |
CD166 | Branch models | M0 (one ratio) | −2713.8934 | ω0 = 0.09913 |  |  |  |
|  |  | Free ratio | −2709.9951 | See Additional file 5 | (M0 vs Free ratio) 7.7966 | 0.4536 |  |
|  |  | Two ratio | −2713.8904 | ω0 = 0.09991, ω1 = 0.09134 | (M0 vs Two ratio) 0.0060 | 0.9383 |  |
|  | Branch-site models | Model A | −2713.8934 | ω0 = 0.09913, ω1 = 1, ω2 = 1 |  |  | Asn-91 |
|  |  | Null model A | −2713.8934 | ω0 = 0.09913, ω1 = 1, ω2 = 1 | (Model A vs Null model A) 0.000 | 1.000 |  |
Thyroglobulin | Branch models | M0 (one ratio) | −15128.0999 | ω0 = 0.35639 |  |  |  |
|  |  | Free ratio | −15121.3529 | See Additional file 6 | (M0 vs Free ratio) 13.4941 | 0.09595 |  |
|  |  | Two ratio | −15124.3983 | ω0 = 0.33454, ω1 = 0.78473 | (M0 vs Two ratio) 7.4033 | 0.006511** |  |
|  | Branch-site models | Model A | −15103.5548 | ω0 = 0.000, ω1 = 1, ω2 = 3.59382 |  |  | Asn-76, Ser-633, Ser-734, Asn-775, Met-911, Ser-913, Gly-1061, Ser-1140, Thr-1204, Met-1242, Thr-1498, Arg-1646, His-1669, Arg-1691, Asp-1795, His-2486, Arg-2530, Asn-2616, Leu-2632, Glu-2702, Thr-2727, Thr-2765 |
|  |  | Null model A | −15104.1308 | ω0 = 0.000, ω1 = 1, ω2 = 1 | (Model A vs Null model A) 1.1520 | 0.2831 |  |