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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  
  1. aHuman-specific N-glycosylation sites are in bold. See Additional files 4, 5, and 6 for details.
  2. **P < 0.05.