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Table 3 Summary of likelihood ratio tests for site-specific positive selection of MHC IIB genes comparing groups of alleles

From: Molecular characterization of MHC class IIB genes of sympatric Neotropical cichlids

Allele Group Models compared LRT (2Δl) p-value Estimate for ω >1 Proportion of PSS PSS
All groups M1a versus M2a 81.738836 1.09E-06 3.71226 0.34292 1, 2, 7, 9, 10, 32, 33, 37, 38, 39, 41, 42, 43, 46, 57, 58, 60, 61, 62
All groups M7 versus M8 84.941740 6.61E-07 3.55150 0.35599 1, 2, 7, 9, 10, 32, 33, 37, 38, 39, 41, 42, 43, 46, 57, 58, 60, 61, 62
All groups M8a versus M8 73.238718 6.12E-07    
All except I M1a versus M2a 83.327546 1.16E-06 3.89788 0.32156 8, 9, 16, 17, 32, 39, 40, 44, 45, 46, 48, 49, 50, 53, 64, 65, 67, 68, 69
All except I M7 versus M8 80.631206 6.74E-07 3.72628 0.33118 8, 9, 14, 16, 17, 32, 39, 40, 44, 45, 46, 48, 49, 50, 53, 64, 65, 67, 68, 69
All except I M8a versus M8 74.046658 8.90E-07    
Group I only M1a versus M2a 4.594664 0.10    
Group I only M7 versus M8 4.594238 0.10    
Group I only M8a versus M8 4.594000 0.10    
Group II only M1a versus M2a 7.702834 0.021 3.16267 0.48401 49, 65
Group II only M7 versus M8 7.706184 0.021 3.16268 0.48401 13, 49, 65
Group II only M8a versus M8 7.702818 0.021    
Group III only M1a versus M2a 14.605000 0.0007 31.27408 0.03609 73
Group III only M7 versus M8 14.663852 0.0007 31.37037 0.03603 73
Group III only M8a versus M8 14.604918 0.0007    
Group IV only M1a versus M2a 20.610518 0.00003 7.27232 0.15698 11, 48, 55, 67, 69, 106
Group IV only M7 versus M8 20.981230 0.00003 7.22462 0.15872 11, 42, 48, 55, 66, 67, 69, 77, 106
  1. The LRT models compared by the likelihood ratio test with five codon substitution models: Beta models M7 (no positive selection), M8 (positive selection), and M8a (no positive selection and ω = 1), and models M1a (nearly neutral) and M2a (positive selection). The 2Δl = 2(lb - la), ω = dN / dS, positively selected sites (PSS) are inferred by empirical Bayesian posterior probabilities. PSS in bold are inferred at 99%
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