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Table 3 Inference of positively selected amino acid sites for golden pheasant MHC class I sequences

From: Balancing selection and recombination as evolutionary forces caused population genetic variations in golden pheasant MHC class I genes

Locus M8 vs. M7 likelihood ratio test Positively selected sites
  df Test statistic Significance OmegaMap PAML REL FEL
IA1        
-E2 2 6.7 <0.01 24 L * 24 L ** 24 L ** -
-E3 2 10.5 <0.001 (9A) 99Y**, 155R** - -
IA2        
-E2 2 105.8 <0.001 (17B) 9E**, 24 L**, 68 V**, 9E**, 24 L**, 9E**, 24 L**,
      71 T**, 74I**, 78D** 70G**, 71 T**, 78D** 71 T**, 74I*, 78D*
-E3 2 47.3 <0.001 (7C) 95 L**, 97 W**, 99Y**, 113H**, 113H**, 155R** 113H**, 155R*
      115 V**, 152Y*, 155R**, 156Q*   
  1. Notes: The test statistic was computed as 2 (Lb-La), where La and Lb are log-likelihood values for the M8 and M7 site model, respectively. *, posterior probability > 0.95; **, posterior probability > 0.99. df, degree of freedom; PAML, phylogenetic analysis by maximum likelihood; REL, random effects likelihood; and FEL, fixed-effects likelihood. A The inferred positively selected amino acid sites by OmegaMap in IA1-E3 were: 99Y*,150P**, 151 T**, 152Y**, 153 V**, 154D**, 155R**, 156Q** and 158 L**. B The inferred positively selected amino acid sites by OmegaMap in IA2-E2 were: 9H**, 24 L**, 40 T*, 41R*, 42R*, 55A**, 56 M*, 57D**, 58Q**, 59Q*, 67I**, 68 V**, 70G**, 71 T**, 74I**, 75Y**, and 78D**. C The inferred positively selected amino acid sites by OmegaMap in IA2-E2 were: 113H**, 115 V*, 150P**, 151 T*, 152Y**, 155R**, and 156Q**