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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**
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BMC Ecology and Evolution

ISSN: 2730-7182

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