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Table 6 Likelihood Ratio Tests for the SULT1A Genes

From: Phylogenomic approaches to common problems encountered in the analysis of low copy repeats: The sulfotransferase 1A gene family example

 

Selection vs. Neutral

Discrete (k = 3) vs. One-ratio

Beta+selection vs. Beta

Model A vs. Neutral

Model B vs. Discrete (k = 2)

Log L1

- 4,884.89

- 4,880.78

- 4,879.97

- 5,013.29

- 4,886.52

Log L0

- 5,021.14

- 5,047.81

- 4,884.27

- 5,021.14

- 4,931.05

2ΔLog L

272.50

334.06

8.60

15.70

89.06

d.f.

2

4

2

2

2

P-value

P < 0.001

P < 0.001

0.01 < P < 0.05

P < 0.001

P < 0.001

  

Positively selected sites*

   
  

3 (0.86)

   
  

7 (0.63)

   
  

30 (0.71)

   
  

35 (0.73)

   
  

71 (0.88)

   
  

77 (0.92)

   
    

84 (0.92)

 
  

85 (0.95)

   
  

86 (0.97)

   
  

89 (0.99)

89 (0.88)

89 (0.99)

89 (0.99)

  

93 (0.97)

   
    

105 (0.72)

105 (0.53)

    

107 (0.82)

107 (0.75)

    

132 (0.87)

132 (0.78)

    

143 (0.51)

 
    

146 (0.80)

146 (0.97)

  

222 (0.99)

222 (0.58)

  
  

236 (0.53)

   
  

245 (0.99)

245 (0.99)

  
  

261 (0.90)

   
  

275 (0.70)

   
  

288 (0.89)

   
  

290 (0.95)

   
  

293 (0.72)

   
  1. *In parentheses for each positively selected site is the posterior probability that the site belongs to the class with KA/KS >1. Posterior probabilities >90% are bold-face. Positively selected sites also experiencing non-synonymous change on the 1A3/1A4 branch are underlined.
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BMC Ecology and Evolution

ISSN: 2730-7182

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