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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%