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Table 3 Branch-site models: estimated parameters and log-likelihood ratio tests

From: Contrasted patterns of selective pressure in three recent paralogous gene pairs in the Medicagogenus (L.)

 

Model (k)

np

LogL

LRT

P-value

prop

clade

ω

 

M3 (2)

58

−2375.94

      

Lax2/Lax4

MD (2)

59

−2369.54

vs. M3 (2)

12.8**

3.47 10-4

0.76

 

0.00

       

0.24

Lax2

0.15

        

Lax4

0.52

 

M3 (3)

60

−2375.94

      
 

MD (3)

61

−2361.85

vs. M3 (3)

28.17**

1.11 10-7

0.77

 

0.005

       

0.03

 

0.97

       

0.20

Lax2

0.55

        

Lax4

0.97

 

M3 (2)

61

−3411.03

      

Pg11/Pg3

MD (2)

62

−3407.95

vs. M3 (2)

6.16*

0.01

0.68

 

0.09

       

0.32

Pg3

0.74

        

Pg11

1.35

 

M3 (3)

63

−3400.58

      
 

MD (3)

64

−3399.59

vs. M3 (3)

1.98

1.16

   
 

M3 (2)

40

−2216.23

      

Pg11a/Pg11c

MD (2)

41

−2214.01

vs. M3 (2)

4.45*

0.03

0.79

 

0.12

       

0.21

Pg11a

1.54

        

Pg11c

3.13

 

M3 (3)

42

−2210.38

      
 

MD (3)

43

−2209.37

vs. M3 (3)

2.01

0.16

   
  1. Note. Models: for M3 (discrete model), ω is free to take the number of values indicated in brackets (k); these values are homogenous in all branches of the tree; for MD, as explained in Figure 1 (b), one category of ω is allowed to differ between the two paralogous genes clades of the tree [33]. np: number of free parameters; logL: log-likelihood; LRT: likelihood ratio test statistic between indicated models; one (respectively two) asterisk indicates that the probability of observing such an LRT or higher under the compared model is <0.05 (respectively <0.01), assuming that the LRT follows a χ2 distribution with the difference of free parameters between the compared models as the number of degrees of freedom.
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BMC Ecology and Evolution

ISSN: 2730-7182

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