
Model (k)

np

LogL

LRT

Pvalue

prop

clade

ω



M_{3} (2)

58

−2375.94
      
Lax2/Lax4

M_{D} (2)

59

−2369.54

vs. M_{3} (2)

12.8**

3.47 10^{4}

0.76
 
0.00

      
0.24

Lax2

0.15

       
Lax4

0.52


M_{3} (3)

60

−2375.94
      

M_{D} (3)

61

−2361.85

vs. M_{3} (3)

28.17**

1.11 10^{7}

0.77
 
0.005

      
0.03
 
0.97

      
0.20

Lax2

0.55

       
Lax4

0.97


M_{3} (2)

61

−3411.03
      
Pg11/Pg3

M_{D} (2)

62

−3407.95

vs. M_{3} (2)

6.16*

0.01

0.68
 
0.09

      
0.32

Pg3

0.74

       
Pg11

1.35


M_{3} (3)

63

−3400.58
      

M_{D} (3)

64

−3399.59

vs. M_{3} (3)

1.98

1.16
   

M_{3} (2)

40

−2216.23
      
Pg11a/Pg11c

M_{D} (2)

41

−2214.01

vs. M_{3} (2)

4.45*

0.03

0.79
 
0.12

      
0.21

Pg11a

1.54

       
Pg11c

3.13


M_{3} (3)

42

−2210.38
      

M_{D} (3)

43

−2209.37

vs. M_{3} (3)

2.01

0.16
   
 Note. Models: for M_{3} (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 M_{D}, 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: loglikelihood; 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 χ^{2} distribution with the difference of free parameters between the compared models as the number of degrees of freedom.