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Table 1 Branch models: estimated parameters and log-likelihood ratio tests

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

Paralog pair

Model

logL

np

Branchs

ω

LRT

p-value

 

M0

−2847.12

58

OG

0.05

   
    

Lax

0.08

   
    

OG

0.05

   
 

MP

−2846.50

59

Lax2

0.07

vs. M0

1.24

0.26

    

Lax4

0.10

   
    

OG

0.05

   

 Lax2/Lax4

MA

−2840.62

59

Lax early

0.14

vs. M0

13.0**

0.00031

    

Lax late

0.05

   
    

OG

0.05

   
    

Lax2 early

0.19

vs. MP

13.8**

0.001

 

MPA

−2839.60

61

Lax4 early

0.11

   
    

Lax2 late

0.04

vs. MA

2.04

0.36

    

Lax4 late

0.06

   
 

M0

−4127.20

62

OG

0.06

   
    

Pg

0.33

   
    

OG

0.06

   
 

MP

−4125.06

63

Pg3

0.25

vs. M0

4.28*

0.04

    

Pg11

0.41

   
    

OG

0.06

   

 Pg3/Pg11

MA

−4124.78

63

Pg early

0.22

vs. M0

4.84*

0.03

    

Pg late

0.38

   
    

OG

0.06

   
    

Pg3 early

0.24

vs. MP

3.68

0.16

 

MPA

−4123.22

65

Pg11 early

0.21

   
    

Pg3 late

0.29

vs. MA

3.12

0.21

    

Pg11 late

0.44

   
 

M0

−3604.36

40

OG

0.27

   
    

Pg11

0.44

   
    

OG

0.27

   
 

MP

−3603.75

41

Pg11a

0.38

vs. M0

1.22

0.27

    

Pg11c

0.50

   
    

OG

0.27

   

 Pg11a/Pg11c

MA

−3604.19

41

Pg11 early

0.50

vs. M0

0.34

0.57

    

Pg11 late

0.42

   
    

OG

0.27

   
    

Pg11a early

0.50

vs. MP

0.72

0.70

 

MPA

−3603.39

43

Pg11c early

0.54

   
    

Pg11a late

0.35

vs. MA

1.60

0.45

    

Pg11c late

0.49

   
  1. *Note. Models: for M0, ω is allowed to take a different value only in the branch of the outgroup (OG); for MP, MA and MPA ω is allowed to take a different values according to the tested effect, i.e. “paralogs”, “age” or combined as explained in Figure 1. 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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