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Table 2 Results of Clade models testing for divergent selection among codons between Ungulate (Clade 0) and Cetacean (Clade 1)

From: Evolution of toll-like receptors in the context of terrestrial ungulates and cetaceans diversification

 

Clade model

Branch-site model

 

lnL

Site classes

 

Gene

M2a_rel (np)

Clade model C (np)

LRT

0

1

2

P- value

LRT

P-value

TLR2

−8561.3 (28)

−8561.1 (29)

0.4

P 0 = 0.66

ω0 = 0.08

P 1 = 0.31

ω1 = 1

P 2 = 0.03

ω Clade 0 = 4.6

ω Clade 1 =2.78

0.5

  

TLR3

−9856.6 (42)

−9850.5 (43)

12.2

P 0 = 0.77

ω0 = 0.1

P 1= 0.21

ω1 = 1

P 2 = 0.02

ω Clade 0 = 2.7

ω Clade 1 = 4.7

<0.001

0.000

>0.05

TLR4

−10128.7 (34)

−10128.7 (35)

0.0

P 0 = 0.6

ω0 = 0.08

P 1 = 0.3

ω1 = 1

P 2 = 0.1

ω Clade 0 = 2.85

ω Clade 1 =2.67

0.8

  

TLR5

−10467.5 (38)

−10467.3 (39)

0.3

P 0 = 0.6

ω0 = 0.09

P 1 = 0.3

ω1 = 1

P 2 = 0.1

ω Clade 0 = 2.98

ω Clade 1 =3.71

0.6

  

TLR7

−9947.7 (43)

−9946.8 (42)

1.8

P 0 = 0.0

ω0 = 0.0

P 1 = 0.2

ω1 = 1

P 2 = 0.8

ω Clade 0 = 0.05

ω Clade 1 = 0.00

0.2

  

TLR9

−10345.2 (30)

−10345.1 (31)

0.2

P 0 = 0.57

ω0 = 0.00

P 1 = 0.12

ω1 = 1

P 2 = 0.31

ω Clade 0 = 0.17

ω Clade 1 = 0. 20

0.7

  

TLR10

−8606.2 (40)

−8605.4 (41)

1.5

P 0 = 0.61

ω0 = 0.10

P 1 = 0.38

ω1 = 1

P 2 = 0.01

ω Clade 0 = 4.99

ω Clade 1 =0.00

0.2

  
  1. The TLR with significant divergent selection was further subjected to branch-site analysis to determine if divergent selection corresponds to positive selection in the foreground (Cetacean) branch