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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