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