Table 1 Likelihood ratio tests of various models on the selective pressures on Tas1r1 , Tas1r2 , Pkd2l1 , and Scnn1g

Dataset I:

All branches have one ω (A)

0.2919

12711.16

28

All branches have one ω = 1(B)

1

13033.12

27

B vs. A

643.92

0

The branches with pseudogenized Tas1r1 has ω₂, others have ω₁ (C)

ω₁ = 0.25599

12686.76

29

A vs. C

48.81

2.82E-12

ω₂ = 0.68390

The branches with pseudogenized Tas1r1 has ω₂ = 1, others have ω₁ (D)

ω₁ = 0.25589

12690.33

28

D vs. C

7.15

0.01

ω₂ = 1.00000

Each branch has its own ω(E)

Variable ω by branch

12655.22

53

C vs. E

63.06

2.33E-05

Dataset II:

All branches have one ω (A)

0.20585

11866.17

24

All branches have one ω = 1(B)

1

12287.21

23

B vs. A

842.08

0

The branches with pseudogenized Tas1r2 has ω₂, others have ω₁ (C)

ω₁ = 0.17096 ω₂ = 0.49085

11838.26

25

A vs. C

55.81

7.97E-14

The branches with pseudogenized Tas1r2 has ω₂ = 1, others have ω₁ (D)

ω₁ = 0.16972 ω₂ = 1.00000

11850.23

24

D vs. C

23.95

9.90E-07

Each branch has its own ω(E)

Variable ω by branch

11809.99

45

C vs. E

56.54

2.41E-05

Dataset III:

Pkd2l1

All branches have one ω(A)

0.28788

8723.86

28

All branches have one ω = 1(B)

1

8907.34

27

B vs. A

366.97

0

The branches with pseudogenized Pkd2l1 has ω₂, others have ω₁ (C)

ω₁ = 0.24058 ω₂ = 0.55166

8709.97

29

A vs. C

27.79

1.35E-07

The branches with pseudogenized Pkd2l1 has ω₂ = 1, others have ω₁ (D)

ω₁ = 0.23991

8718.11

28

D vs. C

16.29

5.45E-05

ω₂ = 1.00000

Each branch has its own ω (E)

Variable ω by branch

8673.30

53

C vs. E

73.33

6.78E-07

Dataset IV:

Scnn1g

All branches in cetaceans have a ω₃, other branches have a ω₂. (F)

ω₂ = 0.19790

8999.60

46

ω₃ = 1.05041

M2a-rel: All branches in cetaceans have a ω₃, other branches have a ω₂, ω₂ = ω₃. (G)

ω₂ = ω₃ = 0.25665

9036.40

45

F vs G

73.58

0

M1a (nearly neutral)

ω₀ = 0.05745 ω₁ = 1.00000

9068.93

43

M2a (positive selection)

ω₀ = 0.05745 ω₁ = 1.00000 ω₂ = 1.00000

9068.93

45

M1a VS M2a

0

1

M8a

ω = 1.00000

9037.05

44

M8

ω = 1.35413

9036.59

45

M8a VS M8

0.93

0.33