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Table 3 Summary of Likelihood Ratio Test (LRTs) for selection tests

From: Daily activity patterns influence retinal morphology, signatures of selection, and spectral tuning of opsin genes in colubrid snakes

Opsins

Comparisons

2ΔLn L

Df

P value

Positive Sites

LWS

Branch Models

free model x 1ω

639

146

<10−5

–

2ω x 1ω

218

1

<10−5

–

3ω x 2ω

27

1

<10−5

–

4ω x 3ω

8

1

0.006

–

4ω (D x N) x 3ω

1

1

0.28

–

Branch-Site Models

Model A (diurnal) x null

45.9

2

<10−5

39 L(0.97) 49 V(0.89) 112 L(0.81) 119A(0.99) 165C(0.95) 195S(0.97) 213A(0.99) 276 V(1.0)

Model A (nocturnal) x null

100.9

2

<10−5

39 L(0.94) 119A(0.73) 124A(0.99) 137 V(0.82) 146 V(0.98) 166A(0.99) 199G(1.0) 209I(0.79) 213A(1.0) 218 V(1.0) 221I(0.85) 269 T *(1.0) 270F(0.77) 282A(0.99) 290 L(0.97)

Site Models

Model 3 x Model 0

726

4

<10−5

–

Model 2a x Model 1a

156

2

<10−5

39 L(1.0) 49 V(0.95) 104 V(0.99) 112 V(1.0) 119 V(1.0) 124A(0.98) 154 V(1.0) 158 L(0.87) 164S*(0.6) 165C(1.0) 166A(1.0) 195S(0.97) 205 V(0.99) 209I(0.98) 213A(0.99) 218 V(0.94) 228 L(0.87) 269 T*(0.79) 270F(0.7) 290 L(1.0)

Model 8 x Model 7

172

2

<10−5

39 L(1.0) 45 V(0.99) 49 V(0.99) 81I(0.83) 104 V(1.0) 109 L(0.69) 112 L(1.0) 119A(1.0) 124A(1.0) 137 V(0.88) 146 V(0.96) 154 L(1.0) 158 L(0.98) 164S*(0.98) 165C(1.0) 166A(1.0) 195S(0.99) 198P(0.95) 199G(0.9) 205 V(1.0) 206 V(0.85) 209I(0.99) 213A(1.0) 214I(0.8) 218 V(1.0) 221I(0.97) 228 L(0.99) 269 T *(0.99) 270F(0.99) 276 V(0.87) 287 T(0.9) 317 L(1.0)

RH1

Branch Models

free model x 1ω

427

142

<10−5

–

2ω x 1ω

121

1

<10−5

–

3ω x 2ω

6

1

0.015

–

4ω x 3ω

2

1

0.14

–

4ω (D x N) x 3ω

22

1

<10−5

–

Branch-Site Models

Model A (diurnal) x null

8.5

2

0.01

155 M(0.99)

Model A (nocturnal) x null

49.5

2

<10−5

159 L(0.9) 213 V(0.7) 214 T(1.0) 292S *(1.0)

Site Models

Model 3 x Model 0

427

4

<10−5

–

Model 2a x Model 1a

29

2

<10−5

81 V(0.8) 112 V(0.7) 133 V(0.8) 158S(0.9) 159 L(0.8) 209 L(0.7) 213 V(0.99) 217 T(0.99) 290 V(0.96) 292S*(0.7) 299A*(0.9)

Model 8 x Model 7

35

2

<10−5

46 L(0.8) 60Y(0.66) 81 V(0.9) 83 N*(0.7) 107 T(0.7) 112 V(0.9) 133 V(0.9) 158S(0.98) 159 L(0.9) 169A(0.6) 173I(0.8) 185S(0.6) 209 L(0.9) 213 V(1.0) 217 T(1.0) 290I(0.99) 292S*(0.9) 299A*(0.97)

SWS1

Branch Models

free model x 1ω

496

150

<10−5

–

2ω x 1ω

39

1

<10−5

–

3ω x 2ω

12

1

<10−4

–

4ω x 3ω

7

1

0.01

–

4ω (D x N) x 3ω

8

1

0.004

–

Branch-Site Models

Model A (diurnal) x null

46.6

2

<10−5

57I(0.97) 86 V*(0.75) 91I(0.97) 118 T*(0.9) 122 L(0.9) 143 L(0.96) 178Y(0.76) 213 L(0.8) 217 T(0.8) 255 V(0.6) 258I(0.6) 282G(1.0) 315A(0.8)

Model A (nocturnal) x null

21.3

2

<10−5

105 L(0.68) 109 V(0.87) 124I(0.9) 137I(0.8) 149 N(0.9) 213 L(0.99) 259G(0.98)

Site Models

Model 3 x Model 0

437

4

<10−5

–

Model 2a x Model 1a

0

2

1.0

–

Model 8 x Model 7

0

2

1.0

–

  1. Note – Underlined model fits the data significantly better. Sites inferred to be under positive selection at the 99% level are listed in bold; numbers after each site indicate the posterior probability value
  2. *Known spectral tuning sites. Sites are numbered based on the bovine RH1
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BMC Ecology and Evolution

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