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Table 2 Parameter estimates of branch-site models and predicted positively selected sites

From: Evolutionary ecology of the visual opsin gene sequence and its expression in turbot (Scophthalmus maximus)

Opsin

Clade

lnL

LRT

P

Positively selected sites

Null

modelA

RH2

a

− 10,169.10

− 10,169.10

0

1

–

b

− 10,166.54

− 10,164.23

4.62

0.0315

19 (0.881) 31 (0.628) 95 (0.945) 109 (0.882) 122 (0.511) 169 (0.501) 207 (0.966) 266 (0.604) 273 (0.949) 320 (0.578)

c

− 10,169.10

− 10,169.10

0

1

–

d

− 10,167.62

− 10,165.03

5.16

0.0230

105 (0.612) 217 (0.993)

e

− 10,168.60

− 10,168.58

0.03

0.8636

–

f

− 10,166.92

− 10,162.26

9.32

0.0022

49 (0.944) 95 (0.733) 270 (0.982) 307 (0.907)

g

− 10,148.85

− 10,136.84

24.01

< 0.001

14 (0.875) 33 (0.514) 50 (0.946) 65 (0.770) 84 (0.948) 151 (0.523) 195 (0.951) 197 (0.845) 198 (0.600) 217 (0.945) 239 (0.528) 254 (0.952) 286 (0.502) 290 (0.594) 297 (0.581) 321 (0.757) 322 (0.966) 323 (0.990) 325 (0.979) 328 (0.649) 329(0.770) 330 (0.772)

RH1

a

− 3629.453904

− 3625.696675

7.51

0.0061

35 (0.769) 126 (0.674) 196 (0.858) 210 (0.879) 235 (0.911) 236 (0.959) 281 (0.773)

b

− 3632.72

− 3632.72

0

1

–

c

− 3632.72

− 3632.72

0

1

–

d

− 3630.82

− 3630.82

4E-06

1

–

SWS2

a

− 7840.16

− 7831.84

16.63

< 0.001

2 (0.572) 5 (0.605) 10 (0.815) 14 (0.801) 15 (0.575) 21 (0.841) 22 (0.579) 25 (0.507) 27 (0.805) 42 (0.552) 44 (0.889) 45 (0.598) 51 (0.605) 55 (0.623) 87 (0.570) 88 (0.617) 91 (0.567) 95 (0.613) 99 (0.510) 123 (0.556) 125 (0.539) 156 (0.601)162 (0.619) 166 (0.598) 244 (0.600) 257 (0.600) 269 (0.670) 279 (0.604) 283 (0.853) 301 (0.685) 315 (0.708) 328 (0.858)329 (0.818) 332 (0.577) 335 (0.596) 339 (0.533) 341 (0.545) 346 (0.659) 349 (0.687)

b

− 7851.02

− 7848.07

5.88

0.0152

38 (0.560) 99 (0.904) 276 (0.687) 299 (0.983)

c

− 7852.17

− 7850.19

3.97

0.0463

18 (0.894)

d

− 7852.21

− 7852.21

0

1

–

e

− 7852.13

− 7852.10

0.06

0.8135

–

f

− 7852.21

− 7851.96

0.50

0.4798

–

SWS1

a

− 4194.06

− 4194.06

0

1

–

b

− 4194.59

− 4193.82

1.54

0.2146

–

c

− 4189.36

− 4185.92

6.87

0.0087

8 (0.895) 9 (0.860) 10 (0.788) 11 (0.765) 16 (0.704) 27 (0.895) 56 (0.678) 70 (0.888) 125 (0.746) 145 (0.751) 185 (0.881) 194 (0.766) 263 (0.792) 342 (0.512)

LWS

a

− 4828.06

− 4828.06

0

1

–

b

− 4828.06

− 4828.06

0

1

–

c

− 4828.06

− 4828.06

0

1

–

d

− 4828.06

− 4828.06

0

1

–

  1. lnL ln likelihood, LRT likelihood ratio test, – no positively selected sites
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BMC Ecology and Evolution

ISSN: 2730-7182

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