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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