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Table 1 Substitution frequencies and rate heterogeneity parameters

From: Short-wavelength sensitive opsin (SWS1) as a new marker for vertebrate phylogenetics

   A↔C A↔G A↔T C↔G C↔Ta αb I (ML)c Id
All sites Fish 0.778 2.419 1.328 0.984 3.192 1.203 0.262 0.412
  Reptiles 1.081 4.598 0.907 3.330 2.516 0.392 0.000 0.611
  Mammals 1.322 4.876 0.838 0.727 4.672 1.473 0.345 0.530
  Tetrapods 1.091 4.120 0.969 1.431 3.341 1.029 0.244 0.367
  Vertebrates 0.987 3.326 1.084 1.298 3.115 1.014 0.166 0.263
Codon #1 Fish 2.338 2.645 1.434 0.793 2.877 0.422 0.000 0.334
  Reptiles 2.383 2.148 0.777 0.579 1.313 0.312 0.000 0.629
  Mammals 2.504 4.097 0.739 0.828 3.515 1.445 0.447 0.646
  Tetrapods 2.051 2.781 0.935 0.602 1.891 0.780 0.212 0.457
  Vertebrates 2.188 2.473 1.008 0.741 2.256 0.837 0.122 0.319
Codon #2 Fish 5.561 9.417 3.878 23.904 10.450 0.411 0.000 0.629
  Reptiles 0.411 7.219 0.549 5.696 3.547 1.936 0.666 0.806
  Mammals 1.654 11.198 2.489 6.140 7.073 0.364 0.298 0.747
  Tetrapods 1.727 8.563 1.226 6.564 4.313 0.403 0.119 0.593
  Vertebrates 2.435 7.089 1.480 7.343 4.679 0.647 0.108 0.435
Codon #3 Fish 0.454 2.419 1.878 0.286 3.282 3.877 0.013 0.103
  Reptiles 0.377 4.589 0.000 0.431 4.089 1.002 0.000 0.343
  Mammals 0.985 5.023 0.810 0.194 4.248 2.907 0.000 0.197
  Tetrapods 0.623 4.283 0.973 0.679 3.599 3.058 0.028 0.050
  Vertebrates 0.521 3.386 1.169 0.622 3.027 4.665 0.032 0.036
  1. a Parameters are reversible and measured against the G↔T parameter with a value of 1
  2. b Shape parameter for the gamma distribution.
  3. c Proportion of invariant sites estimated using maximum likelihood methods
  4. d Proportion of invariant sites calculated from raw alignment data using MEGA3 [131].