## Table 2 |
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Results of PAML analyses for the vertebrate dataset |
|||||

Data set |
2ΔlnL |
df |
P-value |
Proportion of sites with ω > 1 (average ω for these sites) |
Positively selected codons^{a} |

All vertebrates (n= 77) |
|||||

M1a vs. M2a | 15.22 | 2 | P= 0.0005 |
0.017 (ω = 2.0) | |

M7 vs. M8 | 34.89 | 2 | P< 0.0001 |
0.050 (ω = 1.3) | 97**, 98*, 104*, 286* |

M0 vs. free ratios | 510.67 | 142 | P< 0.0001 |
||

Mammals (n= 55) |
|||||

M1a vs. M2a | 31.27 | 2 | P< 0.0001 |
0.027 (ω = 2.3) | |

M7 vs. M8 | 47.39 | 2 | P< 0.0001 |
0.066 (ω = 1.6) | 97**, 98*, 104*, 214*, 286** |

M0 vs. free ratios | 265.71 | 100 | P< 0.0001 |
||

Primates (n= 17) |
|||||

M1a vs. M2a | 0 | 2 | P = 1.0 |
none | |

M7 vs. M8 | 0 | 2 | P = 1.0 |
none | |

M0 vs. free ratios | 36.45 | 28 | P = 0.13 |

*n*, number of sequences; 2Δln*L*, twice the log-likelihood difference of the models compared; df, degrees of freedom;
*P*-value, level of significance (*P*-values < 0.05 are shown in bold).

^{a} Sites pinpointed to be under positive selection under the selection model with the
highest likelihood (M8 for the vertebrate and mammalian datasets) by Bayes Empirical
Bayes (BEB) analysis. Only sites with posterior probability greater than 0.95 (*)
or 0.99 (**) are shown. Sites are numbered according to the full human coding sequence.

Sabbagh * et al.*

Sabbagh * et al.* *BMC Evolutionary Biology* 2013 **13**:62 doi:10.1186/1471-2148-13-62