Table 5.
Selection test
| Log-likelihood | dN/dS | P-value Chi-square | PSS | ||
|---|---|---|---|---|---|
| Actinopterygii | Log-likelihood M1a | -21118.741643 | 0.1331 | 1 | - |
| Log-likelihood M2a | -21118.741643 | 0.1331 | |||
| Amphibia | Log-likelihood M1a | -22490.686927 | 0.1049 | 1 | - |
| Log-likelihood M2a | -22490.686928 | 0.1049 | 33 T | ||
| Aves | Log-likelihood M1a | -16728.712033 | 0.1695 | 10-7* | 76 W |
| Log-likelihood M2a | -16714.234740 | 0.1807 | |||
| Chondrichthyes | Log-likelihood M1a | -6993.815583 | 0.1783 | 1 | - |
| Log-likelihood M2a | -6993.815583 | 0.1783 | |||
| Crocodylia | Log-likelihood M1a | -3538.892722 | 0.2144 | 1 | - |
| Log-likelihood M2a | -3538.892722 | 0.2144 | |||
| Lepidosauria | Log-likelihood M1a | -38632.722264 | 0.2632 | 0.032* | 159 H |
| Log-likelihood M2a | -38629.286234 | 0.2665 | |||
| Mammalia | Log-likelihood M1a | -10175.360951 | 0.0713 | 1 | - |
| Log-likelihood M2a | -10175.360951 | 0.0713 | |||
| Testudines | Log-likelihood M1a | -10208.575616 | 0.1653 | 0.1145 | 23 V |
| Log-likelihood M2a | -10206.408516 | 0.1730 |
Test for positive selection using the M1a (neutral) and M2a (positive) models, and a maximum of 60 Rag1 sequences for each vertebrate lineage (see Methods for further explanations). "dN/dS" indicates the substitution rate ratio averaged across all sites and lineages. "PSS" indicates the positively selected sites (calculated as in [47]). We indicate the position of the amino acid under positive selection (based on the within group alignment used for this analysis) and the corresponding amino acid. * indicates the statistically significant p-values (<0.05) in the Chi-square test.