Table 3.
Analysis of the amino acid substitutions in positively selected sites. Evidence of positive selection from BEB posterior probabilities in branch-site PAML and P-values from FEL HyPhy analysis. The functional impact of the substitutions was assessed using four scores (PROVEAN, MAPP, PolyPhen2, and SIFT) and considered deleterious when the prediction was supported by at least three predictions. See extended results in Table S2. Amino acid substitutions position relative to the human protein sequence.
| A. EDA positively selected substitutions in Hawaiian monk seal (N.schauinslandi) | |||
| Evidence of positive selection | |||
| Substitution | BEB Post.Prob. | FEL P -values | Functional prediction |
| A134R | 1.000 | 0.016 | Deleterious |
| L136R | 1.000 | 0.001 | Neutral |
| N137S | 1.000 | 0.014 | Deleterious |
| D142P | 1.000 | 0.005 | Neutral |
| P145N | 1.000 | <0.001 | Neutral |
| V154E | 1.000 | 0.008 | Neutral |
| S162V | 0.999 | 0.012 | Neutral |
| B. EDA positively selected substitutions in sea otter (E.lutris) | |||
| Evidence of positive selection | |||
| Substitution | BEB Post.Prob. | FEL P -values | Functional prediction |
| E148L | 0.999 | 0.013 | Neutral |
| R152F | 0.995 | 0.004 | Neutral |
| C. EDAR positively selected substitutions in Yangtze finless porpoise (N.asiaoeorientalis) | |||
| Evidence of positive selection | |||
| Substitution | BEB Post.Prob. | FEL P -values | Functional prediction |
| H224A | 0.991 | <0.001 | Neutral |
| G226W | 0.992 | 0.002 | Neutral |
| K227A | 1.000 | 0.015 | Deleterious |
| V229G | 0.984 | 0.002 | Neutral |
| E230R | 1.000 | <0.001 | Deleterious |
| S234T | 0.995 | 0.003 | Neutral |
| K235P | 0.980 | 0.022 | Neutral |
| D236P | 0.999 | <0.001 | Neutral |
| E237R | 1.000 | 0.024 | Neutral |
| E238L | 1.000 | <0.001 | Deleterious |
| K239A | 1.000 | 0.018 | Deleterious |
| K240P | 1.000 | <0.001 | Neutral |
| E241V | 0.974 | 0.011 | Neutral |