Table S1.
Analysis of positive selection for the Chinese tree shrew MDA5 and LGP2 genes
| Foreground | lnL (null) | np1 | lnL (alternative) | np2 | 2ΔlnL | P value | PSSs* (BEB analysis) | Parameters |
| Branch analysis | ||||||||
| Tree shrew MDA5 (M0 vs. M2) | −9,394.433345 | 12 | −9,392.138604 | 13 | 4.589482 | 0.032 | / | M0: All branches have the same ω0 = 0.22283 |
| M2: The tree shrew branch has ω2= 0.30320, other branches have ω1= 0.20895 | ||||||||
| Tree shrew LGP2 (M0 vs. M2) | −6,660.077474 | 12 | −6,657.787937 | 13 | 4.579074 | 0.032 | / | M0: All branches have the same ω0 = 0.17109 |
| M2: The tree shrew branch has ω2= 0.24227, other branches have ω1 = 0.15777 | ||||||||
| Branch-site analysis | ||||||||
| Tree shrew MDA5 | −9,433.609553 | 14 | −9,429.916706 | 15 | 7.385694 | 0.007 | 188 Q 0.732, 402 K 0.800 | p0 = 0.77887 p1 = 0.21476 p2a = 0.00499 p2b = 0.00138 ω0 = 0.06695 ω1 = 1.00000 ω2= 957.32532 |
| Tree shrew LGP2 | −6,626.184812 | 14 | −6,626.184812 | 15 | 0 | 1 | 95 R 0.602, 318 T 0.677, 513 V 0.616, 683 L 0.793 | p0 = 0.70426 p1 = 0.19775 p2a = 0.07651 p2b = 0.02148 ω0= 0.05436 ω1 = 1.00000 ω2 = 1.00000 |
BEB analysis, Bayes Empirical Bayes analysis (44); lnL, log-likelihood value; np, number of parameters; 2ΔlnL, twice the difference of ln(likelihood) values (2ΔlnL) between the two models compared; PSSs, positively selected sites; A P value < 0.05 is marked in bold.
*
The amino acid positions are called based on the tree shrew MDA5.