Table 2.
Likelihood and omega values estimated under two ratio branch model of selective pressures on tooth-related genes
| Models and special branches | ω | − ln L | np | Models comparison | 2Δ (ln L) | P-value |
|---|---|---|---|---|---|---|
| AMBN | ||||||
| A. All branches have one ω | 0.459 | 22,143.52 | 124 | |||
| B. All branches have one ω = 1 | 1 | 22,429.33 | 123 | B vs A | 571.622 | 0 |
| C. The terminal branch of Orycteropus afer afer with pseudogenized AMBN has ω2, others have ω1 | ω1 = 0.454 ω2 = 0.894 | 22,140.4 | 125 | A vs C | 6.224 | 0.013 |
| D. The terminal branch of Orycteropus afer afer with pseudogenized AMBN has ω2 = 1, others have ω1 | ω1 = 0.454 ω2 = 1 | 22,140.48 | 124 | D vs C | 0.156 | 0.693 |
| E. The ancestral branch of Pholidota has ω2, others have ω1 | ω1 = 0.450 ω2 = 1.009 | 22,136.21 | 125 | A vs E | 14.618 | < 0.001 |
| F. The ancestral branch of Pholidota has ω2 = 1, others have ω1 | ω1 = 0.450 ω2 = 1 | 22,136.21 | 124 | F vs E | 0.002 | 0.964 |
| ENAM | ||||||
| A. All branches have one ω | 0.472 | 64,566.98 | 128 | |||
| B. All branches have one ω = 1 | 1 | 65,277.19 | 127 | B vs A | 1420.43 | 0 |
| C. The terminal branch of Manis javanica with pseudogenized ENAM has ω2, others have ω1 | ω1 = 0.470 ω2 = 1.034 | 64,563.42 | 129 | A vs C | 7.112 | 0.008 |
| D. The terminal branch of Manis javanica with pseudogenized ENAM has ω2 = 1, others have ω1 | ω1 = 0.470 ω2 = 1 | 64,563.43 | 128 | D vs C | 0.01 | 0.92 |
| E. The ancestral branch of Pholidota has ω2, others have ω1 | ω1 = 0.468 ω2 = 0.806 | 64,561.14 | 129 | A vs E | 11.67 | < 0.001 |
| F. The ancestral branch of Pholidota has ω2 = 1, others have ω1 | ω1 = 0.468 ω2 = 1 | 64,561.98 | 128 | F vs E | 1.674 | 0.196 |
| G.The terminal branch of Choloepus hoffmanni with pseudogenized ENAM has ω2, others have ω1 | ω1 = 0.469 ω2 = 0.914 | 64,562.17 | 129 | A vs G | 9.61 | 0.002 |
| H. The terminal branch of Choloepus hoffmanni with pseudogenized ENAM has ω2 = 1, others have ω1 | ω1 = 0.469 ω2 = 1 | 64,562.25 | 128 | H vs G | 0.154 | 0.695 |
| I. The terminal branch of Dasypus novemcinctuswith pseudogenized ENAM has ω2, others have ω1 | ω1 = 0.468 ω2 = 0.743 | 64,562.4 | 129 | A vs I | 9.162 | 0.002 |
| J. The terminal branch of Dasypus novemcinctus with pseudogenized ENAM has ω2 = 1, others have ω1 | ω1 = 0.467 ω2 = 1 | 64,564.07 | 128 | J vs I | 3.346 | 0.067 |
| MMP20 | ||||||
| A. All branches have one ω | 0.18 | 20,392.24 | 128 | |||
| B. All branches have one ω = 1 | 1 | 21,668.04 | 127 | B vs A | 2551.59 | 0 |
| C. The terminal branch of Manis javanica with pseudogenized MMP20 has ω2, others have ω1 | ω1 = 0.179 ω2 = 0.864 | 20,388.99 | 129 | A vs C | 6.502 | 0.011 |
| D. The terminal branch of Manis javanica with pseudogenized MMP20 has ω2 = 1, others have ω1 | ω1 = 0.179 ω2 = 1 | 20,389.01 | 128 | D vs C | 0.043 | 0.836 |
| E. The ancestral branch of Pholidota has ω2, others have ω1 | ω1 = 0.174 ω2 = 0.966 | 20,372.19 | 129 | A vs E | 40.104 | < 0.001 |
| F. The ancestral branch of Pholidota has ω2 = 1, others have ω1 | ω1 = 0.174 ω2 = 1 | 20,372.2 | 128 | F vs E | 0.012 | 0.913 |
| DSPP | ||||||
| A. All branches have one ω | 0.385 | 58,713.76 | 114 | |||
| B. All branches have one ω = 1 | 1 | 59,730.58 | 113 | B vs A | 2033.64 | 0 |
| C. The terminal branch of Dasypus novemcinctus with pseudogenized DSPP has ω2, others have ω1 | ω1 = 0.380 ω2 = 0.771 | 58,702.61 | 115 | A vs C | 22.298 | < 0.001 |
| D. The terminal branch of Dasypus novemcinctus with pseudogenized DSPP has ω2 = 1, others have ω1 | ω1 = 0.380 ω2 = 1 | 58,704.01 | 114 | D vs C | 2.786 | 0.095 |