Table 5 Parameter estimates and LRT of MA1 vs. MA in DEF-like genes from Poales.
Clade | Model | Estimate of parameters | Positive selection | L |
|---|---|---|---|---|
Poales (P1) | A | ω0 = 0.08303, f0 = 0.89319 ω1 = 1.00000, f1 = 0.03486 ω2a fore =936.29115, ω2a back =0.08303, f2a = 0.06925 ω2b fore =936.29115, ω2b back =1.00000, f2b = 0.00270 | 45 L 0.612 50 S 0.703 54 L 0.531 55 S 0.996** 77 I 0.556 82 A 0.588 86 K 0.583 89 N 0.991** 92 N 0.517 103 K 0.689 116 I 0.573 117 K 0.976* 126 L 0.625 132 L 0.993** 152 V 0.604 159 H 0.535 164 R 0.899← 167 E 0.742 170 N 0.931← 175 E 0.639 177 Y 0.996** 181 L 0.610 | -9975.021057 |
A1 | ω0 = 0.08196, f0 = 0.78512 ω1 = 1.00000, f1 = 0.03088 ω2a fore =1.00000, ω2a back =0.08196, f2a = 0.17704 ω2b fore =1.00000, ω2b back =1.00000, f2b = 0.00696 | -9979.237754 | ||
LRT | 2δ = 8.433394 df = 1 P = 0.0037 | |||
Poales (P2) | A | ω0 = 0.08281, f0 = 0.86235 ω1 = 1.00000, f1 = 0.03283 ω2a fore =4.43236, ω2a back =0.08281, f2a = 0.10097 ω2b fore =4.43236, ω2b back =1.00000, f2b = 0.00384 | 14 S 0.813 42 E 0.747 44 S 0.846 50 S 0.993** 54 L 0.571 57 F 0.799 64 T 0.787 75 S 0.992** 78 N 0.706 81 S 0.788 103 K 0.893 128 E 0.892 142 N 0.821 154 N 0.736 171 Y 0.801 | -9983.412368 |
A1 | ω0 = 0.08278, f0 = 0.76740 ω1 = 1.00000, f1 = 0.02922 ω2a fore =1.00000, ω2a back =0.08278, f2a = 0.19592 ω2b fore =1.00000, ω2b back =1.00000, f2b = 0.00746 | -9984.514801 | ||
LRT | 2δ = 2.204866 df = 1 P = 0.1376 | |||
Poales (P3) | A | ω0 = 0.08393, f0 = 0.95687 ω1 = 1.00000, f1 = 0.03593 ω2a fore =8.40943, ω2a back =0.08393, f2a = 0.00694 ω2b fore =8.40943, ω2b back =1.00000, f2b = 0.00026 | 33 T 0.517 183 L 0.954* | -9987.927062 |
A1 | ω0 = 0.08401, f0 = 0.95276 ω1 = 1.00000, f1 = 0.03571 ω2a fore =1.00000, ω2a back =0.08401, f2a = 0.01111 ω2b fore =1.00000, ω2b back =1.00000, f2b = 0.00042 | -9988.396587 | ||
LRT | 2δ = 0.93905 df = 1 P = 0.3325 |